Changes

[//]: # (NOTES:) [//]: # ( - comments are added here this way because comments in ‘.bumpversion.cfg’ get wiped when it self-updates) [//]: # ( - headers at level 2 must be with ‘—’, not ##, to avoid comment-interpretation errors with bumpversion) [//]: # ( see: https://github.com/c4urself/bump2version/issues/99) [//]: # ( - bump2version will not tag automatically, so it must be done manually after PR is merged and approved) [//]: # ( This is to ensure that new tags are applied directly on merge-commit, an not a commit within the PR) [//]: # ( see decission: https://github.com/bird-house/birdhouse-deploy/pull/161#discussion_r661746230)

[//]: # (DEFINE LATEST CHANGES UNDER BELOW ‘Unreleased’ SECTION - THEY WILL BE INTEGRATED IN NEXT RELEASE VERSION) [//]: # ( bump2version will take care to generate a new empty ‘Unreleased’ section after version bump)

Unreleased (latest)

[//]: # (list changes here, using ‘-’ for each new entry, remove this when items are added)

2.28.1 (2026-06-02)

Fixes

  • Fix compose env resolution to preserve internal DELAYED_EVAL list when re-applying caller environment.

    Calling read_configs re-applies exported variables from the caller process using reset_process_env. If the caller shell had already exported DELAYED_EVAL preemptively (by mistake or by sourcing a file exporting it), that step could overwrite the internally assembled delayed-eval list, causing following invocations to rely on a stale list of variables. Many derived paths (e.g.: ${BIRDHOUSE_DATA_PERSIST_ROOT}/...) would then remain unresolved. Notably, this could fail compose commands (not files using .template, but directly including delayed-eval variables) with errors such as undefined volume ${BIRDHOUSE_DATA_PERSIST_ROOT}/... due to invalid portions of volume mounts (e.g.: ${COWBIRD_MONGODB_DATA_DIR}:/data/db becomes ${BIRDHOUSE_DATA_PERSIST_ROOT}/mongodb_cowbird_persist:/data/db) because the environment variables are used directly in the compose files rather than by shell/templating resolution.

    The fix filters DELAYED_EVAL from the staged caller environment before running reset_process_env, ensuring the internally computed list (if any) is not overwritten by caller values breaking following references.

  • Cowbird: Fix missing export for COWBIRD_MONGODB_DATA_DIR default delayed-eval variable.

2.28.0 (2026-05-15)

Fixes

  • Postgres container healthchecks were logging error messages

    The postgres healthchecks were written in docker’s exec syntax instead of the shell syntax which meant that the environment variables were not actually being interpreted. This didn’t cause the healthcheck to fail but it did cause the postgres logger to write an error message saying that the provided posgtres user could not be found.

    This changes the healthcheck syntax to shell style to ensure that the environment variables are actually used.

Changes

  • Update documentation only, no “stack” feature

    • Update doc links and cross-references to work both on GitHub (direct sections links) and rendered Sphinx docs (things resolve where expected).

    • Remove the :download: and :ref: for a unified |<ref>|_ structure. Since all files are provided as-is for quick access, there is no need for explicit download. Because of relative references, the URIs are rendered correctly on GitHub as well, rather than plain :ref: that do not resolve when rendered by GitHub.

    • Update some code blocks to use expected lexers, which identified some syntax errors embedded within their code

    • Add Makefile docs-... targets for convenience.

    • Reorder certain components to make reading more consistent (WPS/birds/data services, followed by auth, followed by proxies/data/volumes) rather than mixed all over the place.

    • Move scheduler jobs under optional-components README to align with their actual location.

    • Fix multiple links. For example bin/birdhouse not resolving.

    • Fix inconsistent single/double code-quotes for italic/code fragments.

    • Fix some typos found along the way.

  • Reduce number of metrics exported by prometheus log parser

    The optional-components/prometheus-log-parser was creating way too many metrics and it was taking a really long time for prometheus to scrape the metrics from the log parser. This reduces the number of metrics created by:

    • turning off the _created metrics by default (can be turned on by setting PROMETHEUS_LOG_PARSER_PROMETHEUS_DISABLE_CREATED_SERIES=False)

    • moving the tds_service label to its own counter named thredds_transfer_size_by_service_bytes

    This means that the thredds_transfer_size_bytes counter no longer contains information about which TDS service was used to download the data. Instead the total amount of data downloaded per-service is calculated in the new counter.

  • Add title field to all docker image links in service-config.json files

    Each service definition has a link to the docker image used by that service but not all links had a title. This add the title in every case so that we’re consistent. This is not strictly necessary but it makes things a bit cleaner.

  • Magpie / Twitcher / Cowbird: Address error with permission synchronization under a special user.

    When a special user with reserved keyword such as the main Magpie “administrator” was applied a permission, the registration process of the permissions could, in certain cases, yield an error causing the procedure to fail. Notably, if the admin user already exists, which is typically the case since it is required and the service auto-generates it if missing on startup, the permission registration would cause an error since it itself tries to create the user, which is forbidden by the API. This is normally automatically handled by 409 conflict by the registration script, but another 400 error code is used for the special user case, which was not caught.

    In most deployments, this error is not observed since the administrator group is typically employed to apply permissions on multiple “admins” simultaneously, and it does not have the same error handling conditions.

    Because the registration procedure is leveraged by Cowbird to perform a batch multi-permission/resource update, which is the same operation employed by the loaded Magpie configurations, it needs to align with the Magpie API. Cowbird happened to have been using a slightly outdated (although compatible) Magpie 4.3.0 version. Because Magpie and Twitcher have synchronized releases, it is also updated. Both Cowbird, Twitcher and Magpie itself are now aligned with version 5.1.0. These updates also include various dependency security fixes that they share.

  • The birdhouse/birdhouse-deploy repository now makes more effective use of GitHub Workflows in order to automate the release procedure.

    When preparing a new version, the tagging and release steps are now handled by the create-tag.yml and release.yml workflows, respectively. When changes are detected to RELEASE.txt on pushes to master, a new tag is created (create-tag.yml); this then triggers the second workflow (release.yml) to automatically publish the new tag with an autogenerated summary of changes. Developers should no longer tag new releases manually.

  • New GitHub Workflow for automatically accepting minor/patch GitHub Actions updates.

    The auto-accept-ci-changes.yml workflow will now automatically approve and set to auto-merge minor and patch updates of existing GitHub Actions. The approval and merge is performed with a short-lived token created by the Bird-house Helper App, and should handle most updates automatically.

  • Pull Request titles and commits containing [skip jenkins] will no longer trigger Jenkins on CRIM infrastructure.

    Updates to GitHub Workflows from Dependabot are now prefixed with [skip jenkins] in order to prevent redundant testing.

  • pre-commit has been replaced by prek in dependencies and workflows. prek is Rust-built reimplementation of pre-commit that can use the same configuration files and runs much faster with less storage usage.

  • All workflow jobs/steps have names for easier-to-understand build summaries as well as constrained permissions for less potentially attack surface.

  • Update jupyterhub version to 5.4.5-20260506

    This update includes bug fixes and a fix for CVE-2026-33709.

    This update also removes the source code for the magpie authenticator from the jupyterhub package since that code is now maintained in this repo since version 2.22.0.

2.27.0 (2026-04-21)

Changes

  • STAC Browser: update to 5.0.0-rc.0-crim.

    • Adds a code snippet generator to help users obtain a working program in various languages using their search parameters.

    • Includes various UI rendering improvements.

    • Includes dependency and security updates.

  • STAC API: update to crim-ca/stac-app:2.3.1.

    Fix issue related to STAC Item search paging of next links due to token parameter misinterpretation (relates to https://github.com/crim-ca/stac-app/pull/85).

  • STAC Populator: update to crim-ca/stac-populator:0.15.0.

  • Update long-term Prometheus metrics: replace increase by rate and rename metrics. Filter THREDDS downloads to keep only values larger than 0.

2.26.4 (2026-04-16)

Fixes

  • Avoid excessive command logging from birdhouse/scripts/bootstrap-instance-for-testsuite and related scripts.

    Because set -x was used before invoking read_configs and all its nested calls which prints large list of variables and component definitions to configure them, produced logs would reach excessive lengths (tens of thousands of lines) before even reaching the relevant portion of the script to be debugged. The options are moved after the call and each nested script reset its state to better manage their verbosity independently.

    Fixes #673.

2.26.3 (2026-04-15)

Changes

  • Jupyter env: Updated jupyter image (py312-260415). The image has undergone some notable changes:

    • The base Python version has been updated to Python3.12.

    • The image now includes common build tools (x86_64-conda-linux-gnu-{gcc|g++|gfortran}, make, cmake) installed via conda. They are exposed to the userspace via their expected tool names so that common build tools use them by default.

    • The “birdy” ipython kernel has been removed. There are still two conda environments (base and birdy), but the kernels offered to users are now python and the xeus-python kernels (xpython and xpython-raw).

    • jupyterlab has been upgraded from v3.x to v4.x (v4.5.6). This allowed for the removal of several workarounds required for legacy jupyterlab plugins. Modern jupyterlab plugin support no longer requires explicit build/install steps.

    • Updates to all Ouranos software libraries: xclim (v0.60.0), xsdba (v0.6.1), xscen (v0.14.0), figanos (v0.6.0)

    • The latest ravenpy (v0.21.0) conda package now requires the raven model to be explicitly installed (raven-hydro). This was done to more easily allow for users installing custom raven binaries in their environments.

    • Most PyPI-based packages have been removed with the exception of new jupyterlab interface plugins (jupyterlab-logout and jupyterlab-theme-toggler).

    See Ouranosinc/PAVICS-e2e-workflow-tests#161 and Ouranosinc/PAVICS-e2e-workflow-tests#157 for more info.

2.26.2 (2026-04-15)

Fixes

  • New ./optional-components/robots in 2.26.0 broke the stack

    Enabling ./optional-components/robots result in the error services must be a mapping when bringing up the stack with birdhouse compose up -d.

    The new config var ROBOTS_TXT_FILE is not an env var so it is not visible to docker compose.

  • Display warning message for proxy log rotation properly

    Since the ./optional-components/proxy-log-volume can be enabled as a component dependency of ./components/canarie-api we should be checking for it’s presence in ALL_CONF_DIRS. Previously we were checking for it in BIRDHOUSE_EXTRA_CONF_DIRS which is manually set by the user and doesn’t include dynamically added components that are dependants of others.

2.26.1 (2026-04-09)

Changes

2.26.0 (2026-04-09)

Fixes

  • Catch delayed eval variables that get processed multiple times

    If the read_configs function gets called multiple times then delayed eval variables can cause errors.

    For example, if X='$(echo '"')' where X is a delayed eval variable then when it is first processed it will evaluate to X='"' as expected. However if it is run through the delayed eval process again it will raise an error because it treats the " as an unterminated quoted string. This is not the only way to get an error here but it is a simple example to illustrate the issue.

    In order to avoid this, the code now checks if a delayed eval variable was set successfully and if not it falls back to the original value and warns the user. So in the example above the result of running the delayed eval process multiple times will always result in X='"'.

Changes

  • Mount THREDDS data to S3

    Automatically mount data in THREDDS to the S3 service when the optional-components/mount-thredds-to-s3 component is enabled. The S3 service must be enabled as well.

    This creates a new bucket named thredds by default (can be changed by setting the THREDDS_S3_BUCKET_NAME variable) which contains a symlink to the thredds data which is mounted separately to the s3 container.

    A symlink is used so that the THREDDS data itself does not get added as a subdirectory of S3 data which is itself mounted to the S3 component from a bind mount on the host machine.

    A user accessing this data through S3 has the same permissions as if they were accessing the file through THREDDS. Users are currently not permitted to list the files in the thredds bucket since there is no good way to check whether the user has permission to list specific files according to the Magpie resource permissions for THREDDS.

  • Better management of service-config.json files

    Previously the service-config.json files were mounted to the /static/services/ directory on the proxy docker container.

    This mostly worked except that the /static directory was itself mounted from a directory on the host machine. This meant that the files mounted to /static/services were also visible from the host machine and would remain on the host filesystem after the stack was brought down or updated. To fix this the old files were removed in proxy/pre-docker-compose-up but occasionally these files could be owned by the root user which meant that they could not be properly removed. This happens when the docker daemon restarts.

    In order to prevent this, this change instead mounts these files to a different directory (/static-services) on the proxy docker container that is not within a directory also mounted from the host. This means that there is no additional cleanup required to manage these files.

  • Better management of the S3 data files

    Previously the data/ and meta/ subdirectories of the files specified by the S3_DATA_STORE variable were created in a pre-docker-compose-up file that ran on the host machine.

    This works only if these directories can be created as the user executing pre-docker-compose-up which is not the case if the parent folder is root owned. If this is the case, then an error is raised when the stack is brought up and the S3 service is not started.

    In order to prevent this, these subdirectories are now mounted directly as bind mounts to the S3 container which guarantees that they can be created since the user running docker will have permission to create these as bind mounts.

  • Add optional component to mount a robots.txt file

    This adds a robots.txt file to the birdhouse stack which can be used to ask bots and web crawlers to not scrape this website.

    By default it uses a file that disallows crawling by most major AI crawler bots. To specify a custom robots.txt file set the absolute path to the file as the ROBOTS_TXT_FILE configuration variable.

2.25.0 (2026-03-17)

Changes

  • Create S3 service

    Introduces a new service that allows users to download data using an S3 interface. This S3 interface is read-only for users and it’s intended purpose is to serve data (like Thredds, Geoserver, or the secure data proxy).

    Administrators can create buckets on S3 using the make-s3-bucket.sh script. This will create a bucket and create a Magpie resource for that bucket. By default, only admin users will be able to interact with a new bucket but additional read permissions can be added to users and groups through Magpie.

    For example, to create a bucket named “birdhouse”:

    ./birdhouse/scripts/make-s3-bucket.sh birdhouse

    Administrators can interact with the S3 interface with admin permissions through the s3-cli service. This uses the AWS CLI tool and supports all subcommands.

    For example, to list all buckets:

    ./bin/birdhouse compose run --rm s3-cli s3 ls

    or to upload some files to the “birdhouse” bucket

    ./bin/birdhouse compose run --rm -v ./files-to-upload:/data:ro s3-cli s3 cp /data s3://birdhouse

    Administrators can also add files to the birdhouse bucket by adding them directly to the directory specified by the S3_DATA_STORE config variable. For example, if S3_DATA_STORE=/data/s3-data and I want to add the same files in the example above to the “birdhouse” bucket:

    cp -r ./files-to-upload /data/s3-data/birdhouse/

    Note that when setting permission in Magpie that write permissions are ignored and read permissions only apply for buckets and individual files. For example, I can set read permissions on the “birdhouse” bucket and a file in that bucket at “birdhouse/subdir/file.nc” and that will effect whether a user can see the files in “birdhouse” and whether they can read that one file. However, if I set a read permission on “birdhouse/subdir/” this will have no effect on whether the user can or cannot read or browse files in the “subdir/” folder.

  • Add Nvidia MPS component for managing Nvidia GPU resources

    This creates a container running Nvidia’s Multi Process Service (MPS) which helps manage multi-user GPU access. It runs an alternative CUDA interface which manages resource allocation when multiple processes are running simultaneously on the same GPU. It also allows the node admin to set additional per-user limits through the JUPYTERHUB_RESOURCE_LIMITS variable which configures Jupyterlab containers:

    • "gpu_device_mem_limit": sets the CUDA_MPS_PINNED_DEVICE_MEM_LIMIT environment variable

    • "gpu_active_thread_percentage": sets the CUDA_MPS_ACTIVE_THREAD_PERCENTAGE environment variable

    For example, the following will give all users in the group named "users" access to three GPUs in their Jupyterlab container. On the first one (id = 0) only 1GB of memory is available, on the second (id = 1) only 5GB, and on the third (id = 2) only 10GB. Additionally, the container will be able to use 10% of available threads on the GPUs.

    export JUPYTERHUB_RESOURCE_LIMITS='
[{
      "type": "group",
      "name": "users",
      "limits": {
        "gpu_ids": ["0", "1", "2"],
        "gpu_count": 3,
        "gpu_device_mem_limit": "0=1G,1=5G,2=10G",
        "gpu_active_thread_percentage": "10"
      }
}]
'

    Note that leaving any of these limits unset will default to allowing the user full access to the given resource.

  • Update CustomDockerSpawner to make pre spawn hooks and resource limits more configurable

    Introduce builtin_pre_spawn_hooks and resource_limit_callbacks attributes to the CustomDockerSpawner class which can be used to further customize the CustomDockerSpawner from optional components. This gives us a way to add additional functionality without having to directly modify existing functions which may be overwritten by the user when they configure the spawner in JUPYTERHUB_CONFIG_OVERRIDE.

    This also introduces the JUPYTERHUB_CONFIG_OVERRIDE_INTERNAL variable which is identical to the JUPYTERHUB_CONFIG_OVERRIDE variable except that it is intended to only be set by other components (not by the user in the local environment file). This allows components to customize Jupyterhub deployments without interfering with custom settings created by the user.

    Note that the contents of JUPYTERHUB_CONFIG_OVERRIDE have precedence over the contents of JUPYTERHUB_CONFIG_OVERRIDE_INTERNAL. So for example if you create a volume mount named my_volume in both, only the one defined in JUPYTERHUB_CONFIG_OVERRIDE will be applied.

Fixes

  • Update GPU limit examples to show expected syntax

    Fixes some examples that showed that gpu_ids could be given as integers if they were meant to be indexes. However, due to limitation of docker they must be strings. This modifies examples so that it is clear that strings must be used and also updates the code to ensure that string values are only ever passed to docker when spawning a new jupyterlab server.

  • Improve prometheus-longterm-metrics scraping

    The prometheus-longterm-metrics service scrapes longterm data rules from the prometheus service. However, the scrape interval was set too long (1 hour) which meant that some data was probably lost in between scrapes. Also, the prometheus documentation recommends setting unique external_labels when exporting data to a different federated prometheus instance.

    Note that I don’t know how long is too long for a scrape interval before data starts being lost but with some experimentation it seems that 5 minutes is at least below that threshold and it’s not so frequent that it seems like a waste to be polling so often.

2.24.1 (2026-03-04)

Changes

  • CanarieAPI: update to version 1.1.0.

    • Reduces the Docker image size by >50%.

    • Rebuild the Docker image for security fixes.

2.24.0 (2026-03-03)

Changes

  • Update magpie to version 5.0.1

    This update to Magpie introduces network mode.

    This is disabled by default to ensure backwards compatibility but can be enabled by setting MAGPIE_NETWORK_ENABLED=true in your local environment file. Note that enabling network mode also requires setting MAGPIE_NETWORK_INSTANCE_NAME to a unique name within the network.

    Upgrading to this version does not require any database migration and is fully backwards compatible with previous versions.

    This change also introduces the ability to set all configuration options for Magpie’s network mode as environment variables in the local environment file. Note that all of these configuration options will be ignored if MAGPIE_NETWORK_ENABLED is false.

2.23.3 (2026-02-26)

Fixes

  • generic_bird: wrong DB credential provided

    Missing template explansion (since 2.4.0) and wrong credential file (since the beginning!).

    docker logs generic_bird had this error:

    sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) connection to server at "postgres_generic_bird" (172.23.0.20),
port 5432 failed: FATAL:  database "generic_bird" does not exist

    When upgrading from a working existing generic_bird, it is fine but when spinning up a brand new instance, it does not work.

2.23.2 (2026-02-20)

Fixes

  • Unable to set custom homepage due to a missing back-compat config var mapping

    Only when back-compat mode is used. Regression since 2.4.0.

    Missing mapping PROXY_ROOT_LOCATION=BIRDHOUSE_PROXY_ROOT_LOCATION.

2.23.1 (2026-02-17)

Changes

  • STAC API: Security update, minor OpenAPI version reporting fixes, and stac-fastapi/starlette compatibility fix using version 2.3.0 (relates to crim-ca/stac-app#65, crim-ca/stac-app#69 and crim-ca/stac-app#74).

  • Cowbird: Security update using version 2.6.0 (relates to Ouranosinc/cowbird#98).

  • Magpie: Security update using version 4.3.1 (relates to Ouranosinc/Magpie#640 and Ouranosinc/Magpie#642).

  • Twitcher: Security update using version 0.11.0 (relates to bird-house/twitcher#143, bird-house/twitcher#145, bird-house/twitcher#146 and bird-house/twitcher#148).

  • Weaver: Security and dependency fix update using version 6.8.3 (relates to crim-ca/weaver#868, crim-ca/weaver#869, crim-ca/weaver#877 and crim-ca/weaver#881).

  • Weaver: Update post-docker-compose-up script.

    • Handle multiple Magpie cookies in response. This can happen depending on specific internal HTTP libraries versions of the services. To retain backward/forward compatibility, all cookies returned from Magpie are chained in following curl commands.

    • Use birdhouse log utility to report operations produced by the script rather than custom “echo level”.

  • Weaver: Job Result Proxy Buffers

    • The Job Results responses of weaver can return a lot of Link headers. This is done to provide job metadata references and provenance traceability details, but also for actual results locations that can vary in quantity depending on the actual process execution. Therefore, the Ngnix proxy_buffer_size and proxy_buffers directives of the proxy service must be added with sufficiently large values to avoid HTTP 502 errors when the response headers exceed the default buffer sizes. The WEAVER_PROXY_RESPONSE_BUFFER_SIZE and WEAVER_PROXY_RESPONSE_BUFFER_COUNT variables are added to allow further customization as needed by the server. Their defaults are reasonable values to meet minimal requirements by weaver’s metadata Link and a few result outputs.

  • Birdhouse: Allow log <LEVEL> -n ... and log <LEVEL> -p ... to generate log outputs without newline/prefixes.

    These options allow writing multiple log entries onto the same line for correct visual rendering of distinct log calls separated to allow some intermediate logic. The log function invocations with these options respect the log levels in order to make the messages consistent with enabled redirections and verbosity.

2.23.0 (2026-02-13)

Changes

  • DGGS: Update API metadata and version from v0.1.6-rc7 to v0.1.6-rc12.

2.22.1 (2026-02-09)

Changes

  • STAC: add environment variables to facilitate customization of the API’s landing page and OpenAPI metadata.

    • Adds STAC_FASTAPI_VERSION, STAC_FASTAPI_TITLE, STAC_FASTAPI_DESCRIPTION, STAC_FASTAPI_LANDING_ID variables. These names are purposely selected to align natively with stac-fastapi settings. Implementations previously had to manually inject the variables using a docker-compose-extra.yml configuration extending the stac service with the relevant environment variables and values.

2.22.0 (2026-02-09)

Fixes

  • Service files not properly deleted when bringing up the stack

    The service files served by the proxy container as static JSON files were not properly deleted because the command used a path with * in quotes which matches the * character instead of treating it as a glob pattern. This meant that the rm command was trying to remove a file named * instead of all files in the directory.

    The files were also being removed by a plain rm command which is often an alias for rm -i in some shell environments meaning that the deletion could be run interactively. By changing this to rm -f we can ensure that the rm in this script is always in non-interactive mode and it also lets us remove the || true since the -f flag ensures that the return code from rm will always be 0 regardless of whether the command succeeded or failed.

  • Prometheus sends alertmanager API requests to correct path

    Prometheus communicates with alertmanager through its API which is accessible on docker’s bridge network at http://altermanager:9093/alertmanager/api/v2. But, prometheus was not configured to include the /alertmanager subpath so it was actually sending alerts to http://alertmanager:9093/api/v2 which returned a 404 error.

    This fix updates the prometheus configuration so that it sends alerts to the correct URL.

Changes

  • Update cadvisor image version

    Docker engine version 29.0 dropped support for docker API versions <1.44. That means that the docker client used by the cadvisor component cannot be used with modern versions of docker engine. To fix this, the cadvisor component’s image has been updated to the most recent cAdvisor version v0.54.1 which uses a modern version of the docker client.

  • Refactor Jupyterhub configuration files

    Previously the jupyterhub configuration was defined in components/jupyterhub/jupyterhub_config.py.template except for the custom authenticator which was included in the pavics/jupyterhub docker image. This was fine, except that the configuration was split across two projects and as the configuration got more complex, maintaining these was getting more difficult.

    This moves all configuration code including the authenticator to a python package named jupyterhub_custom located at components/jupyterhub/jupyterhub_custom/. It moves all configurations for the authenticator to the magpie_authenticator.py file and all the configurations for the spawner to the custom_spawner.py file. All variables that are settable by environment variables are moved to the constants.py file. This makes it much easier to see which variables are configurable using environment variables all in one place.

    This change introduces unit tests and style policies (enforced by ruff and pre-commit) for this package to encourage better code practices.

    This change should be fully backwards compatible with the exception of the change to how settings for deprecated-components/catalog is handled (see below). However, it does deprecate some environment variables in favour of better configuration solutions:

    • using the JUPYTERHUB_ENABLE_MULTI_NOTEBOOKS variable to set the DockerSpawner.allowed_images variable is deprecated.

      • why?: this variable could be used to insert any python code into the middle of the jupyterhub_config.py.template file. This makes it too easy to accidentally insert code that breaks the configuration settings later on. We should avoid code insertion like this whenever possible.

      • new method: by default DockerSpawner.allowed_images will be set based on the values of JUPYTERHUB_IMAGE_SELECTION_NAMES and JUPYTERHUB_DOCKER_NOTEBOOK_IMAGES. If more than one image is specified by those variables then the user will be able to select which one they want. If you want to specify images other than those in the default, those can be set using the JUPYTERHUB_ALLOWED_IMAGES which is a yaml or JSON mapping of image names to jupyterlab docker image tags.

    • using the JUPYTERHUB_ADMIN_USERS variable to set the DockerSpawner.admin_users variable is deprecated.

      • why?: this also executes arbitrary code (like above). Also, jupyterhub encourages assigning admin permissions based on roles, not by assigning them to the admin_users attribute. This makes it possible to easily revoke admin permissions as well and does not require us to restart Jupyterhub to do so.

      • new method: a new Magpie group is created. Its name is determined by the JUPYTERHUB_ADMIN_GROUP_NAME variable (default is “jupyterhub-admin”). Add users to this group in Magpie in order to give them admin permissions on Jupyterhub.

    • using lowercase constants in JUPYTERHUB_CONFIG_OVERRIDE is deprecated.

      • why?: PEP8 recommends constants be written with capitals with underscores separating them.

      • new method: all the constants that were previously named with lowercase have an uppercase equivalent in constants.py. For example: notebook_dir == constants.NOTEBOOK_DIR. The uppercase version is preferred.

    Note: if your deployment is still using the deprecated-components/catalog component. You may want to manually set the following in JUPYTERHUB_CONFIG_OVERRIDE since the automatic addition of the the CATALOG_USERNAME to the blocked_users set is no longer part of the default settings (since the deprecated-components/catalog component has been deprecated for a long time):

    c.MagpieAuthenticator.blocked_users.add("${CATALOG_USERNAME}")

  • Introduce a scheduler job to delete old files that may accumulate over time

    Creates the optional-component/clean_old_files job that deletes old THREDDS log files and WPS output files. Allows individual cleanup jobs to be enabled for each of raven, finch, hummingbird, and thredds components. Allows the user to configure how old a file must be before it is deleted (age in days) and how to calculate the age of the file (time since last modified, time since last accessed, time since created).

    (see env.local.example or the scheduler documentation for details).

2.21.2 (2026-02-05)

Fixes

  • Bug fixes for healthchecks and update-postgres.sh

    • Fix healthchecks for finch, raven, and postgres-magpie containers

    • update scripts/update-postgres.sh to ensure that the user calling the script has permissions to move directories that may be owned by root.

Changes

  • Set GPU access on Jupyterlab containers based on Magpie user or group name

    Adds to the feature that lets resource allocations to Jupyterlab containers be assigned based on username or group membership.

    New settings for the JUPYTERHUB_RESOURCE_LIMITS variable are gpu_ids and gpu_count.

    gpu_ids are an array of the GPU uuids or zero based indexes of the GPUs that you want to make available to the user or group. GPU uuids and indexes can be discovered by running the nvidia-smi --list-gpus command or similar (such as amd-smi list for AMD GPUs). Uuids are preferred as they remain stable across the life of the GPU. Mixing indexes and uuids is possible but discouraged since it makes it possible to select the same GPU multiple times. If gpu_count is also specified, this is an integer indicating how many GPUs to make available to that user or group. If gpu_count is not specified, then exactly one GPU will be randomly selected. For example, if {"gpu_ids": [1,2,6], "gpu_count": 2} then two GPUs will be randomly selected from the gpu_ids list.

    Also changes the format for JUPYTERHUB_RESOURCE_LIMITS to a yaml or JSON string.

2.21.1 (2026-02-02)

Fixes

  • Services: Update and fix certain /services/... definitions.

    • Fix incorrectly defined links reporting OpenAPI or Docker URIs inappropriately or without adequate media-type.

    • Add /services/canarie definition to provide metadata about CanarieAPI component if enabled.

    • Fix outdated service-config.json definitions sometimes incorrectly detected by docker-compose due to reused inode.

2.21.0 (2026-01-27)

Changes

  • Remove proxy component’s dependency on scheduler and scheduler-job-logrotate-nginx

    Creates new settings in optional-components/proxy-log-volume that create the proxy-logs docker volume as well as instructing Nginx to write access logs to an additional log file (specified by PROXY_LOG_PATH). These settings are included as a COMPONENT_DEPENDENCY in components that require access to the the proxy access logs as a regular file. If no components require access to these logs as a regular file then the proxy component will only write access logs to the stdout stream for that container.

    Right now, the only components that require access to logs in this way are components/canarie-api and optional-components/prometheus-log-parser. Both of these now include optional-components/proxy-log-volume as a COMPONENT_DEPENDENCY.

    Note: this means that if no optional components require optional-components/proxy-log-volume as a dependency then logs from the proxy container will only be written to stdout/stderr. This means that there is no need for any additional custom log rotation handling since the logs are handled directly by docker. This means that the proxy service itself no longer need to be dependant on the scheduler and scheduler-job-logrotate-nginx components.

    Note: a previous discussion suggested that logs could be parsed directly from the stdout stream of the proxy container. However, there is no way to do so that doesn’t require very hacky workarounds. Possible solutions that were explored and rejected include:

    • Mounting the log file from the proxy container from the host to the relevant containers. Rejected because this practice is highly discouraged by docker as the actual storage location of log files is not standardized and may be changed in future versions.

    • Writing logs to a named pipe or socket within the proxy container. Rejected because this is very difficult to set up and is untested when then mounted to other containers. Also, a different named pipe would be required for each consumer which is currently very difficult to set up using birdhouse’s deployment tools.

    Breaking Change: if a custom component (not included in this repository) uses the proxy-logs named volume. It must now include optional-components/proxy-log-volume as a COMPONENT_DEPENDENCY for that custom component.

    Breaking Change: if SCHEDULER_JOB_BACKUP_ARGS specifies -l proxy explicitly (not -l '*') then this should be changed to -l proxy-log-volume since the backup script has been moved. Note that it is not necessary to specify -l proxy-log-volume if --birdhouse-logs is also specified because the log data is identical in both.

  • Make docker compose logging options configurable

    Introduce a new component components/logging that sets default logging options for all docker compose services started by birdhouse-deploy. This component is enabled by default.

    The default value is set by the BIRDHOUSE_DOCKER_LOGGING_DEFAULT environment variable. To change the default value, set the BIRDHOUSE_DOCKER_LOGGING_DEFAULT to a JSON string in the local environment file that contains a valid docker compose logging configuration.

    For example, to set the default driver to “local” set the following in your local environment file:

    export BIRDHOUSE_DOCKER_LOGGING_DEFAULT='{"driver": "local"}'

    You can also override logging options for a single service using environment variables using a variable BIRDHOUSE_DOCKER_LOGGING_<service_name> where <service_name> is the uppercase name of the docker compose service with hyphens replaced with underscores. For example, to set the default driver to “local” only for the weaver-worker service:

    export BIRDHOUSE_DOCKER_LOGGING_WEAVER_WORKER='{"driver": "local"}'

    Logging options can can also be set directly in a component’s docker-compose-extra.yml file. The order of precedence for logging options are as follows:

    1. logging options specified by BIRDHOUSE_DOCKER_LOGGING_<service_name> environment variable

    2. logging options set in a docker-compose-extra.yml file

    3. logging options specified by BIRDHOUSE_DOCKER_LOGGING_DEFAULT environment variable

  • Add script that automatically updates postgres databases to a later version

    In anticipation of upgrading postgres databases in the future, this introduces a script that automatically upgrades postgres databases using the backup/restore process.

    This includes magpie and all WPS birds that use the postgres component. This does not include test component like optional-components/generic_bird and will not update custom components (ones not from this repository).

    Test components are not assumed to have persistent data that needs to be updated and we cannot guarantee that other postgres databases used by components outside this repository do not require additional steps (data migrations) in order to comply with a different version of postgres.

    It will update postgres databases to the version specified by the POSTGRES_VERSION_UPDATE environment variable. All of the old database files will be copied to a temporary directory in case you want to inspect them or revert this operation later on. To specify which directory to write these backups to set the BIRDHOUSE_BACKUP_DATA_DIR variable (default: ${TMPDIR:-/tmp}/birdhouse-postgres-migrate-backup/)

    Note that backups in the form of database dumps will also be written to the named volume or directory specified by the BIRDHOUSE_BACKUP_VOLUME variable.

    For example, to update the current postgres databases to version 18.1 and write backups to /tmp/test/

    $ POSTGRES_VERSION_UPDATE=18.1 BIRDHOUSE_BACKUP_DATA_DIR=/tmp/test/ birdhouse/scripts/update-postgresh.sh

    In a future update we can update the postgres versions and tell users to run this script first in order to safely migrate data from one version to the next.

2.20.4 (2026-01-16)

Fixes

  • Update scheduler image version

    Docker engine version 29.0 dropped support for docker API versions <1.44. That means that the docker client used by the scheduler component cannot be used with modern versions of docker engine. To fix this, the scheduler component’s image has been updated to version 0.6-rc3 which uses a modern version of the docker client.

2.20.3 (2026-01-13)

Fixes

  • Fix bugs in get-components-json.include.sh and simplify get-services-json.include.sh

    get-components-json.include.sh was unable to handle the case where a component was commented out in the BIRDHOUSE_EXTRA_CONF_DIRS variable.

    This also simplifies the code in both files to make it easier to maintain:

    • removed unnecessary variable declarations

    • simplify component discovery get-components-json.include.sh

  • Incorrect usage checks for birdhouse backup create

    Running birdhouse backup create was failing without either the --no-restic or --snapshot options specified. However, --snapshot is only required for the restore subargument (not create) and so create would often fail with a confusing error message.

    This fixes the issue by moving the check so that it is only triggered when restoring a backup.

2.20.2 (2026-01-05)

Changes

  • STAC API: Improve reported service links.

    • Add STAC_LICENSE_URL to define the relevant license metadata location of the selected implementation.

    • Add STAC_OPENAPI_SPEC_PATH and STAC_OPENAPI_DOCS_PATH to define endpoints of OpenAPI specification.

    • Update the /services/stac response to provide more metadata links, including license details and better API metadata references. Notably, replace the generic STAC API Core OpenAPI definition by the implementation-specific definition self-served by the selected docker image to document API extensions.

2.20.1 (2025-12-16)

Fixes

  • Add log rotation scheduler job for the nginx logs

    Currently, the nginx logs are not rotated so they can build up to quite a large size.

    Previously, they were rotated by the canarie-api component but that is no longer a required component and CanarieAPI hasn’t handled log rotation since CanarieAPI version 1.0.0 (see https://github.com/bird-house/birdhouse-deploy/pull/452 for details).

    Fixes https://github.com/bird-house/birdhouse-deploy/issues/593. Here is a summary of the issue:

    • CanarieApi parses the log file every minute starting from the beginning of the file

    • If the log file is really big it uses a lot of CPU and memory to read through the whole file

    • This would use a lot less CPU and memory if the log file was smaller

    This quick and least disruptive fix to get the production server out of the water should be a temporary solution until a better solution using container STDOUT parsing is implemented for the CanarieAPI and prometheus-log-parser (https://github.com/bird-house/birdhouse-deploy/issues/618). Then we can deprecate this scheduler job.

2.20.0 (2025-12-10)

Changes

  • STAC API: update to version 2.1.0.

    • Fix paging error on /collections responses causing requests with limit query or catalogs with more than 10 collections (by default) to never return collections beyond the first page.

  • STAC Browser: update to version 4.0.0-rc.2-crim.

    Apply upstream fixes, notably:

    • Logo resizing issue when embedded in contact details.

    • Handling of geojson.io external viewer references from compatible GeoJSON STAC Assets.

    • Improvements to UI for better locales, content positioning and browsing experience.

    • Alignment with latest OGC APIs requirements and conformance classes.

    • Added support for multiple additional data representations and visualization.

2.19.0 (2025-12-05)

Changes

  • DGGS: Add the new components/dggs providing an OGC API for Discrete Global Grid Systems.

    • DGGS API available through /dggs-api path (default, configurable via DGGS_API_PATH).

    • Redirects available for /ogcapi/dggs/... and /ogcapi/collections/.../dggs/....

    • Sample configuration (minimum 1 resolvable data provider required) uses the new feature of optional-components/secure-data-proxy on CRIM’s Hirondelle server.

  • Data: Allow optional-components/secure-data-proxy to define generic and flexible locations.

    • SECURE_DATA_PROXY_ROOT can be defined as mount directory inside the proxy service.

    • SECURE_DATA_PROXY_LOCATIONS can be defined with any amount of custom locations.

    • All locations can be configured (as desired) under Magpie secure-data-proxy service for access control.

    • Other components (wps_output-volume, stac-data-proxy) that can optionally use this security middleware via SECURE_DATA_PROXY_AUTH_INCLUDE can still do so. Their mount points are handled separately.

  • Weaver: Modified /ogcapi/... redirections strategy via WEAVER_ALT_PREFIX_PROXY_LOCATION.

    • Allows other OGC APIs to reuse the same prefix to provide a unified location to access them.

2.18.16 (2025-12-05)

Changes

  • Proxy: Allow Access-Control-Allow-Origin header to be configured using BIRDHOUSE_PROXY_CORS_ALLOW_ORIGIN variable.

    • A defaults.include.template file is introduced to setup global nginx server defaults that can be overridden by more specialized definitions in location blocks of components.

    • The default BIRDHOUSE_PROXY_CORS_ALLOW_ORIGIN="*" is used to retain the previous behaviour.

    • The BIRDHOUSE_PROXY_CORS_ALLOW_ORIGIN variable can reference other variables to allow dynamic configuration (notably, to reference BIRDHOUSE_FQDN_PUBLIC for same-origin allowance).

    • Align the documentation with corresponding STAC_CORS_ORIGINS header implications.

    • Avoids Nginx warnings flagged from using uninitialized access_control_allow_origin variable (fixes https://github.com/bird-house/birdhouse-deploy/issues/610).

2.18.15 (2025-12-01)

Changes

  • README: remind the user to source control env.local securely as it may contain passwords.

Fixes

  • Autodeploy broken due to new config variable precedence order.

    Broken since 2.18.8 (https://github.com/bird-house/birdhouse-deploy/pull/600).

    Example breakage scenario:

    Autodeploy starts and calls read_configs, then git pull a newer version of env.local (which might modify EXTRA_CONF_DIRS to enable new components for example). But since the new var precedence locked all the values to the first call of read_configs, the new change to EXTRA_CONF_DIRS (or any vars in env.local) never went into effect at the end of the autodeploy process when we start the full stack.

    This is because read_configs returns all variables as environment variables and the new variable precedence order gives environment variables precedence higher than the values in env.local. So after the first call to read_configs (or read_basic_configs_only), all the values are “locked” for all child processes even if they try to call read_configs again to get the newest values from env.local.

    The fix is to avoid getting these config variables as environment variables which will avoid “locking” their values for child processes.

  • Autodeploy broken due to attempt to be compat with changing the location of env.local via BIRDHOUSE_LOCAL_ENV.

    Broken since 2.18.9 (https://github.com/bird-house/birdhouse-deploy/pull/601).

    It was working for the first run of autodeploy but on the next run, the value of BIRDHOUSE_LOCAL_ENV in optional-components/scheduler-job-autodeploy/config.yml is wrong !

    Good value in first run:

    --volume /real/path/to/env.local:/tmp/birdhouse-local-env

    Bad value in subsequent run:

    --volume /tmp/birdhouse-local-env:/tmp/birdhouse-local-env

    This is because we override --env BIRDHOUSE_LOCAL_ENV=/tmp/birdhouse-local-env in optional-components/scheduler-job-autodeploy/config.yml.template as env var so on the subsequent runs the bad value persists because it is an env var.

    This BIRDHOUSE_LOCAL_ENV is meant to be set “outside” the stack as env var so there is nothing in the stack that will fix this value if it is bad.

    The fix is to revert that attempt. So autodeploy only supports changing the location of env.local via symlink, or by manually adding the folder containing the file env.local to BIRDHOUSE_AUTODEPLOY_EXTRA_REPOS if env.local is set by BIRDHOUSE_LOCAL_ENV environment variable and not via symlink.

  • One feature of autodeploy is broken due to a missing mapping in back-compat config var name change.

    Broken since 2.4.0 but only if back-compat var name mode is required.

    The AUTODEPLOY_CODE_OWNERSHIP old name mapping is missing in BIRDHOUSE_BACKWARDS_COMPATIBLE_VARIABLES.

    Autodeploy is missing the chown step to the good code owner because it does not “see” the value of the old variable name since the mapping to the new variable name is missing.

  • Missing default value for BIRDHOUSE_HTTP_ONLY causing inconsistent behavior when the var is used in env.local then removed from env.local. The behavior never revert back as if it has never been initially used in env.local. See discussion.

2.18.14 (2025-12-01)

Fixes

  • Ensure Jupyterlab container healthchecks don’t fail because of leftover files

    Leftover files from Jupyterlab containers that didn’t shut down properly could cause the healthcheck to always fail. Old files are now removed when the container starts up so this is avoided.

    The full explanation:

    If a Jupyterlab container is not shut down properly then it does not have a chance to clean up old runtime files. These runtime files are stored in the user’s home directory which is persisted between containers as a bind-mount.

    When the Jupyterlab container is created again, it will create new versions of some of these files. One of which is the jpserver JSON files which contains a URL used by the healthchecks.

    This URL contains the hostname of the Jupyterlab container which is different each time a new container is created. Different files will have different hostnames, only one of which will be the hostname for the current container.

    Since the healthchecks use glob which returns files in an arbitrary order, the healthcheck can easily choose an old file with an old hostname. If that is the case, the healthcheck will always fail.

2.18.13 (2025-12-01)

Changes

  • Update prometheus-log-parser component to use version 1.1.1 of the log-parser

    See changes for versions 1.1.0 and 1.1.1.

    The most relevant changes to this project are support for parsing logs from streams (like stdout) and a safer way to kill the running log-parser container.

2.18.12 (2025-11-25)

Changes

  • Add mechanism to set CPU and memory limits on Jupyterlab containers based on Magpie user or group name

    Creates a new variable JUPYTERHUB_RESOURCE_LIMITS which sets resource limits for JupyterLab containers per Magpie user or group.

    The value for this variable is a whitespace delimited string. Each section is delimited by colons (:) where the first element is either group or user and the second element is the name of the user or group to apply the limits to. The rest are resource limits of the form limit=amount. For example:

    export JUPYTERHUB_RESOURCE_LIMITS="
   user:user1:mem_limit=30G
   group:group1:mem_limit=10G:cpu_limit=1
   group:group2:cpu_limit=3
"

    Supported limits are: mem_limit and cpu_limit.

    Note that this will not create the groups in Magpie, that must be done by some other means (through configuration files or the Magpie API or UI).

    Note that if a user belongs to multiple groups, later values in JUPYTERHUB_RESOURCE_LIMITS will take precedence. For example, if a user named user1 belongs to group1 and group2 then the following limits will apply:

    • mem_limit=10G (because group1 is later in the list)

    • cpu_limit=3 (because group2 is later in the list)

2.18.11 (2025-11-13)

Changes

  • Update $schema in all service.config.json.template files to version 1.3.0

    Version 1.3.0 replaces “keywords” with “types” and allow keywords to be any string.

  • Fix bin/birdhouse configs --default flag usage description

    Previously the description made it seem like the local environment file would not be read if this option was specified. In fact, it’s the components that won’t be read.

    Also rename the --default flag to --basic to reflect the function it calls (read_basic_configs_only) but keep the old version for backwards compatibility.

2.18.10 (2025-11-12)

Changes

  • Allow each service to specify values for Access-Control-Allow-Origin

    Previously, if a location block in the nginx configuration for a given service included the cors helper configuration (with include /etc/nginx/conf.d/cors.include;) then all origins were allowed by default.

    This was done by setting the header Access-Control-Allow-Origin: * which works well but is a bit too permissive since it allowed all origins.

    This change introduces a mechanism to specify specific additional allowed origins by setting the $access_control_allow_origin nginx variable in the location block before including the cors.include file.

    For example:

    set $access_control_allow_origin http://example.com;
include /etc/nginx/conf.d/cors.include;

    will set the value of the Access-Control-Allow-Origin response header to http://example.com.

    By default, the header value will be * if $access_control_allow_origin is not set (to maintain backwards compatibility).

    To specify multiple allowed origins, use a map directive (see the implementation for components/stac for an example).

  • Set allowed CORS origins for stac through an environment variable

    This change implements this flexibility for the components/stac component. By setting the STAC_CORS_ORIGINS variable a user can specify allowed origins for responses from the components/stac component.

    For example, setting the following:

    export STAC_CORS_ORIGINS='https://example.com ~^https?://(www\.)?other\.example\.com$'

    then requests from https://example.com and http://other.example.com will get a response with the Access-Control-Allow-Origin header set to their origin, but http://example.ca will not.

    Note that this breaks backwards compatibility slightly since previously all origins were allowed for /stac by default. To match all origins and keep the backwards compatible behaviour you can set:

    export STAC_CORS_ORIGINS='~.*'

2.18.9 (2025-11-10)

Changes

  • Centralize management of docker-compose image version needed by birdhouse-compose.sh script.

    To simplify future version update and to easily shared by other future components.

    Backward compatible change:

    • Added config variables

      • BIRDHOUSE_COMPOSE_DOCKER

      • BIRDHOUSE_COMPOSE_VERSION

      • BIRDHOUSE_COMPOSE_IMAGE

  • Update DOCKER_CLI_IMAGE version.

    Simply to match BIRDHOUSE_COMPOSE_IMAGE version. Previous version was not causing any problems.

  • Centralized usage of DOCKER_CLI_IMAGE in all scheduler jobs.

    To ease future version update and for all jobs to be consistent.

    Backward compatible change:

    • Added config variables

      • DOCKER_CLI_DOCKER

      • DOCKER_CLI_VERSION

  • scheduler-job-autodeploy: make compatible with change of BIRDHOUSE_LOCAL_ENV via env var and not symlink

    See https://github.com/bird-house/birdhouse-deploy/pull/597#issuecomment-3428179549.

Fixes

  • scheduler-job-deploy_xclim_testdata wrongly used variables from scheduler-job-deploy_raven_testdata.

  • scheduler-jobs: fix deploy raven and xclim testdata missing logs, forgot delayed eval

2.18.8 (2025-10-30)

Changes

  • Allow configuration options to be set as environment variables

    Previously configuration options must be set in the local environment file (birdhouse/env.local by default). This change allows configuration options to be set as environment variables which would take precedence over those set in the local environment file.

    For example, you can now set the BIRDHOUSE_FQDN variable when starting the stack like so:

    BIRDHOUSE_FQDN=myhost.example.com bin/birdhouse compose up -d

# OR

export BIRDHOUSE_FQDN=myhost.example.com
bin/birdhouse compose up -d

    This change has the following advantages:

    • flexibility: the user has more options for how they can customize their deployment

    • good dev-ops: this change further aligns birdhouse with the 12 factor app principles, specifically the Config principle which recommends that configuration options be settable as environment variables.

    • security: sensitive settings (credentials, secrets) can be set as environment variables, ensuring that they are not easily visible in the plain text local environment file.

    • consistency: users can store non-sensitive settings in the local environment file and share that file freely without worrying that sensitive setting will be leaked.

2.18.7 (2025-10-17)

Fixes

  • Autodeploy unable to git pull the newer env.local file.

    Previously the env.local file could be a symlink to a file anywhere on the disk.

    Now env.local can only be a symlink to a file under a folder listed in BIRDHOUSE_AUTODEPLOY_EXTRA_REPOS.

    This is a new restriction from the newer autodeploy docker image in the previous release 2.18.5 below. We can not volume-mount both the parent dir and the file at the same time and have write access. We can only volume-mount one of the two. For read-only access, it is still okay to volume-mount both.

2.18.6 (2025-10-17)

Fixes

  • STAC Browser: fix resolution against the pre-built prefix path to align with proxy configuration.

    • Add STAC_BROWSER_PATH_PREFIX variable that makes the mapping more easily configurable. However, changing its value requires building the corresponding docker wih the same prefix. The change will not be effective “simply” by modifying the variable.

    • Revert to crim-ca/stac-browser:3.3.5 (rather than crim-ca/stac-browser:3.4.0-dev) without need of the temporary patch (relates to https://github.com/radiantearth/stac-browser/pull/653).

2.18.5 (2025-10-15)

Fixes

  • Modify Prometheus Thredds counter to record bytes instead of kb.

  • Change longterm rule names to follow naming conventions.

Changes

  • Update autodeploy image to latest version

    This makes autodeploy compatible with newer Docker engine installed on the host #246.

    Also makes autodeploy compatible with newer docker-compose syntax version #505.

2.18.4 (2025-10-01)

Fixes

2.18.3 (2025-09-26)

Fixes

  • Fix various bugs with backward-compatibility mode

    • Missing template expansion for old variable names

      This bug only affect external repos still using old variable names for template expansion.

    • Missing delayed eval for old variable names

      This bug only affect external repos still using old variable names for delayed eval.

    • Lost new lines when new value is transfered to old value and vice-versa

      Example: if ENABLE_JUPYTERHUB_MULTI_NOTEBOOKS (old var) is set in env.local, the new matching var JUPYTERHUB_ENABLE_MULTI_NOTEBOOKS is automatically set but lost the new lines from the old var.

      This is bad because subsequently, when new var JUPYTERHUB_ENABLE_MULTI_NOTEBOOKS is used in components/jupyterhub/jupyterhub_config.py.template for template expansion, it will generate badly formatted code since the new lines are lost.

      The reverse case: external repos still using old vars for template expansion but in env.local the new var is used, the value transfered from the new var to the old var is missing all the new lines and also generate broken code.

    • Wrong old var overriding new var during child invocation, even when new var is set properly in env.local.

      This bug is mostly visible with child invocation. First level invocation, to be affected, need to use the old var name, which means external repos only because the current repo has all switched to use the new var names.

      Previously set_old_backwards_compatible_variables was called before read_env_local which means old var names were initialized with default values only, not the updated values from env.local. On child invocation, since the old var already exists, it overrides the new var even if the new var is properly set in env.local.

      For the autodeploy process, triggerdeploy.sh is the first level invocation and autodeploy.sh is the child invocation. It blows up in the child invocation when BIRDHOUSE_LOG_DIR resets to the default value even when BIRDHOUSE_LOG_DIR (new var) is sets properly in env.local.

      Most other scripts do not have a child invocation so they all work fine and that’s why this back-compat bug is discovered so late.

    • New var reset to default in child invocation even when old var is set properly in env.local

      This bug happens for child invocation only.

      Example: in autodeploy, triggerdeploy.sh is the first level invocation and deploy.sh is the child invocation. SSL_CERTIFICATE (old var) is properly set in env.local but BIRDHOUSE_SSL_CERTIFICATE (new var) resets to default value in deploy.sh and breaks autodepploy.

      In process_backwards_compatible_variables(), it has to change to process all old vars and not just those old vars not set in set_old_backwards_compatible_variables().

      Technically this is safe because all the old vars set in set_old_backwards_compatible_variables() are set from new var values or default values so setting “new_var = old_value” back in process_backwards_compatible_variables() is basically setting the same value again.

  • Fix process_delayed_eval() losing new lines and leading empty space after being eval’ed

    Example: if AUTODEPLOY_PLATFORM_EXTRA_DOCKER_ARGS is set in env.local and added to DELAYED_EVAL in env.local because it uses other variables, the new lines and the 4 front spaces must be kept for proper yaml syntax when template expanding in components/scheduler/config.yml.template.

Changes

  • Remove 5 duplicate intermediate unused SERVER_ vars

    The back-compat code and mapping syntax only support one rename. Those 5 SERVER_ vars are intermediate rename (orig -> SERVER_orig -> BIRDHOUSE_orig) and not fully supported in the current state.

    • SERVER_DOC_URL=BIRDHOUSE_DOC_URL

    • SERVER_SUPPORT_EMAIL=BIRDHOUSE_SUPPORT_EMAIL

    • SERVER_SSL_CERTIFICATE=BIRDHOUSE_SSL_CERTIFICATE

    • SERVER_DATA_PERSIST_SHARED_ROOT=BIRDHOUSE_DATA_PERSIST_SHARED_ROOT

    • SERVER_WPS_OUTPUTS_DIR=BIRDHOUSE_WPS_OUTPUTS_DIR

    Those 5 SERVER_ were intermediate rename inside a same PR so they never made it to any release. Nobody should ever have been aware of them.

2.18.2 (2025-09-24)

Fixes

2.18.1 (2025-09-23)

Fixes

2.18.0 (2025-09-19)

Changes

  • STAC: Split the services API/UI into distinct components/stac and components/stac-browser.

    • Enabling only components/stac will not provide /stac-browser/ endpoint anymore. It must be explicitly enabled.

    • Enabling components/stac-browser will enforce enabling components/stac as a dependency.

    • Add missing STAC_BROWSER_DOCKER variable to respect the standard naming convention used by other components.

    • Each component has their respective service-config.json.template definition.

  • Twitcher: Define variables in the standard naming convention used by other components.

    • TWITCHER_VERSION, TWITCHER_DOCKER, TWITCHER_IMAGE

    • TWITCHER_RELEASE is used to resolve the version property of service-config.json.template which has special consideration with MAGPIE_VERSION

  • Cowbird: Define variables in the standard naming convention used by other components.

    • COWBIRD_DOCKER, COWBIRD_IMAGE, COWBIRD_IMAGE_API, COWBIRD_IMAGE_WORKER, COWBIRD_IMAGE_URI

  • Services: Add more links and references.

    • Add a /services/{serviceId} endpoint to retrieve individual service metadata definitions.

    • Add missing service-config.json.template files for Magpie, Twitcher and Cowbird.

    • Extend the provided metadata links for multiple services.

    • Change all service-config.json.template definition to be directly the JSON object rather than an array. This allows reporting these objects directly on /services/{serviceId}, while /services combines them.

Fixes

  • Proxy: Fix lost HTTP method on redirect to HTTPS.

2.17.2 (2025-09-12)

Fixes

  • Magpie: Fix trailing slash redirect handling between the proxy and magpie.

2.17.1 (2025-09-10)

Fixes

  • Weaver: Fix invalid JSON/HTML media-types for reported /services links without explicit format indicator.

2.17.0 (2025-09-02)

Changes

  • STAC: Update STAC Browser to crim-ca/stac-browser:3.4.0-dev.

    • Dockers are now built directly with the GitHub CI releases (see https://github.com/crim-ca/stac-browser/pkgs/container/stac-browser).

    • Synchronize with latest changes (as of 2025-08-16).

      • Beside the necessary prefixPath override for Nginx Proxy redirect and a minor HTML file resolution fix, the image is entirely up-to-date with the official upstream code.

      • Supports STAC 1.1.0.

      • Supports language locales.

      • Greatly improves parsing of STAC metadata and their visual rendering.

      • Allows dynamic runtime config.js overrides. For the time being, only the required catalogUrl is overridden, but further settings could be added later on.

  • STAC: Update STAC API to crim-ca/stac-app:2.0.1.

    • Changes in crim-ca/stac-app:2.0.0 includes:

      • migration to stac-fastapi==6.0.0 and corresponding fixes to support it

      • add q parameter free-text search on /search, /collections and /collections/{collectionId}/items endpoints

      • enforce JSON schema validation of all stac_extensions referenced by published STAC Items and Collections

      • multiple dependency updates

    • Minor package dependency fix in crim-ca/stac-app:2.0.1.

  • STAC: Update stac-db and stac-migration to version 0.9.8.

  • STAC: Add optional/stac-db-persist and STAC_DB_PERSIST_DIR to allow custom STAC DB metadata storage location.

  • Drop unsupported pytest-lazy-fixture python package for tests

    This package is no longer maintained and breaks for pytest versions 8+. We do not need it for our tests so it was dropped. In the future if we need to support lazy fixtures we should use the pytest-lazy-fixtures package instead (which is actively maintained).

  • Dependabot automated updates for Python dependencies.

    The following Python dependencies were updated to their most recent compatible releases:

    • jsonschema: 4.17.1 -> 4.25.1

    • prometheus-client: 0.22.0 -> 0.22.1

    • pytest: 7.2.2 -> 8.4.1

    • python-dotenv: 1.0.1 -> 1.1.1

    • requests: 2.32.4 -> 2.32.5

Fixes

  • Backup: Fix STAC representative data restore operation (birdhouse backup restore -r stac).

    • Change the default STAC_POPULATOR_BACKUP_VERSION=0.9.0 to employ the Dockerfile of ``stac-populator` <https://github.com/crim-ca/stac-populator/blob/master/docker/Dockerfile>`_ fix with preconfigured PYESSV_ARCHIVE_HOME directory.

    • Add stac-migration along stac-db to the list of stopped/restored containers to ensure that the stac-db volume used by both does not yield a docker daemon error of “volume in use”, and to apply any relevant migration scripts on the recreated stac-db volume.

2.16.14 (2025-08-27)

Fixes

  • Updated configuration of .github/labeler.yml to follow the new actions/labeler v5.0 conventions.

    In Birdhouse-deploy v2.16.11, the actions/labeler action was updated to v5.0 which introduced a new configuration format for the .github/labeler.yml file. This change updates the configuration to follow the new format. See: actions/labeler v5.0 release notes.

2.16.13 (2025-08-27)

Changes

  • Updated the finch service to v0.12.1.

    This is a significant jump from the previous version (v0.9.2) and includes many bug fixes and dependency updates:

    • anyascii (replacement for unidecode)

    • xclim v0.43.0 (previously xclim v0.37)

2.16.12 (2025-08-27)

Fixes

  • User kernels directory should always be writable

    The destination used to symlink user kernels (/usr/local/share/jupyter) is not always writable depending on the jupyterlab docker image that is used to spawn the jupyterlab containers. To ensure that it is always writable this places the link under /var/tmp which is guaranteed to be writable.

2.16.11 (2025-08-22)

Changes

  • Added a Dependabot configuration for tracking version updates for pip and for GitHub Actions

    GitHub Actions have been updated to their most recent versions and their versions now point to commit hashes instead of version tags for security purposes. Dependabot has been configured to perform periodic updates on these actions. Python requirements (requirements.txt) now use commit hashes generated via the pip-tools library for security purposes as well. The list of Python library requirements has been moved to requirements.in and is also managed by Dependabot.

  • Added nodefaults to the environment-dev.yml to ensure that the Anaconda “default” repository is never used for environment creation

  • Replaced bump2version with a maintained fork (bump-my-version) in the development dependencies and the top-level Makefile

    Migrated the .bumpversion.cfg to use newer TOML format (.bumpversion.toml) and removed the logic in Makefile centred on tracking and updating the date of last version bump as this is now handled dynamically via bump-my-version

2.16.10 (2025-08-16)

Changes

  • Proxy: allow to add parameters to Nginx listen directives via env.local

    One usage is to add the parameter “http2” to enable HTTP/2 protocol.

    Before

    $ curl --silent --include https://${BIRDHOUSE_FQDN_PUBLIC}/ | head -1
HTTP/1.1 200 OK

    After export PROXY_LISTEN_443_PARAMS="http2" is set in env.local and proxy container restarted

    $ curl --silent --include https://${BIRDHOUSE_FQDN_PUBLIC}/ | head -1
HTTP/2 200

2.16.9 (2025-08-15)

Changes

  • Backup: Allow BIRDHOUSE_BACKUP_VOLUME to be employed directly as directory.

    This feature *requires* using the --no-restic option to avoid it being involved by --snapshot override. Combining a directory path and omitting --no-restic can lead to undesired side effects. However, it allows using backup/restore operations for quick data manipulations on alternate locations than a volume to offer flexibility or to bypass restic operations. This can be employed for fixing problematic service data migrations or file system limitations with volumes.

    The directory structure must match exactly with BIRDHOUSE_BACKUP_VOLUME when used as volume (e.g.: /tmp/backup/{component}-{backup_type}/...).

    This feature also disables the automatic cleanup of the volume (since the directory is used directly). Therefore, users have to manage the contents of BIRDHOUSE_BACKUP_VOLUME on their own and consistently.

  • Backup: Avoid birdhouse backup restore operation to complain about missing -s|--snapshot when not required.

    For example, BIRDHOUSE_BACKUP_VOLUME=/tmp/backup birdhouse backup restore --no-restic -r stac only operates on local data contents to be restored into the server instance. No remote restic snapshot is required to run the operation.

  • Backup: Unification of script shebangs, variables names and function names with invoked operations.

    • Renames related to backup [create|restore|restic] when they apply to many operations simultaneously. This helps highlight that a variable with explicitly CREATE, RESTORE or RESTIC only applies to that specific operation, whereas others are shared.

      • parse_backup_restore_common_args => parse_backup_common_args

      • BIRDHOUSE_BACKUP_RESTORE_NO_RESTIC => BIRDHOUSE_BACKUP_NO_RESTIC

      • BIRDHOUSE_BACKUP_RESTORE_COMMAND => BIRDHOUSE_BACKUP_COMMAND

    • Renames to match the common BIRDHOUSE_BACKUP_[...] prefix employed by other “backup” variables:

      • BIRDHOUSE_RESTORE_SNAPSHOT => BIRDHOUSE_BACKUP_RESTORE_SNAPSHOT

  • Backup: Add stac-migration image to the list of containers to stop on birdhouse backup restore -r stac.

    Because the service was not stopped, and that it links to stac-db and its corresponding volume, the following docker volume rm stac-db step would fail as the volume was still in use. This would lead to a restore operation dealing with dirty database contents and potentially conflicting restore data that would not be applied. Relates to added service stac-migration in #534.

  • Backup: Allow BIRDHOUSE_LOG_LEVEL to override the stac-populator log level involved with -r stac.

2.16.8 (2025-08-13)

Fixes

  • Allow user generated jupyterlab kernels to persist between sessions

    If a jupyterlab user wants to create a virtual environment to use as a kernel they can do so by creating a new virtual environment and installing it as a kernel with the python -m ipykernel install command.

    By default this command installs the kernel metadata in /usr/local/share/jupyter/kernels which is not persisted to a docker volume and so the kernel is no longer visible when the jupyterlab container restarts. Alternatively, the command can be run with the --user flag which installs the kernel metadata to the user’s home directory (which is persisted to a docker volume) but the jupyterlab API does not recognize kernels installed in this way for some reason.

    To solve this issue, this creates a symlink from the kernels metadata folder in the user’s home directory to a location outside of the user’s home directory (/usr/local/share/jupyter/user-kernels/kernels) which can be detected by the juptyerlab API.

  • Ensure jupyterlab container healthchecks don’t fail by default

    The healthchecks assume that the jupyter data directory is in /home/$NB_USER/.local regardless of the value of $HOME. This means that healthechecks for the jupyterlab containers were always failing even if the container was actually healthy.

    This fixes the issue by symlinking the relevant folder to /home/$NB_USER/.local within the container so that the healthchecks can run as expected.

  • Thanos-minio container should always restart on failure

    Since this container wasn’t restarting automatically it could make the entire stack unavailable if it failed. The proxy container would refuse to start since it could not connect to the upstream thanos-minio server.

2.16.7 (2025-08-05)

Fixes

  • Fixed a malformed rsync command in deploy-data-raven-testdata-to-thredds.yml workflow.

    The --exclude option was not used properly which would cause the rsync command to fail. This is now fixed.

2.16.6 (2025-08-01)

Changes

  • Jupyter env: Updated jupyter image (py311-250423-update250730) with new dependency intake-esgf, significantly changed ravenpy (v0.19.0), as well as marginal updates to Ouranos core libraries: xclim (v0.57.0), xsdba (v0.12.3), and xscen (v0.5.0).

    See Ouranosinc/PAVICS-e2e-workflow-tests#150 for more info.

  • Updated deploy-data-raven-testdata-to-thredds.yml to reflect the new raven-testdata repository structure.

    The deploy-data-raven-testdata-to-thredds.yml workflow was updated to reflect the new structure of the raven-testdata repository. The new structure includes a data directory that contains all the test data files and provides more granular control by setting tagged commits as targets for the test data required for a specific version of raven and RavenPy. This new layout emulates the same control functionality employed in xclim/xclim-testdata.

2.16.5 (2025-07-18)

Changes

Fixes

  • Fix empty newlines displayed on COMPOSE_CONF_LIST output.

2.16.4 (2025-07-03)

Fixes

  • Fix invalid STAC_POPULATOR_BACKUP_IMAGE='${STAC_POPULATOR_BACKUP_DOCKER}:${STAC_POPULATOR_BACKUP_VERSION}'.

    The STAC_POPULATOR_BACKUP_IMAGE variable was referring other variables missing their _BACKUP part.

2.16.3 (2025-06-25)

Fixes

  • Fix thredds_transfer_size_kb_total name in optional-components/prometheus-longterm-rules.

    Counter names have the suffix _total. Without this suffix, the counter value is not discovered properly in a rule and the prometheus rule will never return valid data.

  • Fix bugs in prometheus-log-exporter.

  • Avoid tput: No value for $TERM and no -T specified warnings if terminal is undefined.

2.16.2 (2025-06-23)

Changes

  • Add option to backup “representative” application data

    Representative data is an application agnostic version of the stateful data used by components to store the current state of the running service.

    This includes an option to backup and restore representative data for the stac component. Other components should be added in future updates.

  • Add additional documentation for backups

    Also include a new script birdhouse/scripts/create-restic-keypair.sh to help users create and test SSH keypairs for use by restic when accessing restic repositories over SFTP.

2.16.1 (2025-06-17)

Changes

  • Allow to set Prometheus log level for the monitoring and prometheus-longterm-metrics components

Fixes

  • Fix typo in prometheus-longterm-rules “thredds:kb_transfer_size_kb:increase_1h rule”

    Fix the follow error

    ts=2025-06-17T05:09:00.903Z caller=manager.go:201 level=error component="rule manager" msg="loading groups failed" err="/etc/prometheus/prometheus-longterm-metrics.rules: 41:17: group \"longterm-metrics-hourly\", rule 6, \"thredds:kb_transfer_size_kb:increase_1h\": could not parse expression: 1:40: parse error: unexpected right parenthesis ')'"

2.16.0 (2025-06-16)

Changes

  • Add backup command in bin/birdhouse to backup and restore data to a restic repository

    This allows users to backup and restore:

    • application data, user data, and log data for all components

    • birdhouse logs

    • docker container logs

    • local environement file

    Restoring data either involves restoring it to a named volume (determined by BIRDHOUSE_BACKUP_VOLUME) or in the case of user data and application data, to overwrite the current data with the backup.

    For full details run the bin/birdhouse backup --help command.

    Backups are stored in a restic repository which can be configured by creating a file at BIRDHOUSE_BACKUP_RESTIC_ENV_FILE (default: birdhouse/restic.env) which contains the environment variables necessary for restic to create, and access a repository (see birdhouse/restic.env.example for details).

    The backup and restore commands can be further customized by setting any of the following variables:

    • BIRDHOUSE_BACKUP_SSH_KEY_DIR:

      • The location of a directory that contains an SSH key used to access a remote machine where the restic repository is hosted. Required if accessing a restic repository using the sftp protocol.

    • BIRDHOUSE_BACKUP_RESTIC_BACKUP_ARGS:

      • Additional options to pass to the restic backup command when running the birdhouse backup create command. For example: BIRDHOUSE_BACKUP_RESTIC_BACKUP_ARGS='--skip-if-unchanged --exclude-file "file-i-do-not-want-backedup.txt"

    • BIRDHOUSE_BACKUP_RESTIC_FORGET_ARGS:

      • Additional options to pass to the restic forget command after running the backup job. This allows you to ensure that restic deletes old backups according to your backup retention policy. If this is set, then restic will also run the restic prune command after every backup to clean up old backup files. For example, to store backups daily for 1 week, weekly for 1 month, and monthly for a year: BIRDHOUSE_BACKUP_RESTIC_FORGET_ARGS='--keep-daily=7 --keep-weekly=4 --keep-monthly=12'

  • Add scheduler job to automatically backup data

    Create a new scheduler job at optional-components/scheduler-job-backup which runs the bin/birdhouse backup create command at regular intervals to ensure that the birdhouse stack’s data is regularly backed up.

    To configure this job you must set the following variables:

    • SCHEDULER_JOB_BACKUP_FREQUENCY:

      • Cron schedule when to run this scheduler job (default is '1 1 * * *', at 1:01 am daily)

    • SCHEDULER_JOB_BACKUP_ARGS:

      • Extra arguments to pass to the ‘bin/birdhouse backup create’ command when backing up data. For example, to back up everything set it to '-a \* -u \* -l \* --birdhouse-logs --local-env-file'

  • Add configs --print-log-command option in bin/birdhouse

    This allows users to print a command that can be used to load the birdhouse logging functions in the current process. This is very similar to the bin/birdhouse configs --print-config-command except that it only loads the logging functions.

    Example usage:

    eval $(bin/birdhouse configs --print-log-command)
log INFO 'here is an example log message'

    It is important to have a distinct option to just load the log commands because functions are not inherited by subprocesses which means that if you do something like:

    eval $(bin/birdhouse configs --print-config-command)
log INFO 'this one works'
sh -c 'log ERROR "this one does not"'

    the log command in the subprocess does not work. We would have to re-run the eval in the subprocess which would unnecessarily redefine all the existing configuration variables. Instead we can now do this:

    eval $(bin/birdhouse configs --print-log-command)
log INFO 'this one works'
sh -c 'eval $(bin/birdhouse configs --print-log-command); log INFO "this one does work now"'

    which is much quicker and does not require redefining all configuration variables.

    Note: this was introduced as a helper for the bin/birdhouse backup commands but was made part of the public interface because it is potentially very useful for other scripts that want to use the birdhouse logging mechanism. For example, the components/weaver/post-docker-compose-up script defines its own logging functions which could now be easily replaced using this method.

  • Add BIRDHOUSE_COMPOSE_TEMPLATE_SKIP environment variable to explicitly skip rebuilding template files if true

    This gives us the option to skip re-building template files even if the command to bin/birdhouse compose is up or restart. This is essentially the opposite of BIRDHOUSE_COMPOSE_TEMPLATE_FORCE.

    This option is necessary when running a command while the birdhouse stack is already running and we don’t want to change the template files for the running stack.

  • Add Prometheus rules defining long-term metrics (hourly and daily).

Fixes

  • Replace non-portable sed -z option

    The birdhouse/scripts/get-services-json.include.sh script includes the sed command using the -z flag. The -z flag is non-standard and is not supported by several well-used versions of sed.

    This became apparent when this script is run by the optional-components/scheduler-job-backup job which runs in an alpine based docker container.

  • Fix bugs in Prometheus log parser meant to measure download volume.

  • Fix issue where the current environment is printed to stdout if no shell exec flags are set.

2.15.1 (2025-06-04)

Changes

  • Stop build when a build step fails

    If a command exits with a non-zero exit code when deploying the stack (i.e. running birdhouse-compose.sh) the build process should stop and report that an unexpected error occurs.

    This is enforced by setting the -e flag when birdhouse-compose.sh is run by default. Several commands have been updated so that they are followed by || true so that if they exit with a non-zero status it will not stop the script.

    Also a new environment variable BIRDHOUSE_DEBUG_MODE is introduced which can be set to true to set the -x flag which will write every command that is run by birdhouse-compose.sh to stderr. Previously, setting the BIRDHOUSE_LOG_LEVEL to DEBUG would set the -x flag whenever pre-docker-compose-up and post-docker-compose-up scripts are executed. Please use the BIRDHOUSE_DEBUG_MODE instead from now on. BIRDHOUSE_LOG_LEVEL should only be used to set the log level of the birdhouse logger.

2.15.0 (2025-05-27)

Changes

  • Make scheduler jobs configurable

    The scheduler component automatically enables three jobs (autodeploy, logrotate, notebookdeploy). If someone wants to use the scheduler component but does not want these jobs, there is no obvious way to disable any one of these jobs.

    This change makes it possible to enable/disable jobs as required by the user and adds documentation to explain how to do this.

    This change also converts existing jobs to be optional components. This makes the jobs more in-line with the way the stack is deployed (since version 1.24.0) and ensures that settings set as environment variables in the local environment file are not so sensitive to the order that they were declared in.

    Breaking Change:

    • the three jobs that were automatically enabled previously are now no longer enabled by default.

    • to re-enable these three jobs, source the relevant component in the optional-components subdirectory.

    Deprecations

    • setting additional scheduler jobs using the BIRDHOUSE_AUTODEPLOY_EXTRA_SCHEDULER_JOBS variable. Users should create additional jobs by adding them as custom components instead.

    What about… ?

    • just schedule these jobs for a non-existant day like February 31st?

      • Answer: This would technically work but is not obvious to the user. It is better to make this explicit.

    • just set the schedule to the '#' string?

      • Answer: This is a hack that would work based on the specific way that the docker-crontab image sets schedules. However, this is not obvious to the user and is unreliable since it is not documented.

2.14.0 (2025-05-12)

Changes

  • Weaver: update weaver component default version to 6.6.0.

    Notable changes include:

    • Added HTML representation of job status.

    • Added alternate job Profile representations for interoperability with other clients like WPS and openEO.

    • Adjust job status value for successful instead of succeeded in accordance to latest OGC API standard edits. If clients were defined with explicit checks of the older value, they can request that job representation using query parameters ?profile=wps&f=json. Otherwise, it is preferable that scripts are updated to allow either value to ensure the statuses are resolved correctly regardless of Weaver version employed by the server.

    • Docker build employs Provenance and Software Bill of Materials (SBOM) for traceable dependencies, validation of references, and trust for replicable execution pipelines.

    • Update Python 3.11 to Python 3.12 in the distributed Docker image.

    • Various bug fixes and security vulnerability fixes.

    For full changelog details, see Weaver Changes.

  • Cowbird: Update version 2.5.1 for security fixes.

2.13.5 (2025-05-08)

Changes

  • Script extract-jupyter-users-from-magpie-db: allow to customize the query

    An example query is provided if we want to list all users, except if they belong to some groups.

2.13.4 (2025-05-05)

Changes

  • Update stac service to use crim-ca/stac-app:1.1.0 image

    This updates the version of stac-fastapi to version 5 (currently the latest) and resolves and issue where paging links did not work properly.

    See more details here.

Fixes

  • Forward correct headers through twitcher for the stac service

    The nginx configuration for twitcher was creating a Forwarded header to help stac construct a base_url behind the reverse proxy. However, with newer versions of stac-fastapi (the application running the stac service), the Forwarded header is being parsed incorrectly which means that the base_url was incorrectly formed.

    This change removes the problematic Forwarded header and instead send the information to the stac application using the X-Forwarded-Port, X-Forwarded-Proto, and X-Forwarded-Host headers. This technique allows stac to generate the correct base_url for all versions (up to the current version 5).

2.13.3 (2025-05-03)

Fixes

  • Makefile: Ensure the bin/birdhouse path employed by default resolves from anywhere.

    Previously, if make -C path/to/birdhouse-deploy {target} was invoked from anywhere else than within the birdhouse-deploy directory, the invoked script path would be invalid. Path resolution is improved to allow calls from anywhere, as well as, including the Makefile within an external one seamlessly.

2.13.2 (2025-05-02)

Changes

  • Log multiple lines

    Allow the log command (defined in scripts/logging.include.sh) to log messages that span multiple lines. This also adds unit tests for the scripts/logging.include.sh file.

Fixes

  • Logging bug fixes:

    • Setting NO_COLOR or setting BIRDHOUSE_COLOR to a non-integer value raised an error since BIRDHOUSE_COLOR was tested with the numeric comparison -eq. This has now been fixed.

    • Providing an invalid log message level (e.g. log BADLEVEL message) would log a critical error message but not exit unless the set -o pipefail option was set. This has been updated so that the script will exit as intended even if the pipefail option is not set.

2.13.1 (2025-04-28)

Changes

2.13.0 (2025-04-04)

Changes

  • Deprecate portainer component

    The portainer component is not currently being used and is not actually usable outside of a very specific host machine configuration. This change deprecates the component by moving it to the deprecated-components directory. It can still be enabled from that path if desired.

2.12.0 (2025-04-03)

Changes

  • THREDDS: provide service information page details

    • Add multiple metadata variables (THREDDS_ORGANIZATION_[...], THREDDS_SUPPORT_[...], THREDDS_ABSTRACT and THREDDS_KEYWORDS) allowing customization of the THREDDS server information page.

    • Add a cross-reference to the service-config.json to the service information /thredds/info/serverInfo.html page.

    • Resolve the Magpie ServiceTHREDDS configuration disallowing access to /twitcher/ows/proxy/thredds/info/serverInfo.html by default. Every content under the THREDDS /info/ prefix will be considered a Magpie BROWSE permission of “metadata”. It is up to the organization to make this endpoint visible, either using optional-components/all-public-access or a similar custom Magpie permission definition.

2.11.2 (2025-03-31)

Fixes

  • Make sure that authentication routes use the correct scheme

    Two components that were added after the BIRDHOUSE_PROXY_SCHEME environment variable was introduced did not use it when checking whether a user was authenticated to view a resource using twitcher’s verify route. This is now fixed so that the proper scheme is used.

  • Fix bug where generated docker compose file is appended to not written

    Fixes a bug introduced when the version string was removed from the generated docker compose file. The previous line used > which truncated the file before writing. Now that the previous line is removed, the truncation logic needed to be applied elsewhere.

2.11.1 (2025-03-27)

Fixes

  • Remove deprecated version field from generated docker-compose files

    The env-local optional component generates a docker compose file that contained a version field which are deprecated. This fixes the issue by removing the code that generates the deprecated field.

    Also updates a declaration of an external volume in prometheus-longterm-metrics to use the compose v2 syntax.

  • Fix bug where compose directory can’t be found in bin/birdhouse script

    The COMPOSE_DIR variable cannnot be discovered properly if:

    • the bin/birdhouse script is called with the configs --print-config-command options.

    • the result of that call is ``eval``ed in order to load the birdhouse configuration settings into the calling process’s environment.

    • this is done from a directory outside of the birdhouse-deploy source code directory.

    For example:

    cd /
eval $(birdhouse configs --print-config-command)

    This is fixed by explicitly giving a value for the COMPOSE_DIR variable when using the --print-config-command option. The value is already correctly set in the bin/birdhouse script so it is easy to pass that value on to the user.

2.11.0 (2025-03-24)

Fixes

  • Wrong compose up extra arguments given to compose restart

    • For example, when setting BIRDHOUSE_COMPOSE_UP_EXTRA_OPTS="--remove-orphans" in env.local, that --remove-orphans flag is not supposed to be used with compose restart. Fix regression from PR #492.

Changes

  • Improve handling of .template files generation

    • Change the templating mechanism to run by default for the docker compose restart command instead of only up.

    • Add BIRDHOUSE_COMPOSE_TEMPLATE_FORCE variable that allows enforcing the generation of the .template files instead of only when compose up or restart command is passed by default.

    • Add automatic removal of empty directories conflicting with .template destinations. This occurs only if a docker compose command ran early, and it generated volume mount directories to the yet non-existing files.

    • Add logs when template generation occurs, is skipped, or edge case directories are removed.

  • Deprecate the docker-compose command as default

    Sets the default compose command to docker compose using the new DOCKER_COMPOSE environment variable. This uses compose v2 by default (instead of v1 which is very old and has been deprecated for a while). For backwards compatibility, you can set DOCKER_COMPOSE=docker-compose in the local environment file to use the previous default.

  • Remove deprecated catalog crawler code

    Code related to the solr catalog in the birdhouse-compose.sh file has been deprecated for a while and is not currently usable with the current stack anyway so it is removed

    Also there is commented out old code that relates to the presence of an SSL certificate which is not use and no longer relevant as of version 2.7.0.

  • Update Docker Compose syntax to version 2 in all docker compose files

    Breaking Change: as of birdhouse-deploy version 2.7.3, the stack could not be deployed with a docker compose version <2.20.2. However, that was not specified in the release notes so we’re stating it here. The incompatibility is due to the addition of various additional keys under healthcheck in the docker compose files including interval, timeout, start_period, and start_interval.

    The version 1 compose specification that docker uses is out of date and no longer maintained by docker. We currently have a mix of version 1 syntax and version 2 (specifically ``2.20.2``+) syntax in our docker compose files.

    This means that the stack will not properly run with a docker compose version <2.20.2. For any version >``2.20.2`` the stack runs properly but displays lots of deprecation warnings about deprecated version strings, external volumes and external network definitions.

    This PR updates all version 1 syntax so that these deprecation warnings are not displayed. Documentation has been updated to make this dependency on a modern version of docker explicit.

    Migration Steps:

    • if you are using a version of docker compose <2.20.2 update your docker compose version

    • if you deploy any external components that use any of the old docker compose syntax you may want to update those docker compose files as well so that you aren’t bombarded by deprecation warnings whenever you start the birdhouse stack.

2.10.1 (2025-03-10)

Changes

  • Update STAC app version to 1.0.1

    This update includes a bug fix which treats date-time values as ranges instead of strings when building JSON schemas for use in queryables or collection summaries. See https://github.com/crim-ca/stac-app/pull/24 for more details.

2.10.0 (2025-02-24)

Changes

  • Add the prometheus-longterm-metrics and thanos optional components

    The prometheus-longterm-metrics component collects longterm monitoring metrics from the original prometheus instance (the one created by the components/monitoring component).

    Longterm metrics are any prometheus rule that have the label group: longterm-metrics or in other words are selectable using prometheus’s '{group="longterm-metrics"}' query filter. To see which longterm metric rules are added by default see the optional-components/prometheus-longterm-metrics/config/monitoring/prometheus.rules.template file.

    To configure this component:

    • update the PROMETHEUS_LONGTERM_RETENTION_TIME variable to set how long the data will be kept by prometheus

    Enabling the prometheus-longterm-metrics component creates the additional endpoint /prometheus-longterm-metrics.

    The thanos component enables better storage of longterm metrics collected by the optional-components/prometheus-longterm-metrics component. Data will be collected from the prometheus-longterm-metrics and stored in an S3 object store indefinitely.

    When enabling this component, please change the default values for the THANOS_MINIO_ROOT_USER and THANOS_MINIO_ROOT_PASSWORD by updating the env.local file. These set the login credentials for the root user that runs the minio object store.

  • Enabling the thanos component creates the additional endpoints:

    • /thanos-query: a prometheus-like query interface to inspect the data stored by thanos

    • /thanos-minio: a minio web console to inspect the data stored by minio.

2.9.1 (2025-02-10)

Changes

  • STAC: update stac component to version 1.0.0

    This update makes the /queryables endpoint run much more quickly by stashing the queryables data in the database instead of building it from scratch every time the /queryables endpoint was accessed.

    It also adds two new endpoints PATCH /queryables and PATCH /summaries which automatically update the queryables and collection summaries based on the data that is currently present in the database. See the documentation for more details.

2.9.0 (2025-02-03)

Changes

  • JupyterHub: update jupyterhub component default version to 5.2.1

    This implements all changes between JupyterHub version 4.1.6 and 5.2.1.

    Breaking backward incompatible change: This update requires the following manual upgrade steps:

    • If your local environment file sets the c.DockerSpawner.image_whitelist config option in the JUPYTERHUB_ENABLE_MULTI_NOTEBOOKS environnment variable. Change c.DockerSpawner.image_whitelist to c.DockerSpawner.allowed_images.

    If you have changed any of the default jupyterhub settings you may need to consult the JupyterHub upgrade guide to see if any of those settings have been changed.

2.8.2 (2025-01-30)

Fixes

  • Generic_bird broken because a DELAYED_EVAL is missing

    • Generic_bird consumes FINCH_IMAGE which is a delayed eval variable so generic_bird variable should also be a delayed eval variable.

Changes

  • Allow to override certbot image in env.local to easily test newer version and update to latest version.

2.8.1 (2025-01-20)

Fixes

  • Weaver: adjust missing WEAVER_MANAGER_NAME in healthchecks expecting matching SCRIPT_NAME configuration

    • Weaver’s own healthcheck definition did not resolve to the expected endpoint.

    • Canarie-API monitoring endpoint for Weaver did not resolve to the expected endpoint.

2.8.0 (2025-01-17)

Changes

  • Weaver: update weaver component default version to 6.1.1.

    • Add support of OGC API - Processes - Part 3: Workflows and Chaining with Nested Process ad-hoc workflow.

    • Add support of OGC API - Processes - Part 3: Workflows and Chaining with Remote Collection (STAC and OGC).

    • Add support of OGC API - Processes - Part 4: Job Management endpoints for job “pending” creation and execution.

    • Add support of OGC API - Processes - Part 4: Job Management endpoints for job provenance as W3C PROV metadata.

    • Multiple alignment and fixes related to latest OGC API - Processes - Part 1: Core definitions regarding handling of input parameters and headers when submitting jobs to obtain alternate result representations and behavior.

    • Add HTML responses by default via web browsers or as requested by Accept headers or f query parameter.

    • Add improved CWL schema validation with Weaver-specific definitions where applicable (see https://github.com/crim-ca/weaver/tree/master/weaver/schemas/cwl).

  • Weaver: modifications to proxy configurations for weaver

    • Add WEAVER_ALT_PREFIX optional variable that auto-configures WEAVER_ALT_PREFIX_PROXY_LOCATION, which allows setting an alternate endpoint to redirect requests to weaver. It uses /ogcapi by default which is a very common expectation from servers supporting OGC standards.

    • Use the TWITCHER_VERIFY_PATH approach to accelerate access of weaver resources authorization.

    • Modify proxy pass definitions and URL prefixes to resolve correctly with HTML resources.

2.7.3 (2025-01-17)

Changes

  • Add integration test framework

    This update adds a framework for testing the deployed stack using pytest. This will allow developers to check that their changes are consistent with the existing stack and to add additionally tests when new functionality is introduced.

    Changes to implement this include:

    • existing unit tests are moved to the tests/unit/ directory

    • new integration tests are written in the tests/integration/ directory. More tests will be added in the future!

    • conftest.py scripts updated to bring the stack up/down in a consistent way for the integration tests.

    • unit tests updated to accomodate new testing infrastructure as needed.

    • unit tests updated to test logging outputs better

    • birdhouse interface script updated to support testing infrastructure (this should not change anything for other end-users).

    • additional documentation added to birdhouse interface to improve user experience.

    • docker healthchecks added to more components so that the readiness of the stack can be determined with or without the use of the canarie-api component.

    • deprecates the optional-components/wps-healthchecks component since the healthchecks are now added by default to all WPS components.

    Next steps:

    • add more integration tests as needed

    • add a framework for testing migrating the stack from one version to another

2.7.2 (2025-01-16)

Fixes

  • Jupyterhub: allow users created before Cowbird was enabled to spawn jupyterlab

    Users created before Cowbird was enabled will not have a “workspace directory” created. A workspace directory is a symlink to the directory that contains their Jupyterhub data.

    When Cowbird is enabled, Jupyterhub checks if the workspace directory exists and raises an error if it doesn’t.

    This change allows Jupyterhub to create the symlink if it doesn’t exist instead of raising an error. This means that users without a “workspace directory” will be able to continue using Jupyterhub as they did before without the need for manual intervention by a system administrator who would otherwise need to manually create the symlink for them.

  • Add resolver for http nginx configuration

    Nginx requires a resolver to be explicity defined when using proxy_pass with a variable in the argument passed to proxy_pass. This resolver is defined explicitly for the https server block but not for the http server block.

    This adds the explicit resolver for the http server block as well so that proxy_pass works when called using using http URLs as well.

2.7.1 (2024-12-20)

Changes

2.7.0 (2024-12-19)

Changes

  • Enable local deployment to improve development and testing

    The Birdhouse stack can now be deployed locally and accessed on a browser on the host machine without the need for an SSL certificate. This is useful for local development and for running tests against the full stack while developing and in CI environments.

    To enable this, add the new optional-components/local-dev-test component to BIRDHOUSE_EXTRA_CONF_DIRS and set the following environment variables in the local environment file:

    • export BIRDHOUSE_FQDN=host.docker.internal

    • export BIRDHOUSE_HTTP_ONLY=True

    You should also add host.docker.internal to your /etc/hosts file pointing to the loopback address so that URLs generated by Birdhouse that refer to host.docker.internal will resolve properly in a browser:

    echo '127.0.0.1    host.docker.internal' | sudo tee -a /etc/hosts

    After deploying the stack, you can now interact with the Birdhouse software at http://host.docker.internal from the machine that is the docker host.

    In order to implement the changes above, the following non-breaking changes have been made to the deployment code:

    • added a configuration variable BIRDHOUSE_HTTP_ONLY which is not set by default. If set to True the proxy component will only serve content over http (not https).

    • added the following configuration variables. These should not be set directly unless you really know what you’re doing:

      • BIRDHOUSE_PROXY_SCHEME: default remains https. If BIRDHOUSE_HTTP_ONLY is True then the default becomes http

      • PROXY_INCLUDE_HTTPS: default remains include /etc/nginx/conf.d/https.include;. If BIRDHOUSE_HTTP_ONLY is True, the default is that the variable is unset.

    • changed the default values for the following configuration variables:

      • BIRDHOUSE_ALLOW_UNSECURE_HTTP: default remains "". If BIRDHOUSE_HTTP_ONLY is True then the default becomes True.

    • logs are written to stderr by default. Previously they were written to stdout.

      • this allows us to call scripts and programmatically use their outputs. Previously log entries would need to be manually filtered out before program outputs could be used.

      • added the --log-stdout and --log-file flags to the bin/birdhouse interface to allow redirecting logs to stdout or to a specific file instead.

      • log redirection can also now be set using environment variables:

        • BIRDHOUSE_LOG_FD can be used to redirect logs to a file descriptor (ex: BIRDHOUSE_LOG_FD=3)

        • BIRDHOUSE_LOG_FILE can be used to redirect logs to file (ex: BIRDHOUSE_LOG_FILE=/some/file/on/disk.log)

        • Note that the variables here should not be set in the local environment file since that file is sourced after some logs are written. Instead, set these by exporting them in the parent process that calls bin/birdhouse.

      • for backwards compatibility, if scripts are not called through the bin/birdhouse interface, logs will still be written to stdout.

2.6.5 (2024-12-18)

Fixes

  • Fix incorrect Geoserver URL in Cowbird configuration

    The Geoserver URL in the Cowbird configuration was incorrect as it used a non-standard port. This changes the URL to the one used by docker compose internally. This allows Cowbird to execute webhooks that target Geoserver.

2.6.4 (2024-12-09)

Fixes

2.6.3 (2024-12-05)

Changes

  • Update Thredds to supported version

    Unidata has dropped support for TDS versions < 5.x. This updates Thredds to version 5.5.

    This Thredds v5 actually have 2 minors issues

    They are considered minor and not blocking the release because

    • Magpie top-level Allow or Deny still work across the board, exception under top-level also works across the board, except for NCSS only and NCSS is not widely used.

    • WMS is not widely used, similar to NCSS.

    Other features from this newer Thredds

    • Security fixes (newer Tomcat) and if there is a critical vulnerability, we won’t be able to stay on v4 series because it is not even available on DockerHub anymore as Unidata has dropped support.

    • New experimental Zarr support.

2.6.2 (2024-12-03)

Changes

  • Fix help string description for bin/birdhouse configs command

    Update description of the configs subcommand to better describe it. The description when calling bin/birdhouse -h now matches the description when calling bin/birdhouse configs -h

  • Jupyterhub: Update recommended paths for public share folders

    The recommended public share folders in the env.local.example file create a conflict with the default PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR path when both are enabled and mounted on a Jupyterlab container. This change updates the recommended paths for the public share folders to avoid this conflict and adds a warning helping users to avoid this conflict.

    Note: the conflict arises when PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR is mounted to a container as read-only volume and then Jupyterhub tries to mount the public share folder within that volume. Since the parent volume is read-only, the second volume mount fails.

Fixes

  • Correct docker image for stac-populator optional component

    This sets the docker image for the stac-populator component to a version that actually contains the code that is executed when stac-populator is called. The previous image no longer contained the relevant code.

2.6.1 (2024-11-22)

Fixes

  • Fix regressions introduced by PR #359 “Flexible locations for data served by thredds”

    In PR #359:

    secure-thredds/config/magpie/permissions.cfg started to use variable but was never renamed to .template so those variable never get template expanded (commit 317d96c3).

    bootstrap-testdata default value was removed but did not source read-configs.include.sh so the variable stayed blank (commit 4ab0fc74). The default value was there initially so the script can be used in standalone situation (not inside a checkout).

2.6.0 (2024-11-19)

Changes

  • Add the prometheus-log-parser optional component

    This component parses log files from other components and converts their logs to prometheus metrics that are then ingested by the monitoring Prometheus instance (the one created by the components/monitoring component).

    For more information on how this component reads log files and converts them to prometheus components see the log-parser documentation.

    To configure this component:

    • set the PROMETHEUS_LOG_PARSER_POLL_DELAY variable to a number of seconds to set how often the log parser checks if new lines have been added to log files (default: 1)

    • set the PROMETHEUS_LOG_PARSER_TAIL variable to "true" to only parse new lines in log files. If unset, this will parse all existing lines in the log file as well (default: "true")

    To view all metrics exported by the log parser:

    • Navigate to the https://<BIRDHOUSE_FQDN>/prometheus/graph search page

    • Put {job="log_parser"} in the search bar and click the “Execute” button

  • Update the prometheus version to the current latest v2.53.3. This is required to support loading multiple prometheus scrape configuration files with the scrape_config_files configuration option.

2.5.5 (2024-11-14)

Changes

2.5.4 (2024-10-31)

Changes

  • THREDDS: add more options to configure catalog.xml

    • The default THREDDS configuration creates two default datasets, the Service Data dataset and the Main dataset. The Service Data dataset is used internally and hosts WPS outputs. The Main dataset is the place where users can access data served by THREDDS. Both of these are configured to serve files with the following extensions: .nc .ncml .txt .md .rst .csv

    • In order to allow the THREDDS server to serve files with additional extensions, this introduces two new variables:

      • THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS: this allows users to specify additional filter elements to the Service Data dataset. This is especially useful if a WPS outputs files with an extension other than the default (eg: .h5) to the wps_outputs/ directory.

      • THREDDS_DATASET_DATASETSCAN_BODY: this allows users to specify the whole body of the Main dataset’s element. This allows users to fully customize how this dataset serves files.

    • We limit the configuration options for the Service Data dataset more than the Main dataset because the Service Data dataset requires a basic configuration in order to properly serve WPS outputs. Making significant changes to this configuration could have unexpected negative impacts on WPS usage.

    • In order to allow customization of the Magpie THREDDS configuration in case new file extensions are added we introduce two additional variables:

      • THREDDS_MAGPIE_EXTRA_METADATA_PREFIXES: additional file prefixes (ie. regular expression match patterns) that Magpie should treat as metadata (accessible with “browse” permissions).

      • THREDDS_MAGPIE_EXTRA_DATA_PREFIXES: additional file prefixes (ie. regular expression match patterns) that Magpie should treat as data (accessible with “read” permissions).

    • The defaults for these new variables are fully backwards compatible. Without changing these variables, the THREDDS server should behave exactly the same as before except that .md files and .rst files are now considered metadata files according to the Magpie configuration, meaning that they can now be viewed with “browse” permissions.

2.5.3 (2024-09-11)

Changes

  • Magpie/Twitcher: update Python packages and base Docker image to address security vulnerabilities

  • xclim-testdata: adapt repository cloning script to the new data structure

    The xclim-testdata repo has been restructured to include the data in a data subdirectory. This change updates the cloning script to account for this new structure and to ensure that the user experience is consistent with the previous version.

    See:

2.5.2 (2024-07-19)

Changes

2.5.1 (2024-07-10)

  • Cowbird: bump version to 2.4.0.

    • Includes multiple dependency updates for latest security and performance improvements.

2.5.0 (2024-06-20)

Changes

  • Weaver: bump version to 5.6.1.

    • See full changes details in Weaver changes

    • In summary:

      • multiple control setting options to customize some behaviors

      • improved OGC API - Processes standard conformance

      • improved support of Common Workflow Language (CWL) features (secrets, sub-workflow, auth-propagation, etc.)

  • Weaver: WPS retry logic on post-compose step.

    • Apply --network birdhouse_default to the Docker curl image to allow HTTP requests to properly resolve against the running services (WPS bird providers, Weave and Magpie). In some cases, this network would not be automatically resolved.

    • Fix the index used during HTTP request retry to avoid going one step over the intended retry attempts.

2.4.2 (2024-06-12)

Changes

  • deploy-data: allow more flexibility to deploy files from other checkout in same config file

    Given the config file can specify multiple checkouts, this flexibility to have SRC_DIR be an absolute path will allow one checkout to take files from other checkouts, using absolute path to the other checkouts. SRC_DIR can still be a relative path of the current checkout, as before, to preserve backward-compatibility.

    Possible use-case: re-organize the layout of various files from the various checkouts in an intermediate location before rsyncing this intermediate location to the final destination.

2.4.1 (2024-06-05)

Fixes

  • Weaver: Adjust invalid data_sources.yml definitions.

    • Add the missing data_sources.yml volume mount for weaver-worker.

    • When weaver-worker runs a Workflow, the nested step process locations need to be resolved according to the current "localhost" instance. However, the Web API running in weaver service is not visible from the worker. Since the configuration is shared between weaver and weaver-worker, use the public endpoint of weaver to make process URL resolution consistent, and also provide more useful references in job logs when resolution fails.

2.4.0 (2024-06-04)

Changes

  • Rename variables, constants and files from PAVICS to Birdhouse

    For historical reasons the name PAVICS was used in variable names, constants and filenames in this repo to refer to the software stack in general. This was because, for a long time, the PAVICS deployment of this stack was the only one that was being used in production. However, now that multiple deployments of this software exist in production (that are not named PAVICS), we remove unnecessary references to PAVICS in order to reduce confusion for maintainers and developers who may not be aware of the historical reasons for the PAVICS name.

    This update makes the following changes:

    • The string PAVICS in environment variables, constant values, and file names have been changed to BIRDHOUSE (case has been preserved where possible).

      • For example:

        • PAVICS_FQDN -> BIRDHOUSE_FQDN

        • pavics_compose.sh -> birdhouse_compose.sh

        • THREDDS_DATASET_LOCATION_ON_CONTAINER='/pavics-ncml' -> THREDDS_DATASET_LOCATION_ON_CONTAINER='/birdhouse-ncml'

    • Comment strings and documentation that refers to the software stack as PAVICS have been changed to use Birdhouse.

    • Recreated the pavics-compose.sh script that runs birdhouse-compose.sh in backwards compatible mode.

      • Backwards compatible mode means that variables in env.local that contain the string PAVICS will be used to set the equivalent variable that contains BIRDHOUSE. For example, the PAVICS_FQDN variable set in the env.local file will be used to set the value of BIRDHOUSE_FQDN.

    • Removed unused variables:

      • CMIP5_THREDDS_ROOT

  • Create a new CLI entrypoint in bin/birdhouse that can be used to invoke pavics-compose.sh or birdhouse-compose.sh from one convenient location. This script also includes some useful options and provides a generic entrypoint to the stack that can be extended in the future. In the future, users should treat this entrypoint as the only stable CLI for interacting with the Birdhouse software.

Migration Guide

  • Update env.local file to replace all variables that contain PAVICS with BIRDHOUSE. Variable names have also been updated to ensure that they start with the prefix BIRDHOUSE_.

    • see env.local.example to see new variable names

    • see the BIRDHOUSE_BACKWARDS_COMPATIBLE_VARIABLES variable (defined in default.env) for a full list of changed environment variable names.

  • Update any external scripts that access the old variable names directly to use the updated variable names.

  • Update any external scripts that access any of the following files to use the new file name:

    old file name | new file name |

    |-------------------------|—————————-| | pavics-compose.sh | birdhouse-compose.sh | | PAVICS-deploy.logrotate | birdhouse-deploy.logrotate | | configure-pavics.sh | configure-birdhouse.sh | | trigger-pavicscrawler | trigger-birdhousecrawler |

  • Update any external scripts that called pavics-compose.sh or read-configs.include.sh to use the CLI entrypoint in bin/birdhouse instead.

  • The following default values have changed. If your deployment was using the old default value, update your env.local file to explicitly set the old default values.

    old variable name | new variable name | old default value | new default value |

    |--------------------------------------------|————————————–|-------------------------|:—————————| | POSTGRES_PAVICS_USERNAME | BIRDHOUSE_POSTGRES_USERNAME | postgres-pavics | postgres-birdhouse | | THREDDS_DATASET_LOCATION_ON_CONTAINER | (no change) | /pavics-ncml | /birdhouse-ncml | | THREDDS_SERVICE_DATA_LOCATION_ON_CONTAINER | (no change) | /pavics-data | /birdhouse-data | | (hardcoded) | BIRDHOUSE_POSTGRES_DB | pavics | birdhouse | | PAVICS_LOG_DIR | BIRDHOUSE_LOG_DIR | /var/log/PAVICS | /var/log/birdhouse | | (hardcoded) | GRAFANA_DEFAULT_PROVIDER_FOLDER | Local-PAVICS | Local-Birdhouse | | (hardcoded) | GRAFANA_DEFAULT_PROVIDER_FOLDER_UUID | local-pavics | local-birdhouse | | (hardcoded) | GRAFANA_PROMETHEUS_DATASOURCE_UUID | local_pavics_prometheus | local_birdhouse_prometheus |

    Note that the PAVICS_LOG_DIR variable was actually hardcoded as /var/log/PAVICS in some scripts. If PAVICS_LOG_DIR was set to anything other than /var/log/PAVICS you’ll end up with inconsistent log outputs as previously some logs would have been sent to PAVICS_LOG_DIR and others to /var/log/PAVICS. We recommend merging these two log files. Going forward, all logs will be sent to BIRDHOUSE_LOG_DIR.

  • Update any jupyter notebooks that make use of the PAVICS_HOST_URL environment variable to use the new BIRDHOUSE_HOST_URL instead.

  • Set the BIRDHOUSE_POSTGRES_DB variable to pavics in the env.local file. This value was previously hardcoded to the string pavics so to maintain backwards compatibility with any existing databases this should be kept the same. If you do want to update to the new database name, you will need to rename the existing database. For example, the following will update the existing database named pavics to birdhouse (assuming the old default values for the postgres username):

    docker exec -it postgres psql -U postgres-pavics -d postgres -c 'ALTER DATABASE pavics RENAME TO birdhouse'

    You can then update the env.local file to the new variable name and restart the stack

  • Set the BIRDHOUSE_POSTGRES_USER variable to postgres-pavics in the env.local file if you would like to preserve the old default value. If you would like to change the value of BIRDHOUSE_POSTGRES_USER then also update the name for any running postgres instances. For example, the following will update the user named postgres-pavics to postgres-birdhouse:

    docker exec -it postgres psql -U postgres-pavics -d postgres -c 'CREATE USER "tmpsuperuser" WITH SUPERUSER'
docker exec -it postgres psql -U tmpsuperuser -d postgres -c 'ALTER ROLE "postgres-pavics" RENAME TO "postgres-birdhouse"'
docker exec -it postgres psql -U tmpsuperuser -d postgres -c 'ALTER ROLE "postgres-birdhouse" WITH PASSWORD '\''postgres-qwerty'\'
docker exec -it postgres psql -U postgres-birdhouse -d postgres -c 'DROP ROLE "tmpsuperuser"'

    Note that the postgres-qwerty value is meant just for illustration, you should replace this with the value of the BIRDHOUSE_POSTGRES_PASSWORD variable. Note that you’ll need to do the same for the stac-db service as well (assuming that you weren’t previously overriding the STAC_POSTGRES_USER with a custom value).

2.3.3 (2024-05-29)

Changes

  • Bump cadvisor version to the latest version: v0.49.1

    • See the cadvisor repo for all changes: https://github.com/google/cadvisor/compare/v0.36.0…v0.49.1

    • This updated was prompted by the fact that the previously installed version of cadvisor (v0.36.0) did not support newer versions of docker. When deploying this repo with recent docker version, cadvisor was unable to discover or monitor running containers.

2.3.2 (2024-05-27)

Changes

  • Make the monitoring component docker images configurable

    • The following variables have been added to the components/monitoring/default.env file and can be overridden in env.local to change the docker image for one of the services enabled by the monitoring component:

      • GRAFANA_VERSION

      • GRAFANA_DOCKER

      • CADVISOR_VERSION

      • CADVISOR_DOCKER

      • PROMETHEUS_VERSION

      • PROMETHEUS_DOCKER

      • NODE_EXPORTER_VERSION

      • NODE_EXPORTER_DOCKER

      • ALERTMANAGER_VERSION

      • ALERTMANAGER_DOCKER

    • Note that the defaults are the same as the previous hardcoded versions so this change is fully backwards compatible.

2.3.1 (2024-05-21)

Fixes

  • Scripts that read configuration settings and that exit early on error fail unexpectedly

    • Scripts that call set -e before reading configuration settings were failing early because some lines are intentionally returning a non-zero value when setting variable defaults. This change modifies lines that may return a non-zero status but should not cause the script to exit early.

    • Scripts that were exiting early prior to this change include:

      • birdhouse/deployment/fix-geoserver-data-dir-perm

      • birdhouse/deployment/fix-write-perm

      • birdhouse/deployment/trigger-deploy-notebook

2.3.0 (2024-05-14)

Changes

  • bump canarie-api version to 1.0.0

    • This version of canarie-api permits running the proxy (nginx) container independently of the canarie-api application. This makes it easier to monitor the logs of canarie-api and proxy containers simultaneously and allows for the configuration files for canarie-api to be mapped to the canarie-api containers where appropriate.

2.2.2 (2024-05-11)

Changes

2.2.1 (2024-05-01)

Changes

  • bump jupyterhub version to 4.1.5-20240426

    • This is the latest bugfix update to jupyterhub after the release of version 4.1.0. There haven’t been any additional updates for a few weeks now, so we can assume that this version is relatively stable now. See the jupyterhub changelog for details.

Fixes

2.2.0 (2024-04-18)

Changes

  • Node Services: Add definitions and variables for every service represented by the DACCS-Climate/Marble-node-registry.

    • Add version field using the corresponding <SERVICE>_VERSION variables.

    • Add types field restricted by specific values instead of previous keywords expected to be extendable.

    • Add <SERVICE>_IMAGE_URI variables to provide rel: service-meta link for every service.

    • Update all $schema references of service node registry to 1.2.0 instead of main. During unit tests, specific $schema reference in the respective service configuration will be used for validation.

    See bird-house/birdhouse-deploy#441 for more details.

2.1.3 (2024-04-09)

Fixes

  • GeoServer: fix invalid media-type specified for the service’s endpoint in service-config.json.template

  • Jupyterhub: fix authentication bug when changing settings

    If the JUPYTERHUB_AUTHENTICATOR_AUTHORIZATION_URL variable or JUPYTERHUB_CRYPT_KEY is unset without clearing the jupyterhub database, users could no longer spawn jupyterlab servers.

2.1.2 (2024-03-25)

Fixes

  • Weaver: celery-healthcheck: update regular expression

    The celery-healthcheck file which checks if celery node is online when weaver starts up was using an outdated regular expression to check if a node was online or not. This has been fixed so that this script can now reliably check whether the node is available or not.

2.1.1 (2024-03-06)

Changes

  • logging: decrease logging level for empty optional vars from WARN to DEBUG

    To avoid drowning real WARN messages. Many optional vars can be valid if empty.

  • config: add sample config to configure docker-compose to remove orphans

    To remove orphans containers when components are disabled. Also link to full documentations if other env var can be used.

  • compose script: allow to pass extra options to up operation

    The previous docker-compose built-in env var was not working so had to add this homegrown solution.

    When disabling components, their existing containers will not be removed unless option --remove-orphans is given together with ./pavics-compose.sh up -d.

    This change allow any additional options, not just --remove-orphans.

  • compose script: exit early when any errors occurred during invocation

    Before, all the post-docker-compose-up would still execute after docker-compose has an error.

2.1.0 (2024-02-23)

Changes

  • Compose script utilities:

    • Add BIRDHOUSE_COLOR option and various logging/messaging definitions in birdhouse/scripts/logging.include.sh.

    • Replace all explicit color “logging” related echo in scripts by a utility log {LEVEL} {message} function that employs variables LOG_DEBUG, LOG_INFO, LOG_WARN, LOG_ERROR and LOG_CRITICAL as applicable per respective messages to report logging messages in a standard approach. Colors can be disabled with BIRDHOUSE_COLOR=0 and logging level can be set with BIRDHOUSE_LOG_LEVEL={LEVEL} where all levels above or equal to the configured one will be displayed (default logging level is INFO).

    • Unify all birdhouse/scripts utilities to employ the same COMPOSE_DIR variable (auto-resolved or explicitly set) in order to include or source any relevant dependencies they might have within the birdhouse-deploy repository.

    • Add info option (ie: pavics-compose.sh info) that will stop processing just before docker-compose call. This can be used to perform a “dry-run” of the command and validate that was is loaded is as expected, by inspecting provided log messages.

    • Replace older backtick (`) executions by $(...) representation except for eval calls that require them for backward compatibility of sh on some server instances.

    • Modify the sh -x calls to scripts listed in COMPONENT_PRE_COMPOSE_UP and COMPONENT_POST_COMPOSE_UP to employ the -x flag (showing commands) only when BIRDHOUSE_LOG_LEVEL=DEBUG.

  • Defaults:

    • Add multiple SERVER_[...] variables with defaults using previously hard coded values referring to PAVICS. These variables use a special combination of DELAYED_EVAL and OPTIONAL_VARS definitions that can make use of a variable formatted as <ANY_NAME>='${__DEFAULT__<ANY_NAME>}' that will print a warning messages indicating that the default is employed, although STRONGLY recommended to be overridden. This allows a middle ground between backward-compatible env.local while flagging potentially misused configurations.

Fixes

  • Canarie-API: updated references

  • Magpie: ensure that the MAGPIE_ADMIN_USERNAME variable is respected

    • When determining the JUPYTERHUB_ADMIN_USERS variable

    • Double check that it is being respected everywhere else

  • env.local.example: fix JUPYTERHUB_CONFIG_OVERRIDE comment section

    JUPYTERHUB_CONFIG_OVERRIDE was disconnected from its sample code.

2.0.6 (2024-02-15)

Changes

  • Weaver: add option to automatically unregister old providers

    Introduces the WEAVER_UNREGISTER_DROPPED_PROVIDERS variable. If set to “True”, Weaver providers that are no longer working (not responding when deployed) and are not named in WEAVER_WPS_PROVIDERS will be unregistered. This is useful when deploying Weaver with fewer providers than a previous deployment.

    For example, if the stack is deployed with the Weaver, Finch, and Raven components. Then later deployed with just Weaver and Raven, the Finch provider will be unregistered from weaver.

    Previously, the Finch provider would have remained as a Weaver provider despite the fact that it has been removed from the stack.

2.0.5 (2024-01-22)

Changes

2.0.4 (2024-01-18)

Fixes

  • Allow users to log in to Jupyterhub with their email address

    Previously, JupyterHub’s MagpieAuthenticator class treated the email address entered into the username field as the username itself. This led to a mismatch between the username in JupyterHub and the username in Magpie. To resolve this, we update the JupyterHub docker image to a version where this bug is fixed.

    See https://github.com/Ouranosinc/jupyterhub/pull/26 and https://github.com/Ouranosinc/Magpie/issues/598 for reference.

2.0.3 (2024-01-16)

Fixes

  • Autodeploy broken due to instanciated left-over files in ./config/ dir

    The .gitignore syntax was wrong. Regression from v2.0.0.

2.0.2 (2023-12-15)

Fixes

  • Cowbird README file disappears now that cowbird is a default component

    The settings to enable the Cowbird README file (added in version 1.41.0) assumed that the cowbird component would be loaded after the juptyerhub component. Now that the cowbird component is part of the DEFAULT_CONF_DIRS and therefore will always be loaded first, this updates the settings so that the README file will be enabled given the new component load order.

2.0.1 (2023-12-11)

Changes

  • Code documentation: provide an additional reason to not exit early if a directory listed in the EXTRA_CONF_DIRS variable does not exist.

Fixes

  • Twitcher: unable to change log level because of typo in qualname config

2.0.0 (2023-12-11)

Changes

  • Update DEFAULT_CONF_DIRS to the minimal components required to deploy the stack

    Changes DEFAULT_CONF_DIRS to refer exclusively to the proxy, magpie, twitcher, stac, and cowbird components. Also moves all components that were previously under the birdhouse/config directory to the birdhouse/components directory. This removes the arbitrary distinction between these groups of components that didn’t have any functional or logical reason.

    Because this change updates the default components, this is not backwards compatible unless the following changes are made to the local environment file (birdhouse/env.local by default):

    • add any components no longer in the DEFAULT_CONF_DIRS list to the EXTRA_CONF_DIRS list. For example, to keep the jupyterhub component enabled, add ./components/jupyterhub to the EXTRA_CONF_DIRS list.

    • update the PROXY_ROOT_LOCATION to redirect the root path / to an enabled component. By default, this will redirect to Magpie’s landing page, unless jupyterhub is enabled, in which case it will redirect to jupyterhub’s landing page. If any other behaviour is desired, PROXY_ROOT_LOCATION should be updated in the env.local file.

1.42.2 (2023-12-08)

Changes

1.42.1 (2023-12-07)

Changes

  • Allow user to access their Magpie cookie programmatically

    When the user logs in to jupyterhub, their Magpie cookie is stored in the jupyterhub database. This allows the user to access this variable to programmatically access resources protected by magpie without having to copy/paste these cookies from their browser session or add a username and password in plaintext to the file.

    For example, to access a dataset behind a secured URL with xarray.open_dataset using a username and password. (this is not recommended as it makes it much easier to accidentally leak user credentials):

    import requests
from request_magpie import MagpieAuth
import xarray

with requests.session() as session:
     session.auth = MagpieAuth("https://mynode/magpie", "myusername", "myverysecretpassword")
     store = xarray.backends.PydapDataStore.open("https://mynode/thredds/some/secure/dataset.nc", session=session)
     dataset = xarray.open_dataset(store)

    And to do the same thing using the current magpie cookie already used to log in the current user (no need to include username and password, this is strongly recommended over the technique above):

    import os
import requests
import xarray

with requests.session() as session:
    r = requests.get(f"{os.getenv('JUPYTERHUB_API_URL')}/users/{os.getenv('JUPYTERHUB_USER')}",
                     headers={"Authorization": f"token {os.getenv('JUPYTERHUB_API_TOKEN')}"})
    for name, value in r.json().get("auth_state", {}).get("magpie_cookies", {}).items():
        session.cookies.set(name, value)
    store = xarray.backends.PydapDataStore.open("https://mynode/thredds/some/secure/dataset.nc", session=session)
    dataset = xarray.open_dataset(store)

    Note that users who are already logged in to jupyterhub will need to log out and log in for these changes to take effect.

1.42.0 (2023-11-30)

Changes

1.41.0 (2023-11-30)

Changes

  • New optional-component optional-components/test-cowbird-jupyter-access that executes a script to set up a test user along with different test files. This component is used for the related e2e test from the PAVICS-e2e-workflow-tests repo.

  • Update cowbird service from 2.1.0 to 2.2.0.

  • Add new README file to be used on jupyterhub when cowbird is activated. The file describes to the user the different directories and permissions found in its workspace.

Fixes

  • Updates incorrect WPS outputs resource name in the cowbird config.

1.40.0 (2023-11-30)

  • optional-components/stac-data-proxy: add a new feature to allow hosting of local STAC assets.

    The new component defines variables STAC_DATA_PROXY_DIR_PATH (default ${DATA_PERSIST_ROOT}/stac-data) and STAC_DATA_PROXY_URL_PATH (default /data/stac) that are aliased (mapped) under nginx to provide a URL where locally hosted STAC assets can be downloaded from. This allows a server node to be a proper data provider, where its STAC-API can return Catalog, Collection and Item definitions that points at these local assets available through the STAC_DATA_PROXY_URL_PATH endpoint.

    When enabled, this component can be combined with optional-components/secure-data-proxy to allow per-resource access control of the contents under STAC_DATA_PROXY_DIR_PATH by setting relevant Magpie permissions under service secure-data-proxy for children resources that correspond to STAC_DATA_PROXY_URL_PATH. Otherwise, the path and all of its contents are publicly available, in the same fashion that WPS outputs are managed without optional-components/secure-data-proxy. More details are provided under the component’s README.

  • optional-components/stac-public-access: add public write permission for POST /stac/search request.

    Since pystac_client, a common interface to interact with STAC API, employs POST method by default to perform search, the missing permission caused an unexpected error for users that are not aware of the specific permission control of Magpie. Since nothing is created by that endpoint, but rather, the POST’ed body employs the convenient JSON format to provide search criteria, it is safe to set this permission when the STAC service was configured to be publicly searchable.

1.39.2 (2023-11-30)

Changes

  • Jupyterhub: periodically check whether the logged-in user still have permission to access

    By setting the JUPYTERHUB_CRYPT_KEY environment variable in the env.local file, jupyterhub will store user’s authentication information (session cookie) in the database. This allows jupyterhub to periodically check whether the user still has permission to access jupyterhub (the session cookie is not expired and the permission have not changed).

    The minimum duration between checks can be set with the JUPYTERHUB_AUTHENTICATOR_REFRESH_AGE variable which is an integer (in seconds).

    Note that users who are already logged in to jupyterhub will need to log out and log in for these changes to take effect.

    To forcibly log out all users currently logged in to jupyterhub you can run the following command to force the recreation of the cookie secret:

    docker exec jupyterhub rm /persist/jupyterhub_cookie_secret && docker restart jupyterhub

1.39.1 (2023-11-29)

Changes

  • Limit usernames in Magpie to match restrictions by Jupyterhub’s Dockerspawner

    When Jupyterhub spawns a new jupyterlab container, it escapes any non-ascii, non-digit character in the username. This results in a username that may not match the expected username (as defined by Magpie). This mismatch results in the container failing to spawn since expected volumes cannot be mounted to the jupyterlab container.

    This fixes the issue by ensuring that juptyerhub does not convert the username that is receives from Magpie.

    Note that this updates the Magpie version.

1.39.0 (2023-11-27)

Changes

  • Add a Magpie Webhook to create the Magpie resources corresponding to the STAC-API path elements when a STAC-API POST /collections/{collection_id} or POST /collections/{collection_id}/items/{item_id} request is accomplished.

    • When creating the STAC Item, the source entry in links corresponding to a THREDDS file on the same instance is used to define the Magpie resource_display_name corresponding to a file to be mapped later on (eg: a NetCDF birdhouse/test-data/tc_Anon[...].nc).

    • Checking same instance source path is necessary because STAC could refer to external assets, and we do not want to inject Magpie resource that are not part of the active instance where the hook is running.

1.38.0 (2023-11-21)

Changes

Flexible locations for data served by THREDDS. This PR adds two capabilities:

  • Makes it possible to configure all aspects of the two default top-level THREDDS catalogs that has been available on Birdhouse (conventionally referred to as Birdhouse and Datasets on PAIVCS). This is done by defining the following two sets of new environment variables. The THREDDS_DATASET_ set of variables are meant to control properties of the Datasets catalog:

    • THREDDS_DATASET_LOCATION_ON_CONTAINER

    • THREDDS_DATASET_LOCATION_ON_HOST

    • THREDDS_DATASET_LOCATION_NAME

    • THREDDS_DATASET_URL_PATH

    The THREDDS_SERVICE_DATA_ set of variables control properties of the Birdhouse catalog.

    • THREDDS_SERVICE_DATA_LOCATION_ON_CONTAINER

    • THREDDS_SERVICE_DATA_LOCATION_ON_HOST

    • THREDDS_SERVICE_DATA_LOCATION_NAME

    • THREDDS_SERVICE_DATA_URL_PATH

    These new variables are defined in thredds/default.env and included in env.local.example. Their default values have been chosen to ensure the behaviours of the two catalogs remain unchanged (for reasons of backward compatibility).

  • Adds the ability to define additional top-level THREDDS catalogs. This is achieved by introducing the THREDDS_ADDITIONAL_CATALOG variable in thredds/default.env that can be used to inject custom XML configuration for a new catalog. This information is picked up by the THREDDS server. An example is provided in env.local.example.

1.37.2 (2023-11-10)

  • Fix weaver and cowbird inconsistencies for public WPS outputs directory handling.

    Because cowbird needs to mount multiple directories within the user-workspace for jupyterhub, it needs to define a dedicated public/wps_outputs sub-directory to distinguish it from other public files not part of WPS outputs. However, for WPS birds, other files than WPS outputs are irrelevant, and are therefore mounted directly in their container. The variable PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR was being misused in the context of weaver, causing WPS output URLs for public context to be nested as /wpsoutputs/weaver/public/wps_outputs/{jobID} instead of the intended location /wpsoutputs/weaver/public/{jobID}, in contrast to user-context WPS outputs located under /wpsoutputs/weaver/users/{userID}/{jobID}.

    Relates to Ouranosinc/pavics-sdi#314.

1.37.1 (2023-11-03)

Fixes

  • optional-components/all-public-access: remove erroneous Magpie route permission properties for GeoServer.

1.37.0 (2023-11-01)

Changes

  • Geoserver: protect web interface and ows routes behind magpie/twitcher

    Updates Magpie version to 3.35.0 in order to take advantage of updated Geoserver Service.

    The geoserverwms Magpie service is now deprecated. If a deployment is currently using this service, it is highly recommended that the permissions are transferred from the deprecated geoserverwms service to the geoserver service.

    The /geoserver endpoint is now protected by default. If a deployment currently assumes open access to Geoserver and would like to keep the same permissions after upgrading to this version, please update the permissions for the geoserver service in Magpie to allow the anonymous group access.

    A Magpie service named geoserver with type wfs exists already and must be manually deleted before the new Magpie service created here can take effect.

    The optional-components/all-public-access component provides full access to the geoserver service for the anonymous group in Magpie. Please note that this includes some permissions that will allow anonymous users to perform destructive operations. Because of this, please remember that enabling the optional-components/all-public-access component is not recommended in a production environment.

    Introduces the GEOSERVER_SKIP_AUTH environment variable. If set to True, then requests to the geoserver endpoint will not be authorized through twitcher/magpie at all. This is not recommended at all. However, it will slightly improve performance when accessing geoserver endpoints.

    See https://github.com/bird-house/birdhouse-deploy/issues/333 for details.

1.36.0 (2023-10-31)

Changes

  • Protect jupyterhub behind twitcher authentication

    • Sets magpie cookies whenever a user logs in or out through jupyterhub so that they are automatically logged in or out through magpie as well.

    • Ensures that the user has permission to access jupyterhub according to magpie when logging in.

1.35.2 (2023-10-24)

Fixes

  • Fix warning from JupyterHub regarding DockerSpawner method never awaited.

1.35.1 (2023-10-18)

Fixes

  • Jupyterhub cull interval setting must be an integer:

    • Previously, the default jupyter_idle_kernel_cull_interval setting is calculated by dividing the jupyter_idle_kernel_cull_timeout setting by 2 using float division. This meant that the result was a float instead of the expected integer value. This caused and error when the jupyterlab server spawned. In order to fix this, the value is cast to an integer after division.

1.35.0 (2023-10-16)

Changes

  • Jupyterhub configurable idle server culling.

    • Add optional variables JUPYTER_IDLE_SERVER_CULL_TIMEOUT, JUPYTER_IDLE_KERNEL_CULL_TIMEOUT and JUPYTER_IDLE_KERNEL_CULL_INTERVAL that allows fined-grained configuration of user-kernel and server-wide docker image culling when their activity status reached a certain idle timeout threshold.

    • Enable idle kernel culling by default with a timeout of 1 day, and user server culling with timeout of 3 days.

    • Avoids the need for custom JUPYTERHUB_CONFIG_OVERRIDE specifically for idle server culling. If similar argument parameters should be defined using an older JUPYTERHUB_CONFIG_OVERRIDE definition, the new configuration strategy can be skipped by setting JUPYTER_IDLE_KERNEL_CULL_TIMEOUT=0.

1.34.0 (2023-10-10)

Changes

  • Allow users to submit a Weaver job requesting to store outputs to the public location instead of their user-workspace.

  • Update default Weaver version from 4.22.0 to 4.32.0.

  • Add COWBIRD_LOG_LEVEL environment variable to allow control over logging level of Cowbird services.

1.33.5 (2023-10-02)

Changes

  • Adding a description for the STAC service that will be served at the /services endpoint

1.33.4 (2023-10-02)

Fixes

  • Clean up: Make bind-mount locations more flexible

    Clean up unused variables and correct file paths from the changes made in 1.33.2

1.33.3 (2023-09-29)

Changes

  • Add test data and volume for test-geoserver-secured-access

1.33.2 (2023-09-27)

Changes

  • Make bind-mount locations more flexible

    Previously, most bind mount locations on the host machine were subdirectories of the folder specified by the DATA_PERSIST_ROOT environment variable (/data by default). This change allows the user to set custom locations for the following additional variables, so that they don’t need to be all under the same common directory.

    • LOGROTATE_DATA_DIR (default: ${DATA_PERSIST_ROOT}/logrotate)

    • MONGODB_DATA_DIR (default: ${DATA_PERSIST_ROOT}/mongodb_persist)

    • COWBIRD_MONGODB_DATA_DIR (default: ${DATA_PERSIST_ROOT}/mongodb_cowbird_persist)

    • POSTGRES_DATA_DIR (default ${DATA_PERSIST_ROOT}/frontend_persist)

    • WEAVER_MONGODB_DATA_DIR (default ${DATA_PERSIST_ROOT}/mongodb_weaver_persist)

    The following variable is also added which is another location on disk where files that may contain links are placed. Because the links need to be mounted together in order to resolve properly, the subdirectories of this directory are not configurable:

    • DATA_PERSIST_SHARED_ROOT (default: same as DATA_PERSIST_ROOT)

    The following variables now create subdirectories under DATA_PERSIST_SHARED_ROOT (previously they were created under DATA_PERSIST_ROOT by default):

    • USER_WORKSPACES (default user_workspaces)

    • WEAVER_WPS_OUTPUTS_DIR (default wps_outputs/weaver)

1.33.1 (2023-09-25)

Fixes

  • Docker compose version missing in stac/config/magpie/ compose file

    • The version: key was not set in the stac/config/magpie/docker-compose-extra.yml file which caused docker-compose to report a version mismatch and fail to start.

1.33.0 (2023-09-25)

Changes

  • Add public WPS outputs directory to Cowbird and add corresponding volume mount to JupyterHub.

  • Update cowbird service from 1.2.0 to 2.1.0.

  • Require MongoDB==5.0 Docker image for Cowbird’s database.

  • Add WPS_OUTPUTS_DIR env variable to manage the location of the WPS outputs data.

Important

Because of the new MongoDB==5.0 database requirement for Cowbird that uses (potentially) distinct version from other birds, a separate Docker image is employed only for Cowbird. If some processes, jobs, or other Cowbird-related data was already defined on one of your server instances, manual transfer between the generic ${DATA_PERSIST_ROOT}/mongodb_persist to new ${DATA_PERSIST_ROOT}/mongodb_cowbird_persist directory must be accomplished. The data in the new directory should then be migrated to the new version following the same procedure as described for Weaver in Database Migration.

1.32.0 (2023-09-22)

Changes

  • Changes JUPYTERHUB_VERSION from 1.4.0-20210506 to 4.0.2-20230816.

    • This upgrade is needed to resolve a compatibility issue when using Spawner.disable_user_config = True in Jupyterhub config and the new image which run jupyter-server 2.7.3.

  • Add an image to the list of images that can be launched from JupyterHub which will be used to start an instance of MLflow.

    • Note that the jupyter lab google drive extension is not supported with this image.

1.31.3 (2023-09-21)

Fixes

  • Move initial stac service Magpie definition under its component configuration.

    • Before this change, optional-components/stac-public-access was mandatory since the stac service under Magpie was not created otherwise, leading to “service not found” error when requesting the /stac endpoint.

    • Ensure that the first stac resource under stac service in Magpie is created by default. Without this resource being defined initially, it is very easy to forget creating it, which would not take into account the required /stac/stac request path to properly resolve the real endpoints where STAC API is served.

  • Remove optional-components/stac-public-access dependency under optional-components/all-public-access to avoid indirectly enforcing components/stac when optional-components/all-public-access is enabled. Users that desire using optional-components/stac-public-access will have to add it explicitly to the list of EXTRA_CONF_DIRS.

  • Rename optional-components/stac-public-access/config/magpie/config.yml.template to optional-components/stac-public-access/config/magpie/permissions.cfg in order to align with permissions-specific contents as accomplished with other components.

  • Fix invalid endpoint redirect for STAC when using Twitcher/Magpie.

  • Apply Magpie permission on /stac/stac since the second /stac is needed to secure access properly.

1.31.2 (2023-09-13)

Fixes

  • Fix invalid templated configurations of flyingpigeon that could remain in the old location (birdhouse/config/flyingpigeon) when updating an existing instance to 1.31.0.

1.31.1 (2023-09-13)

Changes

1.31.0 (2023-09-13)

Changes:

1.30.1 (2023-09-11)

Fixes

  • Fix incorrect tag X-Robots-Tags header to appropriate X-Robots-Tag (no final s) name. Optional component name optional-components/x-robots-tag-header and variable X_ROBOTS_TAG_HEADER have also been adjusted accordingly.

1.30.0 (2023-09-06)

Changes

1.29.2 (2023-08-24)

Changes

  • Monitoring: allow access to magpie members of group monitoring

    To allow accessing the various monitoring WebUI without having full blown magpie admin priviledge to add and remove users.

    Add existing users to this new monitoring group to allow them access to the various monitoring WebUI. This way, we do not need to share the admin user account and do not have to add them to the administrators group.

1.29.1 (2023-08-15)

Changes

  • Small STAC changes

    • This PR includes some changes that were suggested in a review for #297. But because the PR was already merged, further updates are included here:

      • removes extra block to include in docker compose files (no longer needed)

      • moves docker compose file in stac-public-access component to the correct location

      • uses PAVICS_FQDN_PUBLIC for public facing URLs in all places

1.29.0 (2023-08-10)

Changes

  • Do not expose additional ports:

    • Docker compose no longer exposes any container ports outside the default network except for ports 80 and 443 from the proxy container. This ensures that ports that are not intended for external access are not exposed to the wider internet even if firewall rules are not set correctly.

    • Note that if the monitoring component is used then port 9100 will be exposed from the node-exporter container. This is because this container must be run on the host machine’s network and unfortunately there is no known workaround that would not require this port to be exposed on the host machine.

    • Fixes https://github.com/bird-house/birdhouse-deploy/issues/222

1.28.0 (2023-08-10)

Changes

1.27.1 (2023-07-10)

Changes

  • Add Magpie webhook definitions for permission creation and deletion cases to be processed by Cowbird.

  • Add USER_WORKSPACE_UID and USER_WORKSPACE_GID env variables to manage ownership of the user workspaces used by Cowbird, JupyterHub and others.

  • Update magpie service from 3.31.0 to 3.34.0

  • Update cowbird service from 1.1.1 to 1.2.0

1.27.0 (2023-07-06)

  • Deprecate unused/unmaintained components

    Move unused and unmaintained components to a separate deprecated-components/ subdirectory and remove them from the DEFAULT_CONF_DIRS list if required.

1.26.11 (2023-07-04)

Fixes

  • Components endpoint now returns valid json

    The JSON string reported by the /components/ path was not valid JSON due to a misconfigured regular expression used to generate the content. The issue was that integers were not being properly parsed by the regular expression meaning that paths that contained integers other than 0 were not recognized as valid paths.

    This fixes https://github.com/bird-house/birdhouse-deploy/issues/339

1.26.10 (2023-07-04)

Changes

  • Move canarie-api configuration for cowbird from proxy to canarie-api config directory

    • The canarie-api configuration for cowbird was being loaded whenever the proxy component was enabled instead of when the canarie-api component was enabled. Since these components can now be enabled separately, the configuration has to be moved to ensure that canarie-api configuration files aren’t unintentionally mounted to a container that is just running an nginx proxy.

1.26.9 (2023-07-04)

Fixes

  • Fix Cowbird’s sync_permissions config which used invalid Magpie service types.

1.26.8 (2023-06-22)

Fixes

  • Tests: some tests fail to run when CWD is not COMPOSE_DIR

    The root cause is the automatic COMPOSE_DIR detection in read-configs.include.sh missed one case and the detection ordering was wrong for one other case as well.

    This was not found before because the checkout was properly named “birdhouse-deploy”. When the checkout is named something else, then we hit this error.

    Fixes the error found here https://github.com/bird-house/birdhouse-deploy/pull/329#pullrequestreview-1480211502

Changes

  • Autodeploy: document test procedure

  • Dev environment: add Conda environment-dev.yml to easily install all the dev tools required

  • Tests: make test runs more robust, able to run from any CWD

    Before, test runs can only be started from inside the checkout, at some “popular” locations inside the checkout. Now it can be started from litterally anywhere.

1.26.7 (2023-06-19)

Changes

  • A new endpoint /services is added that provides a JSON string describing each of the user facing services currently enabled on the stack. This is a static string and serves a different purpose than the endpoints served by canarie-api (monitoring status). This endpoint is meant to be polled by the node registry scripts (https://github.com/DACCS-Climate/DACCS-node-registry) to provide information about what services are meant to be available without having to poll other endpoints directly.

  • A new endpoint /version is added that provides a string containing the current version number of the stack (e.g. “1.26.0”). This endpoint is meant to be polled by the node registry scripts (https://github.com/DACCS-Climate/DACCS-node-registry).

1.26.6 (2023-06-16)

Fixes

  • components/ endpoint displays intended information after auto-deploy

    Previously, the script that generates the content for the components/ endpoint was using a feature of grep that is not supported by all versions of grep. This meant that this script running in the auto-deployment docker container was not able to properly parse the running components using grep. This fixes the issue by making the script compliant with all versions of grep.

    Resolves https://github.com/bird-house/birdhouse-deploy/issues/342

1.26.5 (2023-06-16)

Fixes

  • Autodeploy: optionally fix file permissions

    The autodeploy mechanism creates new files owned by root. If this is not desired then users have to manually update the file ownership after each autodeployment. This adds an option to change the ownership of all files to a specific user after each autodeployment.

    For example, if the code in this repo is currently owned by a user named birduser with uid 1002, then by setting export AUTODEPLOY_CODE_OWNERSHIP="1002:1002" in env.local, all files and folders in this repo will continue to be owned by birduser after each autodeployment.

1.26.4 (2023-06-06)

Changes

1.26.3 (2023-06-01)

Changes

Fixes

  • Notebook autodeploy: unable to read the env.local

    When env.local is a symlink we need to volume-mount the destination of the symlink so it resolves inside the notebook autodeploy container.

    This will allow notebook autodeploy config variable to be set in env.local.

    Also had someone changed the value of JUPYTERHUB_USER_DATA_DIR in env.local, it would not have worked without this fix.

    This is a non-breaking fix.

1.26.2 (2023-05-25)

Changes

  • Update Zenodo config

    • Add Misha to creators

    • Add birdhouse community

  • Licence: update copyright line with year and ownership

1.26.1 (2023-04-26)

Changes

  • Zenodo: A configuration file for Zenodo was added to the source code, listing all contributing authors on the birdhouse-deploy repository.

1.26.0 (2023-04-20)

Breaking changes

  • CanarieAPI: update to 0.7.1.

    • The Docker running CanarieAPI is now using Python 3 (since 0.4.x tags). Configurations need to be updated if any specific Python 2 definitions were used. See 2to3 to help migrate configurations automatically if necessary.

    • Update the CanarieAPI configuration to use Python 3.x executable code.

Changes

  • CanarieAPI: update to 0.7.1.

    • The server node now provides a generic server configuration for the current platform definition.

    • Added multiple missing docuementation references for all the services included within CanarieAPI configurations.

    • With new CanarieAPI version, a slightly improved UI with more service details are provided for the active server:

image

  • Add optional variables witht defaults to define reference Docker image version tags.

    Following optional variables are defined by default. These are used as reference in the respective Docker compose service definition of these components, as well as in their CanarieAPI configuration to retrieve the release time of the tag, and refer to relevant URL references as needed.

    • CATALOG_VERSION

    • FINCH_VERSION

    • FLYINGPIGEON_VERSION

    • GEOSERVER_VERSION

    • HUMMINGBIRD_VERSION

    • MALLEEFOWL_VERSION

    • RAVEN_VERSION

Fixes:

  • CanarieAPI: update to 0.7.1.

    • Fixes an AttributeError raised due to misconfiguration of the Web Application with Flask 2.x definitions (relates to Ouranosinc/CanarieAPI#10).

    • Skip over 0.4.x, 0.5.x, 0.6.x versions to avoid issue related to cron job monitoring and log parser command failures in order to collect configured service statistics and statuses (see also Ouranosinc/CanarieAPI#14).

  • Weaver: update CanarieAPI monitoring definitions

  • Cowbird: update CanarieAPI monitoring definitions

1.25.7 (2023-04-20)

Fixes

  • Fix flaky WPS provider responses (i.e.: other WPS birds) causing failure during their registration in weaver.

    In some cases, the WPS birds would not respond properly when starting the stack, either because they are still initiating or due to other temporary failures such as services being restarted until healthy. This fix introduces a retry mechanism to attempt WPS registration in weaver up to WEAVER_WPS_PROVIDERS_RETRY_COUNT=5 times (1 initial attempt + 5 retries), and with WEAVER_WPS_PROVIDERS_RETRY_AFTER=5 second intervals between each retry. If the maximum number of retries for any WPS provider or the WEAVER_WPS_PROVIDERS_MAX_TIME across all registrations are reached, the operation is aborted.

1.25.6 (2023-04-20)

Fixes

  • Config var PAVICS_FQDN_PUBLIC not usable in component default.env and external scripts

    Currently, PAVICS_FQDN_PUBLIC is only usable in .template files, in docker-compose-extra.yml files and in component pre/post compose scripts because they are handled by pavics-compose.sh.

    It was good enough but now with delayed eval feature, we can do better. PAVICS_FQDN_PUBLIC can be as accessible as the other PAVICS_FQDN var.

    Both vars allow a host to have a different public and internal hostname. Some scripts, certbotwrapper for example, prefer the public hostname than the internal hostname when they are different because Let’s Encrypt only knows about the public hostname.

    With the pluggable nature of this stack, we can have many external scripts from many external repos reading the config vars and they can have the need to specifically access the public hostname.

    Bonus, we now have a sample use of DELAYED_EVAL list, right in the main default.env.

Changes

1.25.5 (2023-04-12)

Fixes

  • Fix disapearing Thredds docker image

    The current docker image version for thredds (4.6.18) is no longer hosted in the Unidata docker repository.

    Pushed the same image from Ouranos production to PAVICS DockerHub, restoring the missing Thredds image.

    Discovered that Unidata is also not keeping their tag immutable, like Kartoza Geoserver image.

    So Ouranos tag has the approximate month of Unidata re-release of 4.6.18.

    On our production server:

    $ docker images |grep thredds|grep 4.6.18
unidata/thredds-docker              4.6.18              25997a1b2893   15 months ago   5.63GB

    On our staging server:

    $ docker images |grep thredds | grep 4.6.18
unidata/thredds-docker              4.6.18              09103737360a   16 months ago   5.62GB

1.25.4 (2023-04-12)

Fixes

  • Enforce the load order of components defined in env.local

    Extra components defined in the EXTRA_CONF_DIRS variables were being loaded before the dependant components defined in the COMPONENT_DEPENDENCIES variables in each default.env file. This meant that if an extra component was meant to override some setting defined in a dependant component, the setting would not be overridden by the extra component.

    This change enforces the following load order rules:

    • components defined in DEFAULT_CONF_DIRS are loaded before those in EXTRA_CONF_DIRS

    • components are loaded in the order they appear in either DEFAULT_CONF_DIRS or EXTRA_CONF_DIRS

    • components that appear in COMPONENT_DEPENDENCIES variable are immediately loaded unless they have already been loaded

    For example, with the following files in place:

    # env.local
DEFAULT_CONF_DIRS="
  ./config/twitcher
  ./config/project-api
  ./config/magpie
"
EXTRA_CONF_DIRS="
  ./optional-components/generic_bird
  ./components/cowbird
"

# config/twitcher/default.env
COMPONENT_DEPENDENCIES="
  ./config/magpie
"
# optional-components/generic_bird/default.env
COMPONENT_DEPENDENCIES="
  ./config/wps_outputs-volume
"

    the load order is:

    • ./config/magpie (loaded as a dependency of twitcher, not loaded a second time after project-api)

    • ./config/twitcher

    • ./config/project-api

    • ./config/wps_outputs-volume (loaded as a dependency of generic_bird)

    • ./optional-components/generic_bird

    • ./components/cowbird

    This load order also applies to the order that docker-compose-extra.yml files are specified. If a component also includes an override file for another component (eg: ./config/finch/config/proxy/docker-compose-extra.yml overrides ./config/proxy/docker-compose-extra.yml), the following additional load order rules apply:

    • if the component that is being overridden has already been loaded, the override file is loaded immediately

    • otherwise, the override files will be loaded immediately after the component that is being overridden has been loaded

    For example, with the following files in place:

    # env.local
DEFAULT_CONF_DIRS="
./config/finch
./config/proxy
"

    # config/proxy/docker-compose-extra.yml
  ...
# config/finch/docker-compose-extra.yml
  ...
# config/finch/config/proxy/docker-compose-extra.yml
  ...

    the docker compose files will be loaded in the following order:

    • config/finch/docker-compose-extra.yml

    • config/proxy/docker-compose-extra.yml

    • config/finch/config/proxy/docker-compose-extra.yml

  • Add tests to ensure override capabilities are preserved which allows all default behaviors of the platform can be customized.

    See birdhouse/README.rst for instruction to run the tests.

1.25.3 (2023-04-12)

Fixes

  • Canarie-api: add old config file into historical gitignore

    In order to maintain backwards compatibility, old files that are no longer present in the code should be kept in the gitignore files. This adds back one file to the relevant .gitignore file that no longer exists under conf.extra-service.d/canarie-api.conf.

1.25.2 (2023-04-12)

Changes

1.25.1 (2023-04-11)

Changes

  • Canarie-api should not be a mandatory component.

    Canarie-api is currently deployed in the same container as the nginx reverse proxy service meaning that it is not possible to deploy nginx without including canarie-api.

    This means that it is currently not possible to run this deployment without canarie-api or use a different monitoring application. This change fully separates the configuration for canarie-api and nginx so that a user can choose to run nginx with or without canarie-api.

    Canarie-api has been kept on the DEFAULT_CONF_DIRS list so that canarie-api is included by default, for backwards-compatibility. In order to run nginx without canarie-api, remove the ./conf/canarie-api line from the DEFAULT_CONF_DIRS environment variable.

    A user can also choose a specific version of the nginx docker image to use by specifying the PROXY_IMAGE environment variable (default is “nginx”). Note that if canarie-api is used (by including the ./conf/canarie-api line in DEFAULT_CONF_DIRS), then the PROXY_IMAGE variable will be ignored.

1.25.0 (2023-04-01)

Fixes

Changes

  • Raven: allow to customize the Geoserver it will use

    Useful to test the local Geoserver or to have your own Geoserver with your own data. Default to PAVICS Geoserver.

    Set RAVEN_GEO_URL in env.local to something like https://host/geoserver/.

  • env.local.example: change default Geoserver admin user from ‘admin’ to ‘admingeo’

    This only impacts new deployment when env.local.example is instanciated to env.local.

    This is to avoid confusion with the admin user of Magpie, which is also ‘admin’.

1.24.1 (2023-03-27)

Fixes

  • Cowbird: Resolve celery tasks not properly registered for dispatching from the API to the worker service.

    When calling the https://${PAVICS_FDQN_PUBLIC}/cowbird/version endpoint, a task is submitted to cowbird-worker to validate that it is responsive and in sync with cowbird. The instance was reporting an error indicating that celery tasks were not properly detected.

    To facilitate detection of this kind of problem, better error log reporting was added to the /version endpoint under cowbird==1.1.1.

1.24.0 (2023-03-22)

Fixes

  • Make all components pluggable

    The default stack was not configurable. This meant that if someone wanted to deploy a subset of the default stack there was no good way of configuring birdhouse-deploy to run this subset only.

    Previously, additional components could be added to the stack (ex: weaver, cowbird, etc.) by adding them to the EXTRA_CONF_DIRS variable. This change extends this functionality to all components.

    For backwards compatibility, all components that were in the original default stack are now listed in the DEFAULT_CONF_DIRS variable (in birdhouse/default.env). To run a subset of the original stack, update DEFAULT_CONF_DIRS to only include the configuration directories for the desired components.

    The components that will be added to the stack are only those whose configuration directory is listed in either DEFAULT_CONF_DIRS or EXTRA_CONF_DIRS. Note that some components are dependent on others to run and will automatically add the other components to the stack as a dependency. For example, twitcher requires magpie so if you only specify twitcher, magpie will be added to the stack as well. To inspect component dependencies, look at the COMPONENT_DEPENDENCIES environment variable that is extended in some default.env files. For example, birdhouse/config/twitcher/default.env contains:

    COMPONENT_DEPENDENCIES="
  $COMPONENT_DEPENDENCIES
  ./config/magpie

    Components can also have optional dependencies. These are additional configuration options to run if both components are deployed in the stack at the same time. These are defined in the config/*/docker-compose-extra.yml files where the * refers to another component that could be deployed. For example, birdhouse/config/raven/config/magpie/docker-compose-extra.yml contains additional configuration settings for the raven docker service that only apply if magpie is also deployed. This relaxes some dependencies between components and allows more flexibility when choosing what parts of the stack to deploy.

Changes:

  • Cowbird: Updated Cowbird config for user workspaces and for working callbacks to Magpie.

    When enabling Cowbird, the config will now mount a different working directory with JupyterHub, which corresponds to the user workspaces created with Cowbird. These workspaces will use symlinks to the Jupyterhub data directories.

    For example, we have the original directory, which is still mounted by default by JupyterHub, which contains the user’s notebooks :

    image

    If Cowbird is enabled, JupyterHub mounts Cowbird’s workspace instead, which has a symlink to the other dir :

    image

    Cowbird’s workspace can also contain other files related to other services. Cowbird’s workspace directory is defined by the added environment variable USER_WORKSPACES.

  • JupyterHub: Updated config to support Cowbird, which uses a different working directory.

    JupyterHub now mounts the variable WORKSPACE_DIR when starting a JupyterLab instance. It will refer to the original JupyterHub data directory by default, and if Cowbird is activated, it will be overridden to refer to Cowbird’s workspace instead.

    In JupyterHub with Cowbird enabled, the writable-workspace is the Cowbird user’s workspace :

    image

    When we open the notebooks dir, it displays the files found at the symlink’s source :

    image

  • Updated eo and nlp images to latest version in the env.local.example config.

1.23.3 (2023-02-17)

Fixes

  • Vagrant: fix mismatch docker-compose version with autodeploy resulting in containers being recreated

    Normally a ./pavics-compose.sh up -d after an autodeploy has run, should only create any new containers, not recreating all the existing containers.

    This is because docker-compose v2 seems to be incompatible with old v1. This is the last v1 version still compatible with the docker-compose in the autodeploy.

    This old docker-compose v1 seems to work just fine with latest docker cli.

    This is the quickest way to get Vagrant boxes up and running without causing backward incompatible changes to existing production deployment.

    If we update the docker-compose inside autodeploy to v2, this will force all existing deployment to also update their installed docker-compose.

    A more long term solution would be to always run ./pavics-compose.sh using the docker-compose image from autodeploy so the version will always match and any docker-compose version update will be transparent.

  • Vagrant: ubuntu version after bionic is missing net-tools package pre-installed

    net-tools package is required to have the route command to set the default gateway. Without the default gateway set, the VM will not be visible outside of its own subnet.

1.23.2 (2023-02-17)

Fixes

1.23.1 (2023-02-13)

[//]: # (list changes here, using ‘-’ for each new entry, remove this when items are added)

Fixes

  • Vars in DELAYED_EVAL list are not expanded properly outside of pavics-compose.sh

    There are other scripts sourcing default.env and env.local and all those scripts have to expand the vars in DELAYED_EVAL list to have their actual values.

    Only scripts using the 3 variables in DELAYED_EVAL list are broken.

    DELAYED_EVAL was previously introduced in PR https://github.com/bird-house/birdhouse-deploy/pull/272.

    Sample errors

    fix-geoserver-data-dir-perm (called at the end of pavics-compose.sh):

    fix GeoServer data dir permission on first run only, when data dir do not exist yet.
+ DATA_DIR='${DATA_PERSIST_ROOT}/geoserver'
+ '[' -n  ]
+ docker run --rm --name fix-geoserver-data-dir-perm --volume '${DATA_PERSIST_ROOT}/geoserver:/datadir' --env FIRST_RUN_ONLY bash:5.1.4 bash -xc 'if [ -z "$FIRST_RUN_ONLY" -o ! -f /datadir/global.xml ]; \
    then chown -R 1000:10001 /datadir; else echo "No execute."; fi'
docker: Error response from daemon: create ${DATA_PERSIST_ROOT}/geoserver: "${DATA_PERSIST_ROOT}/geoserver" includes invalid characters for a local volume name, only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a host directory, use absolute path.

    trigger-deploy-notebook (broke notebook deploy job):

    + TMP_SCRIPT=/tmp/notebookdeploy/notebookdeploy.XXXXXXIfafFK/deploy-notebook
+ cat
+ chmod a+x /tmp/notebookdeploy/notebookdeploy.XXXXXXIfafFK/deploy-notebook
+ docker run --rm --name deploy_tutorial_notebooks -u root -v /tmp/notebookdeploy/notebookdeploy.XXXXXXIfafFK/deploy-notebook:/deploy-notebook:ro -v /tmp/notebookdeploy/notebookdeploy.XXXXXXIfafFK/tutorial-notebooks:/tutorial-notebooks:ro -v '${DATA_PERSIST_ROOT}/jupyterhub_user_data:/notebook_dir:rw' --entrypoint /deploy-notebook bash:5.1.4
docker: Error response from daemon: create ${DATA_PERSIST_ROOT}/jupyterhub_user_data: "${DATA_PERSIST_ROOT}/jupyterhub_user_data" includes invalid characters for a local volume name, only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a host directory, use absolute path.

    Explanation of the fix

    All scripts have to remember to call function process_delayed_eval in order to obtain the real value of each vars in DELAYED_EVAL list.

    Centralized all logic about reading configs (config files reading order, remember to call process_delayed_eval) to avoid mistake and to ease updating logic in the future. Too many scripts were reading the configs themselves and some are not doing it properly, ex: forgot to hide password when reading env.local.

    All scripts should do this going forward

    # Set variable COMPOSE_DIR to the dir containing pavics-compose.sh and docker-compose.yml.

# Source the script providing function read_configs.
# read_configs uses COMPOSE_DIR to find default.env and env.local.
. $COMPOSE_DIR/read-configs.include.sh

# Call function read_configs to read the various config files in the appropriate order and process delayed eval vars properly.
read_configs

1.23.0 (2023-02-10)

Changes:

  • secure-data-proxy: add new secure-data-proxy optional component.

    When enabled, this component will enforce authentication and authorization to be resolved against the /wpsoutputs endpoint prior to accessing the results produced by WPS executions. A Magpie service named secure-data-proxy is created to define the resource and permission hierarchy of directories and files the users and groups can access. When disabled, the original behavior to provide open access to /wpsoutputs is employed.

    A variable named SECURE_DATA_PROXY_AUTH_INCLUDE is dynamically assigned based on the activation or not of this component. Corresponding validation of optional/mandatory/delayed-eval variables used by this component are also applied dynamically, as well as mounting the necessary nginx and docker-compose extended configurations.

  • Weaver: adjust user-context output directory hooks and permissions for secure-data-proxy.

    When a process defined in Weaver (either a WPS provider or a local definition) is executed by a user that was granted authorization to run a job, the corresponding user-context directory under /wpsoutputs/users/{user-id} will be used for storing the execution outputs and will have the appropriate permissions set for that user to grant them access to those outputs.

Fixes:

  • Magpie/Twitcher: update minimum version magpie>=3.31.0 to employ twitcher>=0.8.0 in MapgieAdatepr.

    • Resolve an issue where response.request references were not set in OWS proxy responses when handled by Twitcher. This caused MapgieAdatepr response hooks to fail, which in turn caused failing requests for any non-WPS service that defined any proxy request hook, such as in the case of weaver component.

    • Adds the Twitcher /ows/verify/{service_name}[/{extra_path} endpoint employed for validating authorized access to Magpie service/resources, in the same fashion as the protected proxy endpoint, but without performing the proxied request toward the target service. This is mandatory for using the new secure-data-proxy optional component, otherwise the proxy endpoint triggers data download twice, once for authorization and another for actually accessing the data.

    See also Ouranosinc/Magpie#571 and bird-house/twitcher#118.

1.22.11 (2023-02-03)

Changes:

  • Proxy: add /components endpoint that provides a JSON list of loaded components by the platform.

    Prior to this functionality, it was impossible to know which potential capabilities, services or behaviors were to be expected by a given DACCS/PAVICS/birdhouse instance. Using this endpoint, nodes can obtain minimal machine-readable details about their supported capabilities, allowing better interoperability.

    Furthermore, developers maintaining distinct stacks and integrating different features can have a better understanding of behaviors by the various web services when performing requests against a given node.

1.22.10 (2023-01-31)

Fixes:

  • Weaver: fixes for running post-docker-compose-up operation.

    • When the target curl image was not already available on the machine (each time for ephemeral test instances), the docker pull outputs on the first call would mangle the monitoring messages. An initial pull is done to avoid it.

    • When running on sh (as expected by the script’s shebang), the utility variable $RANDOM is missing. A POSIX portable equivalent is used if $RANDOM could not be resolved.

1.22.9 (2023-01-25)

Changes:

  • Jupyter: allow recursive directory deletion

    This was not possible before since non-empty dir deletion was not possible.

  • Jupyter: re-enable terminal for all users

    It was disabled to avoid malicious usage but with the monitoring in place and the demo account restricted to limited resources, it’s probably safe to try enabling this again.

    For legitimate users, not having the terminal is pretty annoying. Should not penalize legit users for some rogue users.

1.22.8 (2023-01-24)

Fixes:

  • Weaver: fix post script to be compatible with autodeploy

    Autodeploy runs inside its own docker container and curl is not available. Therefore Weaver post script should be using curl from a docker image instead of locally installed flavor.

  • Jupyter: fix the Docker Spawner start function to support JupyterHub image selection names that use the <name>:<version> format.

1.22.7 (2022-12-23)

Fixes:

  • Overriding DATA_PERSIST_ROOT in env.local do not take effect for JUPYTERHUB_USER_DATA_DIR, MAGPIE_PERSIST_DIR, and GEOSERVER_DATA_DIR.

    These 3 vars will have to be delayed evaluated for override in env.local to take effect.

    For a variable to be delayed evaluated, it has to be defined using single-quote and be added to the list of DELAYED_EVAL in default.env.

    If those steps are forgotten in env.local, it will still work since env.local is the last file to be read. However those steps should not be forgotten in any default.env for all components.

    So the impact or burden is on the developpers to write their default.env file properly, not on the users that only modify the env.local file.

    All default.env files header have been updated with notice about this new delayed evaluation feature.

    Fixes https://github.com/bird-house/birdhouse-deploy/issues/270.

Changes:

  • Warn when a dir in EXTRA_CONF_DIRS does not exist.

    Most likely a typo in a new dir. Just warn and not exit directly to avoid leaving the entire platform down during an unattended autodeploy since no one is around to take immediate action.

    Fixes https://github.com/bird-house/birdhouse-deploy/issues/266.

1.22.6 (2022-12-19)

Changes:

1.22.5 (2022-12-02)

Changes:

  • new Jupyter env with latest of everything

    PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/106

    <   - bokeh=2.4.2=py38h578d9bd_1
>   - bokeh=2.4.3=pyhd8ed1ab_3

<   - cartopy=0.20.1=py38hf9a4893_1
>   - cartopy=0.21.0=py38hf6c3373_3

<   - cf_xarray=0.7.2=pyhd8ed1ab_0
>   - cf_xarray=0.7.5=pyhd8ed1ab_0

<   - cftime=1.6.0=py38h71d37f0_1
>   - cftime=1.6.2=py38h26c90d9_1

<   - clisops=0.9.0=pyh6c4a22f_0
>   - clisops=0.9.3=pyh1a96a4e_0

# unpin
<   - dask=2022.1.0=pyhd8ed1ab_0
>   - dask=2022.11.0=pyhd8ed1ab_0

# new
>   - flox=0.6.3=pyhd8ed1ab_0

<   - fiona=1.8.20=py38hbb147eb_2
>   - fiona=1.8.22=py38hc72d8cd_2

<   - gdal=3.3.3=py38hcf2042a_0
>   - gdal=3.5.3=py38h1f15b03_3

<   - geopandas=0.10.2=pyhd8ed1ab_1
>   - geopandas=0.12.1=pyhd8ed1ab_1

# new
>   - geopy=2.3.0=pyhd8ed1ab_0
>   - pyston_lite=2.3.4=py38h0a891b7_1
>   - python-pptx=0.6.21=pyhd8ed1ab_0

<   - ravenpy=0.7.8=pyh8a188c0_0
>   - ravenpy=0.9.0=pyha21a80b_0

# pip to conda
<     - requests-magpie==0.1.1
>   - requests-magpie=0.2.0=pyhd8ed1ab_0

<   - rioxarray=0.11.1=pyhd8ed1ab_0
>   - rioxarray=0.13.1=pyhd8ed1ab_0

<   - roocs-utils=0.6.1=pyh6c4a22f_0
>   - roocs-utils=0.6.3=pyh1a96a4e_0

# unpin
<   - shapely=1.7.1=py38hb7fe4a8_5
>   - shapely=1.8.5=py38hafd38ec_2

# new
>   - streamlit=1.15.0=pyhd8ed1ab_0

<   - xarray=2022.3.0=pyhd8ed1ab_0
>   - xarray=2022.10.0=pyhd8ed1ab_0

<   - xclim=0.36.0=pyhd8ed1ab_0
>   - xclim=0.39.0=pyhd8ed1ab_0

<   - xesmf=0.6.2=pyhd8ed1ab_0
>   - xesmf=0.6.3=pyhd8ed1ab_1

# new
>     - jupyterlab-tabular-data-editor==1.0.0

  • documentation:

    • Add Weaver component diagram to better illustrate its interactions with other birdhouse services.

    • Move monitoring component images under its respective component directory.

1.22.4 (2022-11-08)

Changes:

  • autodeploy: allow repos to optionally decide if a deploy is required

    Useful when only a subset of file changes in a repo will actually impact deployment.

    Without this mechanism any file changes in a repo will trigger a deployment, which would cost a full platform restart for no reason.

    Var GIT_CHANGED_FILES is given to optional script <repo_root>/autodeploy/conditional-trigger and only an exit code 0 will trigger deploy.

  • fix-geoserver-data-dir-perm: allow overriding data dir to use on another instance of Geoserver

1.22.3 (2022-10-25)

Fixes:

  • jupyter env: reap defunct processes with proper pid 1 init process

    Before, process hierarchy:

    $ docker exec jupyter-lvu ps -efH
UID          PID    PPID  C STIME TTY          TIME CMD
jenkins       88       0  0 21:01 ?        00:00:00 ps -efH
jenkins        1       0  0 18:57 ?        00:00:00 /opt/conda/bin/python /opt/conda/bin/conda run -n birdy /usr/local/bin/start-notebook.sh --ip=0.0.0.0 --port=8888 --notebook-dir=/notebook_dir --SingleUserNotebookApp.default_url=/lab --debug --disable-user-config --NotebookApp.terminals_enabled=False --NotebookApp.shutdown_no_activity_timeout=345600 --MappingKernelManager.cull_idle_timeout=86400 --MappingKernelManager.cull_connected=True
jenkins        7       1  0 18:57 ?        00:00:00   /bin/bash /tmp/tmpmx46emji
jenkins       21       7  0 18:57 ?        00:00:27     /opt/conda/envs/birdy/bin/python3.8 /opt/conda/envs/birdy/bin/jupyterhub-singleuser --ip=0.0.0.0 --port=8888 --notebook-dir=/notebook_dir --SingleUserNotebookApp.default_url=/lab --debug --disable-user-config --NotebookApp.terminals_enabled=False --NotebookApp.shutdown_no_activity_timeout=345600 --MappingKernelManager.cull_idle_timeout=86400 --MappingKernelManager.cull_connected=True

    Before, reproducible defunct firefox-esr processes:

    True
[{'pid': 302, 'create_time': 1666550504.76, 'name': 'firefox-esr'}, {'pid': 303, 'create_time': 1666550504.8, 'name': 'firefox-esr'}]

True
[{'pid': 302, 'create_time': 1666550504.76, 'name': 'firefox-esr'}, {'pid': 303, 'create_time': 1666550504.8, 'name': 'firefox-esr'}, {'pid': 692, 'create_time': 1666550867.43, 'name': 'firefox-esr'}, {'pid': 693, 'create_time': 1666550867.45, 'name': 'firefox-esr'}]

$ docker exec jupyter-lvu ps
    PID TTY          TIME CMD
      1 ?        00:00:00 conda
      7 ?        00:00:00 bash
     21 ?        00:00:20 jupyterhub-sing
    296 ?        00:00:00 geckodriver <defunct>
    302 ?        00:00:00 firefox-esr <defunct>
    303 ?        00:00:45 firefox-esr <defunct>
    379 ?        00:00:00 Web Content <defunct>
    407 ?        00:00:04 WebExtensions <defunct>
    486 ?        00:00:00 Web Content <defunct>
    507 ?        00:00:38 file:// Content <defunct>
    581 ?        00:00:15 python
    686 ?        00:00:00 geckodriver
    692 ?        00:00:00 firefox-esr <defunct>
    693 ?        00:00:34 firefox-esr
    768 ?        00:00:00 Web Content
    796 ?        00:00:04 WebExtensions
    874 ?        00:00:13 file:// Content
    902 ?        00:00:00 Web Content
    961 ?        00:00:00 ps

    After, process hierarchy:

    $ docker exec jupyter-lvu2 ps -efH
UID          PID    PPID  C STIME TTY          TIME CMD
jenkins       49       0  0 21:01 ?        00:00:00 ps -efH
jenkins        1       0  0 21:00 ?        00:00:00 /sbin/docker-init -- conda run -n birdy /usr/local/bin/start-notebook.sh --ip=0.0.0.0 --port=8888 --notebook-dir=/notebook_dir --SingleUserNotebookApp.default_url=/lab --debug --disable-user-config --NotebookApp.terminals_enabled=False --NotebookApp.shutdown_no_activity_timeout=345600 --MappingKernelManager.cull_idle_timeout=86400 --MappingKernelManager.cull_connected=True
jenkins        7       1  0 21:00 ?        00:00:00   /opt/conda/bin/python /opt/conda/bin/conda run -n birdy /usr/local/bin/start-notebook.sh --ip=0.0.0.0 --port=8888 --notebook-dir=/notebook_dir --SingleUserNotebookApp.default_url=/lab --debug --disable-user-config --NotebookApp.terminals_enabled=False --NotebookApp.shutdown_no_activity_timeout=345600 --MappingKernelManager.cull_idle_timeout=86400 --MappingKernelManager.cull_connected=True
jenkins        8       7  0 21:00 ?        00:00:00     /bin/bash /tmp/tmp6chrvz_j
jenkins       22       8  9 21:00 ?        00:00:06       /opt/conda/envs/birdy/bin/python3.8 /opt/conda/envs/birdy/bin/jupyterhub-singleuser --ip=0.0.0.0 --port=8888 --notebook-dir=/notebook_dir --SingleUserNotebookApp.default_url=/lab --debug --disable-user-config --NotebookApp.terminals_enabled=False --NotebookApp.shutdown_no_activity_timeout=345600 --MappingKernelManager.cull_idle_timeout=86400 --MappingKernelManager.cull_connected=True

    After, unable to reproduce defunct firefox-esr processes:

    False
[]

True
[{'create_time': 1666550929.17, 'pid': 962, 'name': 'firefox-esr'}]

$ docker exec jupyter-lvu2 ps
    PID TTY          TIME CMD
      1 ?        00:00:00 docker-init
      6 ?        00:00:00 conda
      7 ?        00:00:00 bash
     21 ?        00:00:20 jupyterhub-sing
    928 ?        00:00:11 python
    955 ?        00:00:00 geckodriver
    962 ?        00:00:46 firefox-esr
   1035 ?        00:00:00 Web Content
   1061 ?        00:00:03 WebExtensions
   1176 ?        00:00:00 Web Content
   1223 ?        00:00:21 file:// Content
   1327 ?        00:00:00 ps

    How to reproduce defunct firefox-esr processes (run twice to create defunct processes from first run):

    import psutil
import panel as pn
import numpy as np
import xarray as xr

pn.extension()

def checkIfProcessRunning(processName):
    '''
    Check if there is any running process that contains the given name processName.
    '''
    #Iterate over the all the running process
    for proc in psutil.process_iter():

        # Check if process name contains the given name string.
        if processName.lower() in proc.name().lower():
            return True

    return False;

def findProcessIdByName(processName):
    '''
    Get a list of all the PIDs of a all the running process whose name contains
    the given string processName
    '''
    listOfProcessObjects = []
    #Iterate over the all the running process
    for proc in psutil.process_iter():

       pinfo = proc.as_dict(attrs=['pid', 'name', 'create_time'])
       # Check if process name contains the given name string.
       if processName.lower() in pinfo['name'].lower() :
           listOfProcessObjects.append(pinfo)

    return listOfProcessObjects;

print(checkIfProcessRunning('firefox-esr'))
print(findProcessIdByName('firefox-esr'))

import hvplot.xarray
panel = pn.Column()
data = xr.DataArray(np.random.rand(200,400), name='data')
app = pn.Column(data.hvplot.quadmesh())
app.save('test.html')
for ii in range(0,10):
    data = xr.DataArray(np.random.rand(200,400), name='data')
    app = pn.Column(data.hvplot.quadmesh())
    app.save(f"test{ii}.png")
print(checkIfProcessRunning('firefox-esr'))
print(findProcessIdByName('firefox-esr'))

1.22.2 (2022-09-19)

Changes:

  • deploy-data: allow post_actions to vary depending on files changed on subsequent run

    Useful for post_actions to know the git version change between the current and the previous run and which files are impacted.

    Actions can perform extra git commands if needed or simply used the provide git diff output and/or rsync output to decide what to do next.

    Non-breaking changes

    • deploy-data script: add new vars GIT_PREVIOUS_COMMIT_HASH, GIT_NEW_COMMIT_HASH, GIT_CHANGED_FILES, RSYNC_OUTPUT, accessible to post_actions scripts.

1.22.1 (2022-09-01)

Changes:

  • birdhouse-deploy: fix bump versioning methodology to auto-update releaseTime accordingly.

    • Adds Makefile to run basic DevOps maintenance commands on the repository.

    • Adds RELEASE.txt with the active release tag and datetime.

    • Replace now: directives by utcnow: to report time properly according to employed ISO format.

    • Update contribution guidelines regarding methodology to create a new revision.

1.22.0 (2022-08-24)

Changes:

  • Geoserver: Adds ./optional-components/test-geoserver-secured-access, to test Twitcher-protected access to Geoserver

    Relevant changes:

    • New Provider (Magpie) : geoserver-secured

    • New Location (Proxy) : /geoserver-secured

    • Copied current WFS GetCapabilities and DescribeFeatureType permissions to new Provider

1.21.1 (2022-08-24)

Changes

  • birdhouse-deploy: fix invalid canarie-api-full-monitoring endpoints adding double / when substituting variables.

  • birdhouse-deploy: add optional variables MAGPIE_LOG_LEVEL and TWITCHER_LOG_LEVEL (both INFO by default) to allow instead to customize reported details by instances for debugging purposes. Note that setting DEBUG will leak sensible details in their logs and should be reserved only for testing environments.

1.21.0 (2022-08-19)

Changes

  • Cowbird: add new service Ouranosinc/cowbird to the stack.

    • Cowbird can be integrated to the instance using components/cowbird when added to in EXTRA_CONF_DIRS in the env.local variable definitions.

    • Offers syncing operations between various other birds in order to apply user/group permissions between corresponding files, granting access to them seamlessly through distinct services.

    • Allows event and callback triggers to sync permissions and volume paths between API endpoints and local storages.

  • Nginx: add missing X-Forwarded-Host header to allow Twitcher to report the proper server host location when the service to be accessed uses an internal Docker network reference through the service private URL defined in Magpie.

  • birdhouse-deploy: fix missing GEOSERVER_ADMIN_USER variable templating from pavics-compose.sh.

1.20.4 (2022-08-19)

Changes:

  • Weaver: update weaver component default version to 4.22.0.

    • Minor improvements to facilitate retrieval of XML and JSON Process definition and their seamless execution with XML or JSON request contents using either WPS or OGC API - Processes REST endpoints interchangeably.

    • Fixes to WPS remote provider parsing registered in Weaver to successfully perform the relevant process executions.

    • Add WPS remote provider retry conditions to handle known problematic cases during process execution (on remote) that can lead to sporadic failures of the monitored job. When possible, retried submission leading to successful execution will result in the monitored job to complete successfully and transparently to the user. Relevant errors and retry attempts are provided in the job logs.

    • Add WPS remote provider status exception response as XML message from the failed remote execution within the monitored local job logs to help users understand how to resolve any encountered issue on the remote service.

    • Bump version OWSLib==0.26.0 to fix processVersion attribute resolution from WPS remote provider definition to populate Process.version property employed in converted Process description to OGC API - Process schema (relates to geopython/OWSLib#794).

1.20.3 (2022-08-18)

Fixes:

  • Canarie-api: fix unable to verify LetsEncrypt SSL certs

    LetsEncrypt older root certificate “DST Root CA X3” expired on September 30, 2021, see https://letsencrypt.org/docs/dst-root-ca-x3-expiration-september-2021/

    All the major browsers and OS platform has previously added the new root certificate “ISRG Root X1” ahead of time so the transition to the new root certificate is seemless for all clients.

    Python requests package bundle their own copy of known root certificates and is late to add this new root cert “ISRG Root X1”. Had it automatically fallback to the OS copy of the root cert bundle, this would have been seemless.

    The fix is to force requests to use the OS copy of the root cert bundle.

    Fix for this error:

    $ docker exec proxy python -c "import requests; requests.request('GET', 'https://lvupavicsmaster.ouranos.ca/geoserver')"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/requests/api.py", line 50, in request
    response = session.request(method=method, url=url, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/requests/sessions.py", line 468, in request
    resp = self.send(prep, **send_kwargs)
  File "/usr/local/lib/python2.7/dist-packages/requests/sessions.py", line 576, in send
    r = adapter.send(request, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/requests/adapters.py", line 433, in send
    raise SSLError(e, request=request)
requests.exceptions.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)

    Default SSL root cert bundle of requests:

    $ docker exec proxy python -c "import requests; print requests.certs.where()"
/usr/local/lib/python2.7/dist-packages/requests/cacert.pem

    Confirm the fix works:

    $ docker exec -it proxy bash
root@37ed3a2a03ae:/opt/local/src/CanarieAPI/canarieapi# REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt python -c "import requests; requests.request('GET', 'https://lvupavicsmaster.ouranos.ca/geoserver')"
root@37ed3a2a03ae:/opt/local/src/CanarieAPI/canarieapi#

$ docker exec proxy env |grep REQ
REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt

    Fixes https://github.com/bird-house/birdhouse-deploy/issues/198

1.20.2 (2022-08-17)

Changes:

  • birdhouse-deploy: fix missing bump of server version reported in canarie service configuration

1.20.1 (2022-08-11)

Changes:

1.20.0 (2022-08-10)

Changes

  • Weaver: update weaver component default version from 4.12.0 to 4.20.0. See full CHANGELOG for details.

    • Docker commands that target weaver-worker to start or use celery must be adjusted according to how its new CLI resolves certain global parameters. Since the celery-healthcheck script uses this CLI, celery commands were adjusted to consider those changes. If custom scripts or command overrides are used to call celery, similar changes will need to be applied according to employed Weaver version. See details in Weaver 4.15.0 changes.

    • Support OpenAPI-based schema field for Process I/O definitions to align with latest OGC API - Processes changes.

    • Support Prefer header to define execution mode of jobs according to latest OGC API - Processes recommendations.

    • Support transmissionMode to return file-based outputs by HTTP Link header references as desired.

    • Support deployment of new processes using YAML and CWL based request contents directly to remove the need to convert and indirectly embed their definitions in specific JSON schema structures.

    • Support process revisions allowing users to iteratively update process metadata and their definitions without full un/re-deployment of the complete process for each change. This also allows multiple process revisions to live simultaneously on the instance, which can be described or launched for job executions with specific tagged versions.

    • Add control query parameters to retrieve outputs in different JSON schema variations according to desired structure.

    • Add statistics collection following job execution to obtain machine resource usage by the executed process.

    • Improve handling of Content-Type definitions for reporting inputs, outputs and logs retrieval from job executions.

    • Fixes related to reporting of job results with different formats and URL references based on requested execution methods and control parameters.

    • Fixes to resolve pending vulnerabilities or feature integrations by package dependencies (celery, pywps, etc.).

    • Fixes related to parsing of WPS-1/2 remote providers URL from a CWL definition using GetCapabilities endpoint.

    • Fixes and addition of multiple Weaver CLI capabilities to employ new features.

1.19.2 (2022-07-20)

Changes

  • Finch: new release for new Xclim

    Finch release notes:

    • Fix Finch unable to startup in the Docker image.

    • Avoid using a broken version of libarchive in the Docker image.

    • Fix use of output_name, add output_format to xclim indicators.

    • Change all outputs to use output as the main output field name (instead of output_netcdf).

    • Updated to xclim 0.37:

      • Percentile inputs of xclim indicators have been renamed with generic names, excluding an explicit mention to the target percentile.

      • In ensemble processes, these percentiles can now be chosen through perc_[var] inputs. The default values are inherited from earlier versions of xclim.

    • Average shape process downgraded to be single-threaded, as ESMF seems to have issues with multithreading.

    • Removed deprecated processes subset_ensemble_bbox_BCCAQv2, subset_ensemble_BCCAQv2 and BCCAQv2_heat_wave_frequency_gridpoint.

    • Added csv_precision to all processes allowing CSV output. When given, it controls the number of decimal places in the output.

1.19.1 (2022-07-19)

Changes

  • Various changes to get the new production host up and running

    Non-breaking changes

    • Bootstrap testsuite: only crawl the subset enough to pass canarie-api monitoring: faster when system under test has too much other stuff.

    • New script: check-autodeploy-repos: to ensure autodeploy will trigger normally.

    • New script: sync-data: to pull data from existing production host to a new production host or to a staging host to emulate the production host.

    • thredds, geoserver, generic_bird: set more appropriate production values, taken from https://github.com/Ouranosinc/birdhouse-deploy/commit/316439e310e915e0a4ef35d25744cab76722fa99

    • monitoring: fix redundant network_mode: host and ports binding since host network_mode will already automatically perform port bindings

    Breaking changes

    • None

1.19.0 (2022-06-08)

Changes:

  • Magpie/Twitcher: update magpie service from 3.21.0 to 3.26.0 and bundled twitcher from 0.6.2 to 0.7.0.

    • Adds Service Hooks allowing Twitcher to apply HTTP pre-request/post-response modifications to requested services and resources in accordance to MagpieAdapter implementation and using plugin Python scripts when matched against specific request parameters.

    • Using Service Hooks, inject X-WPS-Output-Context header in Weaver job submission requests through the proxied request by Twitcher and MagpieAdapter. This header contains the user ID that indicates to Weaver were to store job output results, allowing to save them in the corresponding user’s workspace directory under wpsoutputs path. More details found in PR https://github.com/bird-house/birdhouse-deploy/pull/244.

    • Using Service Hooks, filter processes returned by Weaver in JSON response from /processes endpoint using respective permissions applied onto each /processes/{processID} for the requesting user. Users will only be able to see processes for which they have read access to retrieve the process description. More details found in PR https://github.com/bird-house/birdhouse-deploy/pull/245.

    • Using Service Hooks, automatically apply permissions for the user that successfully deployed a Weaver process using POST /processes request, granting it direct access to this process during process listing, process description request and for submitting job execution of this process. Only this user deploying the process will have access to it until further permissions are added in Magpie to share or publish it with other users, groups and/or publicly. The user must have the necessary permission to deploy a new process in the first place. More details found in PR https://github.com/bird-house/birdhouse-deploy/pull/247.

1.18.13 (2022-06-07)

Changes:

  • deploy-data: new env var DEPLOY_DATA_RSYNC_USER_GRP to avoid running cronjobs as root

    When deploy-data is used by the scheduler component, it is run as root. This new env var will force the rsync process to run as a regular user to follow security best practice to avoid running as root when not needed.

    Note that the git checkout step done by deploy-data is still run as root. This is because deploy-data is currently still run as root so it can execute docker commands (ex: spawning the rsync command above in its own docker container).

    To fix this limitation, the regular user inside the deploy-data container need to have docker access inside the container and outside on the host at the same time. If we make that regular user configurable so the script deploy-data is generic and can work for any organisations, this is tricky for the moment so will have to be handle in another PR.

    So for the moment we have not achieved full non-root user in cronjobs launched by the scheduler compoment but the most important part, the part that perform the actual job (rsync or execute custom command using an external docker container) is running as non-root.

    See PR https://github.com/bird-house/birdhouse-deploy-ouranos/pull/18 that make use of this new env var.

    When deploy-data is invoking an external script that itself spawn a new docker run, then it is up to this external script to ensure the proper non-root user is used by docker run. See PR https://github.com/Ouranosinc/pavics-vdb/pull/50 that handle that case.

1.18.12 (2022-05-05)

Changes:

  • Jupyter env: new build for new XClim and to get Dask dashboard and Panel server app to work

    Deploy new Jupyter env from PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/105 on PAVICS.

    Detailed changes can be found at https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/105.

    Dask dashboard no manual URL mangling required:

    Screenshot from 2022-04-13 22-37-49

    “Render with Panel” button works:

    Screenshot from 2022-05-04 15-18-03

    Relevant changes:

    # new
>   - dask-labextension=5.2.0=pyhd8ed1ab_0
>   - jupyter-panel-proxy=0.2.0a2=py_0
>   - jupyter-server-proxy=3.2.1=pyhd8ed1ab_0

# removed, interfere with panel
<     - handcalcs==1.4.1

<   - xclim=0.34.0=pyhd8ed1ab_0
>   - xclim=0.36.0=pyhd8ed1ab_0

<   - cf_xarray=0.6.3=pyhd8ed1ab_0
>   - cf_xarray=0.7.2=pyhd8ed1ab_0

<   - clisops=0.8.0=pyh6c4a22f_0
>   - clisops=0.9.0=pyh6c4a22f_0

# downgrade by clisops
<   - pandas=1.4.1=py38h43a58ef_0
>   - pandas=1.3.5=py38h43a58ef_0

<   - rioxarray=0.10.3=pyhd8ed1ab_0
>   - rioxarray=0.11.1=pyhd8ed1ab_0

<   - nc-time-axis=1.4.0=pyhd8ed1ab_0
>   - nc-time-axis=1.4.1=pyhd8ed1ab_0

<   - roocs-utils=0.5.0=pyh6c4a22f_0
>   - roocs-utils=0.6.1=pyh6c4a22f_0

<   - panel=0.12.7=pyhd8ed1ab_0
>   - panel=0.13.1a2=py_0

<   - plotly=5.6.0=pyhd8ed1ab_0
>   - plotly=5.7.0=pyhd8ed1ab_0

1.18.11 (2022-04-21)

Changes:

1.18.10 (2022-04-07)

Changes:

  • Jupyter env: new xlrd, pre-commit, pin dask, distributed, cf_xarray, latest of everything else

    Deploy new Jupyter env from PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/101 on PAVICS.

    Detailed changes can be found at https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/101.

    Relevant changes:

    >   - pre-commit=2.17.0=py38h578d9bd_0
>   - xlrd=2.0.1=pyhd8ed1ab_3

<   - xclim=0.32.1=pyhd8ed1ab_0
>   - xclim=0.34.0=pyhd8ed1ab_0

<   - cfgrib=0.9.9.1=pyhd8ed1ab_1
>   - cfgrib=0.9.10.1=pyhd8ed1ab_0

<   - cftime=1.5.1.1=py38h6c62de6_1
>   - cftime=1.6.0=py38h3ec907f_0

<   - intake-xarray=0.5.0=pyhd8ed1ab_0
>   - intake-xarray=0.6.0=pyhd8ed1ab_0

<   - pandas=1.3.5=py38h43a58ef_0
>   - pandas=1.4.1=py38h43a58ef_0

<   - regionmask=0.8.0=pyhd8ed1ab_1
>   - regionmask=0.9.0=pyhd8ed1ab_0

<   - rioxarray=0.9.1=pyhd8ed1ab_0
>   - rioxarray=0.10.3=pyhd8ed1ab_0

<   - xarray=0.20.2=pyhd8ed1ab_0
>   - xarray=2022.3.0=pyhd8ed1ab_0

<   - zarr=2.10.3=pyhd8ed1ab_0
>   - zarr=2.11.1=pyhd8ed1ab_0

1.18.9 (2022-03-16)

Changes:

  • Finch: update finch component from 0.7.7 to 0.8.2

    Relevant Changes:

    • v0.8.0

      • Add hourly_to_daily process

      • Avoid annoying warnings by updating birdy (environment-docs)

      • Upgrade to clisops 0.8.0 to accelerate spatial averages over regions.

      • Upgrade to xesmf 0.6.2 to fix spatial averaging bug not weighing correctly cells with varying areas.

      • Update to PyWPS 4.5.1 to allow the creation of recursive directories for outputs.

    • v0.8.2

      • Add geoseries_to_netcdf process, converting a geojson (like a OGC-API request) to a CF-compliant netCDF.

      • Add output_name argument to most processes (excepted subsetting and averaging processes), to control the name (or prefix) of the output file.

      • New dependency python-slugify to ensure filenames are safe and valid.

      • Pinning dask to <=2022.1.0 to avoid a performance issue with 2022.1.1.

1.18.8 (2022-03-09)

Changes:

  • Weaver: fix tests

    Relevant changes:

    • Increase default timeout (60s -> 120s) for components/weaver/post-docker-compose-up script to allow it to complete with many WPS bird taking a long time to boot. Before this fix, test instances only managed to register catalog, finch, and flyingpigeon providers, but timed out for hummingbird and following WPS birds.

      This resolves the first few cell tests by having birds ready for use:

      [2022-03-09T02:13:34.966Z] pavics-sdi-master/docs/source/notebook-components/weaver_example.ipynb . [ 57%]
[2022-03-09T02:13:46.069Z] .......FF.                                                               [ 61%]

    • Add override request_options.yml in birdhouse/optional-components/test-weaver that disables SSL verification specifically for the remaining 2 F cell above. Error is related to the job execution itself on the test instance, which fails when Weaver sends requests to hummingbird’s ncdump process. An SSL verification error happens, because the test instance uses a self-signed SSL certificate.

1.18.7 (2022-03-08)

Changes:

  • Weaver: update weaver component from 4.5.0 to 4.12.0.

    Relevant changes:

    • Adds WeaverClient and Weaver CLI. Although not strictly employed by the platform itself to offer Weaver as a service, these can be employed to interact with Weaver using Python or shell commands, providing access to all WPS birds offered by the platform using the common OGC API - Processes interface through Weaver Providers.

    • Adds Vault functionality allowing temporary and secure storage to upload files for single-use process execution.

    • Various bugfixes and conformance resolution related to OGC API - Processes.

    • Fix weaver-mongodb link references for weaver-worker. New default variables WEAVER_MONGODB_[HOST|PORT|URL] are defined to construct different INI configuration formats employed by weaver and weaver-worker images.

    • Fix missing EXTRA_VARS variables in Weaver’s default.env.

    • Fix celery-healthcheck of weaver-worker to consider multiple tasks.

1.18.6 (2022-03-08)

  • Magpie: update magpie service from 3.19.1 to 3.21.0.

    Relevant changes:

    • Update WFS, WMS and WPS related services to properly implement the relevant Permissions and Resources according to their specific implementation details. For example, GeoServer-based WMS implementation supports Workspaces and additional operations that are not offered by standard OGC-based WMS. Some of these implementation specific operations can be taken advantage of with improved Permissions and Resources resolution.

    • Add multi-Resource effective access resolution for Services that support it. For example, accessing multiple Layers under a permission-restricted WFS with parameters that allow multiple values within a single request is now possible, if the user is granted to all specified Resources. Previously, users would require to access each Layer Resource individually with distinct requests.

    • Magpie’s API and UI are more verbose about supported hierarchical Resource structure under a given Service type. When creating Resources, specific structures have to be respected, and only valid cases are proposed in the UI.

    • Minor UI fixes.

1.18.5 (2022-01-27)

Changes:

  • Jupyter: update Jupyter env for latest XClim, RavenPy and all packages

    Deploy new Jupyter env from PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/95 on PAVICS.

    Detailed changes can be found at https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/95.

    Relevant changes:

    <   - xclim=0.31.0=pyhd8ed1ab_0
>   - xclim=0.32.1=pyhd8ed1ab_0

<   - ravenpy=0.7.5=pyhff6ddc9_0
>   - ravenpy=0.7.8=pyh8a188c0_0

<   - python=3.7.12=hb7a2778_100_cpython
>   - python=3.8.12=hb7a2778_2_cpython

# removed
<   - vcs=8.2.1=pyh9f0ad1d_0

<   - numpy=1.21.4=py37h31617e3_0
>   - numpy=1.21.5=py38h87f13fb_0

<   - xarray=0.20.1=pyhd8ed1ab_0
>   - xarray=0.20.2=pyhd8ed1ab_0

<   - rioxarray=0.8.0=pyhd8ed1ab_0
>   - rioxarray=0.9.1=pyhd8ed1ab_0

<   - cf_xarray=0.6.1=pyh6c4a22f_0
>   - cf_xarray=0.6.3=pyhd8ed1ab_0

<   - gdal=3.3.2=py37hd5a0ba4_2
>   - gdal=3.3.3=py38hcf2042a_0

<   - rasterio=1.2.6=py37hc20819c_2
>   - rasterio=1.2.10=py38hfd64e68_0

<   - climpred=2.1.6=pyhd8ed1ab_1
>   - climpred=2.2.0=pyhd8ed1ab_0

<   - clisops=0.7.0=pyh6c4a22f_0
>   - clisops=0.8.0=pyh6c4a22f_0

<   - xesmf=0.6.0=pyhd8ed1ab_0
>   - xesmf=0.6.2=pyhd8ed1ab_0

<   - birdy=v0.8.0=pyh6c4a22f_1
>   - birdy=0.8.1=pyh6c4a22f_1

<   - cartopy=0.20.0=py37hbe109c4_0
>   - cartopy=0.20.1=py38hf9a4893_1

<   - dask=2021.11.2=pyhd8ed1ab_0
>   - dask=2022.1.0=pyhd8ed1ab_0

<   - numba=0.53.1=py37hb11d6e1_1
>   - numba=0.55.0=py38h4bf6c61_0

<   - pandas=1.3.4=py37he8f5f7f_1
>   - pandas=1.3.5=py38h43a58ef_0

1.18.4 (2022-01-25)

Changes:

  • vagrant: support RockyLinux

    RockyLinux 8 is the successor to Centos 7.

    Centos 8 has become like a “RHEL 8 beta” than the equivalent of RHEL 8.

    RockyLinux 8 is the new equivalent of RHEL 8, following the original spirit of the Centos project.

    More info at https://rockylinux.org/about.

1.18.3 (2021-12-17)

Changes:

  • Jupyter: new build with latest changes

    See PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/94 for more info.

    Change summary:

    <   - xclim=0.28.1=pyhd8ed1ab_0
>   - xclim=0.31.0=pyhd8ed1ab_0

<   - ravenpy=0.7.4=pyh7f9bfb9_0
>   - ravenpy=0.7.5=pyhff6ddc9_0

<   - xarray=0.19.0=pyhd8ed1ab_1
>   - xarray=0.20.1=pyhd8ed1ab_0

<   - rasterio=1.2.1=py37ha549118_0
>   - rasterio=1.2.6=py37hc20819c_2

<   - bokeh=2.3.3=py37h89c1867_0
>   - bokeh=2.4.2=py37h89c1867_0

<   - cartopy=0.19.0.post1=py37h0c48da3_1
>   - cartopy=0.20.0=py37hbe109c4_0

<   - cffi=1.14.6=py37hc58025e_0
>   - cffi=1.15.0=py37h036bc23_0

<   - climpred=2.1.5.post1=pyhd8ed1ab_0
>   - climpred=2.1.6=pyhd8ed1ab_1

<   - clisops=0.6.5=pyh6c4a22f_0
>   - clisops=0.7.0=pyh6c4a22f_0

<   - dask=2021.9.0=pyhd8ed1ab_0
>   - dask=2021.11.2=pyhd8ed1ab_0

<   - gdal=3.1.4=py37h2ec2946_8
>   - gdal=3.3.2=py37hd5a0ba4_2

<   - geopandas=0.9.0=pyhd8ed1ab_1
>   - geopandas=0.10.2=pyhd8ed1ab_0

<   - nc-time-axis=1.3.1=pyhd8ed1ab_2
>   - nc-time-axis=1.4.0=pyhd8ed1ab_0

<   - pandas=1.2.5=py37h219a48f_0
>   - pandas=1.3.4=py37he8f5f7f_

<   - poppler=0.89.0=h2de54a5_5
>   - poppler=21.09.0=ha39eefc_3

<   - rioxarray=0.7.0=pyhd8ed1ab_0
>   - rioxarray=0.8.0=pyhd8ed1ab_0

<   - roocs-utils=0.4.2=pyh6c4a22f_0
>   - roocs-utils=0.5.0=pyh6c4a22f_0

1.18.2 (2021-12-13)

Fixes

  • Thredds: update for Log4j Vulnerability CVE-2021-44228

    Quebec gouvernment has shutdown its website due to this vulnerability so it’s pretty serious (https://montrealgazette.com/news/quebec/quebec-government-shutting-down-websites-report).

    Thredds release notes: https://github.com/Unidata/thredds/releases

    https://www.oracle.com/security-alerts/alert-cve-2021-44228.html

    Oracle Security Alert Advisory - CVE-2021-44228 Description

    This Security Alert addresses CVE-2021-44228, a remote code execution vulnerability in Apache Log4j. It is remotely exploitable without authentication, i.e., may be exploited over a network without the need for a username and password.

    Due to the severity of this vulnerability and the publication of exploit code on various sites, Oracle strongly recommends that customers apply the updates provided by this Security Alert as soon as possible.

    Affected Products and Versions Apache Log4j, versions 2.0-2.14.1

    We have 4 Java component but only 1 is vulnerable: Thredds:

    After fix:

    $ docker run -it --rm unidata/thredds-docker:4.6.18 bash
root@f65aadd2955c:/usr/local/tomcat# find -iname '**log4j**'
./webapps/thredds/WEB-INF/classes/log4j2.xml
./webapps/thredds/WEB-INF/lib/log4j-api-2.15.0.jar
./webapps/thredds/WEB-INF/lib/log4j-core-2.15.0.jar
./webapps/thredds/WEB-INF/lib/log4j-slf4j-impl-2.15.0.jar
./webapps/thredds/WEB-INF/lib/log4j-web-2.15.0.jar

    Before fix (unidata/thredds-docker:4.6.15):

    $ docker exec -it thredds find / -iname '**log4j**'
find: ‘/proc/1/map_files’: Operation not permitted
find: ‘/proc/12/map_files’: Operation not permitted
find: ‘/proc/20543/map_files’: Operation not permitted
/usr/local/tomcat/webapps/twitcher#ows#proxy#thredds/WEB-INF/classes/log4j2.xml
/usr/local/tomcat/webapps/twitcher#ows#proxy#thredds/WEB-INF/lib/log4j-api-2.13.3.jar
/usr/local/tomcat/webapps/twitcher#ows#proxy#thredds/WEB-INF/lib/log4j-core-2.13.3.jar
/usr/local/tomcat/webapps/twitcher#ows#proxy#thredds/WEB-INF/lib/log4j-slf4j-impl-2.13.3.jar
/usr/local/tomcat/webapps/twitcher#ows#proxy#thredds/WEB-INF/lib/log4j-web-2.13.3.jar

    Other components (ncwms2, geoserver, solr) have log4j older than version 2.0 so supposedly not affected:

    $ docker exec -it ncwms2 find / -iname '**log4j**'
/opt/conda/envs/birdhouse/opt/apache-tomcat/webapps/ncWMS2/WEB-INF/classes/log4j.properties
/opt/conda/envs/birdhouse/opt/apache-tomcat/webapps/ncWMS2/WEB-INF/lib/log4j-1.2.17.jar
/opt/conda/envs/birdhouse/opt/apache-tomcat/webapps/ncWMS2/WEB-INF/lib/slf4j-log4j12-1.7.2.jar

$ docker exec -it geoserver find / -iname '**log4j**'
/build_data/log4j.properties
find: ‘/etc/ssl/private’: Permission denied
find: ‘/proc/tty/driver’: Permission denied
find: ‘/proc/1/map_files’: Operation not permitted
find: ‘/proc/15/task/47547’: No such file or directory
find: ‘/proc/15/map_files’: Operation not permitted
find: ‘/proc/47492/map_files’: Operation not permitted
find: ‘/root’: Permission denied
/usr/local/tomcat/log4j.properties
/usr/local/tomcat/webapps/geoserver/WEB-INF/lib/log4j-1.2.17.jar
/usr/local/tomcat/webapps/geoserver/WEB-INF/lib/metrics-log4j-3.0.2.jar
/usr/local/tomcat/webapps/geoserver/WEB-INF/lib/slf4j-log4j12-1.6.4.jar
find: ‘/var/cache/apt/archives/partial’: Permission denied
find: ‘/var/cache/ldconfig’: Permission denied

$ docker exec -it solr find / -iname '**log4j**'
/data/solr/log4j.properties
/opt/birdhouse/eggs/birdhousebuilder.recipe.solr-0.1.5-py2.7.egg/birdhousebuilder/recipe/solr/templates/log4j.properties
/opt/conda/envs/birdhouse/opt/solr/docs/solr-core/org/apache/solr/logging/log4j
/opt/conda/envs/birdhouse/opt/solr/docs/solr-core/org/apache/solr/logging/log4j/Log4jInfo.html
/opt/conda/envs/birdhouse/opt/solr/docs/solr-core/org/apache/solr/logging/log4j/Log4jWatcher.html
/opt/conda/envs/birdhouse/opt/solr/docs/solr-core/org/apache/solr/logging/log4j/class-use/Log4jInfo.html
/opt/conda/envs/birdhouse/opt/solr/docs/solr-core/org/apache/solr/logging/log4j/class-use/Log4jWatcher.html
/opt/conda/envs/birdhouse/opt/solr/example/resources/log4j.properties
/opt/conda/envs/birdhouse/opt/solr/licenses/log4j-1.2.17.jar.sha1
/opt/conda/envs/birdhouse/opt/solr/licenses/log4j-LICENSE-ASL.txt
/opt/conda/envs/birdhouse/opt/solr/licenses/log4j-NOTICE.txt
/opt/conda/envs/birdhouse/opt/solr/licenses/slf4j-log4j12-1.7.7.jar.sha1
/opt/conda/envs/birdhouse/opt/solr/server/lib/ext/log4j-1.2.17.jar
/opt/conda/envs/birdhouse/opt/solr/server/lib/ext/slf4j-log4j12-1.7.7.jar
/opt/conda/envs/birdhouse/opt/solr/server/resources/log4j.properties
/opt/conda/envs/birdhouse/opt/solr/server/scripts/cloud-scripts/log4j.properties
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/docs/solr-core/org/apache/solr/logging/log4j
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/docs/solr-core/org/apache/solr/logging/log4j/Log4jInfo.html
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/docs/solr-core/org/apache/solr/logging/log4j/Log4jWatcher.html
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/docs/solr-core/org/apache/solr/logging/log4j/class-use/Log4jInfo.html
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/docs/solr-core/org/apache/solr/logging/log4j/class-use/Log4jWatcher.html
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/example/resources/log4j.properties
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/licenses/log4j-1.2.17.jar.sha1
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/licenses/log4j-LICENSE-ASL.txt
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/licenses/log4j-NOTICE.txt
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/licenses/slf4j-log4j12-1.7.7.jar.sha1
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/server/lib/ext/log4j-1.2.17.jar
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/server/lib/ext/slf4j-log4j12-1.7.7.jar
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/server/resources/log4j.properties
/opt/conda/pkgs/solr-5.2.1-1/opt/solr/server/scripts/cloud-scripts/log4j.properties

1.18.1 (2021-12-08)

Fixes

1.18.0 (2021-12-08)

Changes

  • Upgrade default Weaver version to 4.5.0 (from 4.2.1) for new features and fixes. Most notable changes are:

    • Adds support of X-WPS-Output-Context header to define the WPS output nested directory (for user context).

    • Adds support of X-Auth-Docker header to define a private Docker registry authentication token when the referenced Docker image in the deployed Application Package requires it to fetch it for Process execution.

    • Require MongoDB==5.0 Docker image for Weaver’s database.

    • Fixes related to handling dismiss operation of job executions and retrieval of their results.

    • Fixes related to fetching remote files and propagation of intermediate results between Workflow steps.

Important

Because of the new MongoDB==5.0 database requirement for Weaver that uses (potentially) distinct version from other birds (notably phoenix with MongoDB==3.4), a separate Docker image is employed only for Weaver. If some processes, jobs, or other Weaver-related data was already defined on one of your server instances, manual transfer between the generic ${DATA_PERSIST_ROOT}/mongodb_persist to new ${DATA_PERSIST_ROOT}/mongodb_weaver_persist directory must be accomplished. The data in the new directory should then be migrated to the new version following the procedure described in Database Migration.

1.17.6 (2021-12-03)

Changes

  • Upgrade Magpie/Twitcher to 3.19.0, and add new related environment variables.

    • Adjust Twitcher runner to employ gunicorn instead of waitress.

    • Add new environment variables to handle email usage, used for features such as user registration/approval and user assignment to groups with terms and conditions.

    • Add expiration variable for temporary tokens.

1.17.5 (2021-11-16)

Changes

1.17.4 (2021-11-03)

Fixes

  • Add missing config/canarie-api/weaver_config.py entry to .gitignore of ./components/weaver that is generated from the corresponding template file.

    If upgrading from previous 1.17.x version, autodeploy will not resume automatically even with this fix because of the dirty state of the repository. A manual git pull will be required to fix subsequent autodeploy triggers.

1.17.3 (2021-11-03)

Fixes

  • Minor fix to install-docker.sh and comment update for other scripts due to Magpie upgrade

    install-docker.sh: fix to work with users with sudo privilege. Before it needed user root.

    Other comments in scripts are due to new Magpie in PR https://github.com/bird-house/birdhouse-deploy/pull/107.

1.17.2 (2021-11-03)

Changes

  • scripts: add extract-jupyter-users-from-magpie-db

    Extract Jupyter users from Magpie DB so we can send announcements to all Jupyter users.

    Sample output:

    $ ./scripts/extract-jupyter-users-from-magpie-db  > /tmp/out
+ echo SELECT email,user_name FROM users ORDER BY email
+ docker exec -i postgres-magpie psql -U postgres-magpie magpiedb

$ cat /tmp/out
         email          |   user_name
------------------------+---------------
 admin-catalog@mail.com | admin-catalog
 admin@mail.com         | admin
 anonymous@mail.com     | anonymous
 authtest@example.com   | authtest
(4 rows)

1.17.1 (2021-11-02)

Fixes

  • Apply mongodb network to mongodb image in order to allow phoenix to properly reference it.

  • Remove mongodb definition from ./components/weaver since the extended mongodb network is already provided.

1.17.0 (2021-11-01)

Changes

  • Adds Weaver to the stack (optional) when ./components/weaver is added to EXTRA_CONF_DIRS. For more details, refer to Weaver Component Following happens when enabled:

    • Service weaver (API) gets added with endpoints /twitcher/ows/proxy/weaver and /weaver.

    • All birds offering a WPS 1.x/2.x endpoint are automatically added as providers known by Weaver (birds: catalog, finch, flyingpigeon, hummingbird, malleefowl and raven). This offers an automatic mapping of WPS 1.x/2.x requests of process descriptions and execution nested under the birds to corresponding OGC-API - Processes RESTful interface (and added functionalities).

    • New processes can be deployed and executed using Dockerized Application Packages. Additionally, all existing processes (across bird providers and Dockerized Application Packages) can be chained into Workflows

    • Images weaver-worker (Weaver’s job executor) and docker-proxy (sibling Docker container dispatcher) are added to the stack to support above functionalities.

    • Adds Magpie permissions and service for Weaver endpoints.

    • Adds ./optional-components/test-weaver for even more Magpie extended permissions for Weaver for getting access to resources for functionalities required by Weaver Testing notebook.

1.16.2 (2021-10-27)

Changes

  • geoserver: enable geopkg plugin

    https://docs.geoserver.org/latest/en/user/community/geopkg/

    This plugin brings in the ability to write GeoPackage files in GeoServer. Reading GeoPackage files is part of the core functionality of GeoServer, and does not require this extension.

    GeoPackage is an SQLite based standard format that is able to hold multiple vector and raster data layers in a single file.

    GeoPackage can be used as an output format for WFS GetFeature (creating one vector data layer) as well as WMS GetMap (creating one raster data layer). The GeoServer GeoPackage extension also allows to create a completely custom made GeoPackage with multiple layers, using the GeoPackage process.

    Concretely this plugin adds a new GeoPackage download format, see screenshot below:

    Screenshot from 2021-10-27 17-09-05

1.16.1 (2021-10-25)

Changes

  • Thredds: Enable Netcdf Subset Service (NCSS)

    “The Netcdf Subset Service (NCSS) is one of the ways that the TDS can serve data. It is an experimental REST protocol for returning subsets of CDM datasets.” https://www.unidata.ucar.edu/software/tds/current/reference/NetcdfSubsetServiceConfigure.html

    More NCSS docs: https://www.unidata.ucar.edu/software/tds/current/reference/NetcdfSubsetServiceReference.html

    Briefly, the advantage to enable NCSS is to be able to perform subsetting directly in the browser (manipulating URL parameters), avoiding the overhead for using OpenDAP (needs another client than the existing browser). This even works for .ncml files.

    Recall previously using “HTTPServer” link type, we were able to download directly the .nc files but for .ncml we got the xml content instead. With this new “NetcdfSubset” link type, we can actually download the NetCDF content of a .ncml file directly from the browser.

    Sample screenshots:

    Screenshot 2021-10-21 at 21-32-14 Catalog Services Screenshot 2021-10-21 at 21-31-13 NetCDF Subset Service for Grids

    dataset.xml:

    <?xml version="1.0" encoding="UTF-8"?>
<gridDataset location="/twitcher/ows/proxy/thredds/ncss/birdhouse/testdata/flyingpigeon/cmip3/tasmin.sresa2.miub_echo_g.run1.atm.da.nc" path="path">
  <axis name="lat" shape="6" type="double" axisType="Lat">
    <attribute name="units" value="degrees_north"/>
    <attribute name="long_name" value="latitude"/>
    <attribute name="standard_name" value="latitude"/>
    <attribute name="bounds" value="lat_bnds"/>
    <attribute name="axis" value="Y"/>
    <attribute name="_ChunkSizes" type="int" value="6"/>
    <attribute name="_CoordinateAxisType" value="Lat"/>
    <values>42.67760468 46.38855743 50.09945297 53.81027222 57.52099228 61.2315712</values>
  </axis>
  <axis name="lon" shape="7" type="double" axisType="Lon">
    <attribute name="units" value="degrees_east"/>
    <attribute name="long_name" value="longitude"/>
    <attribute name="standard_name" value="longitude"/>
    <attribute name="bounds" value="lon_bnds"/>
    <attribute name="axis" value="X"/>
    <attribute name="_ChunkSizes" type="int" value="7"/>
    <attribute name="_CoordinateAxisType" value="Lon"/>
    <values start="281.25" increment="3.75" npts="7"/>
  </axis>
  <axis name="time" shape="7200" type="double" axisType="Time">
    <attribute name="units" value="days since 1860-1-1"/>
    <attribute name="calendar" value="360_day"/>
    <attribute name="bounds" value="time_bnds"/>
    <attribute name="_ChunkSizes" type="int" value="7200"/>
    <attribute name="_CoordinateAxisType" value="Time"/>
    <values start="66960.5" increment="1.0" npts="7200"/>
  </axis>
  <gridSet name="time lat lon">
    <projectionBox>
      <minx>279.375</minx>
      <maxx>305.625</maxx>
      <miny>40.82210731506348</miny>
      <maxy>63.08675956726074</maxy>
    </projectionBox>
    <axisRef name="time"/>
    <axisRef name="lat"/>
    <axisRef name="lon"/>
    <grid name="tasmin" desc="Minimum Daily Surface Air Temperature" shape="time lat lon" type="float">
      <attribute name="original_name" value="T2MIN"/>
      <attribute name="coordinates" value="height"/>
      <attribute name="long_name" value="Minimum Daily Surface Air Temperature"/>
      <attribute name="standard_name" value="air_temperature"/>
      <attribute name="cell_methods" value="time: minimum (interval: 30 minutes)"/>
      <attribute name="units" value="K"/>
      <attribute name="missing_value" type="float" value="1.0E20"/>
      <attribute name="history" value="tas=max(195,tas) applied to raw data; min of 194.73 detected;"/>
      <attribute name="_ChunkSizes" type="int" value="7200 6 7"/>
    </grid>
  </gridSet>
  <LatLonBox>
    <west>-78.7500</west>
    <east>-56.2500</east>
    <south>42.6776</south>
    <north>61.2315</north>
  </LatLonBox>
  <TimeSpan>
    <begin>2046-01-01T12:00:00Z</begin>
    <end>2065-12-30T12:00:00Z</end>
  </TimeSpan>
  <AcceptList>
    <GridAsPoint>
      <accept displayName="xml">xml</accept>
      <accept displayName="xml (file)">xml_file</accept>
      <accept displayName="csv">csv</accept>
      <accept displayName="csv (file)">csv_file</accept>
      <accept displayName="geocsv">geocsv</accept>
      <accept displayName="geocsv (file)">geocsv_file</accept>
      <accept displayName="netcdf">netcdf</accept>
      <accept displayName="netcdf4">netcdf4</accept>
    </GridAsPoint>
    <Grid>
      <accept displayName="netcdf">netcdf</accept>
      <accept displayName="netcdf4">netcdf4</accept>
    </Grid>
  </AcceptList>
</gridDataset>

1.16.0 (2021-10-20)

Changes

1.15.2 (2021-09-22)

Changes

1.15.1 (2021-09-21)

Changes

  • Finch: Increase maxrequestsize from 100mb to 400mb to enable ERA5 data subset. Should be possible to bring this back down with smarter averaging processes.

1.15.0 (2021-09-20)

Changes

  • Backward-incompatible change: do not, by default, volume-mount the Jupyter env README file since that file has been deleted in this repo. That file is fairly specific to Ouranos while we want this repo to be generic. PR https://github.com/Ouranosinc/PAVICS-landing/pull/31 restored that file in PAVICS-landing repo that is Ouranos specific.

    • Previous default added as a comment in env.local for existing deployment to restore the previous behavior. Although the README file has been deleted in this PR, it has already been previously deployed so existing system can restore the previous behavior of having the existing README file. This file will simply be not updated anymore.

  • Delete the deployment of that README file as well since that README file is deleted. PR https://github.com/bird-house/birdhouse-deploy-ouranos/pull/15 restore the deployment for Ouranos.

  • Each Org will be responsible for the deployment of their own README file. PR https://github.com/bird-house/birdhouse-deploy-ouranos/pull/15 can be used as a working example from Ouranos.

  • Add sample code for simple and naive notebook sharing between Jupyter users.

Notebook sharing details

Shared notebooks will be visible to all users logged in, even the public demo user so do not share any notebooks containing sensitive private info.

Can not share to a specific user.

Anyone will see the login id of everyone else so if the login id needs to be kept private, change this sample code.

Inside Jupyter, user will have the following additional folders:

.
├── mypublic/  # writable by current user
│   ├── current-user-public-share-file.ipynb
│   ├── (...)
├── public/  # read-only for everyone
│   ├── loginid-1-public/
│   │   └── loginid-1-shared-file.ipynb
│   │   └── (...)
│   ├── loginid-2-public/
│   │   └── loginid-2-shared-file.ipynb
│   │   └── (...)
│   ├── (...)-public/
│   │   └── (...)

User can drop their files to be shared under folder mypublic and see other users share under public/{other-loginid}-public.

Matching PR https://github.com/Ouranosinc/PAVICS-landing/pull/31 updating README inside the Jupyter env to explain this new sharing mechanism.

Deployed to https://medus.ouranos.ca/jupyter/ for acceptance testing.

1.14.4 (2021-09-10)

Changes

  • Jupyter: update for new RavenPy and other new packages

    Bokeh png export now also works.

    Other noticeable changes:

    <   - ravenpy=0.7.0=pyh1bb2064_0
>   - ravenpy=0.7.4=pyh7f9bfb9_0

<   - xclim=0.28.0=pyhd8ed1ab_0
>   - xclim=0.28.1=pyhd8ed1ab_0

>   - geckodriver=0.29.1=h3146498_0
>   - selenium=3.141.0=py37h5e8e339_1002
>   - nested_dict=1.61=pyhd3deb0d_0
>   - paramiko=2.7.2=pyh9f0ad1d_0
>   - scp=0.14.0=pyhd8ed1ab_0
>   - s3fs=2021.8.1=pyhd8ed1ab_0

# Downgrade !
<   - pandas=1.3.1=py37h219a48f_0
>   - pandas=1.2.5=py37h219a48f_0

<   - owslib=0.24.1=pyhd8ed1ab_0
>   - owslib=0.25.0=pyhd8ed1ab_0

<   - cf_xarray=0.6.0=pyh6c4a22f_0
>   - cf_xarray=0.6.1=pyh6c4a22f_0

<   - rioxarray=0.5.0=pyhd8ed1ab_0
>   - rioxarray=0.7.0=pyhd8ed1ab_0

<   - climpred=2.1.4=pyhd8ed1ab_0
>   - climpred=2.1.5.post1=pyhd8ed1ab_0

<   - dask=2021.7.1=pyhd8ed1ab_0
>   - dask=2021.9.0=pyhd8ed1ab_0

    See PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/89 for more info.

1.14.3 (2021-09-08)

Changes

1.14.2 (2021-09-01)

Changes

1.14.1 (2021-08-31)

  • monitoring: make some prometheus alert threshold configurable via env.local

    Default values are previous hardcoded values so this is fully backward compatible.

    Different organizations with different policies and hardware can now adapt the alert threshold to their specific needs, decreasing false positive alerts.

    Too much false positive alerts will decrease the importance and usefulness of each alert. Alerts should not feel like spams.

    Not all alert thresholds are changed to make configurable. Only thresholds that are most likely to need customization or that logically should be configurable are made configurable.

    Fixes https://github.com/bird-house/birdhouse-deploy/issues/66.

1.14.0 (2021-08-02)

Changes

  • Add request caching settings in TWitcher INI configuration to work with Magpie to help reduce permission and access control computation time.

  • Add magpie logger under Twitcher INI configuration to provide relevant logging details provided by MagpieAdapter it employs for service and resource access resolution.

  • Change logging level of sqlalchemy.engine under Magpie INI configuration to WARN in order to avoid by default over verbose database queries.

  • Update Magpie version to 3.14.0 with corresponding Twitcher using MagpieAdapter to obtain fixes about request caching and logging improvements during Twitcher security check failure following raised exception.

    Please note that because the previous default version was 3.12.0, a security fix introduced in 3.13.0 is included. (see details here: 3.13.0 (2021-06-29))

    This security fix explicitly disallows duplicate emails for different user accounts, which might require manual database updates if such users exist on your server instance. To look for possible duplicates, the following command can be used. Duplicate entries must be updated or removed such that only unique emails are present.

    echo "select email,user_name from users" | \
docker exec -i postgres-magpie psql -U $POSTGRES_MAGPIE_USERNAME magpiedb | \
sort > /tmp/magpie_users.txt

Fixes

  • Adjust incorrect magpie.url value in Magpie INI configuration.

1.13.14 (2021-07-29)

  • jupyter: update for JupyterLab v3, fix memory monitor display and RavenPy-0.7.0

    See PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/85 for more info.

    Relevant changes:

    <   - jupyterlab=2.2.9=pyhd8ed1ab_0
>   - jupyterlab=3.1.0=pyhd8ed1ab_0

<   - jupyterlab_server=1.2.0=py_0
>   - jupyterlab_server=2.6.1=pyhd8ed1ab_0

<   - jupyter-archive=2.2.0=pyhd8ed1ab_0
>   - jupyter-archive=3.0.1=pyhd8ed1ab_0

<   - jupyter_bokeh=2.0.4=pyhd8ed1ab_0
>   - jupyter_bokeh=3.0.2=pyhd8ed1ab_0

<   - jupyterlab-git=0.24.0=pyhd8ed1ab_0
>   - jupyterlab-git=0.31.0=pyhd8ed1ab_0

<   - nbdime=2.1.0=py_0
>   - nbdime=3.1.0=pyhd8ed1ab_0

# Pip to Conda package
<     - nbresuse==0.4.0
>   - nbresuse=0.4.0=pyhd8ed1ab_0

>   - nbclassic=0.3.1=pyhd8ed1ab_1

>   - jupyterlab-system-monitor=0.8.0=pyhd8ed1ab_1
>   - jupyter-resource-usage=0.5.1=pyhd8ed1ab_0
>   - jupyterlab-topbar=0.6.1=pyhd8ed1ab_2
>     - jupyterlab-logout=0.5.0

<   - jupyter_conda=5.1.1=hd8ed1ab_0

<   - ravenpy=0.6.0=pyh1bb2064_2
>   - ravenpy=0.7.0=pyh1bb2064_0

<   - pandas=1.2.5=py37h219a48f_0
>   - pandas=1.3.1=py37h219a48f_0

<   - xarray=0.18.2=pyhd8ed1ab_0
>   - xarray=0.19.0=pyhd8ed1ab_1

<   - dask=2021.7.0=pyhd8ed1ab_0
>   - dask=2021.7.1=pyhd8ed1ab_0

<   - regionmask=0.6.2=pyhd8ed1ab_0
>   - regionmask=0.7.0=pyhd8ed1ab_0

1.13.13 (2021-07-26)

Changes

  • jupyter: update for RavenPy-0.6.0, Xclim-0.28.0 and latest of everything else

    See PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/84 for more info.

    Relevant changes:

    <   - ravenpy=0.5.2=pyh7f9bfb9_0
>   - ravenpy=0.6.0=pyh1bb2064_2

<   - xclim=0.27.0=pyhd8ed1ab_0
>   - xclim=0.28.0=pyhd8ed1ab_0

# birdy rebuild
<   - birdy=v0.8.0=pyh6c4a22f_0
>   - birdy=v0.8.0=pyh6c4a22f_1

<   - cf_xarray=0.5.2=pyh6c4a22f_0
>   - cf_xarray=0.6.0=pyh6c4a22f_0

<   - cftime=1.4.1=py37h902c9e0_0
>   - cftime=1.5.0=py37h6f94858_0

<   - dask=2021.6.0=pyhd8ed1ab_0
>   - dask=2021.7.0=pyhd8ed1ab_0

<   - nc-time-axis=1.2.0=py_1
>   - nc-time-axis=1.3.1=pyhd8ed1ab_2

<   - rioxarray=0.4.1.post0=pyhd8ed1ab_0
>   - rioxarray=0.5.0=pyhd8ed1ab_0

<   - numpy=1.20.3=py37h038b26d_1
>   - numpy=1.21.1=py37h038b26d_0

<   - pandas=1.2.4=py37h219a48f_0
>   - pandas=1.2.5=py37h219a48f_0

<   - plotly=4.14.3=pyh44b312d_0
>   - plotly=5.1.0=pyhd8ed1ab_1

<     - nbconvert==5.6.1
>   - nbconvert=6.1.0=py37h89c1867_0

1.13.12 (2021-07-13)

Changes

  • Add csv files to Thredds filter

1.13.11 (2021-07-06)

Changes

1.13.10 (2021-06-30)

Changes

  • Add bump2version configuration to allow self-update of files that refer to new version releases and apply update of features listed in this changelog.

  • Add this CHANGES.md file with all previous version details extracted for PR merge commit messages.

  • Add listing of change history to generated documentation on bird-house/birdhouse-deploy ReadTheDocs.

  • Update CONTRIBUTING.rst file to include note about updating this changelog for future PR.

Fixes

1.13.9 (2021-06-18)

  • jupyter: update for raven notebooks

    To deploy the new Jupyter env to PAVICS.

    Given it’s an incremental build, these are the only differences:

    >   - intake-geopandas=0.2.4=pyhd8ed1ab_0
>   - intake-thredds=2021.6.16=pyhd8ed1ab_0
>   - intake-xarray=0.5.0=pyhd8ed1ab_0

    See PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/76.

1.13.8 (2021-06-15)

  • jupyter: new version for updated ravenpy, birdy and xclim

    PR to deploy the new Jupyter env to PAVICS.

    See PR Ouranosinc/PAVICS-e2e-workflow-tests#75 for more details.

    <   - ravenpy=0.4.2=py37_1
>   - ravenpy=0.5.2=pyh7f9bfb9_0

# Renamed.
<   - raven=3.0.4.318=hc9bffa2_2
>   - raven-hydro=3.0.4.322=h516393e_0

<   - ostrich=21.03.16=h2bc3f7f_0
>   - ostrich=21.03.16=h4bd325d_1

<   - xclim=0.25.0=pyhd8ed1ab_0
>   - xclim=0.27.0=pyhd8ed1ab_0

# Old version was from pip.
<     - birdhouse-birdy==0.7.0
>   - birdy=v0.8.0=pyh6c4a22f_0

# Was previously included in another package, now it is standalone.
>   - pydantic=1.8.2=py37h5e8e339_0

# New libs for upcoming Raven notebooks
>   - gcsfs=2021.6.0=pyhd8ed1ab_0
>   - intake=0.6.2=pyhd8ed1ab_0
>   - intake-esm=2021.1.15=pyhd8ed1ab_0
>   - zarr=2.8.3=pyhd8ed1ab_0

<   - xarray=0.17.0=pyhd8ed1ab_0
>   - xarray=0.18.2=pyhd8ed1ab_0

<   - owslib=0.23.0=pyhd8ed1ab_0
>   - owslib=0.24.1=pyhd8ed1ab_0

<   - cf_xarray=0.5.1=pyh44b312d_0
>   - cf_xarray=0.5.2=pyh6c4a22f_0

<   - clisops=0.6.3=pyh44b312d_0
>   - clisops=0.6.5=pyh6c4a22f_0

<   - dask=2021.2.0=pyhd8ed1ab_0
>   - dask=2021.6.0=pyhd8ed1ab_0

# Downgrade !
<   - gdal=3.2.1=py37hc5bc4e4_7
>   - gdal=3.1.4=py37h2ec2946_8

# Downgrade !
<   - rasterio=1.2.2=py37hd5c4cce_0
>   - rasterio=1.2.1=py37ha549118_0

<   - hvplot=0.7.1=pyh44b312d_0
>   - hvplot=0.7.2=pyh6c4a22f_0

<   - rioxarray=0.3.1=pyhd8ed1ab_0
>   - rioxarray=0.4.1.post0=pyhd8ed1ab_0

# Downgrade !
<   - xskillscore=0.0.19=pyhd8ed1ab_0
>   - xskillscore=0.0.18=py_1

    Full diff of conda env export: 210415-210527.1-update210615-conda-env-export.diff.txt

    Full new conda env export: 210527.1-update210615-conda-env-export.yml.txt

1.13.7 (2021-06-10)

  • jupyterhub: allow config override via env.local

    This is basically the same as ENABLE_JUPYTERHUB_MULTI_NOTEBOOKS but at the bottom of the file so it can override everything.

    ENABLE_JUPYTERHUB_MULTI_NOTEBOOKS is kept for backward-compat.

    First useful application is to enable server culling for auto shutdown of idle kernels and idle jupyter single server, hopefully fixes #67.

    The culling settings will only take effect the next time user restart their personal Jupyter server because it seems that the Jupyter server is the one culling itself. JupyterHub do not perform the culling, it simply forwards the culling settings to the Jupyter server.

    $ docker inspect jupyter-lvu --format '{{ .Args }}'
[run -n birdy /usr/local/bin/start-notebook.sh --ip=0.0.0.0 --port=8888 --notebook-dir=/notebook_dir --SingleUserNotebookApp.default_url=/lab --debug --disable-user-config --NotebookApp.terminals_enabled=False --NotebookApp.shutdown_no_activity_timeout=180 --MappingKernelManager.cull_idle_timeout=180 --MappingKernelManager.cull_connected=True]

    Non-breaking changes

    • jupyterhub: allow config override via env.local

    Deployed to https://lvupavicsdev.ouranos.ca/jupyter (timeout set to 5 mins)

1.13.6 (2021-06-02)

  • Bugfix for autodeploy job

    The new code added with this merge created a new bug for the autodeploy job.

    From the autodeploy job’s log :

    triggerdeploy START_TIME=2021-05-13T14:00:03+0000
Error: DEPLOY_DATA_JOB_SCHEDULE not set

    If the AUTODEPLOY_NOTEBOOK_FREQUENCY variable is not set in the env.local file, it would create the error above. The variable is set in the default.env file, in case it is not defined in the env.local, and is then used for the new env file from pavics-jupyter-base here. The error happens because the default.env was not called in the triggerdeploy.sh script, and the variable was not set when running the env.local.

    Solution was tested in a test environment and the cronjob seems to be fixed now.

    Tests were executed to see if the same situation could be found anywhere else. From what was observed, default.env seems to be called consistently before the env.local. Only here, default.env doesn’t seem to be called. A default.env call has also been added in that file.

1.13.5 (2021-05-19)

  • magpie 3.x + gunicorn bind

1.13.4 (2021-05-18)

  • Update to raven 0.13.0

1.13.3 (2021-05-11)

    • Add new docker-compose optional components

      • optional-components/database-external-ports

      • optional-components/wps-healthchecks

    Following is the output result when using optional-components/wps-healthcheck .. code-block:

    ubuntu@daccs-instance-26730-daccsci:~$ pavics-compose ps
reading './components/monitoring/default.env'
reading './optional-components/testthredds/default.env'
COMPOSE_CONF_LIST=-f docker-compose.yml -f ./components/monitoring/docker-compose-extra.yml -f ./optional-components/canarie-api-full-monitoring/docker-compose-extra.yml -f ./optional-components/all-public-access/docker-compose-extra.yml -f ./optional-components/testthredds/docker-compose-extra.yml -f ./optional-components/secure-thredds/docker-compose-extra.yml -f ./optional-components/wps-healthchecks/docker-compose-extra.yml -f ./optional-components/database-external-ports/docker-compose-extra.yml
     Name                    Command                  State                                                                                Ports
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
alertmanager      /bin/alertmanager --config ...   Up             0.0.0.0:9093->9093/tcp
cadvisor          /usr/bin/cadvisor -logtostderr   Up (healthy)   0.0.0.0:9999->8080/tcp
catalog           /bin/sh -c python /home/do ...   Up (healthy)   0.0.0.0:8086->80/tcp
finch             gunicorn --bind=0.0.0.0:50 ...   Up (healthy)   0.0.0.0:8095->5000/tcp
flyingpigeon      /bin/bash -c source activa ...   Up (healthy)   0.0.0.0:8093->8093/tcp
frontend          /bin/sh -c /bin/bash ./bin ...   Up             0.0.0.0:3000->3000/tcp
geoserver         /entrypointwrapper               Up             0.0.0.0:8087->8080/tcp
grafana           /run.sh                          Up             0.0.0.0:3001->3000/tcp
hummingbird       /usr/bin/tini -- make upda ...   Up (healthy)   0.0.0.0:28097->28097/tcp, 0.0.0.0:38097->38097/tcp, 8000/tcp, 8080/tcp, 0.0.0.0:8097->8097/tcp, 8443/tcp, 0.0.0.0:48097->9001/tcp
jupyterhub        jupyterhub                       Up             0.0.0.0:8800->8000/tcp
magpie            /bin/sh -c crond -c $CRON_ ...   Up             0.0.0.0:2001->2001/tcp
malleefowl        /usr/bin/tini -- make upda ...   Up (healthy)   0.0.0.0:28091->28091/tcp, 0.0.0.0:38091->38091/tcp, 8000/tcp, 8080/tcp, 0.0.0.0:8091->8091/tcp, 8443/tcp, 0.0.0.0:48091->9001/tcp
mongodb           /entrypoint.sh bash -c cho ...   Up             0.0.0.0:27017->27017/tcp
ncwms2            /usr/bin/tini -- make upda ...   Up             0.0.0.0:8080->8080/tcp, 0.0.0.0:48080->9001/tcp
node-exporter     /bin/node_exporter --path. ...   Up
phoenix           /usr/bin/tini -- make upda ...   Up             0.0.0.0:38443->38443/tcp, 8000/tcp, 8080/tcp, 0.0.0.0:8081->8081/tcp, 0.0.0.0:8443->8443/tcp, 0.0.0.0:9001->9001/tcp
portainer         /portainer                       Up             0.0.0.0:9000->9000/tcp
postgis           /bin/sh -c /start-postgis.sh     Up             5432/tcp
postgres          docker-entrypoint.sh postgres    Up             0.0.0.0:5432->5432/tcp
postgres-magpie   docker-entrypoint.sh postgres    Up             0.0.0.0:5433->5432/tcp
project-api       /bin/sh -c npm run bootstr ...   Up             0.0.0.0:3005->3005/tcp
prometheus        /bin/prometheus --config.f ...   Up             0.0.0.0:9090->9090/tcp
proxy             /entrypoint                      Up             0.0.0.0:443->443/tcp, 0.0.0.0:80->80/tcp, 0.0.0.0:58079->8079/tcp, 0.0.0.0:58086->8086/tcp, 0.0.0.0:58091->8091/tcp, 0.0.0.0:58093->8093/tcp,
                                                                  0.0.0.0:58094->8094/tcp
raven             /bin/bash -c source activa ...   Up (healthy)   0.0.0.0:8096->9099/tcp
solr              /usr/bin/tini -- /bin/sh - ...   Up             0.0.0.0:8983->8983/tcp, 0.0.0.0:48983->9001/tcp
testthredds       /entrypointwrapper               Up (healthy)   0.0.0.0:8084->8080/tcp, 8443/tcp
thredds           /entrypointwrapper               Up (healthy)   0.0.0.0:8083->8080/tcp, 8443/tcp
twitcher          pserve /opt/birdhouse/src/ ...   Up             0.0.0.0:8000->8000/tcp, 8080/tcp, 8443/tcp, 9001/tcp

1.13.2 (2021-05-11)

  • Custom notebooks

1.13.1 (2021-05-10)

1.13.0 (2021-05-06)

  • bump default log retention to 500m instead of 2m, more suitable for prod

    Bump default log retention to 500m instead of 2m, more suitable for prod

    Forgot to push during PR #152.

    Non-breaking changes

    • Bump default log retention to 500m instead of 2m, more suitable for prod

1.12.4 (2021-05-06)

1.12.3 (2021-05-04)

  • Change overview:

    • allow customization of /data persistence root on disk, retaining current default for existing deployment

    • add data persistence for mongodb container

1.12.2 (2021-04-28)

  • Add contributions guideline and policy

1.12.1 (2021-04-28)

  • proxy: allow homepage (location /) to be configurable

1.12.0 (2021-04-19)

  • Magpie upgrade strike II

    Strike II of this original PR https://github.com/bird-house/birdhouse-deploy/pull/107.

    Matching notebook fix https://github.com/Ouranosinc/pavics-sdi/pull/218

    Performed test upgrade on staging (Medus) using prod (Boreas) Magpie DB, everything went well and Jenkins passed (http://jenkins.ouranos.ca/job/ouranos-staging/job/medus.ouranos.ca/80/parameters/). This Jenkins build uses the corresponding branch in https://github.com/Ouranosinc/pavics-sdi/pull/218 and with TEST_MAGPIE_AUTH enabled.

    Manual upgrade migration procedure:

    1. Save /data/magpie_persist folder from prod pavics.ouranos.ca: cd /data; tar czf magpie_persist.prod.tgz magpie_persist

    2. scp magpie_persist.prod.tgz to medus

    3. login to medus

    4. cd /path/to/birdhouse-deploy/birdhouse

    5. ./pavics-compose.sh down

    6. git checkout master

    7. cd /data

    8. rm -rf magpie_persist

    9. tar xzf magpie_persist.prod.tgz # restore Magpie DB with prod version

    10. cd /path/to/birdhouse-deploy/birdhouse

    11. ./pavics-compose.sh up -d

    12. Update env.local MAGPIE_ADMIN_PASSWORD with prod passwd for Twitcher to be able to access Magpie since we juste restore the Magpie DB from prod

    13. ./pavics-compose.sh restart twitcher # for Twitcher to get new Magpie admin passwd

    14. Baseline working state: trigger Jenkins test suite, ensure all pass except pavics_thredds.ipynb that requires new Magpie

    15. Baseline working state: view existing services permissions on group Anonymous (https://medus.ouranos.ca/magpie/ui/groups/anonymous/default)

    16. git checkout restore-previous-broken-magpie-upgrade-so-we-can-work-on-a-fix # This current branch

    17. ./pavics-compose.sh up -d # upgrade to new Magpie

    18. docker logs magpie: check no DB migration error

    19. Trigger Jenkins test suite again

1.11.29 (2021-04-16)

  • Update Raven and Jupyter env for Raven demo

    Raven release notes in PR Ouranosinc/raven#374 and Ouranosinc/raven#382

    Jupyter env update in PR Ouranosinc/PAVICS-e2e-workflow-tests#71

    Other fixes:

    • Fix intermittent Jupyter spawning error by doubling various timeouts config (it’s intermittent so hard to test so we are not sure which ones of timeout fixed it)

    • Fix Finch and Raven “Broken pipe” error when the request size is larger than default 3mb (bumped to 100mb) (fixes Ouranosinc/raven#361 and Finch related comment)

    • Lower chance to have “Max connection” error for Finch and Raven (bump parallelprocesses from 2 to 10). In prod, the server has the CPU needed to run 10 concurrent requests if needed so this prevent users having to “wait” after each other.

1.11.28 (2021-04-09)

  • jupyter: update for new clisops, xclim, ravenpy

    Matching PR to deploy the new Jupyter env to PAVICS.

    See PR Ouranosinc/PAVICS-e2e-workflow-tests#68 for more info.

    Relevant changes:

    <   - clisops=0.5.1=pyhd3deb0d_0
>   - clisops=0.6.3=pyh44b312d_0

<   - xclim=0.23.0=pyhd8ed1ab_0
>   - xclim=0.25.0=pyhd8ed1ab_0

>   - ostrich=0.1.2=h2bc3f7f_0
>   - raven=0.1.1=h2bc3f7f_0

<     - ravenpy==0.2.3  # from pip
>   - ravenpy=0.3.1=py37_0  # from conda

>   - aiohttp=3.7.4=py37h5e8e339_0

<   - roocs-utils=0.1.5=pyhd3deb0d_1
>   - roocs-utils=0.3.0=pyh6c4a22f_0

<   - cf_xarray=0.4.0=pyh44b312d_0
>   - cf_xarray=0.5.1=pyh44b312d_0

<   - rioxarray=0.2.0=pyhd8ed1ab_0
>   - rioxarray=0.3.1=pyhd8ed1ab_0

<   - xarray=0.16.2=pyhd8ed1ab_0
>   - xarray=0.17.0=pyhd8ed1ab_0

<   - geopandas=0.8.2=pyhd8ed1ab_0
>   - geopandas=0.9.0=pyhd8ed1ab_0

<   - gdal=3.1.4=py37h2ec2946_5
>   - gdal=3.2.1=py37hc5bc4e4_7

<   - jupyter_conda=4.1.0=hd8ed1ab_1
>   - jupyter_conda=5.0.0=hd8ed1ab_0

<   - python=3.7.9=hffdb5ce_100_cpython
>   - python=3.7.10=hffdb5ce_100_cpython

1.11.27 (2021-04-01)

1.11.26 (2021-03-31)

  • Update canarieAPI doc links

    • Updated components’ version number.

    • Replaced links to githubio docs to readthedocs.

    • renderer is provided by THREDDS-WMS.

    • slicer is provided by finch.

1.11.25 (2021-03-26)

  • finch: update to version 0.7.1

    See Finch release PR https://github.com/bird-house/finch/pull/164 for more release info.

    This update will fix the following Jenkins error introduced by https://github.com/bird-house/finch/pull/161#discussion_r601975311:

    12:37:00  _________ finch-master/docs/source/notebooks/finch-usage.ipynb::Cell 1 _________
12:37:00  Notebook cell execution failed
12:37:00  Cell 1: Cell outputs differ
12:37:00
12:37:00  Input:
12:37:00  help(wps.frost_days)
12:37:00
12:37:00  Traceback:
12:37:00   mismatch 'stdout'
12:37:00
12:37:00   assert reference_output == test_output failed:
12:37:00
12:37:00    'Help on meth...ut files.\n\n' == 'Help on meth...ut files.\n\n'
12:37:00    Skipping 70 identical leading characters in diff, use -v to show
12:37:00    - min=None, missing_options=None, check_missing='any', thresh='0 degC', freq='YS', variable=None, output_formats=None) method of birdy.client.base.WPSClient instance
12:37:00    + min=None, check_missing='any', cf_compliance='warn', data_validation='raise', thresh='0 degC', freq='YS', missing_options=None, variable=None, output_formats=None) method of birdy.client.base.WPSClient instance
12:37:00          Number of days where daily minimum temperatures are below 0.
12:37:00
12:37:00          Parameters
12:37:00          ----------
12:37:00          tasmin : ComplexData:mimetype:`application/x-netcdf`, :mimetype:`application/x-ogc-dods`
12:37:00              NetCDF Files or archive (tar/zip) containing netCDF files.
12:37:00          thresh : string
12:37:00              Freezing temperature.
12:37:00          freq : {'YS', 'MS', 'QS-DEC', 'AS-JUL'}string
12:37:00              Resampling frequency.
12:37:00          check_missing : {'any', 'wmo', 'pct', 'at_least_n', 'skip', 'from_context'}string
12:37:00              Method used to determine which aggregations should be considered missing.
12:37:00          missing_options : ComplexData:mimetype:`application/json`
12:37:00              JSON representation of dictionary of missing method parameters.
12:37:00    +     cf_compliance : {'log', 'warn', 'raise'}string
12:37:00    +         Whether to log, warn or raise when inputs have non-CF-compliant attributes.
12:37:00    +     data_validation : {'log', 'warn', 'raise'}string
12:37:00    +         Whether to log, warn or raise when inputs fail data validation checks.
12:37:00          variable : string
12:37:00              Name of the variable in the NetCDF file.
12:37:00
12:37:00          Returns
12:37:00          -------
12:37:00          output_netcdf : ComplexData:mimetype:`application/x-netcdf`
12:37:00              The indicator values computed on the original input grid.
12:37:00          output_log : ComplexData:mimetype:`text/plain`
12:37:00              Collected logs during process run.
12:37:00          ref : ComplexData:mimetype:`application/metalink+xml; version=4.0`
12:37:00              Metalink file storing all references to output files.

    Jenkins build with Finch notebooks passing against newer Finch: http://jenkins.ouranos.ca/job/ouranos-staging/job/lvupavics.ouranos.ca/45/console

1.11.24 (2021-03-19)

  • Avoid docker pull since pull rate limit on dockerhub

    Pin bash tag so it is reproducible (previously it was more or less reproducible since we always ensure “latest” tag).

    Avoid the following error:

    + docker pull bash
Using default tag: latest
Error response from daemon: toomanyrequests: You have reached your pull rate limit. You may increase the limit by authenticating and upgrading: https://www.docker.com/increase-rate-limit

1.11.23 (2021-03-17)

  • Custom Jupyter user images

    Adds CRIM’s nlp and eo images to the available list of images in JupyterHub

    The base image (pavics-jupyter-base) wasn’t added to the list, because it is assumed the users will always be using the other more specialized images.

    We were already able to add/override Jupyter images but this PR makes it more integrated: those image will also be pulled in advanced so startup is much faster for big images since these images will already be cached.

    Backward incompatible changes: DOCKER_NOTEBOOK_IMAGE renamed to DOCKER_NOTEBOOK_IMAGES and is now a space separated list of images. Any existing override in env.local using the old name will have to switch to the new name.

1.11.22 (2021-03-16)

1.11.21 (2021-02-19)

  • Configurable Jupyterhub README

    While the README.ipynb provided by birdhouse-deploy is good, it does not quite fit our needs at PCIC. This PR allows users to configure their own README for Jupyterhub.

    • Adds JUPYERHUB_README as configuration option in the appropriate spots

1.11.20 (2021-02-19)

1.11.19 (2021-02-10)

  • proxy: proxy_read_timeout config should be configurable

    We have a performance problem with the production deployment at Ouranos so we need a longer timeout. Being an Ouranos specific need, it should not be hardcoded as in previous PR https://github.com/bird-house/birdhouse-deploy/pull/122.

    The previous increase was sometime not enough !

    The value is now configurable via env.local as most other customizations. Documentation updated.

    Timeout in Prod:

    WPS_URL=https://pavics.ouranos.ca/twitcher/ows/proxy/raven/wps FINCH_WPS_URL=https://pavics.ouranos.ca/twitcher/ows/proxy/finch/wps FLYINGPIGEON_WPS
_URL=https://pavics.ouranos.ca/twitcher/ows/proxy/flyingpigeon/wps pytest --nbval-lax --verbose docs/source/notebooks/Running_HMETS_with_CANOPEX_datas
et.ipynb --sanitize-with docs/source/output-sanitize.cfg --ignore docs/source/notebooks/.ipynb_checkpoints

HTTPError: 504 Server Error: Gateway Time-out for url: https://pavics.ouranos.ca/twitcher/ows/proxy/raven/wps

===================================================== 11 failed, 4 passed, 1 warning in 249.80s (0:04:09) ===========================================

    Pass easily on my test VM with very modest hardware (10G ram, 2 cpu):

    WPS_URL=https://lvupavicsmaster.ouranos.ca/twitcher/ows/proxy/raven/wps FINCH_WPS_URL=https://lvupavicsmaster.ouranos.ca/twitcher/ows/proxy/finch/wp
s FLYINGPIGEON_WPS_URL=https://lvupavicsmaster.ouranos.ca/twitcher/ows/proxy/flyingpigeon/wps pytest --nbval-lax --verbose docs/source/notebooks/Runni
ng_HMETS_with_CANOPEX_dataset.ipynb --sanitize-with docs/source/output-sanitize.cfg --ignore docs/source/notebooks/.ipynb_checkpoints

=========================================================== 15 passed, 1 warning in 33.84s ===========================================================

    Pass against Medus:

    WPS_URL=https://medus.ouranos.ca/twitcher/ows/proxy/raven/wps FINCH_WPS_URL=https://medus.ouranos.ca/twitcher/ows/proxy/finch/wps FLYINGPIGEON_WPS_URL=https://medus.ouranos.ca/twitcher/ows/proxy/flyingpigeon/wps pytest --nbval-lax --verbose docs/source/notebooks/Running_HMETS_with_CANOPEX_dataset.ipynb --sanitize-with docs/source/output-sanitize.cfg --ignore docs/source/notebooks/.ipynb_checkpoints

============================================== 15 passed, 1 warning in 42.44s =======================================================

    Pass against hirondelle.crim.ca:

    WPS_URL=https://hirondelle.crim.ca/twitcher/ows/proxy/raven/wps FINCH_WPS_URL=https://hirondelle.crim.ca/twitcher/ows/proxy/finch/wps FLYINGPIGEON_WPS_URL=https://hirondelle.crim.ca/twitcher/ows/proxy/flyingpigeon/wps pytest --nbval-lax --verbose docs/source/notebooks/Running_HMETS_with_CANOPEX_dataset.ipynb --sanitize-with docs/source/output-sanitize.cfg --ignore docs/source/notebooks/.ipynb_checkpoints

=============================================== 15 passed, 1 warning in 35.61s ===============================================

    For comparison, a run on Prod without Twitcher (PR https://github.com/bird-house/birdhouse-deploy-ouranos/pull/5):

    WPS_URL=https://pavics.ouranos.ca/raven/wps FINCH_WPS_URL=https://pavics.ouranos.ca/twitcher/ows/proxy/finch/wps FLYINGPIGEON_WPS_URL=https://pavics
.ouranos.ca/twitcher/ows/proxy/flyingpigeon/wps pytest --nbval-lax --verbose docs/source/notebooks/Running_HMETS_with_CANOPEX_dataset.ipynb --sanitize
-with docs/source/output-sanitize.cfg --ignore docs/source/notebooks/.ipynb_checkpoints

HTTPError: 504 Server Error: Gateway Time-out for url: https://pavics.ouranos.ca/raven/wps

================================================ 11 failed, 4 passed, 1 warning in 248.99s (0:04:08) =================================================

    A run on Prod without Twitcher and Nginx (direct hit Raven):

    WPS_URL=http://pavics.ouranos.ca:8096/ FINCH_WPS_URL=https://pavics.ouranos.ca/twitcher/ows/proxy/finch/wps FLYINGPIGEON_WPS_URL=https://pavics.oura
nos.ca/twitcher/ows/proxy/flyingpigeon/wps pytest --nbval-lax --verbose docs/source/notebooks/Running_HMETS_with_CANOPEX_dataset.ipynb --sanitize-with
 docs/source/output-sanitize.cfg --ignore docs/source/notebooks/.ipynb_checkpoints

===================================================== 15 passed, 1 warning in 218.46s (0:03:38) ======================================================

1.11.18 (2021-02-02)

  • update Raven and Jupyter env

    See https://github.com/Ouranosinc/raven/compare/v0.10.0…v0.11.1 for change details.

    Jupyter env change details: https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/60

    Jenkins run (this Jupyter env pavics/workflow-tests:210201.2 against a devel version of Raven 0.11.1 + --nbval-lax) http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/test-nbval-lax-DO_NOT_MERGE/4/console

    Only known error:

    20:25:45  =========================== short test summary info ============================
20:25:45  FAILED pavics-sdi-master/docs/source/notebooks/WMS_example.ipynb::Cell 1
20:25:45  FAILED pavics-sdi-master/docs/source/notebooks/WMS_example.ipynb::Cell 2
20:25:45  FAILED pavics-sdi-master/docs/source/notebooks/WMS_example.ipynb::Cell 3
20:25:45  FAILED pavics-sdi-master/docs/source/notebooks/WMS_example.ipynb::Cell 4
20:25:45  FAILED pavics-sdi-master/docs/source/notebooks/WMS_example.ipynb::Cell 5
20:25:45  FAILED pavics-sdi-master/docs/source/notebooks/WMS_example.ipynb::Cell 6
20:25:45  FAILED pavics-sdi-master/docs/source/notebooks/WMS_example.ipynb::Cell 7
20:25:45  FAILED raven-master/docs/source/notebooks/Bias_correcting_climate_data.ipynb::Cell 8
20:25:45  FAILED raven-master/docs/source/notebooks/Bias_correcting_climate_data.ipynb::Cell 9
20:25:45  FAILED raven-master/docs/source/notebooks/Bias_correcting_climate_data.ipynb::Cell 10
20:25:45  FAILED raven-master/docs/source/notebooks/Bias_correcting_climate_data.ipynb::Cell 11
20:25:45  FAILED raven-master/docs/source/notebooks/Full_process_example_1.ipynb::Cell 13
20:25:45  FAILED raven-master/docs/source/notebooks/Full_process_example_1.ipynb::Cell 17
20:25:45  FAILED raven-master/docs/source/notebooks/Full_process_example_1.ipynb::Cell 18
20:25:45  FAILED raven-master/docs/source/notebooks/Full_process_example_1.ipynb::Cell 19
20:25:45  FAILED raven-master/docs/source/notebooks/Full_process_example_1.ipynb::Cell 20
20:25:45  FAILED raven-master/docs/source/notebooks/Full_process_example_1.ipynb::Cell 21
20:25:45  FAILED raven-master/docs/source/notebooks/Multiple_watersheds_simulation.ipynb::Cell 1
20:25:45  FAILED raven-master/docs/source/notebooks/Multiple_watersheds_simulation.ipynb::Cell 3
20:25:45  FAILED raven-master/docs/source/notebooks/Multiple_watersheds_simulation.ipynb::Cell 4
20:25:45  FAILED raven-master/docs/source/notebooks/Multiple_watersheds_simulation.ipynb::Cell 5
20:25:45  FAILED raven-master/docs/source/notebooks/Region_selection.ipynb::Cell 7
20:25:45  FAILED raven-master/docs/source/notebooks/Region_selection.ipynb::Cell 8
20:25:45  FAILED raven-master/docs/source/notebooks/Subset_climate_data_over_watershed.ipynb::Cell 5
20:25:45  ============ 24 failed, 226 passed, 2 skipped in 2528.69s (0:42:08) ============

1.11.17 (2021-01-28)

1.11.16 (2021-01-14)

1.11.15 (2021-01-14)

  • jupyter: update to version 201214

    Matching PR to deploy the new Jupyter env in PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/56 to PAVICS.

    Relevant changes:

    >   - cfgrib=0.9.8.5=pyhd8ed1ab_0

<   - clisops=0.3.1=pyh32f6830_1
>   - clisops=0.4.0=pyhd3deb0d_0

<   - dask=2.30.0=py_0
>   - dask=2020.12.0=pyhd8ed1ab_0

<   - owslib=0.20.0=py_0
>   - owslib=0.21.0=pyhd8ed1ab_0

<   - xarray=0.16.1=py_0
>   - xarray=0.16.2=pyhd8ed1ab_0

<   - xclim=0.21.0=py_0
>   - xclim=0.22.0=pyhd8ed1ab_0

<   - jupyter_conda=3.4.1=pyh9f0ad1d_0
>   - jupyter_conda=4.1.0=hd8ed1ab_1

1.11.14 (2020-12-17)

  • Add ability to execute post actions for deploy-data script.

    Script deploy-data was previously introduced in PR #72 to deploy any files from any git repos to the local host it runs.

    Now it grows the ability to run commands from the git repo it just pulls.

    Being able to run commands open new possibilities:

    Combining this deploy-data with the scheduler component means we have a way for cronjobs to automatically always execute the most up-to-date version of any scripts from any git repos.

1.11.13 (2020-12-14)

  • jupyterhub: update to version 1.3.0 to include login terms patch

    This version of jupyterhub includes the login terms patch originally introduced in commit 8be8eeac211d3f5c2de620781db8832fdb8f9093 of PR #104.

    This official login terms feature has a few enhancements (see https://github.com/jupyterhub/jupyterhub/pull/3264#discussion_r530466178):

    • no javascript dependency

    • pop-up reminder for user to check the checkbox

    Behavior change is the “Sign in” button is not longer disabled if unchecked. It simply does not work and reminds the user to check the checkbox if unchecked.

    Before:

    recorded

    After:

    recorded

1.11.12 (2020-11-25)

1.11.11 (2020-11-20)

  • Various small fixes.

    monitoring: prevent losing stats when VM auto start from a power failure

    check-instance-ready: new script to smoke test instance (use in bootstrap-instance-for-testsuite for our automation pipeline).

    jupyter: add CATALOG_USERNAME and anonymous to blocked_users list for security See comment https://github.com/bird-house/birdhouse-deploy/pull/102#issuecomment-730109547 and comment https://github.com/bird-house/birdhouse-deploy/pull/102#issuecomment-730407914

    They are not real Jupyter users and their password is known.

See config/magpie/permissions.cfg.template that created those users.

Tested:
```
[W 2020-11-20 13:25:18.924 JupyterHub auth:487] User 'admin-catalog' blocked. Stop authentication
[W 2020-11-20 13:25:18.924 JupyterHub base:752] Failed login for admin-catalog

[W 2020-11-20 13:49:18.069 JupyterHub auth:487] User 'anonymous' blocked. Stop authentication
[W 2020-11-20 13:49:18.070 JupyterHub base:752] Failed login for anonymous
```

1.11.10 (2020-11-18)

  • Add terms conditions to JupyterHub login page and update to latest JupyterHub version.

    User have to check the checkbox agreeing to the terms and conditions in order to login (fixes Ouranosinc/pavics-sdi#188).

    User will have to accept the terms and conditions (the checkbox) each time he needs to login. However, if user do not logout or wipe his browser cookies, the next time he navigate to the login page, he’ll just log right in, no password is asked so no terms and conditions to accept either.

    This behavior is optional and only enabled if JUPYTER_LOGIN_TERMS_URL in env.local is set.

    Had to patch the login.html template from jupyterhub docker image for this feature (PR jupyterhub/jupyterhub#3264).

    Also update jupyterhub docker image to latest version.

    Deployed to my test server https://lvupavics.ouranos.ca/jupyter/hub/login (pointing to a bogus terms and conditions link for now).

    Tested on Firefox and Google Chrome.

    Tested that upgrade from jupyterhub 1.0.0 to 1.2.1 is completely transparent to already logged in jupyter users.

    [D 2020-11-18 19:53:52.517 JupyterHub app:2055] Verifying that lvu is running at http://172.18.0.3:8888/jupyter/user/lvu/
[D 2020-11-18 19:53:52.523 JupyterHub utils:220] Server at http://172.18.0.3:8888/jupyter/user/lvu/ responded with 302
[D 2020-11-18 19:53:52.523 JupyterHub _version:76] jupyterhub and jupyterhub-singleuser both on version 1.2.1
[I 2020-11-18 19:53:52.524 JupyterHub app:2069] lvu still running
    recorded

1.11.9 (2020-11-13)

1.11.8 (2020-11-06)

  • bump finch to version-0.5.3

1.11.7 (2020-11-06)

  • bump thredds-docker to 4.6.15

1.11.6 (2020-11-06)

  • Prepare fresh deployment for automated tests.

    @MatProv is building an automated pipeline that will provision and deploy a full PAVICS stack and run our Jenkins test suite for each PR here.

    So each time his new fresh instance comes up, there are a few steps to perform for the Jenkins test suite to pass. Those steps are captured in scripts/bootstrap-instance-for-testsuite. @MatProv please call this script, do not perform each steps yourself so any future changes to those steps will be transparent to your pipeline. A new optional components was also required, done in PR https://github.com/bird-house/birdhouse-deploy/pull/92.

    For security reasons, Jupyterhub will block the test user to login since its password is known publicly.

    Each step are also in their own script so can be assembled differently to prepare the fresh instance if desired.

    Solr query in the canarie monitoring also updated to target the minimal dataset from bootstrap-testdata so the canarie monitoring page works on all PAVICS deployment (fixes https://github.com/bird-house/birdhouse-deploy/issues/6). @MatProv you can use this canarie monitoring page (ex: https://pavics.ouranos.ca/canarie/node/service/status) to confirm the fresh instance is ready to run the Jenkins test suite.

1.11.5 (2020-10-27)

1.11.4 (2020-10-15)

  • Sync Raven testdata to Thredds for Raven tutorial notebooks.

    Leveraging the cron daemon of the scheduler component, sync Raven testdata to Thredds for Raven tutorial notebooks.

    Activation of the pre-configured cronjob is via env.local as usual for infra-as-code.

    New generic deploy-data script can clone any number of git repos, sync any number of folders in the git repo to any number of local folders, with ability to cherry-pick just the few files needed (Raven testdata has many types of files, we only need to sync .nc files to Thredds, to avoid polluting Thredds storage /data/datasets/testdata/raven).

    Limitation of the first version of this deploy-data script:

    • Do not handle re-organizing file layout, this is a pure sync only with very limited rsync filtering for now (tutorial notebooks deploy from multiple repos, need re-organizing the file layout)

    So the script has room to grow. I see it as a generic solution to the repeated problem “take files from various git repos and deploy them somewhere automatically”. If we need to deploy another repo, juste write a new config file, stop writing boilerplate code again.

    Minor unrelated change in this PR:

    • README update to reference the new birdhouse-deploy-ouranos.

    • Make sourcing the various pre-configured cronjob backward-compat with older version of the repo where those cronjob did not exist yet.

1.11.3 (2020-09-28)

1.11.2 (2020-09-15)

  • Auto-renew LetsEncrypt SSL certificate.

    Auto-renew LetsEncrypt SSL certificate leveraging the cron jobs of the “scheduler” component. Meaning this feature is self-contained in the PAVICS stack, no dependency on the host’s cron jobs.

    Default behavior is to attempt renewal everyday. certbot client in renew mode will not hit LetsEncrypt server if renewal is not allowed (not within 1 month of expiry) so this should not put too much stress on LetsEncrypt server. However, this gives us 30 retry opportunities (1 month) if something is wrong on the first try.

    All configs are centralized in env.local, easing reproducibility on multiple deployments of PAVICS and following infra-as-code.

    User can still perform the renewal manually by calling certbotwrapper directly. User is not forced to enable the “scheduler” component but will miss out on the automatic renewal.

    Documentation for activating this automatic renewal is in env.local.example.

    See vagrant-utils/configure-pavics.sh for how it’s being used for real in a Vagrant box.

    Logs (/var/log/PAVICS/renew_letsencrypt_ssl.log) when no renewal is necessary, proxy down time less than 1 minute: certbot-renew-no-ops.txt

    ==========
certbotwrapper START_TIME=2020-09-11T01:20:02+0000
+ realpath /vagrant/birdhouse/deployment/certbotwrapper
+ THIS_FILE=/vagrant/birdhouse/deployment/certbotwrapper
+ dirname /vagrant/birdhouse/deployment/certbotwrapper
+ THIS_DIR=/vagrant/birdhouse/deployment
+ pwd
+ SAVED_PWD=/
+ . /vagrant/birdhouse/deployment/../default.env
+ export 'DOCKER_NOTEBOOK_IMAGE=pavics/workflow-tests:200803'
+ export 'FINCH_IMAGE=birdhouse/finch:version-0.5.2'
+ export 'THREDDS_IMAGE=unidata/thredds-docker:4.6.14'
+ export 'JUPYTERHUB_USER_DATA_DIR=/data/jupyterhub_user_data'
+ export 'JUPYTER_DEMO_USER=demo'
+ export 'JUPYTER_DEMO_USER_MEM_LIMIT=2G'
+ export 'JUPYTER_DEMO_USER_CPU_LIMIT=0.5'
+ export 'JUPYTER_LOGIN_BANNER_TOP_SECTION='
+ export 'JUPYTER_LOGIN_BANNER_BOTTOM_SECTION='
+ export 'CANARIE_MONITORING_EXTRA_CONF_DIR=/conf.d'
+ export 'THREDDS_ORGANIZATION=Birdhouse'
+ export 'MAGPIE_DB_NAME=magpiedb'
+ export 'VERIFY_SSL=true'
+ export 'AUTODEPLOY_DEPLOY_KEY_ROOT_DIR=/root/.ssh'
+ export 'AUTODEPLOY_PLATFORM_FREQUENCY=7 5 * * *'
+ export 'AUTODEPLOY_NOTEBOOK_FREQUENCY=@hourly'
+ ENV_LOCAL_FILE=/vagrant/birdhouse/deployment/../env.local
+ set +x
+ CERT_DOMAIN=
+ '[' -z  ]
+ CERT_DOMAIN=lvupavicsmaster.ouranos.ca
+ '[' '!' -z 1 ]
+ cd /vagrant/birdhouse/deployment/..
+ docker stop proxy
proxy
+ cd /
+ CERTBOT_OPTS=
+ '[' '!' -z 1 ]
+ CERTBOT_OPTS=renew
+ docker run --rm --name certbot -v /etc/letsencrypt:/etc/letsencrypt -v /var/lib/letsencrypt:/var/lib/letsencrypt -v /var/log/letsencrypt:/var/log/letsencrypt -p 443:443 -p 80:80 certbot/certbot:v1.3.0 renew
Saving debug log to /var/log/letsencrypt/letsencrypt.log

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Processing /etc/letsencrypt/renewal/lvupavicsmaster.ouranos.ca.conf
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Cert not yet due for renewal

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

The following certs are not due for renewal yet:
  /etc/letsencrypt/live/lvupavicsmaster.ouranos.ca/fullchain.pem expires on 2020-11-02 (skipped)
No renewals were attempted.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ RC=0
+ '[' '!' -z 1 ]
+ TMP_SSL_CERT=/tmp/tmp_certbotwrapper_ssl_cert.pem
+ CERTPATH=/etc/letsencrypt/live/lvupavicsmaster.ouranos.ca
+ cd /vagrant/birdhouse/deployment/..
+ docker run --rm --name copy_cert -v /etc/letsencrypt:/etc/letsencrypt bash cat /etc/letsencrypt/live/lvupavicsmaster.ouranos.ca/fullchain.pem /etc/letsencrypt/live/lvupavicsmaster.ouranos.ca/privkey.pem
+ diff /home/vagrant/certkey.pem /tmp/tmp_certbotwrapper_ssl_cert.pem
+ rm -v /tmp/tmp_certbotwrapper_ssl_cert.pem
removed '/tmp/tmp_certbotwrapper_ssl_cert.pem'
+ '[' -z  ]
+ docker start proxy
proxy
+ cd /
+ set +x

certbotwrapper finished START_TIME=2020-09-11T01:20:02+0000
certbotwrapper finished   END_TIME=2020-09-11T01:20:21+0000

    Logs when renewal is needed but failed due to firewall, certbot adds a random delay so proxy could be down up to 10 mins: certbot-renew-error.txt

    ==========
certbotwrapper START_TIME=2020-09-11T13:00:04+0000
+ realpath /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ THIS_FILE=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ dirname /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ THIS_DIR=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment
+ pwd
+ SAVED_PWD=/
+ . /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/../default.env
+ export 'DOCKER_NOTEBOOK_IMAGE=pavics/workflow-tests:200803'
+ export 'FINCH_IMAGE=birdhouse/finch:version-0.5.2'
+ export 'THREDDS_IMAGE=unidata/thredds-docker:4.6.14'
+ export 'JUPYTERHUB_USER_DATA_DIR=/data/jupyterhub_user_data'
+ export 'JUPYTER_DEMO_USER=demo'
+ export 'JUPYTER_DEMO_USER_MEM_LIMIT=2G'
+ export 'JUPYTER_DEMO_USER_CPU_LIMIT=0.5'
+ export 'JUPYTER_LOGIN_BANNER_TOP_SECTION='
+ export 'JUPYTER_LOGIN_BANNER_BOTTOM_SECTION='
+ export 'CANARIE_MONITORING_EXTRA_CONF_DIR=/conf.d'
+ export 'THREDDS_ORGANIZATION=Birdhouse'
+ export 'MAGPIE_DB_NAME=magpiedb'
+ export 'VERIFY_SSL=true'
+ export 'AUTODEPLOY_DEPLOY_KEY_ROOT_DIR=/root/.ssh'
+ export 'AUTODEPLOY_PLATFORM_FREQUENCY=7 5 * * *'
+ export 'AUTODEPLOY_NOTEBOOK_FREQUENCY=@hourly'
+ ENV_LOCAL_FILE=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/../env.local
+ set +x
+ CERT_DOMAIN=
+ '[' -z  ]
+ CERT_DOMAIN=medus.ouranos.ca
+ '[' '!' -z 1 ]
+ cd /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/..
+ docker stop proxy
proxy
+ cd /
+ CERTBOT_OPTS=
+ '[' '!' -z 1 ]
+ CERTBOT_OPTS=renew
+ docker run --rm --name certbot -v /etc/letsencrypt:/etc/letsencrypt -v /var/lib/letsencrypt:/var/lib/letsencrypt -v /var/log/letsencrypt:/var/log/letsencrypt -p 443:443 -p 80:80 certbot/certbot:v1.3.0 renew
Saving debug log to /var/log/letsencrypt/letsencrypt.log

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Processing /etc/letsencrypt/renewal/medus.ouranos.ca.conf
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Cert is due for renewal, auto-renewing...
Non-interactive renewal: random delay of 10.77459918236335 seconds
Plugins selected: Authenticator standalone, Installer None
Renewing an existing certificate
Performing the following challenges:
http-01 challenge for medus.ouranos.ca
Waiting for verification...
Challenge failed for domain medus.ouranos.ca
http-01 challenge for medus.ouranos.ca
Cleaning up challenges
Attempting to renew cert (medus.ouranos.ca) from /etc/letsencrypt/renewal/medus.ouranos.ca.conf produced an unexpected error: Some challenges have failed.. Skipping.
All renewal attempts failed. The following certs could not be renewed:
  /etc/letsencrypt/live/medus.ouranos.ca/fullchain.pem (failure)

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

All renewal attempts failed. The following certs could not be renewed:
  /etc/letsencrypt/live/medus.ouranos.ca/fullchain.pem (failure)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
1 renew failure(s), 0 parse failure(s)
IMPORTANT NOTES:
 - The following errors were reported by the server:

   Domain: medus.ouranos.ca
   Type:   connection
   Detail: Fetching
   http://medus.ouranos.ca/.well-known/acme-challenge/F-_TzoOMcgoo5WC9FQvi_QdKuoqdsrQFa7MR2bEdnJE:
   Timeout during connect (likely firewall problem)

   To fix these errors, please make sure that your domain name was
   entered correctly and the DNS A/AAAA record(s) for that domain
   contain(s) the right IP address. Additionally, please check that
   your computer has a publicly routable IP address and that no
   firewalls are preventing the server from communicating with the
   client. If you're using the webroot plugin, you should also verify
   that you are serving files from the webroot path you provided.
+ RC=1
+ '[' '!' -z 1 ]
+ TMP_SSL_CERT=/tmp/tmp_certbotwrapper_ssl_cert.pem
+ CERTPATH=/etc/letsencrypt/live/medus.ouranos.ca
+ cd /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/..
+ docker run --rm --name copy_cert -v /etc/letsencrypt:/etc/letsencrypt bash cat /etc/letsencrypt/live/medus.ouranos.ca/fullchain.pem /etc/letsencrypt/live/medus.ouranos.ca/privkey.pem
+ diff /etc/letsencrypt/live/medus.ouranos.ca/certkey.pem /tmp/tmp_certbotwrapper_ssl_cert.pem
+ rm -v /tmp/tmp_certbotwrapper_ssl_cert.pem
removed '/tmp/tmp_certbotwrapper_ssl_cert.pem'
+ '[' -z  ]
+ docker start proxy
proxy
+ cd /
+ set +x

certbotwrapper finished START_TIME=2020-09-11T13:00:04+0000
certbotwrapper finished   END_TIME=2020-09-11T13:00:49+0000

    Logs when renewal is successful, again proxy could be down up to 10 mins due to random delay by certbot client: certbot-renew-success-in-2-run-after-file-copy-fix.txt

    ==========
certbotwrapper START_TIME=2020-09-11T13:10:04+0000
+ realpath /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ THIS_FILE=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ dirname /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ THIS_DIR=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment
+ pwd
+ SAVED_PWD=/
+ . /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/../default.env
+ export 'DOCKER_NOTEBOOK_IMAGE=pavics/workflow-tests:200803'
+ export 'FINCH_IMAGE=birdhouse/finch:version-0.5.2'
+ export 'THREDDS_IMAGE=unidata/thredds-docker:4.6.14'
+ export 'JUPYTERHUB_USER_DATA_DIR=/data/jupyterhub_user_data'
+ export 'JUPYTER_DEMO_USER=demo'
+ export 'JUPYTER_DEMO_USER_MEM_LIMIT=2G'
+ export 'JUPYTER_DEMO_USER_CPU_LIMIT=0.5'
+ export 'JUPYTER_LOGIN_BANNER_TOP_SECTION='
+ export 'JUPYTER_LOGIN_BANNER_BOTTOM_SECTION='
+ export 'CANARIE_MONITORING_EXTRA_CONF_DIR=/conf.d'
+ export 'THREDDS_ORGANIZATION=Birdhouse'
+ export 'MAGPIE_DB_NAME=magpiedb'
+ export 'VERIFY_SSL=true'
+ export 'AUTODEPLOY_DEPLOY_KEY_ROOT_DIR=/root/.ssh'
+ export 'AUTODEPLOY_PLATFORM_FREQUENCY=7 5 * * *'
+ export 'AUTODEPLOY_NOTEBOOK_FREQUENCY=@hourly'
+ ENV_LOCAL_FILE=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/../env.local
+ set +x
+ CERT_DOMAIN=
+ '[' -z  ]
+ CERT_DOMAIN=medus.ouranos.ca
+ '[' '!' -z 1 ]
+ cd /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/..
+ docker stop proxy
proxy
+ cd /
+ CERTBOT_OPTS=
+ '[' '!' -z 1 ]
+ CERTBOT_OPTS=renew
+ docker run --rm --name certbot -v /etc/letsencrypt:/etc/letsencrypt -v /var/lib/letsencrypt:/var/lib/letsencrypt -v /var/log/letsencrypt:/var/log/letsencrypt -p 443:443 -p 80:80 certbot/certbot:v1.3.0 renew
Saving debug log to /var/log/letsencrypt/letsencrypt.log

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Processing /etc/letsencrypt/renewal/medus.ouranos.ca.conf
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Cert is due for renewal, auto-renewing...
Non-interactive renewal: random delay of 459.45712705256506 seconds
Plugins selected: Authenticator standalone, Installer None
Renewing an existing certificate
Performing the following challenges:
http-01 challenge for medus.ouranos.ca
Waiting for verification...
Cleaning up challenges

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
new certificate deployed without reload, fullchain is
/etc/letsencrypt/live/medus.ouranos.ca/fullchain.pem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Congratulations, all renewals succeeded. The following certs have been renewed:
  /etc/letsencrypt/live/medus.ouranos.ca/fullchain.pem (success)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ RC=0
+ '[' '!' -z 1 ]
+ TMP_SSL_CERT=/tmp/tmp_certbotwrapper_ssl_cert.pem
+ CERTPATH=/etc/letsencrypt/live/medus.ouranos.ca
+ cd /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/..
+ docker run --rm --name copy_cert -v /etc/letsencrypt:/etc/letsencrypt bash cat /etc/letsencrypt/live/medus.ouranos.ca/fullchain.pem /etc/letsencrypt/live/medus.ouranos.ca/privkey.pem
+ diff /etc/letsencrypt/live/medus.ouranos.ca/certkey.pem /tmp/tmp_certbotwrapper_ssl_cert.pem
--- /etc/letsencrypt/live/medus.ouranos.ca/certkey.pem
+++ /tmp/tmp_certbotwrapper_ssl_cert.pem
@@ -1,33 +1,33 @@
 -----BEGIN CERTIFICATE-----

REMOVED for Privacy.

 -----END PRIVATE KEY-----
+ '[' 0 -eq 0 ]
+ cp -v /tmp/tmp_certbotwrapper_ssl_cert.pem /etc/letsencrypt/live/medus.ouranos.ca/certkey.pem
cp: can't create '/etc/letsencrypt/live/medus.ouranos.ca/certkey.pem': File exists
+ rm -v /tmp/tmp_certbotwrapper_ssl_cert.pem
removed '/tmp/tmp_certbotwrapper_ssl_cert.pem'
+ '[' -z  ]
+ docker start proxy
proxy
+ cd /
+ set +x

certbotwrapper finished START_TIME=2020-09-11T13:10:04+0000
certbotwrapper finished   END_TIME=2020-09-11T13:18:10+0000
==========
certbotwrapper START_TIME=2020-09-11T15:00:06+0000
+ realpath /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ THIS_FILE=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ dirname /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/certbotwrapper
+ THIS_DIR=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment
+ pwd
+ SAVED_PWD=/
+ . /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/../default.env
+ export 'DOCKER_NOTEBOOK_IMAGE=pavics/workflow-tests:200803'
+ export 'FINCH_IMAGE=birdhouse/finch:version-0.5.2'
+ export 'THREDDS_IMAGE=unidata/thredds-docker:4.6.14'
+ export 'JUPYTERHUB_USER_DATA_DIR=/data/jupyterhub_user_data'
+ export 'JUPYTER_DEMO_USER=demo'
+ export 'JUPYTER_DEMO_USER_MEM_LIMIT=2G'
+ export 'JUPYTER_DEMO_USER_CPU_LIMIT=0.5'
+ export 'JUPYTER_LOGIN_BANNER_TOP_SECTION='
+ export 'JUPYTER_LOGIN_BANNER_BOTTOM_SECTION='
+ export 'CANARIE_MONITORING_EXTRA_CONF_DIR=/conf.d'
+ export 'THREDDS_ORGANIZATION=Birdhouse'
+ export 'MAGPIE_DB_NAME=magpiedb'
+ export 'VERIFY_SSL=true'
+ export 'AUTODEPLOY_DEPLOY_KEY_ROOT_DIR=/root/.ssh'
+ export 'AUTODEPLOY_PLATFORM_FREQUENCY=7 5 * * *'
+ export 'AUTODEPLOY_NOTEBOOK_FREQUENCY=@hourly'
+ ENV_LOCAL_FILE=/home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/../env.local
+ set +x
+ CERT_DOMAIN=
+ '[' -z  ]
+ CERT_DOMAIN=medus.ouranos.ca
+ '[' '!' -z 1 ]
+ cd /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/..
+ docker stop proxy
proxy
+ cd /
+ CERTBOT_OPTS=
+ '[' '!' -z 1 ]
+ CERTBOT_OPTS=renew
+ docker run --rm --name certbot -v /etc/letsencrypt:/etc/letsencrypt -v /var/lib/letsencrypt:/var/lib/letsencrypt -v /var/log/letsencrypt:/var/log/letsencrypt -p 443:443 -p 80:80 certbot/certbot:v1.3.0 renew
Saving debug log to /var/log/letsencrypt/letsencrypt.log

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Processing /etc/letsencrypt/renewal/medus.ouranos.ca.conf
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Cert not yet due for renewal

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

The following certs are not due for renewal yet:
  /etc/letsencrypt/live/medus.ouranos.ca/fullchain.pem expires on 2020-12-10 (skipped)
No renewals were attempted.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ RC=0
+ '[' '!' -z 1 ]
+ TMP_SSL_CERT=/tmp/tmp_certbotwrapper_ssl_cert.pem
+ CERTPATH=/etc/letsencrypt/live/medus.ouranos.ca
+ cd /home/mourad/PROJECTS/birdhouse-deploy/birdhouse/deployment/..
+ docker run --rm --name copy_cert -v /etc/letsencrypt:/etc/letsencrypt bash cat /etc/letsencrypt/live/medus.ouranos.ca/fullchain.pem /etc/letsencrypt/live/medus.ouranos.ca/privkey.pem
+ diff /etc/letsencrypt/live/medus.ouranos.ca/certkey.pem /tmp/tmp_certbotwrapper_ssl_cert.pem
--- /etc/letsencrypt/live/medus.ouranos.ca/certkey.pem
+++ /tmp/tmp_certbotwrapper_ssl_cert.pem
@@ -1,33 +1,33 @@
 -----BEGIN CERTIFICATE-----

REMOVED for Privacy.

 -----END PRIVATE KEY-----
+ '[' 0 -eq 0 ]
+ cp -v /tmp/tmp_certbotwrapper_ssl_cert.pem /etc/letsencrypt/live/medus.ouranos.ca/certkey.pem
'/tmp/tmp_certbotwrapper_ssl_cert.pem' -> '/etc/letsencrypt/live/medus.ouranos.ca/certkey.pem'
+ rm -v /tmp/tmp_certbotwrapper_ssl_cert.pem
removed '/tmp/tmp_certbotwrapper_ssl_cert.pem'
+ '[' -z  ]
+ docker start proxy
proxy
+ cd /
+ set +x

certbotwrapper finished START_TIME=2020-09-11T15:00:06+0000
certbotwrapper finished   END_TIME=2020-09-11T15:00:31+0000

1.11.1 (2020-09-15)

1.11.0 (2020-08-25)

1.10.4 (2020-08-05)

  • jupyter: new update image with hvplot pinned to older version for violin plot

    See PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/48 (commit https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/commit/4ad6ba6fa2a4ecf6d5d78e0602b39202307bcb76) for more detailed info.

    Deployed to Medus for testing (as regular PAVICS image, not the devel image). @aulemahal reported back that violin plot still do not work even with the old hvplot pinned in this image.

    I’ll release this image as-is since violin plot is also not working in the previous image that had hvplot 0.6.0 so no new regression there. Will unpin hvplot on next image build because pinning it did not fix violin plot (probably interference from other newer packages in this build).

    Noticeable changes:

    <   - hvplot=0.6.0=pyh9f0ad1d_0
>   - hvplot=0.5.2=py_0

<   - dask=2.20.0=py_0
>   - dask=2.22.0=py_0

<   - geopandas=0.8.0=py_1
>   - geopandas=0.8.1=py_0

<   - pandas=1.0.5=py37h0da4684_0
>   - pandas=1.1.0=py37h3340039_0

<   - matplotlib=3.2.2=1
>   - matplotlib=3.3.0=1

<   - numpy=1.18.5=py37h8960a57_0
>   - numpy=1.19.1=py37h8960a57_0

<   - cryptography=2.9.2=py37hb09aad4_0
>   - cryptography=3.0=py37hb09aad4_0

<   - python=3.7.6=h8356626_5_cpython
>   - python=3.7.8=h6f2ec95_1_cpython

<   - nbval=0.9.5=py_0
>   - nbval=0.9.6=pyh9f0ad1d_0

<   - pytest=5.4.3=py37hc8dfbb8_0
>   - pytest=6.0.1=py37hc8dfbb8_0

1.10.3 (2020-07-21)

  • proxy: increase timeout for reading a response from the proxied server

    Fixes https://github.com/Ouranosinc/raven/issues/286

    “there seems to be a problem with the size of the ncml and the timeout if I use more than 10-12 years as the historical data. I get a : “Netcdf: DAP failure” error if I use too many years.”

    ________________________________________________________ TestBiasCorrect.test_bias_correction ________________________________________________________
Traceback (most recent call last):
  File "/zstore/repos/raven/tests/test_bias_correction.py", line 20, in test_bias_correction
    ds = (xr.open_dataset(hist_data).sel(lat=slice(lat + 1, lat - 1),lon=slice(lon - 1, lon + 1), time=slice(dt.datetime(1991,1,1), dt.datetime(2010,12,31))).mean(dim={"lat", "lon"}, keep_attrs=True))
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/common.py", line 84, in wrapped_func
    func, dim, skipna=skipna, numeric_only=numeric_only, **kwargs
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/dataset.py", line 4313, in reduce
    **kwargs,
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/variable.py", line 1586, in reduce
    input_data = self.data if allow_lazy else self.values
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/variable.py", line 349, in data
    return self.values
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/variable.py", line 457, in values
    return _as_array_or_item(self._data)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/variable.py", line 260, in _as_array_or_item
    data = np.asarray(data)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/numpy/core/_asarray.py", line 83, in asarray
    return array(a, dtype, copy=False, order=order)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/indexing.py", line 677, in __array__
    self._ensure_cached()
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/indexing.py", line 674, in _ensure_cached
    self.array = NumpyIndexingAdapter(np.asarray(self.array))
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/numpy/core/_asarray.py", line 83, in asarray
    return array(a, dtype, copy=False, order=order)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/indexing.py", line 653, in __array__
    return np.asarray(self.array, dtype=dtype)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/numpy/core/_asarray.py", line 83, in asarray
    return array(a, dtype, copy=False, order=order)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/indexing.py", line 557, in __array__
    return np.asarray(array[self.key], dtype=None)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/backends/netCDF4_.py", line 73, in __getitem__
    key, self.shape, indexing.IndexingSupport.OUTER, self._getitem
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/core/indexing.py", line 837, in explicit_indexing_adapter
    result = raw_indexing_method(raw_key.tuple)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/backends/netCDF4_.py", line 85, in _getitem
    array = getitem(original_array, key)
  File "/home/lvu/.conda/envs/raven/lib/python3.7/site-packages/xarray/backends/common.py", line 54, in robust_getitem
    return array[key]
  File "netCDF4/_netCDF4.pyx", line 4408, in netCDF4._netCDF4.Variable.__getitem__
  File "netCDF4/_netCDF4.pyx", line 5352, in netCDF4._netCDF4.Variable._get
  File "netCDF4/_netCDF4.pyx", line 1887, in netCDF4._netCDF4._ensure_nc_success
RuntimeError: NetCDF: DAP failure

1.10.2 (2020-07-18)

1.10.1 (2020-07-11)

  • Monitoring: add alert rules and alert handling (deduplicate, group, route, silence, inhibit).

    This is a follow up to the previous PR https://github.com/bird-house/birdhouse-deploy/pull/56 that added the monitoring itself.

    Added cAdvisor and Node-exporter collection of alert rules found here https://awesome-prometheus-alerts.grep.to/rules with a few fixing because of errors in the rules and tweaking to reduce false positive alarms (see list of commits). Great collection of sample of ready-made rules to hit the ground running and learn PromML query language on the way.

    2020-07-08-090953_474x1490_scrot

    Added Alertmanager to handle the alerts (deduplicate, group, route, silence, inhibit). Currently the only notification route configured is email but Alertmanager is able to route alerts to Slack and any generic services accepting webhooks.

    2020-07-08-091150_1099x669_scrot 2020-07-08-091302_1102x1122_scrot

    This is an initial attempt at alerting. There are several ways to tweak the system without changing the code:

    • To add more Prometheus alert rules, volume-mount more *.rules files to the prometheus container.

    • To disable existing Prometheus alert rules, add more Alertmanager inhibition rules using ALERTMANAGER_EXTRA_INHIBITION via env.local file.

    • Other possible Alertmanager configs via env.local: ALERTMANAGER_EXTRA_GLOBAL, ALERTMANAGER_EXTRA_ROUTES, ALERTMANAGER_EXTRA_RECEIVERS.

    What more could be done after this initial attempt:

    • Possibly add more graphs to Grafana dashboard since we have more alerts on metrics that we do not have matching Grafana graph. Graphs are useful for historical trends and correlation with other metrics, so not required if we do not need trends and correlation.

    • Only basic metrics are being collected currently. We could collect more useful metrics like SMART status and alert when a disk is failing.

    • The autodeploy mechanism can hook into this monitoring system to report pass/fail status and execution duration, with alerting for problems. Then we can also correlate any CPU, memory, disk I/O spike, when the autodeploy runs and have a trace of previous autodeploy executions.

    I had to test these alerts directly in prod to tweak for less false positive alert and to debug not working rules to ensure they work on prod so these changes are already in prod ! This also test the SMTP server on the network.

    See rules on Prometheus side: http://pavics.ouranos.ca:9090/rules, http://medus.ouranos.ca:9090/rules

    Manage alerts on Alertmanager side: http://pavics.ouranos.ca:9093/#/alerts, http://medus.ouranos.ca:9093/#/alerts

    Part of issue https://github.com/bird-house/birdhouse-deploy/issues/12

1.10.0 (2020-07-02)

  • Monitoring for host and each docker container.

    Screenshot_2020-06-19 Docker and system monitoring - Grafana

    For host, using Node-exporter to collect metrics:

    • uptime

    • number of container

    • used disk space

    • used memory, available memory, used swap memory

    • load

    • cpu usage

    • in and out network traffic

    • disk I/O

    For each container, using cAdvisor to collect metrics:

    • in and out network traffic

    • cpu usage

    • memory and swap memory usage

    • disk usage

    Useful visualisation features:

    • zoom in one graph and all other graph update to match the same “time range” so we can correlate event

    • view each graph independently for more details

    • mouse over each data point will show value at that moment

    Prometheus is used as the time series DB and Grafana is used as the visualization dashboard.

    Node-exporter, cAdvisor and Prometheus are exposed so another Prometheus on the network can also scrape those same metrics and perform other analysis if required.

    The whole monitoring stack is a separate component so user is not forced to enable it if there is already another monitoring system in place. Enabling this monitoring stack is done via env.local file, like all other components.

    The Grafana dashboard is taken from https://grafana.com/grafana/dashboards/893 with many fixes (see commits) since most of the metric names have changed over time. Still it was much quicker to hit the ground running than learning the Prometheus query language and Grafana visualization options from scratch. Not counting there are lots of metrics exposed, had to filter out which one are relevant to graph. So starting from a broken dashboard was still a big win. Grafana has a big collection of existing but probably un-maintained dashboards we can leverage.

    So this is a first draft for monitoring. Many things I am not sure or will need tweaking or is missing:

    • Probably have to add more metrics or remove some that might be irrelevant, with time we will see.

    • Probably will have to tweak the scrape interval and the retention time, to keep the disk storage requirement reasonable, again we’ll see with time.

    • Missing alerting. With all the pretty graph, we are not going to look at them all day, we need some kind of alerting mechanism.

    Test system: http://lvupavicsmaster.ouranos.ca:3001/d/pf6xQMWGz/docker-and-system-monitoring?orgId=1&refresh=5m, user: admin, passwd: the default passwd

    Also tested on Medus: http://medus.ouranos.ca:3001/d/pf6xQMWGz/docker-and-system-monitoring?orgId=1&refresh=5m (on Medus had to perform full yum update to get new kernel and new docker engine for cAdvisor to work properly).

    Part of issue https://github.com/bird-house/birdhouse-deploy/issues/12

1.9.6 (2020-06-15)

1.9.5 (2020-06-12)

1.9.4 (2020-06-03)

1.9.3 (2020-05-07)

1.9.2 (2020-04-29)

1.9.1 (2020-04-24)

  • Fix notebook autodeploy wipe already deployed notebook when GitHub down.

    Fixes https://github.com/bird-house/birdhouse-deploy/issues/43

    Fail early with any unexpected error to not wipe already deployed notebooks.

    Check source dir not empty before wiping dest dir containing already deployed notebooks.

    Reduce cleaning verbosity for more concise logging.

    To fix this error found in production logs when Github is down today:

    notebookdeploy START_TIME=2020-04-23T10:01:01-0400
++ mktemp -d -t notebookdeploy.XXXXXXXXXXXX
+ TMPDIR=/tmp/notebookdeploy.ICk70Vto2LaE
+ cd /tmp/notebookdeploy.ICk70Vto2LaE
+ mkdir tutorial-notebooks
+ cd tutorial-notebooks
+ wget --quiet https://raw.githubusercontent.com/Ouranosinc/PAVICS-e2e-workflow-tests/master/downloadrepos
+ chmod a+x downloadrepos
chmod: cannot access ‘downloadrepos’: No such file or directory
+ wget --quiet https://raw.githubusercontent.com/Ouranosinc/PAVICS-e2e-workflow-tests/master/default_build_params
+ wget --quiet https://raw.githubusercontent.com/Ouranosinc/PAVICS-e2e-workflow-tests/master/binder/reorg-notebooks
+ chmod a+x reorg-notebooks
chmod: cannot access ‘reorg-notebooks’: No such file or directory
+ wget --quiet --output-document - https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/archive/master.tar.gz
+ tar xz

gzip: stdin: unexpected end of file
tar: Child returned status 1
tar: Error is not recoverable: exiting now
+ ./downloadrepos
/etc/cron.hourly/PAVICS-deploy-notebooks: line 63: ./downloadrepos: No such file or directory
+ ./reorg-notebooks
/etc/cron.hourly/PAVICS-deploy-notebooks: line 64: ./reorg-notebooks: No such file or directory
+ mv -v 'PAVICS-e2e-workflow-tests-master/notebooks/*.ipynb' ./
mv: cannot stat ‘PAVICS-e2e-workflow-tests-master/notebooks/*.ipynb’: No such file or directory
+ rm -rfv PAVICS-e2e-workflow-tests-master
+ rm -rfv downloadrepos default_build_params reorg-notebooks
+ TMP_SCRIPT=/tmp/notebookdeploy.ICk70Vto2LaE/deploy-notebook
+ cat
+ chmod a+x /tmp/notebookdeploy.ICk70Vto2LaE/deploy-notebook
+ docker pull bash
Using default tag: latest
latest: Pulling from library/bash
Digest: sha256:febb3d74f41f2405fe21b7c7b47ca1aee0eda0a3ffb5483ebe3423639d30d631
Status: Image is up to date for bash:latest
+ docker run --rm --name deploy_tutorial_notebooks -u root -v /tmp/notebookdeploy.ICk70Vto2LaE/deploy-notebook:/deploy-notebook:ro -v /tmp/notebookdeploy.ICk70Vto2LaE/tutorial-notebooks:/tutorial-notebooks:ro -v /data/jupyterhub_user_data:/notebook_dir:rw --entrypoint /deploy-notebook bash
+ cd /notebook_dir
+ rm -rf tutorial-notebooks/WCS_example.ipynb tutorial-notebooks/WFS_example.ipynb tutorial-notebooks/WMS_example.ipynb tutorial-notebooks/WPS_example.ipynb tutorial-notebooks/catalog_search.ipynb tutorial-notebooks/dap_subset.ipynb tutorial-notebooks/esgf-compute-api-examples-devel tutorial-notebooks/esgf-dap.ipynb tutorial-notebooks/finch-usage.ipynb tutorial-notebooks/hummingbird.ipynb tutorial-notebooks/opendap.ipynb tutorial-notebooks/pavics_thredds.ipynb tutorial-notebooks/raven-master tutorial-notebooks/rendering.ipynb tutorial-notebooks/subsetting.ipynb
+ cp -rv '/tutorial-notebooks/*' tutorial-notebooks
cp: can't stat '/tutorial-notebooks/*': No such file or directory
+ chown -R root:root tutorial-notebooks
+ set +x
removed directory: ‘/tmp/notebookdeploy.ICk70Vto2LaE/tutorial-notebooks’
removed ‘/tmp/notebookdeploy.ICk70Vto2LaE/deploy-notebook’
removed directory: ‘/tmp/notebookdeploy.ICk70Vto2LaE’

notebookdeploy finished START_TIME=2020-04-23T10:01:01-0400
notebookdeploy finished   END_TIME=2020-04-23T10:02:12-0400

1.9.0 (2020-04-24)

  • vagrant: add centos7 and LetsEncrypt SSL cert support, fix scheduler autodeploy remaining issues

    Fixes https://github.com/bird-house/birdhouse-deploy/issues/27.

    Centos7 support added to Vagrant to reproduce problems found on Medus in PR https://github.com/bird-house/birdhouse-deploy/pull/39 (commit https://github.com/bird-house/birdhouse-deploy/commit/6036dbd5ff072544d902e7b84b5eff361b00f78b):

    Problem 1: wget httpS url not working in bash docker image breaking the notebook autodeploy when running under the new scheduler autodeploy: not reproducible

    Problem 2: all containers are destroyed and recreated when alternating between manually running ./pavics-compose.sh up -d locally and when the same command is executed automatically by the scheduler autodeploy inside its own container: not reproducible

    Problem 3: sysctl: error: 'net.ipv4.tcp_tw_reuse' is an unknown key on ./pavics-compose.sh up -d when executed automatically by the scheduler autodeploy inside its own container: reproduced but seems harmless so not fixing it.

    Problem 4: current user lose write permission to birdhouse-deploy checkout and other checkout in AUTODEPLOY_EXTRA_REPOS when using scheduler autodeploy: fixed

    Problem 5: no documentation for the new scheduler autodeploy: fixed

    Another autodeploy fix found while working on this PR: notebook autodeploy broken when /data/jupyterhub_user_data/tutorial-notebooks dir do not pre-exist. Regression from this commit https://github.com/bird-house/birdhouse-deploy/pull/16/commits/6ddaddc74d384299e45b0dc8d50a63e59b3cc0d5 (PR https://github.com/bird-house/birdhouse-deploy/pull/16): before that commit the entire dir was copied, not just the content, so the dir was created automatically.

    Centos7 Vagrant box experience is not completely automated as Ubuntu box, even when using the same vagrant-disksize Vagrant plugin as Ubuntu box. Manual disk resize instruction is provided. Candidate for automation later if we destroy and recreate Centos7 box very often. Hopefully the problem is not there for Centos8 so we can forget about this annoyance.

    Automatic generation of SSL certificate from LetsEncrypt is also added for both Ubuntu and Centos Vagrant box. Can be used outside of Vagrant so Medus and Boreas can also benefit next time, if needed. Later docker image of certbot is used so should already be using ACMEv2 protocol (ACMEv1 is being deprecated).

    Pagekite is also preserved for both boxes for when exposing port 80 and 443 directly on the internet is not possible but PAVICS still need a real SSL certificate.

    Test server: https://lvupavicsmaster.ouranos.ca (Centos7, on internet with LetsEncrypt SSL cert).

    Jenkins run only have known errors: http://jenkins.ouranos.ca/job/ouranos-staging/job/lvupavicsmaster.ouranos.ca/4/console

    2020-04-22-070604_1299x1131_scrot

1.8.10 (2020-04-09)

  • Autodeploy the autodeploy phase 2: everything operational but a few compatibility issues remain

    Part of https://github.com/bird-house/birdhouse-deploy/issues/27

    Activating the ./components/scheduler will do everything. All configurations are centralized in the env.local file.

    One missing feature is piece-wise choice of platform or notebook autodeploy only, like with the old manual install-* stcripts under https://github.com/bird-house/birdhouse-deploy/tree/master/birdhouse/deployment. Right now it’s all or nothing. I can work on this if you guys think it’s needed.

    Remaining compatibility issues with Medus (Vagrant box works fine):

    • Notebook autodeploy do not work. It looks like using the bash docker image, I am unable to wget any httpS address. This same docker run command works fine on my Vagrant box as well. So there’s something on Medus.

    $ docker run --rm --name debug_wget_httpS -u root bash bash -c "wget https://google.com -O -"
Connecting to google.com (172.217.13.206:443)
wget: error getting response: Connection reset by peer

    • All the containers are being recreated when ./pavics-compose.sh runs inside the container (first migration to the new autodeploy mechanism). To investigate but I suspect this might be due to older version of docker and docker-compose on Medus.

    • This one looks like due to older kernel on Medus:

    sysctl: error: 'net.ipv4.tcp_tw_reuse' is an unknown key
sh: 0: unknown operand

    • All the files updated by git pull are now owned by root (the user inside the container). I’ll have to undo this ownership change, somehow. This one is super weird, I should have got it on my Vagrant box. Probably Vagrant did some magic to always ensure files under /vagrant is always owned by the user even if changed by user root.

    • Documentation: update README and list relevant configuration variables in env.local for this new ./component/scheduler.

    Migrating to this new mechanism requires manual deletion of all the artifacts created by the old install scripts: sudo rm /etc/cron.d/PAVICS-deploy /etc/cron.hourly/PAVICS-deploy-notebooks /etc/logrotate.d/PAVICS-deploy /usr/local/sbin/triggerdeploy.sh. Both can not co-exist at the same time.

    Maximum backward-compatibility has been kept with the old existing install scripts style:

    • Still log to the same existing log files under /var/log/PAVICS.

    • Old single ssh deploy key is still compatible, but the new mechanism allows for different ssh deploy keys for each extra repos (again, public repos should use https clone path to avoid dealing with ssh deploy keys in the first place)

    • Old install scripts are kept

    Features missing in old existing install scripts or how this improves on the old install scripts:

    • Autodeploy of the autodeploy itself ! This is the biggest win. Previously, if triggerdeploy.sh or PAVICS-deploy-notebooks script changes, they have to be deployed manually. It’s very annoying. Now they are volume-mount in so are fresh on each run.

    • env.local now drive absolutely everything, source control that file and we’ve got a true DevOPS pipeline.

    • Configurable platform and notebook autodeploy frequency. Previously, this means manually editing the generated cron file, less ideal.

    • Do not need any support on the local host other than docker and docker-compose. cron/logrotate/git/ssh versions are all locked-down in the docker images used by the autodeploy. Recall previously we had to deal with git version too old on some hosts.

    • Each cron job run in its own docker image meaning the runtime environment is traceable and reproducible.

    • The newly introduced scheduler component is made extensible so other jobs can added into it as well (ex: backup), via env.local, which should source control, meaning all surrounding maintenance related tasks can also be traceable and reproducible.

    This is a rather large PR. For a less technical overview, start with the diff of README.md, env.local.example, common.env. If a change looks funny to you, read the commit description that introduce that change, the reasoning should be there.

1.8.9 (2020-04-08)

  • finch: update to 0.5.2

    Fix following 2 Jenkins failures:

    Tested in this Jenkins run http://jenkins.ouranos.ca/job/ouranos-staging/job/lvupavics-lvu.pagekite.me/20/console

    _________ finch-master/docs/source/notebooks/dap_subset.ipynb::Cell 9 __________
Notebook cell execution failed
Cell 9: Cell outputs differ

Input:
resp = wps.sdii(pr + sub)
out = resp.get(asobj=True)
out.output_netcdf.sdii

Traceback:
 mismatch 'text/html'

 assert reference_output == test_output failed:

  '<pre>&lt;xar...vera...</pre>' == '<pre>&lt;xar...vera...</pre>'
  Skipping 350 identical leading characters in diff, use -v to show
    m/day
  -     cell_methods:   time: mean (interval: 30 minutes)
        history:        pr=max(0,pr) applied to raw data;\n[DATE_TIME] ...
  +     cell_methods:   time: mean (interval: 30 minutes)
        standard_name:  lwe_thickness_of_precipitation_amount
        long_name:      Average precipitation during wet days (sdii)
        description:    Annual simple daily intensity index (sdii) : annual avera...</pre>

    _________ finch-master/docs/source/notebooks/finch-usage.ipynb::Cell 1 _________
Notebook cell execution failed
Cell 1: Cell outputs differ

Input:
help(wps.frost_days)

Traceback:
 mismatch 'stdout'

 assert reference_output == test_output failed:

  'Help on meth...ut files.\n\n' == 'Help on meth...ut files.\n\n'
  Skipping 399 identical leading characters in diff, use -v to show
  -    freq : string
  +    freq : {'YS', 'MS', 'QS-DEC', 'AS-JUL'}string
            Resampling frequency

        Returns
        -------
        output_netcdf : ComplexData:mimetype:`application/x-netcdf`
            The indicator values computed on the original input grid.
        output_log : ComplexData:mimetype:`text/plain`
            Collected logs during process run.
        ref : ComplexData:mimetype:`application/metalink+xml; version=4.0`
            Metalink file storing all references to output files.

1.8.8 (2020-03-20)

  • jupyter: make configurable public demo user name, passwd, resource limit, login banner

    For security reasons, the public demo username and password are not hardcoded anymore.

    Compromising of one PAVICS deployment should not compromise all other PAVICS deployments if each deployment use a different password.

    The password is set when the public demo user is created in Magpie, see the birdhouse/README.md update.

    The login banner do not display the public demo password anymore. If one really want to display the password, can use the top or bottom section of the login banner that is customizable via env.local.

    Login banner is updated with more notices, please review wording.

    Resource limits (only memory limit seems to work with the DockerSpawner) is also customizable.

    All changes to env.local are live after a ./pavics-compose.sh up -d.

    Test server: https://lvupavics-lvu.pagekite.me/jupyter/ (ask me privately for the password :D)

1.8.7 (2020-03-19)

  • finch: update to v0.5.1

1.8.6 (2020-03-16)

1.8.5 (2020-03-13)

  • jupyter: update to pavics/workflow-tests:200312 for Raven notebooks

1.8.4 (2020-03-10)

  • raven: upgrade to pavics/raven:0.10.0

1.8.3 (2020-02-17)

1.8.2 (2020-02-10)

  • Optionally monitor all components behind Twitcher using canarie api.

    Fixes https://github.com/bird-house/birdhouse-deploy/issues/8

    The motivation was the need for some quick dashboard for the working state of all the components, not to get more stats.

    Right now we bypassing Twitcher, which is not real life, it’s not what real users will experience.

    This is ultra cheap to add and provide very fast and up-to-date (every minute) result. It’s like an always on sanity check that can quickly help debugging any connectivity issues between the components.

    It is optional because it assumes all components are publicly accessible. Might not be the case for everyone. We can also override the override :D

    All components in config/canarie-api/docker_configuration.py.template that do not have public (behind Twitcher) monitoring are added.

    Also added Hummingbird and ncWMS2 public monitoring.

    @tlogan2000 This will catch accidental Thredds public url breakage like last time and will leverage the existing monitoring on https://pavics.ouranos.ca/canarie/node/service/stats by @moulab88.

    @davidcaron @dbyrns This is optional so if the CRIM do not want to enable it, it’s fine.

    New node monitoring page:

    Screenshot_2020-02-07 Ouranos - Node Service

1.8.1 (2020-02-06)

  • Increase JupyterHub security.

    ab56994 jupyter: limit memory of public user to 500 MB 90c1950 jupyter: prevent user from loading user-owned config at spawner server startup e8f2fa3 jupyter: avoid terminating user running jobs on Hub update 3f97cc7 jupyter: get ready to prevent browser session re-use even if password changed e2ebcc3 jupyter: disable notebook terminal for security reasons

1.8.0 (2020-02-03)

1.7.1 (2020-01-30)

  • jupyter: update various packages and add threddsclient

    Noticeable changes:

    <     - bokeh==1.4.0
>   - bokeh=1.4.0=py36_0

<   - python=3.7.3=h33d41f4_1
>   - python=3.6.7=h357f687_1006

>   - threddsclient=0.4.2=py_0

<     - xarray==0.13.0
>   - xarray=0.14.1=py_1

<     - dask==2.8.0
>     - dask==2.9.2

<     - xclim==0.12.2
>     - xclim==0.13.0

    See PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/34 for more info.

1.7.0 (2020-01-22)

  • backup solr: should save all of /data/solr, not just the index

Prior Versions

All versions prior to 1.7.0 were not officially tagged. Is it strongly recommended employing later versions to ensure better traceability of changes that could impact behavior and potential issues on new server instances.