bird-house · ChaamC · Sep 25, 2023 · Jul 18, 2023 · Jul 25, 2023 · Jul 25, 2023
@@ -19,14 +19,15 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optionally set the Python requirements required to build your docs
 python:
-  version: 3.6
   install:
     - requirements: docs/requirements.txt
 
 #conda:
 #  environment: environment-docs.yml
 
 build:
-  image: stable
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.6"
@@ -15,7 +15,22 @@
 [Unreleased](https://github.com/bird-house/birdhouse-deploy/tree/master) (latest)
 ------------------------------------------------------------------------------------------------------------------
 
-[//]: # (list changes here, using '-' for each new entry, remove this when items are added)
+## Changes
+
+- Add public WPS outputs directory to Cowbird and add corresponding volume mount to JupyterHub.
+- Update `cowbird` service from [1.2.0](https://github.com/Ouranosinc/cowbird/tree/1.2.0)
+  to [2.1.0](https://github.com/Ouranosinc/cowbird/tree/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](https://pavics-weaver.readthedocs.io/en/latest/installation.html?#database-migration).
 
 [1.31.2](https://github.com/bird-house/birdhouse-deploy/tree/1.31.2) (2023-09-13)
 ------------------------------------------------------------------------------------------------------------------
@@ -147,11 +162,6 @@
   [CMIP Dataset Ingestion Workflows](https://github.com/cedadev/stac-generator-example/tree/master/conf).
 
 - Adds ``optional-components/stac-public-access`` to give public access to the STAC catalog.
-- Add public wps outputs directory to Cowbird and add corresponding volume mount to JupyterHub.
-- Update `cowbird` service from [1.2.0](https://github.com/Ouranosinc/cowbird/tree/1.2.0)
-  to [2.0.0](https://github.com/Ouranosinc/cowbird/tree/2.0.0)
-- 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.
 
 [1.27.1](https://github.com/bird-house/birdhouse-deploy/tree/1.27.1) (2023-07-10)
 ------------------------------------------------------------------------------------------------------------------

@@ -33,7 +33,11 @@ handlers:
     workspace_dir: ${WORKSPACE_DIR}
     jupyterhub_user_data_dir: ${JUPYTERHUB_USER_DATA_DIR}
     wps_outputs_dir: ${WPS_OUTPUTS_DIR}
-    wps_outputs_public_subdir: ${WPS_OUTPUTS_PUBLIC_SUBDIR}
+    secure_data_proxy_name: ${SECURE_DATA_PROXY_NAME}
+    # wps_outputs_res_name: ${WPS_OUTPUTS_RES_NAME}
+    public_workspace_wps_outputs_subdir: ${PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR}
+    # notebooks_dir_name: ${NOTEBOOKS_DIR_NAME}
+    # user_wps_outputs_dir_name: ${USER_WPS_OUTPUTS_DIR_NAME}
 
 # [Required] This section defines how to synchronize permissions between services when they share resources
 sync_permissions:

@@ -14,6 +14,6 @@ services:
   jupyterhub:
     environment:
       WORKSPACE_DIR: ${DATA_PERSIST_ROOT}/${USER_WORKSPACES}
-      WPS_OUTPUTS_PUBLIC_SUBDIR: ${WPS_OUTPUTS_PUBLIC_SUBDIR}
+      PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR: ${PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR}
     volumes:
       - "${DATA_PERSIST_ROOT}/${USER_WORKSPACES}:${DATA_PERSIST_ROOT}/${USER_WORKSPACES}"
@@ -13,11 +13,11 @@
 EXTRA_VARS='
     ${COWBIRD_VERSION}
     ${COWBIRD_MONGODB_VERSION}
-    ${COWBIRD_MONGODB_SERVICE}
     ${COWBIRD_MONGODB_HOST}
     ${COWBIRD_MONGODB_PORT}
     ${USER_WORKSPACES}
-    ${WPS_OUTPUTS_PUBLIC_SUBDIR}
+    ${PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR}
+    ${SECURE_DATA_PROXY_NAME}
 '
 # extend the original 'VARS' from 'birdhouse/pavics-compose.sh' to employ them for template substitution
 # adding them to 'VARS', they will also be validated in case of override of 'default.env' using 'env.local'
@@ -27,7 +27,7 @@ VARS="$VARS $EXTRA_VARS"
 # Cowbird Configuration
 # =====================
 
-export COWBIRD_VERSION="2.0.0"
+export COWBIRD_VERSION="2.1.0"
 
 # default release of the MongoDB version employed by Cowbird
 # note that MongoDB>=5.0 is REQUIRED for Cowbird>=2.0.0
@@ -36,19 +36,21 @@ export COWBIRD_MONGODB_VERSION=5.0
 # or use another service (e.g.: dedicated mongodb)
 # the 'host' is the mongo 'service' inter-docker network connection in this case
 # the selected 'mongo' service should be member of a network of same name
-export COWBIRD_MONGODB_SERVICE=cowbird-mongodb
-export COWBIRD_MONGODB_HOST=${COWBIRD_MONGODB_SERVICE}
+export COWBIRD_MONGODB_HOST=cowbird-mongodb
 export COWBIRD_MONGODB_PORT=27017
 
 # Subdirectory containing the user workspaces used by Cowbird
 export USER_WORKSPACES="user_workspaces"
 
-# Subdirectory containing the hardlinks to the public wpsoutputs data
+# Subdirectory containing the hardlinks to the public WPS outputs data
 # This directory will be mounted on the JupyterLab instances and is located by default
 # in the ${USER_WORKSPACES} directory.
-export WPS_OUTPUTS_PUBLIC_SUBDIR="public/wpsoutputs"
+export PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR="public/wps_outputs"
 
-# this dependency is only required if COWBIRD_MONGODB_SERVICE is the one provided in config/mongodb.
+# Default name for the secure-data-proxy service from Magpie.
+export SECURE_DATA_PROXY_NAME="secure-data-proxy"
+
+# this dependency is only required if the mongo instance is the one provided in config/mongodb.
 # (include this for Cowbird<2.0.0)
 #COMPONENT_DEPENDENCIES="
 #  $COMPONENT_DEPENDENCIES

@@ -23,18 +23,19 @@ services:
       # root user
       COWBIRD_FILESYSTEM_ADMIN_UID: 0
       COWBIRD_FILESYSTEM_ADMIN_GID: 0
+      PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR: ${PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR}
+      SECURE_DATA_PROXY_NAME: ${SECURE_DATA_PROXY_NAME}
       # Note that WPS_OUTPUTS_DIR and WORKSPACE_DIR must both point to paths from the same volume.
       # This is to allow the creation of hardlinks between the wpsoutputs and the user workspace.
       WPS_OUTPUTS_DIR: ${WPS_OUTPUTS_DIR}
-      WPS_OUTPUTS_PUBLIC_SUBDIR: ${WPS_OUTPUTS_PUBLIC_SUBDIR}
       WORKSPACE_DIR: ${DATA_PERSIST_ROOT}/${USER_WORKSPACES}
     links:
-      - "${COWBIRD_MONGODB_SERVICE}"
+      - cowbird-mongodb
     networks:
       - default
-      - "${COWBIRD_MONGODB_SERVICE}"
+      - cowbird-mongodb
     depends_on:
-      - "${COWBIRD_MONGODB_SERVICE}"
+      - cowbird-mongodb
     volumes:
       - ./components/cowbird/config/cowbird/config.yml:/opt/local/src/cowbird/config/cowbird.yml
       - ./components/cowbird/config/cowbird/cowbird.ini:/opt/local/src/cowbird/config/cowbird.ini
@@ -58,12 +59,12 @@ services:
       COWBIRD_FILESYSTEM_ADMIN_GID: 0
       WORKSPACE_DIR: ${DATA_PERSIST_ROOT}/${USER_WORKSPACES}
     links:
-      - "${COWBIRD_MONGODB_SERVICE}"
+      - cowbird-mongodb
     networks:
       - default
-      - "${COWBIRD_MONGODB_SERVICE}"
+      - cowbird-mongodb
     depends_on:
-      - "${COWBIRD_MONGODB_SERVICE}"
+      - cowbird-mongodb
       - cowbird  # if not started first, sometimes celery misbehaves and will not pick jobs in queue
     volumes:
       - ./components/cowbird/config/cowbird/config.yml:/opt/local/src/cowbird/config/cowbird.yml
@@ -76,9 +77,9 @@ services:
   # Dedicated database for Cowbird, since other 'mongodb' image does not employ the same version.
   cowbird-mongodb:
     image: mongo:${COWBIRD_MONGODB_VERSION}
-    container_name: ${COWBIRD_MONGODB_SERVICE}
+    container_name: cowbird-mongodb
     networks:
-      - "${COWBIRD_MONGODB_SERVICE}"
+      - cowbird-mongodb
     volumes:
       - ${DATA_PERSIST_ROOT}/mongodb_cowbird_persist:/data/db
     restart: always

@@ -81,8 +81,8 @@ export WEAVER_WPS_PATH=/wps
 export WEAVER_WPS_OUTPUTS_PATH="/wpsoutputs/weaver"
 # data persistence of wps outputs (directory path)
 # NOTE:
-#   follow the same convension of 'wps_outputs/<bird>' as the rest of the stact
-export WEAVER_WPS_OUTPUTS_DIR='${DATA_PERSIST_ROOT}/wps_outputs/weaver'
+#   follow the same convention of 'wps_outputs/<bird>' as the rest of the stack
+export WEAVER_WPS_OUTPUTS_DIR='${WPS_OUTPUTS_DIR}/weaver'
 export WEAVER_WPS_WORKDIR="/tmp/wps_workdir/weaver"
 
 # logging

@@ -88,8 +88,8 @@ if os.environ['WORKSPACE_DIR'] != jupyterhub_data_dir:
         "bind": join(jupyterhub_data_dir, "{username}"),
         "mode": "rw"
     }
-    c.DockerSpawner.volumes[join(os.environ['WORKSPACE_DIR'], os.environ['WPS_OUTPUTS_PUBLIC_SUBDIR'])] = {
-        "bind": join(notebook_dir, os.environ['WPS_OUTPUTS_PUBLIC_SUBDIR']),
+    c.DockerSpawner.volumes[join(os.environ['WORKSPACE_DIR'], os.environ['PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR'])] = {
+        "bind": join(notebook_dir, os.environ['PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR']),
         "mode": "ro"
     }
 

@@ -53,4 +53,4 @@ export DEFAULT_CONF_DIRS='
 export USER_WORKSPACE_UID=1000
 export USER_WORKSPACE_GID=1000
 
-export WPS_OUTPUTS_DIR="/data/wpsoutputs"
+export WPS_OUTPUTS_DIR="${DATA_PERSIST_ROOT}/wps_outputs"