Merge branch 'main' into add_media

tethysplatform · Apr 15, 2024 · 7302123 · 7302123
2 parents 5b41419 + 9d5c55b
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diff --git a/.github/workflows/tethys-release.yml b/.github/workflows/tethys-release.yml
@@ -137,7 +137,7 @@ jobs:
           cd ..
           . ~/miniconda/etc/profile.d/conda.sh;
           conda activate tethys;
-          tethys gen metayaml -p minor --overwrite;
+          tethys gen metayaml -p ${CONDA_BUILD_PIN_LEVEL} --overwrite;
       # Show Tethys Meta
       - name: Show Tethys Meta
         run: |
@@ -179,7 +179,7 @@ jobs:
           cd ..
           . ~/miniconda/etc/profile.d/conda.sh;
           conda activate tethys;
-          tethys gen metayaml -p minor --micro --overwrite;
+          tethys gen metayaml -p ${CONDA_BUILD_PIN_LEVEL} --micro --overwrite;
       # Show Tethys Meta
       - name: Show Tethys Meta - micro
         run: |

diff --git a/Dockerfile b/Dockerfile
@@ -3,6 +3,7 @@ FROM mambaorg/micromamba:bullseye
 # BUILD ARGUMENTS #
 ###################
 ARG PYTHON_VERSION=3.*
+ARG MICRO_TETHYS=false
 
 ###############
 # ENVIRONMENT #
@@ -14,6 +15,7 @@ ENV TETHYS_APPS_ROOT="/var/www/tethys/apps"
 ENV TETHYS_PORT=8000
 ENV NGINX_PORT=80
 ENV POSTGRES_PASSWORD="pass"
+ENV SKIP_DB_SETUP=false
 ENV TETHYS_DB_ENGINE='django.db.backends.postgresql'
 ENV TETHYS_DB_NAME='tethys_platform'
 ENV TETHYS_DB_USERNAME="tethys_default"
@@ -114,14 +116,14 @@ RUN echo "force-unsafe-io" > /etc/dpkg/dpkg.cfg.d/02apt-speedup \
 
 # Install APT packages
 RUN rm -rf /var/lib/apt/lists/*\
- && apt-get update \
- && apt-get -y install curl \
- && mkdir /etc/apt/keyrings \
- && curl -fsSL -o /etc/apt/keyrings/salt-archive-keyring-2023.gpg https://repo.saltproject.io/salt/py3/debian/11/amd64/SALT-PROJECT-GPG-PUBKEY-2023.gpg \
- && echo "deb [signed-by=/etc/apt/keyrings/salt-archive-keyring-2023.gpg arch=amd64] https://repo.saltproject.io/salt/py3/debian/11/amd64/latest bullseye main" | tee /etc/apt/sources.list.d/salt.list \
- && apt-get update \
- && apt-get -y install bzip2 git nginx supervisor gcc salt-minion procps pv \
- && rm -rf /var/lib/apt/lists/*
+  && apt-get update \
+  && apt-get -y install curl \
+  && mkdir /etc/apt/keyrings \
+  && curl -fsSL -o /etc/apt/keyrings/salt-archive-keyring-2023.gpg https://repo.saltproject.io/salt/py3/debian/11/amd64/SALT-PROJECT-GPG-PUBKEY-2023.gpg \
+  && echo "deb [signed-by=/etc/apt/keyrings/salt-archive-keyring-2023.gpg arch=amd64] https://repo.saltproject.io/salt/py3/debian/11/amd64/latest bullseye main" | tee /etc/apt/sources.list.d/salt.list \
+  && apt-get update \
+  && apt-get -y install bzip2 git nginx supervisor gcc salt-minion procps pv \
+  && rm -rf /var/lib/apt/lists/*
 
 # Remove default NGINX site
 RUN rm -f /etc/nginx/sites-enabled/default
@@ -132,10 +134,21 @@ RUN ln -s /bin/micromamba ${CONDA_HOME}/bin/conda
 
 # Setup Conda Environment
 COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml ${TETHYS_HOME}/tethys/
+COPY --chown=$MAMBA_USER:$MAMBA_USER micro_environment.yml ${TETHYS_HOME}/tethys/
+
 WORKDIR ${TETHYS_HOME}/tethys
-RUN sed -i "s/- python$/- python=${PYTHON_VERSION}/g" environment.yml \
- && micromamba create -n "${CONDA_ENV_NAME}" --yes --file "environment.yml" \
- && micromamba clean --all --yes
+
+RUN if [ "${MICRO_TETHYS}" = "true" ]; then \
+  sed -i "s/- python$/- python=${PYTHON_VERSION}/g" micro_environment.yml && \
+  micromamba create -n "${CONDA_ENV_NAME}" --yes --file "micro_environment.yml" && \
+  micromamba clean --all --yes && \
+  rm -rf environment.yml; \
+  else \
+  sed -i "s/- python$/- python=${PYTHON_VERSION}/g" environment.yml && \
+  micromamba create -n "${CONDA_ENV_NAME}" --yes --file "environment.yml" && \
+  micromamba clean --all --yes && \
+  rm -rf micro_environment.yml; \
+  fi
 
 ###########
 # INSTALL #

diff --git a/docker/run.sh b/docker/run.sh
@@ -12,6 +12,8 @@ db_max_count=24;
 no_daemon=true;
 skip_perm=false;
 test=false;
+db_engine=${TETHYS_DB_ENGINE} # Get the DB engine from environment variable
+skip_db_setup=${SKIP_DB_SETUP} # Get the DB setup flag from environment variable
 USAGE="USAGE: . run.sh [options]
 OPTIONS:
 --background              \t run supervisord in background.
@@ -44,32 +46,42 @@ done
 
 echo_status "Starting up..."
 
-# Create Salt Config
-echo "file_client: local" > /etc/salt/minion
-echo "postgres.host: '${TETHYS_DB_HOST}'" >> /etc/salt/minion
-echo "postgres.port: '${TETHYS_DB_PORT}'" >> /etc/salt/minion
-echo "postgres.user: '${TETHYS_DB_USERNAME}'" >> /etc/salt/minion
-echo "postgres.pass: '${TETHYS_DB_PASSWORD}'" >> /etc/salt/minion
-echo "postgres.bins_dir: '${CONDA_HOME}/envs/${CONDA_ENV_NAME}/bin'" >> /etc/salt/minion
 
 if [[ $test = false ]]; then
   # Set extra ENVs
   export NGINX_USER=$(grep 'user .*;' /etc/nginx/nginx.conf | awk '{print $2}' | awk -F';' '{print $1}')
 
   # Apply States
-  echo_status "Checking if DB is ready"
-
-  db_check_count=0
-
-  until ${CONDA_HOME}/envs/${CONDA_ENV_NAME}/bin/pg_isready -h ${TETHYS_DB_HOST} -p ${TETHYS_DB_PORT} -U postgres; do
-    if [[ $db_check_count -gt $db_max_count ]]; then
-      >&2 echo "DB was not available in time - exiting"
-      exit 1
+  if [[ $skip_db_setup != true ]]; then
+    echo_status "Checking if DB is ready"
+    if [[ $db_engine == "django.db.backends.postgresql" ]]; then
+        # Create Salt Config for PostgreSQL
+        echo "postgres.host: '${TETHYS_DB_HOST}'" >> /etc/salt/minion
+        echo "postgres.port: '${TETHYS_DB_PORT}'" >> /etc/salt/minion
+        echo "postgres.user: '${TETHYS_DB_USERNAME}'" >> /etc/salt/minion
+        echo "postgres.pass: '${TETHYS_DB_PASSWORD}'" >> /etc/salt/minion
+        echo "postgres.bins_dir: '${CONDA_HOME}/envs/${CONDA_ENV_NAME}/bin'" >> /etc/salt/minion
+
+        db_check_count=0
+
+        until ${CONDA_HOME}/envs/${CONDA_ENV_NAME}/bin/pg_isready -h ${TETHYS_DB_HOST} -p ${TETHYS_DB_PORT} -U postgres; do
+          if [[ $db_check_count -gt $db_max_count ]]; then
+            >&2 echo "DB was not available in time - exiting"
+            exit 1
+          fi
+          >&2 echo "DB is unavailable - sleeping"
+          db_check_count=`expr $db_check_count + 1`
+          sleep 5
+        done
+
+
+    else
+      echo_status "Using SQLite3 as the database"
     fi
-    >&2 echo "DB is unavailable - sleeping"
-    db_check_count=`expr $db_check_count + 1`
-    sleep 5
-  done
+  else
+    # Database setup should be skipped
+    echo "Skipping database setup: check SKIP_DB_SETUP environment variable."
+  fi
 fi
 
 echo_status "Enforcing start state... (This might take a bit)"

diff --git a/docker/salt/tethyscore.sls b/docker/salt/tethyscore.sls
@@ -14,6 +14,7 @@
 {% set POSTGRES_PASSWORD = salt['environ.get']('POSTGRES_PASSWORD') %}
 {% set TETHYS_DB_PORT = salt['environ.get']('TETHYS_DB_PORT') %}
 {% set TETHYS_DB_USERNAME = salt['environ.get']('TETHYS_DB_USERNAME') %}
+{% set SKIP_DB_SETUP = salt['environ.get']('SKIP_DB_SETUP') %}
 {% set TETHYS_HOME = salt['environ.get']('TETHYS_HOME') %}
 {% set TETHYS_PORT = salt['environ.get']('TETHYS_PORT') %}
 {% set OTHER_SETTINGS = salt['environ.get']('OTHER_SETTINGS') %}
@@ -72,20 +73,12 @@
 
 {% set TETHYS_SITE_CONTENT = TETHYS_SITE_CONTENT_LIST|join(' ') %}
 
-
-
 Generate_Tethys_Settings_TethysCore:
   cmd.run:
     - name: >
         tethys settings
         --set DEBUG {{ DEBUG }}
         --set ALLOWED_HOSTS {{ ALLOWED_HOSTS }}
-        --set DATABASES.default.ENGINE "{{ TETHYS_DB_ENGINE }}"
-        --set DATABASES.default.NAME "{{ TETHYS_DB_NAME }}"
-        --set DATABASES.default.USER "{{ TETHYS_DB_USERNAME }}"
-        --set DATABASES.default.PASSWORD "{{ TETHYS_DB_PASSWORD }}"
-        --set DATABASES.default.HOST "{{ TETHYS_DB_HOST }}"
-        --set DATABASES.default.PORT "{{ TETHYS_DB_PORT }}"
         --set INSTALLED_APPS {{ ADD_DJANGO_APPS }}
         --set SESSION_CONFIG.SECURITY_WARN_AFTER {{ SESSION_WARN }}
         --set SESSION_CONFIG.SECURITY_EXPIRE_AFTER {{ SESSION_EXPIRE }}
@@ -102,6 +95,24 @@ Generate_Tethys_Settings_TethysCore:
         --set CHANNEL_LAYERS.default.CONFIG {{ CHANNEL_LAYERS_CONFIG }}
         --set CAPTCHA_CONFIG.RECAPTCHA_PRIVATE_KEY "{{ RECAPTCHA_PRIVATE_KEY }}"
         --set CAPTCHA_CONFIG.RECAPTCHA_PUBLIC_KEY "{{ RECAPTCHA_PUBLIC_KEY }}"
+        {%- if TETHYS_DB_ENGINE %}
+        --set DATABASES.default.ENGINE "{{ TETHYS_DB_ENGINE }}"
+        {%- endif %}
+        {%- if TETHYS_DB_NAME %}
+        --set DATABASES.default.NAME "{{ TETHYS_DB_NAME }}"
+        {%- endif %}
+        {%- if TETHYS_DB_USERNAME %}
+        --set DATABASES.default.USER "{{ TETHYS_DB_USERNAME }}"
+        {%- endif %}
+        {%- if TETHYS_DB_PASSWORD %}
+        --set DATABASES.default.PASSWORD "{{ TETHYS_DB_PASSWORD }}"
+        {%- endif %}          
+        {%- if TETHYS_DB_HOST %}
+        --set DATABASES.default.HOST "{{ TETHYS_DB_HOST }}"
+        {%- endif %}
+        {%- if TETHYS_DB_PORT %}
+        --set DATABASES.default.PORT "{{ TETHYS_DB_PORT }}"
+        {%- endif %}                   
         {{ OTHER_SETTINGS }}
     - unless: /bin/bash -c "[ -f "{{ TETHYS_PERSIST }}/setup_complete" ];"
 
@@ -144,6 +155,7 @@ Generate_ASGI_Service_TethysCore:
     - replace: False
     - makedirs: True
 
+{% if TETHYS_DB_ENGINE == 'django.db.backends.postgresql' %}
 Create_Database_User_and_SuperUser_TethysCore:
   cmd.run:
     - name: >
@@ -153,7 +165,8 @@ Create_Database_User_and_SuperUser_TethysCore:
         -N "{{ TETHYS_DB_SUPERUSER }}"
         -P "{{ TETHYS_DB_SUPERUSER_PASS }}"
     - shell: /bin/bash
-    - unless: /bin/bash -c "[ -f "{{ TETHYS_PERSIST }}/setup_complete" ];"
+    - unless: /bin/bash -c "[ -f '{{ TETHYS_PERSIST }}/setup_complete' ] || {{ SKIP_DB_SETUP | lower }};"
+{% endif %}
 
 Migrate_Database_TethysCore:
   cmd.run:

diff --git a/docs/installation/production/docker/tethys_docker_reference.rst b/docs/installation/production/docker/tethys_docker_reference.rst
@@ -98,6 +98,8 @@ Use these build arguments with the ``build`` command to customize how the image
 +===========================+==========================================================================================+
 | PYTHON_VERSION            | The version of Python to build the Tethys environment with. Defaults to "3.*".           |
 +---------------------------+------------------------------------------------------------------------------------------+
+| MICRO_TETHYS              | Set to True to use `micro-tethys` environment. Defaults to False.                        |
++---------------------------+------------------------------------------------------------------------------------------+
 
 Important Paths
 ---------------
@@ -142,32 +144,34 @@ Database Parameters
 
 These environment variables are used to configure the database and database users Tethys Portal will use. If the database doesn't exist, then it will be created using the ``postgres`` user.
 
-+---------------------------+------------------------------------------------------------------------------------------+
-| Environment Variable      | Description                                                                              |
-+===========================+==========================================================================================+
-| POSTGRES_PASSWORD         | Password of the postgres user. Used to initialize the Tethys Portal database.            |
-|                           | Defaults to "pass".                                                                      |
-+---------------------------+------------------------------------------------------------------------------------------+
-| TETHYS_DB_HOST            | Host of the database server where the primary Tethys Portal database resides.            |
-|                           | Defaults to "db".                                                                        |
-+---------------------------+------------------------------------------------------------------------------------------+
-| TETHYS_DB_PORT            | Port of the database server where the primary Tethys Portal database resides.            |
-|                           | Defaults to "5432".                                                                      |
-+---------------------------+------------------------------------------------------------------------------------------+
-| TETHYS_DB_ENGINE          | Type of database backend to use for the primary Tethys Portal database.                  |
-|                           | Defaults to "django.db.backends.postgresql".                                             |
-+---------------------------+------------------------------------------------------------------------------------------+
-| TETHYS_DB_NAME            | Name of the primary Tethys Portal database. Defaults to "tethys_platform".               |
-+---------------------------+------------------------------------------------------------------------------------------+
-| TETHYS_DB_USERNAME        | Username of the owner of the primary Tethys Portal database.                             |
-|                           | Defaults to "tethys_default".                                                            |
-+---------------------------+------------------------------------------------------------------------------------------+
-| TETHYS_DB_PASSWORD        | Password of the owner of the primary Tethys Portal database. Defaults to "pass".         |
-+---------------------------+------------------------------------------------------------------------------------------+
-| TETHYS_DB_SUPERUSER       | Name of the database superuser used by Tethys Portal. Defaults to "tethys_super".        |
-+---------------------------+------------------------------------------------------------------------------------------+
-| TETHYS_DB_SUPERUSER_PASS  | Password of the database superuser used by Tethys Portal. Defaults to "pass".            |
-+---------------------------+------------------------------------------------------------------------------------------+
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| Environment Variable     | Description                                                                                                                         |
++==========================+=====================================================================================================================================+
+|| POSTGRES_PASSWORD       || Password of the postgres user. Used to initialize the Tethys Portal database.                                                      |
+||                         || Defaults to "pass".                                                                                                                |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+|| TETHYS_DB_HOST          || Host of the database server where the primary Tethys Portal database resides.                                                      |
+||                         || Defaults to "db".                                                                                                                  |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+|| TETHYS_DB_PORT          || Port of the database server where the primary Tethys Portal database resides.                                                      |
+||                         || Defaults to "5432".                                                                                                                |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+|| TETHYS_DB_ENGINE        || Type of database backend to use for the primary Tethys Portal database.                                                            |
+||                         || Defaults to "django.db.backends.postgresql".                                                                                       |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| TETHYS_DB_NAME           | Name of the primary Tethys Portal database. Defaults to "tethys_platform".                                                          |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+|| TETHYS_DB_USERNAME      || Username of the owner of the primary Tethys Portal database.                                                                       |
+||                         || Defaults to "tethys_default".                                                                                                      |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| TETHYS_DB_PASSWORD       | Password of the owner of the primary Tethys Portal database. Defaults to "pass".                                                    |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| TETHYS_DB_SUPERUSER      | Name of the database superuser used by Tethys Portal. Defaults to "tethys_super".                                                   |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| TETHYS_DB_SUPERUSER_PASS | Password of the database superuser used by Tethys Portal. Defaults to "pass".                                                       |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
+| SKIP_DB_SETUP            | Set to True to skip database creation, useful for existing databases configured for Tethys. Defaults to False.                      |
++--------------------------+-------------------------------------------------------------------------------------------------------------------------------------+
 
 Tethys Portal Admin User
 ------------------------

diff --git a/docs/tethys_portal/admin_pages.rst b/docs/tethys_portal/admin_pages.rst
@@ -309,7 +309,7 @@ Proxy apps are links to external web applications or websites. They are represen
 
 * **Name**: The name of the app that will appear on the app tile on the Apps Library page (e.g.: "My Proxy App").
 * **Endpoint**: The URL that will be opened when the user clicks on the app tile of the proxy app (e.g.: ``https://my.proxy.app/foo/``).
-* **Logo url**: The URL of the image that will be displayed on the app tile of the Proxy App (e.g.: ``https://my.proxy.app/static/foo-logo.org``).
+* **Icon**: Override the icon/logo of the proxy app with a different icon. Accepts a relative path to a static file (e.g.: ``my-first-app/images/other-logo.png``) or a URL to an externally hosted image (e.g.: ``https://some.other-site.org/static/other-logo.png``).
 * **Back url**: A URL to suggest as the back URL; usually points to the referring portal. If the Proxy App is a Tethys App on another Tethys Portal (>4.0.0), the Exit button for the app will be set to this URL (e.g.: ``https://this.portal.org/apps/``).
 * **Description**: A description of the app that will be displayed when the user clicks on the info icon on the app tile.
 * **Tags**: One or more tags for an app. Wrap each tag in double quotes and separate by commas (e.g.: ``"Hydrology","Grided Data","THREDDS"``).

diff --git a/docs/tethys_sdk/app_class.rst b/docs/tethys_sdk/app_class.rst
@@ -104,4 +104,10 @@ Class Methods
 
 .. automethod:: tethys_apps.base.TethysAppBase.create_persistent_store
 
-.. automethod:: tethys_apps.base.TethysAppBase.drop_persistent_store
+.. automethod:: tethys_apps.base.app_base.TethysAppBase.render
+
+.. automethod:: tethys_apps.base.app_base.TethysBase.redirect
+
+.. automethod:: tethys_apps.base.app_base.TethysBase.reverse
+
+.. automethod:: tethys_apps.base.app_base.TethysBase.render_to_string