Add scripts to extract workflows from WorkflowHub and UseGalaxy servers

.github/workflows/fetch_filter_resources.yaml

@@ -101,6 +101,12 @@ jobs:
       - name: Generate wordcloud and interactive table
         run: |
           bash sources/bin/format_tools.sh
+      - name: Fetch all workflows
+        run: | 
+          bash sources/bin/extract_all_workflows.sh 
+      - name: Filter workflows for communities
+        run: | 
+          bash sources/bin/get_community_workflows.sh
       - name: Fetch all tutorials
         run: | 
           bash sources/bin/extract_all_tutorials.sh

.github/workflows/lint.yaml

@@ -6,14 +6,11 @@ concurrency:
 jobs:
   lint:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.11']
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: ${{ matrix.python-version }}
+          python-version: '3.11'
     - name: Install tox
       run: python -m pip install 'tox>=1.8.0'
     - name: Lint

.github/workflows/run_tests.yaml

@@ -1,16 +1,19 @@
 name: Run tests
-on: [push, pull_request_target]
+on: [push, pull_request]
 
 jobs:
   test-tools:
     runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: ['3.11']
     environment: fetch-tools
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: ${{ matrix.python-version }}
       - name: Install requirement
         run: python -m pip install -r requirements.txt
       - name: Tool extraction
@@ -26,12 +29,15 @@ jobs:
           bash sources/bin/format_tools.sh
   test-tutorials:
     runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: ['3.11']
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: ${{ matrix.python-version }}
       - name: Install requirement
         run: python -m pip install -r requirements.txt
       - name: Tutorial extraction
@@ -41,4 +47,23 @@ jobs:
           PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }}
       - name: Tutorial filtering
         run: | 
-          bash sources/bin/get_community_tutorials.sh test
+          bash sources/bin/get_community_tutorials.sh test
+  test-workflows:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install requirement
+        run: python -m pip install -r requirements.txt
+      - name: Workflow extraction
+        run: | 
+          bash sources/bin/extract_all_workflows.sh test
+      - name: Workflow filtering
+        run: | 
+          bash sources/bin/get_community_workflows.sh test

README.md

@@ -6,4 +6,4 @@ Galaxy Communities Dock aka Galaxy Codex is a catalog of Galaxy resources (tools
 This repository stores the sources to build this catalog. The catalog is automatically updated every week.
 
 
-Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN toturial**. 
+Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN tutorial**. 

communities/microgalaxy/metadata/workflow_tags

@@ -0,0 +1,15 @@
+name:microgalaxy
+bacteria
+bacterial-genomics
+antimicrobial-resistance
+metagenomics
+virology
+amr
+microbiome
+asaim
+pathogfair
+abromics
+bacterial
+microgalaxy
+name:metatranscriptomics
+name:amplicon

pyproject.toml

@@ -7,10 +7,12 @@ include = '\.pyi?$'
 isort = true
 
 [tool.ruff]
+target-version = "py38"
+
+[tool.ruff.lint]
 # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
 # flake8-logging-format (G) and pyupgrade (UP)
 select = ["E", "F", "B", "G", "UP"]
-target-version = "py38"
 # Exceptions:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # B9 flake8-bugbear opinionated warnings

sources/README.md

@@ -240,6 +240,20 @@ To make a test run of the tool to check its functionalities follow [Usage](#Usag
     $ bash sources/bin/get_community_tutorials.sh test
     ```
 
+### Workflows
+
+1. Workflow extraction
+
+    ```bash
+    $ bash bin/extract_all_workflows.sh test 
+    ```
+
+2. Workflow filtering
+
+    ```bash
+    $ bash bin/get_community_workflowss.sh test
+    ```
+
 # Galaxy Labs framework
 
 ## What is a Galaxy Lab?

sources/bin/extract_all_workflows.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+if [ ! -z $1 ] 
+then
+        python sources/bin/extract_galaxy_workflows.py extract \
+                --all communities/all/resources/workflows.json \
+                --tools communities/all/resources/tools.json \
+                --test
+else
+        python sources/bin/extract_galaxy_workflows.py extract \
+                --all communities/all/resources/workflows.json \
+                --tools communities/all/resources/tools.json
+fi