Merge branch 'main' into deploy-results-to-different-branch

galaxyproject · Jul 18, 2024 · a7d8855 · a7d8855
2 parents 5f8f62a + 08b1ba1
commit a7d8855
Show file tree

Hide file tree

Showing 4 changed files with 49 additions and 14 deletions.
diff --git a/.github/workflows/fetch_all_tools.yaml b/.github/workflows/fetch_all_tools.yaml
@@ -20,8 +20,18 @@ jobs:
     runs-on: ubuntu-20.04
     name: Fetch list of all available servers
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout main
+        uses: actions/checkout@v4
+        with:
+          ref: main #pull latest code produced by job 1, not the revision that started the workflow (https://github.com/actions/checkout/issues/439)
+      - name: Checkout results
+        uses: actions/checkout@v4
+        with:
+          ref: results
+          path: results
       - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
       - name: Install requirement
         run: python -m pip install -r requirements.txt
       - name: Run script 
@@ -42,14 +52,22 @@ jobs:
     name: Fetch all tool stepwise
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.11]
         subset:
          - repositories01.list
          - repositories02.list
          - repositories03.list
          - repositories04.list
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout main
+        uses: actions/checkout@v4
+        with:
+          ref: main #pull latest code produced by job 1, not the revision that started the workflow (https://github.com/actions/checkout/issues/439)
+      - name: Checkout results
+        uses: actions/checkout@v4
+        with:
+          ref: results
+          path: results
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
@@ -84,6 +102,8 @@ jobs:
         ref: results
         path: results
     - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
     - name: Install requirement
       run: |
         python -m pip install -r requirements.txt

diff --git a/.github/workflows/fetch_all_tutorials.yaml b/.github/workflows/fetch_all_tutorials.yaml
@@ -21,7 +21,15 @@ jobs:
     environment: fetch-tutorials
     name: Fetch all tutorials
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout main
+        uses: actions/checkout@v4
+        with:
+          ref: main #pull latest code produced by job 1, not the revision that started the workflow (https://github.com/actions/checkout/issues/439)
+      - name: Checkout results
+        uses: actions/checkout@v4
+        with:
+          ref: results
+          path: results
       - uses: actions/setup-python@v5
         with:
           python-version: '3.11'

diff --git a/.github/workflows/filter_communities.yaml b/.github/workflows/filter_communities.yaml
@@ -39,7 +39,7 @@ jobs:
         path: results
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.8' 
+        python-version: '3.11' 
     - name: Install requirement
       run: python -m pip install -r requirements.txt
     - name: Run script
@@ -66,10 +66,10 @@ jobs:
       uses: actions/checkout@v4
       with:
         ref: results
-        sparse-checkout: results
+        path: results
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.8' 
+        python-version: '3.11' 
     - name: Install requirement
       run: python -m pip install -r requirements.txt
     - name: Run script
@@ -96,10 +96,10 @@ jobs:
       uses: actions/checkout@v4
       with:
         ref: results
-        sparse-checkout: results
+        path: results
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.8' 
+        python-version: '3.11' 
     - name: Install requirement
       run: python -m pip install -r requirements.txt
     - name: Run script

diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py
@@ -761,9 +761,16 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]:
 
         # filter tool lists
         ts_filtered_tools, filtered_tools = filter_tools(tools, categories, status)
-        export_tools_to_tsv(ts_filtered_tools, args.ts_filtered, format_list_col=True)
-        # if there are no filtered tools return the ts filtered tools
-        if filtered_tools:
-            export_tools_to_tsv(filtered_tools, args.filtered, format_list_col=True)
+
+        if ts_filtered_tools:
+
+            export_tools_to_tsv(ts_filtered_tools, args.ts_filtered, format_list_col=True)
+            # if there are no filtered tools return the ts filtered tools
+            if filtered_tools:
+                export_tools_to_tsv(filtered_tools, args.filtered, format_list_col=True)
+            else:
+                export_tools_to_tsv(ts_filtered_tools, args.filtered, format_list_col=True)
+
         else:
-            export_tools_to_tsv(ts_filtered_tools, args.filtered, format_list_col=True)
+            # if there are no ts filtered tools
+            print(f"No tools found for category {args.filtered}")