Merge pull request #15 from paulzierep/deploy-results-to-different-br…

…anch

Deploy results to different branch

.github/workflows/fetch_all_tools.yaml

@@ -16,42 +16,13 @@ permissions:
   contents: write
 
 jobs:
-  fetch-available-servers:
-    runs-on: ubuntu-20.04
-    name: Fetch list of all available servers
-    steps:
-      - 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 
-        run: | 
-          python bin/get_public_galaxy_servers.py -o results/available_public_servers.csv
-      - name: Commit servers 
-        uses: s0/git-publish-subdir-action@develop
-        env:
-          BRANCH: results
-          FOLDER: results
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          REPO: self
-          SKIP_EMPTY_COMMITS: true
 
   fetch-all-tools-stepwise:
     runs-on: ubuntu-20.04
     environment: fetch-tools
     name: Fetch all tool stepwise
     strategy:
-      max-parallel: 1
+      max-parallel: 1 #need to run one after another, since otherwise there is a chance, that mulitple jobs want to push to the results branch at the same time (which fails due to merge)
       matrix:
         python-version: [3.11]
         subset:

.github/workflows/utilities.yml

@@ -0,0 +1,46 @@
+name: Utilities
+on:
+  workflow_dispatch:
+  schedule:
+    #Every Sunday at 7:00 am
+    - cron: "0 7 * * 0" 
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "tools"
+  cancel-in-progress: false
+
+permissions:
+  contents: write
+
+jobs:
+    fetch-available-servers:
+      runs-on: ubuntu-20.04
+      name: Fetch list of all available servers
+      steps:
+        - 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 
+          run: | 
+            python bin/get_public_galaxy_servers.py -o results/available_public_servers.csv
+        - name: Commit servers 
+          uses: s0/git-publish-subdir-action@develop
+          env:
+            BRANCH: results
+            FOLDER: results
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            REPO: self
+            SKIP_EMPTY_COMMITS: true

README.md

@@ -77,7 +77,7 @@ A GitHub action performs every week the following steps:
 3. Run the script to extract all tools
 
     ```
-    $ python bin/extract_all_tools.sh
+    $ bash bin/extract_all_tools.sh
     ```
 
 The script will generate a TSV file with each tool found in the list of GitHub repositories and metadata for these tools:
@@ -152,7 +152,7 @@ A GitHub action performs every week the following steps:
 3. Run the script
 
     ```
-    $ python bin/extract_all_tutorials.sh
+    $ bash bin/extract_all_tutorials.sh
     ```
 
 ## Filter tutorials based on tags outside a GitHub Action

bin/extract_all_tools.sh

@@ -4,7 +4,7 @@ mkdir -p 'results/'
 
 if [ ! -z $1 ] 
 then 
-        if [ $1=="test" ]
+        if [ $1 == "test" ]
         then 
                 echo "Test tool extraction"
                 python bin/extract_galaxy_tools.py \

bin/get_community_tools.sh

@@ -3,7 +3,7 @@
 # stop on error
 set -e 
 
-if [[ ! -z $1  && $1=="test" ]]; then
+if [[ ! -z $1  && $1 == "test" ]]; then
         python bin/extract_galaxy_tools.py \
                 filter \
                 --all "results/all_tools.json" \