spread dois on Wed Mar 11 12:11:23 UTC 2020

.github/workflows/biii-import.yaml

@@ -0,0 +1,45 @@
+name: import Neubias biii.eu content
+
+on:
+  push:
+  #schedule:
+  #  - cron: '40 10 * * * '
+
+jobs:
+
+  build-biii-raw-bioschemas:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{ github.head_ref }}
+    - uses: geertvdc/setup-hub@master
+    - name: Setup Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: "3.7"
+    - name: Install dependencies
+      run:
+        pip install -r scripts/neubias/requirements.txt
+    - name: dump Neubias biii.eu data as bioschemas and raw files
+      run: |
+        cd scripts/neubias
+        python biseEU_LD_export.py -td http://test.biii.eu -dump
+    - name: commit new data and push to new PR
+      env:
+        GITHUB_USER: ${{ secrets.GITHUB_USER }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        git config --local user.email "tpe-bot@github.com"
+        git config --local user.name "Tools Platform Ecosystem bot"
+        cd data
+        git add .
+        if git commit -m "import from neubias biii.eu on $(date)"; then
+          git checkout -b biii_import_${{ github.run_id }}
+          hub pull-request -m "import from biii.eu on $(date)"
+          echo "successfully created new data"
+        else
+            echo "nothing new to add, exiting"
+        fi

.github/workflows/bioschemas-build.yml

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+name: build bioschemas jsonld from bio.tools files
+
+on:
+  pull_request:
+    types: [assigned, opened, synchronize, reopened]
+  issue_comment:
+    types: [created]
+
+jobs:
+
+  build-bioschemas:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{ github.head_ref }}
+    - uses: geertvdc/setup-hub@master
+    - name: test if pull-request (automated) or pull-request comment with "bioschemas"
+      if: github.event_name == 'pull_request' && github.event.action == 'unassigned'
+      uses: Khan/pull-request-comment-trigger@1.0.0
+      with:
+        # The string to look for in pull-request descriptions and comments. For example "#build/android"
+        trigger: bioschemas
+    - name: Setup Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: "3.7"
+    - name: Install dependencies
+      run:
+        pip install -r scripts/bioschemas/requirements.txt
+    - name: publish bio.tools data as bioschemas files
+      run: |
+        cd scripts/bioschemas
+        python biotools_to_bioschemas.py
+    - name: commit new data
+      env:
+        GITHUB_USER: ${{ secrets.GITHUB_USER }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        cd data
+        git config --local user.email "tpe-bot@github.com"
+        git config --local user.name "Tools Platform Ecosystem bot"
+        git add .
+        if git commit -m "build bioschemas on $(date)"; then
+            git push origin HEAD
+            echo "successfully created new data"
+        else
+            echo "nothing new to add, exiting"            
+        fi

.github/workflows/biotools-import.yml

@@ -0,0 +1,41 @@
+name: import bio.tools contents
+
+on: 
+  push:
+  schedule:
+    - cron: '0 0 * * * '
+
+jobs:
+  import-biotools:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: geertvdc/setup-hub@master
+    - name: Setup Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: "3.7"
+    - name: Install dependencies
+      run:
+        pip install -r scripts/biotools-import/requirements.txt
+    - name: import bio.tools using the API
+      run: |
+        cd scripts/biotools-import
+        python import.py
+    - name: commit new data and push to new PR
+      env:
+        GITHUB_USER: ${{ secrets.GITHUB_USER }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |  
+        git config --local user.email "tpe-bot@github.com"
+        git config --local user.name "Tools Platform Ecosystem bot"
+        cd data
+        git add .
+        if git commit -m "import from bio.tools on $(date)"; then
+          git checkout -b biotools_import_${{ github.run_id }}
+          git push --set-upstream origin "biotools_import_${{ github.run_id }}"
+          hub pull-request -m "import from bio.tools on $(date)"
+          echo "successfully created new data"
+        else
+            echo "nothing new to add, exiting"
+        fi

.github/workflows/biotools-pullrequest-analyzer.yml

@@ -0,0 +1,51 @@
+name: analyze how many biotools have change on pullrequest
+
+on:
+  pull_request:
+
+jobs:
+  analyze:
+    name: Analyze biotools differences 
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: analyze biotools difference
+      env:
+        GITHUB_USER: ${{ secrets.GITHUB_USER }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        sudo apt install python3-pip
+        sudo apt install python3-setuptools git
+        pip3 install gitpython
+        git remote add biotools-content${{ github.run_id }} https://github.com/bio-tools/content.git
+        git fetch biotools-content${{ github.run_id }}
+        git fetch origin pull/${{ github.event.number }}/head:${{ github.run_id }}
+        git checkout ${{ github.run_id }}
+        python3 scripts/biotools-pullrequest-bot/biotools_pullrequest_analyzer.py $GITHUB_WORKSPACE biotools-content${{ github.run_id }}/master ${{ github.run_id }} > output.txt
+        cat output.txt
+    - name: Upload output
+      uses: actions/upload-artifact@v1
+      with:
+          name: output
+          path: output.txt
+  comment:
+    needs: analyze
+    name: Add PR comments
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Download output
+        uses: actions/download-artifact@v1
+        with:
+          name: output
+      - name: copy output to workflow dir
+        run: |
+         cat /home/runner/work/content/content/output/output.txt
+         mkdir -p .github/workflows/
+         cp /home/runner/work/content/content/output/output.txt .github/workflows/output.txt 
+      - name: comment under pr  
+        uses: harupy/comment-on-pr@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          filename: output.txt

.github/workflows/biotools-testrunregistry.yml

@@ -0,0 +1,54 @@
+name: launch a test bio.tools server and perform import tests
+
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+
+  build-bioschemas:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{ github.head_ref }}
+    - uses: geertvdc/setup-hub@master
+    - name: test if pull-request (automated) or pull-request comment with "bioschemas"
+      if: github.event_name == 'pull_request' && github.event.action == 'unassigned'
+      uses: Khan/pull-request-comment-trigger@1.0.0
+      with:
+        # The string to look for in pull-request descriptions and comments. For example "#build/android"
+        trigger: runbiotools
+    - name: checkout bio.tools registry
+      uses: actions/checkout@v2
+      with:
+        # Repository name with owner. For example, actions/checkout
+        # Default: ${{ github.repository }}
+        repository: 'bio-tools/biotoolsRegistry'
+        path: ${{ github.repository }}/biotoolsRegistry
+    - name: Shutdown Ubuntu MySQL (SUDO)
+      run: sudo service mysql stop # Shutdown the Default MySQL, "sudo" is necessary, please not remove it
+    - name: build docker containers for bio.tools registry
+      run: |
+        cd ${{ github.repository }}/biotoolsRegistry
+        docker-compose build
+    - name: run docker containers for bio.tools registry
+      run: |
+        cd ${{ github.repository }}/biotoolsRegistry
+        docker-compose up -d
+    - name: setup running docker containers for bio.tools registry
+      run: |
+        cd ${{ github.repository }}/biotoolsRegistry
+        docker cp initial_db.sql biotools-mysql:/root
+        docker cp load_initial_db.sh biotools-mysql:/root
+        docker exec biotools-mysql bash /root/load_initial_db.sh
+        docker exec biotools-backend python manage.py makemigrations
+        docker exec biotools-backend python manage.py migrate
+        docker exec biotools-backend python manage.py es_purge
+        docker exec biotools-backend python manage.py es_regenerate
+    - name: test that bio.tools registry is up and running
+      run:
+        cd /tmp
+        wget --spider http://localhost:8000

.github/workflows/debian-yaml-validator.yaml

@@ -0,0 +1,21 @@
+name: validate debian yaml files
+
+on: 
+  push:
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron:  '00 20 * * *'
+jobs:
+  validate:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: validate debian yaml files
+      run: |
+        sudo apt install python3-pip
+        sudo apt install python3-setuptools
+        sudo pip3 install virtualenv
+        cd scripts/files-validator/
+        python3 debian_validator.py $GITHUB_WORKSPACE/data/

.github/workflows/doi-load.yaml

@@ -0,0 +1,43 @@
+
+name: spread doi among sources
+
+on: 
+  push:
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron:  '00 20 * * *'
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: geertvdc/setup-hub@master
+    - name: spread doi among sources
+      env:
+        GITHUB_USER: ${{ secrets.GITHUB_USER }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        sudo apt install python3-pip
+        sudo apt install python3-setuptools
+        sudo pip3 install virtualenv
+        virtualenv -p python3 venv
+        . venv/bin/activate	
+        pip3 install setuptools wheel
+        pip3 install ruamel.yaml
+        pwd
+        cd scripts/doi-collector
+        python3 doi_collector.py $GITHUB_WORKSPACE/data/
+        cd ../../data
+        git config --local user.email "tpe-bot@github.com"
+        git config --local user.name "Tools Platform Ecosystem bot"
+        git add .
+        if git commit -m "spread dois on $(date)"; then
+          git checkout -b doi_update${{ github.run_id }}
+          git push --set-upstream origin "doi_update${{ github.run_id }}"
+          hub pull-request -m "spread dois on $(date)"
+          echo "successfully created new data"
+        else
+            echo "nothing new to add, exiting"
+        fi

data/-cnn/-cnn.oeb.json

@@ -0,0 +1,60 @@
+
+{
+    "credit": [
+    ],
+    "function": [
+        {
+            "operation": [
+                {
+                    "term": "Peak detection",
+                    "uri": "http://edamontology.org/operation_3215"
+                },
+                {
+                    "term": "Peak calling",
+                    "uri": "http://edamontology.org/operation_3222"
+                },
+                {
+                    "term": "Pathway or network prediction",
+                    "uri": "http://edamontology.org/operation_3439"
+                }
+            ]
+        }
+    ],
+    "labels": {
+        "language": [
+            "Python"
+        ],
+        "license": "MIT",
+        "topic": [
+            {
+                "term": "ChIP-seq",
+                "uri": "http://edamontology.org/topic_3169"
+            },
+            {
+                "term": "Transcription factors and regulatory sites",
+                "uri": "http://edamontology.org/topic_0749"
+            },
+            {
+                "term": "Machine learning",
+                "uri": "http://edamontology.org/topic_3474"
+            },
+            {
+                "term": "Epigenetics",
+                "uri": "http://edamontology.org/topic_3295"
+            }
+        ]
+    },
+    "publication": [
+        {
+            "doi": "10.1093/BIOINFORMATICS/BTZ843",
+            "pmid": "31742318"
+        }
+    ],
+    "summary": {
+        "biotoolsCURIE": "biotools:-CNN",
+        "biotoolsID": "-CNN",
+        "description": "An Integrative Approach for Fine-Mapping Chromatin Interactions.\n\nComputational method for fine-mapping chromatin interactions, e.g., Hi-C.\n\n||| CORRECT NAME OF TOOL COULD ALSO BE 'CNN', 'Hi-C'",
+        "homepage": "https://github.com/ernstlab/X-CNN",
+        "name": "-CNN"
+    }
+}