Merge pull request #133 from oncokb/update-annotation-action

Split github action for annotation tests

.github/workflows/compare-genomic-change-study-annotation.yml

@@ -0,0 +1,93 @@
+# This workflow will install Python dependencies, run annotation against the master annotation for a particular study
+
+name: Compare Study Genomic Change Annotation
+
+on:
+  push:
+    branches:
+      - master
+jobs:
+  build:
+    if: github.repository == 'oncokb/oncokb-annotator'
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8
+          pip install -r requirements/common.txt -r requirements/pip3.txt
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Annotate msk_impact_2017 study
+        id: annotate
+        env:
+          ONCOKB_API_TOKEN: ${{ secrets.ONCOKB_BOT_API_TOKEN }}
+          ONCOKB_OAUTH_TOKEN: ${{ secrets.ONCOKB_OAUTH_TOKEN }}
+        run: |
+          git checkout -b compare
+
+          STUDY=msk_impact_2017
+          DATAHUB_URL=https://media.githubusercontent.com/media/cBioPortal/datahub/42afc279efb8d9104aba36fa35bad3ec41921949/public/$STUDY
+
+          MUTATION_DATA_NAME=data_mutations_extended.txt
+          CLINICAL_DATA_NAME=data_clinical_sample.txt
+
+          cd data
+          curl -s $DATAHUB_URL/$MUTATION_DATA_NAME -O
+          curl -s $DATAHUB_URL/$CLINICAL_DATA_NAME -O
+          cd ..
+
+          # create compare folder to add all annotated files
+          mkdir compare
+
+          PREFIX=oncokb
+
+          OGCMAF="$PREFIX"_genomic_change_$MUTATION_DATA_NAME
+
+          python MafAnnotator.py -i data/$MUTATION_DATA_NAME -o compare/$OGCMAF -c data/$CLINICAL_DATA_NAME -b $ONCOKB_API_TOKEN -q Genomic_Change
+
+          git config user.name oncokb-bot
+          git config user.email dev.oncokb@gmail.com
+
+          git add .
+          git commit -m 'add analysis'
+
+          echo "::set-output name=STUDY::$STUDY"
+          echo "::set-output name=FILE_NAME::$OGCMAF"
+
+      - name: Compare annotation result with the ones from master
+        id: compare
+        env:
+          STUDY: ${{steps.annotate.outputs.STUDY}}
+          FILE_NAME: ${{steps.annotate.outputs.FILE_NAME}}
+          ONCOKB_OAUTH_TOKEN: ${{ secrets.ONCOKB_OAUTH_TOKEN }}
+        run: |
+          # remove everything under compare folder and replace wiht the ones from oncokb-data
+          rm -f compare/*.txt
+
+          cd compare
+          curl -s -H "Authorization: token ${ONCOKB_OAUTH_TOKEN}" https://api.github.com/repos/knowledgesystems/oncokb-data/contents/annotation/$STUDY | jq -r '.[] | .download_url + " " + .name' | while IFS=' ' read -r downloadurl name; do
+            if [[ "$name" == "$FILE_NAME" ]]; then
+              curl -s "$downloadurl" -o $name
+            fi
+          done
+          cd ..
+
+          # compare
+          CHANGED=$(git diff --name-only HEAD --)
+
+          if [ -n "$CHANGED" ]
+          then
+            git diff
+            exit 1
+          fi
+            

.github/workflows/compare-study-annotation.yml

@@ -4,8 +4,8 @@ name: Compare Study Annotation
 
 on:
   push:
-    branches: [ master ]
-
+    branches:
+      - master
 jobs:
   build:
     if: github.repository == 'oncokb/oncokb-annotator'
@@ -57,9 +57,6 @@ jobs:
           IMAF=data/$MUTATION_DATA_NAME
           OMAF=compare/"$PREFIX"_$MUTATION_DATA_NAME
 
-          IGCMAF=data/$MUTATION_DATA_NAME
-          OGCMAF=compare/"$PREFIX"_genomic_change_$MUTATION_DATA_NAME
-
           IC=data/$CLINICAL_DATA_NAME
           OC=compare/"$PREFIX"_$CLINICAL_DATA_NAME
 
@@ -70,7 +67,6 @@ jobs:
           OCNA=compare/"$PREFIX"_$CNA_DATA_NAME
 
           python MafAnnotator.py -i $IMAF -o $OMAF -c $IC -b $ONCOKB_API_TOKEN
-          python MafAnnotator.py -i $IGCMAF -o $OGCMAF -c $IC -b $ONCOKB_API_TOKEN -q Genomic_Change
           python FusionAnnotator.py -i $IF -o $OF -c $IC -b $ONCOKB_API_TOKEN
           python CnaAnnotator.py -i $ICNA -o $OCNA -c $IC -b $ONCOKB_API_TOKEN
           python ClinicalDataAnnotator.py -i $IC -o $OC -a $OMAF,$OCNA,$OF
@@ -88,13 +84,16 @@ jobs:
         env:
           STUDY: ${{steps.annotate.outputs.STUDY}}
           ONCOKB_OAUTH_TOKEN: ${{ secrets.ONCOKB_OAUTH_TOKEN }}
+          FIEL_NAME_PREFIX: 'oncokb_data'
         run: |
           # remove everything under compare folder and replace wiht the ones from oncokb-data
           rm -f compare/*.txt
 
           cd compare
           curl -s -H "Authorization: token ${ONCOKB_OAUTH_TOKEN}" https://api.github.com/repos/knowledgesystems/oncokb-data/contents/annotation/$STUDY | jq -r '.[] | .download_url + " " + .name' | while IFS=' ' read -r downloadurl name; do
-            curl -s "$downloadurl" -o $name
+            if [[ "$name" == "$FIEL_NAME_PREFIX"* ]]; then
+              curl -s "$downloadurl" -o $name
+            fi
           done
           cd ..
 

AnnotatorCore.py

@@ -158,7 +158,7 @@ class ReferenceGenome(Enum):
 }
 
 POST_QUERIES_THRESHOLD = 1000
-POST_QUERIES_THRESHOLD_GC_HGVSG = 100
+POST_QUERIES_THRESHOLD_GC_HGVSG = 1000
 
 def getOncokbInfo():
     ret = ['Files annotated on ' + date.today().strftime('%m/%d/%Y') + "\nOncoKB API URL: "+oncokbapiurl]