Merge pull request #135 from oncokb/fix-bash-warnings

Update bash scripts format following ShellCheck
oncokb · Aug 23, 2021 · c0f001a · c0f001a
2 parents 77a2544 + 3c90953
commit c0f001a
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diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,5 +1,5 @@
-name-template: 'v$NEXT_PATCH_VERSION'
-tag-template: 'v$NEXT_PATCH_VERSION'
+name-template: 'v$NEXT_MINOR_VERSION'
+tag-template: 'v$NEXT_MINOR_VERSION'
 categories:
   - title: '🧬 Features'
     labels:
@@ -31,4 +31,4 @@ template: |
   ## Changes
   $CHANGES
   ## 🕵️‍♀️ Full commit logs
-  - https://github.com/oncokb/oncokb-annotator/compare/$PREVIOUS_TAG...v$NEXT_PATCH_VERSION
+  - https://github.com/oncokb/oncokb-annotator/compare/$PREVIOUS_TAG...v$NEXT_MINOR_VERSION
diff --git a/.github/workflows/compare-study-annotation.yml b/.github/workflows/compare-study-annotation.yml
@@ -36,40 +36,40 @@ jobs:
           git checkout -b compare
 
           STUDY=msk_impact_2017
-          DATAHUB_URL=https://media.githubusercontent.com/media/cBioPortal/datahub/42afc279efb8d9104aba36fa35bad3ec41921949/public/$STUDY
+          DATAHUB_URL=https://media.githubusercontent.com/media/cBioPortal/datahub/42afc279efb8d9104aba36fa35bad3ec41921949/public/"$STUDY"
 
           MUTATION_DATA_NAME=data_mutations_extended.txt
           CLINICAL_DATA_NAME=data_clinical_sample.txt
           FUSION_DATA_NAME=data_fusions.txt
           CNA_DATA_NAME=data_CNA.txt
 
-          cd data
-          curl -s $DATAHUB_URL/$MUTATION_DATA_NAME -O
-          curl -s $DATAHUB_URL/$CLINICAL_DATA_NAME -O
-          curl -s $DATAHUB_URL/$FUSION_DATA_NAME -O
-          curl -s $DATAHUB_URL/$CNA_DATA_NAME -O
+          cd data || exit
+          curl -s "$DATAHUB_URL"/"$MUTATION_DATA_NAME" -O
+          curl -s "$DATAHUB_URL"/"$CLINICAL_DATA_NAME" -O
+          curl -s "$DATAHUB_URL"/"$FUSION_DATA_NAME" -O
+          curl -s "$DATAHUB_URL"/"$CNA_DATA_NAME" -O
           cd ..
 
           # create compare folder to add all annotated files
           mkdir compare
 
           PREFIX=oncokb
-          IMAF=data/$MUTATION_DATA_NAME
-          OMAF=compare/"$PREFIX"_$MUTATION_DATA_NAME
+          IMAF=data/"$MUTATION_DATA_NAME"
+          OMAF=compare/"$PREFIX"_"$MUTATION_DATA_NAME"
 
-          IC=data/$CLINICAL_DATA_NAME
-          OC=compare/"$PREFIX"_$CLINICAL_DATA_NAME
+          IC=data/"$CLINICAL_DATA_NAME"
+          OC=compare/"$PREFIX"_"$CLINICAL_DATA_NAME"
 
-          IF=data/$FUSION_DATA_NAME
-          OF=compare/"$PREFIX"_$FUSION_DATA_NAME
+          IF=data/"$FUSION_DATA_NAME"
+          OF=compare/"$PREFIX"_"$FUSION_DATA_NAME"
 
-          ICNA=data/$CNA_DATA_NAME
-          OCNA=compare/"$PREFIX"_$CNA_DATA_NAME
+          ICNA=data/"$CNA_DATA_NAME"
+          OCNA=compare/"$PREFIX"_"$CNA_DATA_NAME"
 
-          python MafAnnotator.py -i $IMAF -o $OMAF -c $IC -b $ONCOKB_API_TOKEN
-          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,$OF
+          python MafAnnotator.py -i "$IMAF" -o "$OMAF" -c "$IC" -b "$ONCOKB_API_TOKEN"
+          python FusionAnnotator.py -i "$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"
 
           git config user.name oncokb-bot
           git config user.email dev.oncokb@gmail.com
@@ -89,7 +89,7 @@ jobs:
           # remove everything under compare folder and replace wiht the ones from oncokb-data
           rm -f compare/*.txt
 
-          cd compare
+          cd compare || exit
           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 [[ "$name" == "$FIEL_NAME_PREFIX"* ]]; then
               curl -s "$downloadurl" -o $name

diff --git a/example.sh b/example.sh
@@ -1,36 +1,44 @@
 #!/usr/bin/env bash
 IMAF="data/example_maf.txt"
 OMAF="data/example_maf.oncokb.txt"
+
 IMAF38="data/example_maf_grch38.txt"
 OMAF38="data/example_maf_grch38.oncokb.txt"
+
 OMAFHGVSPSHORT="data/example_maf_hgsp_short.oncokb.txt"
 OMAFHGVSP="data/example_maf_hgsp.oncokb.txt"
 OMAFHGVSG="data/example_maf_hgsg.oncokb.txt"
 OMAFGC="data/example_maf_genomic_change.oncokb.txt"
+
 IATYPICALALT="data/example_atypical_alterations.txt"
 OATYPICALALT="data/example_atypical_alterations.oncokb.txt"
+
 IF="data/example_fusions.txt"
 OF="data/example_fusions.oncokb.txt"
+
 ICNA="data/example_cna.txt"
 OCNA="data/example_cna.oncokb.txt"
+
 IC="data/example_clinical.txt"
 OC="data/example_clinical.oncokb.txt"
+
 OCPDF="data/example_clinical.oncokb.pdf"
+
 TOKEN="" #OncoKB API Token
 README="data/example_README.txt"
 
-python MafAnnotator.py -i $IMAF -o $OMAF -c $IC -b $TOKEN
-python MafAnnotator.py -i $IMAF -o $OMAFHGVSPSHORT -c $IC -b $TOKEN -q hgvsp_short
-python MafAnnotator.py -i $IMAF -o $OMAFHGVSP -c $IC -b $TOKEN -q hgvsp
-python MafAnnotator.py -i $IMAF -o $OMAFHGVSG -c $IC -b $TOKEN -q hgvsg
-python MafAnnotator.py -i $IMAF -o $OMAFGC -c $IC -b $TOKEN -q genomic_change
+python MafAnnotator.py -i "$IMAF" -o "$OMAF" -c "$IC" -b "$TOKEN"
+python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSPSHORT" -c "$IC" -b "$TOKEN" -q hgvsp_short
+python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSP" -c "$IC" -b "$TOKEN" -q hgvsp
+python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSG" -c "$IC" -b "$TOKEN" -q hgvsg
+python MafAnnotator.py -i "$IMAF" -o "$OMAFGC" -c "$IC" -b "$TOKEN" -q genomic_change
 
-python MafAnnotator.py -i $IMAF38 -o $OMAF38 -c $IC -b $TOKEN
+python MafAnnotator.py -i "$IMAF38" -o "$OMAF38" -c "$IC" -b "$TOKEN"
 
-python MafAnnotator.py -i $IATYPICALALT -o $OATYPICALALT -c $IC -b $TOKEN
+python MafAnnotator.py -i "$IATYPICALALT" -o "$OATYPICALALT" -c "$IC" -b "$TOKEN"
 
-python FusionAnnotator.py -i $IF -o $OF -c $IC -b $TOKEN
-python CnaAnnotator.py -i $ICNA -o $OCNA -c $IC -b $TOKEN
-python ClinicalDataAnnotator.py -i $IC -o $OC -a $OMAF,$OATYPICALALT,$OCNA,$OF
-python OncoKBPlots.py -i $OC -o $OCPDF -c ONCOTREE_CODE #-n 10
-python GenerateReadMe.py -o $README
+python FusionAnnotator.py -i "$IF" -o "$OF" -c "$IC" -b "$TOKEN"
+python CnaAnnotator.py -i "$ICNA" -o "$OCNA" -c "$IC" -b "$TOKEN"
+python ClinicalDataAnnotator.py -i "$IC" -o "$OC" -a "$OMAF,$OATYPICALALT,$OCNA,$OF"
+python OncoKBPlots.py -i "$OC" -o "$OCPDF" -c ONCOTREE_CODE #-n 10
+python GenerateReadMe.py -o "$README"