feat: upgrade clinvar-this for new ClinVar XML format (#72)

varfish-org · May 27, 2024 · 1547249 · 1547249
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commit 1547249
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Showing 7 changed files with 18 additions and 18 deletions.
diff --git a/.github/actions/acmg-class-by-freq/action.yml b/.github/actions/acmg-class-by-freq/action.yml
@@ -25,7 +25,7 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/acmg-class-by-freq
-        key: acmg-class-by-freq-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: acmg-class-by-freq-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         lookup-only: true
 
     - name: Create requirements.txt
@@ -50,15 +50,15 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/acmg-class-by-freq
-        key: acmg-class-by-freq-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: acmg-class-by-freq-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
 
     - name: Retrieve cached ClinVar JSONL file
       if: |
         (steps.check-cache-acmg-class-by-freq-output.outputs.cache-hit != 'true')
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/convert-clinvar
-        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         fail-on-cache-miss: true
 
     - name: Run the ACMG class by freq. generation

diff --git a/.github/actions/convert-clinvar/action.yml b/.github/actions/convert-clinvar/action.yml
@@ -25,7 +25,7 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/convert-clinvar
-        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         lookup-only: true
 
     - name: Create requirements.txt
@@ -50,7 +50,7 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/convert-clinvar
-        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
 
     - name: Retrieve cached ClinVar file
       if: |

diff --git a/.github/actions/convert-clinvar/run.sh b/.github/actions/convert-clinvar/run.sh
@@ -11,8 +11,8 @@ df -h
 clinvar-this data xml-to-jsonl \
     ${CLINVAR_DIR}/ClinVarFullRelease_00-latest_weekly.xml.gz \
     ${OUTPUT_DIR}/convert-clinvar/clinvar-full-release.jsonl.gz \
-    $(if [[ "$MAX_RCVS" != "" ]] && [[ "$MAX_RCVS" != "0" ]]; then \
-        echo --max-records $MAX_RCVS;
+    $(if [[ "$MAX_RECORDS" != "" ]] && [[ "$MAX_RECORDS" != "0" ]]; then \
+        echo --max-records $MAX_RECORDS;
     fi)
 
 

diff --git a/.github/actions/extract-vars/action.yml b/.github/actions/extract-vars/action.yml
@@ -25,7 +25,7 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/extract-vars
-        key: extract-vars-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: extract-vars-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         lookup-only: true
 
     - name: Create requirements.txt
@@ -50,15 +50,15 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/extract-vars
-        key: extract-vars-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: extract-vars-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
 
     - name: Retrieve cached ClinVar JSONL file
       if: |
         (steps.check-cache-extract-vars-output.outputs.cache-hit != 'true')
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/convert-clinvar
-        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         fail-on-cache-miss: true
 
     - name: Run the variant extraction generation

diff --git a/.github/actions/gene-variant-report/action.yml b/.github/actions/gene-variant-report/action.yml
@@ -25,7 +25,7 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/gene-variant-report
-        key: gene-variant-report-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: gene-variant-report-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         lookup-only: true
 
     - name: Create requirements.txt
@@ -50,15 +50,15 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/gene-variant-report
-        key: gene-variant-report-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: gene-variant-report-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
 
     - name: Retrieve cached ClinVar JSONL file
       if: |
         (steps.check-cache-gene-variant-report-output.outputs.cache-hit != 'true')
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/convert-clinvar
-        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         fail-on-cache-miss: true
 
     - name: Run the gene variant report generation

diff --git a/.github/actions/phenotype-links/action.yml b/.github/actions/phenotype-links/action.yml
@@ -25,7 +25,7 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/phenotype-links
-        key: phenotype-links-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: phenotype-links-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         lookup-only: true
 
     - name: Create requirements.txt
@@ -50,15 +50,15 @@ runs:
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/phenotype-links
-        key: phenotype-links-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: phenotype-links-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
 
     - name: Retrieve cached ClinVar JSONL file
       if: |
         (steps.check-cache-phenotype-links-output.outputs.cache-hit != 'true')
       uses: actions/cache@v3
       with:
         path: ${{ env.OUTPUT_DIR }}/convert-clinvar
-        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output
+        key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output
         fail-on-cache-miss: true
 
     - name: Run the phenotype links generation

diff --git a/.github/workflows/-build-artifacts.yml b/.github/workflows/-build-artifacts.yml
@@ -29,8 +29,8 @@ env:
   CLINVAR_THIS_VERSION: "0.14.3"
   # Helper to get unique cache keys
   CACHE_SEED: "0"
-  # Maximal number of RCVs to process (0 = no limit).
-  MAX_RCVS: "0"
+  # Maximal number of records to process (0 = no limit).
+  MAX_RECORDS: "0"
   # Lower verbosity of TQDM progress bar
   TQDM_MININTERVAL: "5"