Fix missing vat schema JSONs [VS-699]

.dockstore.yml

@@ -209,7 +209,7 @@ workflows:
        branches:
          - master
          - ah_var_store
-         - vs_688_fix_integration_for_alpine
+         - vs_699_fix_missing_vat_schema_jsons
    - name: GvsIngestTieout
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl

scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl

@@ -264,7 +264,7 @@ task Add_AS_MAX_VQSLOD_ToVcf {
     File input_vcf
     String output_basename
 
-    String docker = "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+    String docker = "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
     Int cpu = 1
     Int memory_mb = 3500
     Int disk_size_gb = ceil(2*size(input_vcf, "GiB")) + 50

scripts/variantstore/wdl/GvsCallsetCost.wdl

@@ -62,7 +62,7 @@ task WorkflowComputeCosts {
     >>>
 
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
     }
 
     output {

scripts/variantstore/wdl/GvsCreateVAT.wdl

@@ -124,7 +124,7 @@ task MakeSubpopulationFilesAndReadSchemaFiles {
     # ------------------------------------------------
     # Runtime settings:
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
         memory: "1 GB"
         preemptible: 3
         cpu: "1"

scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl

@@ -169,7 +169,7 @@ task ExtractAnAcAfFromVCF {
     # ------------------------------------------------
     # Runtime settings:
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
         maxRetries: 3
         memory: "16 GB"
         preemptible: 3
@@ -291,7 +291,7 @@ task PrepAnnotationJson {
     # ------------------------------------------------
     # Runtime settings:
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
         memory: "8 GB"
         preemptible: 5
         cpu: "1"

scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl

@@ -286,7 +286,7 @@ task GenerateHailScripts {
         File hail_create_vat_inputs_script = 'hail_create_vat_inputs.py'
     }
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
         disks: "local-disk 500 HDD"
     }
 }

scripts/variantstore/wdl/GvsPopulateAltAllele.wdl

@@ -243,7 +243,7 @@ task PopulateAltAlleleTable {
     done
   >>>
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+    docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
     memory: "3 GB"
     disks: "local-disk 10 HDD"
     cpu: 1

scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl

@@ -105,7 +105,7 @@ task PrepareRangesCallsetTask {
   }
 
   runtime {
-    docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+    docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
     memory: "3 GB"
     disks: "local-disk 100 HDD"
     bootDiskSizeGb: 15

scripts/variantstore/wdl/GvsUtils.wdl

@@ -347,7 +347,7 @@ task ScaleXYBedValues {
     }
 
     runtime {
-        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-12-alpine"
+        docker: "us.gcr.io/broad-dsde-methods/variantstore:2022-10-25-alpine"
         maxRetries: 3
         memory: "7 GB"
         preemptible: 3

scripts/variantstore/wdl/extract/Dockerfile

@@ -7,7 +7,7 @@
 # Because this is an Alpine-based image it is more bare-bones than its Debian-based peers. Key components missing here
 # are the Apache Arrow library (a requirement for pyarrow which in turn is a requirement for the google-cloud-bigquery
 # Python module) and bcftools.
-FROM gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine as build
+FROM gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-alpine as build
 
 RUN apk update && apk upgrade
 RUN python3 -m ensurepip --upgrade
@@ -95,7 +95,7 @@ RUN mkdir /bcftools bcftools-build && \
     make install
 
 # The main layer does not install development tools, instead copies artifacts from the build layer above.
-FROM gcr.io/google.com/cloudsdktool/cloud-sdk:404.0.0-alpine as main
+FROM gcr.io/google.com/cloudsdktool/cloud-sdk:406.0.0-alpine as main
 
 RUN apk update && apk upgrade
 RUN python3 -m ensurepip --upgrade
@@ -114,7 +114,7 @@ COPY *.py /app
 COPY *.sql /app
 
 # Copy the schema files needed for VAT creation.
-COPY *.json /data/variant_annotation_table/schema/
+COPY ./variant_annotation_table/schema/*.json /data/variant_annotation_table/schema/
 
 ENV PATH=/bcftools/bin\:$PATH
 WORKDIR /app