Create a Docker image for topic generator (#505)

https://ucsc-cgl.atlassian.net/browse/SEAB-6653

---------

Co-authored-by: Kathy Tran <kathylevtran@gmail.com>

.github/workflows/deploy_tagged.yml

@@ -14,4 +14,6 @@ jobs:
     uses: dockstore/workflow-actions/.github/workflows/deploy_tagged.yaml@main
     with:
       changelist: ${{ inputs.changelist }}
+      createDockerImage: true
+      dockerTagPrefix: 'quay.io/dockstore/dockstore-support'
     secrets: inherit

.github/workflows/maven.yml

@@ -7,8 +7,6 @@ on:
   push:
     branches: [ '**' ]
     tags: [ '**' ]
-  pull_request:
-    branches: [ '**' ]
 
 jobs:
   build:
@@ -34,3 +32,33 @@ jobs:
         run: ./mvnw -B clean install
       - name: code coverage
         run: bash <(curl -s https://codecov.io/bash)
+
+      - if: github.ref == 'refs/heads/develop'
+        name: Set S3 folder name and quay tag name
+        run: |
+          S3_FOLDER=${GITHUB_REF##refs/tags/}
+          if [ $GITHUB_REF == $S3_FOLDER ]; then
+           # If this isn't a tag, it must be a branch
+           S3_FOLDER=${GITHUB_REF##refs/heads/}
+          fi
+          # QUAY_TAG differs from S3_FOLDER because it only contains the git ref with no short hash. It also replaces slashes with underscores.
+          echo "QUAY_TAG=${S3_FOLDER//\//_}" >> $GITHUB_ENV
+          echo "S3_FOLDER=${S3_FOLDER}-$(echo $GITHUB_SHA | cut -c -7)" >> $GITHUB_ENV
+          
+      # neat, quay itself uses manual github actions https://github.com/quay/quay/blob/master/.github/workflows/build-and-publish.yaml
+      - if: github.ref == 'refs/heads/develop'
+        name: Login to Quay.io
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USER }}
+          password: ${{ secrets.QUAY_TOKEN }}
+
+      - if: github.ref == 'refs/heads/develop'
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: quay.io/dockstore/dockstore-support:${{env.QUAY_TAG}}

Dockerfile

@@ -0,0 +1,17 @@
+FROM eclipse-temurin:21.0.2_13-jdk-jammy
+
+# Update the APT cache
+# Prepare for Java download
+RUN apt-get update \
+    && apt-get upgrade -y \
+    && apt-get install unzip jq -y --no-install-recommends
+
+# Install aws cli so dockstore-deploy can use the aws cli to upload files to S3
+RUN curl -s "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o /tmp/awscliv2.zip
+RUN unzip -q /tmp/awscliv2.zip -d /tmp
+RUN /tmp/aws/install
+RUN rm -f /tmp/awscliv2.zip
+RUN rm -fr /tmp/aws
+
+# Copy, for example, topicgenerator-1.16.0-SNAPSHOT.jar, but not topicgenerator-1.16.0-SNAPSHOT-sources.jar
+COPY topicgenerator/target/topicgenerator*[^s].jar /home/topic-generator.jar

topicgenerator/src/main/java/io/dockstore/topicgenerator/client/cli/TopicGeneratorClient.java

@@ -14,6 +14,7 @@
 import com.beust.jcommander.ParameterException;
 import com.google.common.collect.Lists;
 import io.dockstore.common.NextflowUtilities;
+import io.dockstore.common.NextflowUtilities.NextflowParsingException;
 import io.dockstore.openapi.client.ApiClient;
 import io.dockstore.openapi.client.ApiException;
 import io.dockstore.openapi.client.api.ExtendedGa4GhApi;
@@ -320,7 +321,13 @@ private FileWrapper getDescriptorFile(Ga4Ghv20Api ga4Ghv20Api, String trsId, Str
     }
 
     private Optional<FileWrapper> getNextflowMainScript(String nextflowConfigFileContent, Ga4Ghv20Api ga4Ghv20Api, String trsId, String versionId, DescriptorTypeEnum descriptorType) {
-        final String mainScriptPath = NextflowUtilities.grabConfig(nextflowConfigFileContent).getString("manifest.mainScript", "main.nf");
+        final String mainScriptPath;
+        try {
+            mainScriptPath = NextflowUtilities.grabConfig(nextflowConfigFileContent).getString("manifest.mainScript", "main.nf");
+        } catch (NextflowParsingException e) {
+            LOG.error("Could not grab config", e);
+            return Optional.empty();
+        }
         try {
             return Optional.of(ga4Ghv20Api.toolsIdVersionsVersionIdTypeDescriptorRelativePathGet(trsId, descriptorType.toString(), versionId, mainScriptPath));
         } catch (ApiException exception) {

topicgenerator/src/main/java/io/dockstore/topicgenerator/helper/AIModelType.java

@@ -3,8 +3,8 @@
 import com.knuddels.jtokkit.api.ModelType;
 
 public enum AIModelType {
-    CLAUDE_3_5_SONNET("anthropic.claude-3-5-sonnet-20240620-v1:0", 0.003, 0.015, 200000),
-    CLAUDE_3_HAIKU("anthropic.claude-3-haiku-20240307-v1:0", 0.00025, 0.00125, 200000),
+    CLAUDE_3_5_SONNET("us.anthropic.claude-3-5-sonnet-20240620-v1:0", 0.003, 0.015, 200000),
+    CLAUDE_3_HAIKU("us.anthropic.claude-3-haiku-20240307-v1:0", 0.00025, 0.00125, 200000),
     GPT_4O_MINI(ModelType.GPT_4O_MINI.getName(), 0.000150, 0.000600, ModelType.GPT_4O_MINI.getMaxContextLength());
 
     private final String modelId;