Develop - test run for deployment

.github/workflows/build_publish.yml

@@ -1,6 +1,6 @@
 # Github action to Build cda service artifact, add/promote semantic tagging
 
-name: cda-service-build-tag-publish
+name: Tag, Build, and Push Image
 
 on:
   push:
@@ -31,7 +31,7 @@ jobs:
         env:
           DEFAULT_BUMP: patch
           GITHUB_TOKEN: ${{ secrets.BROADBOT_TOKEN }}
-          RELEASE_BRANCHES: master
+          RELEASE_BRANCHES: develop
           WITH_V: true
 
       - name: debug outputs
@@ -91,4 +91,19 @@ jobs:
     permissions:
       contents: 'read'
       id-token: 'write'
-#    inputs: '{ "bee-name": "${{ github.event.repository.name }}-${{ github.run_id }}-${{ matrix.terra-env }}" }'
+
+#    inputs: '{ "bee-name": "${{ github.event.repository.name }}-${{ github.run_id }}-${{ matrix.terra-env }}" }'
+
+  set-version-in-dev:
+    if: ${{ github.event_name != 'pull_request' }}
+    # Put new cda version in Broad dev environment
+    uses: broadinstitute/sherlock/.github/workflows/client-set-environment-app-version.yaml@main
+    needs: [tag-build-publish, report-to-sherlock]
+    with:
+      new-version: ${{ needs.tag-build-publish.outputs.tag }}
+      chart-name: 'cancerdata'
+      environment-name: 'dev'
+    secrets:
+      sync-git-token: ${{ secrets.BROADBOT_TOKEN }}
+    permissions:
+      id-token: 'write'

.github/workflows/tests.yml

@@ -27,23 +27,18 @@ jobs:
         restore-keys: ${{ runner.os }}-gradle
     - name: Run tests
       run: ./gradlew test --scan
-    - name: Run SonarQube scan
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
-        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-      run: ./gradlew sonarqube --info
     - name: Run Coverage
       run: |
         chmod +x gradlew
         ./gradlew jacocoTestReport
     - name: Upload Report
-      uses: 'actions/upload-artifact@v2'
+      uses: 'actions/upload-artifact@v4'
       with:
         name: report.xml
         path: ${{ github.workspace }}/build/reports/jacoco/test/jacocoTestReport.xml
     - name: Add coverage to PR
       id: jacoco
-      uses: madrapps/jacoco-report@v1.2
+      uses: madrapps/jacoco-report@v1.6.1
       with:
         paths: ${{ github.workspace }}/build/reports/jacoco/test/jacocoTestReport.xml
         token: ${{ secrets.GITHUB_TOKEN }}

build.gradle

@@ -1,11 +1,12 @@
 import org.openapitools.generator.gradle.plugin.tasks.GenerateTask
 
+
 buildscript {
 	repositories {
 		mavenCentral()
 	}
 	dependencies {
-		classpath("org.springframework.boot:spring-boot-gradle-plugin:2.7.4.RELEASE")
+		classpath("org.springframework.boot:spring-boot-gradle-plugin:2.7.18")
 		classpath("com.google.guava:guava:30.1.1-jre")
 	}
 	configurations.all {
@@ -18,7 +19,7 @@ buildscript {
 plugins {
 	id 'java'
 	id 'idea'
-	id 'org.springframework.boot' version '2.7.4'
+	id 'org.springframework.boot' version '2.7.18'
 	id 'io.spring.dependency-management' version '1.0.11.RELEASE'
 	id 'com.google.cloud.tools.jib' version '2.8.0'
 	id 'org.openapi.generator' version '6.0.1'
@@ -63,9 +64,11 @@ dependencies {
 	// These dependencies are required to load the logback config file.
 	implementation group: 'org.codehaus.groovy', name: 'groovy', version: '3.0.7'
 	implementation group: 'org.springframework.cloud', name: 'spring-cloud-gcp-starter-logging', version: '1.2.8.RELEASE'
+	implementation group: 'ch.qos.logback', name: 'logback-classic', version: '1.2.13'
+	implementation group: 'ch.qos.logback', name: 'logback-core', version: '1.2.13'
 
 	// These are temporary until the including library catches up with these vulnerability fixes
-	implementation group: 'org.yaml', name: 'snakeyaml', version: '1.33'
+	implementation group: 'org.yaml', name: 'snakeyaml', version: '2.0'
 	implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.14.0-rc1'
 
 	// -- OpenAPI CodeGen dependencies --
@@ -273,13 +276,13 @@ requires = ["setuptools", "wheel"]  # PEP 508 specifications.
 			pyprojectTomlTemplate += line + "\n"
 		}
 
-		for( line  in new File("./build/generated-client/requirements.txt")){
+		for( line in new File( System.getenv().get('PWD') + "/build/generated-client/requirements.txt" ) ) {
 					String[] parts = line.split("[><=]")
 					String op = "="
 			pyprojectTomlTemplate += "${parts[0].trim()} ${op} \"${parts[parts.length - 1].trim()}\" \n"
 		}
 
-		new File("./build/generated-client/pyproject.toml").write(pyprojectTomlTemplate)
+		new File( System.getenv().get('PWD') + "/build/generated-client/pyproject.toml" ).write( pyprojectTomlTemplate )
 		println pyprojectTomlTemplate
 	}
 }

src/main/java/bio/terra/cda/app/builders/JoinBuilder.java

@@ -96,7 +96,7 @@ protected boolean foundMatch(ForeignKey key, String toTable) {
 
   protected ForeignKey getMatchingMappingFK(ForeignKey key, String toTable, String toFieldname) {
     TableInfo destTable = dataSetInfo.getTableInfo(key.getDestinationTableName());
-    if (destTable.isMapppingTable()) {
+    if (destTable.isMappingTable()) {
       // remove the FK that got us to this mapping table
       return
           destTable.getForeignKeys().stream()

src/main/java/bio/terra/cda/app/builders/ParameterBuilder.java

@@ -2,18 +2,20 @@
 
 import bio.terra.cda.app.models.QueryField;
 import org.apache.logging.log4j.util.Strings;
-import org.springframework.jdbc.core.SqlParameterValue;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;import org.springframework.jdbc.core.SqlParameterValue;
 import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
 import org.springframework.util.StringUtils;
+import org.yaml.snakeyaml.util.ArrayUtils;
 
 import java.sql.Types;
 import java.util.Arrays;
-import java.util.HashMap;
+import java.util.Collections;
 import java.util.List;
-import java.util.Map;
 import java.util.stream.Collectors;
 
 public class ParameterBuilder {
+  private static final Logger logger = LoggerFactory.getLogger(ParameterBuilder.class);
   private final MapSqlParameterSource parameterValueMap;
   private int index;
 
@@ -28,26 +30,35 @@ public MapSqlParameterSource getParameterValueMap() {
 
   public String addParameterValue(String type, Object value) {
     String parameterName = String.format("parameter_%s", ++index);
+
     if (value.getClass().isArray()) {
       this.parameterValueMap.addValue(parameterName, value, Types.ARRAY);
-    } else
-    if (type.equals("text")) {
+    } else if (type.equals("text")) {
       this.parameterValueMap.addValue(parameterName, value);
-    } else if (type.equals("integer")){
+    } else if (type.equals("integer"))  {
       this.parameterValueMap.addValue(parameterName, value, Types.INTEGER);
+    } else if (type.equals("bigint"))  {
+      this.parameterValueMap.addValue(parameterName, value, Types.BIGINT);
     } else if (type.equals("float")) {
       this.parameterValueMap.addValue(parameterName, value, Types.FLOAT);
+    } else if (type.equals("boolean")) {
+      this.parameterValueMap.addValue(parameterName, value, Types.BOOLEAN);
+    } else {
+      logger.error("Unknown type: {}", type);
+      throw new RuntimeException("Unknown type: " + type);
     }
     return String.format(":%s", parameterName);
   }
 
   public String substituteForReadableString(String sqlStr) {
     String result = sqlStr;
-    for (String key : getParameterValueMap().getParameterNames()) {
+    List<String> reversed_parameters = Arrays.asList(getParameterValueMap().getParameterNames());
+    Collections.reverse(reversed_parameters);
+    for (String key : reversed_parameters) {
       String keyformat = String.format(":%s", key);
       Object value = parameterValueMap.getValue(key);
       int type = parameterValueMap.getSqlType(key);
-      if (type == Types.INTEGER || type == Types.FLOAT) {
+      if (type == Types.INTEGER || type == Types.FLOAT || type == Types.BOOLEAN) {
         result = result.replace(keyformat, value.toString());
       } else if (type == Types.ARRAY) {
         List<String> valueList = Arrays.stream((Object[])value).map(x ->

src/main/java/bio/terra/cda/app/controller/GlobalExceptionHandler.java

@@ -67,6 +67,6 @@ private ResponseEntity<ErrorReport> buildErrorReport(
       errorReport =
           new ErrorReport().message(ex.getMessage()).statusCode(statusCode.value()).causes(causes);
     }
-    return new ResponseEntity<>(errorReport, statusCode);
+    return new ResponseEntity<>(errorReport, HeaderUtils.getNoCacheResponseHeader(), statusCode);
   }
 }

src/main/java/bio/terra/cda/app/controller/HeaderUtils.java

@@ -0,0 +1,15 @@
+package bio.terra.cda.app.controller;
+
+import org.springframework.http.CacheControl;
+import org.springframework.http.HttpHeaders;
+
+public class HeaderUtils {
+
+    public static HttpHeaders getNoCacheResponseHeader(){
+        HttpHeaders responseHeaders = new HttpHeaders();
+        responseHeaders.setCacheControl(CacheControl.noStore());
+        responseHeaders.setPragma("no-cache");
+        return responseHeaders;
+    }
+
+}

src/main/java/bio/terra/cda/app/controller/MetaApiController.java

@@ -22,7 +22,10 @@
 import com.fasterxml.jackson.databind.node.JsonNodeFactory;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.fasterxml.jackson.databind.node.TextNode;
+import org.apache.http.Header;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.CacheControl;
+import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Controller;
@@ -41,35 +44,37 @@ public MetaApiController(ApplicationConfiguration applicationConfiguration) {
   @TrackExecutionTime
   @Override
   public ResponseEntity<SystemStatus> serviceStatus() {
-    //TODO actually validate systems
-    return ResponseEntity.ok(new SystemStatus());
+    return ResponseEntity.ok().headers(HeaderUtils.getNoCacheResponseHeader()).body(queryService.postgresCheck());
   }
 
   // For now, the dataset description is hardcoded. In the future, it will probably be read from a
   // table
   private DatasetDescription createDescription() {
     var dateOfRelease =
-        OffsetDateTime.of(LocalDate.of(2022, 6, 28), LocalTime.MIN, ZoneOffset.UTC).toString();
+        OffsetDateTime.of(LocalDate.of(2024, 3, 21), LocalTime.MIN, ZoneOffset.UTC).toString();
+    Model m = new Model();
+    m.setVersion("1.0");
+    m.setDate(dateOfRelease);
     return new DatasetDescription()
         .addDatasetsItem(
             new DatasetInfo()
                 .version(applicationConfiguration.getVersion())
-                .source("IDC, PDC and GDC")
+                .source("IDC, PDC, GDC and CDS")
                 .date(dateOfRelease))
-        .cdaVersion("MVP")
+        .cdaVersion("4.0")
         .notes("CDA MVP release")
         .releaseDate(dateOfRelease)
-        .cdaModel(new Model());
+        .cdaModel(m);
   }
 
   @Override
   public ResponseEntity<List<DatasetDescription>> allReleaseNotes() {
-    return ResponseEntity.ok(Collections.singletonList(createDescription()));
+    return ResponseEntity.ok().headers(HeaderUtils.getNoCacheResponseHeader()).body(Collections.singletonList(createDescription()));
   }
 
   @Override
   public ResponseEntity<DatasetDescription> latestReleaseNotes() {
-    return ResponseEntity.ok(createDescription());
+    return ResponseEntity.ok().headers(HeaderUtils.getNoCacheResponseHeader()).body(createDescription());
   }
 
 }