Merge pull request #48 from icgc-argo/rc/2.5.0

Rc/2.5.0
icgc-argo · Jan 18, 2021 · 24842f7 · 24842f7
2 parents cfaf782 + 83ce992
commit 24842f7
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Showing 19 changed files with 390 additions and 46 deletions.
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -1,6 +1,6 @@
-def dockerHubRepo = "icgcargo/song-search"
+def dockerRepo = "ghcr.io/icgc-argo/song-search"
 def gitHubRepo = "icgc-argo/song-search"
-def chartVersion = "1.1.0"
+def chartVersion = "1.2.0"
 def commit = "UNKNOWN"
 def version = "UNKNOWN"
 
@@ -69,15 +69,15 @@ spec:
             }
             steps {
                 container('docker') {
-                    withCredentials([usernamePassword(credentialsId:'argoDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
-                        sh 'docker login -u $USERNAME -p $PASSWORD'
+                    withCredentials([usernamePassword(credentialsId:'argoContainers', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
+                        sh 'docker login ghcr.io -u $USERNAME -p $PASSWORD'
                     }
 
                     // DNS error if --network is default
-                    sh "docker build --network=host . -t ${dockerHubRepo}:edge -t ${dockerHubRepo}:${commit}"
+                    sh "docker build --network=host . -t ${dockerRepo}:edge -t ${dockerRepo}:${commit}"
 
-                    sh "docker push ${dockerHubRepo}:${commit}"
-                    sh "docker push ${dockerHubRepo}:edge"
+                    sh "docker push ${dockerRepo}:${commit}"
+                    sh "docker push ${dockerRepo}:edge"
                 }
             }
         }
@@ -93,10 +93,10 @@ spec:
                      [$class: 'StringParameterValue', name: 'AP_HELM_CHART_VERSION', value: "${chartVersion}"],
                      [$class: 'StringParameterValue', name: 'AP_ARGS_LINE', value: "--set-string image.tag=${commit}" ]
                 ])
-                sleep(time:30,unit:"SECONDS")
-                build(job: "/provision/rdpc-gateway-restart", parameters: [
-                    [$class: 'StringParameterValue', name: 'AP_RDPC_ENV', value: 'dev' ],
-                ])
+                // sleep(time:30,unit:"SECONDS")
+                // build(job: "/provision/rdpc-gateway-restart", parameters: [
+                //     [$class: 'StringParameterValue', name: 'AP_RDPC_ENV', value: 'dev' ],
+                // ])
             }
         }
         stage('Build & Publish Release') {
@@ -110,15 +110,15 @@ spec:
                         sh "git push https://${GIT_USERNAME}:${GIT_PASSWORD}@github.com/${gitHubRepo} --tags"
                     }
 
-                    withCredentials([usernamePassword(credentialsId:'argoDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
-                        sh 'docker login -u $USERNAME -p $PASSWORD'
+                    withCredentials([usernamePassword(credentialsId:'argoContainers', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
+                        sh 'docker login ghcr.io -u $USERNAME -p $PASSWORD'
                     }
 
                     // DNS error if --network is default
-                    sh "docker build --network=host . -t ${dockerHubRepo}:latest -t ${dockerHubRepo}:${version}"
+                    sh "docker build --network=host . -t ${dockerRepo}:latest -t ${dockerRepo}:${version}"
 
-                    sh "docker push ${dockerHubRepo}:${version}"
-                    sh "docker push ${dockerHubRepo}:latest"
+                    sh "docker push ${dockerRepo}:${version}"
+                    sh "docker push ${dockerRepo}:latest"
                 }
             }
         }
@@ -134,10 +134,10 @@ spec:
                      [$class: 'StringParameterValue', name: 'AP_HELM_CHART_VERSION', value: "${chartVersion}"],
                      [$class: 'StringParameterValue', name: 'AP_ARGS_LINE', value: "--set-string image.tag=${version}" ]
                 ])
-                sleep(time:30,unit:"SECONDS")
-                build(job: "/provision/rdpc-gateway-restart", parameters: [
-                    [$class: 'StringParameterValue', name: 'AP_RDPC_ENV', value: 'qa' ],
-                ])
+                // sleep(time:30,unit:"SECONDS")
+                // build(job: "/provision/rdpc-gateway-restart", parameters: [
+                //     [$class: 'StringParameterValue', name: 'AP_RDPC_ENV', value: 'qa' ],
+                // ])
             }
         }
     }

diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
     </parent>
     <groupId>bio.overture</groupId>
     <artifactId>song-search</artifactId>
-    <version>2.4.0</version>
+    <version>2.5.0</version>
     <name>song-search</name>
     <description>GQL microservice for searching maestro generated song indexes</description>
 

diff --git a/src/main/java/bio/overture/songsearch/config/constants/EsDefaults.java b/src/main/java/bio/overture/songsearch/config/constants/EsDefaults.java
@@ -0,0 +1,13 @@
+package bio.overture.songsearch.config.constants;
+
+import static lombok.AccessLevel.PRIVATE;
+
+import lombok.NoArgsConstructor;
+
+@NoArgsConstructor(access = PRIVATE)
+public class EsDefaults {
+  // Default values from ES pagination:
+  // https://www.elastic.co/guide/en/elasticsearch/reference/7.x/paginate-search-results.html
+  public static final Integer ES_PAGE_DEFAULT_SIZE = 10;
+  public static final Integer ES_PAGE_DEFAULT_FROM = 0;
+}
diff --git a/...rture/songsearch/config/SearchFields.java → ...search/config/constants/SearchFields.java b/...rture/songsearch/config/SearchFields.java → ...search/config/constants/SearchFields.java
@@ -16,7 +16,7 @@
  * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package bio.overture.songsearch.config;
+package bio.overture.songsearch.config.constants;
 
 import static lombok.AccessLevel.PRIVATE;
 
@@ -39,4 +39,7 @@ public class SearchFields {
   public static final String SUBMITTER_SAMPLE_ID = "submitterSampleId";
   public static final String MATCHED_NORMAL_SUBMITTER_SAMPLE_ID = "matchedNormalSubmitterSampleId";
   public static final String RUN_ID = "runId";
+  public static final String PUBLISHED_AT = "publishedAt";
+  public static final String UPDATED_AT = "updatedAt";
+  public static final String FIRST_PUBLISHED_AT = "firstPublishedAt";
 }
diff --git a/src/main/java/bio/overture/songsearch/graphql/AnalysisDataFetcher.java b/src/main/java/bio/overture/songsearch/graphql/AnalysisDataFetcher.java
@@ -18,9 +18,12 @@
 
 package bio.overture.songsearch.graphql;
 
-import bio.overture.songsearch.model.Analysis;
-import bio.overture.songsearch.model.SampleMatchedAnalysisPair;
+import static bio.overture.songsearch.utils.JacksonUtils.convertValue;
+import static java.util.stream.Collectors.toUnmodifiableList;
+
+import bio.overture.songsearch.model.*;
 import bio.overture.songsearch.service.AnalysisService;
+import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableMap;
 import graphql.schema.DataFetcher;
 import java.util.List;
@@ -42,18 +45,40 @@ public AnalysisDataFetcher(AnalysisService analysisService) {
   }
 
   @SuppressWarnings("unchecked")
-  public DataFetcher<List<Analysis>> getAnalysesDataFetcher() {
+  public DataFetcher<SearchResult<Analysis>> getAnalysesDataFetcher() {
     return environment -> {
       val args = environment.getArguments();
 
       val filter = ImmutableMap.<String, Object>builder();
       val page = ImmutableMap.<String, Integer>builder();
+      val sorts = ImmutableList.<Sort>builder();
 
       if (args != null) {
         if (args.get("filter") != null) filter.putAll((Map<String, Object>) args.get("filter"));
         if (args.get("page") != null) page.putAll((Map<String, Integer>) args.get("page"));
+        if (args.get("sorts") != null) {
+          val rawSorts = (List<Object>) args.get("sorts");
+          sorts.addAll(
+              rawSorts.stream()
+                  .map(sort -> convertValue(sort, Sort.class))
+                  .collect(toUnmodifiableList()));
+        }
+      }
+      return analysisService.searchAnalyses(filter.build(), page.build(), sorts.build());
+    };
+  }
+
+  @SuppressWarnings("unchecked")
+  public DataFetcher<AggregationResult> getAggregateAnalysesDataFetcher() {
+    return environment -> {
+      val args = environment.getArguments();
+
+      val filter = ImmutableMap.<String, Object>builder();
+
+      if (args != null) {
+        if (args.get("filter") != null) filter.putAll((Map<String, Object>) args.get("filter"));
       }
-      return analysisService.getAnalyses(filter.build(), page.build());
+      return analysisService.aggregateAnalyses(filter.build());
     };
   }
 

diff --git a/src/main/java/bio/overture/songsearch/graphql/EntityDataFetcher.java b/src/main/java/bio/overture/songsearch/graphql/EntityDataFetcher.java
@@ -18,8 +18,8 @@
 
 package bio.overture.songsearch.graphql;
 
-import static bio.overture.songsearch.config.SearchFields.ANALYSIS_ID;
-import static bio.overture.songsearch.config.SearchFields.RUN_ID;
+import static bio.overture.songsearch.config.constants.SearchFields.ANALYSIS_ID;
+import static bio.overture.songsearch.config.constants.SearchFields.RUN_ID;
 import static bio.overture.songsearch.utils.CommonUtils.asImmutableMap;
 import static com.google.common.base.Strings.isNullOrEmpty;
 import static java.util.stream.Collectors.toList;

diff --git a/src/main/java/bio/overture/songsearch/graphql/FileDataFetcher.java b/src/main/java/bio/overture/songsearch/graphql/FileDataFetcher.java
@@ -18,8 +18,15 @@
 
 package bio.overture.songsearch.graphql;
 
+import static bio.overture.songsearch.utils.JacksonUtils.convertValue;
+import static java.util.stream.Collectors.toUnmodifiableList;
+
+import bio.overture.songsearch.model.AggregationResult;
 import bio.overture.songsearch.model.File;
+import bio.overture.songsearch.model.SearchResult;
+import bio.overture.songsearch.model.Sort;
 import bio.overture.songsearch.service.FileService;
+import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableMap;
 import graphql.schema.DataFetcher;
 import java.util.List;
@@ -40,18 +47,40 @@ public FileDataFetcher(FileService fileService) {
   }
 
   @SuppressWarnings("unchecked")
-  public DataFetcher<List<File>> getFilesDataFetcher() {
+  public DataFetcher<SearchResult<File>> getFilesDataFetcher() {
     return environment -> {
       val args = environment.getArguments();
 
       val filter = ImmutableMap.<String, Object>builder();
       val page = ImmutableMap.<String, Integer>builder();
+      val sorts = ImmutableList.<Sort>builder();
 
       if (args != null) {
         if (args.get("filter") != null) filter.putAll((Map<String, Object>) args.get("filter"));
         if (args.get("page") != null) page.putAll((Map<String, Integer>) args.get("page"));
+        if (args.get("sorts") != null) {
+          val rawSorts = (List<Object>) args.get("sorts");
+          sorts.addAll(
+              rawSorts.stream()
+                  .map(sort -> convertValue(sort, Sort.class))
+                  .collect(toUnmodifiableList()));
+        }
+      }
+      return fileService.searchFiles(filter.build(), page.build(), sorts.build());
+    };
+  }
+
+  @SuppressWarnings("unchecked")
+  public DataFetcher<AggregationResult> getAggregateFilesDataFetcher() {
+    return environment -> {
+      val args = environment.getArguments();
+
+      val filter = ImmutableMap.<String, Object>builder();
+
+      if (args != null) {
+        if (args.get("filter") != null) filter.putAll((Map<String, Object>) args.get("filter"));
       }
-      return fileService.getFiles(filter.build(), page.build());
+      return fileService.aggregateFiles(filter.build());
     };
   }
 }
diff --git a/src/main/java/bio/overture/songsearch/graphql/GraphQLProvider.java b/src/main/java/bio/overture/songsearch/graphql/GraphQLProvider.java
@@ -127,7 +127,14 @@ private RuntimeWiring buildWiring() {
         .type(
             newTypeWiring("Query")
                 .dataFetcher("analyses", analysisDataFetcher.getAnalysesDataFetcher()))
+        .type(
+            newTypeWiring("Query")
+                .dataFetcher(
+                    "aggregateAnalyses", analysisDataFetcher.getAggregateAnalysesDataFetcher()))
         .type(newTypeWiring("Query").dataFetcher("files", fileDataFetcher.getFilesDataFetcher()))
+        .type(
+            newTypeWiring("Query")
+                .dataFetcher("aggregateFiles", fileDataFetcher.getAggregateFilesDataFetcher()))
         .type(
             newTypeWiring("Query")
                 .dataFetcher(

diff --git a/src/main/java/bio/overture/songsearch/model/AggregationResult.java b/src/main/java/bio/overture/songsearch/model/AggregationResult.java
@@ -0,0 +1,8 @@
+package bio.overture.songsearch.model;
+
+import lombok.Value;
+
+@Value
+public class AggregationResult {
+  Long totalHits;
+}
diff --git a/src/main/java/bio/overture/songsearch/model/Analysis.java b/src/main/java/bio/overture/songsearch/model/Analysis.java
@@ -55,6 +55,12 @@ public class Analysis {
 
   private Workflow workflow;
 
+  private String updatedAt;
+
+  private String publishedAt;
+
+  private String firstPublishedAt;
+
   @SneakyThrows
   public static Analysis parse(@NonNull Map<String, Object> sourceMap) {
     return MAPPER.convertValue(sourceMap, Analysis.class);

diff --git a/src/main/java/bio/overture/songsearch/model/SearchResult.java b/src/main/java/bio/overture/songsearch/model/SearchResult.java
@@ -0,0 +1,22 @@
+package bio.overture.songsearch.model;
+
+import java.util.List;
+import lombok.Value;
+
+@Value
+public class SearchResult<T> {
+  List<T> content;
+  Info info;
+
+  public SearchResult(List<T> content, Boolean hasNextFrom, Long totalHits) {
+    this.content = content;
+    this.info = new Info(hasNextFrom, totalHits, content.size());
+  }
+
+  @Value
+  public static class Info {
+    Boolean hasNextFrom;
+    Long totalHits;
+    Integer contentCount;
+  }
+}
diff --git a/src/main/java/bio/overture/songsearch/model/Sort.java b/src/main/java/bio/overture/songsearch/model/Sort.java
@@ -0,0 +1,9 @@
+package bio.overture.songsearch.model;
+
+import lombok.Data;
+
+@Data
+public class Sort {
+  String fieldName;
+  String order;
+}