core: add new tool externalExecutor object to Job, #TASK-6445

opencb · Sep 20, 2024 · c6df368 · c6df368
1 parent 857b41d
commit c6df368
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Showing 10 changed files with 95 additions and 35 deletions.
diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/binary/BinaryExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/binary/BinaryExecutor.java
@@ -2,7 +2,6 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.StopWatch;
-import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.utils.DockerUtils;
 import org.opencb.opencga.analysis.tools.OpenCgaToolScopeStudy;
 import org.opencb.opencga.catalog.utils.InputFileUtils;
@@ -12,6 +11,7 @@
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.job.JobRunDockerParams;
 import org.opencb.opencga.core.models.job.JobRunParams;
+import org.opencb.opencga.core.models.job.ToolInfoExecutor;
 import org.opencb.opencga.core.tools.annotations.Tool;
 import org.opencb.opencga.core.tools.annotations.ToolParams;
 import org.slf4j.Logger;
@@ -60,13 +60,11 @@ protected void check() throws Exception {
         }
 
         // Update job tags and attributes
-        ObjectMap attributes = new ObjectMap()
-                .append("DOCKER_ID", runParams.getDocker().getId())
-                .append("DOCKER_TAG", runParams.getDocker().getTag());
+        ToolInfoExecutor toolInfoExecutor = new ToolInfoExecutor(runParams.getDocker().getId(), runParams.getDocker().getTag());
         List<String> tags = new LinkedList<>();
         tags.add(ID);
         tags.add(this.dockerImage);
-        updateJobInformation(tags, attributes);
+        updateJobInformation(tags, toolInfoExecutor);
 
         // Build input bindings
         this.inputBindings = new LinkedList<>();

diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaToolScopeStudy.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaToolScopeStudy.java
@@ -18,10 +18,11 @@
 
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.opencga.catalog.db.api.JobDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.StudyManager;
 import org.opencb.opencga.core.api.ParamConstants;
-import org.opencb.opencga.core.models.job.JobUpdateParams;
+import org.opencb.opencga.core.models.job.ToolInfoExecutor;
 
 import java.util.List;
 
@@ -55,11 +56,11 @@ protected final String getStudyFqn() throws CatalogException {
                 getToken()).first().getFqn();
     }
 
-    protected void updateJobInformation(List<String> tags, ObjectMap attributes) throws CatalogException {
-        JobUpdateParams updateParams = new JobUpdateParams()
-                .setTags(tags)
-                .setAttributes(attributes);
-        catalogManager.getJobManager().update(getStudyFqn(), getJobId(), updateParams, QueryOptions.empty(), token);
+    protected void updateJobInformation(List<String> tags, ToolInfoExecutor executor) throws CatalogException {
+        ObjectMap params = new ObjectMap()
+                .append(JobDBAdaptor.QueryParams.TAGS.key(), tags)
+                .append(JobDBAdaptor.QueryParams.TOOL_EXTERNAL_EXECUTOR.key(), executor);
+        catalogManager.getJobManager().update(getStudyFqn(), getJobId(), params, QueryOptions.empty(), token);
     }
 
 }
diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java
@@ -19,6 +19,7 @@
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.file.File;
+import org.opencb.opencga.core.models.job.ToolInfoExecutor;
 import org.opencb.opencga.core.models.workflow.NextFlowRunParams;
 import org.opencb.opencga.core.models.workflow.Workflow;
 import org.opencb.opencga.core.models.workflow.WorkflowScript;
@@ -90,9 +91,7 @@ protected void check() throws Exception {
         }
 
         // Update job tags and attributes
-        ObjectMap attributes = new ObjectMap()
-                .append("WORKFLOW_ID", workflow.getManager().getId())
-                .append("WORKFLOW_VERSION", workflow.getManager().getVersion());
+        ToolInfoExecutor toolInfoExecutor = new ToolInfoExecutor(workflow.getManager().getId().name(), workflow.getManager().getVersion());
         Set<String> tags = new HashSet<>();
         tags.add(ID);
         tags.add(workflow.getManager().getId().name());
@@ -101,7 +100,7 @@ protected void check() throws Exception {
         if (CollectionUtils.isNotEmpty(workflow.getTags())) {
             tags.addAll(workflow.getTags());
         }
-        updateJobInformation(new ArrayList<>(tags), attributes);
+        updateJobInformation(new ArrayList<>(tags), toolInfoExecutor);
 
         this.inputBindings = new LinkedList<>();
         if (MapUtils.isNotEmpty(nextflowParams.getParams())) {

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java
@@ -29,6 +29,7 @@
 import org.opencb.opencga.core.models.job.JobTop;
 import org.opencb.opencga.core.models.job.JobUpdateParams;
 import org.opencb.opencga.core.models.job.ToolInfo;
+import org.opencb.opencga.core.models.job.ToolInfoExecutor;
 import org.opencb.opencga.core.response.QueryType;
 import org.opencb.opencga.core.response.RestResponse;
 import org.opencb.opencga.core.tools.annotations.Tool;

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java
@@ -120,16 +120,16 @@ public class CreateCommandOptions {
         public String toolId;
 
         @Parameter(names = {"--tool-description"}, description = "Users may provide a description for the entry.", required = false, arity = 1)
-        public String toolDescription = "No description available";
+        public String toolDescription;
 
         @Parameter(names = {"--tool-scope"}, description = "Tool info scope can have the values GLOBAL, PROJECT and STUDY.", required = false, arity = 1)
-        public String toolScope = "No description available";
+        public String toolScope;
 
         @Parameter(names = {"--tool-type"}, description = "Tool info type can have the values OPERATION and ANALYSIS.", required = false, arity = 1)
-        public String toolType = "No description available";
+        public String toolType;
 
         @Parameter(names = {"--tool-resource"}, description = "Tool info resource can have the values AUDIT, USER, PROJECT, STUDY, FILE, SAMPLE, JOB, INDIVIDUAL, COHORT, DISEASE_PANEL, FAMILY, CLINICAL_ANALYSIS, INTERPRETATION, VARIANT, ALIGNMENT, CLINICAL, EXPRESSION, RGA and FUNCTIONAL.", required = false, arity = 1)
-        public String toolResource = "No description available";
+        public String toolResource;
 
         @Parameter(names = {"--priority"}, description = "The body web service priority parameter", required = false, arity = 1)
         public String priority;

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/JobDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/JobDBAdaptor.java
@@ -113,6 +113,7 @@ enum QueryParams implements QueryParam {
         TOOL("tool", OBJECT, ""),
         TOOL_ID("tool.id", TEXT, ""),
         TOOL_TYPE("tool.type", TEXT, ""),
+        TOOL_EXTERNAL_EXECUTOR("tool.externalExecutor", OBJECT, ""),
 
         PRIORITY("priority", TEXT, ""),
 

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/JobMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/JobMongoDBAdaptor.java
@@ -441,7 +441,8 @@ private UpdateDocument parseAndValidateUpdateParams(ObjectMap parameters, QueryO
                     Enums.Priority.getPriority(parameters.getString(QueryParams.PRIORITY.key())).getValue());
         }
 
-        String[] acceptedObjectParams = {QueryParams.EXECUTION.key(), QueryParams.STUDY.key(), QueryParams.INTERNAL_STATUS.key()};
+        String[] acceptedObjectParams = {QueryParams.EXECUTION.key(), QueryParams.STUDY.key(), QueryParams.INTERNAL_STATUS.key(),
+                QueryParams.TOOL_EXTERNAL_EXECUTOR.key()};
         filterObjectParams(parameters, document.getSet(), acceptedObjectParams);
 
         if (document.getSet().containsKey(QueryParams.STUDY.key())) {

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
@@ -305,6 +305,8 @@ public class FieldConstants {
     public static final String TOOL_INFO_RESOURCE_DESCRIPTION = "Tool info resource can have the values AUDIT, USER, PROJECT, "
             + "STUDY, FILE, SAMPLE, JOB, INDIVIDUAL, COHORT, DISEASE_PANEL, FAMILY, CLINICAL_ANALYSIS, INTERPRETATION, "
             + "VARIANT, ALIGNMENT, CLINICAL, EXPRESSION, RGA and FUNCTIONAL.";
+    public static final String TOOL_INFO_EXTERNAL_EXECUTOR_DESCRIPTION = "Object containing the id and version of the external tool that"
+            + " is being executed.";
 
     // Workflow
     public static final String WORKFLOW_ID_DESCRIPTION = "Workflow ID.";

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/job/ToolInfo.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/job/ToolInfo.java
@@ -29,43 +29,49 @@ public class ToolInfo {
             description = FieldConstants.GENERIC_ID_DESCRIPTION)
     private String id;
 
-    @DataField(id = "description", defaultValue = "No description available",
-            description = FieldConstants.GENERIC_DESCRIPTION_DESCRIPTION)
+    @DataField(id = "description", description = FieldConstants.GENERIC_DESCRIPTION_DESCRIPTION)
     private String description;
 
-    @DataField(id = "scope", defaultValue = "No description available",
-            description = FieldConstants.TOOL_INFO_SCOPE_DESCRIPTION)
+    @DataField(id = "scope", description = FieldConstants.TOOL_INFO_SCOPE_DESCRIPTION)
     private Scope scope;
 
-    @DataField(id = "type", defaultValue = "No description available",
-            description = FieldConstants.TOOL_INFO_TYPE_DESCRIPTION)
+    @DataField(id = "type", description = FieldConstants.TOOL_INFO_TYPE_DESCRIPTION)
     private Type type;
 
-    @DataField(id = "resource", defaultValue = "No description available",
-            description = FieldConstants.TOOL_INFO_RESOURCE_DESCRIPTION)
+    @DataField(id = "resource", description = FieldConstants.TOOL_INFO_RESOURCE_DESCRIPTION)
     private Enums.Resource resource;
 
+    @DataField(id = "resource", description = FieldConstants.TOOL_INFO_EXTERNAL_EXECUTOR_DESCRIPTION)
+    private ToolInfoExecutor externalExecutor;
+
 
     public ToolInfo() {
     }
 
     public ToolInfo(String id, String description, Scope scope, Type type, Enums.Resource resource) {
+        this(id, description, scope, type, resource, null);
+    }
+
+    public ToolInfo(String id, String description, Scope scope, Type type, Enums.Resource resource, ToolInfoExecutor externalExecutor) {
         this.id = id;
         this.description = description;
         this.scope = scope;
         this.type = type;
         this.resource = resource;
+        this.externalExecutor = externalExecutor;
     }
 
     @Override
     public String toString() {
-        return "ToolInfo{" +
-                "id='" + id + '\'' +
-                ", description='" + description + '\'' +
-                ", scope=" + scope +
-                ", type=" + type +
-                ", resource=" + resource +
-                '}';
+        final StringBuilder sb = new StringBuilder("ToolInfo{");
+        sb.append("id='").append(id).append('\'');
+        sb.append(", description='").append(description).append('\'');
+        sb.append(", scope=").append(scope);
+        sb.append(", type=").append(type);
+        sb.append(", resource=").append(resource);
+        sb.append(", externalExecutor=").append(externalExecutor);
+        sb.append('}');
+        return sb.toString();
     }
 
     public String getId() {
@@ -112,4 +118,13 @@ public ToolInfo setResource(Enums.Resource resource) {
         this.resource = resource;
         return this;
     }
+
+    public ToolInfoExecutor getExternalExecutor() {
+        return externalExecutor;
+    }
+
+    public ToolInfo setExternalExecutor(ToolInfoExecutor externalExecutor) {
+        this.externalExecutor = externalExecutor;
+        return this;
+    }
 }
diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/job/ToolInfoExecutor.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/job/ToolInfoExecutor.java
@@ -0,0 +1,42 @@
+package org.opencb.opencga.core.models.job;
+
+public class ToolInfoExecutor {
+
+    private String id;
+    private String version;
+
+    public ToolInfoExecutor() {
+    }
+
+    public ToolInfoExecutor(String id, String version) {
+        this.id = id;
+        this.version = version;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ToolInfoExecutor{");
+        sb.append("id='").append(id).append('\'');
+        sb.append(", version='").append(version).append('\'');
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public ToolInfoExecutor setId(String id) {
+        this.id = id;
+        return this;
+    }
+
+    public String getVersion() {
+        return version;
+    }
+
+    public ToolInfoExecutor setVersion(String version) {
+        this.version = version;
+        return this;
+    }
+}