Move PRUNE_TO_COLUMN to query_flags

ge-semtk · Jan 10, 2023 · 366515d · 366515d
1 parent aff0a17
commit 366515d
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Showing 11 changed files with 63 additions and 145 deletions.
diff --git a/...a/com/ge/research/semtk/services/nodeGroupExecution/NodeGroupExecutionRestController.java b/...a/com/ge/research/semtk/services/nodeGroupExecution/NodeGroupExecutionRestController.java
@@ -542,8 +542,7 @@ public JSONObject dispatchAnyJobById(@RequestBody DispatchByIdRequestBody reques
 					requestBody.getRuntimeConstraints(), 
 					requestBody.getLimitOverride(),
 					requestBody.getOffsetOverride(),
-					targetId,
-					requestBody.getPruneToColumn());
+					targetId);
 
 			retval.setSuccess(true);
 			retval.addResult(SimpleResultSet.JOB_ID_RESULT_KEY, ngExecutor.getJobID()); 

diff --git a/...a/com/ge/research/semtk/services/nodeGroupExecution/requests/DispatchByIdRequestBody.java b/...a/com/ge/research/semtk/services/nodeGroupExecution/requests/DispatchByIdRequestBody.java
@@ -38,14 +38,6 @@ public class DispatchByIdRequestBody extends DispatchRequestBody {
 			example = "-1")
 	private int offsetOverride = -1;
 
-	// This is custom optional field only available through straight REST
-	// for Saqib @ collins
-	@Schema(
-			description = "Prune select table return down to one column and uniquify.",
-			required = false,
-			example = "favorite_column")
-	private String pruneToColumn = null;
-
 	public int getLimitOverride() {
 		return limitOverride;
 	}
@@ -65,13 +57,6 @@ public String getNodeGroupId(){
 		return this.nodeGroupId;
 	}	
 
-	public void setPruneToColumn(String val) {
-		this.pruneToColumn = val;
-	}
-	public String getPruneToColumn() {
-		return this.pruneToColumn;
-	}
-
 	/**
 	 * Validate request contents.  Throws an exception if validation fails.
 	 */

diff --git a/.../java/com/ge/research/semtk/services/nodeGroupExecution/requests/DispatchRequestBody.java b/.../java/com/ge/research/semtk/services/nodeGroupExecution/requests/DispatchRequestBody.java
@@ -28,19 +28,19 @@
 public class DispatchRequestBody extends SparqlConnRequestBody {
 	@Schema(
 			description = "EDC query constraints json",
-			required = false,
+			requiredMode = Schema.RequiredMode.NOT_REQUIRED,
 			example = "{ optional complex json }")
 	private String externalDataConnectionConstraints;
 
 	@Schema(
 			description = "Query flags array",
-			required = false,
-			example = "[\"FLAG1\", \"FLAG2\"]")
+			requiredMode = Schema.RequiredMode.NOT_REQUIRED,
+			example = "[\"PRUNE_TO_COLUMN:myCol\", \"UNOPTIONALIZE_CONSTRAINED\"]")
 	private String flags; // json array
 
 	@Schema(
 			description = "Runtime constraints json",
-			required = false,
+			requiredMode = Schema.RequiredMode.NOT_REQUIRED,
 			example = "\"[{\"SparqlID\":\"?id\",\"Operator\":\"MATCHES\",\"Operands\":[\"98243-T\"]}]\"")
 	private String runtimeConstraints;
 

diff --git a/...rc/main/java/com/ge/research/semtk/services/dispatch/DispatcherServiceRestController.java b/...rc/main/java/com/ge/research/semtk/services/dispatch/DispatcherServiceRestController.java
@@ -62,6 +62,7 @@
 import com.ge.research.semtk.springutillib.properties.EnvironmentProperties;
 import com.ge.research.semtk.springutillib.properties.ServicesGraphProperties;
 import com.ge.research.semtk.sparqlX.asynchronousQuery.AsynchronousNodeGroupBasedQueryDispatcher;
+import com.ge.research.semtk.sparqlX.dispatch.QueryFlags;
 
 @RestController
 @RequestMapping("/dispatcher")
@@ -326,7 +327,11 @@ public JSONObject queryFromNodeGroup(@RequestBody QueryRequestBody requestBody,
 		try {
 			dsp = getDispatcher(props, jobId, (NodegroupRequestBody) requestBody, useAuth, true);
 			dsp.getJobTracker().incrementPercentComplete(dsp.getJobId(), 1, 10);
-			dsp.addPruneToColumn(requestBody.getPruneToColumn());
+
+			QueryFlags flags = requestBody.getFlags();
+			if (flags != null) {
+				dsp.addPruneToColumn(flags.get(QueryFlags.PRUNE_TO_COL));
+			}
 
 			WorkThread thread = new WorkThread(dsp, requestBody.getExternalConstraints(), requestBody.getFlags(), qt, rt);
 

diff --git a/...spatchService/src/main/java/com/ge/research/semtk/services/dispatch/QueryRequestBody.java b/...spatchService/src/main/java/com/ge/research/semtk/services/dispatch/QueryRequestBody.java
@@ -31,16 +31,9 @@ public class QueryRequestBody extends NodegroupRequestBody {
 	@Schema(required = false,  example = "[{\"SparqlID\":\"?name\",\"Operator\":\"MATCHES\",\"Operands\":[\"Fred\"]}]")
 	private String constraintSet;	
 
-	@Schema(required = false,  example = "[\"UNOPTIONALIZE_CONSTRAINED\"]")
+	@Schema(required = false,  example = "[\"UNOPTIONALIZE_CONSTRAINED\", \"PRUNE_TO_COLUMN:myCol\"]")
 	private String flags;			// a string parseable to a JSONArray
 
-	// This is custom optional field only available through straight REST
-	// for Saqib @ collins
-	@Schema(
-			description = "Prune select table return down to one column and uniquify.",
-			required = false,
-			example = "favorite_column")
-	private String pruneToColumn = null;
 
 	public void setConstraintSet(String constraintSet){
 		this.constraintSet = constraintSet;
@@ -67,11 +60,4 @@ public QueryFlags getFlags() throws Exception{
 		return new QueryFlags(Utility.getJsonArrayFromString(this.flags));
 	}
 
-	public void setPruneToColumn(String val) {
-		this.pruneToColumn = val;
-	}
-	public String getPruneToColumn() {
-		return this.pruneToColumn;
-	}
-
 }
diff --git a/...Library/src/main/java/com/ge/research/semtk/api/nodeGroupExecution/NodeGroupExecutor.java b/...Library/src/main/java/com/ge/research/semtk/api/nodeGroupExecution/NodeGroupExecutor.java
@@ -302,39 +302,6 @@ public void dispatchRawSparqlUpdate(SparqlConnection sc, String sparqlQuery) thr
 		this.setJobID(simpleRes.getResult("requestID"));
 	}
 
-	/**
-	 * Version without queryFlags or pruneToColumn
-	 * @param qt
-	 * @param rt
-	 * @param sc
-	 * @param ng
-	 * @param externalConstraints
-	 * @param runtimeConstraints
-	 * @param targetObjectSparqlID
-	 * @throws Exception
-	 */
-	public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt,SparqlConnection sc, NodeGroup ng, JSONObject externalConstraints, JSONArray runtimeConstraints, String targetObjectSparqlID) throws Exception{
-		this.dispatchJob(qt, rt, sc, ng, externalConstraints, null, runtimeConstraints, -1, -1, targetObjectSparqlID, null);
-	}
-
-	/**
-	 * Version without pruneToColumn
-	 * @param qt
-	 * @param rt
-	 * @param sc
-	 * @param ng
-	 * @param externalConstraints
-	 * @param flags
-	 * @param runtimeConstraints
-	 * @param limitOverride
-	 * @param offsetOverride
-	 * @param targetObjectSparqlID
-	 * @param pruneToColumn
-	 * @throws Exception
-	 */
-	public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, SparqlConnection sc, NodeGroup ng, JSONObject externalConstraints, QueryFlags flags, JSONArray runtimeConstraints, int limitOverride, int offsetOverride, String targetObjectSparqlID) throws Exception{
-		this.dispatchJob(qt, rt, sc, ng, externalConstraints, flags, runtimeConstraints, -1, -1, targetObjectSparqlID, null);
-	}
 
 	/**
 	 * 
@@ -348,11 +315,10 @@ public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, Sparql
 	 * @param limitOverride
 	 * @param offsetOverride
 	 * @param targetObjectSparqlID
-	 * @param pruneToColumn - unusual special : prune a SELECT table result to only this column, uniquified
 	 * @throws Exception
 	 */
 	@SuppressWarnings("unchecked")
-	public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, SparqlConnection sc, NodeGroup ng, JSONObject externalConstraints, QueryFlags flags, JSONArray runtimeConstraints, int limitOverride, int offsetOverride, String targetObjectSparqlID, String pruneToColumn) throws Exception{
+	public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, SparqlConnection sc, NodeGroup ng, JSONObject externalConstraints, QueryFlags flags, JSONArray runtimeConstraints, int limitOverride, int offsetOverride, String targetObjectSparqlID) throws Exception{
 		// externalConstraints as used by executeQueryFromNodeGroup
 
 		LocalLogger.logToStdOut("Sending a " + qt + " query to the dispatcher...");
@@ -396,7 +362,7 @@ public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, Sparql
 		SparqlGraphJson sgjson = new SparqlGraphJson(ng, sc);
 		SimpleResultSet simpleRes = null;
 
-		simpleRes = this.dispatchClient.executeQuery(sgjson, qt, rt, externalConstraints, flags, targetObjectSparqlID, pruneToColumn);
+		simpleRes = this.dispatchClient.executeQuery(sgjson, qt, rt, externalConstraints, flags, targetObjectSparqlID);
 		simpleRes.throwExceptionIfUnsuccessful();
 
 		// set up the Job ID
@@ -405,7 +371,7 @@ public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, Sparql
 	}
 
 	/**
-	 * Version without queryFlags or pruneToColumn
+	 * Version without queryFlags
 	 * @param qt
 	 * @param rt
 	 * @param sc
@@ -416,26 +382,9 @@ public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, Sparql
 	 * @throws Exception
 	 */
 	public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt,SparqlConnection sc, String storedNodeGroupId, JSONObject externalConstraints, JSONArray runtimeConstraints, String targetObjectSparqlID) throws Exception{
-		this.dispatchJob(qt, rt, sc, storedNodeGroupId, externalConstraints, null, runtimeConstraints, -1, -1, targetObjectSparqlID, null);
+		this.dispatchJob(qt, rt, sc, storedNodeGroupId, externalConstraints, null, runtimeConstraints, -1, -1, targetObjectSparqlID);
 	}
 
-	/**
-	 * Version without pruneToColumn
-	 * @param qt
-	 * @param rt
-	 * @param sc
-	 * @param storedNodeGroupId
-	 * @param externalConstraints
-	 * @param flags
-	 * @param runtimeConstraints
-	 * @param limitOverride
-	 * @param offsetOverride
-	 * @param targetObjectSparqlID
-	 * @throws Exception
-	 */
-	public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, SparqlConnection sc, String storedNodeGroupId, JSONObject externalConstraints, QueryFlags flags, JSONArray runtimeConstraints, int limitOverride, int offsetOverride, String targetObjectSparqlID) throws Exception{
-		this.dispatchJob(qt, rt, sc, storedNodeGroupId, externalConstraints, flags, runtimeConstraints, -1, -1, targetObjectSparqlID, null);
-	}
 	/**
 	 * 
 	 * @param qt
@@ -446,7 +395,7 @@ public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, Sparql
 	 * @param targetObjectSparqlID
 	 * @throws Exception
 	 */
-	public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, SparqlConnection sc, String storedNodeGroupId, JSONObject externalConstraints, QueryFlags flags, JSONArray runtimeConstraints, int limitOverride, int offsetOverride, String targetObjectSparqlID, String pruneToColumn) throws Exception{
+	public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, SparqlConnection sc, String storedNodeGroupId, JSONObject externalConstraints, QueryFlags flags, JSONArray runtimeConstraints, int limitOverride, int offsetOverride, String targetObjectSparqlID) throws Exception{
 
 		// get the node group from the remote store
 		TableResultSet trs = this.storeClient.executeGetNodeGroupById(storedNodeGroupId);
@@ -491,7 +440,7 @@ public void dispatchJob(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, Sparql
 		}
 
 		// dispatch the job itself
-		this.dispatchJob(qt, rt, conn, ng, externalConstraints, flags, runtimeConstraints, limitOverride, offsetOverride, targetObjectSparqlID, pruneToColumn);
+		this.dispatchJob(qt, rt, conn, ng, externalConstraints, flags, runtimeConstraints, limitOverride, offsetOverride, targetObjectSparqlID);
 	}
 
 	public URL[] dispatchJobSynchronous(AutoGeneratedQueryTypes qt, SparqlResultTypes rt, SparqlConnection sc, String storedNodeGroupId, JSONObject externalConstraints, JSONArray runtimeConstraints, String targetObjectSparqlID) throws Exception {

diff --git a/...in/java/com/ge/research/semtk/api/nodeGroupExecution/client/NodeGroupExecutionClient.java b/...in/java/com/ge/research/semtk/api/nodeGroupExecution/client/NodeGroupExecutionClient.java
@@ -82,7 +82,6 @@ public class NodeGroupExecutionClient extends SharedIngestNgeClient {
 	private static final String JSON_KEY_RUNTIME_CONSTRAINTS = "runtimeConstraints";
 	private static final String JSON_KEY_EDC_CONSTRAINTS = "externalDataConnectionConstraints";
 	private static final String JSON_KEY_FLAGS = "flags";
-	private static final String JSON_KEY_PRUNE_TO_COLUMN = "pruneToColumn";
 
 	// service mapping
 	private static final String mappingPrefix = "/nodeGroupExecution";
@@ -518,13 +517,12 @@ public Table execDispatchSelectByIdToTable(String nodegroupID, SparqlConnection
 	 * @param runtimeConstraintsJson
 	 * @param limitOverride
 	 * @param offsetOverride
-	 * @param pruneToColumn
 	 * @return
 	 * @throws Exception
 	 */
-	public Table execDispatchByIdToTable(String nodegroupID, SparqlConnection overrideConn, JSONObject edcConstraintsJson, JSONArray flagsJson, JSONArray runtimeConstraintsJson, int limitOverride, int offsetOverride, String pruneToColumn) throws Exception{
+	public Table execDispatchByIdToTable(String nodegroupID, SparqlConnection overrideConn, JSONObject edcConstraintsJson, JSONArray flagsJson, JSONArray runtimeConstraintsJson, int limitOverride, int offsetOverride) throws Exception{
 		// dispatch the job
-		String jobId = this.dispatchByIdToJobId(nodegroupID, overrideConn, edcConstraintsJson, flagsJson, runtimeConstraintsJson, limitOverride, offsetOverride, pruneToColumn);
+		String jobId = this.dispatchByIdToJobId(nodegroupID, overrideConn, edcConstraintsJson, flagsJson, runtimeConstraintsJson, limitOverride, offsetOverride);
 
 		try {
 			return this.waitForJobAndGetTable(jobId);
@@ -1638,12 +1636,11 @@ public Table getRuntimeConstraintsByNodeGroupID(String nodegroupID) throws Excep
 	 * @param runtimeConstraintsJson
 	 * @param limitOverride
 	 * @param offsetOverride
-	 * @param pruneToColumn
 	 * @return String jobId
 	 * @throws Exception
 	 */
-	public String dispatchByIdToJobId(String nodegroupID, SparqlConnection overrideConn, JSONObject edcConstraintsJson, JSONArray flagsJson, JSONArray runtimeConstraintsJson, int limitOverride, int offsetOverride, String pruneToColumn) throws Exception{
-		SimpleResultSet ret =  this.execDispatchById(nodegroupID, overrideConn, edcConstraintsJson, flagsJson, runtimeConstraintsJson, limitOverride, offsetOverride, pruneToColumn);
+	public String dispatchByIdToJobId(String nodegroupID, SparqlConnection overrideConn, JSONObject edcConstraintsJson, JSONArray flagsJson, JSONArray runtimeConstraintsJson, int limitOverride, int offsetOverride) throws Exception{
+		SimpleResultSet ret =  this.execDispatchById(nodegroupID, overrideConn, edcConstraintsJson, flagsJson, runtimeConstraintsJson, limitOverride, offsetOverride);
 		return ret.getResult("JobId");
 	}
 
@@ -1663,7 +1660,7 @@ public String dispatchByIdToJobId(String nodegroupID, SparqlConnection overrideC
 	}
 
 	/**
-	 * Raw call to launch a select query:  version without query flags or pruneToColumn
+	 * Raw call to launch a select query:  version without query flags 
 	 * @param nodegroupID
 	 * @param overrideConn
 	 * @param edcConstraintsJson
@@ -1672,22 +1669,10 @@ public String dispatchByIdToJobId(String nodegroupID, SparqlConnection overrideC
 	 * @throws Exception
 	 */
 	public SimpleResultSet execDispatchById(String nodegroupID, SparqlConnection overrideConn, JSONObject edcConstraintsJson, JSONArray runtimeConstraintsJson) throws Exception{
-		return this.execDispatchById(nodegroupID, overrideConn, edcConstraintsJson, null, runtimeConstraintsJson, -1, -1, null);
+		return this.execDispatchById(nodegroupID, overrideConn, edcConstraintsJson, null, runtimeConstraintsJson, -1, -1);
 	}
 
-	/**
-	 * Raw call to launch a select query:  version without pruneToColumn
-	 * @param nodegroupID
-	 * @param overrideConn
-	 * @param edcConstraintsJson
-	 * @param flagsJson
-	 * @param runtimeConstraintsJson
-	 * @return
-	 * @throws Exception
-	 */
-	public SimpleResultSet execDispatchById(String nodegroupID, SparqlConnection overrideConn, JSONObject edcConstraintsJson, JSONArray flagsJson, JSONArray runtimeConstraintsJson, int limitOverride, int offsetOverride) throws Exception{
-		return this.execDispatchById(nodegroupID, overrideConn, edcConstraintsJson, flagsJson, runtimeConstraintsJson, limitOverride, offsetOverride, null);
-	}
+
 
 	/**
 	 * Raw call to launch a select query
@@ -1698,12 +1683,11 @@ public SimpleResultSet execDispatchById(String nodegroupID, SparqlConnection ove
 	 * @param runtimeConstraintsJson
 	 * @param limitOverride
 	 * @param offsetOverride
-	 * @param pruneToColumn
 	 * @return SimpleResultSet containing "JobId"
 	 * @throws Exception
 	 */
 	@SuppressWarnings("unchecked")
-	public SimpleResultSet execDispatchById(String nodegroupID, SparqlConnection overrideConn, JSONObject edcConstraintsJson, JSONArray flagsJson, JSONArray runtimeConstraintsJson, int limitOverride, int offsetOverride, String pruneToColumn) throws Exception{
+	public SimpleResultSet execDispatchById(String nodegroupID, SparqlConnection overrideConn, JSONObject edcConstraintsJson, JSONArray flagsJson, JSONArray runtimeConstraintsJson, int limitOverride, int offsetOverride) throws Exception{
 		SimpleResultSet retval = null;
 
 		conf.setServiceEndpoint(mappingPrefix + dispatchByIdEndpoint);
@@ -1716,8 +1700,6 @@ public SimpleResultSet execDispatchById(String nodegroupID, SparqlConnection ove
 		this.parametersJSON.put(JSON_KEY_EDC_CONSTRAINTS, edcConstraintsJson == null ? null : edcConstraintsJson.toJSONString());	
 		this.parametersJSON.put(JSON_KEY_FLAGS, flagsJson == null ? null : flagsJson.toJSONString());
 		this.parametersJSON.put(JSON_KEY_RUNTIME_CONSTRAINTS,            runtimeConstraintsJson == null ? null : runtimeConstraintsJson.toJSONString());		
-		if (pruneToColumn != null)
-			this.parametersJSON.put(JSON_KEY_PRUNE_TO_COLUMN, pruneToColumn);
 
 		try{
 			LocalLogger.logToStdErr("sending executeDispatchById request");

diff --git a/...e/research/semtk/sparqlX/asynchronousQuery/AsynchronousNodeGroupBasedQueryDispatcher.java b/...e/research/semtk/sparqlX/asynchronousQuery/AsynchronousNodeGroupBasedQueryDispatcher.java
@@ -47,7 +47,7 @@
  * Base class for dispatchers.
  */
 public abstract class AsynchronousNodeGroupBasedQueryDispatcher {
-	private String pruneToColumn;
+	private String pruneToColumn = null;
 
 	protected NodeGroup queryNodeGroup;
 	protected OntologyInfoClient oInfoClient;
@@ -335,6 +335,10 @@ public JobTracker getJobTracker() {
 		return this.jobTracker;
 	}
 
+	/**
+	 * Add column name for prune feature (prune table to single unique column)
+	 * @param pruneToColumn - column name or null
+	 */
 	public void addPruneToColumn(String pruneToColumn) {
 		this.pruneToColumn = pruneToColumn;