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sparqlGraph use N_TRIPLES as the resultType for all CONSTRUCT queries.
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Paul Cuddihy committed Apr 18, 2023
1 parent eba33bc commit 2425815
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Showing 10 changed files with 402 additions and 95 deletions.
13 changes: 13 additions & 0 deletions connectionUtils/src/main/java/com/ge/research/semtk/sparqlX/SparqlEndpointInterface.java
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Expand Up @@ -620,6 +620,19 @@ public String executeQueryToRdf(String query) throws Exception {
return (String) res.getResult(SparqlResultTypes.RDF.toString());
}

/**
*
* WARNING: see INTERNAL USE notes at top of this file
* @param query
* @return
* @throws Exception
*/
public String executeQueryToNtriples(String query) throws Exception {
SimpleResultSet res = (SimpleResultSet) this.executeQueryAndBuildResultSet(query, SparqlResultTypes.N_TRIPLES);
res.throwExceptionIfUnsuccessful();
return (String) res.getResult(SparqlResultTypes.N_TRIPLES.toString());
}

/**
* Execute query to table
* WARNING: see INTERNAL USE notes at top of this file
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3 changes: 2 additions & 1 deletion ...a/com/ge/research/semtk/services/nodeGroupExecution/NodeGroupExecutionRestController.java
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Expand Up @@ -1038,13 +1038,14 @@ public JSONObject constructConnectedData(@RequestBody ConstructConnectedDataRequ
ResultsClient resClient = results_prop.getClient();

ConnectedDataConstructor constructor = new ConnectedDataConstructor(
requestBody.getInstanceVal(), requestBody.buildInstanceType(),
requestBody.getInstanceVal(), requestBody.buildInstanceType(), requestBody.getResultType(),
conn, this.retrieveOInfo(conn), getJobTracker(), resClient);

constructor.start();

retval.setSuccess(true);
retval.addResult(SimpleResultSet.JOB_ID_RESULT_KEY, constructor.getJobId());
retval.addResult(SimpleResultSet.RESULT_TYPE_KEY, requestBody.getResultType().toString());

} catch(Exception e){
retval.setSuccess(false);
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18 changes: 13 additions & 5 deletions ...ge/research/semtk/services/nodeGroupExecution/requests/ConstructConnectedDataRequest.java
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Expand Up @@ -16,6 +16,7 @@
*/

package com.ge.research.semtk.services.nodeGroupExecution.requests;
import com.ge.research.semtk.sparqlX.SparqlResultTypes;
import com.ge.research.semtk.sparqlX.XSDSupportedType;
import com.ge.research.semtk.springutilib.requests.SparqlConnectionRequest;

Expand All @@ -24,18 +25,25 @@

public class ConstructConnectedDataRequest extends SparqlConnectionRequest {

@Schema(
required = true,
@Schema(requiredMode = Schema.RequiredMode.NOT_REQUIRED,
example = "http://path#this")
private String instanceVal;

@Schema(
required = false,
@Schema(requiredMode = Schema.RequiredMode.NOT_REQUIRED,
example = "node_uri")
private String instanceType = null;

@Schema(requiredMode = Schema.RequiredMode.NOT_REQUIRED,
description = "Defaults to json-ld",
example = "N_TRIPLES")
public SparqlResultTypes resultType = SparqlResultTypes.GRAPH_JSONLD;


public String getInstanceVal() {
public SparqlResultTypes getResultType() {
return resultType;
}

public String getInstanceVal() {
return instanceVal;
}

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45 changes: 25 additions & 20 deletions ...phLibrary/src/main/java/com/ge/research/semtk/ontologyTools/ConnectedDataConstructor.java
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Expand Up @@ -9,13 +9,15 @@
import com.ge.research.semtk.edc.client.ResultsClient;
import com.ge.research.semtk.sparqlToXLib.SparqlToXLibUtil;
import com.ge.research.semtk.sparqlX.SparqlConnection;
import com.ge.research.semtk.sparqlX.SparqlResultTypes;
import com.ge.research.semtk.sparqlX.XSDSupportedType;
import com.ge.research.semtk.utility.LocalLogger;

public class ConnectedDataConstructor extends Thread {

private String instanceVal = null;
private XSDSupportedType instanceType = null;
private SparqlResultTypes resultType = SparqlResultTypes.GRAPH_JSONLD;
private SparqlConnection conn = null;
private OntologyInfo oInfo = null;
private JobTracker tracker = null;
Expand All @@ -34,10 +36,15 @@ public class ConnectedDataConstructor extends Thread {
* @param resClient - "
* @throws Exception
*/
public ConnectedDataConstructor(String instanceVal, XSDSupportedType instanceType, SparqlConnection conn, OntologyInfo oInfo, JobTracker tracker, ResultsClient resClient) throws Exception {
public ConnectedDataConstructor(String instanceVal, XSDSupportedType instanceType, SparqlResultTypes resultType, SparqlConnection conn, OntologyInfo oInfo, JobTracker tracker, ResultsClient resClient) throws Exception {

this.instanceVal = instanceVal;
this.instanceType = instanceType;
this.resultType = resultType;

if (resultType != SparqlResultTypes.GRAPH_JSONLD && resultType != SparqlResultTypes.N_TRIPLES)
throw new Exception("Unsupported result type: " + resultType.toString());

this.conn = conn;
this.oInfo = oInfo;
this.tracker = tracker;
Expand All @@ -49,27 +56,14 @@ public ConnectedDataConstructor(String instanceVal, XSDSupportedType instanceTyp
this.resClient = resClient;
}

public ConnectedDataConstructor(String instanceVal, XSDSupportedType instanceType, SparqlConnection conn) throws Exception {
this(instanceVal, instanceType, conn, null, null, null);
public ConnectedDataConstructor(String instanceVal, XSDSupportedType instanceType, SparqlResultTypes resultType, SparqlConnection conn) throws Exception {
this(instanceVal, instanceType, resultType, conn, null, null, null);
}

public String getJobId() {
return this.jobId;
}
public JSONObject queryJsonLd() throws Exception {
JSONObject ret = null;

if (this.oInfo == null) {
this.oInfo = new OntologyInfo(this.conn);
}
String sparql = SparqlToXLibUtil.generateConstructConnected(this.conn, this.oInfo, this.instanceVal, this.instanceType);
ret = this.conn.getDefaultQueryInterface().executeQueryToJsonLd(sparql);

// TODO: use oInfo to clean stuff out

return ret;
}


public void run() {

try {
Expand All @@ -80,10 +74,21 @@ public void run() {

this.tracker.setJobPercentComplete(this.jobId, 10, "Querying data");

JSONObject jObj = this.queryJsonLd();

tracker.setJobPercentComplete(this.jobId, 90, "Storing results");
resClient.execStoreGraphResults(this.jobId, jObj);

if (this.oInfo == null) {
this.oInfo = new OntologyInfo(this.conn);
}
String sparql = SparqlToXLibUtil.generateConstructConnected(this.conn, this.oInfo, this.instanceVal, this.instanceType);

if (this.resultType == SparqlResultTypes.GRAPH_JSONLD) {
resClient.execStoreGraphResults(this.jobId, this.conn.getDefaultQueryInterface().executeQueryToJsonLd(sparql));

} else if (this.resultType == SparqlResultTypes.N_TRIPLES) {
JSONObject jObj = new JSONObject();
jObj.put(SparqlResultTypes.N_TRIPLES.toString(), this.conn.getDefaultQueryInterface().executeQueryToNtriples(sparql));
resClient.execStoreGraphResults(this.jobId, jObj);
}

this.tracker.setJobSuccess(this.jobId);

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1 change: 1 addition & 0 deletions sparqlGraphWeb/sparqlGraph/js/belmont.js
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Expand Up @@ -1829,6 +1829,7 @@ SemanticNodeGroup.RT_JSONLD = "GRAPH_JSONLD";
SemanticNodeGroup.RT_CONFIRM = "CONFIRM";
SemanticNodeGroup.RT_OWLRDF = "RDF";
SemanticNodeGroup.RT_HTML = "HTML";
SemanticNodeGroup.RT_NTRIPLES = "N_TRIPLES";

SemanticNodeGroup.FUNCTION_MIN = 0;
SemanticNodeGroup.FUNCTION_MAX = 1;
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31 changes: 22 additions & 9 deletions sparqlGraphWeb/sparqlGraph/js/exploretab.js
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Expand Up @@ -763,10 +763,10 @@ define([ // properly require.config'ed
IIDXHelper.progressBarCreate(this.progressDiv, "progress-info progress-striped active");
IIDXHelper.progressBarSetPercent(this.progressDiv, 0, "");
this.busy(true);
client.execAsyncDispatchRawSparql(sparql, gConn, jsonLdCallback, failureCallback, "GRAPH_JSONLD");
client.execAsyncDispatchRawSparql(sparql, gConn, jsonLdCallback, failureCallback, SemanticNodeGroup.RT_NTRIPLES);
},

drawOntologyDetailCallback : function (jsonLdResults) {
drawOntologyDetailCallback : function (res) {
IIDXHelper.progressBarSetPercent(this.progressDiv, 90);

var network = this.networkHash[ExploreTab.MODE_ONTOLOGY_DETAIL];
Expand All @@ -776,16 +776,29 @@ define([ // properly require.config'ed
network.deleteSelected();

// add new
var jsonLd = jsonLdResults.getGraphResultsJsonArr(false, false, false);
var edgeList = [];
var nodeDict = {};
for (var i=0; i < jsonLd.length; i++) {
VisJsHelper.addJsonLdObject(jsonLd[i], nodeDict, edgeList, true);
if (i % 20 == 0) {
network.body.data.nodes.update(Object.values(nodeDict));
network.body.data.edges.update(edgeList);
}

if (res.isJsonLdResults()) {
var jsonLd = res.getGraphResultsJsonArr(false, false, false);
for (var i=0; i < jsonLd.length; i++) {
VisJsHelper.addJsonLdObject(jsonLd[i], nodeDict, edgeList, true);
if (i % 20 == 0) {
network.body.data.nodes.update(Object.values(nodeDict));
network.body.data.edges.update(edgeList);
}
}
} else if (res.isNtriplesResults()) {
triples = res.getNtriplesArray();
for (var i=0; i < triples.length; i++) {
VisJsHelper.addTriple(triples[i], nodeDict, edgeList, true, false);
if (i % 20 == 0) {
network.body.data.nodes.update(Object.values(nodeDict));
network.body.data.edges.update(edgeList);
}
}
}

network.body.data.nodes.update(Object.values(nodeDict));
network.body.data.edges.update(edgeList);

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40 changes: 26 additions & 14 deletions sparqlGraphWeb/sparqlGraph/js/msiclientnodegroupexec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -279,36 +279,47 @@ define([ // properly require.config'ed bootstrap-modal
** You can build a jobIdCallback with one of the
** MsiClientNodeGroupExec.build___Callback() functions
*/
/* deprecated: use execAsyncDisatchQueryFromNodeGroup */
execAsyncDispatchConstructFromNodeGroup : function(nodegroup, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback) {
this.runAsyncNodegroup("dispatchConstructFromNodegroup",
nodegroup, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback);
},

/* deprecated: use execAsyncDisatchQueryFromNodeGroup */
execAsyncDispatchSelectFromNodeGroup : function(nodegroup, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback) {
this.runAsyncNodegroup("dispatchSelectFromNodegroup",
nodegroup, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback);
},
execAsyncDispatchQueryFromNodeGroup : function(nodegroup, conn, queryType, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback) {
var data = JSON.stringify ({
"jsonRenderedNodeGroup": JSON.stringify(nodegroup.toJson()),
"sparqlConnection": JSON.stringify(conn.toJson()),
"queryType" : queryType,
"runtimeConstraints": (typeof runtimeConstraints == "undefined" || runtimeConstraints == null) ? "" : JSON.stringify(runtimeConstraints.toJson()),
"externalDataConnectionConstraints": (typeof edcConstraints == "undefined" || edcConstraints == null) ? "" : JSON.stringify(edcConstraints.toJson())
});

this.runAsync("dispatchQueryFromNodegroup", data, jobIdCallback, failureCallback);
/* === latest: replaces others ===
** execute query from a nodegroup
** query
*/
execAsyncDispatchQueryFromNodeGroup : function(nodegroup, optConn, jobIdCallback, optFailureCallback, optQueryType, optResultType, optRuntimeConstraints, optEdcConstraints, optTargetId, optFlags) {

var data = {};
data["jsonRenderedNodeGroup"] = JSON.stringify(nodegroup.toJson());

if (optQueryType) data["queryType"] = optQueryType;
if (optResultType) data["resultType"] = optResultType;
if (optConn) data["sparqlConnection"] = JSON.stringify(optConn.toJson());
if (optFlags) data["flags"] = optFlags;
if (optTargetId) data["targetObjectSparqlId"] = optTargetId;
if (optRuntimeConstraints) data["runtimeConstraints"] = JSON.stringify(optRuntimeConstraints.toJson());
if (optEdcConstraints) data["externalDataConnectionConstraints"] = JSON.stringify(optEdcConstraints.toJson());

this.runAsync("dispatchQueryFromNodegroup", JSON.stringify(data), jobIdCallback, optFailureCallback);
},

/* deprecated: use execAsyncDisatchQueryFromNodeGroup */
execAsyncDispatchDeleteFromNodeGroup : function(nodegroup, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback) {
this.runAsyncNodegroup("dispatchDeleteFromNodegroup",
nodegroup, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback);
},

/* deprecated: use execAsyncDisatchQueryFromNodeGroup */
execAsyncDispatchCountFromNodeGroup : function(nodegroup, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback) {
this.runAsyncNodegroup("dispatchCountFromNodegroup",
nodegroup, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback);
},

/* deprecated: use execAsyncDisatchQueryFromNodeGroup */
execAsyncDispatchFilterFromNodeGroup : function(nodegroup, conn, sparqlId, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback) {
this.runAsyncNodegroupSparqlId("dispatchFilterFromNodegroup",
nodegroup, sparqlId, conn, edcConstraints, runtimeConstraints, jobIdCallback, failureCallback);
Expand Down Expand Up @@ -352,10 +363,11 @@ define([ // properly require.config'ed bootstrap-modal
sei, jobIdCallback, failureCallback);
},

execAsyncConstructConnectedData : function(instanceVal, instanceType, conn, jobIdCallback, failureCallback) {
execAsyncConstructConnectedData : function(instanceVal, instanceType, resultType, conn, jobIdCallback, failureCallback) {
var data = JSON.stringify ({
"instanceVal" : instanceVal,
"instanceType": instanceType,
"resultType": resultType,
"conn": JSON.stringify(conn.toJson())
});

Expand Down
18 changes: 18 additions & 0 deletions sparqlGraphWeb/sparqlGraph/js/msiresultset.js
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,10 @@ define([ // properly require.config'ed bootstrap-modal
isJsonLdResults : function () {
return this.xhr.hasOwnProperty("@graph") || this.xhr.hasOwnProperty("@id") || this.xhr.hasOwnProperty("@context") || JSON.stringify(this.xhr) === "{}";
},

isNtriplesResults : function () {
return this.xhr.hasOwnProperty("N_TRIPLES");
},

getColumnName : function (x) {
return this.getTable().col_names[x];
Expand Down Expand Up @@ -116,6 +120,20 @@ define([ // properly require.config'ed bootstrap-modal
}
return graphArr;
},

getNtriplesText : function() {
return this.xhr["N_TRIPLES"];
},

getNtriplesArray : function() {
ret = []
for (let line of this.getNtriplesText().split("\n") ) {
f = line.replace(/\s*\.\s*$/, "").split(" ");
if (f[0] && f[1])
ret.push([ f[0], f[1], f.slice(2,).join(" ") ]);
}
return ret;
},

// use json-ld @context to expand a json-ld array
expandJsonArrWithContext : function(jArr) {
Expand Down
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