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passed marklogic junits by having rest clients setUserAndPasswordIfEm…
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…pty()
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Paul Cuddihy committed Sep 11, 2023
1 parent 7b04811 commit 193dc3d
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Showing 20 changed files with 224 additions and 101 deletions.
4 changes: 2 additions & 2 deletions ...onUtils/src/main/java/com/ge/research/semtk/sparqlX/MarkLogicSparqlEndpointInterface.java
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Original file line number Diff line number Diff line change
Expand Up @@ -90,12 +90,12 @@ public class MarkLogicSparqlEndpointInterface extends SparqlEndpointInterface {
* @throws Exception
*/
public MarkLogicSparqlEndpointInterface(String server, String graph) throws Exception {
super(server, graph, "test", "password");
super(server, graph, "", "");

}

public MarkLogicSparqlEndpointInterface(String server, String graph, String user, String pass) throws Exception {
super(server, graph, user!=null?user:"test", pass!=null?pass:"password");
super(server, graph, user, pass);

}
// For MarkLogic, we're storing the database in "endpoint"
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12 changes: 11 additions & 1 deletion connectionUtils/src/main/java/com/ge/research/semtk/sparqlX/SparqlConnection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -245,7 +245,17 @@ public void overrideSparqlServer(String serverAndPort) throws Exception {
* @throws Exception
*/
public static SparqlConnection deepCopy(SparqlConnection other) throws Exception {
return new SparqlConnection(other.toJson().toString());
SparqlConnection ret = new SparqlConnection(other.toJson().toString());
// copy passwords too
for (int i=0; i < other.getModelInterfaceCount(); i++) {
SparqlEndpointInterface osei = other.getModelInterface(i);
ret.modelInterfaces.get(i).setUserAndPassword(osei.getUserName(), osei.getPassword());
}
for (int i=0; i < other.getDataInterfaceCount(); i++) {
SparqlEndpointInterface osei = other.getDataInterface(i);
ret.dataInterfaces.get(i).setUserAndPassword(osei.getUserName(), osei.getPassword());
}
return ret;
}

/**
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55 changes: 39 additions & 16 deletions ...a/com/ge/research/semtk/services/nodeGroupExecution/NodeGroupExecutionRestController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,7 @@
import com.ge.research.semtk.springutillib.properties.StatusServiceProperties;
import com.ge.research.semtk.springutillib.properties.NodegroupStoreServiceProperties;
import com.ge.research.semtk.springutillib.properties.OntologyInfoServiceProperties;
import com.ge.research.semtk.springutillib.properties.QueryServiceProperties;
import com.ge.research.semtk.springutillib.properties.ResultsServiceProperties;
import com.ge.research.semtk.springutillib.properties.ServicesGraphProperties;
import com.ge.research.semtk.utility.LocalLogger;
Expand Down Expand Up @@ -155,6 +156,8 @@ public class NodeGroupExecutionRestController {
private NodegroupStoreServiceProperties ngstore_prop;
@Autowired
private DispatchServiceProperties dispatch_prop;
@Autowired
private QueryServiceProperties query_prop;
@Autowired
private ResultsServiceProperties results_prop;
@Autowired
Expand All @@ -172,6 +175,7 @@ public void init() {
AuthorizationManager.authorizeWithExit(auth_prop);
ngstore_prop.validateWithExit();
dispatch_prop.validateWithExit();
query_prop.validateWithExit();
results_prop.validateWithExit();
status_prop.validateWithExit();
ingest_prop.validateWithExit();
Expand Down Expand Up @@ -531,7 +535,9 @@ public JSONObject dispatchAnyJobById(@RequestBody DispatchByIdRequestBody reques

NodeGroupExecutor ngExecutor = this.getExecutor(null );

SparqlConnection connection = requestBody.buildSparqlConnection();
SparqlConnection connection = requestBody.buildSparqlConnection();
query_prop.setUserAndPasswordIfMissing(connection);

// create a json object from the external data constraints.

// check if this is actually for a filter query
Expand Down Expand Up @@ -588,7 +594,7 @@ private JSONObject dispatchAnyJobFromNodegroup(@RequestBody DispatchFromNodegrou
if (connection == null || NodeGroupExecutor.isUseNodegroupConn(connection)) {
connection = sgJson.getSparqlConn();
}

query_prop.setUserAndPasswordIfMissing(connection);
String targetId = null;
if(requestBody instanceof FilterDispatchFromNodeGroupRequestBody){
// set the target ID
Expand Down Expand Up @@ -934,6 +940,7 @@ public JSONObject dispatchSelectInstanceDataPredicates(@RequestBody InstanceData

try {
SparqlConnection conn = new SparqlConnection(requestBody.getConn());
query_prop.setUserAndPasswordIfMissing(conn);
OntologyInfo oInfo = retrieveOInfo(conn);
ArrayList<String[]> pairsList = requestBody.buildPredicateListPairs();
if (pairsList.size() == 0) {
Expand Down Expand Up @@ -990,6 +997,7 @@ public JSONObject dispatchSelectInstanceDataSubjects(@RequestBody InstanceDataCl

try {
SparqlConnection conn = new SparqlConnection(requestBody.getConn());
query_prop.setUserAndPasswordIfMissing(conn);
OntologyInfo oInfo = retrieveOInfo(conn);
ArrayList<String> classList = requestBody.getClassValues();
if (classList.size() == 0) {
Expand Down Expand Up @@ -1041,6 +1049,7 @@ public JSONObject constructConnectedData(@RequestBody ConstructConnectedDataRequ
try {

SparqlConnection conn = requestBody.buildSparqlConnection();
query_prop.setUserAndPasswordIfMissing(conn);
ResultsClient resClient = results_prop.getClient();

ConnectedDataConstructor constructor = new ConnectedDataConstructor(
Expand Down Expand Up @@ -1076,7 +1085,8 @@ public JSONObject constructInstanceWithPredicates(@RequestBody ConstructInstance

try {
SparqlConnection conn = requestBody.buildSparqlConnection();

query_prop.setUserAndPasswordIfMissing(conn);

// create a nodegroup: instance connecting to given predicates
NodeGroup ng = new NodeGroup();
Node node = ng.addNode(requestBody.getInstanceClassUri(), this.retrieveOInfo(conn)); // add node for given class URI
Expand Down Expand Up @@ -1173,7 +1183,8 @@ public JSONObject dispatchRawSparql(@RequestBody DispatchRawSparqlRequestBody re

// try to create a sparql connection
SparqlConnection connection = requestBody.buildSparqlConnection();

query_prop.setUserAndPasswordIfMissing(connection);

// dispatch the job.
ngExecutor.dispatchRawSparql(connection, requestBody.getSparql(), requestBody.getResultType());
String id = ngExecutor.getJobID();
Expand Down Expand Up @@ -1217,7 +1228,8 @@ public JSONObject dispatchRawSparqlUpdate(@RequestBody DispatchRawSparqlRequestB
NodeGroupExecutor ngExecutor = this.getExecutor(null );
// try to create a sparql connection
SparqlConnection connection = requestBody.buildSparqlConnection();

query_prop.setUserAndPasswordIfMissing(connection);

// dispatch the job.
ngExecutor.dispatchRawSparqlUpdate(connection, requestBody.getSparql());
String id = ngExecutor.getJobID();
Expand Down Expand Up @@ -1262,9 +1274,7 @@ public JSONObject dispatchClearGraph(@RequestBody SparqlEndpointRequestBody requ
SparqlEndpointInterface sei = requestBody.buildSei();
SparqlEndpointInterface jobSei = servicesgraph_props.buildSei();

// PEC TODO security
// borrowing auth username password from the services graph
sei.setUserAndPassword(jobSei.getUserName(), jobSei.getPassword());
query_prop.setUserAndPasswordIfMissing(sei);

ResultsClient resClient = results_prop.getClient();

Expand Down Expand Up @@ -1322,6 +1332,8 @@ public JSONObject ingestFromCsvStrings(@RequestBody IngestByNodegroupCsvStrReque
NodeGroupExecutor nodeGroupExecutor = this.getExecutor(null);

SparqlGraphJson sparqlGraphJson = requestBody.buildSparqlGraphJson();
query_prop.setUserAndPasswordIfMissing(sparqlGraphJson);

retval = nodeGroupExecutor.ingestFromNodegroupAndCsvString(requestBody.buildSparqlConnection(), sparqlGraphJson, requestBody.getCsvContent(), requestBody.getTrackFlag(), requestBody.getOverrideBaseURI());
}catch(Exception e){
LoggerRestClient.easyLog(logger, SERVICE_NAME, ENDPOINT_NAME + " exception", "message", e.toString());
Expand Down Expand Up @@ -1358,6 +1370,7 @@ public JSONObject ingestFromCsvStringsAsync(@RequestBody IngestByNodegroupCsvStr
NodeGroupExecutor nodeGroupExecutor = this.getExecutor(null);

SparqlGraphJson sparqlGraphJson = requestBody.buildSparqlGraphJson();
query_prop.setUserAndPasswordIfMissing(sparqlGraphJson);
String jobId = nodeGroupExecutor.ingestFromNodegroupAndCsvStringAsync(
requestBody.buildSparqlConnection(),
sparqlGraphJson,
Expand Down Expand Up @@ -1403,8 +1416,9 @@ public JSONObject ingestFromCsvStringsById(@RequestBody IngestByIdCsvStrRequestB
RecordProcessResults retval = null;
try{
NodeGroupExecutor nodeGroupExecutor = this.getExecutor(null);

retval = nodeGroupExecutor.ingestFromNodegroupIdAndCsvString(requestBody.buildSparqlConnection(), requestBody.getNodegroupId(), requestBody.getCsvContent(), requestBody.getTrackFlag(), requestBody.getOverrideBaseURI());
SparqlConnection conn = requestBody.buildSparqlConnection();
query_prop.setUserAndPasswordIfMissing(conn);
retval = nodeGroupExecutor.ingestFromNodegroupIdAndCsvString(conn, requestBody.getNodegroupId(), requestBody.getCsvContent(), requestBody.getTrackFlag(), requestBody.getOverrideBaseURI());
}catch(Exception e){
LoggerRestClient.easyLog(logger, SERVICE_NAME, ENDPOINT_NAME + " exception", "message", e.toString());
retval = new RecordProcessResults(false);
Expand Down Expand Up @@ -1437,9 +1451,10 @@ public JSONObject ingestFromCsvStringsByIdAsync(@RequestBody IngestByIdCsvStrAsy
SimpleResultSet retval = null;
try{
NodeGroupExecutor nodeGroupExecutor = this.getExecutor(null);

SparqlConnection conn = requestBody.buildSparqlConnection();
query_prop.setUserAndPasswordIfMissing(conn);
String jobId = nodeGroupExecutor.ingestFromNodegroupIdAndCsvStringAsync(
requestBody.buildSparqlConnection(),
conn,
requestBody.getNodegroupId(),
requestBody.getCsvContent(),
requestBody.getSkipPrecheck(),
Expand Down Expand Up @@ -1479,6 +1494,7 @@ public JSONObject ingestFromCsvStringsByClassTemplateAsync(@RequestBody Ingestio
try {
// pass-through
IngestorRestClient iclient = ingest_prop.getClient();

String jobId = iclient.execFromCsvUsingClassTemplate(requestBody.getClassURI(), requestBody.getIdRegex(), requestBody.getData(), requestBody.getConnection(), requestBody.getTrackFlag(), requestBody.getOverrideBaseURI());

// success: add jobId
Expand Down Expand Up @@ -1701,6 +1717,7 @@ public JSONObject copyGraph(@RequestBody SparqlEndpointsRequestBody requestBody,
tracker.setJobPercentComplete(jobId, 10);
HeadersManager.setHeaders(headers);
SparqlEndpointInterface fromSei = requestBody.buildFromSei();
query_prop.setUserAndPasswordIfMissing(fromSei);

// fromGraph to temp file
String filename = UUID.randomUUID().toString();
Expand All @@ -1714,6 +1731,8 @@ public JSONObject copyGraph(@RequestBody SparqlEndpointsRequestBody requestBody,

// temp file to toGraph
SparqlEndpointInterface toSei = requestBody.buildToSei();
query_prop.setUserAndPasswordIfMissing(toSei);

InputStream fis = new FileInputStream(tempFile);
try {
this.uploadFile(toSei, fis, "temp.owl");
Expand Down Expand Up @@ -1770,7 +1789,9 @@ public JSONObject dispatchConstructToGraphById(@RequestBody DispatchConstructToG
try {
// dispatch
JSONObject simpleResJson = dispatchAnyJobById(requestBody, AutoGeneratedQueryTypes.CONSTRUCT, SparqlResultTypes.RDF);
waitThenStoreRdfToSei(jobId, (new SimpleResultSet(simpleResJson)).getJobId(), requestBody.buildResultsSei());
SparqlEndpointInterface sei = requestBody.buildResultsSei();
query_prop.setUserAndPasswordIfMissing(sei);
waitThenStoreRdfToSei(jobId, (new SimpleResultSet(simpleResJson)).getJobId(), sei);

} catch (Exception e) {
try {
Expand Down Expand Up @@ -1817,7 +1838,9 @@ public JSONObject dispatchConstructToGraphFromNodegroup(@RequestBody DispatchCon
try {
// dispatch
JSONObject simpleResJson = dispatchAnyJobFromNodegroup(requestBody, AutoGeneratedQueryTypes.CONSTRUCT, SparqlResultTypes.RDF);
waitThenStoreRdfToSei(jobId, (new SimpleResultSet(simpleResJson)).getJobId(), requestBody.buildResultsSei());
SparqlEndpointInterface sei = requestBody.buildResultsSei();
query_prop.setUserAndPasswordIfMissing(sei);
waitThenStoreRdfToSei(jobId, (new SimpleResultSet(simpleResJson)).getJobId(), sei);

} catch (Exception e) {
try {
Expand Down Expand Up @@ -1964,6 +1987,7 @@ public JSONObject dispatchCombineEntitiesTable(@RequestBody CombineEntitiesTable
String jobId = JobTracker.generateJobId();

SparqlConnection conn = requestBody.buildSparqlConnection();
query_prop.setUserAndPasswordIfMissing(conn);

new CombineEntitiesTableThread(
tracker, results_prop.getClient(), jobId, this.retrieveOInfo(conn), conn,
Expand Down Expand Up @@ -2001,8 +2025,7 @@ public JSONObject dispatchCombineEntitiesInConn(@RequestBody CombineEntitiesInCo
String jobId = JobTracker.generateJobId();

SparqlConnection conn = requestBody.buildSparqlConnection();


query_prop.setUserAndPasswordIfMissing(conn);
new CombineEntitiesInConnThread(
tracker, results_prop.getClient(), jobId, this.retrieveOInfo(conn), conn,
requestBody.getSameAsClassURI(), requestBody.getTargetPropURI(), requestBody.getDuplicatePropURI(),
Expand Down
7 changes: 7 additions & 0 deletions nodeGroupExecutionService/src/main/resources/application.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,13 @@ ngstore.service.port=${PORT_NODEGROUPSTORE_SERVICE}
dispatch.service.protocol=${DISPATCH_SERVICE_PROTOCOL}
dispatch.service.server=${DISPATCH_SERVICE_HOST}
dispatch.service.port=${PORT_DISPATCH_SERVICE}

query.service.protocol=${SPARQLQUERY_SERVICE_PROTOCOL}
query.service.server=${SPARQLQUERY_SERVICE_HOST}
query.service.port=${PORT_SPARQL_QUERY_SERVICE}
query.service.user=${SPARQLQUERY_SERVICE_USER}
query.service.password=${SPARQLQUERY_SERVICE_PWD}

results.service.protocol=${RESULTS_SERVICE_PROTOCOL}
results.service.server=${RESULTS_SERVICE_HOST}
results.service.port=${PORT_SPARQLGRAPH_RESULTS_SERVICE}
Expand Down
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