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Optimization so service #337

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52f19e4
optimization test
niio972 Feb 24, 2020
31e45c0
remove profiling variables
niio972 Feb 26, 2020
502fcd3
Update config file
niio972 Feb 26, 2020
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2 changes: 1 addition & 1 deletion phis2-ws/src/main/java/opensilex/service/dao/DatasetDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -205,7 +205,7 @@ protected BasicDBObject prepareSearchProvenance() {
private void updateScientificObjectsWithExperimentsScientificObjects() {
ScientificObjectRdf4jDAO agronomicalObjectDao = new ScientificObjectRdf4jDAO();

ArrayList<ScientificObject> scientificObjectsSearched = agronomicalObjectDao.find(null, null, null, null, experiment, null);
ArrayList<ScientificObject> scientificObjectsSearched = agronomicalObjectDao.find(null, null, null, null, experiment, null, true);

scientificObjectsSearched.forEach((scientificObject) -> {
this.scientificObjects.add(scientificObject.getUri());
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47 changes: 26 additions & 21 deletions phis2-ws/src/main/java/opensilex/service/dao/ScientificObjectRdf4jDAO.java
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Expand Up @@ -606,8 +606,9 @@ public ArrayList<Property> findScientificObjectProperties(String uri) {
* @param alias
* @return scientific objects list, result of the user query, empty if no result
*/
public ArrayList<ScientificObject> find(Integer page, Integer pageSize, String uri, String rdfType, String experiment, String alias) {
public ArrayList<ScientificObject> find(Integer page, Integer pageSize, String uri, String rdfType, String experiment, String alias, Boolean withProperties) {
try {

SPARQLQueryBuilder sparqlQuery = prepareSearchQuery(false, page, pageSize, uri, rdfType, experiment, alias);
//SILEX:test
//For pool connection issues
Expand All @@ -618,7 +619,7 @@ public ArrayList<ScientificObject> find(Integer page, Integer pageSize, String u

TupleQuery tupleQuery = getConnection().prepareTupleQuery(QueryLanguage.SPARQL, sparqlQuery.toString());
Map<String, ScientificObject> foundedScientificObjects = new HashMap<>();

try (TupleQueryResult result = tupleQuery.evaluate()) {
while (result.hasNext()) {
BindingSet bindingSet = result.next();
Expand Down Expand Up @@ -652,29 +653,31 @@ public ArrayList<ScientificObject> find(Integer page, Integer pageSize, String u
scientificObject.setRdfType(bindingSet.getValue(RDF_TYPE).stringValue());
}
}

//Get scientific object properties
scientificObject.setProperties(findScientificObjectProperties(actualUri));
if(withProperties){
//Get scientific object properties
scientificObject.setProperties(findScientificObjectProperties(actualUri));
}

foundedScientificObjects.put(actualUri, scientificObject);
}
}

ArrayList<String> scientificObjectsUris = new ArrayList<>();
ArrayList<ScientificObject> scientificObjects = new ArrayList<>();
foundedScientificObjects.entrySet().forEach((entry) -> {
scientificObjects.add(entry.getValue());
scientificObjectsUris.add(entry.getKey());
});

//Get geometries in relational database
//Get geometries in relational database
ScientificObjectSQLDAO scientificObjectDao = new ScientificObjectSQLDAO();
HashMap<String, String> geometries = scientificObjectDao.getGeometries(scientificObjectsUris);

scientificObjects.forEach((scientificObject) -> {
scientificObject.setGeometry(geometries.get(scientificObject.getUri()));
});


return scientificObjects;
} catch (SQLException ex) {
java.util.logging.Logger.getLogger(ScientificObjectRdf4jDAO.class.getName()).log(Level.SEVERE, null, ex);
Expand Down Expand Up @@ -721,7 +724,20 @@ protected SPARQLQueryBuilder prepareSearchQuery(boolean count, Integer page, Int
sparqlQuery.appendAndFilter("REGEX ( str(?" + URI + "),\".*" + uri + ".*\",\"i\")");
}

//Label filter

//Rdf type filter
if (rdfType != null) {
sparqlQuery.appendTriplet("?" + URI, Rdf.RELATION_TYPE.toString(), rdfType, null);
} else {
sparqlQuery.appendTriplet("?" + URI, Rdf.RELATION_TYPE.toString(), "?" + RDF_TYPE, null);
sparqlQuery.appendTriplet(
"?" + RDF_TYPE,
"<" + Rdfs.RELATION_SUBCLASS_OF.toString() + ">*",
Oeso.CONCEPT_SCIENTIFIC_OBJECT.toString(), null);
sparqlQuery.appendSelect(" ?" + RDF_TYPE);
}

//Label filter
sparqlQuery.appendSelect("?" + ALIAS);
if (alias == null && !count) {
sparqlQuery.beginBodyOptional();
Expand All @@ -740,17 +756,6 @@ protected SPARQLQueryBuilder prepareSearchQuery(boolean count, Integer page, Int
sparqlQuery.appendOptional("?" + URI + " <" + Oeso.RELATION_PARTICIPATES_IN.toString() + "> " + "?" + EXPERIMENT + " . ");
}

//Rdf type filter
if (rdfType != null) {
sparqlQuery.appendTriplet("?" + URI, Rdf.RELATION_TYPE.toString(), rdfType, null);
} else {
sparqlQuery.appendSelect(" ?" + RDF_TYPE);
sparqlQuery.appendTriplet("?" + URI, Rdf.RELATION_TYPE.toString(), "?" + RDF_TYPE, null);
sparqlQuery.appendTriplet(
"?" + RDF_TYPE,
"<" + Rdfs.RELATION_SUBCLASS_OF.toString() + ">*",
Oeso.CONCEPT_SCIENTIFIC_OBJECT.toString(), null);
}

if (page != null && pageSize != null) {
sparqlQuery.appendLimit(pageSize);
Expand Down Expand Up @@ -996,7 +1001,7 @@ public void delete(List<ScientificObject> objects) throws DAOPersistenceExceptio
* null if this scientific object does not exist.
*/
public ScientificObject getScientificObjectInContext(String uri, String context) {
ArrayList<ScientificObject> scientificObjects = find(null, null, uri, null, context, null);
ArrayList<ScientificObject> scientificObjects = find(null, null, uri, null, context, null,true);
if (!scientificObjects.isEmpty()) {
return scientificObjects.get(0);
} else {
Expand Down
5 changes: 1 addition & 4 deletions phis2-ws/src/main/java/opensilex/service/dao/ScientificObjectSQLDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -253,10 +253,7 @@ public HashMap<String, String> getGeometries(ArrayList<String> scientificObjects
query.appendSelect("ST_AsGeoJSON(ST_Transform(" + GEOMETRY + ", 4326)), ao." + URI);
query.appendFrom(table, tableAlias);

for (String scientificObjectURI : scientificObjectsURIs) {
query.appendORWhereConditionIfNeeded(URI, scientificObjectURI, "=", null, tableAlias);
}

query.appendINConditions(URI, scientificObjectsURIs, tableAlias);
LOGGER.debug(getTraceabilityLogs() + " quert : " + query.toString());

ResultSet queryResult = statement.executeQuery(query.toString());
Expand Down
14 changes: 10 additions & 4 deletions phis2-ws/src/main/java/opensilex/service/resource/ScientificObjectResourceService.java
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Expand Up @@ -255,11 +255,13 @@ public Response getScientificObjectsBySearch(
@ApiParam(value = "Search by URI", example = DocumentationAnnotation.EXAMPLE_SCIENTIFIC_OBJECT_URI) @QueryParam("uri") String uri,
@ApiParam(value = "Search by experiment URI", example = DocumentationAnnotation.EXAMPLE_EXPERIMENT_URI) @QueryParam("experiment") @URL String experimentURI,
@ApiParam(value = "Search by alias", example = DocumentationAnnotation.EXAMPLE_EXPERIMENT_ALIAS) @QueryParam("alias") String alias,
@ApiParam(value = "Search by rdfType", example = DocumentationAnnotation.EXAMPLE_SCIENTIFIC_OBJECT_TYPE) @QueryParam("rdfType") @URL String rdfType
@ApiParam(value = "Search by rdfType", example = DocumentationAnnotation.EXAMPLE_SCIENTIFIC_OBJECT_TYPE) @QueryParam("rdfType") @URL String rdfType,
@ApiParam(value = "Retreive detailled properties", example = "true") @DefaultValue("true") @QueryParam("withProperties") Boolean withProperties

) {
ArrayList<ScientificObjectDTO> scientificObjectsToReturn = new ArrayList<>();
ArrayList<ScientificObject> scientificObjects = new ArrayList<>();

ArrayList<Status> statusList = new ArrayList<>();
ResultForm<ScientificObjectDTO> getResponse;

Expand All @@ -271,11 +273,13 @@ public Response getScientificObjectsBySearch(
//1. Get count
Integer totalCount = scientificObjectDaoSesame.count(uri, rdfType, experimentURI, alias);


// If scientific objects found
if(totalCount > 0){
//2. Get list of scientific objects
scientificObjects = scientificObjectDaoSesame.find(page, pageSize, uri, rdfType, experimentURI, alias);
scientificObjects = scientificObjectDaoSesame.find(page, pageSize, uri, rdfType, experimentURI, alias, withProperties);
}


if (scientificObjects == null) { //Request failure
getResponse = new ResultForm<>(0, 0, scientificObjectsToReturn, true);
Expand All @@ -284,11 +288,13 @@ public Response getScientificObjectsBySearch(
getResponse = new ResultForm<>(0, 0, scientificObjectsToReturn, true);
return noResultFound(getResponse, statusList);
} else {


//Convert all scientific objects to DTO
scientificObjects.forEach((scientificObject) -> {
scientificObjectsToReturn.add(new ScientificObjectDTO(scientificObject));
});

getResponse = new ResultForm<>(scientificObjectDaoSesame.getPageSize(), scientificObjectDaoSesame.getPage(), scientificObjectsToReturn, true, totalCount);
if (getResponse.getResult().dataSize() == 0) {
return noResultFound(getResponse, statusList);
Expand Down
4 changes: 2 additions & 2 deletions phis2-ws/src/main/java/opensilex/service/resource/brapi/StudiesResourceService.java
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Expand Up @@ -664,7 +664,7 @@ public Response getObservationUnits (
rdfType = Oeso.NAMESPACE + observationLevel;
}

ArrayList<ScientificObject> scientificObjects = scientificObjectsDAO.find(null, null, null, rdfType, studyDbId, null);
ArrayList<ScientificObject> scientificObjects = scientificObjectsDAO.find(null, null, null, rdfType, studyDbId, null, true);

ExperimentSQLDAO experimentDAO = new ExperimentSQLDAO();
experimentDAO.uri = studyDbId;
Expand Down Expand Up @@ -735,7 +735,7 @@ private ArrayList<BrapiObservationDTO> getObservationsList(StudySQLDAO studyDAO,

ArrayList<BrapiObservationDTO> observations = new ArrayList();
ScientificObjectRdf4jDAO objectDAO = new ScientificObjectRdf4jDAO();
ArrayList<ScientificObject> objectsList = objectDAO.find(null, null, null, null, studyDAO.studyDbIds.get(0), null);
ArrayList<ScientificObject> objectsList = objectDAO.find(null, null, null, null, studyDAO.studyDbIds.get(0), null, true);
ArrayList<Variable> variablesList = new ArrayList();

if (variableURIs.isEmpty()) {
Expand Down
2 changes: 1 addition & 1 deletion phis2-ws/src/main/java/opensilex/service/resource/brapi/VariableResourceService.java
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Expand Up @@ -390,7 +390,7 @@ private ArrayList<BrapiObservationDTO> getObservationsList(StudySQLDAO studyDAO,

ArrayList<BrapiObservationDTO> observations = new ArrayList();
ScientificObjectRdf4jDAO objectDAO = new ScientificObjectRdf4jDAO();
ArrayList<ScientificObject> objectsList = objectDAO.find(null, null, null, null, studyDAO.studyDbIds.get(0), null);
ArrayList<ScientificObject> objectsList = objectDAO.find(null, null, null, null, studyDAO.studyDbIds.get(0), null, true);
ArrayList<Variable> variablesList = new ArrayList();

if (variableURIs.isEmpty()) {
Expand Down