/*******************************************************************************
* Copyright 2012 University of Southern California
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* This code was developed by the Information Integration Group as part
* of the Karma project at the Information Sciences Institute of the
* University of Southern California. For more information, publications,
* and related projects, please see: http://www.isi.edu/integration
******************************************************************************/
package edu.isi.karma.er.helper;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import javax.ws.rs.core.UriBuilder;
import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.NameValuePair;
import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.HttpClient;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.client.utils.URIBuilder;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.FileEntity;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.http.message.BasicNameValuePair;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import edu.isi.karma.modeling.Uris;
import edu.isi.karma.util.HTTPUtil;
import edu.isi.karma.webserver.ContextParametersRegistry;
import edu.isi.karma.webserver.KarmaException;
import edu.isi.karma.webserver.ServletContextParameterMap;
public class TripleStoreUtil {
private static Logger logger = LoggerFactory
.getLogger(TripleStoreUtil.class);
public static final String defaultServerUrl;
public static final String defaultModelsRepoUrl;
public static final String defaultDataRepoUrl;
public static final String defaultWorkbenchUrl;
public static final String karma_model_repo = "karma_models";
public static final String karma_data_repo = "karma_data";
static {
String host = ContextParametersRegistry.getInstance().getDefault()
.getParameterValue(ServletContextParameterMap.ContextParameter.JETTY_HOST);
String port = ContextParametersRegistry.getInstance().getDefault()
.getParameterValue(ServletContextParameterMap.ContextParameter.JETTY_PORT);
final String baseURL = host + ":" + port + "/openrdf-sesame";
defaultServerUrl = baseURL + "/repositories";
defaultModelsRepoUrl = defaultServerUrl + "/karma_models";
defaultDataRepoUrl = defaultServerUrl + "/karma_data";
defaultWorkbenchUrl = host + ":" + port
+ "/openrdf-workbench/repositories";
}
protected static HashMap<String, String> mime_types;
public enum RDF_Types {
TriG, BinaryRDF, TriX, N_Triples, N_Quads, N3, RDF_XML, RDF_JSON, Turtle
}
static {
initialize();
mime_types = new HashMap<>();
mime_types.put(RDF_Types.TriG.name(), "application/x-trig");
mime_types.put(RDF_Types.BinaryRDF.name(), "application/x-binary-rdf");
mime_types.put(RDF_Types.TriX.name(), "application/trix");
mime_types.put(RDF_Types.N_Triples.name(), "text/plain");
mime_types.put(RDF_Types.N_Quads.name(), "text/x-nquads");
mime_types.put(RDF_Types.N3.name(), "text/rdf+n3");
mime_types.put(RDF_Types.Turtle.name(), "application/x-turtle");
mime_types.put(RDF_Types.RDF_XML.name(), "application/rdf+xml");
mime_types.put(RDF_Types.RDF_JSON.name(), "application/rdf+json");
}
/**
* This method check for the default karma repositories in the local server
* If not, it creates them
* */
public static boolean initialize() {
boolean retVal = false;
HttpClient httpclient = new DefaultHttpClient();
HttpGet httpget;
HttpResponse response;
HttpEntity entity;
List<String> repositories = new ArrayList<>();
try {
// query the list of repositories
httpget = new HttpGet(defaultServerUrl);
httpget.setHeader("Accept",
"application/sparql-results+json, */*;q=0.5");
response = httpclient.execute(httpget);
entity = response.getEntity();
if (entity != null) {
BufferedReader buf = new BufferedReader(new InputStreamReader(
entity.getContent()));
String s = buf.readLine();
StringBuffer line = new StringBuffer();
while (s != null) {
line.append(s);
s = buf.readLine();
}
JSONObject data = new JSONObject(line.toString());
JSONArray repoList = data.getJSONObject("results")
.getJSONArray("bindings");
int count = 0;
while (count < repoList.length()) {
JSONObject obj = repoList.getJSONObject(count++);
repositories
.add(obj.optJSONObject("id").optString("value"));
}
// check for karama_models repo
if (!repositories.contains(karma_model_repo)) {
logger.info("karma_models not found");
if (create_repo(karma_model_repo,
"Karma default model repository", "native")) {
retVal = true;
} else {
logger.error("Could not create repository : "
+ karma_model_repo);
retVal = false;
}
}
// check for karama_data repo
if (!repositories.contains(karma_data_repo)) {
logger.info("karma_data not found");
if (create_repo(karma_data_repo,
"Karma default data repository", "native")) {
retVal = true;
} else {
logger.error("Could not create repository : "
+ karma_data_repo);
retVal = false;
}
}
}
} catch (Exception e) {
logger.error(e.getMessage());
}
return retVal;
}
public static boolean checkConnection(String url) {
boolean retval = false;
try {
if (url.charAt(url.length() - 1) != '/') {
url = url + "/";
}
url = url + "size";
logger.info(url);
String response = HTTPUtil.executeHTTPGetRequest(url, null);
try {
int i = Integer.parseInt(response.trim());
logger.debug("Connnection to repo : " + url
+ " Successful.\t Size : " + i);
retval = true;
} catch (Exception e) {
logger.error("Could not parse size of repository query result.");
}
} catch (Exception e) {
e.printStackTrace();
}
return retval;
}
public boolean testURIExists(String tripleStoreURL, String context, String uri)
{
tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
try {
testTripleStoreConnection(tripleStoreURL);
} catch (KarmaException e1) {
return false;
}
try {
StringBuilder query = new StringBuilder();
query.append("PREFIX km-dev:<http://isi.edu/integration/karma/dev#> ASK ");
injectContext(context, query);
query.append(" { { ");
formatURI(uri,query);
query.append(" ?y ?z .} union { ?x ?y ");
formatURI(uri,query);
query.append(" } } ");
String queryString = query.toString();
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("query", queryString);
formparams.put("queryLn", "SPARQL");
String responseString = HTTPUtil.executeHTTPPostRequest(
tripleStoreURL, null, "application/sparql-results+json",
formparams);
if (responseString != null) {
JSONObject askResult = new JSONObject(responseString);
return askResult.getBoolean("boolean");
}
} catch (Exception e) {
logger.error(e.getMessage());
}
return false;
}
public Map<String, List<String>> getObjectsForSubjectsAndPredicates(String tripleStoreURL, String context, List<String> subjects, List<String> predicates, List<String> otherClasses, String sameAsProperty) throws KarmaException
{
tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
testTripleStoreConnection(tripleStoreURL);
Map<String, List<String>> results = new HashMap<>();
List<String> resultSubjects = new LinkedList<>();
List<String> resultPredicates = new LinkedList<>();
List<String> resultObjects = new LinkedList<>();
List<String> resultClasses = new LinkedList<>();
results.put("resultSubjects", resultSubjects);
results.put("resultPredicates", resultPredicates);
results.put("resultObjects", resultObjects);
results.put("resultClasses", resultClasses);
try {
StringBuilder query = new StringBuilder();
query.append("PREFIX km-dev:<http://isi.edu/integration/karma/dev#>\n");
query.append("PREFIX rr:<http://www.w3.org/ns/r2rml#>\n");
query.append("SELECT ?s ?p ?o ?filteredtype\n");
injectContext(context, query);
query.append("{\n");
query.append("VALUES ?s { ");
for(String subject : subjects)
{
formatURI(subject, query);
query.append(" ");
}
query.append("}\n");
Iterator<String> predicateIterator = predicates.iterator();
Iterator<String> otherClassIterator = otherClasses.iterator();
String predicate;
String otherClass;
while(predicateIterator.hasNext() && otherClassIterator.hasNext())
{
query.append("{\n");
predicate = predicateIterator.next();
otherClass = otherClassIterator.next();
if(!otherClass.trim().isEmpty())
{
query.append("BIND ( ");
formatURI(otherClass, query);
query.append(" AS ?filteredtype )\n");
}
query.append("BIND ( ");
formatURI(predicate, query);
query.append(" AS ?p )\n");
query.append("{\n");
query.append("?s ");
formatURI(predicate, query);
query.append(" ?o .\n");
query.append("}\n");
if(sameAsProperty != null && !sameAsProperty.isEmpty())
{
query.append("UNION\n");
query.append("{\n");
query.append("?s ");
formatURI(sameAsProperty, query);
query.append("?sprime .\n");
query.append("?sprime ");
formatURI(predicate, query);
query.append(" ?o .\n");
query.append("}\n");
query.append("UNION\n");
query.append("{\n");
query.append("?sprime ");
formatURI(sameAsProperty, query);
query.append("?s .\n");
query.append("?sprime ");
formatURI(predicate, query);
query.append(" ?o .\n");
query.append("}\n");
}
if(!otherClass.trim().isEmpty())
{
query.append("?o a ?filteredtype .\n");
}
query.append("}\n");
if(predicateIterator.hasNext() && otherClassIterator.hasNext())
{
query.append("UNION \n");
}
}
query.append("}\n");
String queryString = query.toString();
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("query", queryString);
formparams.put("queryLn", "SPARQL");
String responseString = HTTPUtil.executeHTTPPostRequest(
tripleStoreURL, null, "application/sparql-results+json",
formparams);
if (responseString != null) {
JSONObject models = new JSONObject(responseString);
JSONArray values = models.getJSONObject("results")
.getJSONArray("bindings");
int count = 0;
while (count < values.length()) {
JSONObject o = values.getJSONObject(count++);
resultSubjects.add(o.getJSONObject("s").getString("value"));
resultPredicates.add(o.getJSONObject("p").getString("value"));
resultObjects.add(o.getJSONObject("o").getString("value"));
if(o.has("filteredtype"))
{
resultClasses.add(o.getJSONObject("filteredtype").getString("value"));
}
else
{
resultClasses.add("");
}
}
}
} catch (Exception e) {
logger.error(e.getMessage());
}
return results;
}
public Map<String, List<String>> getSubjectsForPredicatesAndObjects(String tripleStoreURL, String context, List<String> subjects, List<String> predicates, List<String> otherClasses, String sameAsPredicate) throws KarmaException
{
tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
testTripleStoreConnection(tripleStoreURL);
Map<String, List<String>> results = new HashMap<>();
List<String> resultSubjects = new LinkedList<>();
List<String> resultPredicates = new LinkedList<>();
List<String> resultObjects = new LinkedList<>();
List<String> resultClasses = new LinkedList<>();
results.put("resultSubjects", resultSubjects);
results.put("resultPredicates", resultPredicates);
results.put("resultObjects", resultObjects);
results.put("resultClasses", resultClasses);
try {
StringBuilder query = new StringBuilder();
query.append("PREFIX km-dev:<http://isi.edu/integration/karma/dev#>\n");
query.append("PREFIX rr:<http://www.w3.org/ns/r2rml#>\n");
query.append("SELECT ?s ?p ?o ?filteredtype\n");
injectContext(context, query);
query.append("{\n");
query.append("VALUES ?o { ");
for(String subject : subjects)
{
formatURI(subject, query);
query.append(" ");
}
query.append("}\n");
Iterator<String> predicateIterator = predicates.iterator();
Iterator<String> otherClassIterator = otherClasses.iterator();
String predicate;
String otherClass;
while(predicateIterator.hasNext() && otherClassIterator.hasNext())
{
query.append("{\n");
predicate = predicateIterator.next();
otherClass = otherClassIterator.next();
query.append("BIND ( ");
formatURI(predicate, query);
query.append(" AS ?p )\n");
if(!otherClass.trim().isEmpty())
{
query.append("BIND ( ");
formatURI(otherClass, query);
query.append(" AS ?filteredtype )\n");
}
query.append("{\n");
query.append("?s ?p ?o .\n");
query.append("}\n");
if(sameAsPredicate != null && !sameAsPredicate.isEmpty())
{
query.append("UNION \n");
query.append("{\n");
query.append("?oprime ");
query.append(sameAsPredicate);
query.append(" ?o .\n");
query.append("?s ?p ?oprime .\n");
query.append("}\n");
query.append("UNION \n");
query.append("{\n");
query.append("?o ");
query.append(sameAsPredicate);
query.append(" ?oprime .\n");
query.append("?s ?p ?oprime .\n");
query.append("}\n");
}
if(!otherClass.trim().isEmpty())
{
query.append("?s a ?filteredtype .\n");
}
query.append("}\n");
if(predicateIterator.hasNext() && otherClassIterator.hasNext())
{
query.append("UNION \n");
}
}
query.append("}\n");
String queryString = query.toString();
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("query", queryString);
formparams.put("queryLn", "SPARQL");
String responseString = HTTPUtil.executeHTTPPostRequest(
tripleStoreURL, null, "application/sparql-results+json",
formparams);
if (responseString != null) {
JSONObject models = new JSONObject(responseString);
JSONArray values = models.getJSONObject("results")
.getJSONArray("bindings");
int count = 0;
while (count < values.length()) {
JSONObject o = values.getJSONObject(count++);
resultSubjects.add(o.getJSONObject("s").getString("value"));
resultPredicates.add(o.getJSONObject("p").getString("value"));
resultObjects.add(o.getJSONObject("o").getString("value"));
if(o.has("filteredtype"))
{
resultClasses.add(o.getJSONObject("filteredtype").getString("value"));
}
else
{
resultClasses.add("");
}
}
}
} catch (Exception e) {
logger.error(e.getMessage());
}
return results;
}
public void deleteMappingFromTripleStore(String tripleStoreURL, String context, String mappingURI) throws KarmaException
{
testTripleStoreConnection(tripleStoreURL);
tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL) + "/statements";
try {
StringBuilder query = new StringBuilder();
query.append("PREFIX km-dev:<http://isi.edu/integration/karma/dev#>\n");
query.append("PREFIX rr:<http://www.w3.org/ns/r2rml#>\n");
if (null != context && !context.trim().isEmpty())
{
query.append("WITH ");
formatURI(context, query);
query.append("\n");
}
query.append("DELETE { ?s ?p ?o } \n");
query.append("WHERE\n");
injectMapping(mappingURI, query);
String queryString = query.toString();
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("update", queryString);
String responseString = HTTPUtil.executeHTTPPostRequest(
tripleStoreURL, null, mime_types.get(RDF_Types.N3.name()),
formparams);
System.out.println(responseString);
} catch (Exception e) {
logger.error(e.getMessage());
}
}
protected void injectMapping(String mappingURI, StringBuilder query) {
query.append("{\n");
injectType(mappingURI, query, Uris.RR_TRIPLESMAP_CLASS_URI, Uris.KM_HAS_TRIPLES_MAP_URI);
injectType(mappingURI, query, Uris.RR_SUBJECTMAP_CLASS_URI, Uris.KM_HAS_SUBJECT_MAP_URI);
injectType(mappingURI, query, Uris.RR_PREDICATEOBJECTMAP_CLASS_URI, Uris.KM_HAS_PREDICATE_OBJECT_MAP_URI);
injectType(mappingURI, query, Uris.RR_OBJECTMAP_CLASS_URI, Uris.KM_HAS_OBJECT_MAP_URI);
injectType(mappingURI, query, Uris.RR_LOGICAL_TABLE_CLASS_URI, Uris.KM_HAS_LOGICAL_TABLE_URI);
injectType(mappingURI, query, Uris.RR_TEMPLATE_URI, Uris.RR_CLASS_URI, Uris.KM_HAS_SUBJECT_MAP_URI);
query.append("{\n");
query.append("?s ?p ?o .\n");
query.append("?s owl:sameAs ");
formatURI(mappingURI, query);
query.append(" . \n");
query.append("}\n");
query.append("}\n");
}
protected void injectType(String mappingURI, StringBuilder query,
String type, String hasType) {
query.append("{\n");
query.append("?s a <");
query.append(type);
query.append("> . \n");
query.append("?mapping <");
query.append(hasType);
query.append("> ?s . \n");
query.append("?mapping owl:sameAs ");
formatURI(mappingURI, query);
query.append(" .\n");
query.append("?s ?p ?o . \n");
query.append("}\n");
query.append("UNION\n");
}
protected void injectType(String mappingURI, StringBuilder query,
String type, String hasType, String hasType2) {
query.append("{\n");
query.append("?s <");
query.append(type);
query.append("> ?a . \n");
query.append("?mapping2 <");
query.append(hasType);
query.append("> ?s . \n");
query.append("?mapping <");
query.append(hasType2);
query.append("> ?mapping2 . \n");
query.append("?mapping owl:sameAs ");
formatURI(mappingURI, query);
query.append(" .\n");
query.append("?s ?p ?o . \n");
query.append("}\n");
query.append("UNION\n");
}
public String getMappingFromTripleStore(String tripleStoreURL, String context, String mappingURI) throws KarmaException
{
tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
testTripleStoreConnection(tripleStoreURL);
context = normalizeURI(context);
mappingURI = normalizeURI(mappingURI);
try {
StringBuilder query = new StringBuilder();
query.append("PREFIX km-dev:<http://isi.edu/integration/karma/dev#>\n");
query.append("PREFIX rr:<http://www.w3.org/ns/r2rml#>\n");
query.append("CONSTRUCT { ?s ?p ?o }\n");
injectContext(context, query);
injectMapping(mappingURI, query);
String queryString = query.toString();
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("query", queryString);
formparams.put("queryLn", "SPARQL");
String responseString = HTTPUtil.executeHTTPPostRequest(
tripleStoreURL, null, mime_types.get(RDF_Types.N3.name()),
formparams);
if (responseString != null) {
return responseString;
}
} catch (Exception e) {
logger.error(e.getMessage());
}
return "";
}
protected void injectContext(String context, StringBuilder query) {
if (null != context && !context.trim().isEmpty())
{
query.append("FROM ");
formatURI(context, query);
query.append("\n");
}
}
protected void formatURI(String uri, StringBuilder query) {
uri = uri.trim();
if(!uri.startsWith("<"))
{
query.append("<");
}
query.append(uri);
if(!uri.endsWith(">"))
{
query.append(">");
}
}
public HashMap<String, List<String>> getPredicatesForParentTriplesMapsWithSameClass(String tripleStoreURL, String context, Collection<String> classesToMatch) throws KarmaException
{
tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
testTripleStoreConnection(tripleStoreURL);
List<String> predicates = new LinkedList<>();
List<String> matchingRefObjMaps = new LinkedList<>();
List<String> otherClasses = new LinkedList<>();
try {
StringBuilder query = new StringBuilder();
query.append("PREFIX km-dev:<http://isi.edu/integration/karma/dev#>\n");
query.append("PREFIX rr:<http://www.w3.org/ns/r2rml#>\n");
query.append("SELECT ?predicate ?otherClass (group_concat(?refObjMap; separator = \",\") as ?refObjMaps )\n");
injectContext(context, query);
query.append("{\n");
query.append("?mapping owl:sameAs ?mappingURI . \n");
// query.append("?mappingURI km-dev:hasData \"true\" .\n");
query.append("?mapping km-dev:hasTriplesMap ?triplesMap .\n");
query.append("?triplesMap rr:subjectMap ?subjectMap .\n");
Iterator<String> itr = classesToMatch.iterator();
while(itr.hasNext()) {
String classToMatch = itr.next();
query.append("{?subjectMap rr:class ");
query.append("<").append(classToMatch.trim()).append(">");
query.append("}");
if (itr.hasNext())
query.append(" UNION \n");
else
query.append(". \n");
}
query.append("?refObjMap rr:parentTriplesMap ?triplesMap .\n");
query.append("?pom rr:objectMap ?refObjMap .\n");
query.append("?otherTriplesMap rr:predicateObjectMap ?pom .\n");
query.append("?otherTriplesMap rr:subjectMap ?otherSubjectMap .\n");
query.append("?otherSubjectMap rr:class ?otherClass .\n");
query.append("FILTER NOT EXISTS { ?otherClass rr:template ?z }\n");
query.append("?pom rr:predicate ?predicate .\n");
query.append("}\n");
query.append("GROUP BY ?predicate ?otherClass\n");
String queryString = query.toString();
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("query", queryString);
formparams.put("queryLn", "SPARQL");
String responseString = HTTPUtil.executeHTTPPostRequest(
tripleStoreURL, null, "application/sparql-results+json",
formparams);
if (responseString != null) {
JSONObject models = new JSONObject(responseString);
JSONArray values = models.getJSONObject("results")
.getJSONArray("bindings");
int count = 0;
while (count < values.length()) {
JSONObject o = values.getJSONObject(count++);
predicates.add(o.getJSONObject("predicate").getString("value"));
matchingRefObjMaps.add(o.getJSONObject("refObjMaps").getString("value"));
if(o.has("otherClass"))
{
otherClasses.add(o.getJSONObject("otherClass").getString("value"));
}
else
{
otherClasses.add("");
}
}
}
} catch (Exception e) {
logger.error(e.getMessage());
}
HashMap<String, List<String>> values = new HashMap<>();
values.put("predicates", predicates);
values.put("refObjectMaps", matchingRefObjMaps);
values.put("otherClasses", otherClasses);
return values;
}
public HashMap<String, List<String>> getPredicatesForTriplesMapsWithSameClass(String tripleStoreURL, String context, Collection<String> classesToMatch) throws KarmaException
{
tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
testTripleStoreConnection(tripleStoreURL);
List<String> predicates = new LinkedList<>();
List<String> matchingPOMs = new LinkedList<>();
List<String> otherClasses = new LinkedList<>();
try {
StringBuilder query = new StringBuilder();
query.append("PREFIX km-dev:<http://isi.edu/integration/karma/dev#>\n");
query.append("PREFIX rr:<http://www.w3.org/ns/r2rml#>\n");
query.append("SELECT ?predicate ?otherClass (group_concat(?pom; separator = \",\") as ?poms )\n");
injectContext(context, query);
query.append("{\n");
query.append("?mapping owl:sameAs ?mappingURI . \n");
// query.append("?mappingURI km-dev:hasData \"true\" .\n");
query.append("?mapping km-dev:hasTriplesMap ?triplesMap .\n");
query.append("?triplesMap rr:subjectMap ?subjectMap .\n");
Iterator<String> itr = classesToMatch.iterator();
while (itr.hasNext()) {
String classToMatch = itr.next();
query.append("{?subjectMap rr:class ");
query.append("<").append(classToMatch.trim()).append(">");
query.append("}");
if (itr.hasNext())
query.append(" UNION \n");
else
query.append(". \n");
}
query.append("?triplesMap rr:predicateObjectMap ?pom . \n");
query.append("?pom rr:predicate ?predicate . \n");
query.append("OPTIONAL \n");
query.append("{\n");
query.append("?pom rr:objectMap ?objectMap .\n");
query.append("?objectMap rr:parentTriplesMap ?parentTriplesMap .\n");
query.append("?parentTriplesMap rr:subjectMap ?otherSubjectMap .\n");
query.append("?otherSubjectMap rr:class ?otherClass .\n");
query.append("}\n}\n");
query.append("GROUP BY ?predicate ?otherClass\n");
String queryString = query.toString();
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("query", queryString);
formparams.put("queryLn", "SPARQL");
String responseString = HTTPUtil.executeHTTPPostRequest(
tripleStoreURL, null, "application/sparql-results+json",
formparams);
if (responseString != null) {
JSONObject models = new JSONObject(responseString);
JSONArray values = models.getJSONObject("results")
.getJSONArray("bindings");
int count = 0;
while (count < values.length()) {
JSONObject o = values.getJSONObject(count++);
predicates.add(o.getJSONObject("predicate").getString("value"));
matchingPOMs.add(o.getJSONObject("poms").getString("value"));
if(o.has("otherClass"))
{
otherClasses.add(o.getJSONObject("otherClass").getString("value"));
}
else
{
otherClasses.add("");
}
}
}
} catch (Exception e) {
logger.error(e.getMessage());
}
HashMap<String, List<String>> values = new HashMap<>();
values.put("predicates", predicates);
values.put("predicateObjectMaps", matchingPOMs);
values.put("otherClasses", otherClasses);
return values;
}
public void testTripleStoreConnection(String tripleStoreURL)
throws KarmaException {
// check the connection first
if (checkConnection(tripleStoreURL)) {
logger.info("Connection Test passed");
} else {
logger.info("Failed connection test : " + tripleStoreURL);
throw new KarmaException("Failed connect test : " + tripleStoreURL);
}
}
protected String normalizeTripleStoreURL(String tripleStoreURL) {
if (tripleStoreURL == null || tripleStoreURL.isEmpty()) {
tripleStoreURL = defaultServerUrl + "/" + karma_model_repo + "/" + "statements";
}
if (tripleStoreURL.charAt(tripleStoreURL.length() - 1) == '/') {
tripleStoreURL = tripleStoreURL.substring(0,
tripleStoreURL.length() - 2);
}
logger.info("Repository URL : " + tripleStoreURL);
return tripleStoreURL;
}
/**
* This method fetches all the source names of the models from the triple
* store
*
* @param TripleStoreURL
* : the triple store URL
* */
public HashMap<String, List<String>> getMappingsWithMetadata(String TripleStoreURL, String context) throws KarmaException {
TripleStoreURL = normalizeTripleStoreURL(TripleStoreURL);
testTripleStoreConnection(TripleStoreURL);
List<String> times = new ArrayList<>();
List<String> names = new ArrayList<>();
List<String> urls = new ArrayList<>();
List<String> inputColumns = new ArrayList<>();
List<String> contexts = new ArrayList<>();
try {
StringBuilder query = new StringBuilder();
query.append("PREFIX km-dev:<http://isi.edu/integration/karma/dev#>\n");
query.append("SELECT ?z ?y ?x ?src ?w ?u\n");
injectContext(context, query);
query.append("WHERE \n { \n");
query.append("GRAPH ?src \n { \n");
query.append("?a km-dev:sourceName ?u . \n");
query.append("?a a km-dev:R2RMLMapping . \n");
query.append("?a owl:sameAs ?z . \n");
query.append("?a km-dev:modelPublicationTime ?x \n");
query.append("OPTIONAL \n{?a km-dev:hasInputColumns ?w} \n");
query.append("OPTIONAL \n{?a km-dev:hasModelLabel ?y} \n");
query.append("\n}\n} \nORDER BY ?z ?y ?x ?w ?u ?src");
String queryString = query.toString();
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("query", queryString);
formparams.put("queryLn", "SPARQL");
String responseString = HTTPUtil.executeHTTPPostRequest(
TripleStoreURL, null, "application/sparql-results+json",
formparams);
if (responseString != null) {
JSONObject models = new JSONObject(responseString);
JSONArray values = models.getJSONObject("results")
.getJSONArray("bindings");
int count = 0;
while (count < values.length()) {
JSONObject o = values.getJSONObject(count++);
times.add(o.getJSONObject("x").getString("value"));
urls.add(o.getJSONObject("z").getString("value"));
if (o.has("w"))
inputColumns.add(o.getJSONObject("w").getString("value"));
else
inputColumns.add("");
if (o.has("y"))
names.add(o.getJSONObject("y").getString("value"));
else
names.add(o.getJSONObject("u").getString("value"));
contexts.add(o.getJSONObject("src").getString("value"));
}
}
} catch (Exception e) {
logger.error(e.getMessage());
}
HashMap<String, List<String>> values = new HashMap<>();
values.put("model_publishtimes", times);
values.put("model_names", names);
values.put("model_urls", urls);
values.put("model_contexts", contexts);
values.put("model_inputcolumns", inputColumns);
return values;
}
/**
* This method fetches all the source names of the models from the triple
* store
*
* @param TripleStoreURL
* : the triple store URL
* */
public HashMap<String, List<String>> fetchModelNames(String TripleStoreURL) throws KarmaException {
List<String> names = new ArrayList<>();
List<String> urls = new ArrayList<>();
TripleStoreURL = normalizeTripleStoreURL(TripleStoreURL);
testTripleStoreConnection(TripleStoreURL);
try {
String queryString = "PREFIX km-dev:<http://isi.edu/integration/karma/dev#> SELECT ?y ?z where { ?x km-dev:sourceName ?y . ?x km-dev:serviceUrl ?z . } ORDER BY ?y ?z";
logger.debug("query: " + queryString);
Map<String, String> formparams = new HashMap<>();
formparams.put("query", queryString);
formparams.put("queryLn", "SPARQL");
String responseString = HTTPUtil.executeHTTPPostRequest(
TripleStoreURL, null, "application/sparql-results+json",
formparams);
if (responseString != null) {
JSONObject models = new JSONObject(responseString);
JSONArray values = models.getJSONObject("results")
.getJSONArray("bindings");
int count = 0;
while (count < values.length()) {
JSONObject o = values.getJSONObject(count++);
names.add(o.getJSONObject("y").getString("value"));
urls.add(o.getJSONObject("z").getString("value"));
}
}
} catch (Exception e) {
logger.error(e.getMessage());
e.printStackTrace();
}
HashMap<String, List<String>> values = new HashMap<>();
values.put("model_names", names);
values.put("model_urls", urls);
return values;
}
/**
* @param filePath
* : the url of the file from where the RDF is read
* @param tripleStoreURL
* : the triple store URL
* @param context
* : The graph context for the RDF
* @param replaceFlag
* : Whether to replace the contents of the graph
* @param deleteSrcFile
* : Whether to delete the source R2RML file or not
* @param rdfType
* : The RDF type based on which the headers for the request are
* set
* @param baseURL
* : Specifies the base URI to resolve any relative URIs found in uploaded data against
*
* */
protected boolean saveToStore(HttpEntity entity, String tripleStoreURL,
String context, boolean replaceFlag,
String rdfType, String baseURL) throws KarmaException {
boolean retVal = false;
HttpResponse response;
tripleStoreURL = normalizeTripleStoreURL(tripleStoreURL);
testTripleStoreConnection(tripleStoreURL);
if (tripleStoreURL.charAt(tripleStoreURL.length() - 1) != '/') {
tripleStoreURL += "/";
}
tripleStoreURL += "statements";
try {
URIBuilder builder = new URIBuilder(tripleStoreURL);
// initialize the http entity
HttpClient httpclient = new DefaultHttpClient();
// File file = new File(filePath);
if (mime_types.get(rdfType) == null) {
throw new Exception("Could not find spefied rdf type: "
+ rdfType);
}
// preparing the context for the rdf
if (context == null || context.isEmpty()) {
logger.info("Empty context");
context = "null";
} else {
context = context.trim();
context.replaceAll(">", "");
context.replaceAll("<", "");
builder.setParameter("context", "<" + context + ">");
}
// preapring the base URL
if (baseURL != null && !baseURL.trim().isEmpty()) {
baseURL = baseURL.trim();
baseURL.replaceAll(">", "");
baseURL.replaceAll("<", "");
builder.setParameter("baseURI", "<" + baseURL + ">");
} else {
logger.info("Empty baseURL");
}
// check if we need to specify the context
if (!replaceFlag) {
// we use HttpPost over HttpPut, for put will replace the entire
// repo with an empty graph
logger.info("Using POST to save rdf to triple store");
HttpPost httpPost = new HttpPost(builder.build());
httpPost.setEntity(entity);
// executing the http request
response = httpclient.execute(httpPost);
} else {
// we use HttpPut to replace the context
logger.info("Using PUT to save rdf to triple store");
HttpPut httpput = new HttpPut(builder.build());
httpput.setEntity(entity);
// executing the http request
response = httpclient.execute(httpput);
}
logger.info("request url : " + builder.build().toString());
logger.info("StatusCode: "
+ response.getStatusLine().getStatusCode());
logger.info(response.toString());
int code = response.getStatusLine().getStatusCode();
if (code >= 200 && code < 300) {
retVal = true;
}
} catch (Exception e) {
e.printStackTrace();
logger.error(e.getClass().getName() + " : " + e.getMessage());
}
return retVal;
}
/**
* @param filePath
* : the url of the file from where the RDF is read
* @param tripleStoreURL
* : the triple store URL
* @param context
* : The graph context for the RDF
* @param replaceFlag
* : Whether to replace the contents of the graph deleteSrcFile
* default : false rdfType default: Turtle
* @param baseUri
* : The graph context for the RDF
*
* */
public boolean saveToStoreFromFile(String filePath, String tripleStoreURL,
String context, boolean replaceFlag, String baseUri) throws KarmaException{
File file = new File(filePath);
FileEntity entity = new FileEntity(file, ContentType.create(
mime_types.get(RDF_Types.Turtle.name()), "UTF-8"));
return saveToStore(entity, tripleStoreURL, context, replaceFlag,
RDF_Types.Turtle.name(), baseUri);
}
public boolean saveToStoreFromString(String input, String tripleStoreURL,
String context, Boolean replaceFlag, String baseUri) throws KarmaException{
StringEntity entity = new StringEntity(input, ContentType.create(mime_types.get(RDF_Types.Turtle.name())));
return saveToStore(entity, tripleStoreURL, context, replaceFlag,
RDF_Types.Turtle.name(), baseUri);
}
/**
* Invokes a SPARQL query on the given Triple Store URL and returns the JSON
* object containing the result. The content type of the result is
* application/sparql-results+json.
*
* @param query
* : SPARQL query
* @param tripleStoreUrl
* : SPARQL endpoint address of the triple store
* @param acceptContentType
* : The accept context type in the header
* @param contextType
* :
* @return
* @throws ClientProtocolException
* @throws IOException
* @throws JSONException
*/
public static String invokeSparqlQuery(String query, String tripleStoreUrl,
String acceptContentType, String contextType)
throws ClientProtocolException, IOException, JSONException {
Map<String, String> formParams = new HashMap<>();
formParams.put("query", query);
formParams.put("queryLn", "SPARQL");
String response = HTTPUtil.executeHTTPPostRequest(tripleStoreUrl,
contextType, acceptContentType, formParams);
if (response == null || response.isEmpty())
return null;
return response;
}
public static boolean create_repo(String repo_name, String repo_desc,
String type) {
// TODO : Take the repository type as an enum - native, memory, etc
boolean retVal = false;
if (repo_name == null || repo_name.isEmpty()) {
logger.error("Invalid repo name : " + repo_name);
return retVal;
}
if (repo_desc == null || repo_desc.isEmpty()) {
repo_desc = repo_name;
}
HttpClient httpclient = new DefaultHttpClient();
HttpResponse response;
try {
HttpPost httppost = new HttpPost(defaultWorkbenchUrl
+ "/NONE/create");
List<NameValuePair> formparams = new ArrayList<>();
formparams.add(new BasicNameValuePair("Repository ID", repo_name));
formparams
.add(new BasicNameValuePair("Repository title", repo_name));
formparams
.add(new BasicNameValuePair("Triple indexes", "spoc,posc"));
formparams.add(new BasicNameValuePair("type", "native"));
httppost.setEntity(new UrlEncodedFormEntity(formparams, "UTF-8"));
httppost.setHeader("Content-Type",
"application/x-www-form-urlencoded");
response = httpclient.execute(httppost);
HttpEntity entity = response.getEntity();
if (entity != null) {
StringBuffer out = new StringBuffer();
BufferedReader buf = new BufferedReader(new InputStreamReader(
entity.getContent()));
String line = buf.readLine();
while (line != null) {
logger.info(line);
out.append(line);
line = buf.readLine();
}
logger.info(out.toString());
}
int status = response.getStatusLine().getStatusCode();
if (status >= 200 || status < 300) {
logger.info("Created repository : " + repo_name);
retVal = true;
}
} catch (Exception e) {
e.printStackTrace();
}
return retVal;
}
/**
* This method fetches all the context from the given triplestore Url
* */
public List<String> getContexts(String url) {
if (url == null || url.isEmpty()) {
url = defaultModelsRepoUrl;
}
url += "/contexts";
List<String> graphs = new ArrayList<>();
String responseString;
try {
responseString = HTTPUtil.executeHTTPGetRequest(url,
"application/sparql-results+json");
if (responseString != null) {
JSONObject models = new JSONObject(responseString);
JSONArray values = models.getJSONObject("results")
.getJSONArray("bindings");
int count = 0;
while (count < values.length()) {
JSONObject o = values.getJSONObject(count++);
graphs.add(o.getJSONObject("contextID").getString("value"));
}
}
} catch (Exception e) {
logger.error(e.getMessage());
e.printStackTrace();
graphs = null;
}
return graphs;
}
public boolean isUniqueGraphUri(String tripleStoreUrl, String graphUrl) {
logger.info("Checking for unique graphUri for url : " + graphUrl
+ " at endPoint : " + tripleStoreUrl);
boolean retVal = true;
List<String> urls = this.getContexts(tripleStoreUrl);
if (urls == null) {
return false;
}
// need to compare each url in case-insensitive form
for (String url : urls) {
if (url.equalsIgnoreCase(graphUrl)) {
retVal = false;
break;
}
}
return retVal;
}
/**
* This method clears all the statements from the given context
* */
public static boolean clearContexts(String tripleStoreUrl, String graphUri) {
if (tripleStoreUrl == null || tripleStoreUrl.isEmpty()
|| graphUri == null || graphUri.isEmpty()) {
logger.error("Missing graphUri or tripleStoreUrl");
return false;
}
String responseString;
try {
String url = tripleStoreUrl + "/statements?context="
+ URLEncoder.encode(graphUri, "UTF-8");
logger.info("Deleting from uri : " + url);
responseString = HTTPUtil.executeHTTPDeleteRequest(url);
logger.info("Response=" + responseString);
return true;
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
return false;
}
public String normalizeURI(String uri) {
UriBuilder builder = UriBuilder.fromPath(uri);
return builder.build().toString();
}
}