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grsf-manage-widget/src/main/java/org/gcube/datacatalogue/grsf_manage_widget/server/manage/Utils.java

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package org.gcube.datacatalogue.grsf_manage_widget.server.manage;
import static org.gcube.resources.discovery.icclient.ICFactory.client;
import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpSession;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.gcube.common.portal.PortalContext;
import org.gcube.common.resources.gcore.ServiceEndpoint;
import org.gcube.common.resources.gcore.ServiceEndpoint.AccessPoint;
import org.gcube.common.resources.gcore.utils.XPathHelper;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.datacatalogue.ckanutillibrary.server.ApplicationProfileScopePerUrlReader;
import org.gcube.datacatalogue.ckanutillibrary.server.DataCatalogue;
import org.gcube.datacatalogue.ckanutillibrary.shared.ex.ApplicationProfileNotFoundException;
import org.gcube.datacatalogue.common.Constants;
import org.gcube.datacatalogue.grsf_manage_widget.shared.ConnectedBean;
import org.gcube.datacatalogue.grsf_manage_widget.shared.ManageProductBean;
import org.gcube.datacatalogue.grsf_manage_widget.shared.SimilarGRSFRecord;
import org.gcube.resources.discovery.client.api.DiscoveryClient;
import org.gcube.resources.discovery.client.queries.api.Query;
import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
import org.gcube.resources.discovery.client.queries.impl.QueryBox;
import org.gcube.vomanagement.usermanagement.model.GCubeUser;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import com.liferay.portal.service.UserLocalServiceUtil;
import eu.trentorise.opendata.jackan.internal.org.apache.http.HttpResponse;
import eu.trentorise.opendata.jackan.internal.org.apache.http.client.methods.HttpPost;
import eu.trentorise.opendata.jackan.internal.org.apache.http.entity.StringEntity;
import eu.trentorise.opendata.jackan.internal.org.apache.http.impl.client.CloseableHttpClient;
import eu.trentorise.opendata.jackan.internal.org.apache.http.impl.client.HttpClientBuilder;
import eu.trentorise.opendata.jackan.internal.org.apache.http.util.EntityUtils;
import eu.trentorise.opendata.jackan.model.CkanDataset;
import eu.trentorise.opendata.jackan.model.CkanPair;
/**
* Utility methods for GRSF Management panel widget.
* @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
*/
public class Utils {
private static final String GENERIC_RESOURCE_NAME = "GRSFManageEntries";
private static final String GENERIC_RESOURCE_SECONDARY_TYPE = "ApplicationProfile";
private static final Logger logger = LoggerFactory.getLogger(Utils.class);
private static final String REGEX_UUID = "[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}";
/**
* Look up from the IS other information that can be potentially displayed in read only mode in the management panel.
* @return a list of extra keys to show.
*/
public static Set<String> getLookedUpExtrasKeys() {
Set<String> lookedUpExtrasKeys = new HashSet<String>();
String scope = ScopeProvider.instance.get();
logger.debug("Trying to fetch applicationProfile profile from the infrastructure for " + GENERIC_RESOURCE_NAME + " scope: " + scope);
try {
Query q = new QueryBox("for $profile in collection('/db/Profiles/GenericResource')//Resource " +
"where $profile/Profile/SecondaryType/string() eq '"+ GENERIC_RESOURCE_SECONDARY_TYPE + "' and $profile/Profile/Name/string() " +
" eq '" + GENERIC_RESOURCE_NAME + "'" +
"return $profile");
DiscoveryClient<String> client = client();
List<String> appProfile = client.submit(q);
if (appProfile == null || appProfile.size() == 0)
throw new ApplicationProfileNotFoundException("Your applicationProfile is not registered in the infrastructure");
else {
String elem = appProfile.get(0);
DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Node node = docBuilder.parse(new InputSource(new StringReader(elem))).getDocumentElement();
XPathHelper helper = new XPathHelper(node);
List<String> currValue = null;
currValue = helper.evaluate("/Resource/Profile/Body/text()");
if (currValue != null && currValue.size() > 0) {
String body = currValue.get(0);
String[] splittedSet = body.split(",");
if(splittedSet != null && splittedSet.length > 0)
for (String entry : splittedSet) {
String trimmed = entry.trim();
if(trimmed.isEmpty())
continue;
lookedUpExtrasKeys.add(trimmed);
}
}
}
logger.info("Extras entries are " + lookedUpExtrasKeys);
return lookedUpExtrasKeys;
} catch (Exception e) {
logger.error("Error while trying to fetch applicationProfile profile from the infrastructure", e);
return null;
}
}
/**
* Return a map for converting a key to a namespace:key format by reading a generic resource.
* @param httpSession
* @return a map
*/
@SuppressWarnings("unchecked")
public static Map<String, String> getFieldToFieldNameSpaceMapping(HttpSession httpSession, String resourceName){
// check if this information is available in session
String sessionKey = ScopeProvider.instance.get() + resourceName;
if(httpSession.getAttribute(sessionKey) != null)
return (Map<String, String>) httpSession.getAttribute(sessionKey);
Map<String, String> namespacesMap = new HashMap<String, String>(); // e.g. fishery_identity:Short Title -> Short Title
try {
Query q = new QueryBox("for $profile in collection('/db/Profiles/GenericResource')//Resource " +
"where $profile/Profile/SecondaryType/string() eq '"+ "ApplicationProfile" + "' and $profile/Profile/Name/string() " +
" eq '" + resourceName + "'" +
"return $profile");
DiscoveryClient<String> client = client();
List<String> appProfile = client.submit(q);
if (appProfile == null || appProfile.size() == 0)
throw new Exception("Your applicationProfile is not registered in the infrastructure");
else {
String elem = appProfile.get(0);
DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Node node = docBuilder.parse(new InputSource(new StringReader(elem))).getDocumentElement();
XPathHelper helper = new XPathHelper(node);
NodeList nodeListKeys = helper.evaluateForNodes("//originalKey");
NodeList nodeListModifiedKeys = helper.evaluateForNodes("//modifiedKey");
int sizeKeys = nodeListKeys != null ? nodeListKeys.getLength() : 0;
int sizeKeysModifed = nodeListModifiedKeys != null ? nodeListModifiedKeys.getLength() : 0;
if(sizeKeys != sizeKeysModifed)
throw new Exception("Malformed XML");
logger.debug("Size is " + sizeKeys);
for (int i = 0; i < sizeKeys; i++) {
namespacesMap.put(nodeListModifiedKeys.item(i).getTextContent(), nodeListKeys.item(i).getTextContent());
}
}
logger.debug("Map is " + namespacesMap);
httpSession.setAttribute(sessionKey, namespacesMap);
return namespacesMap;
} catch (Exception e) {
logger.error("Error while trying to fetch applicationProfile profile from the infrastructure", e);
return null;
}
}
/**
* Replace the extras' keys if needed, e.g. fishery_identity:Short Title -> Short Title
* @param extrasAsPairs
* @param namespaces
* @return a map with replaced key value pairs
*/
public static Map<String, List<String>> replaceFieldsKey(List<CkanPair> extrasAsPairs,
Map<String, String> namespaces) {
Map<String, List<String>> toReturn = new HashMap<String, List<String>>();
for (CkanPair ckanPair : extrasAsPairs) {
String pairKey = ckanPair.getKey();
String pairValue = ckanPair.getValue();
String replacedKey = namespaces.containsKey(pairKey) ? namespaces.get(pairKey) : pairKey;
List<String> values = null;
if(toReturn.containsKey(replacedKey))
values = toReturn.get(replacedKey);
else
values = new ArrayList<String>(1);
values.add(pairValue);
toReturn.put(replacedKey, values);
}
return toReturn;
}
/**
* Discover the service endpoint and return its url
* @param context
* @return the url of the service on success, null otherwise
*/
public static String discoverEndPoint(String context){
String oldContext = ScopeProvider.instance.get();
ScopeProvider.instance.set(context);
String toReturn = null;
try{
SimpleQuery query = queryFor(ServiceEndpoint.class);
query.addCondition("$resource/Profile/Name/text() eq '"+ Constants.SERVICE_NAME +"'");
query.addCondition("$resource/Profile/Category/text() eq '"+ Constants.SERVICE_CATEGORY +"'");
DiscoveryClient<ServiceEndpoint> client = clientFor(ServiceEndpoint.class);
List<ServiceEndpoint> resources = client.submit(query);
if (resources.size() == 0){
logger.error("There is no Runtime Resource having name " + Constants.SERVICE_NAME +" and Category " + Constants.SERVICE_CATEGORY + " in this scope.");
throw new Exception("There is no Runtime Resource having name " + Constants.SERVICE_NAME +" and Category " + Constants.SERVICE_CATEGORY + " in this scope.");
}
else {
for (ServiceEndpoint res : resources) {
Iterator<AccessPoint> accessPointIterator = res.profile().accessPoints().iterator();
while (accessPointIterator.hasNext()) {
ServiceEndpoint.AccessPoint accessPoint = (ServiceEndpoint.AccessPoint) accessPointIterator
.next();
// return the path
toReturn = accessPoint.address();
}
}
}
}catch(Exception e){
logger.error("Unable to retrieve such service endpoint information!", e);
}finally{
if(oldContext != null && !oldContext.equals(context))
ScopeProvider.instance.set(oldContext);
}
return toReturn;
}
/**
* Send an update for this bean
* @param baseUrl
* @param bean
* @param username
* @param catalogue
* @return true on success, false otherwise
*/
@SuppressWarnings("unchecked")
public static String updateRecord(String serviceUrl, ManageProductBean bean, DataCatalogue catalogue, String username,
String fullName) throws Exception{
if(serviceUrl == null)
throw new IllegalArgumentException("GRSF Updater service url cannot be null");
if(bean == null)
throw new IllegalArgumentException("Item bean to manage cannot be null");
try(CloseableHttpClient httpClient = HttpClientBuilder.create().build();){
JSONObject obj = new JSONObject();
obj.put(Constants.ADMINISTRATOR_FULLNAME, fullName);
obj.put(Constants.CATALOGUE_ID, bean.getCatalogueIdentifier());
obj.put(Constants.KB_ID, bean.getKnowledgeBaseIdentifier());
obj.put(Constants.NEW_STATUS, bean.getNewStatus().toString().toLowerCase());
obj.put(Constants.OLD_STATUS, bean.getCurrentStatus().toString().toLowerCase());
obj.put(Constants.TRACEABILITY_FLAG, bean.isTraceabilityFlag());
String annotation = bean.getAnnotation();
if(annotation != null)
obj.put(Constants.ANNOTATION, annotation.replaceAll("\"", ""));
obj.put(Constants.SHORT_NAME_OLD, bean.getShortName());
if(bean.getShortNameUpdated() == null || bean.getShortNameUpdated().isEmpty())
bean.setShortNameUpdated(bean.getShortName());
obj.put(Constants.SHORT_NAME_NEW, bean.getShortNameUpdated());
obj.put(Constants.OLD_STATUS, bean.getCurrentStatus().toString().toLowerCase());
// prepare connections
List<ConnectedBean> connections = bean.getConnectTo();
JSONArray connectionsJson = new JSONArray();
for(ConnectedBean c: connections){
JSONObject cc = new JSONObject();
cc.put(Constants.SOURCE_KNOWLEDGE_BASE_ID, c.getSourceKnowledgeBaseId());
cc.put(Constants.DEST_KNOWLEDGE_BASE_ID, c.getDestKnowledgeBaseId());
cc.put(Constants.SOURCE_DOMAIN, c.getSourceDomain());
cc.put(Constants.SUGGESTED, c.isExtra());
cc.put(Constants.TO_BE_KEPT, c.isToBeKept());
connectionsJson.add(cc);
}
obj.put(Constants.CONNECTIONS, connectionsJson);
// prepare similar grsf records
List<SimilarGRSFRecord> similarRecords = bean.getSimilarGrsfRecords();
JSONArray similarRecordsJson = new JSONArray();
for(SimilarGRSFRecord s: similarRecords){
JSONObject ss = new JSONObject();
ss.put(Constants.KB_ID, s.getKnowledgeBaseId());
ss.put(Constants.SUGGESTED, s.isExtra());
ss.put(Constants.TO_BE_KEPT, s.isToBeKept());
ss.put(Constants.MERGE, s.isSuggestedMerge());
similarRecordsJson.add(ss);
}
obj.put(Constants.SIMILAR_GRSF_RECORDS, similarRecordsJson);
logger.debug("Update request looks like " + obj.toJSONString());
HttpPost request = new HttpPost(serviceUrl + Constants.SERVICE_POST_METHOD);
request.setHeader("Accept", "application/json");
request.setHeader("Content-type", "application/json");
StringEntity params = new StringEntity(obj.toJSONString());
request.setEntity(params);
HttpResponse response = httpClient.execute(request);
logger.debug("Response code is " + response.getStatusLine().getStatusCode() + " and response message is " + response.getStatusLine().getReasonPhrase());
String result = EntityUtils.toString(response.getEntity());
JSONParser parser = new JSONParser();
JSONObject parsedJSON = (JSONObject)parser.parse(result);
if(response.getStatusLine().getStatusCode() != Constants.STATUS_SUCCESS){
throw new Exception("Update failed at knowledge base side!");
}else if(!(boolean) parsedJSON.get(Constants.UPDATE_RESULT))
throw new IllegalArgumentException(
"Update failed for the following reason " + parsedJSON.get(Constants.ERROR_MESSAGE));
}catch(Exception e){
logger.error("Unable to update this Item " + e);
throw e;
}
return null;
}
/**
* Get the scope in which ckan information needs to be discovered from the url
* @param httpServletRequest
* @return
*/
public static String getScopeFromClientUrl(HttpServletRequest httpServletRequest){
if(httpServletRequest == null)
throw new IllegalArgumentException("HttpServletRequest is null!");
String scopeToReturn = null;
try{
String clientUrl = getCurrentClientUrl(httpServletRequest).split("\\?")[0];
logger.debug("Client url is " + clientUrl);
// check if this information is in session, otherwise set it and return
HttpSession session = httpServletRequest.getSession();
if((scopeToReturn = (String) session.getAttribute(clientUrl)) != null){
logger.debug("Scope to return is " + scopeToReturn);
}else{
// ask to the ckan library and set it
scopeToReturn = ApplicationProfileScopePerUrlReader.getScopePerUrl(clientUrl);
logger.debug("Scope to return is " + scopeToReturn);
session.setAttribute(clientUrl, scopeToReturn);
}
}catch(Exception e){
scopeToReturn = getCurrentContext(httpServletRequest, true);
logger.warn("Failed to determine the scope from the client url, returning the current one: " + scopeToReturn);
}
return scopeToReturn;
}
/**
* Needed to get the url of the client
* @param httpServletRequest the httpServletRequest object
* @return the instance of the user
* @see the url at client side
*/
public static String getCurrentClientUrl(HttpServletRequest httpServletRequest) {
if(httpServletRequest == null)
throw new IllegalArgumentException("HttpServletRequest is null!");
return httpServletRequest.getHeader(Constants.GCUBE_REQUEST_URL);
}
/**
* Retrieve the current scope by using the portal manager
* @param b
* @return a GcubeUser object
*/
public static String getCurrentContext(HttpServletRequest request, boolean setInThread){
if(request == null)
throw new IllegalArgumentException("HttpServletRequest is null!");
PortalContext pContext = PortalContext.getConfiguration();
String context = pContext.getCurrentScope(request);
logger.debug("Returning context " + context);
if(context != null && setInThread)
ScopeProvider.instance.set(context);
return context;
}
/**
* Retrieve the current user by using the portal manager
* @return a GcubeUser object
*/
public static GCubeUser getCurrentUser(HttpServletRequest request){
if(request == null)
throw new IllegalArgumentException("HttpServletRequest is null!");
PortalContext pContext = PortalContext.getConfiguration();
GCubeUser user = pContext.getCurrentUser(request);
logger.debug("Returning user " + user);
return user;
}
/**
* Given a semantic identifier, check if a record exists and return it
* @param suggestedRecordSemanticIdentifier
* @param catalogue
* @return CkanDataset
* @throws Exception in case no record matches the semantic identifier
*/
public static CkanDataset getRecordBySemanticIdentifier(
String suggestedRecordSemanticIdentifier, DataCatalogue catalogue,
String apiKey) throws Exception {
if(suggestedRecordSemanticIdentifier == null || suggestedRecordSemanticIdentifier.isEmpty())
throw new Exception(Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY + " cannot be null or emtpy");
String query = Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY + "\"" + suggestedRecordSemanticIdentifier+ "\"";
List<CkanDataset> datasets = catalogue.searchForPackageInOrganization(apiKey, query, 0, 10, Constants.GRSF_ADMIN_ORGANIZATION_NAME);
if(datasets == null || datasets.isEmpty()){
String message = "Unable to find dataset with such " + Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY;
logger.warn(message);
throw new Exception(message);
}
logger.info("Result size is " + datasets.size());
if(datasets.size() == 1)
return datasets.get(0);
else{
// worst situation.. we need to check for the right one
for(CkanDataset dataset: datasets)
for(CkanPair extra : dataset.getExtras())
if(extra.getKey().contains(Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY) && extra.getValue().equals(suggestedRecordSemanticIdentifier)){
logger.info("Matching dataset has id " + dataset.getId() + " with value " + Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY);
return dataset;
}
}
// in the end ....
throw new Exception("Unable to find record with " + Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY + " equals to " + suggestedRecordSemanticIdentifier);
}
/**
* Exploits the fact that in GRSF the url of a record contains the name (which is unique) of the record itself
* @param url
* @param clg
* @return
*/
public static CkanDataset getDatasetFromUrl(String url, DataCatalogue clg, String apiKey){
if(url == null || url.isEmpty())
return null;
// Parse url
// Create a Pattern object
Pattern r = Pattern.compile(REGEX_UUID);
// Now create matcher object.
Matcher m = r.matcher(url);
if (m.find()) {
String uuidFound = m.group();
logger.debug("Found match for uuid " + uuidFound);
return clg.getDataset(uuidFound, apiKey);
}
return null;
}
/**
* Exploits the fact that in GRSF the url of a record contains the name (which is unique) of the record itself
* @param url
* @param clg
* @return
*/
public static String getDatasetKnowledgeBaseIdFromUrl(String url){
if(url == null || url.isEmpty())
return null;
// Parse url
// Create a Pattern object
Pattern r = Pattern.compile(REGEX_UUID);
// Now create matcher object.
Matcher m = r.matcher(url);
if (m.find()) {
String uuidFound = m.group();
logger.debug("Found match for uuid " + uuidFound);
return uuidFound;
}
return null;
}
// /**
// * Get extra information to show in the management panel, if any
// * @param extrasAsPairs
// */
// public static void getExtrasToShow(List<CkanPair> extrasAsPairs, ){
//
// Set<String> extrasToShow = getLookedUpExtrasKeys();
// if(extrasToShow != null && !extrasToShow.isEmpty()){
// Map<String, String> extrasKeyValuePair = new HashMap<String, String>();
// = product.getExtras();
// for (CkanPair ckanPair : extrasAsPairs) {
// String key = ckanPair.getKey();
// String value = ckanPair.getValue();
//
// if(extrasToShow.contains(key)){
// String currentValueInMap = extrasKeyValuePair.get(key);
// if(currentValueInMap == null)
// currentValueInMap = value;
// else
// currentValueInMap += ", " + value;
// extrasKeyValuePair.put(key, currentValueInMap);
// }
// }
// toReturn.setExtrasIfAvailable(extrasKeyValuePair);
// }
//
// }
/**
* Get a {@link SimilarGRSFRecord} from a json string
* @param json
* @return {@link SimilarGRSFRecord}
* @throws ParseException
*/
public static SimilarGRSFRecord similarGRSFRecordFromJson(String json) throws ParseException{
if(json == null)
return null;
JSONParser parser = new JSONParser();
JSONObject object = (JSONObject)parser.parse(json);
return new SimilarGRSFRecord(
(String)object.get(Constants.SIMILAR_RECORDS_BEAN_FIELD_DESCRIPTION),
getDatasetKnowledgeBaseIdFromUrl((String)object.get(Constants.SIMILAR_RECORDS_BEAN_FIELD_URL)),
(String)object.get(Constants.SIMILAR_RECORDS_BEAN_FIELD_IDENTIFIER),
(String)object.get(Constants.SIMILAR_RECORDS_BEAN_FIELD_NAME),
(String)object.get(Constants.SIMILAR_RECORDS_BEAN_FIELD_URL)
);
}
/**
* Checks if is into portal.
*
* @return true, if is into portal
*/
public static boolean isIntoPortal() {
try {
UserLocalServiceUtil.getService();
return true;
}catch (Exception ex) {
logger.debug("Development Mode ON");
return false;
}
}
/**
* Get Connected bean from record
* @param json
* @param sourceIdentifier
* @param sourceDomain
* @return
* @throws ParseException
*/
public static ConnectedBean connectedBeanRecordFromJson(String json, String sourceIdentifier, String sourceDomain,
DataCatalogue clg) throws ParseException {
if(json == null)
return null;
JSONParser parser = new JSONParser();
JSONObject object = (JSONObject)parser.parse(json);
String uuidDest = (String)object.get(Constants.CONNECTED_RECORD_KNOWLEDGE_BASE_ID_JSON_KEY);
String url = clg.getUrlFromDatasetIdOrName(uuidDest);
return new ConnectedBean(
sourceIdentifier,
sourceDomain,
(String)object.get(Constants.CONNECTED_RECORD_SHORT_NAME_JSON_KEY),
(String)object.get(Constants.CONNECTED_RECORD_SEMANTIC_IDENTIFIER_JSON_KEY),
uuidDest,
url
);
}
}
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