Java NdexProvenanceEventType类代码示例

import org.ndexbio.model.object.NdexProvenanceEventType; //导入依赖的package包/类
@Override
public void parseFile() throws NdexException  {

	
	try (CXNetworkLoader loader = new CXNetworkLoader(new FileInputStream(fileName), ownerAccountName)) {
		uuid = loader.persistCXNetwork();
		
		try (NetworkDocDAO dao = new NetworkDocDAO()) {
			NetworkSummary currentNetwork = dao.getNetworkSummaryById(uuid.toString());
			
			String uri = NdexDatabase.getURIPrefix();
	        @SuppressWarnings("resource")
			UserDocDAO userDocDAO = new UserDocDAO(dao.getDBConnection()) ;
	        User loggedInUser = userDocDAO.getUserByAccountName(ownerAccountName);
	        	
			ProvenanceEntity provEntity = ProvenanceHelpers.createProvenanceHistory(currentNetwork,
                   uri, NdexProvenanceEventType.FILE_UPLOAD, currentNetwork.getCreationTime(), 
                   (ProvenanceEntity)null);
			Helper.populateProvenanceEntity(provEntity, currentNetwork);
			provEntity.getCreationEvent().setEndedAtTime(currentNetwork.getModificationTime());

			List<SimplePropertyValuePair> l = provEntity.getCreationEvent().getProperties();
			Helper.addUserInfoToProvenanceEventProperties( l, loggedInUser);
			l.add(	new SimplePropertyValuePair ( "filename",description) );

			loader.setNetworkProvenance(provEntity);

		}
	} catch ( Exception e) {
		e.printStackTrace();
		throw new NdexException ("Failed to load CX file. " + e.getMessage());
	} 
	
}
 

import org.ndexbio.model.object.NdexProvenanceEventType; //导入依赖的package包/类
@POST
	//	@PermitAll

	   @Path("")
	   @Produces("text/plain")
	   @Consumes("multipart/form-data")
	   @ApiDoc("Create a network from the uploaded CX stream. The input cx data is expected to be in the CXNetworkStream field of posted multipart/form-data. "
	   		+ "There is an optional 'provenance' field in the form. Users can use this field to pass in a JSON string of ProvenanceEntity object. When a user pass"
	   		+ " in this object, NDEx server will add this object to the provenance history of the CX network. Otherwise NDEx server will create a ProvenanceEntity "
	   		+ "object and add it to the provenance history of the CX network.")
	   public Response createCXNetwork( MultipartFormDataInput input,
			   @QueryParam("visibility") String visibilityStr,
				@QueryParam("indexedfields") String fieldListStr // comma seperated list		
			   ) throws Exception
	   {
	   
		   VisibilityType visibility = null;
		   if ( visibilityStr !=null) {
			   visibility = VisibilityType.valueOf(visibilityStr);
		   }
		   
		   Set<String> extraIndexOnNodes = null;
		   if ( fieldListStr != null) {
			   extraIndexOnNodes = new HashSet<>(10);
			   for ( String f: fieldListStr.split("\\s*,\\s*") ) {
				   extraIndexOnNodes.add(f);
			   }
		   }
		   try (UserDAO dao = new UserDAO()) {
			   dao.checkDiskSpace(getLoggedInUserId());
		   }
		   
		   
		   UUID uuid = storeRawNetwork ( input);
		   String uuidStr = uuid.toString();
		   accLogger.info("[data]\t[uuid:" +uuidStr + "]" );
	   
		   String urlStr = Configuration.getInstance().getHostURI()  + 
		            Configuration.getInstance().getRestAPIPrefix()+"/network/"+ uuidStr;
		   ProvenanceEntity entity = new ProvenanceEntity();
		   entity.setUri(urlStr + "/summary");
		   
		   String cxFileName = Configuration.getInstance().getNdexRoot() + "/data/" + uuidStr + "/network.cx";
		   long fileSize = new File(cxFileName).length();

		   // create entry in db. 
	       try (NetworkDAO dao = new NetworkDAO()) {
	    	   NetworkSummary summary = dao.CreateEmptyNetworkEntry(uuid, getLoggedInUser().getExternalId(), getLoggedInUser().getUserName(), fileSize);
       
			   ProvenanceEvent event = new ProvenanceEvent(NdexProvenanceEventType.CX_CREATE_NETWORK, summary.getModificationTime());

				List<SimplePropertyValuePair> eventProperties = new ArrayList<>();
				eventProperties.add( new SimplePropertyValuePair("user name", this.getLoggedInUser().getUserName()) ) ;
				event.setProperties(eventProperties);

				entity.setCreationEvent(event);
				dao.setProvenance(summary.getExternalId(), entity);
				dao.commit();
	       }
	       
	       NdexServerQueue.INSTANCE.addSystemTask(new CXNetworkLoadingTask(uuid, getLoggedInUser().getUserName(), false, visibility, extraIndexOnNodes));
	       
//		   logger.info("[end: Created a new network based on a POSTed CX stream.]");
		   
		   URI l = new URI (urlStr);

		   return Response.created(l).entity(l).build();

	   	}
 

import org.ndexbio.model.object.NdexProvenanceEventType; //导入依赖的package包/类
@POST
	//	@PermitAll

	   @Path("/asCX")
//	   @Produces("application/json")
	   @Produces("text/plain")
	   @Consumes("multipart/form-data")
	   @ApiDoc("Create a network from the uploaded CX stream. The input cx data is expected to be in the CXNetworkStream field of posted multipart/form-data. "
	   		+ "There is an optional 'provenance' field in the form. Users can use this field to pass in a JSON string of ProvenanceEntity object. When a user pass"
	   		+ " in this object, NDEx server will add this object to the provenance history of the CX network. Otherwise NDEx server will create a ProvenanceEntity "
	   		+ "object and add it to the provenance history of the CX network.")
	   public String createCXNetwork( MultipartFormDataInput input) throws Exception
	   {

//		   logger.info("[start: Creating a new network based on a POSTed CX stream.]");
		   
		   try (UserDAO dao = new UserDAO()) {
			   dao.checkDiskSpace(getLoggedInUserId());
		   }
	   
		   UUID uuid = storeRawNetwork ( input);
		   String uuidStr = uuid.toString();
		   
			accLogger.info("[data]\t[uuid:" +uuidStr + "]" );

		   
		   String urlStr = Configuration.getInstance().getHostURI()  + 
		            Configuration.getInstance().getRestAPIPrefix()+"/network/"+ uuidStr;

		   ProvenanceEntity entity = new ProvenanceEntity();
		   entity.setUri(urlStr + "/summary");
		   
		   String cxFileName = Configuration.getInstance().getNdexRoot() + "/data/" + uuidStr + "/network.cx";
		   long fileSize = new File(cxFileName).length();

		   // create entry in db. 
	       try (NetworkDAO dao = new NetworkDAO()) {
	    	   NetworkSummary summary = dao.CreateEmptyNetworkEntry(uuid, getLoggedInUser().getExternalId(), getLoggedInUser().getUserName(), fileSize);
	    	   
       
			   ProvenanceEvent event = new ProvenanceEvent(NdexProvenanceEventType.CX_CREATE_NETWORK, summary.getModificationTime());

				List<SimplePropertyValuePair> eventProperties = new ArrayList<>();
				eventProperties.add( new SimplePropertyValuePair("user name", this.getLoggedInUser().getUserName()) ) ;
				event.setProperties(eventProperties);

				entity.setCreationEvent(event);
				dao.setProvenance(summary.getExternalId(), entity);
	    	   dao.commit();
	       } catch (Throwable e) {
	    	   e.printStackTrace();
	    	   throw e;
	       }
	       
	       NdexServerQueue.INSTANCE.addSystemTask(new CXNetworkLoadingTask(uuid, getLoggedInUser().getUserName(), false, null,null));
	       
	//	   logger.info("[end: Created a new network based on a POSTed CX stream.]");
		   //return "\"" + uuidStr + "\"";
		   return  uuidStr ;

	   	}
 

import org.ndexbio.model.object.NdexProvenanceEventType; //导入依赖的package包/类
@Override
public void parseFile() throws NdexException {
	this.entityCount = 0;
	this.pubXrefCount = 0;
	this.uXrefCount = 0;
	this.rXrefCount = 0;
//	this.literalPropertyCount = 0;
//	this.referencePropertyCount = 0;
	
	try  {

		this.getMsgBuffer()
				.add("Parsing lines from " + this.getBioPAXURI());

		this.processBioPAX(this.getBioPAXFile());

		// add provenance to network
		NetworkSummary currentNetwork = this.persistenceService
				.getCurrentNetwork();

		// set the source format
		this.persistenceService.setNetworkSourceFormat(NetworkSourceFormat.BIOPAX);

		String uri = NdexDatabase.getURIPrefix();
		this.persistenceService.setNetworkVisibility(VisibilityType.PRIVATE);

           ProvenanceEntity provEntity = ProvenanceHelpers
                   .createProvenanceHistory(currentNetwork, uri, 
                   		NdexProvenanceEventType.FILE_UPLOAD, currentNetwork.getCreationTime(),
                           (ProvenanceEntity) null);
           Helper.populateProvenanceEntity(provEntity, currentNetwork);
           provEntity.getCreationEvent().setEndedAtTime(
                   currentNetwork.getModificationTime());

           List<SimplePropertyValuePair> l = provEntity.getCreationEvent()
                   .getProperties();

           Helper.addUserInfoToProvenanceEventProperties( l, loggedInUser);

           l.add(new SimplePropertyValuePair("filename", this.description));

           this.persistenceService.setNetworkProvenance(provEntity);

		// close database connection
		this.persistenceService.persistNetwork();
           persistenceService.commit();
		
		System.out.println("Network UUID: " + currentNetwork.getExternalId());
		this.networkUUID = currentNetwork.getExternalId().toString();

	} catch (Exception e) {
		// delete network and close the database connection
		e.printStackTrace();
		this.persistenceService.abortTransaction();
		throw new NdexException("Error occurred when loading file "
				+ this.bioPAXFile.getName() + ". " + e.getMessage());
	} 
       finally
       {
           persistenceService.close();
       }
}
 

import org.ndexbio.model.object.NdexProvenanceEventType; //导入依赖的package包/类
@Override
public void parseFile() throws NdexException
   {
       try
       {
           this.processHeaderAndCreateNetwork();
           this.processNamespaces();
           this.processAnnotationDefinitions();
           this.processStatementGroups();
           
		//add provenance to network
		NetworkSummary currentNetwork = this.networkService.getCurrentNetwork();
		
		String uri = NdexDatabase.getURIPrefix();
           
           // set edge count and node count,
           // then close database connection
           this.networkService.persistNetwork();

           ProvenanceEntity provEntity = ProvenanceHelpers.createProvenanceHistory(currentNetwork,
                   uri, NdexProvenanceEventType.FILE_UPLOAD, currentNetwork.getCreationTime(), 
                   (ProvenanceEntity)null);
           Helper.populateProvenanceEntity(provEntity, currentNetwork);
           provEntity.getCreationEvent().setEndedAtTime(currentNetwork.getModificationTime());

           File f = new File (this.xmlFile);
           List<SimplePropertyValuePair> l = provEntity.getCreationEvent().getProperties();
           Helper.addUserInfoToProvenanceEventProperties( l, loggedInUser);
           l.add(	new SimplePropertyValuePair ( "filename",this.description) );

           this.networkService.setNetworkProvenance(provEntity);

           networkService.commit();
       }
       catch (Exception e)
       {
           e.printStackTrace();
           // rollback current transaction and close the database connection
           this.networkService.abortTransaction();
           throw new NdexException ("Error occurred when loading " +
             xmlFile + ". " + e.getMessage());
       }
       finally
       {
           networkService.close();
       }

   }
 

import org.ndexbio.model.object.NdexProvenanceEventType; //导入依赖的package包/类
@Override
public void parseFile() throws NdexException {
       
	try (FileInputStream xgmmlFileStream = new FileInputStream(this.getXgmmlFile())) { 

		try
		{
       	
			setNetwork();
			readXGMML(xgmmlFileStream);

			// set the source format
			this.networkService.setNetworkSourceFormat(NetworkSourceFormat.XGMML);

			//add provenance to network
			NetworkSummary currentNetwork = this.networkService.getCurrentNetwork();
		
			String uri = NdexDatabase.getURIPrefix();

			// close database connection
			this.networkService.persistNetwork();

               ProvenanceEntity provEntity = ProvenanceHelpers.createProvenanceHistory(currentNetwork,
                       uri,NdexProvenanceEventType.FILE_UPLOAD,
                       currentNetwork.getCreationTime(), (ProvenanceEntity)null);
               Helper.populateProvenanceEntity(provEntity, currentNetwork);
               provEntity.getCreationEvent().setEndedAtTime(currentNetwork.getModificationTime());

               List<SimplePropertyValuePair> l = provEntity.getCreationEvent().getProperties();
               Helper.addUserInfoToProvenanceEventProperties( l, loggedInUser);
               l.add(	new SimplePropertyValuePair ( "filename",this.description) );

               this.networkService.setNetworkProvenance(provEntity);

               networkService.commit();
		}
		catch (Exception e)
		{
			// rollback current transaction and close the database connection
			this.networkService.abortTransaction();
			e.printStackTrace();
			throw new NdexException("Error occurred when loading "
           		+ this.xgmmlFile.getName() + ". " + e.getMessage());
		} 
	}	catch (IOException e1) {
       
           e1.printStackTrace();
           log("Could not read " + this.getXgmmlFile() + ": " + e1.getMessage());
           this.networkService.abortTransaction();  
           throw new NdexException("File not found: " + this.xgmmlFile.getName());
       }
       finally
       {
           networkService.close();
       }

}
 

import org.ndexbio.model.object.NdexProvenanceEventType; //导入依赖的package包/类
/**************************************************************************
	 * Whitespace (space or tab) is used to delimit the names in the simple
	 * interaction file format. However, in some cases spaces are desired in a
	 * node name or edge type. The standard is that, if the file contains any
	 * tab characters, then tabs are used to delimit the fields and spaces are
	 * considered part of the name. If the file contains no tabs, then any
	 * spaces are delimiters that separate names (and names cannot contain
	 * spaces).
	 * @throws JsonProcessingException 
	 * @throws NdexException 
	 **************************************************************************/
	@Override
	public void parseFile() throws  NdexException {

		try (BufferedReader bufferedReader = 
				new BufferedReader(new FileReader(this.getSifFile()))){

			this.getMsgBuffer().add("Parsing lines from " + this.getSIFURI());

			boolean extendedBinarySIF = checkForExtendedFormat();
			if (extendedBinarySIF) {
				this.processExtendedBinarySIF(bufferedReader);
//				this.networkService.setFormat("EXTENDED_BINARY_SIF");
			} else {
				boolean tabDelimited = scanForTabs();
				this.processSimpleSIFLines(tabDelimited, bufferedReader);
//				this.networkService.setFormat("BINARY_SIF");
			}

			//add provenance to network
			NetworkSummary currentNetwork = this.persistenceService.getCurrentNetwork();
			
			// set the source format
			this.persistenceService.setNetworkSourceFormat(NetworkSourceFormat.SIF);
			
			String uri = NdexDatabase.getURIPrefix();
			
			// close database connection
			this.persistenceService.persistNetwork();

            ProvenanceEntity provEntity = ProvenanceHelpers.createProvenanceHistory(currentNetwork,
                    uri, NdexProvenanceEventType.FILE_UPLOAD, currentNetwork.getCreationTime(), 
                    (ProvenanceEntity)null);
            Helper.populateProvenanceEntity(provEntity, currentNetwork);
            provEntity.getCreationEvent().setEndedAtTime(currentNetwork.getModificationTime());

            List<SimplePropertyValuePair> l = provEntity.getCreationEvent().getProperties();
            Helper.addUserInfoToProvenanceEventProperties( l, loggedInUser);
            l.add(	new SimplePropertyValuePair ( "filename",taskDescription) );

            this.persistenceService.setNetworkProvenance(provEntity);

            persistenceService.commit();
			
		} catch (Exception e) {
			// delete network and close the database connection
			e.printStackTrace();
			this.persistenceService.abortTransaction();
			throw new NdexException("Error occurred when loading file " +
					this.sifFile.getName() + ". " + e.getMessage() );
		}
        finally
        {
            persistenceService.close();
        }
	}