List of usage examples for java.util.logging Logger log
public void log(Level level, Throwable thrown, Supplier<String> msgSupplier)
From source file:edu.emory.cci.aiw.i2b2etl.dest.I2b2QueryResultsHandler.java
/** * Builds most of the concept tree, truncates the data tables, opens a * connection to the i2b2 project database, and does some other prep. This * method is called before the first call to * {@link #handleQueryResult(String, java.util.List, java.util.Map, java.util.Map, java.util.Map)}. * * @throws QueryResultsHandlerProcessingException *//* w w w . j a va 2 s . c o m*/ @Override public void start(Collection<PropositionDefinition> propDefs) throws QueryResultsHandlerProcessingException { Logger logger = I2b2ETLUtil.logger(); try { this.conceptDimensionHandler = new ConceptDimensionHandler(dataConnectionSpec); this.modifierDimensionHandler = new ModifierDimensionHandler(dataConnectionSpec); this.cache = new KnowledgeSourceCacheFactory().getInstance(this.knowledgeSource, propDefs, true); this.metadata = new MetadataFactory().getInstance(this.qrhId, this.cache, knowledgeSource, collectUserPropositionDefinitions(), this.conceptsSection.getFolderSpecs(), settings, this.data, this.metadataConnectionSpec); this.providerDimensionFactory = new ProviderDimensionFactory(this.metadata, this.settings, this.dataConnectionSpec); this.patientDimensionFactory = new PatientDimensionFactory(this.metadata, this.settings, this.data, this.dataConnectionSpec); this.visitDimensionFactory = new VisitDimensionFactory(this.metadata, this.settings, this.data, this.dataConnectionSpec); DataRemoverFactory f = new DataRemoverFactory(); if (this.query.getQueryMode() == QueryMode.REPLACE) { f.getInstance(this.dataRemoveMethod).doRemoveData(); } f.getInstance(this.metaRemoveMethod).doRemoveMetadata(); this.factHandlers = new ArrayList<>(); addPropositionFactHandlers(); executePreHook(); // disable indexes on observation_fact to speed up inserts disableObservationFactIndexes(); // create i2b2 temporary tables using stored procedures truncateTempTables(); this.dataSchemaConnection = openDataDatabaseConnection(); if (this.settings.getManageCTotalNum()) { try (Connection conn = openMetadataDatabaseConnection()) { try (Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("SELECT DISTINCT C_TABLE_NAME FROM TABLE_ACCESS")) { while (rs.next()) { String tableName = rs.getString(1); try (CallableStatement mappingCall = conn .prepareCall("{ call EUREKA.EK_CLEAR_C_TOTALNUM(?) }")) { logger.log(Level.INFO, "Clearing C_TOTALNUM for query {0}", this.query.getName()); mappingCall.setString(1, tableName); mappingCall.execute(); //commit and rollback are called by stored procedure. } } } } } logger.log(Level.INFO, "Populating observation facts table for query {0}", this.query.getName()); } catch (KnowledgeSourceReadException | SQLException | OntologyBuildException ex) { throw new QueryResultsHandlerProcessingException("Error during i2b2 load", ex); } }
From source file:com.grameenfoundation.ictc.controllers.FarmManagementPlanController.java
/** * Processes requests for both HTTP <code>GET</code> and <code>POST</code> * methods./*from w ww . j a v a 2 s . c om*/ * * @param request servlet request * @param response servlet response * @throws ServletException if a servlet-specific error occurs * @throws IOException if an I/O error occurs */ protected void processRequest(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { response.setContentType("text/html;charset=UTF-8"); Logger log = Logger.getLogger(FarmManagementPlanController.class.getName()); BiodataModel biodataModel = new BiodataModel(); String theString = IOUtils.toString(request.getInputStream(), "UTF-8"); System.out.println("Salesforce data/n " + theString); Transaction tx; tx = ICTCDBUtil.getInstance().getGraphDB().beginTx(); org.neo4j.graphdb.Node farmManagementPlanParent; try (PrintWriter out = response.getWriter()) { System.out.println(" " + request.getContentType()); DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder(); InputSource is = new InputSource(); is.setCharacterStream(new StringReader(theString)); System.out.println("After parsing XML"); Document doc = db.parse(is); System.out.println("Should be normalised now"); doc.getDocumentElement().normalize(); Element ele = doc.getDocumentElement(); //System.out.println("Root element :" + doc.getDocumentElement()); Node node = doc.getDocumentElement(); System.out.println("Root element " + doc.getDocumentElement()); //get fields from objects NodeList sObject = doc.getElementsByTagName("sObject"); // String farmerID = getXmlNodeValue("sf:Farmer_name__c",ele); for (int j = 0; j < sObject.getLength(); j++) { Node rowNode = sObject.item(j); // Map<String,String> m = (Map<String,String>) rowNode.getAttributes(); String salesforceObj = rowNode.getAttributes().getNamedItem("xsi:type").getNodeValue(); System.out.println(salesforceObj); String farmerID = getXmlNodeValue("sf:Farmer_name__c", ele); System.out.println("farmerid " + farmerID); org.neo4j.graphdb.Node FMPNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.FARM_MANAGEMENT_PLAN); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { //System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out .println("id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); FMPNode.setProperty(getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text")) { System.out.println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); FMPNode.setProperty(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } farmManagementPlanParent = ParentNode.FMPlanParentNode(); farmManagementPlanParent.createRelationshipTo(FMPNode, ICTCRelationshipTypes.FARM_MANAGEMENT_PLAN); log.log(Level.INFO, "new node created {0}", FMPNode.getId()); Biodata b = biodataModel.getBiodata("Id", farmerID); biodataModel.BiodataToFMP(b.getId(), FMPNode); tx.success(); out.println(sendAck()); } } catch (ParserConfigurationException ex) { Logger.getLogger(FarmManagementPlanController.class.getName()).log(Level.SEVERE, null, ex); tx.failure(); } catch (SAXException ex) { tx.failure(); Logger.getLogger(FarmManagementPlanController.class.getName()).log(Level.SEVERE, null, ex); } finally { tx.finish(); } }
From source file:com.grameenfoundation.ictc.controllers.SaleforceIntegrationController.java
/** * Processes requests for both HTTP <code>GET</code> and <code>POST</code> * methods./*from ww w. j a va 2s .c om*/ * * @param request servlet request * @param response servlet response * @throws ServletException if a servlet-specific error occurs * @throws IOException if an I/O error occurs */ protected void processRequest(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { Logger log = Logger.getLogger(SaleforceIntegrationController.class.getName()); response.setContentType("text/xml;charset=UTF-8"); BiodataModel biodataModel = new BiodataModel(); try (PrintWriter out = response.getWriter()) { /* TODO output your page here. You may use following sample code. */ String theString = IOUtils.toString(request.getInputStream(), "UTF-8"); System.out.println("Salesforce data/n " + theString); //gets request input stream InputStream in = request.getInputStream(); InputSource input = null; Transaction tx; tx = ICTCDBUtil.getInstance().getGraphDB().beginTx(); org.neo4j.graphdb.Node FarmerParent; try { System.out.println(" " + request.getContentType()); DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder(); InputSource is = new InputSource(); is.setCharacterStream(new StringReader(theString)); System.out.println("After parsing XML"); Document doc = db.parse(is); System.out.println("Should be normalised now"); doc.getDocumentElement().normalize(); Element ele = doc.getDocumentElement(); //System.out.println("Root element :" + doc.getDocumentElement()); Node node = doc.getDocumentElement(); System.out.println("Root element " + doc.getDocumentElement()); //get fields from objects NodeList sObject = doc.getElementsByTagName("sObject"); for (int j = 0; j < sObject.getLength(); j++) { Node rowNode = sObject.item(j); // Map<String,String> m = (Map<String,String>) rowNode.getAttributes(); String salesforceObj = rowNode.getAttributes().getNamedItem("xsi:type").getNodeValue(); System.out.println(salesforceObj); if (salesforceObj.equalsIgnoreCase("sf:Farmer_Biodata__c")) { org.neo4j.graphdb.Node biodataNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.FARMER); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { // System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out.println( "id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); biodataNode.setProperty( getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text")) { System.out .println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); biodataNode.setProperty( getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } FarmerParent = ParentNode.FarmerParentNode(); FarmerParent.createRelationshipTo(biodataNode, ICTCRelationshipTypes.FARMER); log.log(Level.INFO, "new node created {0}", biodataNode.getId()); tx.success(); out.println(sendAck()); } else if (salesforceObj.equals("sf:Harvest__c")) { org.neo4j.graphdb.Node HarvestParent; org.neo4j.graphdb.Node harvestNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.HARVEST); String farmerID = getXmlNodeValue("sf:Farmer_Biodata__c", ele); System.out.println("farmerid " + farmerID); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { //System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out.println( "id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); harvestNode.setProperty( getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text") && !rowNode .getChildNodes().item(k).getNodeName().equals("sf:Farmer_Biodata__c")) { System.out .println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); harvestNode.setProperty( getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } HarvestParent = ParentNode.HarvestParentNode(); HarvestParent.createRelationshipTo(harvestNode, ICTCRelationshipTypes.HARVEST); log.log(Level.INFO, "new node created {0}", harvestNode.getId()); Biodata b = biodataModel.getBiodata("Id", farmerID); biodataModel.BiodataToHarvest(b.getId(), harvestNode); tx.success(); out.println(sendAck()); } else if (salesforceObj.equals("sf:FarmManagement__c")) { org.neo4j.graphdb.Node FarmManagementParent; org.neo4j.graphdb.Node FarmManagementNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.FARM_MANAGEMENT); String farmerID = getXmlNodeValue("sf:Farmer_Biodata__c", ele); System.out.println("farmerid " + farmerID); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { //System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out.println( "id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); FarmManagementNode.setProperty( getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text") && !rowNode .getChildNodes().item(k).getNodeName().equals("sf:Farmer_Biodata__c")) { System.out .println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); FarmManagementNode.setProperty( getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } FarmManagementParent = ParentNode.FMParentNode(); FarmManagementParent.createRelationshipTo(FarmManagementNode, ICTCRelationshipTypes.FARM_MANAGEMENT); log.log(Level.INFO, "new node created {0}", FarmManagementNode.getId()); Biodata b = biodataModel.getBiodata("Id", farmerID); biodataModel.BiodataToFarmManagement(b.getId(), FarmManagementNode); tx.success(); out.println(sendAck()); } else if (salesforceObj.equals("sf:FarmOperations__c")) { org.neo4j.graphdb.Node FarmOperationParent; org.neo4j.graphdb.Node FarmOperationNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.FARM_OPERATION); String farmerID = getXmlNodeValue("sf:Farmer_Biodata__c", ele); System.out.println("farmerid " + farmerID); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { //System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out.println( "id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); FarmOperationNode.setProperty( getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text") && !rowNode .getChildNodes().item(k).getNodeName().equals("sf:Farmer_Biodata__c")) { System.out .println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); FarmOperationNode.setProperty( getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } FarmOperationParent = ParentNode.OperationsParentNode(); FarmOperationParent.createRelationshipTo(FarmOperationNode, ICTCRelationshipTypes.FARM_OPERATION); log.log(Level.INFO, "new node created {0}", FarmOperationNode.getId()); Biodata b = biodataModel.getBiodata("Id", farmerID); biodataModel.BiodataToOperations(b.getId(), FarmOperationNode); tx.success(); out.println(sendAck()); } else if (salesforceObj.equals("sf:Marketing__c")) { org.neo4j.graphdb.Node MarketingParent; org.neo4j.graphdb.Node MarketingNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.MARKETING); String farmerID = getXmlNodeValue("sf:Farmer_Biodata__c", ele); System.out.println("farmerid " + farmerID); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { //System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out.println( "id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); MarketingNode.setProperty( getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text") && !rowNode .getChildNodes().item(k).getNodeName().equals("sf:Farmer_Biodata__c")) { System.out .println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); MarketingNode.setProperty( getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } MarketingParent = ParentNode.MarketingParentNode(); MarketingParent.createRelationshipTo(MarketingNode, ICTCRelationshipTypes.MARKETING); log.log(Level.INFO, "new node created {0}", MarketingNode.getId()); Biodata b = biodataModel.getBiodata("Id", farmerID); biodataModel.BiodataToMarketing(b.getId(), MarketingNode); tx.success(); out.println(sendAck()); } else if (salesforceObj.equals("sf:PostHarvest__c")) { org.neo4j.graphdb.Node PostHarvestParent; org.neo4j.graphdb.Node PostHarvestNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.POSTHARVEST); String farmerID = getXmlNodeValue("sf:Farmer_Biodata__c", ele); System.out.println("farmerid " + farmerID); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { // System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out.println( "id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); PostHarvestNode.setProperty( getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text") && !rowNode .getChildNodes().item(k).getNodeName().equals("sf:Farmer_Biodata__c")) { System.out .println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); PostHarvestNode.setProperty( getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } PostHarvestParent = ParentNode.PostHarvestParentNode(); PostHarvestParent.createRelationshipTo(PostHarvestNode, ICTCRelationshipTypes.POST_HARVEST); log.log(Level.INFO, "new node created {0}", PostHarvestNode.getId()); Biodata b = biodataModel.getBiodata("Id", farmerID); biodataModel.BiodataToPostHarvest(b.getId(), PostHarvestNode); tx.success(); out.println(sendAck()); } else if (salesforceObj.equals("sf:Storage__c")) { org.neo4j.graphdb.Node StorageParent; org.neo4j.graphdb.Node StorageNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.STORAGE); String farmerID = getXmlNodeValue("sf:Farmer_Biodata__c", ele); System.out.println("farmerid " + farmerID); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out.println( "id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); StorageNode.setProperty( getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text") && !rowNode .getChildNodes().item(k).getNodeName().equals("sf:Farmer_Biodata__c")) { System.out .println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); StorageNode.setProperty( getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } StorageParent = ParentNode.StorageParentNode(); StorageParent.createRelationshipTo(StorageNode, ICTCRelationshipTypes.STORAGE); log.log(Level.INFO, "new node created {0}", StorageNode.getId()); Biodata b = biodataModel.getBiodata("Id", farmerID); biodataModel.BiodataToStorage(b.getId(), StorageNode); tx.success(); out.println(sendAck()); } else if (salesforceObj.equals("sf:TechnicalNeeds__c")) { org.neo4j.graphdb.Node TNParent; org.neo4j.graphdb.Node TNNode = ICTCDBUtil.getInstance().getGraphDB() .createNode(Labels.TECHNICAL_NEEDS); String farmerID = getXmlNodeValue("sf:Farmer_Biodata__c", ele); System.out.println("farmerid " + farmerID); for (int k = 0; k < rowNode.getChildNodes().getLength(); k++) { System.out.println("node: " + rowNode.getChildNodes().item(k).getNodeName() + ": " + rowNode.getChildNodes().item(k).getTextContent()); if (rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id")) { System.out.println( "id : " + getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName())); TNNode.setProperty(getObjectFieldId(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } if (!rowNode.getChildNodes().item(k).getNodeName().equals("sf:Id") && !rowNode.getChildNodes().item(k).getNodeName().equals("#text") && !rowNode .getChildNodes().item(k).getNodeName().equals("sf:Farmer_Biodata__c")) { System.out .println(getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName())); TNNode.setProperty( getObjectFieldName(rowNode.getChildNodes().item(k).getNodeName()), rowNode.getChildNodes().item(k).getTextContent()); } } TNParent = ParentNode.TechNeedParentNode(); TNParent.createRelationshipTo(TNNode, ICTCRelationshipTypes.TECHNICAL_NEED); log.log(Level.INFO, "new node created {0}", TNNode.getId()); Biodata b = biodataModel.getBiodata("Id", farmerID); biodataModel.BiodataToTechNeeds(b.getId(), TNNode); tx.success(); out.println(sendAck()); } } } catch (Exception ex) { Logger.getLogger(SaleforceIntegrationController.class.getName()).log(Level.SEVERE, null, ex); tx.failure(); } finally { tx.finish(); } } }