//DB========================================================================
Class.forName("com.mysql.jdbc.Driver");
con = DriverManager.getConnection("jdbc:mysql://IPv4/oss", "root", "root");

ResultSet rs = null;
PreparedStatement ps = null;
String query = "SELECT * from table";
ps = sqlConnection.prepareStatement(query);
rs = ps.executeQuery();
if(!rs.isBeforeFirst())
{
    System.err.println((new StringBuilder("No results returned from the query : ")).append(query).toString());
    System.err.println("Please check the query");
    System.exit(1);
}
ResultSetMetaData metaData = rs.getMetaData();
 Map columnvalueMap;
         for(; rs.next(); jsonmap.put(keyName, columnvalueMap)) //md5
         {
             columnvalueMap = new HashMap();
             for(int columnIndex = 1; columnIndex <= metaData.getColumnCount(); columnIndex++)
                 if(metaData.getColumnLabel(columnIndex).equals("md5"))
                     keyName = rs.getString("md5").toLowerCase();
                 else if(rs.getString(metaData.getColumnName(columnIndex)) != null)
                     columnvalueMap.put(metaData.getColumnLabel(columnIndex), rs.getString(metaData.getColumnName(columnIndex)));
                 else
                     columnvalueMap.put(metaData.getColumnLabel(columnIndex), "");

         }

jsonObject = new JSONObject(JSONValue.toJSONString(jsonmap));
//DB========================================================================

//Protex=====================================================================
ProtexServerProxy myProtexServer = new ProtexServerProxy(serverUri, username, password, connectionTimeout)

ProjectApi projectApi               = myProtexServer.getProjectApi();
IdentificationApi identificationApi = myProtexServer.getIdentificationApi();
BomApi bomApi                       = myProtexServer.getBomApi();
LocalComponentApi localComponentApi = myProtexServer.getLocalComponentApi();
CodeTreeApi codeTreeApi             = myProtexServer.getCodeTreeApi(0L);
LicenseApi licenseApi               = myProtexServer.getLicenseApi();

//get project name
String projectId = projectApi.getProjectByName(projectName).getProjectId()

//get BOM components
List bomComponents = bomApi.getBomComponents(projectId);


//getlocalcomponents

LocalComponentPageFilter componentPageFilter = PageFilterFactory.getAllRows(LocalComponentColumn.COMPONENT_NAME);

List localComponents = localComponentApi.getLocalComponents(projectId, componentPageFilter);

//code tree
 String ROOT = "/";

 Prepare codeTreeNodeRequest
 CodeTreeNodeRequest codeTreeNodeRequest = new CodeTreeNodeRequest();
         codeTreeNodeRequest.getIncludedNodeTypes().addAll(CodeTreeUtilities.ALL_CODE_TREE_NODE_TYPES);
         codeTreeNodeRequest.setDepth(CodeTreeUtilities.INFINITE_DEPTH);
         codeTreeNodeRequest.setIncludeParentNode(Boolean.valueOf(true));
         codeTreeNodeRequest.getCounts().add(NodeCountType.PENDING_ID_ALL);

 List nodes = codeTreeApi.getCodeTreeNodes(projectId, ROOT, codeTreeNodeRequest);

//licenseApi

List typeFilter = new ArrayList();
typeFilter.add(LicenseOriginType.STANDARD);
typeFilter.add(LicenseOriginType.CUSTOM);
typeFilter.add(LicenseOriginType.MODIFIED_STANDARD);

LicenseInfoPageFilter pageFilter = PageFilterFactory.getAllRows(LicenseInfoColumn.LICENSE_NAME);


List licenses = licenseApi.getLicenses(typeFilter, pageFilter);

//perform identification

Prepare identification request
IdentificationRequest identificationRequest = new IdentificationRequest();
identificationRequest.setIdentifiedComponentKey(componentKey);
identificationRequest.setIdentifiedUsageLevel(UsageLevel.COMPONENT_DYNAMIC_LIBRARY);

actual DeclaredIdentification
identificationApi.addDeclaredIdentification(projectId, nodeName, identificationRequest, BomRefreshMode.SKIP);

//Protex=====================================================================

//main========================
rootFolderFileList = CodeTree.fetchCodeTreeNodes(projectId, codeTreeApi);
		Iterator iterator = rootFolderFileList.iterator();
		while(iterator.hasNext())
		{
			CodeTreeNode subFolderFileList = (CodeTreeNode)iterator.next();
			Map countMap = CodeTreeUtilities.getNodeCountMap(subFolderFileList);
			filePendingCount = ((Long)countMap.get(NodeCountType.PENDING_ID_ALL)).longValue();
			nodeName = subFolderFileList.getName();
			if(filePendingCount <= 0L || !subFolderFileList.getNodeType().toString().equalsIgnoreCase("FILE"))
				continue;
			fileIndex++;
			System.out.println((new StringBuilder(String.valueOf(fileIndex))).append(") ").append(subFolderFileList.getName()).toString());
			dllFileName = nodeName.replaceFirst(".*/(\\w+)", "$1");
			sourceFileInfoNodes = codeTreeApi.getFileInfo(projectId, nodeName, CodeTreeUtilities.SINGLE_NODE, Boolean.valueOf(true), null);
			for(Iterator iterator2 = sourceFileInfoNodes.iterator(); iterator2.hasNext();)
			{
				SourceFileInfoNode sourceFileInfoNode = (SourceFileInfoNode)iterator2.next();
				System.out.println((new StringBuilder("MD5:")).append(sourceFileInfoNode.getExactChecksum()).toString());
				dllFileMD5Sum = sourceFileInfoNode.getExactChecksum();
			}

			try
			{
				System.out.println((new StringBuilder("\t Searching for rules from DB for File '")).append(dllFileName).append("'").toString());
				componentDetailsfromRules = dllRulesJSON.getJSONObject(dllFileMD5Sum);
				componentNamefromRules = componentDetailsfromRules.getString("component_name");
				componentVersionfromRules = componentDetailsfromRules.getString("component_version");
				componentHomepagefromRules = componentDetailsfromRules.getString("homepage");
				componentLicenseNamefromRules = componentDetailsfromRules.getString("component_license");
				componentCommentfromRules = componentDetailsfromRules.getString("component_comment");
				System.out.println((new StringBuilder("\t Rules found for File ")).append(dllFileName).toString());
			}
			catch(JSONException e)
			{
				if(e.getMessage().contains("not found"))
				{
					System.err.println((new StringBuilder("\t No rules found for the File : '")).append(nodeName).append("' . Hence Skipping identification").toString());
					continue;
				}
				e.printStackTrace();
			}
			// Boolean bomExists;
			try
			{
				System.out.println((new StringBuilder("\t Searching for already existing BOM for component '")).append(componentNamefromRules).append("' with version '").append(componentVersionfromRules).append("' and homepage '").append(componentHomepagefromRules).append("'").toString());
				componentDetailsfromBom = (Map)bomLocalComponentsMap.get(componentNamefromRules);
				componentVersionfromBom = (String)componentDetailsfromBom.get("component_version");
				componentHomepagefromBom = (String)componentDetailsfromBom.get("component_homepage");
				componentLicenseNamefromBom = (String)componentDetailsfromBom.get("component_license");
				bomComponentKey = (ComponentKey)componentDetailsfromBom.get("component_key");
				if(componentVersionfromRules.equals(componentVersionfromBom) && componentHomepagefromRules.equals(componentHomepagefromBom) && componentLicenseNamefromRules.equals(componentLicenseNamefromBom))
				{
					bomExists = Boolean.valueOf(true);
					System.out.println((new StringBuilder("\t Already BOM exists for the component '")).append(componentNamefromRules).append("'. Hence same BOM Component will be reused").toString());
				} else
				{
					System.out.println((new StringBuilder("\t No components found for File : '")).append(nodeName).append("'. Hence new local component would be created").toString());
					bomExists = Boolean.valueOf(false);
				}
			}
			catch(Exception e)
			{
				System.out.println((new StringBuilder("\t Exception:No components found for File : '")).append(nodeName).append("'. Hence new local component would be created").toString());
				bomExists = Boolean.valueOf(false);
			}
			//ComponentKey localComponentKey;
			if(bomExists.booleanValue())
			{
				localComponentKey = bomComponentKey;
			} else
			{
				System.out.println((new StringBuilder("\t Creating new local component for component name : '")).append(componentNamefromRules).append("'").toString());
				LocalComponentRequest localComponentRequest = new LocalComponentRequest();
				localComponentRequest.setName(componentNamefromRules);
				localComponentRequest.setHomePage(componentHomepagefromRules);
				localComponentRequest.setVersionLabel(componentVersionfromRules);
				String licenseId = licenseJSON.getJSONObject(componentLicenseNamefromRules.toLowerCase()).getString("license_id");
				LocalLicenseRequest localLicenseRequest = new LocalLicenseRequest();
				localLicenseRequest.setBasedOnLicenseId(licenseId);
				try
				{
					localComponentKey = localComponentApi.createLocalComponent(projectId, localComponentRequest, localLicenseRequest);
				}
				catch(SdkFault e)
				{
					System.err.println((new StringBuilder("createLocalComponent() failed: ")).append(e.getMessage()).toString());
					throw new RuntimeException(e);
				}
				Map columnMap = new HashMap();
				columnMap.put("component_id", localComponentKey.getComponentId());
				columnMap.put("component_key", localComponentKey);
				columnMap.put("component_homepage", componentHomepagefromRules);
				columnMap.put("component_version", componentVersionfromRules);
				columnMap.put("license_id", licenseId);
				columnMap.put("component_license", componentLicenseNamefromRules);
				bomLocalComponentsMap.put(componentNamefromRules, columnMap);
			}
			Identification.applyIdentification(projectId, identificationApi, nodeName, localComponentKey);
			ComponentCommentMap.put(localComponentKey, componentCommentfromRules);
		}
		System.out.println("Identification is completed");

//main=========================

//comp comment add
bomApi.setComponentComment(projectId, component key, component comment)

//bom refresh
bomApi.refreshBom(projectId,booleanValue refreshAllFiles,booleanValue asynchronousRefresh);