/**
* Perform operation for the given request using business class(ejb) and return response
*
* @throws I2B2Exception
* @see edu.harvard.i2b2.crc.delegate.RequestHandler#execute()
*/
public BodyType execute() throws I2B2Exception {
QueryProcessorUtil qpUtil = QueryProcessorUtil.getInstance();
String response = null;
BodyType bodyType = new BodyType();
MasterInstanceResultResponseType masterInstanceResponse = null;
try {
StartAnalysisLocal startAnalysisLocal = qpUtil.getStartAnalysisLocal();
DAOFactoryHelper daoFactoryHelper =
new DAOFactoryHelper(
this.getDataSourceLookup().getDomainId(),
getDataSourceLookup().getProjectPath(),
getDataSourceLookup().getOwnerId());
IDAOFactory daoFactory = daoFactoryHelper.getDAOFactory();
// response = queryManagerLocal.processQuery(requestXml);
masterInstanceResponse = startAnalysisLocal.start(daoFactory, requestXml);
// processQuery(this.getDataSourceLookup(), requestXml);
// masterInstanceResponse.setStatus(this.buildCRCStausType(
// RequestHandlerDelegate.DONE_TYPE, "DONE"));
// response = this.buildResponseMessage(requestXml, bodyType);
} catch (I2B2Exception e) {
masterInstanceResponse = new MasterInstanceResultResponseType();
masterInstanceResponse.setStatus(
this.buildCRCStausType(RequestHandlerDelegate.ERROR_TYPE, e.getMessage()));
} finally {
edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory psmObjFactory =
new edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory();
bodyType.getAny().add(psmObjFactory.createResponse(masterInstanceResponse));
}
return bodyType;
}
private DataSource getDataSource(String dataSourceName) {
DataSource ds = null;
try {
ds = OntologyUtil.getInstance().getDataSource(dataSourceName);
} catch (I2B2Exception e2) {
log.error(e2.getMessage());
;
}
return ds;
}
/** Perform operation for the given request using business class(ejb) and return response */
public BodyType execute() throws I2B2Exception {
// call ejb and pass input object
QueryProcessorUtil qpUtil = QueryProcessorUtil.getInstance();
String responseString = null;
BodyType bodyType = new BodyType();
InstanceResponseType instanceResponseType = null;
try {
QueryRunLocalHome queryRunLocalHome = qpUtil.getQueryRunLocalHome();
QueryRunLocal queryRunLocal = queryRunLocalHome.create();
UserType userType = headerType.getUser();
String userId = null;
if (userType != null) {
userId = userType.getLogin();
}
instanceResponseType =
queryRunLocal.getQueryInstanceFromMasterId(
getDataSourceLookup(), userId, masterRequestType);
instanceResponseType.setStatus(
this.buildCRCStausType(RequestHandlerDelegate.DONE_TYPE, "DONE"));
// ResponseMessageType responseMessageType = new ResponseMessageType();
// responseMessageType.setMessageBody(bodyType);
// responseString = getResponseString(responseMessageType);
} catch (I2B2Exception e) {
instanceResponseType = new InstanceResponseType();
instanceResponseType.setStatus(
this.buildCRCStausType(RequestHandlerDelegate.ERROR_TYPE, e.getMessage()));
} catch (ServiceLocatorException e) {
log.error(e);
throw new I2B2Exception("Servicelocator exception", e);
} catch (CreateException e) {
log.error(e);
throw new I2B2Exception("Ejb create exception", e);
} finally {
edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory of =
new edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory();
bodyType.getAny().add(of.createResponse(instanceResponseType));
}
return bodyType;
}
public List getCategories() {
List concepts = null;
try {
// GetReturnType request = new GetReturnType();
// request.setType("limited");
GetCategoriesType request = new GetCategoriesType();
request.setType("core");
request.setHiddens(false);
request.setSynonyms(false);
OntologyResponseMessage msg = new OntologyResponseMessage();
StatusType procStatus = null;
while (procStatus == null || !procStatus.getType().equals("DONE")) {
String response = OntServiceDriver.getCategories(request, "FIND");
procStatus = msg.processResult(response);
// if other error codes
// TABLE_ACCESS_DENIED and USER_INVALID, DATABASE ERROR
if (procStatus.getType().equals("ERROR")) {
System.setProperty("errorMessage", procStatus.getValue());
return concepts;
}
procStatus.setType("DONE");
}
ConceptsType allConcepts = msg.doReadConcepts();
if (allConcepts != null) concepts = allConcepts.getConcept();
} catch (AxisFault e) {
log.error(e.getMessage());
System.setProperty("errorMessage", "Ontology cell unavailable");
} catch (I2B2Exception e) {
log.error(e.getMessage());
System.setProperty("errorMessage", e.getMessage());
} catch (Exception e) {
log.error(e.getMessage());
System.setProperty("errorMessage", "Remote server unavailable");
}
return concepts;
}
public List findCodeInfo(
final VocabRequestType vocabType, final List categories, ProjectType projectInfo)
throws DataAccessException, I2B2Exception {
DataSource ds = null;
try {
ds = OntologyUtil.getInstance().getDataSource("java:OntologyLocalDS");
} catch (I2B2Exception e2) {
log.error(e2.getMessage());
throw e2;
}
SimpleJdbcTemplate jt = new SimpleJdbcTemplate(ds);
// find return parameters
String parameters = DEFAULT;
if (vocabType.getType().equals("core")) {
parameters = CORE;
} else if (vocabType.getType().equals("all")) {
parameters = ALL;
}
if (vocabType.isBlob() == true) parameters = parameters + BLOB;
// extract table code
String tableCd = vocabType.getCategory();
// log.info(tableCd);
// table code to table name conversion
// Get metadata schema name from properties file.
String metadataSchema = "";
try {
metadataSchema = OntologyUtil.getInstance().getMetaDataSchemaName();
} catch (I2B2Exception e1) {
log.error(e1.getMessage());
throw e1;
}
List tableNames = null;
if (tableCd != null) {
// table code to table name conversion
String tableSql =
"select distinct(c_table_name) from "
+ metadataSchema
+ "table_access where c_table_cd = ? ";
ParameterizedRowMapper<String> map =
new ParameterizedRowMapper<String>() {
public String mapRow(ResultSet rs, int rowNum) throws SQLException {
String name = (rs.getString("c_table_name"));
return name;
}
};
tableNames = jt.query(tableSql, map, tableCd);
} else { // tableCd is null, so query all tables user has access to
String whereClause = "where ";
Iterator it = categories.iterator();
while (it.hasNext()) {
ConceptType entry = null;
if (whereClause.equals("where ")) {
entry = (ConceptType) it.next();
whereClause =
whereClause + " c_table_cd = '" + StringUtil.getTableCd(entry.getKey()) + "' ";
} else {
entry = (ConceptType) it.next();
whereClause =
whereClause
+ " or "
+ " c_table_cd = '"
+ StringUtil.getTableCd(entry.getKey())
+ "' ";
}
}
String tableSql =
"select distinct(c_table_name) from " + metadataSchema + "table_access " + whereClause;
ParameterizedRowMapper<String> map =
new ParameterizedRowMapper<String>() {
public String mapRow(ResultSet rs, int rowNum) throws SQLException {
String name = (rs.getString("c_table_name"));
return name;
}
};
try {
tableNames = jt.query(tableSql, map);
} catch (DataAccessException e) {
log.error(e.getMessage());
throw e;
}
}
String hidden = "";
if (vocabType.isHiddens() == false) hidden = " and c_visualattributes not like '_H%'";
String synonym = "";
if (vocabType.isSynonyms() == false) synonym = " and c_synonym_cd = 'N'";
String codeInfoSql = null;
if (tableNames != null) {
Iterator it = tableNames.iterator();
String table = (String) it.next();
String tableCdSql =
", (select distinct(c_table_cd) from "
+ metadataSchema
+ "TABLE_ACCESS where c_table_name = '"
+ table
+ "') as tableCd";
String basecode = " '" + vocabType.getMatchStr().getValue() + "' ";
codeInfoSql =
"select "
+ parameters
+ tableCdSql
+ " from "
+ metadataSchema
+ table
+ " where upper(c_basecode) = "
+ basecode.toUpperCase()
+ hidden
+ synonym;
;
while (it.hasNext()) {
table = (String) it.next();
tableCdSql =
", (select distinct(c_table_cd) from "
+ metadataSchema
+ "TABLE_ACCESS where c_table_name = '"
+ table
+ "') as tableCd";
codeInfoSql =
codeInfoSql
+ " union select "
+ parameters
+ tableCdSql
+ " from "
+ metadataSchema
+ table
+ " where upper(c_basecode) = "
+ basecode.toUpperCase()
+ hidden
+ synonym;
}
codeInfoSql = codeInfoSql + " order by c_name ";
} else return null;
log.debug(codeInfoSql);
final boolean obfuscatedUserFlag = Roles.getInstance().isRoleOfuscated(projectInfo);
ParameterizedRowMapper<ExpandedConceptType> mapper =
new ParameterizedRowMapper<ExpandedConceptType>() {
public ExpandedConceptType mapRow(ResultSet rs, int rowNum) throws SQLException {
ExpandedConceptType entry = new ExpandedConceptType();
// TODO fix this for all/+blob
entry.setName(rs.getString("c_name"));
entry.setTableCd(rs.getString("tablecd"));
if (vocabType.getType().equals("core")) {
entry.setKey(rs.getString("c_fullname"));
entry.setBasecode(rs.getString("c_basecode"));
entry.setLevel(rs.getInt("c_hlevel"));
entry.setSynonymCd(rs.getString("c_synonym_cd"));
entry.setVisualattributes(rs.getString("c_visualattributes"));
Integer totalNum = rs.getInt("c_totalnum");
if (obfuscatedUserFlag == false) {
entry.setTotalnum(totalNum);
}
entry.setFacttablecolumn(rs.getString("c_facttablecolumn"));
entry.setTablename(rs.getString("c_tablename"));
entry.setColumnname(rs.getString("c_columnname"));
entry.setColumndatatype(rs.getString("c_columndatatype"));
entry.setOperator(rs.getString("c_operator"));
entry.setDimcode(rs.getString("c_dimcode"));
entry.setTooltip(rs.getString("c_tooltip"));
}
if ((vocabType.getType().equals("all"))) {
DTOFactory factory = new DTOFactory();
// make sure date isnt null before converting to XMLGregorianCalendar
Date date = rs.getDate("update_date");
if (date == null) entry.setUpdateDate(null);
else entry.setUpdateDate(factory.getXMLGregorianCalendar(date.getTime()));
date = rs.getDate("download_date");
if (date == null) entry.setDownloadDate(null);
else entry.setDownloadDate(factory.getXMLGregorianCalendar(date.getTime()));
date = rs.getDate("import_date");
if (date == null) entry.setImportDate(null);
else entry.setImportDate(factory.getXMLGregorianCalendar(date.getTime()));
entry.setSourcesystemCd(rs.getString("sourcesystem_cd"));
entry.setValuetypeCd(rs.getString("valuetype_cd"));
}
return entry;
}
};
List queryResult = null;
try {
if (tableNames != null) queryResult = jt.query(codeInfoSql, mapper);
} catch (DataAccessException e) {
log.error(e.getMessage());
throw e;
}
log.debug("result size = " + queryResult.size());
if (queryResult != null) {
if (parameters != DEFAULT) {
// fix the key so it equals "\\tableCd\fullname"
// in all cases but default
Iterator it = queryResult.iterator();
while (it.hasNext()) {
ExpandedConceptType entry = (ExpandedConceptType) it.next();
entry.setKey("\\\\" + entry.getTableCd() + entry.getKey());
}
}
// Cant gather clobs when you perform unions....
// So you have to loop through all the results and gather clobs
if (vocabType.isBlob() == true) {
Iterator itr = queryResult.iterator();
while (itr.hasNext()) {
ConceptType child = (ConceptType) itr.next();
Iterator it = tableNames.iterator();
while (it.hasNext()) {
String clobSql =
"select c_metadataxml, c_comment from "
+ metadataSchema
+ (String) it.next()
+ " where c_name = ? and "
+ synonym;
ParameterizedRowMapper<ConceptType> map =
new ParameterizedRowMapper<ConceptType>() {
public ConceptType mapRow(ResultSet rs, int rowNum) throws SQLException {
ConceptType concept = new ConceptType();
try {
if (rs.getClob("c_metadataxml") == null) {
concept.setMetadataxml(null);
} else {
String c_xml = JDBCUtil.getClobString(rs.getClob("c_metadataxml"));
if ((c_xml != null)
&& (c_xml.trim().length() > 0)
&& (!c_xml.equals("(null)"))) {
SAXBuilder parser = new SAXBuilder();
java.io.StringReader xmlStringReader = new java.io.StringReader(c_xml);
Element rootElement = null;
try {
org.jdom.Document metadataDoc = parser.build(xmlStringReader);
org.jdom.output.DOMOutputter out = new DOMOutputter();
Document doc = out.output(metadataDoc);
rootElement = doc.getDocumentElement();
} catch (JDOMException e) {
log.error(e.getMessage());
concept.setMetadataxml(null);
}
if (rootElement != null) {
XmlValueType xml = new XmlValueType();
xml.getAny().add(rootElement);
concept.setMetadataxml(xml);
}
} else {
concept.setMetadataxml(null);
}
}
} catch (IOException e) {
log.error(e.getMessage());
concept.setMetadataxml(null);
}
try {
if (rs.getClob("c_comment") == null) {
concept.setComment(null);
} else {
concept.setComment(JDBCUtil.getClobString(rs.getClob("c_comment")));
}
} catch (IOException e) {
log.error(e.getMessage());
concept.setComment(null);
}
return concept;
}
};
List clobResult = null;
try {
clobResult = jt.query(clobSql, map, child.getName(), child.getTooltip());
} catch (DataAccessException e) {
log.error(e.getMessage());
throw e;
}
if (clobResult != null) {
if ((((ConceptType) (clobResult.get(0))).getMetadataxml() != null)
|| (((ConceptType) (clobResult.get(0))).getComment() != null)) {
child.setMetadataxml(((ConceptType) (clobResult.get(0))).getMetadataxml());
child.setComment(((ConceptType) (clobResult.get(0))).getComment());
break;
}
} else {
child.setMetadataxml(null);
child.setComment(null);
}
}
}
}
}
return queryResult;
}