/**
* Needed for hyperlink form switches...
*
* @param request
* @throws DatabaseException
*/
private void doXrefselect(Tuple request) throws DatabaseException {
// also set the parent menu
if (getParent() != null && getParent() instanceof MenuController) {
// set the filter to select the xref-ed entity
pager.resetFilters();
getModel().setUserRules(new ArrayList<QueryRule>());
QueryRule rule =
new QueryRule(
request.getString("attribute"),
QueryRule.Operator.valueOf(request.getString("operator")),
request.getString("value"));
pager.addFilter(rule);
// tell "my" menu to select me
Tuple parentRequest = new SimpleTuple();
String aChildName = getModel().getName();
ScreenController<?> aParent = getParent();
while (aParent != null) {
if (aParent instanceof MenuModel) {
parentRequest.set("select", aChildName);
MenuController c = (MenuController) aParent;
c.doSelect(parentRequest);
}
aChildName = aParent.getName();
aParent = aParent.getParent();
}
}
}
private void handleShowNextMutation(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
MutationSummaryDTO mutationSummaryDTO =
searchService.findNextMutation(request.getString("mid"));
request.set("mid", mutationSummaryDTO.getIdentifier());
this.handleShowMutation(request);
}
@Override
public ScreenModel.Show handleRequest(Database db, Tuple request, OutputStream downloadStream)
throws Exception {
logger.debug(this.getName());
// check if in dialog
if (request.getString(FormModel.INPUT_SHOW) == null) {
ScreenMessage msg = null;
try {
CsvToDatabase<? extends Entity> csvReader = this.getFormScreen().getCsvReader();
int updatedRows =
csvReader.importCsv(
db,
new CsvFileReader(request.getFile("filefor___csvdata")),
request,
DatabaseAction.ADD);
// for (E entity : entities)
// logger.debug("parsed: " + entity);
// view.getDatabase().add(entities);
msg = new ScreenMessage("CSV UPLOAD SUCCESS: added " + updatedRows + " rows", null, true);
logger.debug("CSV UPLOAD SUCCESS: added " + updatedRows + " rows");
getFormScreen().getPager().resetFilters();
getFormScreen().getPager().last(db);
} catch (Exception e) {
e.printStackTrace();
msg = new ScreenMessage("CSV UPLOAD FAILED: " + e.getMessage(), null, false);
logger.error("CSV UPLOAD FAILED: " + e.getMessage());
}
getFormScreen().getMessages().add(msg);
}
// show result in the main screen
return ScreenModel.Show.SHOW_MAIN;
}
private void handleShowPrevExon(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
ExonDTO exonDTO = searchService.findPrevExon(request.getInt("exon_id"));
request.set("__action", "showExon");
request.set("exon_id", exonDTO.getId());
this.handleShowExon(request);
}
private void handleFindMutationsByTerm(Tuple request) {
// if (StringUtils.isNotEmpty(request.getString("term")) && request.getString("term").length()
// < 3)
// throw new SearchException("Search term is too general. Please use a more specific one.");
if (StringUtils.isNotEmpty(request.getString("result")))
this.getModel().setResult(request.getString("result"));
else this.getModel().setResult("mutations"); // Default: Show mutations
this.getModel().setMutationSummaryVOHash(new HashMap<String, String>());
this.getModel().setPatientSummaryVOHash(new HashMap<String, String>());
SearchService searchService = ServiceLocator.instance().getSearchService();
if (this.getModel().getResult().equals("patients")) {
HashMap<String, List<PatientSummaryDTO>> result =
searchService.findPatientsByTerm(request.getString("term"));
int numPatients = 0;
for (String key : result.keySet()) {
if (CollectionUtils.isNotEmpty(result.get(key))) {
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("patientSummaryVOs", result.get(key));
this.getModel()
.getPatientSummaryVOHash()
.put(" " + key + " ", this.include(request, this.getModel().getPatientPager()));
numPatients += result.get(key).size();
}
}
this.getModel().setHeader(numPatients + " patients found.");
} else if (this.getModel().getResult().equals("mutations")) {
HashMap<String, List<MutationSummaryDTO>> result =
searchService.findMutationsByTerm(request.getString("term"));
int numMutations = 0;
for (String key : result.keySet()) {
if (CollectionUtils.isNotEmpty(result.get(key))) {
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryDTOList", result.get(key));
this.getModel()
.getMutationSummaryVOHash()
.put(" " + key + " ", this.include(request, this.getModel().getMutationPager()));
numMutations += result.get(key).size();
}
}
this.getModel().setHeader(numMutations + " mutations found.");
}
this.setView(new FreemarkerView("freetext.ftl", this.getModel()));
}
private void handleShowPatient(Tuple request) {
if (StringUtils.isNotEmpty(request.getString("pid"))) {
String patientIdentifier = request.getString("pid");
SearchService searchService = ServiceLocator.instance().getSearchService();
PatientSummaryDTO patientSummaryVO =
searchService.findPatientByPatientIdentifier(patientIdentifier);
this.getModel().setPatientSummaryVO(patientSummaryVO);
this.getModel().setHeader("Details for patient " + patientIdentifier);
this.setView(new FreemarkerView(this.getModel().getPatientViewer(), getModel()));
}
}
/**
* Function to build a datastructure filled with rows from a {@link TupleTable}, to be serialised
* by Gson and displayed from there by a jqGrid.
*
* @param rowCount The number of rows to select.
* @param totalPages The total number of pages of data (ie. dependent on size of dataset and nr.
* of rows per page)
* @param page The selected page.
* @param table The Tupletable from which to read the data.
* @return
*/
public static JQGridResult buildJQGridResults(
final int rowCount, final int totalPages, final int page, final TupleTable table)
throws TableException {
final JQGridResult result = new JQGridResult(page, totalPages, rowCount);
for (final Tuple row : table.getRows()) {
System.out.println("check: " + row);
final LinkedHashMap<String, String> rowMap = new LinkedHashMap<String, String>();
final List<String> fieldNames = row.getFieldNames();
for (final String fieldName : fieldNames) {
final String rowValue = !row.isNull(fieldName) ? row.getString(fieldName) : "null";
rowMap.put(fieldName, rowValue); // TODO encode to HTML
}
result.rows.add(rowMap);
}
return result;
}
private void handleFindPatients(Tuple request) {
if (StringUtils.isNotEmpty(request.getString("mid"))) {
String mutationIdentifier = request.getString("mid");
SearchService searchService = ServiceLocator.instance().getSearchService();
List<PatientSummaryDTO> patientSummaryVOList =
searchService.findPatientsByMutationIdentifier(mutationIdentifier);
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("patientSummaryVOs", patientSummaryVOList);
this.getModel().setRawOutput(this.include(request, this.getModel().getPatientPager()));
this.getModel().setHeader(patientSummaryVOList.size() + " results for " + mutationIdentifier);
this.setView(new FreemarkerView("included.ftl", this.getModel()));
}
}
private void handleShowPhenotypeDetails(Tuple request) throws Exception {
if (StringUtils.isNotEmpty(request.getString("pid"))) {
String patientIdentifier = request.getString("pid");
PhenoService phenoService = ServiceLocator.instance().getPhenoService();
SearchService searchService = ServiceLocator.instance().getSearchService();
PatientSummaryDTO patientSummaryVO =
searchService.findPatientByPatientIdentifier(patientIdentifier);
this.getModel()
.setIndividualDTO(phenoService.findPhenotypeDetails(patientSummaryVO.getPatientId()));
this.getModel().setHeader("Phenotypic details for Patient " + patientIdentifier);
this.setView(new FreemarkerView("phenotypedetails.ftl", getModel()));
}
}
/**
* Helper function to add a record from UI
*
* @param request
* @return true if add was successfull, false if it wassen't
* @throws ParseException
* @throws DatabaseException
* @throws IOException
*/
public boolean doAdd(Database db, Tuple request)
throws ParseException, DatabaseException, IOException {
ScreenMessage msg = null;
Entity entity = getModel().create();
boolean result = false;
try {
db.beginTx();
entity.set(request, false);
int updatedRows = 0;
if (request.getObject(FormModel.INPUT_BATCHADD) != null
&& request.getInt(FormModel.INPUT_BATCHADD) > 1) {
// batch
int i;
for (i = 0; i < request.getInt(FormModel.INPUT_BATCHADD); i++) {
updatedRows += db.add(entity);
}
} else {
updatedRows = db.add(entity);
}
db.commitTx();
msg = new ScreenMessage("ADD SUCCESS: affected " + updatedRows, null, true);
result = true;
// navigate to newly added record
pager.last(db);
} catch (Exception e) {
db.rollbackTx();
msg = new ScreenMessage("ADD FAILED: " + e.getMessage(), null, false);
result = false;
}
getModel().getMessages().add(msg);
/* make sure the user sees the newly added record(s) */
// view.setMode(FormScreen.Mode.RECORD_VIEW);
// pager.setLimit(1);
pager.resetOrderBy();
pager.last(db);
// should reset to an order that shows the record on the end
return result;
}
/**
* Tries to set the values of all the inputs in the TablePanel to the corresponding ones in the
* request tuple.
*
* @param request
*/
@SuppressWarnings("unchecked")
public void setValuesFromRequest(Tuple request) {
Object object;
List<HtmlInput<?>> inputList = new ArrayList<HtmlInput<?>>();
fillList(inputList, this);
for (@SuppressWarnings("rawtypes") HtmlInput input : inputList) {
object = request.getObject(input.getName());
if (object != null) {
input.setValue(object);
}
}
}
private void handleShowProteinDomain(Tuple request) throws Exception {
if (StringUtils.isNotEmpty(request.getString("domain_id")))
this.getModel().getMutationSearchCriteriaVO().setProteinDomainId(request.getInt("domain_id"));
if (StringUtils.isNotEmpty(request.getString("snpbool")))
if (request.getString("snpbool").equals("hide"))
this.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);
SearchService searchService = ServiceLocator.instance().getSearchService();
this.getModel()
.setProteinDomainDTO(searchService.findProteinDomain(request.getInt("domain_id"), false));
this.getModel()
.setMutationSummaryDTOList(
searchService.findMutationsByDomainId(request.getInt("domain_id")));
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryVOList", this.getModel().getMutationSummaryDTOList());
this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));
this.getModel().setHeader((this.getModel().getProteinDomainDTO() == null) ? "Unknown id." : "");
this.getModel().getMbrowse().setProteinDomainDTO(this.getModel().getProteinDomainDTO());
if (this.getModel().getMbrowse().getExonDTOList() == null)
this.getModel().getMbrowse().setExonDTOList(searchService.findAllExons());
this.setView(new FreemarkerView("proteindomain.ftl", getModel()));
}
/** NOTE: Copied from InvestigationExcelReader */
private void writeSheetToFile(Sheet sheet, File file) throws FileNotFoundException {
List<String> headers = new ArrayList<String>();
Cell[] headerCells = sheet.getRow(0); // assume headers are on first
// line
ArrayList<Integer> namelessHeaderLocations = new ArrayList<Integer>(); // allow
// for
// empty
// columns,
// also
// column
// order
// does
// not
// matter
for (int i = 0; i < headerCells.length; i++) {
if (!headerCells[i].getContents().equals("")) {
headers.add(headerCells[i].getContents());
} else {
headers.add("nameless" + i);
namelessHeaderLocations.add(i);
}
}
PrintWriter pw = new PrintWriter(file);
CsvWriter cw = new CsvWriter(pw, headers);
cw.setMissingValue("");
cw.writeHeader();
for (int rowIndex = 1; rowIndex < sheet.getRows(); rowIndex++) {
Tuple t = new SimpleTuple();
int colIndex = 0;
for (Cell c : sheet.getRow(rowIndex)) {
if (!namelessHeaderLocations.contains(colIndex)) {
t.set(headers.get(colIndex), c.getContents());
}
colIndex++;
}
cw.writeRow(t);
}
cw.close();
}
private void handleShowMutation(Tuple request) {
if (StringUtils.isNotEmpty(request.getString("mid"))) {
String mutationIdentifier = request.getString("mid");
// if (StringUtils.isNotEmpty(request.getString("snpbool")))
// if (request.getString("snpbool").equals("hide"))
// this.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);
SearchService searchService = ServiceLocator.instance().getSearchService();
MutationSummaryDTO mutationSummaryDTO =
searchService.findMutationByIdentifier(mutationIdentifier);
this.getModel().setMutationSummaryVO(mutationSummaryDTO);
this.getModel().setPositionMutations(searchService.findPositionMutations(mutationSummaryDTO));
this.getModel().setCodonMutations(searchService.findCodonMutations(mutationSummaryDTO));
this.getModel().setHeader("Details for mutation " + mutationIdentifier);
this.setView(new FreemarkerView("mutation.ftl", getModel()));
}
}
private boolean writeSheetToFile(Sheet sheet, File file) throws FileNotFoundException {
List<String> headers = new ArrayList<String>();
Cell[] headerCells = sheet.getRow(0); // assume headers are on first line
if (headerCells.length == 0) {
return false;
}
ArrayList<Integer> namelessHeaderLocations =
new ArrayList<Integer>(); // allow for empty columns, also column order does not matter
for (int i = 0; i < headerCells.length; i++) {
if (!headerCells[i].getContents().equals("")) {
headers.add(headerCells[i].getContents());
} else {
headers.add("nameless" + i);
namelessHeaderLocations.add(i);
}
}
PrintWriter pw = new PrintWriter(file);
CsvWriter cw = new CsvWriter(pw, headers);
cw.setMissingValue("");
cw.writeHeader();
for (int rowIndex = 1; rowIndex < sheet.getRows(); rowIndex++) {
Tuple t = new SimpleTuple();
int colIndex = 0;
for (Cell c : sheet.getRow(rowIndex)) {
if (!namelessHeaderLocations.contains(colIndex)
&& colIndex < headers.size()
&& c.getContents() != null) {
t.set(headers.get(colIndex), c.getContents());
}
colIndex++;
}
cw.writeRow(t);
}
cw.close();
return true;
}
private Show addFilters(DatabasePager<E> pager, Database db, Tuple request)
throws DatabaseException, MolgenisModelException {
List<QueryRule> userRules = new ArrayList<QueryRule>();
for (int i = 0; i < MAX_FILTERS; ++i) {
// suffix: __filter_value, __filter_value1, __filter_value2 etc.
String suffix = i > 0 ? i + "" : "";
String filterAttr = request.getString("__filter_attribute" + suffix);
if (filterAttr == null) break;
String operatorStr = request.getString("__filter_operator" + suffix);
Operator operator = QueryRule.Operator.valueOf(operatorStr);
String filterValue = request.getString("__filter_value" + suffix);
QueryRule filterRule;
if (filterAttr.equals(FILTER_ATTRIBUTE_ALL)) {
filterRule = createFilterRule(db, operator, filterValue);
} else {
String fieldName = toFieldName(filterAttr);
filterRule = createFilterRule(db, fieldName, operator, filterValue);
}
userRules.add(filterRule);
}
FormModel<E> model = getModel();
model.getUserRules().addAll(userRules);
// reset pager
List<QueryRule> rules = new ArrayList<QueryRule>();
rules.addAll(model.getUserRules());
rules.addAll(model.getSystemRules());
pager.resetFilters(rules);
pager.first(db);
return Show.SHOW_MAIN;
}
private void handleShowExon(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
Integer exonId = request.getInt("exon_id");
this.getModel().setExonDTO(searchService.findExonById(exonId));
if (this.getModel().getQueryParametersVO().getShowMutations()) {
this.getModel().setMutationSummaryDTOList(searchService.findMutationsByExonId(exonId));
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryDTOList", this.getModel().getMutationSummaryDTOList());
this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));
}
this.getModel().setHeader("");
this.getModel().getMbrowse().setExonDTO(this.getModel().getExonDTO());
this.getModel()
.getMbrowse()
.setMutationSummaryDTOList(this.getModel().getMutationSummaryDTOList());
this.setView(new FreemarkerView("exon.ftl", getModel()));
}
/**
* Get all MAP file entries
*
* @return
* @throws Exception
*/
public List<MapEntry> getAllEntries() throws Exception {
reader.reset();
final ArrayList<MapEntry> result = new ArrayList<MapEntry>();
int line_number = 0;
for (Tuple tuple : reader) {
line_number++;
for (int objIndex = 0; objIndex < 4; objIndex++) {
if (tuple.getObject(objIndex) == null)
throw new Exception(Helper.errorMsg(line_number, objIndex));
}
MapEntry me =
new MapEntry(
tuple.getString(0), tuple.getString(1), tuple.getDouble(2), tuple.getLong(3));
result.add(me);
}
return result;
}
@Override
public void handleRequest(Database db, Tuple request) {
try {
String action = request.getString("__action");
if (action.equals("load")) {
String filename = request.getString("zip");
String legacy = request.getString("source");
if (legacy.equals("prefill")) {
PrefillAnimalDB myPrefill = new PrefillAnimalDB(db, this.getLogin());
myPrefill.prefillFromZip(filename);
this.setSuccess("Pre-filling AnimalDB successful");
} else if (legacy.equals("ulidb")) {
ConvertUliDbToPheno myLoadUliDb = new ConvertUliDbToPheno(db, this.getLogin());
myLoadUliDb.convertFromFile(filename);
this.setSuccess("Legacy import from Uli Eisel DB successful");
} else if (legacy.equals("oldadb")) {
LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db, this.getLogin());
myLoadAnimalDB.convertFromZip(filename);
this.setSuccess("Legacy import from old AnimalDB successful");
} else if (legacy.equals("rhutdb")) {
ConvertRhutDbToPheno myLoadRhutDb = new ConvertRhutDbToPheno(db, this.getLogin());
myLoadRhutDb.convertFromZip(filename);
this.setSuccess("Legacy import from Roelof Hut DB successful");
}
}
// if( action.equals("loadUliBackgrounds") )
// {
// String filename = request.getString("ulibackgroundtable");
// ConvertUliDbToPheno myLoadUliDb = new ConvertUliDbToPheno(db,
// this.getLogin());
// myLoadUliDb.populateBackground(filename);
// }
//
// if( action.equals("loadUliGenes") )
// {
// String filename = request.getString("uligenetable");
// ConvertUliDbToPheno myLoadUliDb = new ConvertUliDbToPheno(db,
// this.getLogin());
// myLoadUliDb.populateGene(filename);
// }
//
// if( action.equals("loadUliLines") )
// {
// String filename = request.getString("ulilinetable");
// ConvertUliDbToPheno myLoadUliDb = new ConvertUliDbToPheno(db,
// this.getLogin());
// myLoadUliDb.populateLine(filename);
// }
//
// if( action.equals("loadUliAnimals") )
// {
// String filename = request.getString("ulianimaltable");
// //String filename =
// "C:/Documents and
// Settings/Administrator/workspace/molgenis_apps/data/AnimalDB/legacy/20110429_UliEisel/Tierdetails.csv";
// ConvertUliDbToPheno myLoadUliDb = new ConvertUliDbToPheno(db,
// this.getLogin());
// //myLoadUliDb.populateLine("C:/Documents and
// Settings/Administrator/workspace/molgenis_apps/data/AnimalDB/legacy/20110429_UliEisel/Linie.csv");
// //myLoadUliDb.populateGene("C:/Documents and
// Settings/Administrator/workspace/molgenis_apps/data/AnimalDB/legacy/20110429_UliEisel/Gen.csv");
// //myLoadUliDb.populateBackground("C:/Documents and
// Settings/Administrator/workspace/molgenis_apps/data/AnimalDB/legacy/20110429_UliEisel/GenetischerHintergrund.csv");
// myLoadUliDb.populateAnimal(filename);
// myLoadUliDb.populateProtocolApplication();
// myLoadUliDb.populateValue(filename);
// myLoadUliDb.parseParentRelations(filename);
// myLoadUliDb.writeToDb();
//
// CommonService cs = CommonService.getInstance();
// cs.setDatabase(db);
// cs.makeObservationTargetNameMap(this.getLogin().getUserName(),
// true);
// }
//
// if( action.equals("loadAnimals") )
// {
// String filename = request.getString("animaltable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populateAnimal(filename);
// }
//
// if( action.equals("loadLocations") )
// {
// String filename = request.getString("locationtable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populateLocation(filename);
// }
//
// if( action.equals("loadLitters") )
// {
// String filename = request.getString("littertable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populateLitter(filename);
// }
//
// if( action.equals("loadExperiments") )
// {
// String filename = request.getString("experimenttable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populateExperiment(filename);
// }
//
// if( action.equals("loadDECApplications") )
// {
// String filename = request.getString("decapplicationtable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populateDECApplication(filename);
// }
//
// if( action.equals("loadAnimalsInExperiments") )
// {
// String filename = request.getString("experimentanimaltable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populateAnimalsInExperiments(filename);
// }
//
// if( action.equals("loadPresets") )
// {
// String filename = request.getString("presettable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populatePreset(filename);
// }
//
// if( action.equals("loadPresetAnimals") )
// {
// String filename = request.getString("presetanimaltable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populatePresetAnimals(filename);
// }
//
// if( action.equals("loadEvents") )
// {
// String filename = request.getString("eventtable");
// LoadAnimalDB myLoadAnimalDB = new LoadAnimalDB(db,
// this.getLogin());
// myLoadAnimalDB.populateEvents(filename);
// }
} catch (Exception e) {
e.printStackTrace();
this.setError("Something went wrong while loading your legacy database: " + e.getMessage());
}
}
public void service(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// Create object to assist a servlet in sending a response to the client
OutputStream out = response.getOutputStream();
// PrintWriter out = response.getWriter();
response.setContentType("application/spss");
response.setHeader("Content-disposition", "attachment; filename=Matrix.sav");
PrintStream p = new PrintStream(new BufferedOutputStream(out), false, "UTF8");
response.setStatus(HttpServletResponse.SC_OK);
String content = "";
// In case we retrieve the data form DB
/*
boolean databaseIsAvailable = false;
JDBCDatabase db = null;
try {
db = (JDBCDatabase) this.getDatabase();
databaseIsAvailable = true;
}
catch (Exception e) {
content += "Database unavailable.";
content += e.getStackTrace();
}
if (databaseIsAvailable) {
try {
} catch (Exception e) {
content += displayUsage(db);
content += "\n\n";
content += e.getStackTrace();
}
*/
try {
Tuple req =
new HttpServletRequestTuple(
request); // the HttpServletRequestTuple should be defined in another servlet ? In
// ordert to actually return the matrix contents .
// Get the requested id from the user & and get data from DB
int matrixId = req.getInt("id");
// TODO: Danny OLD code ??
/*QueryRule q = */ new QueryRule("id", Operator.EQUALS, matrixId);
// Data data = db.find(Data.class, q).get(0);
content += "TEST write in spss file .";
response.setContentLength(content.length());
p.print(content);
p.flush();
p.close();
} catch (Exception e) {
e.printStackTrace();
}
response.setContentType("application/spss");
response.setHeader("Content-disposition", "attachment; filename=Matrix.sav");
System.out.println("SPSSExport begin....");
// exportToSpss(getMatrix(), out);
/* flush it to HTTP */
out.flush();
out.close();
System.out.println("SPSSExport end....");
}
/**
* Imports UploadBatch from tab/comma delimited File
*
* @param db database to import into
* @param reader csv reader to load data from
* @param defaults to set default values for each row
* @param dbAction indicating wether to add,update,remove etc
* @param missingValues indicating what value in the csv is treated as 'null' (e.g. "" or "NA")
* @return number of elements imported
*/
public int importCsv(
final Database db,
CsvReader reader,
final Tuple defaults,
final DatabaseAction dbAction,
final String missingValues)
throws DatabaseException, IOException, Exception {
// cache for entities of which xrefs couldn't be resolved (e.g. if there
// is a self-refence)
// these entities can be updated with their xrefs in a second round when
// all entities are in the database
// final List<UploadBatch> uploadBatchsMissingRefs = new
// ArrayList<UploadBatch>();
final MutationService mutationService = new MutationService();
mutationService.setDatabase(db);
final UploadService uploadService = new UploadService();
uploadService.setDatabase(db);
final Submission submission = new Submission();
DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
submission.setDate(dateFormat.format(new Date()));
submission.setReleasedate(dateFormat.format(new Date()));
submission.setIdentifier("S" + new Date());
if (db instanceof JDBCDatabase) {
List<Integer> submitters = new ArrayList<Integer>();
submitters.add(db.getLogin().getUserId());
submission.setSubmitters_Id(submitters);
} else if (db instanceof JpaDatabase) {
List<MolgenisUser> submitters = new ArrayList<MolgenisUser>();
submitters.add(db.findById(MolgenisUser.class, db.getLogin().getUserId()));
// submission.setSubmitters(submitters);
}
db.add(submission);
// cache for objects to be imported from file (in batch)
// TODO: Danny: Use or loose
/* final List<PatientSummaryVO> patientList = */ new ArrayList<PatientSummaryVO>(BATCH_SIZE);
// wrapper to count
final IntegerWrapper total = new IntegerWrapper(0);
reader.setMissingValues(missingValues);
Integer mutationIdentifier = uploadService.getMaxMutationIdentifier();
Integer patientIdentifier = uploadService.getMaxPatientIdentifier();
for (Tuple tuple : reader) {
// parse object, setting defaults and values from file
// if (lineNo > 5) return;
PatientSummaryVO patientSummaryVO = new PatientSummaryVO();
patientSummaryVO.setSubmissionDate(submission.getDate());
patientSummaryVO.setPatientNumber(tuple.getString("Local patient number"));
patientSummaryVO.setPatientGender(
ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Gender")), "unknown"));
patientSummaryVO.setPatientEthnicity(tuple.getString("Ethnicity"));
patientSummaryVO.setPatientAge(ObjectUtils.toString(tuple.getString("Age"), "unknown"));
patientSummaryVO.setPatientDeceased(
ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Deceased")), "unknown"));
patientSummaryVO.setPatientConsent(
ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Signed consent")), "no"));
patientSummaryVO.setVariantSummaryVOList(new ArrayList<MutationSummaryVO>());
if (StringUtils.isNotEmpty(tuple.getString("cDNA change_1"))) {
MutationUploadVO mutationUploadVO = new MutationUploadVO();
mutationUploadVO.setGeneSymbol("COL7A1");
mutationUploadVO.setMutation(new Mutation());
mutationUploadVO.getMutation().setCdna_Notation("c." + tuple.getString("cDNA change_1"));
mutationService.assignValuesFromNotation(mutationUploadVO);
if (StringUtils.isNotEmpty(tuple.getString("Protein change_1")))
mutationUploadVO.getMutation().setAa_Notation("p." + tuple.getString("Protein change_1"));
if (StringUtils.isNotEmpty(tuple.getString("Consequence_1")))
mutationUploadVO
.getMutation()
.setConsequence(ObjectUtils.toString(tuple.getString("Consequence_1"), ""));
mutationUploadVO
.getMutation()
.setInheritance(
ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Inheritance_1")), ""));
mutationIdentifier = mutationIdentifier + 1;
mutationUploadVO.getMutation().setIdentifier("M" + mutationIdentifier);
mutationUploadVO.getMutation().setName("M" + mutationIdentifier);
// Insert mutation if it does not exist already
MutationSearchCriteriaVO criteria = new MutationSearchCriteriaVO();
criteria.setVariation(mutationUploadVO.getMutation().getCdna_Notation());
List<MutationSummaryVO> results = mutationService.findMutations(criteria);
if (results.size() != 1) {
uploadService.insert(mutationUploadVO);
System.out.println(">>>Inserted mutation: " + mutationUploadVO.getMutation().toString());
}
MutationSummaryVO mutationSummaryVO = new MutationSummaryVO();
mutationSummaryVO.setCdnaNotation(mutationUploadVO.getMutation().getCdna_Notation());
patientSummaryVO.getVariantSummaryVOList().add(mutationSummaryVO);
}
// Second mutation can be 'NA' or 'unknown':
// Leave xref == null and add remark in mutation2remark
if (StringUtils.isNotEmpty(tuple.getString("cDNA change_2"))) {
if (tuple.getString("cDNA change_2").equalsIgnoreCase("na"))
patientSummaryVO.setVariantComment(tuple.getString("cDNA change_2").toUpperCase());
else if (tuple.getString("cDNA change_2").equalsIgnoreCase("unknown"))
patientSummaryVO.setVariantComment(tuple.getString("cDNA change_2").toUpperCase());
else {
MutationUploadVO mutationUploadVO = new MutationUploadVO();
mutationUploadVO.setGeneSymbol("COL7A1");
mutationUploadVO.setMutation(new Mutation());
mutationUploadVO.getMutation().setCdna_Notation("c." + tuple.getString("cDNA change_2"));
mutationService.assignValuesFromNotation(mutationUploadVO);
if (StringUtils.isNotEmpty(tuple.getString("Protein change_2")))
mutationUploadVO
.getMutation()
.setAa_Notation("p." + tuple.getString("Protein change_2"));
if (StringUtils.isNotEmpty(tuple.getString("Consequence_2")))
mutationUploadVO
.getMutation()
.setConsequence(ObjectUtils.toString(tuple.getString("Consequence_2"), ""));
mutationUploadVO
.getMutation()
.setInheritance(
ObjectUtils.toString(
StringUtils.lowerCase(tuple.getString("Inheritance_2")), ""));
mutationIdentifier = mutationIdentifier + 1;
mutationUploadVO.getMutation().setIdentifier("M" + mutationIdentifier);
mutationUploadVO.getMutation().setName("M" + mutationIdentifier);
// Insert mutation if it does not exist already
MutationSearchCriteriaVO criteria = new MutationSearchCriteriaVO();
criteria.setVariation(mutationUploadVO.getMutation().getCdna_Notation());
List<MutationSummaryVO> results = mutationService.findMutations(criteria);
if (results.size() != 1) {
uploadService.insert(mutationUploadVO);
System.out.println(
">>>Inserted mutation: " + mutationUploadVO.getMutation().toString());
}
MutationSummaryVO mutationSummaryVO = new MutationSummaryVO();
mutationSummaryVO.setCdnaNotation(mutationUploadVO.getMutation().getCdna_Notation());
patientSummaryVO.getVariantSummaryVOList().add(mutationSummaryVO);
}
}
patientSummaryVO.setPhenotypeMajor(
StringUtils.upperCase(tuple.getString("Phenotype major type")));
patientSummaryVO.setPhenotypeSub(StringUtils.lowerCase(tuple.getString("Phenotype Subtype")));
// PhenotypeDetailsVO phenotypeDetailsVO = new PhenotypeDetailsVO();
// patientSummaryVO.getPhenotypeDetails().setLocation(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Location")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setBlistering(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Blistering")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setHands(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Hands")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setFeet(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Feet")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setArms(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Arms")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setLegs(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Legs")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setProximal_Body_Flexures(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Proximal body flexures")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setTrunk(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Trunk")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setMucous_Membranes(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Mucosa")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setSkin_Atrophy(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Skin atrophy")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setMilia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Milia")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setNail_Dystrophy(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Nail dystrophy")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setAlbopapuloid_Papules(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Albopapuloid papules")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setPruritic_Papules(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Pruritic papules")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setAlopecia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Alopecia")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setSquamous_Cell_Carcinomas(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Squamous cell carcinoma(s)")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setRevertant_Skin_Patch(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Revertant skin patch(es)")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setMechanism(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Mechanism")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setFlexion_Contractures(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Flexion contractures")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setPseudosyndactyly_Hands(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Pseudosyndactyly (hands)")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setMicrostomia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Microstomia")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setAnkyloglossia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Ankyloglossia")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setDysphagia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Swallowing difficulties/ dysphagia/ oesophagus strictures")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setGrowth_Retardation(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Growth retardation")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setAnemia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Anaemia")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setRenal_Failure(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Renal failure")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setDilated_Cardiomyopathy(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Dilated cardiomyopathy")),
// "unknown"));
//
// patientSummaryVO.getPhenotypeDetails().setColoboma(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Coloboma")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setCongenital_Heart_Defect(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Congenital heart defect")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setClp(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("C(L)P")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setChoanal_Anomaly(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Choanal anomaly")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setMental_Retardation(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Mental retardation")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setGrowth_Retardation(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Growth retardation")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setGenital_Hypoplasia(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Genital hypoplasia")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setExternal_Ear_Anomaly(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("External ear anomaly")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setSemicircular_Canal_Anomaly(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Semicircular canal anomaly")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setHearing_Loss(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("Hearing loss")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setTe_Anomaly(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("TE anomaly")),
// "unknown"));
// patientSummaryVO.getPhenotypeDetails().setCn_Dysfunction(ObjectUtils.toString(StringUtils.lowerCase(tuple.getString("CN dysfunction")),
// "unknown"));
// for (String field :
// patientSummaryVO.getPhenotypeDetails().getFields(true))
// {
// if ("".equals(patientSummaryVO.getPhenotypeDetails().get(field)))
// patientSummaryVO.getPhenotypeDetails().set(field, "unknown");
// }
// patientSummaryVO.getPhenotypeDetails().set(tuple.getString(""));
if (tuple.getString("PubMed ID") != null && tuple.getString("Reference") != null) {
List<PublicationVO> publicationVOs = new ArrayList<PublicationVO>();
String[] pubmeds = tuple.getString("PubMed ID").split(";");
String[] titles = tuple.getString("Reference").split(";");
for (int i = 0; i < pubmeds.length; i++) {
PublicationVO publicationVO = new PublicationVO();
publicationVO.setPubmedId(pubmeds[i]);
publicationVO.setName(titles[i]);
publicationVO.setTitle(titles[i]);
publicationVOs.add(publicationVO);
}
patientSummaryVO.setPublicationVOList(publicationVOs);
patientSummaryVO.setPatientConsent("publication");
}
patientIdentifier = patientIdentifier + 1;
patientSummaryVO.setPatientIdentifier("P" + patientIdentifier);
patientSummaryVO.setPatientName("P" + patientIdentifier);
patientSummaryVO.setObservedValueVOList(new ArrayList<ObservedValueVO>());
ObservedValueVO observedValueVO;
observedValueVO = new ObservedValueVO();
observedValueVO.setFeatureName("LH7:2 Amount of type VII collagen");
observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier());
observedValueVO.setValue(ObjectUtils.toString(tuple.getString("IF LH7:2"), "unknown"));
patientSummaryVO.getObservedValueVOList().add(observedValueVO);
observedValueVO = new ObservedValueVO();
observedValueVO.setFeatureName("IF Retention of type VII Collagen in basal cells");
observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier());
observedValueVO.setValue(
ObjectUtils.toString(tuple.getString("IF Retention COLVII"), "unknown"));
patientSummaryVO.getObservedValueVOList().add(observedValueVO);
observedValueVO = new ObservedValueVO();
observedValueVO.setFeatureName("Anchoring fibrils Number");
observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier());
observedValueVO.setValue(ObjectUtils.toString(tuple.getString("EM AF_no"), "unknown"));
patientSummaryVO.getObservedValueVOList().add(observedValueVO);
observedValueVO = new ObservedValueVO();
observedValueVO.setFeatureName("Anchoring fibrils Ultrastructure");
observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier());
observedValueVO.setValue(ObjectUtils.toString(tuple.getString("EM AF_structure"), "unknown"));
patientSummaryVO.getObservedValueVOList().add(observedValueVO);
observedValueVO = new ObservedValueVO();
observedValueVO.setFeatureName("EM Retention of type VII Collagen in basal cells");
observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier());
observedValueVO.setValue(
ObjectUtils.toString(tuple.getString("EM_Retention COLVII"), "unknown"));
patientSummaryVO.getObservedValueVOList().add(observedValueVO);
for (int i = 34; ; i++) {
System.out.println(">>>i==" + i);
String colName = tuple.getColName(i);
System.out.println(">>>colName==" + colName);
if (colName == null) break;
observedValueVO = new ObservedValueVO();
observedValueVO.setFeatureName(colName);
observedValueVO.setTargetName(patientSummaryVO.getPatientIdentifier());
observedValueVO.setValue(ObjectUtils.toString(tuple.getString(colName), "unknown"));
patientSummaryVO.getObservedValueVOList().add(observedValueVO);
}
uploadService.insert(patientSummaryVO);
total.set(total.get() + 1);
// patientList.add(patientSummaryVO);
//
// //add to db when batch size is reached
// if(patientList.size() == BATCH_SIZE)
// {
// //resolve foreign keys and copy those entities that could not be
// resolved to the missingRefs list
// uploadBatchsMissingRefs.addAll(resolveForeignKeys(db,
// uploadBatchList));
//
// //update objects in the database using xref_label defined
// secondary key(s) 'id' defined in xref_label
// db.update(uploadBatchList,dbAction, "id");
//
// //clear for next batch
// uploadBatchList.clear();
//
// //keep count
// total.set(total.get() + BATCH_SIZE);
// }
}
// add remaining elements to the database
// if(!uploadBatchList.isEmpty())
// {
// //resolve foreign keys, again keeping track of those entities that
// could not be solved
// uploadBatchsMissingRefs.addAll(resolveForeignKeys(db,
// uploadBatchList));
// //update objects in the database using xref_label defined secondary
// key(s) 'id' defined in xref_label
// db.update(uploadBatchList,dbAction, "id");
// }
//
// //second import round, try to resolve FK's for entities again as they
// might have referred to entities in the imported list
// List<UploadBatch> uploadBatchsStillMissingRefs =
// resolveForeignKeys(db, uploadBatchsMissingRefs);
//
// //if there are still missing references, throw error and rollback
// if(uploadBatchsStillMissingRefs.size() > 0){
// throw new
// Exception("Import of 'UploadBatch' objects failed: attempting to resolve in-list references,
// but there are still UploadBatchs referring to UploadBatchs that are neither in the database
// nor in the list of to-be imported UploadBatchs. (the first one being:
// "+uploadBatchsStillMissingRefs.get(0)+")");
// }
// //else update the entities in the database with the found references
// and return total
// else
// {
// db.update(uploadBatchsMissingRefs,DatabaseAction.UPDATE, "id");
//
// //output count
// total.set(total.get() + uploadBatchList.size());
// logger.info("imported "+total.get()+" uploadBatch from CSV");
//
// return total.get();
// }
return total.get();
}
/**
* Handle a particular {@link MolgenisRequest}, and render into an {@link OutputStream}.
* Particulars handled:
*
* <ul>
* <li>Wrap the desired data source in the appropriate instantiation of {@link TupleTable}.
* <li>Determine which {@link Operation} the request is asking to handle.
* <li>Apply proper sorting and filter rules.
* <li>Select the appropriate view towards which to export/render.
* <li>Select and render the data.
* </ul>
*
* @param db The database to connect to
* @param request The {@link MolgenisRequest} tuple that encodes the request to handle
* @param out The {@link OutputStream} to render to.
*/
public void handleRequest(Database db, Tuple request, OutputStream out)
throws HandleRequestDelegationException {
try {
final TupleTable tupleTable = tupleTableBuilder.create(db, request);
final Operation operation =
StringUtils.isNotEmpty(request.getString(OPERATION))
? Operation.valueOf(request.getString(OPERATION))
: Operation.RENDER_DATA;
switch (operation) {
case LOAD_CONFIG:
loadTupleTableConfig(db, (MolgenisRequest) request, tupleTable);
break;
case LOAD_TREE:
// risky: we give it all columns which would fail if there
// are many
final String treeNodes = JQueryUtil.getDynaTreeNodes(tupleTable.getAllColumns());
((MolgenisRequest) request).getResponse().getOutputStream().print(treeNodes);
break;
case RENDER_DATA:
final List<QueryRule> rules = new ArrayList<QueryRule>();
// parse the request into post data
final JQGridPostData postData = new JQGridPostData(request);
// convert any filters to query rules
final List<QueryRule> filterRules = createQueryRulesFromJQGridRequest(postData.filters);
if (CollectionUtils.isNotEmpty(filterRules)) {
if (tupleTable instanceof FilterableTupleTable) {
rules.addAll(filterRules);
((FilterableTupleTable) tupleTable).setFilters(rules);
}
}
final int rowCount = tupleTable.getCount();
final int totalPages = (int) Math.ceil(rowCount / postData.rows);
// update page
postData.page = Math.min(postData.page, totalPages);
final int offset = Math.max((postData.page - 1) * postData.rows, 0);
final String exportSelection = request.getString("exportSelection");
if (!StringUtils.equalsIgnoreCase(exportSelection, "ALL")) {
// data.rows == limit
tupleTable.setLimit(postData.rows);
// data.rows * data.page
tupleTable.setOffset(offset);
}
if (StringUtils.isNotEmpty(postData.sidx) && tupleTable instanceof FilterableTupleTable) {
final Operator sortOperator =
StringUtils.equals(postData.sord, "asc")
? QueryRule.Operator.SORTASC
: QueryRule.Operator.SORTDESC;
rules.add(new QueryRule(sortOperator, postData.sidx));
}
if (tupleTable instanceof FilterableTupleTable) {
((FilterableTupleTable) tupleTable).setFilters(rules);
}
renderData(((MolgenisRequest) request), postData, totalPages, tupleTable);
}
} catch (final Exception e) {
throw new HandleRequestDelegationException(e);
}
}
@Override
public Show handleRequest(Database db, Tuple request, OutputStream out) {
logger.debug("handleRequest(" + request + ")");
// clear the old messages
FormModel<E> model = getModel();
model.setMessages(new Vector<ScreenMessage>()); // clear messsages
try {
String action = request.getString(FormModel.INPUT_ACTION);
if (request.getString(FormModel.INPUT_COMMAND) != null) {
action = request.getString(FormModel.INPUT_COMMAND);
}
// get the selected ids into the screen list (if any)
model.setSelectedIds(request.getList(FormModel.INPUT_SELECTED));
// if none selected, make empty list
if (model.getSelectedIds() == null) model.setSelectedIds(new ArrayList<Object>());
// get the current command if any
ScreenCommand command = model.getCommand(action);
if (action == null || action.isEmpty()) {
logger.debug("action or command does not exist");
return Show.SHOW_MAIN;
}
// delegate to a command
else if (command != null && command instanceof SimpleCommand) {
logger.debug("delegating to PluginCommand");
model.setCurrentCommand(command);
return command.handleRequest(db, request, out);
} else if (action.equals("filter_add")) {
this.addFilters(pager, db, request);
} else if (action.equals("filter_remove")) {
// remove filter
int index = request.getInt("filter_id");
model.getUserRules().remove(index);
// update pager
List<QueryRule> rules = new ArrayList<QueryRule>();
rules.addAll(model.getUserRules());
rules.addAll(model.getSystemRules());
pager.resetFilters(rules);
} else if (action.equals("filter_set")) {
// remove all existing filters and than add this as a new one.
model.setUserRules(new ArrayList<QueryRule>());
this.addFilters(pager, db, request);
} else if (action.equals("update")) {
this.doUpdate(db, request);
} else if (action.equals("remove")) {
this.doRemove(db, request);
} else if (action.equals("add")) {
this.doAdd(db, request);
} else if (action.equals("prev")) {
pager.prev(db);
} else if (action.equals("next")) {
pager.next(db);
} else if (action.equals("first")) {
pager.first(db);
} else if (action.equals("last")) {
pager.last(db);
} else if (action.equals("sort")) {
String attribute = getSearchField(request.getString("__sortattribute"));
if (pager.getOrderByField().equals(attribute)) {
if (pager.getOrderByOperator().equals(Operator.SORTASC)) {
pager.setOrderByOperator(Operator.SORTDESC);
} else {
pager.setOrderByOperator(Operator.SORTASC);
}
} else {
pager.setOrderByField(attribute);
pager.setOrderByOperator(Operator.SORTASC);
}
} else if (action.equals("xref_select")) // this is used to link from
// one
// form to another based on an xref
{
this.doXrefselect(request);
} else if (action.equals("hideColumn")) {
List<String> UserHiddencols = model.getUserHiddenColumns();
String attribute = request.getString("attribute");
if (!UserHiddencols.contains(attribute)) UserHiddencols.add(attribute);
model.setUserHiddenColumns(UserHiddencols);
} else if (action.equals("showColumn")) {
List<String> UserHiddencols = model.getUserHiddenColumns();
String attribute = request.getString("attribute");
if (UserHiddencols.contains(attribute)) UserHiddencols.remove(attribute);
model.setUserHiddenColumns(UserHiddencols);
} else {
logger.debug("action '" + action + "' unknown");
}
logger.debug("handleRequest finished.");
} catch (Exception e) {
e.printStackTrace();
logger.error(e);
}
return Show.SHOW_MAIN;
}
private void handleFindMutations(Tuple request) {
this.getModel().setMutationSearchCriteriaVO(new MutationSearchCriteriaDTO());
if (StringUtils.isNotEmpty(request.getString("variation")))
this.getModel().getMutationSearchCriteriaVO().setVariation(request.getString("variation"));
if (StringUtils.isNotEmpty(request.getString("consequence")))
this.getModel()
.getMutationSearchCriteriaVO()
.setConsequence(request.getString("consequence"));
if (StringUtils.isNotEmpty(request.getString("mutation_id")))
this.getModel().getMutationSearchCriteriaVO().setMutationId(request.getInt("mutation_id"));
if (StringUtils.isNotEmpty(request.getString("mid")))
this.getModel().getMutationSearchCriteriaVO().setMid(request.getString("mid"));
if (StringUtils.isNotEmpty(request.getString("nuclno")))
this.getModel().getMutationSearchCriteriaVO().setCdnaPosition(request.getInt("nuclno"));
if (StringUtils.isNotEmpty(request.getString("aano")))
this.getModel().getMutationSearchCriteriaVO().setCodonChangeNumber(request.getInt("aano"));
if (StringUtils.isNotEmpty(request.getString("exon_id")))
this.getModel().getMutationSearchCriteriaVO().setExonId(request.getInt("exon_id"));
if (StringUtils.isNotEmpty(request.getString("exon")))
this.getModel().getMutationSearchCriteriaVO().setExonName(request.getString("exon"));
if (StringUtils.isNotEmpty(request.getString("type")))
this.getModel().getMutationSearchCriteriaVO().setType(request.getString("type"));
if (StringUtils.isNotEmpty(request.getString("domain_id")))
this.getModel().getMutationSearchCriteriaVO().setProteinDomainId(request.getInt("domain_id"));
if (StringUtils.isNotEmpty(request.getString("phenotype")))
this.getModel()
.getMutationSearchCriteriaVO()
.setPhenotypeName(request.getString("phenotype"));
if (StringUtils.isNotEmpty(request.getString("inheritance")))
this.getModel()
.getMutationSearchCriteriaVO()
.setInheritance(request.getString("inheritance"));
if (StringUtils.isNotEmpty(request.getString("snpbool")))
if (request.getString("snpbool").equals("hide"))
this.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);
SearchService searchService = ServiceLocator.instance().getSearchService();
this.getModel()
.setMutationSummaryDTOList(
searchService.findMutations(this.getModel().getMutationSearchCriteriaVO()));
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryDTOList", this.getModel().getMutationSummaryDTOList());
this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));
this.getModel().setHeader(this.getModel().getMutationSummaryDTOList().size() + " results.");
this.setView(new FreemarkerView("included.ftl", this.getModel()));
}
// @Implements
public void set(org.molgenis.util.Tuple tuple, boolean strict) throws Exception {
// optimization :-(
if (tuple instanceof org.molgenis.util.ResultSetTuple) {
// set Id
this.setId(tuple.getInt("id"));
// set __Type
this.set__Type(tuple.getString("__Type"));
// set Name
this.setName(tuple.getString("name"));
} else if (tuple != null) {
// set Id
if (strict || tuple.getInt("id") != null) this.setId(tuple.getInt("id"));
if (tuple.getInt("MolgenisRole_id") != null) this.setId(tuple.getInt("MolgenisRole_id"));
// set __Type
if (strict || tuple.getString("__Type") != null) this.set__Type(tuple.getString("__Type"));
if (tuple.getString("MolgenisRole___Type") != null)
this.set__Type(tuple.getString("MolgenisRole___Type"));
// set Name
if (strict || tuple.getString("name") != null) this.setName(tuple.getString("name"));
if (tuple.getString("MolgenisRole_name") != null)
this.setName(tuple.getString("MolgenisRole_name"));
}
// org.apache.log4j.Logger.getLogger("test").debug("set "+this);
}
@Override
public Show handleRequest(Database db, Tuple request, OutputStream out) {
ServiceLocator.instance()
.getContext()
.getAutowireCapableBeanFactory()
.initializeBean(db, "org.molgenis.framework.db.Database");
try {
if (StringUtils.isEmpty(request.getAction())) this.getModel().setAction("init");
else this.getModel().setAction(request.getAction());
if ("1".equals(request.getString("expertSearch")))
this.getModel().getQueryParametersVO().setExpertSearch(true);
else this.getModel().getQueryParametersVO().setExpertSearch(false);
if (this.getModel().getAction().equals("findMutationsByTerm")) {
this.handleFindMutationsByTerm(request);
} else if (this.getModel().getAction().equals("findMutations")) {
this.handleFindMutations(request);
} else if (this.getModel().getAction().equals("findPatients")) {
this.handleFindPatients(request);
} else if (this.getModel().getAction().equals("listAllMutations")) {
this.listAllMutations(request);
} else if (this.getModel().getAction().equals("listAllPatients")) {
this.listAllPatients(request);
} else if (this.getModel().getAction().equals("showProteinDomain")) {
this.handleShowProteinDomain(request);
} else if (this.getModel().getAction().equals("showExon")) {
this.handleShowExon(request);
} else if (this.getModel().getAction().equals("showFirstExon")) {
this.handleShowFirstExon(request);
} else if (this.getModel().getAction().equals("showPrevExon")) {
this.handleShowPrevExon(request);
} else if (this.getModel().getAction().equals("showNextExon")) {
this.handleShowNextExon(request);
} else if (this.getModel().getAction().equals("showLastExon")) {
this.handleShowLastExon(request);
} else if (this.getModel().getAction().equals("showMutation")) {
this.handleShowMutation(request);
} else if (this.getModel().getAction().equals("showFirstMutation")) {
this.handleShowFirstMutation(request);
} else if (this.getModel().getAction().equals("showPrevMutation")) {
this.handleShowPrevMutation(request);
} else if (this.getModel().getAction().equals("showNextMutation")) {
this.handleShowNextMutation(request);
} else if (this.getModel().getAction().equals("showLastMutation")) {
this.handleShowLastMutation(request);
} else if (this.getModel().getAction().equals("showPatient")) {
this.handleShowPatient(request);
} else if (this.getModel().getAction().equals("showPhenotypeDetails")) {
this.handleShowPhenotypeDetails(request);
} else if (this.getModel().getAction().startsWith("mutationsFirstPage")) {
this.getModel().getPager().first();
} else if (this.getModel().getAction().startsWith("mutationsPrevPage")) {
this.getModel().getPager().prev();
} else if (this.getModel().getAction().startsWith("mutationsNextPage")) {
this.getModel().getPager().next();
} else if (this.getModel().getAction().startsWith("mutationsLastPage")) {
this.getModel().getPager().last();
} else {
this.setView(new FreemarkerView("init.ftl", this.getModel()));
}
this.populateDisplayOptionsForm();
// for (ScreenController<?> child : this.getChildren())
// {
// child.handleRequest(db, request, out);
// }
} catch (Exception e) {
String message =
"Oops, an error occurred. We apologize and will work on fixing it as soon as possible. <a href=\"molgenis.do?__target=SearchPlugin&__action=init&expertSearch=0\">Return to home page</a>";
this.getModel().getMessages().add(new ScreenMessage(message, false));
for (StackTraceElement el : e.getStackTrace()) logger.error(el.toString());
// this.getMessages().add(new ScreenMessage(el.toString(), false));
}
return Show.SHOW_MAIN;
}
private void handleShowFirstExon(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
ExonDTO exonDTO = searchService.findFirstExon();
request.set("exon_id", exonDTO.getId());
this.handleShowExon(request);
}