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()));
}
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()));
}
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);
}
/**
* 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;
}
// @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);
}
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()));
}
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....");
}
@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;
}