/**
* Builds the SRA elements that are related to this ISATAB assay. It adds runs and an experiment
* to the respective set.
*
* @return true if it could successfully build the exported items.
*/
protected boolean buildExportedAssay(
Assay assay,
SubmissionType.FILES xsubFiles,
RunSetType xrunSet,
ExperimentSetType xexperimentSet,
SampleSetType xsampleSet) {
String assayAcc = assay.getAcc();
// Now create an experiment for the input material and link it to the run
// get Material associated to the assay and get its identifier
Material material = assay.getMaterial();
String materialAcc = material.getAcc();
// create a new SRA Experiment and assign ISA Material name as SRA Experiment Title
ExperimentType xexp = ExperimentType.Factory.newInstance();
xexp.setAlias(materialAcc);
xexp.setTITLE("experiment made with the sample " + material.getName());
xexp.setCenterName(centerName);
xexp.setBrokerName(brokerName);
PlatformType xplatform = buildExportedPlatform(assay);
if (xplatform == null) {
return false;
}
xexp.setPLATFORM(xplatform);
xexp.setPROCESSING(buildExportedProcessing(assay));
STUDYREF xstudyRef = STUDYREF.Factory.newInstance();
xstudyRef.setRefname(assay.getStudy().getAcc());
xexp.setSTUDYREF(xstudyRef);
EXPERIMENTREF xexpRef = EXPERIMENTREF.Factory.newInstance();
xexpRef.setRefname(materialAcc);
DESIGN xdesign = DESIGN.Factory.newInstance();
xdesign.setDESIGNDESCRIPTION("See study and sample descriptions for details");
SAMPLEDESCRIPTOR xsampleRef = buildExportedAssaySample(assay, xsampleSet);
if (xsampleRef == null) {
return false;
}
xdesign.setSAMPLEDESCRIPTOR(xsampleRef);
LIBRARYDESCRIPTOR xlib = buildExportedLibraryDescriptor(assay);
if (xlib == null) {
return false;
}
xdesign.setLIBRARYDESCRIPTOR(xlib);
SpotDescriptorType xspotd = buildExportedSpotDescriptor(assay);
if (xspotd == null) {
return false;
}
xdesign.setSPOTDESCRIPTOR(xspotd);
xexp.setDESIGN(xdesign);
// For each file, builds one run, with one data block and one file
// TODO: We should introduce something like "Run Name", so that multiple files associated to a
// single run can be
// specified
//
for (AssayResult ar : ProcessingUtils.findAssayResultsFromAssay(assay)) {
Data data = ar.getData();
String url = StringUtils.trimToNull(data.getUrl());
Study study = ar.getStudy();
if (url == null) {
String msg =
MessageFormat.format(
"The assay file of type {0} / {1} for study {2} has a data file node without file name, ignoring",
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc());
nonRepeatedMessages.add(msg + ". Data node is " + data.getName());
log.trace(msg);
return false;
}
FILE.Filetype.Enum xfileType = null;
String fileType =
StringUtils.trimToNull(data.getSingleAnnotationValue("comment:SRA File Type"));
if (fileType == null) {
// Let's try to get it from the file extension
//
fileType = StringUtils.trimToNull(FilenameUtils.getExtension(url));
if (fileType != null) {
xfileType = FILE.Filetype.Enum.forString(fileType.toLowerCase());
}
if (xfileType == null) {
String msg =
MessageFormat.format(
"The assay file of type {0} / {1} for study {2} has a data file node without the annotation "
+ "'SRA file type' and I cannot compute the file type from the file name, ignoring the assay",
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc());
nonRepeatedMessages.add(msg);
log.trace(msg + ". Data node is " + data.getName());
return false;
}
}
if (xfileType == null) {
// fileType is certainly non null at this point, cause it was explicitly provided and so we
// have to process it
//
xfileType = FILE.Filetype.Enum.forString(fileType.toLowerCase());
if (xfileType == null) {
String msg =
MessageFormat.format(
"The assay file of type {0} / {1} for study {2} has a bad 'SRA File Type' annotation: '"
+ fileType
+ "'"
+ ", ignoring the assy",
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc());
nonRepeatedMessages.add(msg);
log.trace(msg + ". Data node is " + data.getName());
return false;
}
}
RunType xrun = RunType.Factory.newInstance();
xrun.setAlias(assayAcc);
xrun.setCenterName(centerName);
xrun.setBrokerName(brokerName);
DATABLOCK dataBlock = DATABLOCK.Factory.newInstance();
FILES xfiles = FILES.Factory.newInstance();
FILE xfile = FILE.Factory.newInstance();
xfile.setFiletype(xfileType);
xfile.setFilename(url);
xfiles.addNewFILE();
xfiles.setFILEArray(0, xfile);
dataBlock.setFILES(xfiles);
xrun.addNewDATABLOCK();
xrun.setDATABLOCKArray(xrun.sizeOfDATABLOCKArray() - 1, dataBlock);
addExportedSubmissionFile(xsubFiles, url);
// TODO: remove, it's deprecated now xrun.setTotalDataBlocks ( BigInteger.ONE );
xrun.setEXPERIMENTREF(xexpRef);
xrunSet.addNewRUN();
xrunSet.setRUNArray(xrunSet.sizeOfRUNArray() - 1, xrun);
}
xexperimentSet.addNewEXPERIMENT();
xexperimentSet.setEXPERIMENTArray(xexperimentSet.sizeOfEXPERIMENTArray() - 1, xexp);
return true;
}