/**
* Builds the SRA {@link LIBRARYDESCRIPTOR}, this is taken from the ISATAB "library construction"
* protocol that has been used for this assay.
*
* <p>Some of these parameters are mandatory in SRA, and/or constrained to certain values, so the
* method raises an exception in case they're not defined.
*/
protected LIBRARYDESCRIPTOR buildExportedLibraryDescriptor(Assay assay) {
ProtocolApplication papp = getProtocol(assay, "library construction");
if (papp == null) {
return null;
}
LIBRARYDESCRIPTOR xlib = LIBRARYDESCRIPTOR.Factory.newInstance();
xlib.setLIBRARYNAME(getParameterValue(assay, papp, "Library Name", true));
// TODO check it is one of the Enum types
xlib.setLIBRARYSTRATEGY(
LIBRARYSTRATEGY.Enum.forString(getParameterValue(assay, papp, "Library Strategy", true)));
xlib.setLIBRARYSOURCE(
LIBRARYSOURCE.Enum.forString(getParameterValue(assay, papp, "Library Source", true)));
xlib.setLIBRARYSELECTION(
LIBRARYSELECTION.Enum.forString(getParameterValue(assay, papp, "Library Selection", true)));
String pdescription = StringUtils.trimToNull(papp.getProtocol().getDescription());
if (pdescription != null) {
xlib.setLIBRARYCONSTRUCTIONPROTOCOL(pdescription);
}
String libLayout = getParameterValue(assay, papp, "Library Layout", true);
LIBRARYLAYOUT xlibLayout = LIBRARYLAYOUT.Factory.newInstance();
if ("single".equalsIgnoreCase(libLayout)) {
xlibLayout.addNewSINGLE();
xlib.setLIBRARYLAYOUT(xlibLayout);
} else if ("paired".equalsIgnoreCase(libLayout)) {
// todo check with philippe about these parameters
xlibLayout.addNewPAIRED();
xlib.setLIBRARYLAYOUT(xlibLayout);
} else {
throw new TabInvalidValueException(
i18n.msg(
"sra_invalid_param",
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc(),
"Library Layout/type",
libLayout));
}
xlib.setLIBRARYLAYOUT(xlibLayout);
LIBRARYDESCRIPTOR.TARGETEDLOCI xtargetedloci =
LIBRARYDESCRIPTOR.TARGETEDLOCI.Factory.newInstance();
LIBRARYDESCRIPTOR.TARGETEDLOCI.LOCUS xlocus =
LIBRARYDESCRIPTOR.TARGETEDLOCI.LOCUS.Factory.newInstance();
String locus = getParameterValue(assay, papp, "target_gene", true);
if (locus != null) {
if (locus.toLowerCase().contains("16s")) {
xlocus.setLocusName(LIBRARYDESCRIPTOR.TARGETEDLOCI.LOCUS.LocusName.X_16_S_R_RNA);
} else {
xlocus.setLocusName(LIBRARYDESCRIPTOR.TARGETEDLOCI.LOCUS.LocusName.OTHER);
}
}
LIBRARYDESCRIPTOR.TARGETEDLOCI.LOCUS[] xlocusArray =
new LIBRARYDESCRIPTOR.TARGETEDLOCI.LOCUS[] {xlocus};
xtargetedloci.setLOCUSArray(xlocusArray);
xlib.setTARGETEDLOCI(xtargetedloci);
String pooling = getParameterValue(assay, papp, "mid", true);
if (pooling != null) {
LIBRARYDESCRIPTOR.POOLINGSTRATEGY xpoolingstrategy =
LIBRARYDESCRIPTOR.POOLINGSTRATEGY.Factory.newInstance();
xlib.setPOOLINGSTRATEGY(LIBRARYDESCRIPTOR.POOLINGSTRATEGY.MULTIPLEXED_LIBRARIES);
}
return xlib;
}
/**
* Builds the SRA {@link PlatformType}, this is partly taken from the ISATAB "sequencing" protocol
* and partly from the "platform" field in the ISATAB assay section (investigation file).
*
* <p>Some of these parameters are mandatory in SRA, and/or constrained to certain values, so the
* method raises an exception in case they're not defined. TODO: this could be replaced by relying
* on the ISA Parameter Value[sequencing instrument] available from latest configuration
*/
protected PlatformType buildExportedPlatform(final Assay assay) {
ProtocolApplication pApp = getProtocol(assay, "sequencing");
if (pApp == null) {
return null;
}
Protocol proto = pApp.getProtocol();
// Get the instrument information associated to that sequencing protocol
// TODO: PRS: rely on a ISA Parameter Value[sequencing instrument] instead to obtain the
// information
// TODO: PRS: check against the declared ISA assay platform
String sequencinginst = getParameterValue(assay, pApp, "sequencing instrument", true);
PlatformType.LS454.INSTRUMENTMODEL.Enum.forString(sequencinginst);
if (("454 GS".equalsIgnoreCase(sequencinginst)
|| "454 GS 20".equalsIgnoreCase(sequencinginst)
|| "454 GS FLX".equalsIgnoreCase(sequencinginst)
|| "454 GS FLX Titanium".equalsIgnoreCase(sequencinginst)
|| "454 GS Junior".equalsIgnoreCase(sequencinginst)
|| "GS20".equalsIgnoreCase(sequencinginst)
|| "GS FLX".equalsIgnoreCase(sequencinginst))) {
// todo finish
}
String xinstrument = null;
for (ProtocolComponent pcomp : proto.getComponents()) {
for (OntologyTerm ctype : pcomp.getOntologyTerms()) {
String pctypeStr = ctype.getName().toLowerCase();
if (pctypeStr.contains("instrument") || pctypeStr.contains("sequencer")) {
xinstrument = pcomp.getValue();
break;
}
}
}
if (xinstrument == null) {
String msg =
MessageFormat.format(
"The assay file of type {0} / {1} for study {2} has no Instrument declared in the ISA Sequencing Protocol",
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc());
throw new TabMissingValueException(msg);
}
PlatformType xplatform = PlatformType.Factory.newInstance();
String platform = StringUtils.upperCase(assay.getAssayPlatform());
if (platform.toLowerCase().contains("454")) {
// if ("LS454".equalsIgnoreCase(platform)) {
PlatformType.LS454 ls454 = PlatformType.LS454.Factory.newInstance();
ls454.setINSTRUMENTMODEL(PlatformType.LS454.INSTRUMENTMODEL.Enum.forString(xinstrument));
ls454.setKEYSEQUENCE(getParameterValue(assay, pApp, "Key Sequence", false));
ls454.setFLOWSEQUENCE(getParameterValue(assay, pApp, "Flow Sequence", false));
String flowCountStr = getParameterValue(assay, pApp, "Flow Count", false);
ls454.setFLOWCOUNT(new BigInteger(checkNumericParameter(flowCountStr)));
xplatform.setLS454(ls454);
} else if (platform.toLowerCase().contains("illumina")) {
PlatformType.ILLUMINA illumina = PlatformType.ILLUMINA.Factory.newInstance();
illumina.setINSTRUMENTMODEL(
PlatformType.ILLUMINA.INSTRUMENTMODEL.Enum.forString(xinstrument));
illumina.setCYCLESEQUENCE(getParameterValue(assay, pApp, "Cycle Sequence", true));
illumina.setCYCLECOUNT(
new BigInteger(
checkNumericParameter(getParameterValue(assay, pApp, "Cycle Count", true))));
xplatform.setILLUMINA(illumina);
} else if (platform.toLowerCase().contains("helicos")) {
// ("HELICOS".equalsIgnoreCase(platform)) {
PlatformType.HELICOS helicos = PlatformType.HELICOS.Factory.newInstance();
helicos.setINSTRUMENTMODEL(PlatformType.HELICOS.INSTRUMENTMODEL.Enum.forString(xinstrument));
helicos.setFLOWSEQUENCE(getParameterValue(assay, pApp, "Flow Sequence", true));
helicos.setFLOWCOUNT(
new BigInteger(
checkNumericParameter(getParameterValue(assay, pApp, "Flow Count", true))));
xplatform.setHELICOS(helicos);
} else if (platform.toLowerCase().contains("solid")) {
// ("ABI SOLID".equalsIgnoreCase(platform) || "ABI_SOLID".equalsIgnoreCase(platform)) {
PlatformType.ABISOLID abisolid = PlatformType.ABISOLID.Factory.newInstance();
abisolid.setINSTRUMENTMODEL(
PlatformType.ABISOLID.INSTRUMENTMODEL.Enum.forString(xinstrument));
{
String colorMatrix = getParameterValue(assay, pApp, "Color Matrix", false);
// single dibase colours are semicolon-separated
if (colorMatrix != null) {
PlatformType.ABISOLID.COLORMATRIX xcolorMatrix =
PlatformType.ABISOLID.COLORMATRIX.Factory.newInstance();
String dibases[] = colorMatrix.split("\\;");
if (dibases != null && dibases.length > 0) {
PlatformType.ABISOLID.COLORMATRIX.COLOR xcolors[] =
new PlatformType.ABISOLID.COLORMATRIX.COLOR[dibases.length];
int i = 0;
for (String dibase : dibases) {
PlatformType.ABISOLID.COLORMATRIX.COLOR xcolor =
PlatformType.ABISOLID.COLORMATRIX.COLOR.Factory.newInstance();
xcolor.setDibase(dibase);
xcolors[i++] = xcolor;
}
xcolorMatrix.setCOLORArray(xcolors);
abisolid.setCOLORMATRIX(xcolorMatrix);
}
}
}
{
String colorMatrixCode = getParameterValue(assay, pApp, "Color Matrix Code", false);
if (colorMatrixCode != null) {
abisolid.setCOLORMATRIXCODE(colorMatrixCode);
}
}
// TODO: remove, deprecated abisolid.setCYCLECOUNT ( new BigInteger ( getParameterValue (
// assay, papp, "Cycle Count", true ) ) );
abisolid.setSEQUENCELENGTH(
new BigInteger(
checkNumericParameter(getParameterValue(assay, pApp, "Cycle Count", false))));
xplatform.setABISOLID(abisolid);
} else {
throw new TabInvalidValueException(
MessageFormat.format(
"The SRA platform ''{0}'' for the assay ''{1}''/''{2}'' in the study ''{3}'' is invalid. Please supply the Platform information for the Assay in the Investigation file",
platform,
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc()));
}
return xplatform;
}
/**
* 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;
}