/**
* Builds the SRA {@link SpotDescriptorType}, this is taken from the ISATAB "sequencing" 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 SpotDescriptorType buildExportedSpotDescriptor(Assay assay) {
ProtocolApplication pApp = getProtocol(assay, "sequencing");
if (pApp == null) {
return null;
}
String barcode = getParameterValue(assay, pApp, "barcode", false);
System.out.println("barcode: " + barcode);
String adapterSpec = getParameterValue(assay, pApp, "Adapter Spec", false);
String numOfSpotReads = getParameterValue(assay, pApp, "Number of reads per spot", false);
boolean usesBarcode = (barcode != null);
SRATemplate sraTemplateToInject =
getSRATemplateToInject(SRASection.SPOT_DESCRIPTOR, assay, pApp, usesBarcode);
SpotDescriptorType xspotd = SpotDescriptorType.Factory.newInstance();
Map<SRAAttributes, String> userDefinedAttributes = new HashMap<SRAAttributes, String>();
if (!StringUtils.isEmpty(adapterSpec)) {
userDefinedAttributes.put(SRAAttributes.ADAPTER_SPEC, adapterSpec);
}
if (!StringUtils.isEmpty(numOfSpotReads)) {
userDefinedAttributes.put(SRAAttributes.NUMBER_OF_READS_PER_SPOT, numOfSpotReads);
}
if (!StringUtils.isEmpty(barcode)) {
userDefinedAttributes.put(SRAAttributes.READ_GROUP_TAG, barcode);
}
try {
String sraTemplate =
sraTemplateLoader.getSRAProcessingTemplate(sraTemplateToInject, userDefinedAttributes);
System.out.println(sraTemplate);
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setDocumentType(SpotDescriptorType.Factory.newInstance().schemaType());
XmlObject parsedAttr = XmlObject.Factory.parse(sraTemplate, xmlOptions);
xspotd.set(parsedAttr);
return xspotd;
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (XmlException e) {
e.printStackTrace();
}
return xspotd;
}
/**
* Builds the SRA {@link PROCESSING}, this is taken from the ISATAB "sequencing" 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 PROCESSING buildExportedProcessing(final Assay assay) {
ProtocolApplication pApp = getProtocol(assay, "sequencing");
SRATemplate sraTemplateToInject = getSRATemplateToInject(SRASection.PROCESSING, assay, pApp);
String seqSpaceStr = getParameterValue(assay, pApp, "Sequence space", false);
String baseCaller = getParameterValue(assay, pApp, "Base caller", false);
String qualityScorer = getParameterValue(assay, pApp, "Quality scorer", false);
String numberOfLevels = getParameterValue(assay, pApp, "Number of levels", false);
String multiplier = getParameterValue(assay, pApp, "Multiplier", false);
Map<SRAAttributes, String> userDefinedAttributes = new HashMap<SRAAttributes, String>();
if (!StringUtils.isEmpty(seqSpaceStr)) {
userDefinedAttributes.put(SRAAttributes.SEQUENCE_SPACE, seqSpaceStr);
}
if (!StringUtils.isEmpty(baseCaller)) {
userDefinedAttributes.put(SRAAttributes.BASE_CALLER, baseCaller);
}
if (!StringUtils.isEmpty(qualityScorer)) {
userDefinedAttributes.put(SRAAttributes.QUALITY_SCORER, qualityScorer);
}
if (!StringUtils.isEmpty(numberOfLevels)) {
userDefinedAttributes.put(SRAAttributes.NUMBER_OF_LEVELS, numberOfLevels);
}
if (!StringUtils.isEmpty(multiplier)) {
userDefinedAttributes.put(SRAAttributes.MULTIPLIER, multiplier);
}
// TODO: modify to pull out the technology and library using Parameter Value[platform] &
// ParameterValue[library layout] respectively
// TODO: PRS-> according to new configuration for sequencing, Parameter Value[library layout] is
// moved to the library construction protocol
// TODO: PRS-> replace Parameter Value[platform] with Parameter Value[sequencing instrument] and
// checks on values.
// TODO: PRS-> add support for Immunoprecipitation techniques, requires detection of Protocol
// TODO: PRS-> add support for 'Targeted Loci' in SRA experiment and find in ISA-TAB file if
// assay is environmental gene survey
try {
String sraTemplate =
sraTemplateLoader.getSRAProcessingTemplate(sraTemplateToInject, userDefinedAttributes);
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setDocumentType(PROCESSING.Factory.newInstance().schemaType());
PROCESSING processing = PROCESSING.Factory.newInstance();
XmlObject processingObject = XmlObject.Factory.parse(sraTemplate, xmlOptions);
processing.set(processingObject);
return processing;
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (XmlException e) {
e.printStackTrace();
}
return PROCESSING.Factory.newInstance();
}
