@Test
public void testOESourceAddNew() throws Exception {
ReferenceSource source = new ReferenceSource("My fancy test ontology");
source.setAcc("bii:tests:MY-SRC-1");
OntologyTerm oe = new OntologyTerm("biionto:1010", "test oe", source);
OntologyTerm oenew = persister.persist(oe);
transaction.commit();
assertNotNull("Uh?! No object returned by the persister!", oenew);
assertTrue("Ouch!? The OE returned by the persister should be the same!", oe == oenew);
assertTrue("Urp! The OE was not saved!", entityManager.contains(oenew));
assertNotNull("Oh! The saved object should have an ID", oenew.getId());
ReferenceSource sourceDB = oenew.getSource();
assertNotNull("Ouch! No source for the persisted OE!", sourceDB);
assertNotNull("Argh! The source of the persisted object should have an ID", source.getId());
}
@Test
public void testOESourceExisting() throws Exception {
ReferenceSource source = new ReferenceSource(null);
source.setAcc("BII-1");
source.setName("TEST ONTOLOGY");
OntologyTerm oe = new OntologyTerm("OBI-EO1", "organism", source);
OntologyTerm oenew = persister.persist(oe);
transaction.commit();
assertNotNull("Uh?! No object returned by the persister!", oenew);
assertTrue("Urp! The OE was not saved!", entityManager.contains(oenew));
assertTrue("Ouch!? The OE returned by the persister should be different!", oe != oenew);
assertTrue("Oh! The saved object should have ID=501", oenew.getId() == 501);
ReferenceSource sourceDB = oenew.getSource();
assertNotNull("Ouch! No source for the persisted OE!", sourceDB);
assertTrue(
"Argh! The source of the persisted object should have ID=100", sourceDB.getId() == 100);
}
/**
* 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;
}
