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Fixes to access generated XmlBeans because of schema update #67
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@djcomlab
djcomlab committed Jul 29, 2016
1 parent f4d6ff0 commit a4a9063
Showing 1 changed file with 19 additions and 19 deletions.
38 changes: 19 additions & 19 deletions import_layer/src/main/java/org/isatools/isatab/export/sra/SraExportPipelineComponent.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1254,17 +1254,17 @@ protected PlatformType buildExportedPlatform(final Assay assay) {
sequencinginst.equalsIgnoreCase("454 GS FLX Titanium") ||
sequencinginst.equalsIgnoreCase("454 GS Junior")) {

ls454.setINSTRUMENTMODEL(PlatformType.LS454.INSTRUMENTMODEL.Enum.forString(sequencinginst));
ls454.setINSTRUMENTMODEL(PlatformType.LS454.Factory.newInstance().getINSTRUMENTMODEL().forString(sequencinginst));
}
//otherwise, we fall back on the 'unspecified' value to avoid falling over
else {
ls454.setINSTRUMENTMODEL(PlatformType.LS454.INSTRUMENTMODEL.Enum.forString("unspecified"));
ls454.setINSTRUMENTMODEL(PlatformType.LS454.Factory.newInstance().getINSTRUMENTMODEL().forString("unspecified"));
}

//ls454.setFLOWSEQUENCE("TACG");
//ls454.setFLOWCOUNT(BigInteger.valueOf(800));
xplatform.setLS454(ls454);
} else if (sequencinginst.toLowerCase().contains("illumina") || sequencinginst.toLowerCase().contains("HiSeq") || sequencinginst.toLowerCase().contains("NextSeq")) {
} else if (sequencinginst.toLowerCase().contains("illumina") || sequencinginst.toLowerCase().contains("hiseq") || sequencinginst.toLowerCase().contains("nextseq")) {

PlatformType.ILLUMINA illumina = PlatformType.ILLUMINA.Factory.newInstance();

Expand All @@ -1286,11 +1286,11 @@ protected PlatformType buildExportedPlatform(final Assay assay) {
sequencinginst.equalsIgnoreCase("NextSeq 500") ||
sequencinginst.equalsIgnoreCase("NextSeq 550"))
{
illumina.setINSTRUMENTMODEL(PlatformType.ILLUMINA.INSTRUMENTMODEL.Enum.forString(sequencinginst));
illumina.setINSTRUMENTMODEL(TypeIlluminaModel.Enum.forString(sequencinginst));
}
//otherwise, we fall back on the 'unspecified' value to avoid falling over
else {
illumina.setINSTRUMENTMODEL(PlatformType.ILLUMINA.INSTRUMENTMODEL.Enum.forString("unspecified"));
illumina.setINSTRUMENTMODEL(TypeIlluminaModel.Enum.forString("unspecified"));
}

// illumina.setCYCLESEQUENCE(getParameterValue(assay, pApp, "Cycle Sequence", true));
Expand All @@ -1302,9 +1302,9 @@ protected PlatformType buildExportedPlatform(final Assay assay) {
PlatformType.HELICOS helicos = PlatformType.HELICOS.Factory.newInstance();

if (sequencinginst.equalsIgnoreCase("Helicos HeliScope")) {
helicos.setINSTRUMENTMODEL(PlatformType.HELICOS.INSTRUMENTMODEL.Enum.forString(sequencinginst));
helicos.setINSTRUMENTMODEL(TypeHelicosModel.Enum.forString(sequencinginst));
} else {
helicos.setINSTRUMENTMODEL(PlatformType.HELICOS.INSTRUMENTMODEL.Enum.forString("unspecified"));
helicos.setINSTRUMENTMODEL(TypeHelicosModel.Enum.forString("unspecified"));
}

//helicos.setFLOWSEQUENCE(getParameterValue(assay, pApp, "Flow Sequence", true));
Expand All @@ -1317,20 +1317,20 @@ protected PlatformType buildExportedPlatform(final Assay assay) {

if (sequencinginst.equalsIgnoreCase("Ion Torrent PGM") || sequencinginst.equalsIgnoreCase("Ion Torrent Proton") ) {

iontorrent.setINSTRUMENTMODEL(PlatformType.IONTORRENT.INSTRUMENTMODEL.Enum.forString(sequencinginst));
iontorrent.setINSTRUMENTMODEL(TypeIontorrentModel.Enum.forString(sequencinginst));
} else {
iontorrent.setINSTRUMENTMODEL(PlatformType.IONTORRENT.INSTRUMENTMODEL.Enum.forString("unspecified"));
iontorrent.setINSTRUMENTMODEL(TypeIontorrentModel.Enum.forString("unspecified"));
}

xplatform.setIONTORRENT(iontorrent);

} else if (sequencinginst.equalsIgnoreCase("MinION") || sequencinginst.equalsIgnoreCase("GridION") ) {
PlatformType.OXFORDNANOPORE oxfordnanopore = PlatformType.OXFORDNANOPORE.Factory.newInstance();
oxfordnanopore.setINSTRUMENTMODEL(PlatformType.OXFORDNANOPORE.INSTRUMENTMODEL.Enum.forString(sequencinginst));
oxfordnanopore.setINSTRUMENTMODEL(TypeOxfordNanoporeModel.Enum.forString(sequencinginst));
xplatform.setOXFORDNANOPORE(oxfordnanopore);
}

else if (sequencinginst.toLowerCase().contains("AB ")) {
else if (sequencinginst.toLowerCase().contains("ab ")) {

PlatformType.ABISOLID abisolid = PlatformType.ABISOLID.Factory.newInstance();

Expand All @@ -1348,9 +1348,9 @@ else if (sequencinginst.toLowerCase().contains("AB ")) {
sequencinginst.equalsIgnoreCase("AB 5500xl-W Genetic Analysis System")
) {

abisolid.setINSTRUMENTMODEL(PlatformType.ABISOLID.INSTRUMENTMODEL.Enum.forString(sequencinginst));
abisolid.setINSTRUMENTMODEL(TypeAbiSolidModel.Enum.forString(sequencinginst));
} else {
abisolid.setINSTRUMENTMODEL(PlatformType.ABISOLID.INSTRUMENTMODEL.Enum.forString("unspecified"));
abisolid.setINSTRUMENTMODEL(TypeAbiSolidModel.Enum.forString("unspecified"));
}

//{
Expand Down Expand Up @@ -1388,7 +1388,7 @@ else if (sequencinginst.toLowerCase().contains("AB ")) {
}


//PlatformType.LS454.INSTRUMENTMODEL.Enum.forString(sequencinginst);
//PlatformType.LS454.Factory.newInstance().getINSTRUMENTMODEL().forString(sequencinginst);

// if ( ("454 GS".equalsIgnoreCase(sequencinginst) ||
// "454 GS 20".equalsIgnoreCase(sequencinginst) ||
Expand All @@ -1397,7 +1397,7 @@ else if (sequencinginst.toLowerCase().contains("AB ")) {
// "454 GS Junior".equalsIgnoreCase(sequencinginst))) {
//
// PlatformType.LS454 ls454 = PlatformType.LS454.Factory.newInstance();
// ls454.setINSTRUMENTMODEL(PlatformType.LS454.INSTRUMENTMODEL.Enum.forString(sequencinginst));
// ls454.setINSTRUMENTMODEL(PlatformType.LS454.Factory.newInstance().getINSTRUMENTMODEL().forString(sequencinginst));
// // todo finish
// }

Expand Down Expand Up @@ -1434,7 +1434,7 @@ else if (sequencinginst.toLowerCase().contains("AB ")) {
// //if ("LS454".equalsIgnoreCase(platform)) {
//
// PlatformType.LS454 ls454 = PlatformType.LS454.Factory.newInstance();
// ls454.setINSTRUMENTMODEL(PlatformType.LS454.INSTRUMENTMODEL.Enum.forString(xinstrument));
// ls454.setINSTRUMENTMODEL(PlatformType.LS454.Factory.newInstance().getINSTRUMENTMODEL().forString(xinstrument));
//
// //String keyseqStr = "TACG";
//
Expand All @@ -1449,23 +1449,23 @@ else if (sequencinginst.toLowerCase().contains("AB ")) {
//
// } else if (platform.toLowerCase().contains("illumina")) {
// PlatformType.ILLUMINA illumina = PlatformType.ILLUMINA.Factory.newInstance();
// illumina.setINSTRUMENTMODEL(PlatformType.ILLUMINA.INSTRUMENTMODEL.Enum.forString(xinstrument));
// illumina.setINSTRUMENTMODEL(PlatformType.ILLUMINA.Factory.newInstance().getINSTRUMENTMODEL().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.setINSTRUMENTMODEL(PlatformType.HELICOS.Factory.newInstance().getINSTRUMENTMODEL().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));
// abisolid.setINSTRUMENTMODEL(PlatformType.ABISOLID.Factory.newInstance().getINSTRUMENTMODEL().forString(xinstrument));
//
// {
// String colorMatrix = getParameterValue(assay, pApp, "Color Matrix", false);
Expand Down

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