diff --git a/build.gradle b/build.gradle index 3eeda5c..f1b2d6b 100644 --- a/build.gradle +++ b/build.gradle @@ -8,7 +8,7 @@ plugins { group = 'uk.ac.ebi.ena.sra' archivesBaseName = 'webin-xml' -version = '2.0.0' +version = '2.1.0' sourceCompatibility = 1.8 targetCompatibility = 1.8 @@ -93,9 +93,7 @@ task generateXMLBeanSources () { } } -compileGeneratedJava.dependsOn generateXMLBeanSources -compileTestJava.dependsOn compileGeneratedJava -jar.dependsOn compileGeneratedJava +compileJava.dependsOn generateXMLBeanSources publish.dependsOn build task classes (overwrite: true) { diff --git a/src/main/java/uk/ac/ebi/ena/webin/xml/transformation/fixers/InstrumentModelEnumFixer.java b/src/main/java/uk/ac/ebi/ena/webin/xml/transformation/fixers/InstrumentModelEnumFixer.java index 2100075..6323c5b 100644 --- a/src/main/java/uk/ac/ebi/ena/webin/xml/transformation/fixers/InstrumentModelEnumFixer.java +++ b/src/main/java/uk/ac/ebi/ena/webin/xml/transformation/fixers/InstrumentModelEnumFixer.java @@ -17,16 +17,21 @@ import uk.ac.ebi.ena.sra.xml.TypeCapillaryModel; import uk.ac.ebi.ena.sra.xml.TypeDnbSeqModel; import uk.ac.ebi.ena.sra.xml.TypeElementModel; +import uk.ac.ebi.ena.sra.xml.TypeGenapsysModel; +import uk.ac.ebi.ena.sra.xml.TypeGeneMindModel; import uk.ac.ebi.ena.sra.xml.TypeHelicosModel; import uk.ac.ebi.ena.sra.xml.TypeIlluminaModel; import uk.ac.ebi.ena.sra.xml.TypeIontorrentModel; import uk.ac.ebi.ena.sra.xml.TypeOxfordNanoporeModel; import uk.ac.ebi.ena.sra.xml.TypePacBioModel; +import uk.ac.ebi.ena.sra.xml.TypeTapestriModel; import uk.ac.ebi.ena.sra.xml.TypeUltimaModel; +import uk.ac.ebi.ena.sra.xml.TypeVelaDiagnosticsModel; public class InstrumentModelEnumFixer extends EnumValueFixer { public InstrumentModelEnumFixer() { + /** Any addition or removal of models in SRA.common.xsd should be reflected here. */ add(Type454Model.Factory.newInstance().schemaType().getStringEnumEntries()); add(TypeIlluminaModel.Factory.newInstance().schemaType().getStringEnumEntries()); add(TypeHelicosModel.Factory.newInstance().schemaType().getStringEnumEntries()); @@ -40,6 +45,10 @@ public InstrumentModelEnumFixer() { add(TypeOxfordNanoporeModel.Factory.newInstance().schemaType().getStringEnumEntries()); add(TypeElementModel.Factory.newInstance().schemaType().getStringEnumEntries()); add(TypeUltimaModel.Factory.newInstance().schemaType().getStringEnumEntries()); + add(TypeVelaDiagnosticsModel.Factory.newInstance().schemaType().getStringEnumEntries()); + add(TypeGenapsysModel.Factory.newInstance().schemaType().getStringEnumEntries()); + add(TypeGeneMindModel.Factory.newInstance().schemaType().getStringEnumEntries()); + add(TypeTapestriModel.Factory.newInstance().schemaType().getStringEnumEntries()); add("none", "unspecified"); add("AB SOLiD System 3 Plus", "AB SOLiD 3 Plus System"); diff --git a/src/main/java/uk/ac/ebi/ena/webin/xml/transformation/fixers/PlatformEnumFixer.java b/src/main/java/uk/ac/ebi/ena/webin/xml/transformation/fixers/PlatformEnumFixer.java index a9b1b34..54ea8e8 100644 --- a/src/main/java/uk/ac/ebi/ena/webin/xml/transformation/fixers/PlatformEnumFixer.java +++ b/src/main/java/uk/ac/ebi/ena/webin/xml/transformation/fixers/PlatformEnumFixer.java @@ -18,16 +18,20 @@ import uk.ac.ebi.ena.sra.xml.TypeCapillaryModel; import uk.ac.ebi.ena.sra.xml.TypeDnbSeqModel; import uk.ac.ebi.ena.sra.xml.TypeElementModel; +import uk.ac.ebi.ena.sra.xml.TypeGenapsysModel; +import uk.ac.ebi.ena.sra.xml.TypeGeneMindModel; import uk.ac.ebi.ena.sra.xml.TypeHelicosModel; import uk.ac.ebi.ena.sra.xml.TypeIlluminaModel; import uk.ac.ebi.ena.sra.xml.TypeIontorrentModel; import uk.ac.ebi.ena.sra.xml.TypeOxfordNanoporeModel; import uk.ac.ebi.ena.sra.xml.TypePacBioModel; +import uk.ac.ebi.ena.sra.xml.TypeTapestriModel; import uk.ac.ebi.ena.sra.xml.TypeUltimaModel; +import uk.ac.ebi.ena.sra.xml.TypeVelaDiagnosticsModel; public class PlatformEnumFixer extends EnumValueFixer { public PlatformEnumFixer() { - + /** Any addition or removal of models in SRA.common.xsd should be reflected here. */ addValueList(Type454Model.Factory.newInstance().schemaType().getStringEnumEntries(), "LS454"); addValueList( TypeIlluminaModel.Factory.newInstance().schemaType().getStringEnumEntries(), "ILLUMINA"); @@ -55,6 +59,15 @@ public PlatformEnumFixer() { TypeElementModel.Factory.newInstance().schemaType().getStringEnumEntries(), "ELEMENT"); addValueList( TypeUltimaModel.Factory.newInstance().schemaType().getStringEnumEntries(), "ULTIMA"); + addValueList( + TypeVelaDiagnosticsModel.Factory.newInstance().schemaType().getStringEnumEntries(), + "VELA_DIAGNOSTICS"); + addValueList( + TypeGenapsysModel.Factory.newInstance().schemaType().getStringEnumEntries(), "GENAPSYS"); + addValueList( + TypeGeneMindModel.Factory.newInstance().schemaType().getStringEnumEntries(), "GENEMIND"); + addValueList( + TypeTapestriModel.Factory.newInstance().schemaType().getStringEnumEntries(), "TAPESTRI"); } private void addValueList(SchemaStringEnumEntry[] keys, String value) { diff --git a/src/main/resources/uk/ac/ebi/ena/sra/schema/SRA.common.xsd b/src/main/resources/uk/ac/ebi/ena/sra/schema/SRA.common.xsd index 1be5972..fcbc5ba 100644 --- a/src/main/resources/uk/ac/ebi/ena/sra/schema/SRA.common.xsd +++ b/src/main/resources/uk/ac/ebi/ena/sra/schema/SRA.common.xsd @@ -10,8 +10,7 @@ ~ specific language governing permissions and limitations under the License. --> - + @@ -192,6 +191,7 @@ + @@ -235,6 +235,7 @@ + @@ -334,7 +335,6 @@ - @@ -689,8 +689,41 @@ + + + semi-conductor based sequencing technology. + + + + + + + + + + Chip based electronic sensing of polymerase extension reaction + + + + + + + + + + + + + + + + + + + + + - @@ -725,7 +758,6 @@ - The PipelineType identifies the sequence or tree of actions to @@ -785,6 +817,7 @@ + Reference assembly details. @@ -852,6 +885,7 @@ + Reference assembly and sequence details. @@ -897,6 +931,7 @@ + @@ -1073,6 +1108,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +