ENA-5911

- added new platforms VELA_DIAGNOSTICS, GENAPSYS, GENEMIND and TAPESTRI along with their instrument models.
enasequence · Oct 6, 2023 · 9d836ed · 9d836ed
1 parent 13f0fc9
commit 9d836ed
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Showing 4 changed files with 97 additions and 10 deletions.
diff --git 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
@@ -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
@@ -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
@@ -10,8 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common"
-    targetNamespace="SRA.common">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common" targetNamespace="SRA.common">
 
     <xs:complexType name="ObjectType">
         <xs:sequence>
@@ -192,6 +191,7 @@
             </xs:element>
         </xs:sequence>
     </xs:complexType>
+
     <xs:complexType name="XRefType">
         <xs:all>
             <xs:element name="DB" type="xs:string" minOccurs="1" maxOccurs="1">
@@ -235,6 +235,7 @@
             </xs:element>
         </xs:all>
     </xs:complexType>
+
     <xs:complexType name="AttributeType">
         <xs:annotation>
             <xs:documentation>
@@ -334,7 +335,6 @@
         </xs:choice>
     </xs:complexType>
 
-
     <xs:complexType name="SpotDescriptorType">
         <xs:annotation>
             <xs:documentation>
@@ -689,8 +689,41 @@
                     </xs:sequence>
                 </xs:complexType>
             </xs:element>
+            <xs:element name="VELA_DIAGNOSTICS">
+                <xs:annotation>
+                    <xs:documentation> semi-conductor based sequencing technology. </xs:documentation>
+                </xs:annotation>
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="INSTRUMENT_MODEL" maxOccurs="1" minOccurs="1" type="com:typeVelaDiagnosticsModel"/>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="GENAPSYS">
+                <xs:annotation>
+                    <xs:documentation> Chip based electronic sensing of polymerase extension reaction </xs:documentation>
+                </xs:annotation>
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="INSTRUMENT_MODEL" maxOccurs="1" minOccurs="1" type="com:typeGenapsysModel"/>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="GENEMIND">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="INSTRUMENT_MODEL" maxOccurs="1" minOccurs="1" type="com:typeGeneMindModel"/>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="TAPESTRI">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="INSTRUMENT_MODEL" maxOccurs="1" minOccurs="1" type="com:typeTapestriModel"/>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
         </xs:choice>
-
     </xs:complexType>
 
     <xs:complexType name="SequencingDirectivesType">
@@ -725,7 +758,6 @@
         </xs:all>
     </xs:complexType>
 
-
     <xs:complexType name="PipelineType">
         <xs:annotation>
             <xs:documentation> The PipelineType identifies the sequence or tree of actions to
@@ -785,6 +817,7 @@
             </xs:element>
         </xs:sequence>
     </xs:complexType>
+
     <xs:complexType name="ReferenceAssemblyType">
         <xs:annotation>
             <xs:documentation>Reference assembly details.</xs:documentation>
@@ -852,6 +885,7 @@
             </xs:element>
         </xs:choice>
     </xs:complexType>
+
     <xs:complexType name="ReferenceSequenceType">
         <xs:annotation>
             <xs:documentation>Reference assembly and sequence details.                              </xs:documentation>
@@ -897,6 +931,7 @@
             </xs:element>
         </xs:sequence>
     </xs:complexType>
+
     <xs:complexType name="ProcessingType">
         <xs:sequence>
             <xs:element name="PIPELINE" type="com:PipelineType" minOccurs="0" maxOccurs="1">
@@ -1073,6 +1108,38 @@
         </xs:restriction>
     </xs:simpleType>
 
+    <xs:simpleType name="typeVelaDiagnosticsModel">
+        <xs:restriction base="xs:string">
+            <xs:enumeration value="Sentosa SQ301"/>
+            <xs:enumeration value="unspecified"/>
+        </xs:restriction>
+    </xs:simpleType>
+
+    <xs:simpleType name="typeGenapsysModel">
+        <xs:restriction base="xs:string">
+            <xs:enumeration value="GENIUS"/>
+            <xs:enumeration value="Genapsys Sequencer"/>
+            <xs:enumeration value="GS111"/>
+            <xs:enumeration value="unspecified"/>
+        </xs:restriction>
+    </xs:simpleType>
+
+    <xs:simpleType name="typeGeneMindModel">
+        <xs:restriction base="xs:string">
+            <xs:enumeration value="GenoCare 1600"/>
+            <xs:enumeration value="GenoLab M"/>
+            <xs:enumeration value="FASTASeq 300"/>
+            <xs:enumeration value="unspecified"/>
+        </xs:restriction>
+    </xs:simpleType>
+
+    <xs:simpleType name="typeTapestriModel">
+        <xs:restriction base="xs:string">
+            <xs:enumeration value="Tapestri"/>
+            <xs:enumeration value="unspecified"/>
+        </xs:restriction>
+    </xs:simpleType>
+
     <!-- STRING ENUMERATIONS END -->
 
 </xs:schema>