Merge pull request #299 from CSCfi/update/ena-schemas-1.11.0

Update/ena schemas 1.11.0
CSCfi · Nov 30, 2021 · c2a7b04 · c2a7b04
2 parents 0e80b7e + a848b52
commit c2a7b04
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Showing 17 changed files with 49 additions and 17 deletions.
diff --git a/metadata_backend/helpers/schemas/EGA.dac.xsd b/metadata_backend/helpers/schemas/EGA.dac.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
 	<xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 
@@ -23,7 +23,7 @@
 			<xs:extension base="com:ObjectType">
 				<xs:sequence>
 
-					<xs:element name="TITLE" type="xs:string" minOccurs="0" maxOccurs="1">
+					<xs:element name="TITLE" type="xs:string" minOccurs="1" maxOccurs="1">
 						<xs:annotation>
 							<xs:documentation>
             Short text that can be used to call out DAC records in searches or in displays.

diff --git a/metadata_backend/helpers/schemas/EGA.dataset.xsd b/metadata_backend/helpers/schemas/EGA.dataset.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
 	<xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 

diff --git a/metadata_backend/helpers/schemas/EGA.policy.xsd b/metadata_backend/helpers/schemas/EGA.policy.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
 	<xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 

diff --git a/metadata_backend/helpers/schemas/ENA.assembly.xsd b/metadata_backend/helpers/schemas/ENA.assembly.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:com="SRA.common" xmlns:xs="http://www.w3.org/2001/XMLSchema">
     <xs:import namespace="SRA.common" schemaLocation="SRA.common.xsd"/>
     <xs:complexType name="AssemblySetType">

diff --git a/metadata_backend/helpers/schemas/ENA.checklist.xsd b/metadata_backend/helpers/schemas/ENA.checklist.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
     <xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 

diff --git a/metadata_backend/helpers/schemas/ENA.project.xsd b/metadata_backend/helpers/schemas/ENA.project.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
     <xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
     <xs:complexType name="OrganismType">

diff --git a/metadata_backend/helpers/schemas/SRA.analysis.xsd b/metadata_backend/helpers/schemas/SRA.analysis.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:com="SRA.common" xmlns:xs="http://www.w3.org/2001/XMLSchema">
     <xs:import namespace="SRA.common" schemaLocation="SRA.common.xsd"/>
 
@@ -349,6 +349,8 @@
                                 </xs:element>
                                 <xs:element name="AMR_ANTIBIOGRAM"/>
                                 <xs:element name="PATHOGEN_ANALYSIS"/>
+                                <xs:element name="COVID19_CONSENSUS"/>
+                                <xs:element name="COVID19_FILTERED_VCF"/>
                                 <xs:element name="TRANSCRIPTOME_ASSEMBLY">
                                     <xs:complexType>
                                         <xs:sequence>

diff --git a/metadata_backend/helpers/schemas/SRA.common.xsd b/metadata_backend/helpers/schemas/SRA.common.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common"
     targetNamespace="SRA.common">
 
@@ -928,6 +928,7 @@
             <xs:enumeration value="Illumina HiSeq 2500"/>
             <xs:enumeration value="Illumina HiSeq 3000"/>
             <xs:enumeration value="Illumina HiSeq 4000"/>
+            <xs:enumeration value="Illumina HiSeq X"/>
             <xs:enumeration value="Illumina iSeq 100"/>
             <xs:enumeration value="Illumina MiSeq"/>
             <xs:enumeration value="Illumina MiniSeq"/>
@@ -976,7 +977,9 @@
 
     <xs:simpleType name="typeBGISEQModel">
         <xs:restriction base="xs:string">
+            <xs:enumeration value="BGISEQ-50"/>
             <xs:enumeration value="BGISEQ-500"/>
+            <xs:enumeration value="MGISEQ-2000RS"/>
         </xs:restriction>
     </xs:simpleType>
 
@@ -996,6 +999,10 @@
             <xs:enumeration value="Ion Torrent Proton"/>
             <xs:enumeration value="Ion Torrent S5"/>
             <xs:enumeration value="Ion Torrent S5 XL"/>
+            <xs:enumeration value="Ion Torrent Genexus"/>
+            <xs:enumeration value="Ion GeneStudio S5"/>
+            <xs:enumeration value="Ion GeneStudio S5 Prime"/>
+            <xs:enumeration value="Ion GeneStudio S5 Plus"/>
             <xs:enumeration value="unspecified"/>
         </xs:restriction>
     </xs:simpleType>

diff --git a/metadata_backend/helpers/schemas/SRA.experiment.xsd b/metadata_backend/helpers/schemas/SRA.experiment.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
   <xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 

diff --git a/metadata_backend/helpers/schemas/SRA.receipt.xsd b/metadata_backend/helpers/schemas/SRA.receipt.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
     <xs:complexType name="ID">
         <xs:sequence>
@@ -58,10 +58,14 @@
         <xs:attribute name="status" use="optional">
             <xs:simpleType>
                 <xs:restriction base="xs:string">
+                    <xs:enumeration value="DRAFT"/>
                     <xs:enumeration value="PRIVATE"/>
+                    <xs:enumeration value="CANCELLED"/>
                     <xs:enumeration value="PUBLIC"/>
-                    <xs:enumeration value="KILLED"/>
                     <xs:enumeration value="SUPPRESSED"/>
+                    <xs:enumeration value="KILLED"/>
+                    <xs:enumeration value="TEMPORARY_SUPPRESSED"/>
+                    <xs:enumeration value="TEMPORARY_KILLED"/>
                 </xs:restriction>
             </xs:simpleType>
         </xs:attribute>

diff --git a/metadata_backend/helpers/schemas/SRA.run.xsd b/metadata_backend/helpers/schemas/SRA.run.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
     <xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 

diff --git a/metadata_backend/helpers/schemas/SRA.sample.xsd b/metadata_backend/helpers/schemas/SRA.sample.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
   <xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 

diff --git a/metadata_backend/helpers/schemas/SRA.study.xsd b/metadata_backend/helpers/schemas/SRA.study.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
   <xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 

diff --git a/metadata_backend/helpers/schemas/SRA.submission.xsd b/metadata_backend/helpers/schemas/SRA.submission.xsd
@@ -10,7 +10,7 @@
   ~ specific language governing permissions and limitations under the License.
   -->
 
-<!-- version:1.8.0 -->
+<!-- version:1.11.0 -->
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:com="SRA.common">
   <xs:import schemaLocation="SRA.common.xsd" namespace="SRA.common"/>
 

diff --git a/metadata_backend/helpers/schemas/ena_dac.json b/metadata_backend/helpers/schemas/ena_dac.json
@@ -176,7 +176,8 @@
     },
     "type": "object",
     "required": [
-        "contacts"
+        "contacts",
+        "title"
     ],
     "properties": {
         "contacts": {

diff --git a/metadata_backend/helpers/schemas/ena_experiment.json b/metadata_backend/helpers/schemas/ena_experiment.json
@@ -723,6 +723,9 @@
                 "AB 3500xL Genetic Analyzer",
                 "AB 3730 Genetic Analyzer",
                 "AB 3730xL Genetic Analyzer",
+                "BGISEQ-50",
+                "BGISEQ-500",
+                "MGISEQ-2000RS",
                 "Complete Genomics",
                 "Helicos HeliScope",
                 "HiSeq X Five",
@@ -737,6 +740,7 @@
                 "Illumina HiSeq 2500",
                 "Illumina HiSeq 3000",
                 "Illumina HiSeq 4000",
+                "Illumina HiSeq X",
                 "Illumina MiSeq",
                 "Illumina MiniSeq",
                 "Illumina NovaSeq 6000",
@@ -746,6 +750,10 @@
                 "Ion Torrent Proton",
                 "Ion Torrent S5",
                 "Ion Torrent S5 XL",
+                "Ion Torrent Genexus",
+                "Ion GeneStudio S5",
+                "Ion GeneStudio S5 Prime",
+                "Ion GeneStudio S5 Plus",
                 "454 GS",
                 "454 GS 20",
                 "454 GS FLX",
@@ -758,6 +766,7 @@
                 "PacBio RS",
                 "PacBio RS II",
                 "Sequel",
+                "Sequel II",
                 "unspecified"
             ]
         },

diff --git a/metadata_backend/helpers/schemas/ena_run.json b/metadata_backend/helpers/schemas/ena_run.json
@@ -638,6 +638,9 @@
                 "AB 3500xL Genetic Analyzer",
                 "AB 3730 Genetic Analyzer",
                 "AB 3730xL Genetic Analyzer",
+                "BGISEQ-50",
+                "BGISEQ-500",
+                "MGISEQ-2000RS",
                 "Complete Genomics",
                 "Helicos HeliScope",
                 "HiSeq X Five",
@@ -652,6 +655,7 @@
                 "Illumina HiSeq 2500",
                 "Illumina HiSeq 3000",
                 "Illumina HiSeq 4000",
+                "Illumina HiSeq X",
                 "Illumina MiSeq",
                 "Illumina MiniSeq",
                 "Illumina NovaSeq 6000",
@@ -661,6 +665,10 @@
                 "Ion Torrent Proton",
                 "Ion Torrent S5",
                 "Ion Torrent S5 XL",
+                "Ion Torrent Genexus",
+                "Ion GeneStudio S5",
+                "Ion GeneStudio S5 Prime",
+                "Ion GeneStudio S5 Plus",
                 "454 GS",
                 "454 GS 20",
                 "454 GS FLX",
@@ -673,6 +681,7 @@
                 "PacBio RS",
                 "PacBio RS II",
                 "Sequel",
+                "Sequel II",
                 "unspecified"
             ]
         },