correct version of schema in current

emdb-empiar · Oct 6, 2023 · 19f2c2e · 19f2c2e
1 parent 8a94da9
commit 19f2c2e
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Showing 8 changed files with 1,926 additions and 124 deletions.
diff --git a/emdb_schemas/current/emdb.py b/emdb_schemas/current/emdb.py
diff --git a/emdb_schemas/current/emdb.xsd b/emdb_schemas/current/emdb.xsd
@@ -3,7 +3,13 @@
     <xs:element name="emd" type="entry_type"/>
     <xs:complexType name="entry_type">
         <xs:sequence>
-            <xs:element name="admin" type="admin_type"/>
+            <xs:element name="admin">
+                <xs:complexType>
+                    <xs:complexContent>
+                        <xs:extension base="admin_type"> </xs:extension>
+                    </xs:complexContent>
+                </xs:complexType>
+            </xs:element>
             <xs:element name="crossreferences" type="crossreferences_type"/>
             <xs:element name="sample" type="sample_type"/>
             <xs:element name="structure_determination_list">
@@ -25,7 +31,7 @@
             </xs:element>
         </xs:sequence>
         <xs:attribute name="emdb_id" type="emdb_id_type" use="required"/>
-        <xs:attribute name="version" type="xs:token" default="3.0.4.0"/>
+        <xs:attribute name="version" type="xs:token" default="3.0.9.0"/>
         <!-- <xs:attribute name="composite_structure" type="xs:boolean"/> -->
     </xs:complexType>
     <xs:complexType name="admin_type">
@@ -136,6 +142,7 @@
             <xs:element name="keywords" type="xs:string" minOccurs="0"/>
             <xs:element name="replace_existing_entry" type="xs:boolean" minOccurs="0"/>
         </xs:sequence>
+        <xs:attribute name="composite_map" type="xs:boolean"/>
     </xs:complexType>
     <xs:complexType name="version_list_type">
         <xs:sequence>
@@ -453,6 +460,7 @@
             </xs:element>
             <xs:element name="emdb_list" type="emdb_cross_reference_list_type" minOccurs="0"/>
             <xs:element name="pdb_list" type="pdb_cross_reference_list_type" minOccurs="0"/>
+            <xs:element name="other_db_list" type="other_db_cross_reference_list_type" minOccurs="0"/>
             <xs:element name="auxiliary_link_list" minOccurs="0">
                 <xs:complexType>
                     <xs:sequence minOccurs="1" maxOccurs="1">
@@ -636,6 +644,20 @@
             <xs:element name="details" type="xs:string" minOccurs="0"/>
         </xs:sequence>
     </xs:complexType>
+    <xs:complexType name="other_db_cross_reference_list_type">
+        <xs:sequence minOccurs="1" maxOccurs="1">
+            <xs:element name="db_reference" type="other_db_cross_reference_type"
+                maxOccurs="unbounded"/>
+        </xs:sequence>
+    </xs:complexType>
+    <xs:complexType name="other_db_cross_reference_type">
+        <xs:sequence>
+            <xs:element name="db_name" type="xs:token"/>
+            <xs:element name="accession_id" type="xs:token"/>
+            <xs:element name="content_type" type="xs:token" minOccurs="0"/>
+            <xs:element name="details" type="xs:string" minOccurs="0"/>
+        </xs:sequence>
+    </xs:complexType>
     <xs:complexType name="auxiliary_link_type">
         <xs:sequence>
             <xs:element name="type">
@@ -776,6 +798,7 @@
             <xs:element name="organism" type="organism_type"/>
             <xs:element name="strain" type="xs:token" minOccurs="0"/>
             <xs:element name="synonym_organism" type="xs:token" minOccurs="0"/>
+            <xs:element name="details" type="xs:string" minOccurs="0"/>
         </xs:sequence>
         <xs:attribute name="database">
             <xs:simpleType>
@@ -784,6 +807,7 @@
                 </xs:restriction>
             </xs:simpleType>
         </xs:attribute>
+        <xs:attribute name="synthetically_produced" type="xs:boolean"/>
     </xs:complexType>
     <xs:complexType name="organism_type">
         <xs:simpleContent>
@@ -2149,6 +2173,7 @@
                         <xs:enumeration value="JEOL 1200EXII"/>
                         <xs:enumeration value="JEOL 1230"/>
                         <xs:enumeration value="JEOL 1400"/>
+                        <xs:enumeration value="JEOL 1400/HR + YPS FEG"/>
                         <xs:enumeration value="JEOL 2000EX"/>
                         <xs:enumeration value="JEOL 2000EXII"/>
                         <xs:enumeration value="JEOL 2010"/>
@@ -2649,6 +2674,7 @@
     <xs:simpleType name="allowed_film_or_detector_model">
         <xs:restriction base="xs:token">
             <xs:enumeration value="AGFA SCIENTA FILM"/>
+            <xs:enumeration value="DECTRIS SINGLA (1k x 1k)"/>
             <xs:enumeration value="DIRECT ELECTRON APOLLO (4k x 4k)"/>
             <xs:enumeration value="DIRECT ELECTRON DE-10 (5k x 4k)"/>
             <xs:enumeration value="DIRECT ELECTRON DE-12 (4k x 3k)"/>

diff --git a/emdb_schemas/current/emdb_relaxed.py b/emdb_schemas/current/emdb_relaxed.py
diff --git a/emdb_schemas/current/emdb_relaxed.xsd b/emdb_schemas/current/emdb_relaxed.xsd
@@ -3,7 +3,13 @@
     <xs:element name="emd" type="entry_type" />
     <xs:complexType name="entry_type">
         <xs:sequence>
-            <xs:element name="admin" type="admin_type" />
+            <xs:element name="admin">
+                <xs:complexType>
+                    <xs:complexContent>
+                        <xs:extension base="admin_type"> </xs:extension>
+                    </xs:complexContent>
+                </xs:complexType>
+            </xs:element>
             <xs:element name="crossreferences" type="crossreferences_type" />
             <xs:element name="sample" type="sample_type" />
             <xs:element name="structure_determination_list">
@@ -24,7 +30,7 @@
             </xs:element>
         </xs:sequence>
         <xs:attribute name="emdb_id" type="emdb_id_type" use="required" />
-        <xs:attribute default="3.0.4.0" name="version" type="xs:token" />
+        <xs:attribute default="3.0.9.0" name="version" type="xs:token" />
 
     </xs:complexType>
     <xs:complexType name="admin_type">
@@ -134,6 +140,7 @@
             <xs:element minOccurs="0" name="keywords" type="xs:string" />
             <xs:element minOccurs="0" name="replace_existing_entry" type="xs:boolean" />
         </xs:sequence>
+        <xs:attribute name="composite_map" type="xs:boolean" />
     </xs:complexType>
     <xs:complexType name="version_list_type">
         <xs:sequence>
@@ -434,6 +441,7 @@
             </xs:element>
             <xs:element minOccurs="0" name="emdb_list" type="emdb_cross_reference_list_type" />
             <xs:element minOccurs="0" name="pdb_list" type="pdb_cross_reference_list_type" />
+            <xs:element minOccurs="0" name="other_db_list" type="other_db_cross_reference_list_type" />
             <xs:element minOccurs="0" name="auxiliary_link_list">
                 <xs:complexType>
                     <xs:sequence maxOccurs="1" minOccurs="1">
@@ -599,6 +607,19 @@
             <xs:element minOccurs="0" name="details" type="xs:string" />
         </xs:sequence>
     </xs:complexType>
+    <xs:complexType name="other_db_cross_reference_list_type">
+        <xs:sequence maxOccurs="1" minOccurs="1">
+            <xs:element maxOccurs="unbounded" name="db_reference" type="other_db_cross_reference_type" />
+        </xs:sequence>
+    </xs:complexType>
+    <xs:complexType name="other_db_cross_reference_type">
+        <xs:sequence>
+            <xs:element name="db_name" type="xs:token" />
+            <xs:element name="accession_id" type="xs:token" />
+            <xs:element minOccurs="0" name="content_type" type="xs:token" />
+            <xs:element minOccurs="0" name="details" type="xs:string" />
+        </xs:sequence>
+    </xs:complexType>
     <xs:complexType name="auxiliary_link_type">
         <xs:sequence>
             <xs:element minOccurs="0" name="type">
@@ -735,6 +756,7 @@
             <xs:element name="organism" type="organism_type" />
             <xs:element minOccurs="0" name="strain" type="xs:token" />
             <xs:element minOccurs="0" name="synonym_organism" type="xs:token" />
+            <xs:element minOccurs="0" name="details" type="xs:string" />
         </xs:sequence>
         <xs:attribute name="database">
             <xs:simpleType>
@@ -743,6 +765,7 @@
                 </xs:restriction>
             </xs:simpleType>
         </xs:attribute>
+        <xs:attribute name="synthetically_produced" type="xs:boolean" />
     </xs:complexType>
     <xs:complexType name="organism_type">
         <xs:simpleContent>
@@ -2038,6 +2061,7 @@
                         <xs:enumeration value="JEOL 1200EXII" />
                         <xs:enumeration value="JEOL 1230" />
                         <xs:enumeration value="JEOL 1400" />
+                        <xs:enumeration value="JEOL 1400/HR + YPS FEG" />
                         <xs:enumeration value="JEOL 2000EX" />
                         <xs:enumeration value="JEOL 2000EXII" />
                         <xs:enumeration value="JEOL 2010" />
@@ -2505,6 +2529,7 @@
     <xs:simpleType name="allowed_film_or_detector_model">
         <xs:restriction base="xs:token">
             <xs:enumeration value="AGFA SCIENTA FILM" />
+            <xs:enumeration value="DECTRIS SINGLA (1k x 1k)" />
             <xs:enumeration value="DIRECT ELECTRON APOLLO (4k x 4k)" />
             <xs:enumeration value="DIRECT ELECTRON DE-10 (5k x 4k)" />
             <xs:enumeration value="DIRECT ELECTRON DE-12 (4k x 3k)" />