Updating Clinvar export schema to 1.7 version (#226).

varfish-org · Jan 12, 2022 · 705b554 · 705b554
1 parent ec17d55
commit 705b554
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Showing 4 changed files with 8 additions and 5 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -25,6 +25,7 @@ End-User Summary
 - Imports via API now are only allowed for projects of type ``PROJECT`` (#237).
 - Fixing ensembl gene link-out to wrong genome build (#156).
 - Added section for developers in manual (#267).
+- Updating Clinvar export schema to 1.7 version (#226).
 - Migrated icons to iconify (#208).
 - Bumped chrome-driver version (#208).
 - VarFish now allows for the import of GRCh38 annotated variants.
@@ -53,6 +54,7 @@ Full Change List
 - Imports via API now are only allowed for projects of type ``PROJECT`` (#237).
 - Fixing ensembl gene link-out to wrong genome build (#156).
 - Added section for developers in manual (#267).
+- Updating Clinvar export schema to the latest 1.7 version (#226).
 - Migrated icons to iconify (#208).
 - Bumped chrome-driver version (#208).
 - Skipping codacy if token is not defined (#275).

diff --git a/clinvar_export/clinvar_xml.py b/clinvar_export/clinvar_xml.py
@@ -4,7 +4,7 @@
 from lxml.builder import ElementMaker
 
 #: URL of the XSD file
-XSD_URL_1_6 = "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xsd_submission/clinvar_submission_1.6.xsd"
+XSD_URL_1_7 = "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xsd_submission/clinvar_submission_1.7.xsd"
 
 
 class SubmissionXmlGenerator:
@@ -18,7 +18,7 @@ def generate_tree(self, submission_set):
             "ClinvarSubmissionSet",
             {
                 "Date": datetime.date.today().isoformat(),
-                "{http://www.w3.org/2001/XMLSchema-instance}noNamespaceSchemaLocation": XSD_URL_1_6,
+                "{http://www.w3.org/2001/XMLSchema-instance}noNamespaceSchemaLocation": XSD_URL_1_7,
             },
         )
         root.append(

diff --git a/...ar_export/data/clinvar_submission_1.6.xsd → ...ar_export/data/clinvar_submission_1.7.xsd b/...ar_export/data/clinvar_submission_1.6.xsd → ...ar_export/data/clinvar_submission_1.7.xsd
@@ -1,4 +1,4 @@
-<xs:schema version="1.6; February 10, 2020" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+<xs:schema version="1.7; May 22, 2020" xmlns:xs="http://www.w3.org/2001/XMLSchema">
     <xs:annotation>
         <xs:documentation> If you have any question about this xsd, please contact us.
             (clinvar@ncbi.nlm.nih.gov). </xs:documentation>
@@ -1515,6 +1515,7 @@
             <xs:enumeration value="Finding"/>
             <xs:enumeration value="InfectionResistance"/>
             <xs:enumeration value="PhenotypeInstruction"/>
+            <xs:enumeration value="NamedProteinVariant"/>
         </xs:restriction>
     </xs:simpleType>
     <xs:simpleType name="typeTraitAttributetype">

diff --git a/clinvar_export/views_ajax.py b/clinvar_export/views_ajax.py
@@ -29,7 +29,7 @@
 
 from geneinfo.models import Hpo, HpoName
 from variants.queries import SmallVariantUserAnnotationQuery
-from .clinvar_xml import SubmissionXmlGenerator, XSD_URL_1_6
+from .clinvar_xml import SubmissionXmlGenerator, XSD_URL_1_7
 from .models import (
     SubmissionSet,
     Submission,
@@ -64,7 +64,7 @@ def _read(filename):
 
 #: Submission XSD URL to XSD string
 XSD_CONTENTS = {
-    XSD_URL_1_6: _read(XSD_URL_1_6.rsplit("/", 1)[1]),
+    XSD_URL_1_7: _read(XSD_URL_1_7.rsplit("/", 1)[1]),
 }