diff --git a/HISTORY.rst b/HISTORY.rst index dfed61b57..74cf3ab8e 100644 --- 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 index 52534e212..7fd07ec9d 100644 --- 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/clinvar_export/data/clinvar_submission_1.6.xsd b/clinvar_export/data/clinvar_submission_1.7.xsd similarity index 99% rename from clinvar_export/data/clinvar_submission_1.6.xsd rename to clinvar_export/data/clinvar_submission_1.7.xsd index 7feac33be..eb76894f9 100644 --- a/clinvar_export/data/clinvar_submission_1.6.xsd +++ b/clinvar_export/data/clinvar_submission_1.7.xsd @@ -1,4 +1,4 @@ - + If you have any question about this xsd, please contact us. (clinvar@ncbi.nlm.nih.gov). @@ -1515,6 +1515,7 @@ + diff --git a/clinvar_export/views_ajax.py b/clinvar_export/views_ajax.py index 4eb8abaa1..b0cd9f761 100644 --- 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]), }