Merge pull request #549 from NBISweden/feature/drop-var-call-ref

Remove var_call_ref from database.
NBISweden · Apr 25, 2019 · f716868 · f716868
2 parents 65d0d26 + 940c0ee
commit f716868
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Showing 5 changed files with 11 additions and 12 deletions.
diff --git a/backend/application.py b/backend/application.py
@@ -172,6 +172,7 @@ def get(self, dataset, version=None):
             future_version = True
 
         ret = build_dataset_structure(version, user)
+        ret['version']['var_call_ref'] = version.reference_set.reference_build
         ret['future'] = future_version
 
         self.finish(ret)

diff --git a/backend/db.py b/backend/db.py
@@ -208,7 +208,6 @@ class Meta:
     version           = CharField(db_column="dataset_version")
     description       = TextField(db_column="dataset_description")
     terms             = TextField()
-    var_call_ref      = CharField(null=True)
     available_from    = DateTimeField()
     ref_doi           = CharField(null=True)
     data_contact_name = CharField(null=True)

diff --git a/sql/data_schema.sql b/sql/data_schema.sql
@@ -128,7 +128,6 @@ CREATE TABLE IF NOT EXISTS data.dataset_versions (
     dataset_version     varchar(20)     NOT NULL,
     dataset_description text            NOT NULL,
     terms               text            NOT NULL,
-    var_call_ref        varchar(50)     DEFAULT NULL,
     available_from      timestamp       DEFAULT current_timestamp,
     ref_doi             varchar(100)    DEFAULT NULL,
     data_contact_name   varchar(100)    DEFAULT NULL,

diff --git a/test/data/browser_test_data.sql b/test/data/browser_test_data.sql
@@ -24,11 +24,11 @@ COPY data.reference_sets (id, reference_build, reference_name, ensembl_version,
 1	\N	swegen	homo_sapiens_core_75_37	19	2.9.3
 \.
 
-COPY data.dataset_versions (id, dataset, reference_set, dataset_version, dataset_description, terms, var_call_ref, available_from, ref_doi, data_contact_name, data_contact_link, num_variants, coverage_levels, portal_avail, file_access, beacon_access) FROM stdin;
-2	1	1	20170823	desc	terms	hg19	2001-01-01 00:00:00	doi	place	email	\N	{1,5,10,15,20,25,30,50,100}	TRUE	REGISTERED	PUBLIC
-3	1	1	20171025	desc	terms	hg19	2001-01-01 00:00:00	doi	place	email	\N	{1,5,10,15,20,25,30,50,100}	TRUE	REGISTERED	PUBLIC
-1	1	1	20161223	desc	terms	hg19	2001-01-01 00:00:00	doi	place	email	\N	{1,5,10,15,20,25,30,50,100}	TRUE	REGISTERED	PUBLIC
-4	1	1	20180409	desc	terms	hg19	2001-01-01 00:00:00	doi	place	email	\N	{1,5,10,15,20,25,30,50,100}	TRUE	REGISTERED	PUBLIC
+COPY data.dataset_versions (id, dataset, reference_set, dataset_version, dataset_description, terms, available_from, ref_doi, data_contact_name, data_contact_link, num_variants, coverage_levels, portal_avail, file_access, beacon_access) FROM stdin;
+2	1	1	20170823	desc	terms	2001-01-01 00:00:00	doi	place	email	\N	{1,5,10,15,20,25,30,50,100}	TRUE	REGISTERED	PUBLIC
+3	1	1	20171025	desc	terms	2001-01-01 00:00:00	doi	place	email	\N	{1,5,10,15,20,25,30,50,100}	TRUE	REGISTERED	PUBLIC
+1	1	1	20161223	desc	terms	2001-01-01 00:00:00	doi	place	email	\N	{1,5,10,15,20,25,30,50,100}	TRUE	REGISTERED	PUBLIC
+4	1	1	20180409	desc	terms	2001-01-01 00:00:00	doi	place	email	\N	{1,5,10,15,20,25,30,50,100}	TRUE	REGISTERED	PUBLIC
 \.
 
 COPY data.coverage (id, dataset_version, chrom, pos, mean, median, coverage) FROM stdin;

diff --git a/test/data/load_dummy_data.sql b/test/data/load_dummy_data.sql
@@ -24,11 +24,11 @@ INSERT INTO data.sample_sets (id, dataset, "collection", sample_size, phenotype)
            (1000002, 1000001, 1000002, 15, 'SamplePheno2 Coll1'),
            (1000003, 1000002, 1000003, 20, 'SamplePheno2 Coll2');
 
-INSERT INTO data.dataset_versions (id, dataset, reference_set, dataset_version, dataset_description, terms, var_call_ref, available_from, ref_doi, data_contact_name, data_contact_link, num_variants, coverage_levels, portal_avail, file_access, beacon_access)
-    VALUES (1000001, 1000001, 1000001, 'Version 1-1', 'Dataset 1-1, description', 'Dataset 1-1, terms', 'CallRef11', '2017-01-01', 'datset11DOI', 'Gunnar Green',     'gunnar.green@example.com', 10, ARRAY[1,5,10], TRUE, 'CONTROLLED', 'PUBLIC'),
-           (1000002, 1000002, 1000001, 'Version 2-1', 'Dataset 2-1, description', 'Dataset 2-1, terms', 'CallRef21', '2017-02-01', 'datset21DOI', NULL, NULL, 100, ARRAY[1,5,10], TRUE, 'CONTROLLED', 'PUBLIC'),
-           (1000003, 1000002, 1000002, 'Version 2-2', 'Dataset 2-2, description', 'Dataset 2-2, terms', 'CallRef22', '2017-02-02', 'datset22DOI', 'Strummer project', 'https://example.com/strummer', 1000, ARRAY[1,5,10], TRUE, 'CONTROLLED', 'PUBLIC'),
-           (1000004, 1000002, 1000002, 'InvVer  2-3', 'Dataset 2-3, description', 'Dataset 2-3, terms', 'CallRef23', '2030-02-03', 'datset23DOI', 'Drummer project',  'https://example.com/drummer', 10000, ARRAY[1,5,10], TRUE, 'CONTROLLED', 'PUBLIC');
+INSERT INTO data.dataset_versions (id, dataset, reference_set, dataset_version, dataset_description, terms, available_from, ref_doi, data_contact_name, data_contact_link, num_variants, coverage_levels, portal_avail, file_access, beacon_access)
+    VALUES (1000001, 1000001, 1000001, 'Version 1-1', 'Dataset 1-1, description', 'Dataset 1-1, terms', '2017-01-01', 'datset11DOI', 'Gunnar Green',     'gunnar.green@example.com', 10, ARRAY[1,5,10], TRUE, 'CONTROLLED', 'PUBLIC'),
+           (1000002, 1000002, 1000001, 'Version 2-1', 'Dataset 2-1, description', 'Dataset 2-1, terms', '2017-02-01', 'datset21DOI', NULL, NULL, 100, ARRAY[1,5,10], TRUE, 'CONTROLLED', 'PUBLIC'),
+           (1000003, 1000002, 1000002, 'Version 2-2', 'Dataset 2-2, description', 'Dataset 2-2, terms', '2017-02-02', 'datset22DOI', 'Strummer project', 'https://example.com/strummer', 1000, ARRAY[1,5,10], TRUE, 'CONTROLLED', 'PUBLIC'),
+           (1000004, 1000002, 1000002, 'InvVer  2-3', 'Dataset 2-3, description', 'Dataset 2-3, terms', '2030-02-03', 'datset23DOI', 'Drummer project',  'https://example.com/drummer', 10000, ARRAY[1,5,10], TRUE, 'CONTROLLED', 'PUBLIC');
 
 INSERT INTO data.dataset_files(id, dataset_version, basename, uri, file_size)
     VALUES (1000001, 1000001, 'File11-1', '/release/file111.txt', 100),