Merge pull request #499 from NBISweden/develop

Changes for v21

backend/modules/browser/browser_handlers.py

@@ -195,9 +195,12 @@ def get(self, dataset, variant):
                     'datasets':{},
                     'total':{}}
         for item in ['ans', 'acs', 'freq', 'homs']:
-            for _dataset, value in variant['pop_' + item].items():
+            key = 'pop_' + item
+            if key not in variant:
+                continue
+            for _dataset, value in variant[key].items():
                 if _dataset not in frequencies['datasets']:
-                    frequencies['datasets'][dataset] = {'pop':_dataset}
+                    frequencies['datasets'][_dataset] = {'pop':_dataset}
                 frequencies['datasets'][_dataset][item] = value
                 if item not in frequencies['total']:
                     frequencies['total'][item] = 0

backend/modules/browser/lookups.py

@@ -40,6 +40,13 @@ def get_variant(db, sdb, xpos, ref, alt):
     return variant
 
 
+def add_rsid_to_variant(sdb, variant):
+    if variant['rsid'] == '.' or variant['rsid'] is None:
+        rsid = sdb.dbsnp.find_one({'xpos': variant['xpos']})
+        if rsid:
+            variant['rsid'] = 'rs%s' % rsid['rsid']
+
+
 def get_variants_by_rsid(db, rsid):
     if not rsid.startswith('rs'):
         return None
@@ -214,7 +221,7 @@ def get_genes_in_region(sdb, chrom, start, stop):
     return list(genes)
 
 
-def get_variants_in_region(db, chrom, start, stop):
+def get_variants_in_region(db, sdb, chrom, start, stop):
     """
     Variants that overlap a region
     Unclear if this will include CNVs
@@ -226,6 +233,7 @@ def get_variants_in_region(db, chrom, start, stop):
     }, projection={'_id': False}, limit=SEARCH_LIMIT))
     add_consequence_to_variants(variants)
     for variant in variants:
+        add_rsid_to_variant(sdb, variant)
         remove_extraneous_information(variant)
     return list(variants)
 
@@ -265,10 +273,11 @@ def remove_extraneous_information(variant):
     del variant['vep_annotations']
 
 
-def get_variants_in_gene(db, gene_id):
+def get_variants_in_gene(db, sdb, gene_id):
     variants = []
     for variant in db.variants.find({'genes': gene_id}, projection={'_id': False}):
         variant['vep_annotations'] = [x for x in variant['vep_annotations'] if x['Gene'] == gene_id]
+        add_rsid_to_variant(sdb, variant)
         add_consequence_to_variant(variant)
         remove_extraneous_information(variant)
         variants.append(variant)
@@ -285,10 +294,11 @@ def get_number_of_variants_in_transcript(db, transcript_id):
     return {'filtered': filtered, 'total': total}
 
 
-def get_variants_in_transcript(db, transcript_id):
+def get_variants_in_transcript(db, sdb, transcript_id):
     variants = []
     for variant in db.variants.find({'transcripts': transcript_id}, projection={'_id': False}):
         variant['vep_annotations'] = [x for x in variant['vep_annotations'] if x['Feature'] == transcript_id]
+        add_rsid_to_variant(sdb, variant)
         add_consequence_to_variant(variant)
         remove_extraneous_information(variant)
         variants.append(variant)

backend/modules/browser/mongodb.py

@@ -44,14 +44,15 @@ def get_variant_list(dataset, datatype, item):
 
     try:
         db = connect_db(dataset, False)
+        db_shared = connect_db(dataset, True)
 
         if datatype == 'gene':
-            variants = lookups.get_variants_in_gene(db, item)
+            variants = lookups.get_variants_in_gene(db, db_shared, item)
         elif datatype == 'region':
             chrom, start, stop = item.split('-')
-            variants = lookups.get_variants_in_region(db, chrom, start, stop)
+            variants = lookups.get_variants_in_region(db, db_shared, chrom, start, stop)
         elif datatype == 'transcript':
-            variants = lookups.get_variants_in_transcript(db, item)
+            variants = lookups.get_variants_in_transcript(db, db_shared, item)
 
         # Format output
         def format_variant(variant):

frontend/templates/ng-templates/dataset-download.html

@@ -72,7 +72,7 @@ <h3>Request access to summary files</h3>
         <div class="col-md-1 column"></div>
         <div class="col-md-8 column">
             <p>By submitting the application for registration you confirm that the information provided in the application is accurate.</p>
-            <p>By submitting the application for registration you also agree to have the information that you submit (Name, affiliation, country and email) handled in accordance with the Swedish Personal Data Act (Personuppgiftslagen, 1998:204). The stored information will only be used for internal administrative purposes and not shared with other parties.</p>
+            <p>By submitting the application for registration you also agree to have the information that you submit (Name, affiliation, country and email) handled in accordance with the General Data Protection Regulation ((EU) 2016/679). The stored information will only be used for internal administrative purposes and not shared with other parties.</p>
         </div>
     </div>
 </div>