remove ability to not define the entire region; avoid exceptions

NBISweden · Mar 27, 2019 · b517459 · b517459
1 parent 4edde8d
commit b517459
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Showing 3 changed files with 13 additions and 30 deletions.
diff --git a/backend/modules/browser/browser_handlers.py b/backend/modules/browser/browser_handlers.py
@@ -126,28 +126,15 @@ def get(self, dataset:str, region:str, ds_version:str=None):
         Returns:
             dict: information about the region and the genes found there
         """
-        region = region.split('-')
-
-        chrom = region[0]
-        start = None
-        stop = None
-
         try:
-            if len(region) > 1:
-                start = int(region[1])
-            if len(region) > 2:
-                stop = int(region[2])
-
+            chrom, start, stop = region.split('-')
+            start = int(start)
+            stop = int(stop)
         except ValueError:
             logging.error('GetRegion: unable to parse region ({})'.format(region))
-            self.send_error(status_code=400)
-            self.set_user_msg('Unable to parse region', 'error')
+            self.send_error(status_code=400, reason='Unable to parse region')
             return
 
-        if not start:
-            start = 0
-        if not stop:
-            stop = start
         ret = {'region':{'chrom': chrom,
                          'start': start,
                          'stop':  stop,
@@ -245,8 +232,7 @@ def get(self, dataset:str, variant:str, ds_version:str=None):
 
         if not variant:
             logging.error('Variant not found ({})'.format(orig_variant))
-            self.send_error(status_code=404)
-            self.set_user_msg('Variant not found', 'error')
+            self.send_error(status_code=404, reason='Variant not found')
             return
 
         # Just get the information we need

diff --git a/backend/modules/browser/tests/test_browser_handlers.py b/backend/modules/browser/tests/test_browser_handlers.py
@@ -109,16 +109,6 @@ def test_get_region():
                                       'geneName': 'PPARA'}]}}
     assert region == expected
 
-    region_def = '22'
-    response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
-    region = json.loads(response.text)
-    assert region == {'region': {'chrom': '22', 'start': 0, 'stop': 20}}
-
-    region_def = '22-1000'
-    response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
-    region = json.loads(response.text)
-    assert region == {'region': {'chrom': '22', 'start': 980, 'stop': 1020}}
-
     region_def = '22-16364870-16366200'
     response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def))
     region = json.loads(response.text)

diff --git a/backend/modules/browser/utils.py b/backend/modules/browser/utils.py
@@ -324,7 +324,14 @@ def get_variant_list(dataset:str, datatype:str, item:str, ds_version:str=None):
     if datatype == 'gene':
         variants = lookups.get_variants_in_gene(dataset, item, ds_version)
     elif datatype == 'region':
-        chrom, start, stop = item.split('-')
+        try:
+            chrom, start, stop = item.split('-')
+            start = int(start)
+            stop = int(stop)
+        except ValueError:
+            self.send_error(status_code=400, reason='Unable to parse region')
+            return
+
         if is_region_too_large(start, stop):
             return {'variants': [], 'headers': [], 'region_too_large': True}
         variants = lookups.get_variants_in_region(dataset, chrom, start, stop, ds_version)