tests and fixes for downloading what is shown

NBISweden · Apr 11, 2019 · 08c2585 · 08c2585
1 parent c5ca6d2
commit 08c2585
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Showing 2 changed files with 24 additions and 8 deletions.
diff --git a/backend/modules/browser/browser_handlers.py b/backend/modules/browser/browser_handlers.py
@@ -35,21 +35,23 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None, filter_t
             filter_type (str): type of filter to apply
         """
         # ctrl.filterVariantsBy~ctrl.filterIncludeNonPass
-        filters = filter_type.split('~')
         dataset, ds_version = utils.parse_dataset(dataset, ds_version)
         filename = "{}_{}_{}.csv".format(dataset, datatype, item)
         self.set_header('Content-Type','text/csv')
         self.set_header('content-Disposition','attachement; filename={}'.format(filename))
 
         data = utils.get_variant_list(dataset, datatype, item, ds_version)
-        logging.error(data)
         # filter variants based on what is shown
-        if filters[1] == 'false':
-            data = [variant for variant in data if variant['filter_string'] == 'PASS']
-        if filters[0] == 'mislof':
-            data = [variant for variant in data if variant['major_consequence'] == 'missense']
-        if 'lof' in filters[0]:
-            data = [variant for variant in data if 'LoF' in variant['filter']]
+        if filter_type:
+            filters = filter_type.split('~')
+            if filters[1] == 'false':
+                data['variants'] = [variant for variant in data['variants'] if variant['filter_string'] == 'PASS']
+            if filters[0] == 'mislof':
+                data['variants'] = [variant for variant in data['variants']
+                                    if variant['major_consequence'] == 'missense'
+                                    or 'LoF' in variant['flags']]
+            elif 'lof' in filters[0]:
+                data['variants'] = [variant for variant in data['variants'] if 'LoF' in variant['flags']]
 
         # Write header
         self.write(','.join([h[1] for h in data['headers']]) + '\n')

diff --git a/backend/modules/browser/tests/test_browser_handlers.py b/backend/modules/browser/tests/test_browser_handlers.py
@@ -29,7 +29,21 @@ def test_download():
     data_type = 'transcript'
     data_item = 'ENST00000438441'
     response = requests.get('{}/api/dataset/{}/browser/download/{}/{}'.format(BASE_URL, dataset, data_type, data_item))
+    assert len(response.text.split('\n')) == 180 # header + 178 + \n
+    response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/all~false'.format(BASE_URL, dataset, data_type, data_item))
+    import logging
+    logging.error(response.text.split('\n'))
+    assert len(response.text.split('\n')) == 8
+    response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/all~true'.format(BASE_URL, dataset, data_type, data_item))
     assert len(response.text.split('\n')) == 180
+    response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/mislof~true'.format(BASE_URL, dataset, data_type, data_item))
+    assert len(response.text.split('\n')) == 2
+    data_type = 'region'
+    data_item = '22-29450622-29465622'
+    response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/mislof~false'.format(BASE_URL, dataset, data_type, data_item))
+    assert len(response.text.split('\n')) == 3
+    response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/lof~false'.format(BASE_URL, dataset, data_type, data_item))
+    assert len(response.text.split('\n')) == 3
 
 
 def test_get_coverage():