+

tests/test_import_data.py

@@ -159,6 +159,34 @@ def test_get_existing_uuid(connection, mocker, returned_vendor_existing_item):
 
 
 def test_combine_set_replicates():
+    post_json = {"aliases": "sample_repset", "description": "sample description"}
+    existing_data = {}
+    dict_replicates = {'sample_repset': [{'replicate_exp': 'awesome_uuid1', 'bio_rep_no': 1.0, 'tec_rep_no': 1.0},
+                                         {'replicate_exp': 'awesome_uuid3', 'bio_rep_no': 1.0, 'tec_rep_no': 2.0}]}
+    post_json2, dict_replicates2 = imp.combine_set(post_json, existing_data, "ExperimentSetReplicate", dict_replicates)
+
+    response = {'experiments_in_set': [{'replicate_exp': 'awesome_uuid1', 'tec_rep_no': 1.0, 'bio_rep_no': 1.0},
+                                       {'replicate_exp': 'awesome_uuid3', 'tec_rep_no': 2.0, 'bio_rep_no': 1.0}],
+                'description': 'sample description',
+                'aliases': 'sample_repset'}
+    assert post_json2 == response
+    assert dict_replicates2 == {}
+
+
+def test_combine_set_expsets():
+    post_json = {"aliases": "sample_expset", "description": "sample description"}
+    existing_data = {}
+    dict_expsets = {'sample_expset': ['awesome_uuid1', 'awesome_uuid4', 'awesome_uuid5']}
+    post_json2, dict_expsets2 = imp.combine_set(post_json, existing_data, "ExperimentSet", dict_expsets)
+
+    response = {'experiments_in_set': ['awesome_uuid4', 'awesome_uuid5', 'awesome_uuid1'],
+                'description': 'sample description',
+                'aliases': 'sample_expset'}
+    assert sorted(post_json2) == sorted(response)
+    assert dict_expsets2 == {}
+
+
+def test_combine_set_replicates_with_existing():
     post_json = {"aliases": "sample_repset", "description": "sample description"}
     existing_data = {"uuid": "sampleuuid", "accession": "sample_accession",
                      'replicate_exps': [{'replicate_exp': 'awesome_uuid', 'bio_rep_no': 1.0, 'tec_rep_no': 6.0},
@@ -177,7 +205,7 @@ def test_combine_set_replicates():
     assert dict_replicates2 == {}
 
 
-def test_combine_set_expsets():
+def test_combine_set_expsets_with_existing():
     post_json = {"aliases": "sample_expset", "description": "sample description"}
     existing_data = {"uuid": "sampleuuid", "accession": "sample_accession",
                      "experiments_in_set": ['awesome_uuid1', 'awesome_uuid2']}

wranglertools/import_data.py

@@ -502,7 +502,7 @@ def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadx
     #     if dict_replicates
 
 
-def get_upload_creds(file_id, connection, file_info):
+def get_upload_creds(file_id, connection, file_info):  # pragma: no cover
     url = "%s%s/upload/" % (connection.server, file_id)
     req = requests.post(url,
                         auth=connection.auth,
@@ -511,24 +511,21 @@ def get_upload_creds(file_id, connection, file_info):
     return req.json()['@graph'][0]['upload_credentials']
 
 
-def upload_file(metadata_post_response, path):
+def upload_file(metadata_post_response, path):  # pragma: no cover
     try:
         item = metadata_post_response['@graph'][0]
         creds = item['upload_credentials']
     except Exception as e:
         print(e)
         return
-
     ####################
     # POST file to S3
-
     env = os.environ.copy()  # pragma: no cover
     env.update({
         'AWS_ACCESS_KEY_ID': creds['access_key'],
         'AWS_SECRET_ACCESS_KEY': creds['secret_key'],
         'AWS_SECURITY_TOKEN': creds['session_token'],
-    })  # pragma: no cover
-
+    })
     # ~10s/GB from Stanford - AWS Oregon
     # ~12-15s/GB from AWS Ireland - AWS Oregon
     print("Uploading file.")
@@ -547,8 +544,6 @@ def upload_file(metadata_post_response, path):
 
 # the order to try to upload / update the items
 # used to avoid dependencies... i.e. biosample needs the biosource to exist
-
-
 def order_sorter(list_of_names):
     ret_list = []
     for i in sheet_order: