Dev (#28)

* Update driver.py (#26)

* adding lims error message to driver and unit tests for changes made (#27)

* adding lims error message to driver and unit tests for changes made

* adding SER : Serum, back into driver

* updating version

* Update driver.py (#26)

* adding lims error message to driver and unit tests for changes made (#27)

* adding lims error message to driver and unit tests for changes made

* adding SER : Serum, back into driver

* updating version

Author: seg1129

CHANGELOG.md

@@ -1,4 +1,8 @@
 
+1.0.4
+  * fixing issue8 - driver execption: adding additional nautilius issue mappings
+  * added additional nautlis mappings -  'SER': 'Serum'
+
 1.0.3
 -----
 * Add additional Nautilus mappings

ehb_datasources/__init__.py

@@ -1,9 +1,9 @@
 __version_info__ = {
     'major': 1,
     'minor': 0,
-    'micro': 2,
+    'micro': 4,
     'releaselevel': 'final',
-    'serial': 23
+    'serial': 25
 }
 
 

ehb_datasources/drivers/nautilus/driver.py

@@ -26,7 +26,16 @@ class ehbDriver(Driver, RequestHandler):
     NAU_ERROR_MAP = {
         '0': 'UNKNOWN ERROR',
         '1': 'Unable to login into LIMS',
-        '8': 'Form data is not valid'
+        '2': 'Username not provided',
+        '3': 'Password not provided',
+        '4': 'Request type not provided',
+        '5': 'Request body not provided',
+        '6': 'Malformed Request',
+        '7': 'Unsupported request type',
+        '8': 'Form data is not valid',
+        '100': 'NAU socket service not found',
+        '101': 'NAU invalid authorization header'
+
     }
 
     def __init__(self, url, user, password, secure):
@@ -175,6 +184,7 @@ def format_aliquots(self, sample_data):
             'CELN': 'Cell Line',
             'CELLFRZ': 'Cell Freeze',
             'SAL': 'Saliva',
+            'SER': 'Serum',
             'SLD': 'Slide',
             'LYS': 'Lysate',
             'XEN': 'Xenograft',

ehb_datasources/tests/unit_tests/test_nautilus_driver.py

@@ -1,4 +1,6 @@
 import pytest
+import json
+
 
 from ehb_datasources.drivers.nautilus.driver import ehbDriver
 from ehb_datasources.drivers.exceptions import RecordCreationError, \
@@ -235,3 +237,40 @@ def test_process_new_record_form_no_sdg(driver, mocker):
         driver.process_new_record_form(request, 'TESTPREFIX', validator_func)
 
     assert excinfo.typename == 'RecordCreationError'
+
+
+# creating parameratized unit tests for testing error message received from lims
+examples = (('expected_error_message', 'status_error_num', 'test_comment'), [
+    # keeping comments blank because 'error message' in this case is sufficient.
+    # Keeping here for best practices in the future.
+    ('Username not provided', "2", ''),
+    ('Password not provided', "3", ''),
+    ('Request type not provided', "4", ''),
+    ('Request body not provided', "5", ''),
+    ('Malformed Request', "6", ''),
+    ('Unsupported request type', "7", ''),
+    ('Form data is not valid', "8", ''),
+    ('NAU socket service not found', "100", ''),
+    ('NAU invalid authorization header', "101", '')
+])
+
+
+@pytest.mark.parametrize(*examples)
+def test_process_new_record_lims(driver, mocker, expected_error_message, status_error_num, test_comment):
+    request = mocker.MagicMock(
+        method='POST',
+        _post={'SDG_NAME': '7316-118', 'csrfmiddlewaretoken': 'foo', 'label_id': '1'}
+    )
+    payload = [
+        {
+            "status": status_error_num,
+        }
+    ]
+    # using .encode() because fn in driver is expecting bytes
+    driver.update = mocker.MagicMock(return_value=json.dumps(payload).encode())
+    validator_func = mocker.MagicMock(return_value=0)
+    with pytest.raises(RecordCreationError) as excinfo:
+        driver.process_new_record_form(request, 'TESTPREFIX', validator_func)
+
+    assert excinfo.typename == 'RecordCreationError'
+    assert excinfo.value.cause == expected_error_message