init log

tests/submission/test_submit.py

@@ -11,18 +11,21 @@ def test_submittable_status():
 
 def test_submit(ctx, mock_server):
 
+    with pytest.raises(Exception):
+        perform_submission(ctx, '///')
+
+    with pytest.raises(AttributeError):
+        submit_dataset(ctx)
+
     ctx.obj['SETTINGS']['ega_submitter_account'] = 'test_account'
     ctx.obj['SETTINGS']['ega_submitter_password'] = 'test_password'
     ctx.obj['SETTINGS']['ega_policy_id'] = 'test_id'
     ctx.obj['CURRENT_DIR'] = os.path.join(os.getcwd(),'tests/data/workspace/unaligned.20170110/')
     ctx.obj['CURRENT_DIR_TYPE'] = "unaligned"
     ctx.obj['EGA_ENUMS'] = EgaEnums()
     ctx.obj['log_file'] = 'tests/data/workspace/unaligned.20170110/ssample_y/.status'
-
-    perform_submission(ctx, '///')
 
-    with pytest.raises(AttributeError):
-        submit_dataset(ctx)
+    perform_submission(ctx, '///')
 
     initial_directory = os.getcwd()
     os.chdir('tests/data/workspace/unaligned.20170110/')

tests/submission/test_submitter.py

@@ -16,6 +16,7 @@ def test_submitter(ctx, mock_server):
     ctx.obj['SUBMISSION']['sessionToken'] = 'X-Token'
     ctx.obj['SETTINGS']['icgc_project_code'] = "abjdh"
 
+    #do not uncomment
     #submitter.submit(unaligned, True)
 
     attributes = [Attribute('tag1', 'value1'), Attribute('tag2', 'value2')]

tests/submission/test_variation.py

@@ -4,6 +4,7 @@
 from egasub.ega.entities import Sample, EgaEnums, \
                                 Analysis as EAnalysis
 from egasub import __version__ as ver
+#from egasub.exceptions import Md5sumFileError
 
 
 def test_variation():
@@ -97,10 +98,9 @@ def test_variation():
     with pytest.raises(Exception):
         variation = Variation('sample_bad_99')
 
-
-    # No /
+    # Cannot contain '/'
     with pytest.raises(Exception):
-        variation = Variation('///')
+        variation = Variation('sdf/df/ff/')
 
     assert variation.status == 'NEW'
 
@@ -109,4 +109,10 @@ def test_variation():
     variation.local_validate(EgaEnums())
 
     os.chdir(initial_directory)
+    os.chdir('tests/data/workspace/alignment.20170115/')
+
+    variation = Variation('test_x')
 
+    variation.local_validate(EgaEnums())
+
+    os.chdir(initial_directory)

tests/test_utils.py

@@ -1,12 +1,20 @@
 
-from egasub.utils import initialize_app, get_current_dir_type, get_settings, find_workspace_root
+from egasub.utils import initialize_app, initialize_log, get_current_dir_type, get_settings, find_workspace_root
 import pytest
 import os
 
 def test_initialize_app(ctx):
     with pytest.raises(KeyError):
         initialize_app(ctx)
 
+    ctx.obj['WORKSPACE_PATH'] = "tests/data/workspace/variation.20170119/test_x"
+    #ctx.obj['WORKSPACE_PATH']['SETTINGS'] =
+
+    #initialize_app(ctx)
+
+def test_initialize_log(ctx):
+    initialize_log(ctx, True, "info")
+
 def test_get_current_dir_type(ctx):
 
     with pytest.raises(KeyError):