Merge pull request #76 from icgc-dcc/testing

Testing

tests/test_init.py → tests/submission/test_init.py

@@ -1,5 +1,7 @@
 from click.testing import CliRunner
-from egasub.submission.init import truncate_string
+from egasub.submission.init import init_workspace, truncate_string, make_dummy_dac, make_dummy_policy
+from egasub.ega.entities import Dac, Policy, EgaEnums
+import pytest
 
 def test_init_function(ctx):
     runner = CliRunner()
@@ -23,4 +25,24 @@ def test_init_function(ctx):
 
 def test_truncate_string():
     assert truncate_string("12345", 4) == "1234..."
-    assert truncate_string("12345", 5) == "12345"
+    assert truncate_string("12345", 5) == "12345"
+
+def test_make_dummy_dac():
+    assert isinstance(make_dummy_dac(), Dac)
+
+def test_make_dummy_policy():
+    assert isinstance(make_dummy_policy(make_dummy_dac()), Policy)
+
+def test_init_workspace(ctx, mock_server):
+    ctx.obj['SETTINGS']['ega_submitter_account'] = 'test_account'
+    ctx.obj['SETTINGS']['ega_submitter_password'] = 'test_password'
+    ctx.obj['EGA_ENUMS'] = EgaEnums()
+    ctx.obj['SETTINGS']['ega_policy_id'] = 'test_id'
+
+    with pytest.raises(KeyError):
+        init_workspace(ctx, 'test_ac', 'test_pass', 'test_token', 'test_code')
+
+
+    ctx.obj['SETTINGS']['ega_submitter_account'] = None
+    ctx.obj['SETTINGS']['ega_submitter_password'] = None
+    ctx.obj['SETTINGS']['ega_policy_id'] = None

tests/submission/test_submit.py

@@ -0,0 +1,33 @@
+from egasub.submission.submit import submittable_status, submit_dataset, perform_submission
+from egasub.ega.entities.ega_enums import EgaEnums
+import pytest
+import os
+
+def test_submittable_status():
+    assert submittable_status("fail") == None
+    assert submittable_status("tests/submission/test_submit.py") == ['']
+
+def test_submit_dataset(ctx, mock_server):
+    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/variation.20170119')
+    ctx.obj['EGA_ENUMS'] = EgaEnums()
+    #ctx.obj['EGA_ENUMS']['_enums'] = ''
+    with pytest.raises(AttributeError):
+        submit_dataset(ctx)
+
+
+
+
+def test_perform_submission(ctx, mock_server):
+    perform_submission(ctx, '///')
+
+    ctx.obj['SETTINGS']['ega_submitter_account'] = None
+    ctx.obj['SETTINGS']['ega_submitter_password'] = None
+
+
+

tests/submission/test_submitter.py

@@ -0,0 +1,25 @@
+from egasub.submission.submitter import Submitter
+import os
+import pytest
+from egasub.submission.submittable import Unaligned
+from egasub.ega.entities.sample import Sample
+from egasub.ega.entities.attribute import Attribute
+
+def test_submitter(ctx, mock_server):
+    initial_directory = os.getcwd()
+    os.chdir('tests/data/workspace/unaligned.20170110/')
+    #unaligned = Unaligned('ssample_y')
+    os.chdir(initial_directory)
+
+    submitter = Submitter(ctx)
+
+    ctx.obj['SUBMISSION']['sessionToken'] = 'X-Token'
+    ctx.obj['SETTINGS']['icgc_project_code'] = "abjdh"
+    #assert submitter.submit(unaligned, True) is None
+
+    attributes = [Attribute('tag1', 'value1'), Attribute('tag2', 'value2')]
+    sample = Sample('an alias','the title','the description',123,2,'head','test line','test region','a phenotype',33,'anonymized name',22,10,'some details',attributes,33)
+    with pytest.raises(Exception):
+        submitter.set_icgc_ids(sample, True)
+
+

tests/submission/test_unaligned.py

@@ -1,14 +1,16 @@
 import pytest
 import os
+import shutil
 from egasub.submission.submittable import Unaligned
-from egasub.ega.entities import Sample, \
+from egasub.ega.entities import Sample, EgaEnums, \
                                 Experiment as EExperiment, \
                                 Run as ERun
 
 def test_unaligned():
     initial_directory = os.getcwd()
     os.chdir('tests/data/workspace/unaligned.20170110/')
     unaligned = Unaligned('ssample_y')
+    #unaligned2 = Unaligned('sample_x')
 
     assert isinstance(unaligned.sample, Sample)
     assert isinstance(unaligned.experiment, EExperiment)
@@ -78,6 +80,7 @@ def test_unaligned():
     assert cmp(unaligned.experiment.to_dict(),reference_experiment)  == 0
     assert cmp(unaligned.run.to_dict(),reference_run)  == 0
 
+
     # Check if the md5 checksum is missing in the file
     with pytest.raises(Exception):
         unaligned = Unaligned('sample_bad')
@@ -94,4 +97,35 @@ def test_unaligned():
     with pytest.raises(Exception):
         unaligned = Unaligned('sample_bad3')
 
+    # Cannot create submission error
+    with pytest.raises(Exception):
+        unaligned = Unaligned('tests')
+    # Name error
+    with pytest.raises(Exception):
+        unaligned = Unaligned('^*#')
+
+    assert unaligned.status == 'NEW'
+
+    assert unaligned.files == unaligned.run.files
+
+    assert unaligned.local_validate(EgaEnums()) is None
+
+    unaligned.record_object_status('none', True, "test", "test")
+
+    assert os.path.isfile(os.path.join(os.getcwd(), 'ssample_y/.status')) == False
+
+    unaligned.restore_latest_object_status('none')
+
+    assert os.path.isfile(os.path.join(os.getcwd(), 'ssample_y/.status')) == False
+
+    unaligned.record_object_status('sample', True, "test", "test")
+
+    assert os.path.isfile(os.path.join(os.getcwd(), 'ssample_y/.status/sample.log')) == True
+
+    unaligned.restore_latest_object_status('sample')
+
+    assert os.path.isfile(os.path.join(os.getcwd(), 'ssample_y/.status')) == False
+
+    shutil.rmtree(os.path.join(os.getcwd(), 'ssample_y/.status'))
+
     os.chdir(initial_directory)

tests/submission/test_variation.py

@@ -1,7 +1,7 @@
 import pytest
 import os
 from egasub.submission.submittable import Variation
-from egasub.ega.entities import Sample, \
+from egasub.ega.entities import Sample, EgaEnums, \
                                 Analysis as EAnalysis
 from egasub import __version__ as ver
 
@@ -97,4 +97,16 @@ def test_variation():
     with pytest.raises(Exception):
         variation = Variation('sample_bad_99')
 
-    os.chdir(initial_directory)
+
+    # No /
+    with pytest.raises(Exception):
+        variation = Variation('///')
+
+    assert variation.status == 'NEW'
+
+    assert variation.files == variation.analysis.files
+
+    variation.local_validate(EgaEnums())
+
+    os.chdir(initial_directory)
+

tests/test_ega_enums.py

@@ -1,5 +1,5 @@
-from egasub.ega.entities.ega_enums import EgaEnums
-
-def test_load_enums():
-    e = EgaEnums()
-    assert len(e.lookup("analysis_types")) == 3
+from egasub.ega.entities.ega_enums import EgaEnums
+
+def test_load_enums():
+    e = EgaEnums()
+    assert isinstance(e.lookup("analysis_types"), list)

tests/test_init_submission_dir.py

@@ -1,4 +1,3 @@
-
 from egasub.submission.init_submission_dir import init_submission_dir
 import pytest