Merge pull request #384 from ISA-tools/develop

Develop final merge for v0.12

Author: Zigur

Diff for: .coveragerc

@@ -1,11 +1,12 @@
 [run]
 source = isatools
 omit =
-    /docs/*
-    /features/*
-    /tests/*
-    /isatools/io/isatab_configurator.py
-    /isatools/io/storage_adapter.py
+    docs/*
+    features/*
+    tests/*
+    isatools/convert/experimental/*
+    isatools/net/storage_adapter.py
+    isatools/io/isatab_configurator.py
 
 [report]
 exclude_lines =

Diff for: isatools/convert/experimental/__init__.py

@@ -3371,7 +3371,8 @@ def next_process(self, val):
         if val is not None and not isinstance(val, Process):
             raise AttributeError(
                 'Process.next_process must be a Process '
-                'or None; got {0}:{1}'.format(val, type(val)))
+                'or None; got {0}:{1}'.format(val, type(val))
+            )
         else:
             self.__next_process = val
 
@@ -3383,12 +3384,6 @@ def __repr__(self):
     def __str__(self):
         return """{0}(name={1.name})""".format(self.__class__.__name__, self)
 
-    # def __repr__(self):
-    #     return 'Process(name="{0.name}", ' \
-    #            'executes_protocol={0.executes_protocol}, ' \
-    #            'date="{0.date}", performer="{0.performer}", ' \
-    #            'inputs={0.inputs}, outputs={0.outputs})'.format(self)
-    #
     def __hash__(self):
         return hash(repr(self))
 

Diff for: isatools/convert/nih-dcc-flux.py renamed to isatools/convert/experimental/nih_dcc_flux.py

@@ -5,6 +5,7 @@
 import tempfile
 import shutil
 
+SLOW_TESTS = int(os.getenv('SLOW_TESTS', '0'))
 
 def setUpModule():
     if not os.path.exists(utils.DATA_DIR):
@@ -24,23 +25,25 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree(self._tmp_dir)
 
-    def test_sampletab2json_test_1(self):
+    def test_sampletab2isatab_test_1(self):
         with open(os.path.join(self._sampletab_dir, "test1.txt")) as sampletab_fp:
             sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir)
 
-    def test_sampletab2json_test_2(self):
+    def test_sampletab2isatab_test_2(self):
         with open(os.path.join(self._sampletab_dir, "test2.txt")) as sampletab_fp:
             sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir)
 
-    def test_sampletab2json_GSB_3(self):
+    @unittest.skipIf(not SLOW_TESTS, "slow")
+    def test_sampletab2isatab_GSB_3(self):
         with open(os.path.join(self._sampletab_dir, "GSB-3.txt")) as sampletab_fp:
             sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir)
 
-    def test_sampletab2json_GSB_537(self):
+    @unittest.skipIf(not SLOW_TESTS, "slow")
+    def test_sampletab2isatab_GSB_537(self):
         with open(os.path.join(self._sampletab_dir, "GSB-537.txt")) as sampletab_fp:
             sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir)
 
-    @unittest.skip("skipping test that hangs on like forever")
-    def test_sampletab2json_GSB_718(self):
+    @unittest.skip("slow")
+    def test_sampletab2isatab_GSB_718(self):
         with open(os.path.join(self._sampletab_dir, "GSB-718.txt")) as sampletab_fp:
             sampletab2isatab.convert(source_sampletab_fp=sampletab_fp, target_dir=self._tmp_dir)

Diff for: isatools/model.py

@@ -5,9 +5,12 @@
 import tempfile
 import zipfile
 
+from unittest.mock import patch
 from isatools.tests import utils
 from isatools.net import sra2isatab
 
+SLOW_TESTS = int(os.getenv('SLOW_TESTS', '0'))
+
 
 def setUpModule():
     if not os.path.exists(utils.DATA_DIR):
@@ -29,10 +32,12 @@ def setUp(self):
     # def tearDown(self):
     #     shutil.rmtree(self._tmp_dir)
 
-   # https://www.ebi.ac.uk/ena/data/view/SRA108974&display=xml
+    # https://www.ebi.ac.uk/ena/data/view/SRA108974&display=xml
 
-    def test_sra_import(self):
+    @unittest.skipIf(not SLOW_TESTS, "slow")
+    def test_sra_import(self, mock_call):
         zipped_bytes = sra2isatab.sra_to_isatab_batch_convert('SRA108974')
+        mock_call.assert_called_with()
         with open(os.path.join(self._tmp_dir, 'o.zip'), 'wb') as zip_fp:
             shutil.copyfileobj(zipped_bytes, zip_fp, length=131072)
 
@@ -42,3 +47,9 @@ def test_sra_import(self):
                 sorted([os.path.basename(x) for x in zip_fp.namelist()]),
                 ['a_wgs-genomic.txt', 'i_SRA108974.txt', 's_SRA108974.txt']
             )
+
+    @patch("subprocess.call")
+    def test_sra_import_mocked(self, mock_call):
+        with self.assertRaises(FileNotFoundError, msg='as subprocess.call is mocked files are nor generated'):
+            sra2isatab.sra_to_isatab_batch_convert('SRA108974')
+            mock_call.assert_called_with('java', '-jar')