pandasGEXpress/concat_gctoo: add tests for main

Author: Dave Lahr

cmapPy/pandasGEXpress/concat_gctoo.py

@@ -98,6 +98,7 @@ def main():
     # get args
     args = build_parser().parse_args(sys.argv[1:])
     setup_logger.setup(verbose=args.verbose)
+    logger.debug("args:  {}".format(args))
 
     # Get files directly
     if args.input_filepaths is not None:
@@ -127,10 +128,12 @@ def main():
 
         # Create concatenated gctoo object
         if args.concat_direction == "horiz":
-            out_gctoo = hstack(gctoos, args.fields_to_remove, args.reset_ids)
+            out_gctoo = hstack(gctoos, args.remove_all_metadata_fields, args.error_report_output_file,
+                               args.fields_to_remove, args.reset_ids)
 
         elif args.concat_direction == "vert":
-            out_gctoo = vstack(gctoos, args.fields_to_remove, args.reset_ids)
+            out_gctoo = vstack(gctoos, args.remove_all_metadata_fields, args.error_report_output_file,
+                               args.fields_to_remove, args.reset_ids)
 
     # Write out_gctoo to file
     logger.info("Writing to output file args.out_name:  {}".format(args.out_name))

cmapPy/pandasGEXpress/tests/functional_tests/test_concat_gctoo/test_main/a.gct

@@ -0,0 +1,5 @@
+#1.3
+2	2	1	0
+id	rhd1	a	b
+rid1	c	1.1	2.2
+rid2	d	3.3	4.4

cmapPy/pandasGEXpress/tests/functional_tests/test_concat_gctoo/test_main/b.gct

@@ -0,0 +1,5 @@
+#1.3
+2	2	1	0
+id	rhd1	g	f
+rid1	e	1.1	2.2
+rid2	d	3.3	4.4

cmapPy/pandasGEXpress/tests/test_concat_gctoo.py

@@ -84,6 +84,8 @@ def test_assemble_common_meta(self):
         self.assertIn("orig_rid", report_df.columns)
         self.assertTrue(set(meta1.columns) < set(report_df.columns))
 
+        os.remove(error_report_file)
+
 
         out_meta1 = cg.assemble_common_meta([meta1, meta2], ["rhd3"], None, False, None)
         logger.debug("out_meta1:\n{}".format(out_meta1))
@@ -330,6 +332,74 @@ def test_build_mismatched_common_meta_report(self):
         self.assertTrue(set(meta1.columns) < set(r.columns))
         self.assertEqual({"r3"}, set(r.orig_rid))
 
+    def test_main(self):
+        test_dir = "functional_tests/test_concat_gctoo/test_main"
+
+        g_a = pg.parse(os.path.join(test_dir, "a.gct"))
+        logger.debug("g_a:  {}".format(g_a))
+        g_b = pg.parse(os.path.join(test_dir, "b.gct"))
+        logger.debug("g_b:  {}".format(g_b))
+
+        save_build_parser = cg.build_parser
+
+        class MockParser:
+            def __init__(self, args):
+                self.args = args
+            def parse_args(self, unused):
+                return self.args
+
+        #unhappy path - write out error report file
+        expected_output_file = tempfile.mkstemp()[1]
+        logger.debug("unhappy path - write out error report file - expected_output_file:  {}".format(expected_output_file))
+
+        args = save_build_parser().parse_args(["-d", "horiz", "-if", g_a.src, g_b.src, "-o", "should_not_be_used",
+                                             "-ot", "gct", "-erof", expected_output_file])
+        logger.debug("args:  {}".format(args))
+
+        my_mock_parser = MockParser(args)
+        cg.build_parser = lambda: my_mock_parser
+
+        with self.assertRaises(cg.MismatchCommonMetadataConcatGctooException) as context:
+            cg.main()
+
+        self.assertTrue(os.path.exists(expected_output_file))
+        report_df = pd.read_csv(expected_output_file, sep="\t")
+        logger.debug("report_df:\n{}".format(report_df))
+        self.assertEqual(2, report_df.shape[0])
+
+        os.remove(expected_output_file)
+
+        print
+        print
+        print
+
+        #happy path
+        args.remove_all_metadata_fields = True
+        args.error_report_output_file = None
+
+        expected_output_file = tempfile.mkstemp(suffix=".gct")[1]
+        logger.debug("happy path - expected_output_file:  {}".format(expected_output_file))
+        args.out_name = expected_output_file
+
+        my_mock_parser = MockParser(args)
+        cg.buid_parser = lambda: my_mock_parser
+
+        cg.main()
+        self.assertTrue(os.path.exists(expected_output_file))
+
+        r = pg.parse(expected_output_file)
+        logger.debug("happy path -r:\n{}".format(r))
+        logger.debug("r.data_df:\n{}".format(r.data_df))
+
+        self.assertEqual((2,4), r.data_df.shape)
+        self.assertEqual({"a", "b", "g", "f"}, set(r.data_df.columns))
+        self.assertEqual({"rid1", "rid2"}, set(r.data_df.index))
+
+        #cleanup
+        os.remove(expected_output_file)
+
+        cg.build_parser = save_build_parser
+
 
 if __name__ == "__main__":
     setup_logger.setup(verbose=True)