added tests for parse module

Author: oena

cmapPy/pandasGEXpress/parse.py

@@ -58,8 +58,9 @@ def parse(file_path, convert_neg_666=True, rid=None, cid=None, ridx=None, cidx=N
         # Ignoring arguments that won't be passed to parse_gct
         for unused_arg in ["rid", "cid", "ridx", "cidx"]:
             if eval(unused_arg):
-                msg = "parse_gct does not use the argument {}. Ignoring it...".format(unused_arg)
-                logger.warning(msg)
+                err_msg = "parse_gct does not use the argument {}. Ignoring it...".format(unused_arg)
+                logger.error(err_msg)
+                raise Exception(err_msg)
         curr = parse_gct.parse(file_path, convert_neg_666, row_meta_only, col_meta_only, make_multiindex)
     elif file_path.endswith(".gctx"):
         curr = parse_gctx.parse(file_path, convert_neg_666, rid, cid, ridx, cidx, row_meta_only, col_meta_only,

cmapPy/pandasGEXpress/tests/test_parse.py

@@ -3,19 +3,110 @@
 import logging
 from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
 import unittest
+import pandas as pd 
 import pandas.util.testing as pandas_testing
+from cmapPy.pandasGEXpress import parse 
+from cmapPy.pandasGEXpress import mini_gctoo_for_testing as mini_gctoo_for_testing
+from cmapPy.pandasGEXpress import slice_gct as slice_gct
+
 from cmapPy.pandasGEXpress import GCToo as GCToo 
 from cmapPy.pandasGEXpress import parse_gctx as parse_gctx
 from cmapPy.pandasGEXpress import mini_gctoo_for_testing as mini_gctoo_for_testing
 
 __author__ = "Oana Enache"
 __email__ = "[email protected]"
 
+FUNCTIONAL_TESTS_PATH = "functional_tests"
+
 logger = logging.getLogger(setup_logger.LOGGER_NAME)
 
 class TestParse(unittest.TestCase):
-	def test_gctx_parsing(self):
-		pass
+    def test_gctx_parsing(self):
+        # parse in gctx, no other arguments        
+        mg1 = mini_gctoo_for_testing.make()
+        mg2 = parse("functional_tests/mini_gctoo_for_testing.gctx")
+
+        pandas_testing.assert_frame_equal(mg1.data_df, mg2.data_df)
+        pandas_testing.assert_frame_equal(mg1.row_metadata_df, mg2.row_metadata_df)
+        pandas_testing.assert_frame_equal(mg1.col_metadata_df, mg2.col_metadata_df) 
+
+        # check convert_neg_666 worked correctly
+        self.assertTrue(mg2.col_metadata_df["mfc_plate_id"].isnull().all())
+
+        # parse w/o convert_neg_666
+        mg2_alt = parse("functional_tests/mini_gctoo_for_testing.gctx", convert_neg_666 = False)
+        self.assertFalse(mg2_alt.col_metadata_df["mfc_plate_id"].isnull().all())        
+
+        # parsing w/rids & cids specified 
+        test_rids = ['LJP007_MCF10A_24H:TRT_CP:BRD-K93918653:3.33', 'LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666']
+        test_cids = ['LJP007_MCF7_24H:TRT_POSCON:BRD-A61304759:10']
+        mg3 = slice_gct.slice_gctoo(mg1, rid=test_rids, cid=test_cids)
+        mg4 = parse("functional_tests/mini_gctoo_for_testing.gctx",
+                               rid=test_rids, cid=test_cids)
+        pandas_testing.assert_frame_equal(mg3.data_df, mg4.data_df)
+        pandas_testing.assert_frame_equal(mg3.row_metadata_df, mg4.row_metadata_df)
+        pandas_testing.assert_frame_equal(mg3.col_metadata_df, mg4.col_metadata_df)
+
+        # parsing w/ridx & cidx specified 
+        mg5 = slice_gct.slice_gctoo(mg1, rid=['LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'],
+                                    cid='LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666')
+        mg6 = parse("functional_tests/mini_gctoo_for_testing.gctx", ridx=[4], cidx=[4])
+
+        pandas_testing.assert_frame_equal(mg5.data_df, mg6.data_df)
+        pandas_testing.assert_frame_equal(mg5.row_metadata_df, mg6.row_metadata_df)
+        pandas_testing.assert_frame_equal(mg5.col_metadata_df, mg6.col_metadata_df)
+
+        # parsing row metadata only
+        mg7 = parse("functional_tests/mini_gctoo_for_testing.gctx", row_meta_only=True)
+        pandas_testing.assert_frame_equal(mg7, mg1.row_metadata_df)
+
+        # parsing col metadata only
+        mg8 = parse("functional_tests/mini_gctoo_for_testing.gctx", col_meta_only=True)
+        pandas_testing.assert_frame_equal(mg8, mg1.col_metadata_df)
+
+        # parsing w/multiindex
+        mg9 = parse("functional_tests/mini_gctoo_for_testing.gctx", make_multiindex=True)
+        self.assertTrue(mg9.multi_index_df is not None)
+
+    def test_gct_parsing(self):
+        # parse in gct, no other arguments
+        mg1 = mini_gctoo_for_testing.make()
+        mg2 = parse("functional_tests/mini_gctoo_for_testing.gct")
+
+        pandas_testing.assert_frame_equal(mg1.data_df, mg2.data_df)
+        pandas_testing.assert_frame_equal(mg1.row_metadata_df, mg2.row_metadata_df)
+        pandas_testing.assert_frame_equal(mg1.col_metadata_df, mg2.col_metadata_df) 
+
+        # check convert_neg_666 worked correctly
+        self.assertTrue(mg2.col_metadata_df["mfc_plate_id"].isnull().all())
+
+        # parse w/o convert_neg_666
+        mg2_alt = parse("functional_tests/mini_gctoo_for_testing.gct", convert_neg_666 = False)
+        self.assertFalse(mg2_alt.col_metadata_df["mfc_plate_id"].isnull().all())        
+
+        # check unused rid argument handling
+        with self.assertRaises(Exception) as context:
+            mg3 = parse("functional_tests/mini_gctoo_for_testing.gct", rid=["a"])
+        self.assertTrue("parse_gct does not use the argument" in str(context.exception))
+
+        # check unused cid argument handling 
+        with self.assertRaises(Exception) as context:
+            mg4 = parse("functional_tests/mini_gctoo_for_testing.gct", cid=["a"])
+        self.assertTrue("parse_gct does not use the argument" in str(context.exception))        
+
+        # check unused ridx argument handling
+        with self.assertRaises(Exception) as context:
+            mg5 = parse("functional_tests/mini_gctoo_for_testing.gct", ridx=[0])
+        self.assertTrue("parse_gct does not use the argument" in str(context.exception))
+
+        # check unused cidx argument handling 
+        with self.assertRaises(Exception) as context:
+            mg6 = parse("functional_tests/mini_gctoo_for_testing.gct", cidx=[0])
+        self.assertTrue("parse_gct does not use the argument" in str(context.exception))
+
+if __name__ == "__main__":
+    setup_logger.setup(verbose=True)
+    unittest.main()
+
+
 
-	def test_gct_parsing(self):
-		pass