Merge pull request #21 from cmap/testing_travis

oena · web-flow · commit fef095f0bbb9 · 2018-01-09T13:47:13.000-05:00
Import statement changes, bug fixes, more tests. Note: Python 3 issues remain for pandasGEXpress tests.
diff --git a/cmapPy/__init__.py b/cmapPy/__init__.py
@@ -1,3 +0,0 @@
-from .clue_api_client import *
-from .pandasGEXpress import *
-from .set_io import *
diff --git a/cmapPy/clue_api_client/cell_queries.py b/cmapPy/clue_api_client/cell_queries.py
@@ -1,5 +1,7 @@
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_logger
+from cmapPy.clue_api_client import setup_logger
 
 __authors__ = "David L. Lahr"
 __email__ = "dlahr@broadinstitute.org"
diff --git a/cmapPy/clue_api_client/clue_api_client.py b/cmapPy/clue_api_client/clue_api_client.py
@@ -1,6 +1,8 @@
+import sys
+sys.path.insert(0, "../..")
 import requests
 import logging
-from . import setup_logger
+from cmapPy.clue_api_client import setup_logger
 import json
 import copy
 
diff --git a/cmapPy/clue_api_client/gene_queries.py b/cmapPy/clue_api_client/gene_queries.py
@@ -1,5 +1,7 @@
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_logger
+from cmapPy.pandasGEXpress import setup_logger
 
 __authors__ = "David L. Lahr"
 __email__ = "dlahr@broadinstitute.org"
diff --git a/cmapPy/clue_api_client/macchiato_queries.py b/cmapPy/clue_api_client/macchiato_queries.py
@@ -1,5 +1,7 @@
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_logger
+from cmapPy.clue_api_client import setup_logger
 
 __authors__ = "David L. Lahr"
 __email__ = "dlahr@broadinstitute.org"
diff --git a/cmapPy/clue_api_client/mock_clue_api_client.py b/cmapPy/clue_api_client/mock_clue_api_client.py
@@ -1,6 +1,8 @@
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_logger
-from . import clue_api_client
+from cmapPy.clue_api_client import setup_logger
+from cmapPy.clue_api_client import clue_api_client
 
 __authors__ = "David L. Lahr"
 __email__ = "dlahr@broadinstitute.org"
diff --git a/cmapPy/clue_api_client/pert_queries.py b/cmapPy/clue_api_client/pert_queries.py
@@ -1,5 +1,7 @@
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_logger
+from cmapPy.clue_api_client import setup_logger
 
 __authors__ = "David L. Lahr"
 __email__ = "dlahr@broadinstitute.org"
diff --git a/cmapPy/clue_api_client/tests/test_cell_queries.py b/cmapPy/clue_api_client/tests/test_cell_queries.py
@@ -1,3 +1,5 @@
+import sys
+sys.path.insert(0, "../../../")
 import unittest
 from cmapPy.clue_api_client import setup_logger as setup_logger
 import logging
diff --git a/cmapPy/clue_api_client/tests/test_clue_api_client.py b/cmapPy/clue_api_client/tests/test_clue_api_client.py
@@ -1,3 +1,5 @@
+import sys
+sys.path.insert(0, "../../../")
 import unittest
 from cmapPy.clue_api_client import setup_logger as setup_logger
 import logging
diff --git a/cmapPy/clue_api_client/tests/test_genes_queries.py b/cmapPy/clue_api_client/tests/test_genes_queries.py
@@ -1,3 +1,5 @@
+import sys
+sys.path.insert(0, "../../../")
 import unittest
 from cmapPy.clue_api_client import  setup_logger as setup_logger
 import logging
diff --git a/cmapPy/clue_api_client/tests/test_macchiato_queries.py b/cmapPy/clue_api_client/tests/test_macchiato_queries.py
@@ -1,3 +1,5 @@
+import sys
+sys.path.insert(0, "../../../")
 import unittest
 from cmapPy.clue_api_client import setup_logger
 import logging
diff --git a/cmapPy/clue_api_client/tests/test_mock_clue_api_client.py b/cmapPy/clue_api_client/tests/test_mock_clue_api_client.py
@@ -1,3 +1,5 @@
+import sys
+sys.path.insert(0, "../../../")
 import unittest
 from cmapPy.clue_api_client import setup_logger as setup_logger 
 import logging
diff --git a/cmapPy/clue_api_client/tests/test_pert_queries.py b/cmapPy/clue_api_client/tests/test_pert_queries.py
@@ -1,3 +1,5 @@
+import sys
+sys.path.insert(0, "../../../")
 import unittest
 from cmapPy.clue_api_client import setup_logger as setup_logger
 import logging
diff --git a/cmapPy/pandasGEXpress/GCToo.py b/cmapPy/pandasGEXpress/GCToo.py
@@ -39,10 +39,12 @@
 - unique
 - matching in both content & order everywhere they're found
 """
+import sys
+sys.path.insert(0, "../..")
 import numpy as np
 import pandas as pd
 import logging
-from . import setup_GCToo_logger as setup_logger
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
 
 
 __authors__ = 'Oana Enache, Lev Litichevskiy, Dave Lahr'
diff --git a/cmapPy/pandasGEXpress/__init__.py b/cmapPy/pandasGEXpress/__init__.py
@@ -1 +1,3 @@
-from cmapPy.pandasGEXpress.parse import parse
+import sys
+sys.path.insert(0, "../..")
+from cmapPy.pandasGEXpress.parse import parse as parse
diff --git a/cmapPy/pandasGEXpress/concat_gctoo.py b/cmapPy/pandasGEXpress/concat_gctoo.py
@@ -30,6 +30,8 @@
 N.B. This script sorts everything!
 
 """
+import sys
+sys.path.insert(0, "../..")
 
 import argparse
 import os
@@ -41,11 +43,11 @@
 import pandas as pd
 from six.moves import range
 
-from . import GCToo
-from . import parse
-from . import setup_GCToo_logger as setup_logger
-from . import write_gct
-from . import write_gctx
+from cmapPy.pandasGEXpress import GCToo
+from cmapPy.pandasGEXpress import parse
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
+from cmapPy.pandasGEXpress import write_gct
+from cmapPy.pandasGEXpress import write_gctx
 
 __author__ = "Lev Litichevskiy"
 __email__ = "lev@broadinstitute.org"
@@ -126,7 +128,7 @@ def main():
         # Parse each file and append to a list
         gctoos = []
         for f in files:
-            gctoos.append(parse.parse(f))
+            gctoos.append(parse(f))
 
         # Create concatenated gctoo object
         if args.concat_direction == "horiz":
diff --git a/cmapPy/pandasGEXpress/gct2gctx.py b/cmapPy/pandasGEXpress/gct2gctx.py
@@ -7,13 +7,13 @@
 
 Note: Only supports v1.3 .gct files. 
 """
-
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_GCToo_logger as setup_logger
 import argparse
-import sys
-from . import parse_gct
-from . import write_gctx
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
+from cmapPy.pandasGEXpress import parse_gct
+from cmapPy.pandasGEXpress import write_gctx
 
 __author__ = "Oana Enache"
 __email__ = "oana@broadinstitute.org"
diff --git a/cmapPy/pandasGEXpress/gctx2gct.py b/cmapPy/pandasGEXpress/gctx2gct.py
@@ -7,14 +7,12 @@
 
 Note: Only supports v1.0 .gctx files. 
 """
-
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_GCToo_logger as setup_logger
 import argparse
-import sys
-from . import parse_gctx
-from . import write_gct
 import os.path
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger, parse_gctx, write_gct
 
 __author__ = "Oana Enache"
 __email__ = "oana@broadinstitute.org"
diff --git a/cmapPy/pandasGEXpress/mini_gctoo_for_testing.py b/cmapPy/pandasGEXpress/mini_gctoo_for_testing.py
@@ -5,12 +5,12 @@
     import mini_gctoo_for testing
     my_mini_gctoo = mini_gctoo_for_testing.make()
 """
-
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_GCToo_logger as setup_logger
 import pandas
 import numpy
-from . import GCToo
+from cmapPy.pandasGEXpress import GCToo, setup_GCToo_logger as setup_logger
 
 __author__ = 'Oana Enache'
 __email__ = 'oana@broadinstitute.org'
diff --git a/cmapPy/pandasGEXpress/parse.py b/cmapPy/pandasGEXpress/parse.py
@@ -6,11 +6,12 @@
 
 Note: Supports GCT1.2, GCT1.3, and GCTX1.0 files. 
 """
-
+import sys
+sys.path.insert(0, "../../")
 import logging
-from . import setup_GCToo_logger as setup_logger
-from . import parse_gct
-from . import parse_gctx
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
+from cmapPy.pandasGEXpress import parse_gct as parse_gct
+from cmapPy.pandasGEXpress import parse_gctx as parse_gctx
 
 __author__ = "Oana Enache"
 __email__ = "oana@broadinstitute.org"
@@ -52,10 +53,11 @@ def parse(file_path, convert_neg_666=True, rid=None, cid=None, ridx=None, cidx=N
     """
     if file_path.endswith(".gct"):
         # Ignoring arguments that won't be passed to parse_gct
-        for unused_arg in ["rid", "cid", "cidx"]:
+        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,
diff --git a/cmapPy/pandasGEXpress/parse_gct.py b/cmapPy/pandasGEXpress/parse_gct.py
@@ -58,13 +58,13 @@
                 -36 = number of data columns   
 
 """
-
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_GCToo_logger as setup_logger
 import pandas as pd
 import numpy as np
 import os.path
-from . import GCToo
+from cmapPy.pandasGEXpress import GCToo, setup_GCToo_logger as setup_logger
 
 __author__ = "Lev Litichevskiy, Oana Enache"
 __email__ = "lev@broadinstitute.org"
diff --git a/cmapPy/pandasGEXpress/parse_gctx.py b/cmapPy/pandasGEXpress/parse_gctx.py
@@ -1,10 +1,12 @@
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_GCToo_logger as setup_logger
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
 import os
 import numpy as np
 import pandas as pd
 import h5py
-from . import GCToo
+from cmapPy.pandasGEXpress import GCToo as GCToo
 
 __author__ = "Oana Enache"
 __email__ = "oana@broadinstitute.org"
diff --git a/cmapPy/pandasGEXpress/random_slice.py b/cmapPy/pandasGEXpress/random_slice.py
@@ -1,10 +1,11 @@
 """
 Slices a random subset of a GCToo instance of a user-specified size. 
 """
+import sys
+sys.path.insert(0, "../..")
 import logging
-from . import setup_GCToo_logger as setup_logger
 import numpy
-from . import GCToo
+from cmapPy.pandasGEXpress import GCToo, setup_GCToo_logger as setup_logger
 
 __author__ = "Oana Enache"
 __email__ = "oana@broadinstitute.org"
diff --git a/cmapPy/pandasGEXpress/slice_gct.py b/cmapPy/pandasGEXpress/slice_gct.py
@@ -6,18 +6,18 @@
 slice method in Python, ids or boolean arrays can be used.
 
 """
-
+import sys
+sys.path.insert(0, "../..")
 import logging
 import sys
 import os
 import argparse
 import pandas as pd
 import re
-
-from . import setup_GCToo_logger as setup_logger
-from . import GCToo
-from . import parse_gct as pg
-from . import write_gct as wg
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
+from cmapPy.pandasGEXpress import GCToo
+from cmapPy.pandasGEXpress import parse_gct as pg
+from cmapPy.pandasGEXpress import write_gct as wg
 
 __author__ = "Lev Litichevskiy"
 __email__ = "lev@broadinstitute.org"
diff --git a/cmapPy/pandasGEXpress/tests/functional_tests/mini_gctoo_for_testing.gct b/cmapPy/pandasGEXpress/tests/functional_tests/mini_gctoo_for_testing.gct
@@ -0,0 +1,14 @@
+#1.3
+6	6	5	5
+id	count_cv	distil_nsample	distil_ss	mfc_plate_id	zmad_ref	LJP007_MCF10A_24H:TRT_CP:BRD-K93918653:3.33	MISC003_A375_24H:TRT_CP:BRD-K93918653:3.33	LJP007_MCF7_24H:TRT_POSCON:BRD-K81418486:10	LJP007_MCF7_24H:TRT_POSCON:BRD-A61304759:10	LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666	LJP007_MCF7_24H:TRT_CP:BRD-K64857848:10
+count_cv	-666	-666	-666	-666	-666	14|15|14	13|14|13	13|15|14|14|15|14|14|13|14|15|15|14|14|15|14|15|14|14|15|14|15|14|14|14|14|14|14|15|14|14|15|14|14|14|14|13|14|14|14|14|14|14|15|14|13|13|15|14|14|15|14|14|14|15|13|13|15|13|14|13|13|14|14|14|14|13	13	13	14
+distil_nsample	-666	-666	-666	-666	-666	3	3	66	2	9	111111
+distil_ss	-666	-666	-666	-666	-666	9.822065353	6.8915205	1.35840559	5.548898697	3.355231762	4.837643147
+mfc_plate_id	-666	-666	-666	-666	-666	-666	-666	-666	-666	-666	-666
+zmad_ref	-666	-666	-666	-666	-666	population	population	population	population	population	population
+LJP007_MCF10A_24H:TRT_CP:BRD-K93918653:3.33	14|15|14	3	9.822065353	-666	population	1.0	2.0	3.0	4.0	5.0	6.0
+MISC003_A375_24H:TRT_CP:BRD-K93918653:3.33	13|14|13	3	6.8915205	-666	population	4.300000190734863	4.5	4.300000190734863	4.300000190734863	4.300000190734863	4.300000190734863
+LJP007_MCF7_24H:TRT_POSCON:BRD-K81418486:10	13|15|14|14|15|14|14|13|14|15|15|14|14|15|14|15|14|14|15|14|15|14|14|14|14|14|14|15|14|14|15|14|14|14|14|13|14|14|14|14|14|14|15|14|13|13|15|14|14|15|14|14|14|15|13|13|15|13|14|13|13|14|14|14|14|13	66	1.35840559	-666	population	7.0	8.0	9.0	0.0	1.234760046005249	9.758319854736328
+LJP007_MCF7_24H:TRT_POSCON:BRD-A61304759:10	13	2	5.548898697	-666	population	0.10999999940395355	3.3456356525421143	2.3456668853759766	9.822065353393555	4.788650989532471	4.788599967956543
+LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666	13	9	3.355231762	-666	population	-0.10999999940395355	-3.3456356525421143	-2.3456668853759766	-9.822065353393555	-4.788650989532471	-4.788599967956543
+LJP007_MCF7_24H:TRT_CP:BRD-K64857848:10	14	111111	4.837643147	-666	population	1.0	-2.0	3.0	-4.0	5.0	-6.0
diff --git a/cmapPy/pandasGEXpress/tests/test_GCToo.py b/cmapPy/pandasGEXpress/tests/test_GCToo.py
@@ -1,9 +1,10 @@
+import sys
+sys.path.insert(0, "../../..")
 import unittest
 import pandas as pd
 import logging
-import cmapPy.pandasGEXpress.setup_GCToo_logger as setup_GCToo_logger
-import cmapPy.pandasGEXpress.GCToo as GCToo
-
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_GCToo_logger
+from cmapPy.pandasGEXpress import GCToo as GCToo
 
 logger = logging.getLogger(setup_GCToo_logger.LOGGER_NAME)
 
diff --git a/cmapPy/pandasGEXpress/tests/test_concat_gctoo.py b/cmapPy/pandasGEXpress/tests/test_concat_gctoo.py
@@ -1,13 +1,15 @@
 from __future__ import print_function
 
+import sys
+sys.path.insert(0, "../../../")
 import os
 import unittest
 import logging
 import numpy as np
 import pandas as pd
-import cmapPy.pandasGEXpress.setup_GCToo_logger as setup_logger
-import cmapPy.pandasGEXpress.concat_gctoo as cg
-import cmapPy.pandasGEXpress.parse_gct as pg
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
+from cmapPy.pandasGEXpress import concat_gctoo as cg
+from cmapPy.pandasGEXpress import parse_gct as pg
 import tempfile
 
 
diff --git a/cmapPy/pandasGEXpress/tests/test_edge_cases.py b/cmapPy/pandasGEXpress/tests/test_edge_cases.py
@@ -2,12 +2,13 @@
 Functional tests comparing gct vs gctx parsing for equivalent file content 
 (stored in gct/text vs gctx/hdf5 format)
 """
-
+import sys
+sys.path.insert(0, "../../..")
 import unittest
 import logging
-import cmapPy.pandasGEXpress.setup_GCToo_logger as setup_logger
-import cmapPy.pandasGEXpress.parse_gct as parse_gct
-import cmapPy.pandasGEXpress.parse_gctx as parse_gctx
+from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
+from cmapPy.pandasGEXpress import parse_gct as parse_gct
+from cmapPy.pandasGEXpress import parse_gctx as parse_gctx
 import pandas.util.testing as pandas_testing
 
 
diff --git a/cmapPy/pandasGEXpress/tests/test_parse.py b/cmapPy/pandasGEXpress/tests/test_parse.py
diff --git a/cmapPy/pandasGEXpress/tests/test_parse_gct.py b/cmapPy/pandasGEXpress/tests/test_parse_gct.py
diff --git a/cmapPy/pandasGEXpress/tests/test_parse_gctx.py b/cmapPy/pandasGEXpress/tests/test_parse_gctx.py
diff --git a/cmapPy/pandasGEXpress/tests/test_random_slice.py b/cmapPy/pandasGEXpress/tests/test_random_slice.py
diff --git a/cmapPy/pandasGEXpress/tests/test_slice_gct.py b/cmapPy/pandasGEXpress/tests/test_slice_gct.py
diff --git a/cmapPy/pandasGEXpress/tests/test_write_gct.py b/cmapPy/pandasGEXpress/tests/test_write_gct.py
diff --git a/cmapPy/pandasGEXpress/tests/test_write_gctx.py b/cmapPy/pandasGEXpress/tests/test_write_gctx.py
diff --git a/cmapPy/pandasGEXpress/write_gct.py b/cmapPy/pandasGEXpress/write_gct.py
diff --git a/cmapPy/pandasGEXpress/write_gctx.py b/cmapPy/pandasGEXpress/write_gctx.py
diff --git a/cmapPy/set_io/tests/test_gmt.py b/cmapPy/set_io/tests/test_gmt.py
diff --git a/cmapPy/set_io/tests/test_grp.py b/cmapPy/set_io/tests/test_grp.py
diff --git a/requirements.txt b/requirements.txt

Original file line number	Diff line number	Diff line change
`@@ -1,3 +0,0 @@`
`1`		`-from .clue_api_client import *`
`2`		`-from .pandasGEXpress import *`
`3`		`-from .set_io import *`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+import sys`
	`2`	`+sys.path.insert(0, "../../../")`
`1`	`3`	`import unittest`
`2`	`4`	`from cmapPy.clue_api_client import setup_logger as setup_logger`
`3`	`5`	`import logging`