def test_parse_data_df(self):
mini_data_df = pd.DataFrame(
[[-0.283359, 0.011270], [0.304119, 1.921061],
[0.398655, -0.144652]],
index=["200814_at", "218597_s_at", "217140_s_at"],
columns=[
"LJP005_A375_24H:DMSO:-666", "LJP005_A375_24H:BRD-K76908866:10"
])
mini_data_df = mini_data_df.astype(np.float32)
mini_data_df.index.name = "rid"
mini_data_df.columns.name = "cid"
# create h5py File instance
mini_gctx = h5py.File(
"cmapPy/pandasGEXpress/tests/functional_tests//mini_gctx_with_metadata_n2x3.gctx",
"r")
data_dset = mini_gctx[data_node]
# get relevant metadata fields
col_meta = parse_gctx.get_column_metadata(
"cmapPy/pandasGEXpress/tests/functional_tests//mini_gctx_with_metadata_n2x3.gctx"
)
row_meta = parse_gctx.get_row_metadata(
"cmapPy/pandasGEXpress/tests/functional_tests//mini_gctx_with_metadata_n2x3.gctx"
)
# case 1: no subsetting
data_df1 = parse_gctx.parse_data_df(data_dset, [0, 1, 2], [0, 1],
row_meta, col_meta)
# note: checks to 3 decimal places
pandas_testing.assert_frame_equal(mini_data_df,
data_df1,
check_exact=False,
check_less_precise=True)
# case 2: subset; ridx < cidx
data_df2 = parse_gctx.parse_data_df(data_dset, [0], [0, 1], row_meta,
col_meta)
pandas_testing.assert_frame_equal(mini_data_df.iloc[[0], [0, 1]],
data_df2,
check_exact=False,
check_less_precise=True)
# case 3: subset; ridx == cidx
data_df3 = parse_gctx.parse_data_df(data_dset, [0], [0], row_meta,
col_meta)
pandas_testing.assert_frame_equal(mini_data_df.iloc[[0], [0]],
data_df3,
check_exact=False,
check_less_precise=True)
# case 4: subset; ridx > cidx
data_df4 = parse_gctx.parse_data_df(data_dset, [0, 1, 2], [0],
row_meta, col_meta)
pandas_testing.assert_frame_equal(mini_data_df.iloc[[0, 1, 2], [0]],
data_df4,
check_exact=False,
check_less_precise=True)
mini_gctx.close()
def test_write_metadata(self):
"""
CASE 1:
- write metadata (has '-666') to file, do not convert -666
- parse in written metadata, don't convert -666
"""
mini_gctoo = mini_gctoo_for_testing.make(convert_neg_666=False)
hdf5_writer = h5py.File(FUNCTIONAL_TESTS_PATH + "/mini_gctoo_metadata.gctx", "w")
write_gctx.write_metadata(hdf5_writer, "row", mini_gctoo.row_metadata_df, False, 6)
write_gctx.write_metadata(hdf5_writer, "col", mini_gctoo.col_metadata_df, False, 6)
hdf5_writer.close()
logger.debug("Wrote mini_gctoo_metadata.gctx to {}".format(
os.path.join(FUNCTIONAL_TESTS_PATH, "mini_gctoo_metadata.gctx")))
# read in written metadata, then close and delete file
mini_gctoo_col_metadata = parse_gctx.get_column_metadata(FUNCTIONAL_TESTS_PATH + "/mini_gctoo_metadata.gctx",
convert_neg_666=False)
mini_gctoo_row_metadata = parse_gctx.get_row_metadata(FUNCTIONAL_TESTS_PATH + "/mini_gctoo_metadata.gctx",
convert_neg_666=False)
os.remove(FUNCTIONAL_TESTS_PATH + "/mini_gctoo_metadata.gctx")
# check row metadata
self.assertTrue(set(mini_gctoo.row_metadata_df.columns) == set(mini_gctoo_row_metadata.columns),
"Mismatch between expected row metadata columns {} and column values written to file: {}".format(
mini_gctoo.row_metadata_df.columns, mini_gctoo_row_metadata.columns))
self.assertTrue(set(mini_gctoo.row_metadata_df.index) == set(mini_gctoo.col_metadata_df.index),
"Mismatch between expect row metadata index {} and index values written to file: {}".format(
mini_gctoo.row_metadata_df.index, mini_gctoo_row_metadata.index))
for c in list(mini_gctoo.row_metadata_df.columns):
logger.debug("C1: For column name: {}".format(c))
logger.debug("C1: populated values: {}".format(set(mini_gctoo_row_metadata[c])))
logger.debug("C1: mini_gctoo values: {}".format(set(mini_gctoo.row_metadata_df[c])))
self.assertTrue(set(mini_gctoo.row_metadata_df[c]) == set(mini_gctoo_row_metadata[c]),
"Values in column {} differ between expected metadata and written row metadata: {} vs {}".format(
c, set(mini_gctoo.row_metadata_df[c]), set(mini_gctoo_row_metadata[c])))
# check col metadata
self.assertTrue(set(mini_gctoo.col_metadata_df.columns) == set(mini_gctoo_col_metadata.columns),
"Mismatch between expected col metadata columns {} and column values written to file: {}".format(
mini_gctoo.col_metadata_df.columns, mini_gctoo_col_metadata.columns))
self.assertTrue(set(mini_gctoo.col_metadata_df.index) == set(mini_gctoo.col_metadata_df.index),
"Mismatch between expect col metadata index {} and index values written to file: {}".format(
mini_gctoo.col_metadata_df.index, mini_gctoo_col_metadata.index))
for c in list(mini_gctoo.col_metadata_df.columns):
self.assertTrue(set(mini_gctoo.col_metadata_df[c]) == set(mini_gctoo_col_metadata[c]),
"Values in column {} differ between expected metadata and written col metadata!".format(c))
"""
CASE 2:
- write metadata (has NaN, not '-666') to file, do convert NaN back to '-666'
- parse in written metadata, don't convert -666
"""
# first convert mini_gctoo's row & col metadata dfs -666s to NaN
converted_row_metadata = mini_gctoo.row_metadata_df.replace([-666, "-666", -666.0],
[numpy.nan, numpy.nan, numpy.nan])
logger.debug("First row of converted_row_metadata: {}".format(converted_row_metadata.iloc[0]))
converted_col_metadata = mini_gctoo.col_metadata_df.replace([-666, "-666", -666.0],
[numpy.nan, numpy.nan, numpy.nan])
# write row and col metadata fields from mini_gctoo_for_testing instance to file
# Note this time does convert back to -666
hdf5_writer = h5py.File(FUNCTIONAL_TESTS_PATH + "/mini_gctoo_metadata.gctx", "w")
write_gctx.write_metadata(hdf5_writer, "row", converted_row_metadata, True, 6)
write_gctx.write_metadata(hdf5_writer, "col", converted_col_metadata, True, 6)
hdf5_writer.close()
# read in written metadata, then close and delete file
mini_gctoo_col_metadata = parse_gctx.get_column_metadata(FUNCTIONAL_TESTS_PATH + "/mini_gctoo_metadata.gctx",
convert_neg_666=False)
mini_gctoo_row_metadata = parse_gctx.get_row_metadata(FUNCTIONAL_TESTS_PATH + "/mini_gctoo_metadata.gctx",
convert_neg_666=False)
os.remove(FUNCTIONAL_TESTS_PATH + "/mini_gctoo_metadata.gctx")
# check row metadata
self.assertTrue(set(mini_gctoo.row_metadata_df.columns) == set(mini_gctoo_row_metadata.columns),
"Mismatch between expected row metadata columns {} and column values written to file: {}".format(
mini_gctoo.row_metadata_df.columns, mini_gctoo_row_metadata.columns))
self.assertTrue(set(mini_gctoo.row_metadata_df.index) == set(mini_gctoo.col_metadata_df.index),
"Mismatch between expect row metadata index {} and index values written to file: {}".format(
mini_gctoo.row_metadata_df.index, mini_gctoo_row_metadata.index))
for c in list(mini_gctoo.row_metadata_df.columns):
logger.debug("C2: For column name: {}".format(c))
logger.debug("C2: populated values: {}".format(set(mini_gctoo_row_metadata[c])))
logger.debug("C2: mini_gctoo values: {}".format(set(mini_gctoo.row_metadata_df[c])))
self.assertTrue(set(mini_gctoo.row_metadata_df[c]) == set(mini_gctoo_row_metadata[c]),
"Values in column {} differ between expected metadata and written row metadata!".format(c))
# check col metadata
self.assertTrue(set(mini_gctoo.col_metadata_df.columns) == set(mini_gctoo_col_metadata.columns),
"Mismatch between expected col metadata columns {} and column values written to file: {}".format(
mini_gctoo.col_metadata_df.columns, mini_gctoo_col_metadata.columns))
self.assertTrue(set(mini_gctoo.col_metadata_df.index) == set(mini_gctoo.col_metadata_df.index),
"Mismatch between expect col metadata index {} and index values written to file: {}".format(
mini_gctoo.col_metadata_df.index, mini_gctoo_col_metadata.index))
for c in list(mini_gctoo.col_metadata_df.columns):
self.assertTrue(set(mini_gctoo.col_metadata_df[c]) == set(mini_gctoo_col_metadata[c]),
"Values in column {} differ between expected metadata and written col metadata!".format(c))