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summarize_networks InvalidIndexError #191

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summarize_networks InvalidIndexError #191

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849ebc4
add repeat edge in pathway.txt test
ntalluri Oct 25, 2024
f55855a
fix InvalidIndexError
ntalluri Oct 25, 2024
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1 change: 1 addition & 0 deletions spras/analysis/ml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@ def summarize_networks(file_paths: Iterable[Union[str, PathLike]]) -> pd.DataFra
str(tup[0]): 1,
}, index=tup[1]
)
dataframe = dataframe[~dataframe.index.duplicated(keep='first')]
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https://pandas.pydata.org/docs/reference/api/pandas.Index.duplicated.html

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Suggested change
dataframe = dataframe[~dataframe.index.duplicated(keep='first')]
# Mark the first occurrence of a duplicate as True and all others as False
# Non-duplicates are also marked as True
dataframe = dataframe[~dataframe.index.duplicated(keep='first')]

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add a warning that edges are being dropped from a file

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If this is hard to do here, we can think about whether it should be handled somewhere else. For instance, should the parse_output functions check for duplicate edges and raise a warning or error?

edge_dataframes.append(dataframe)

# concatenating all the algorithm-specific dataframes together
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32 changes: 16 additions & 16 deletions test/ml/expected/expected-dataframe.csv
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Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
,test-data-s1,test-data-s2,test-data-s3,test-data-longName,test-data-longName2,test-data-empty,test-data-spaces,test-data-mixed-direction
A---B,1,1,0,0,0,0,0,0
C---D,1,1,0,0,0,0,0,1
E---F,1,1,0,0,0,0,0,1
L---M,0,1,1,0,0,0,1,0
M---N,0,0,1,0,0,0,0,0
O---P,0,0,1,0,0,0,1,0
P---Q,0,0,1,0,0,0,0,0
node1---node2,0,0,0,1,0,0,0,0
node1---node3,0,0,0,1,1,0,0,0
node4---node5,0,0,0,1,1,0,0,0
LONGERNAMES---TEST,0,0,0,1,1,0,0,0
node2---node3,0,0,0,0,1,0,0,0
nodes with---spaces in name,0,0,0,0,0,0,1,0
A-->B,0,0,0,0,0,0,0,1
B-->A,0,0,0,0,0,0,0,1
,test-data-s1,test-data-s2,test-data-s3,test-data-longName,test-data-longName2,test-data-empty,test-data-spaces,test-data-mixed-direction,test-repeat-edges
A---B,1,1,0,0,0,0,0,0,1
C---D,1,1,0,0,0,0,0,1,1
E---F,1,1,0,0,0,0,0,1,1
L---M,0,1,1,0,0,0,1,0,0
M---N,0,0,1,0,0,0,0,0,0
O---P,0,0,1,0,0,0,1,0,0
P---Q,0,0,1,0,0,0,0,0,0
node1---node2,0,0,0,1,0,0,0,0,0
node1---node3,0,0,0,1,1,0,0,0,0
node4---node5,0,0,0,1,1,0,0,0,0
LONGERNAMES---TEST,0,0,0,1,1,0,0,0,0
node2---node3,0,0,0,0,1,0,0,0,0
nodes with---spaces in name,0,0,0,0,0,0,1,0,0
A-->B,0,0,0,0,0,0,0,1,0
B-->A,0,0,0,0,0,0,0,1,0
5 changes: 5 additions & 0 deletions test/ml/input/test-repeat-edges/repeat.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
Node1 Node2 Rank Direction
A B 1 U
C D 1 U
E F 1 U
A B 1 U
2 changes: 1 addition & 1 deletion test/ml/test_ml.py
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Expand Up @@ -22,7 +22,7 @@ def setup_class(cls):
def test_summarize_networks(self):
dataframe = ml.summarize_networks([INPUT_DIR + 'test-data-s1/s1.txt', INPUT_DIR + 'test-data-s2/s2.txt', INPUT_DIR + 'test-data-s3/s3.txt',
INPUT_DIR + 'test-data-longName/longName.txt', INPUT_DIR + 'test-data-longName2/longName2.txt',
INPUT_DIR + 'test-data-empty/empty.txt', INPUT_DIR + 'test-data-spaces/spaces.txt', INPUT_DIR + 'test-data-mixed-direction/mixed-direction.txt'])
INPUT_DIR + 'test-data-empty/empty.txt', INPUT_DIR + 'test-data-spaces/spaces.txt', INPUT_DIR + 'test-data-mixed-direction/mixed-direction.txt', INPUT_DIR + 'test-repeat-edges/repeat.txt'])
dataframe.to_csv(OUT_DIR + 'dataframe.csv')
assert filecmp.cmp(OUT_DIR + 'dataframe.csv', EXPECT_DIR + 'expected-dataframe.csv', shallow=False)

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