added parse_output tests and still fixing generate inputs

test/DOMINO/test_domino.py

@@ -9,8 +9,6 @@
 TEST_DIR = 'test/DOMINO/'
 OUT_FILE_DEFAULT = TEST_DIR+'output/domino-output.txt'
 OUT_FILE_OPTIONAL = TEST_DIR+'output/domino-output-thresholds.txt'
-OUT_FILE_PARSE = TEST_DIR+'output/domino-parse-output.txt'
-OUT_FILE_PARSE_EXP = TEST_DIR+'expected_output/domino-parse-output.txt'
 
 
 class TestDOMINO:
@@ -63,18 +61,6 @@ def test_domino_missing_network(self):
                 active_genes=TEST_DIR+'input/domino-active-genes.txt',
                 output_file=OUT_FILE_DEFAULT)
 
-    def test_domino_parse_output(self):
-        # Input is the concatenated module_0.html and module_1.html file from
-        # the DOMINO output of the network dip.sif and the nodes tnfa_active_genes_file.txt
-        # from https://github.com/Shamir-Lab/DOMINO/tree/master/examples
-        # Confirms the generated output matches the expected output
-        out_path = Path(OUT_FILE_PARSE)
-        out_path.unlink(missing_ok=True)
-        DOMINO.parse_output(
-            TEST_DIR+'input/domino-concat-modules.txt',
-            OUT_FILE_PARSE)
-        assert filecmp.cmp(OUT_FILE_PARSE, OUT_FILE_PARSE_EXP, shallow=False)
-
     # Only run Singularity test if the binary is available on the system
     # spython is only available on Unix, but do not explicitly skip non-Unix platforms
     @pytest.mark.skipif(not shutil.which('singularity'), reason='Singularity not found on system')

test/GenerateInputs/test_generate_inputs.py

@@ -31,7 +31,7 @@ def test_prepare_inputs_networks(self):
         for algo in algorithms:
             inputs = runner.get_required_inputs(algo)
             runner.merge_input(data0_dataset, test_file)
-            filename_map = {input_str: os.path.join("test", "PrepareInputs", "output", f"{algo}-{input_str}.txt") for input_str in inputs}
+            filename_map = {input_str: os.path.join("test", "GenerateInputs", "output", f"{algo}-{input_str}.txt") for input_str in inputs}
             runner.prepare_inputs(algo, test_file, filename_map)
             exp_file_name = algo_exp_file[algo]
             assert filecmp.cmp(OUTDIR +f"{algo}-{exp_file_name}.txt", EXPDIR + f"{algo}-{exp_file_name}-expected.txt")

test/ParseOutputs/expected/allpairs-pathway-expected.txt

@@ -0,0 +1,10 @@
+S1	A	1	U
+S1	B	1	U
+A	E	1	U
+A	F	1	U
+E	T1	1	U
+T1	F	1	U
+F	T2	1	U
+F	B	1	U
+B	S2	1	U
+S2	T3	1	U

test/ParseOutputs/expected/meo-pathway-expected.txt

@@ -0,0 +1,2 @@
+GENEA	GENEC	1	U
+GENEC	GENEB	1	U

test/ParseOutputs/expected/mincostflow-pathway-expected.txt

@@ -0,0 +1,2 @@
+B	A	1	D
+D	B	1	D

test/ParseOutputs/expected/omicsintegrator1-pathway-expected.txt

@@ -0,0 +1,2 @@
+A	C	1	U
+C	D	1	U

test/ParseOutputs/expected/omicsintegrator2-pathway-expected.txt

@@ -0,0 +1,2 @@
+B	A	1	U
+B	C	1	U

test/ParseOutputs/expected/pathlinker-pathway-expected.txt

@@ -0,0 +1,17 @@
+S2	T3	1	D
+A	E	2	D
+S1	A	2	D
+E	T1	2	D
+B	F	3	D
+F	T2	3	D
+S2	B	3	D
+C	F	4	D
+S2	C	4	D
+C	G	5	D
+G	T2	5	D
+G	T3	6	D
+E	F	7	D
+B	C	8	D
+F	E	11	D
+G	F	13	D
+F	A	16	D

test/ParseOutputs/input/allpairs-raw-pathway.txt

@@ -0,0 +1,10 @@
+S1	A
+S1	B
+A	E
+A	F
+E	T1
+T1	F
+F	T2
+F	B
+B	S2
+S2	T3

test/ParseOutputs/input/meo-raw-pathway.txt

@@ -0,0 +1,3 @@
+Source	Type	Target	Oriented	Weight
+GENEA	pp	GENEC	true	0.5
+GENEC	pp	GENEB	true	0.5

test/ParseOutputs/input/mincostflow-raw-pathway.txt

@@ -0,0 +1,2 @@
+B	A
+D	B

test/ParseOutputs/input/omicsintegrator1-raw-pathway.txt

@@ -0,0 +1,2 @@
+A	pp	C
+C	pp	D

test/ParseOutputs/input/omicsintegrator2-raw-pathway.txt

@@ -0,0 +1,3 @@
+protein1	protein2	cost	in_solution
+B	A	0.52	True
+B	C	0.73	True

test/ParseOutputs/input/pathlinker-raw-pathway.txt

@@ -0,0 +1,18 @@
+#tail	head	KSP index	path cost
+S2	T3	1	5.00000e-01
+A	E	2	1.25000e-01
+S1	A	2	1.25000e-01
+E	T1	2	1.25000e-01
+B	F	3	1.25000e-01
+F	T2	3	1.25000e-01
+S2	B	3	1.25000e-01
+C	F	4	1.25000e-01
+S2	C	4	1.25000e-01
+C	G	5	1.25000e-01
+G	T2	5	1.25000e-01
+G	T3	6	1.25000e-01
+E	F	7	6.25000e-02
+B	C	8	6.25000e-02
+F	E	11	6.25000e-02
+G	F	13	6.25000e-02
+F	A	16	3.12500e-02

test/ParseOutputs/test_parse_outputs.py

@@ -0,0 +1,47 @@
+import filecmp
+import os
+import shutil
+from pathlib import Path
+
+import yaml
+
+from src import runner
+from src.domino import DOMINO, post_domino_id_transform, pre_domino_id_transform
+INDIR = "test/ParseOutputs/input/"
+OUTDIR = "test/ParseOutputs/output/"
+EXPDIR = "test/ParseOutputs/expected/"
+
+# for domino
+OUT_FILE_PARSE = OUTDIR+'/domino-parse-output.txt'
+OUT_FILE_PARSE_EXP = EXPDIR + '/domino-parse-output.txt'
+
+algorithms = ['mincostflow', 'meo', 'omicsintegrator1', "omicsintegrator2", "pathlinker", "allpairs"]
+class TestParseOutputs:
+    def setup_class(cls):
+        """
+        Create the expected output directory
+        """
+        Path(OUTDIR).mkdir(parents=True, exist_ok=True)
+
+    def test_parse_outputs(self):
+
+        # skip domino
+        for algo in algorithms:
+            # inputs = runner.get_required_inputs(algo)
+            test_file = INDIR + f"{algo}-raw-pathway.txt"
+            out_file = OUTDIR + f"{algo}-pathway.txt"
+            print(out_file)
+            runner.parse_output(algo, test_file, out_file)
+            assert filecmp.cmp(OUTDIR +f"{algo}-pathway.txt", EXPDIR + f"{algo}-pathway-expected.txt")
+
+    def test_domino_parse_output(self):
+        # Input is the concatenated module_0.html and module_1.html file from
+        # the DOMINO output of the network dip.sif and the nodes tnfa_active_genes_file.txt
+        # from https://github.com/Shamir-Lab/DOMINO/tree/master/examples
+        # Confirms the generated output matches the expected output
+        out_path = Path(OUT_FILE_PARSE)
+        out_path.unlink(missing_ok=True)
+        DOMINO.parse_output(
+            INDIR+ 'domino-concat-modules.txt',
+            OUT_FILE_PARSE)
+        assert filecmp.cmp(OUT_FILE_PARSE, OUT_FILE_PARSE_EXP, shallow=False)