diff --git a/docker-wrappers/Cytoscape/cytoscape_util.py b/docker-wrappers/Cytoscape/cytoscape_util.py index 1f386353..dcf110f1 100644 --- a/docker-wrappers/Cytoscape/cytoscape_util.py +++ b/docker-wrappers/Cytoscape/cytoscape_util.py @@ -115,7 +115,7 @@ def load_pathways(pathways: List[str], output: str) -> None: path, name = parse_name(pathway) suid = p4c.networks.import_network_from_tabular_file( file=path, - column_type_list='s,t,x', + column_type_list='s,t,x,ea', delimiters='\t' ) p4c.networks.rename_network(name, network=suid) diff --git a/test/PrepareInputs/expected/allpairs-network-expected.txt b/test/GenerateInputs/expected/allpairs-network-expected.txt similarity index 100% rename from test/PrepareInputs/expected/allpairs-network-expected.txt rename to test/GenerateInputs/expected/allpairs-network-expected.txt diff --git a/test/PrepareInputs/expected/domino-network-expected.txt b/test/GenerateInputs/expected/domino-network-expected.txt similarity index 100% rename from test/PrepareInputs/expected/domino-network-expected.txt rename to test/GenerateInputs/expected/domino-network-expected.txt diff --git a/test/PrepareInputs/expected/meo-edges-expected.txt b/test/GenerateInputs/expected/meo-edges-expected.txt similarity index 100% rename from test/PrepareInputs/expected/meo-edges-expected.txt rename to test/GenerateInputs/expected/meo-edges-expected.txt diff --git a/test/PrepareInputs/expected/mincostflow-edges-expected.txt b/test/GenerateInputs/expected/mincostflow-edges-expected.txt similarity index 100% rename from test/PrepareInputs/expected/mincostflow-edges-expected.txt rename to test/GenerateInputs/expected/mincostflow-edges-expected.txt diff --git a/test/PrepareInputs/expected/omicsintegrator1-edges-expected.txt b/test/GenerateInputs/expected/omicsintegrator1-edges-expected.txt similarity index 100% rename from test/PrepareInputs/expected/omicsintegrator1-edges-expected.txt rename to test/GenerateInputs/expected/omicsintegrator1-edges-expected.txt diff --git a/test/PrepareInputs/expected/omicsintegrator2-edges-expected.txt b/test/GenerateInputs/expected/omicsintegrator2-edges-expected.txt similarity index 100% rename from test/PrepareInputs/expected/omicsintegrator2-edges-expected.txt rename to test/GenerateInputs/expected/omicsintegrator2-edges-expected.txt diff --git a/test/PrepareInputs/expected/pathlinker-network-expected.txt b/test/GenerateInputs/expected/pathlinker-network-expected.txt similarity index 100% rename from test/PrepareInputs/expected/pathlinker-network-expected.txt rename to test/GenerateInputs/expected/pathlinker-network-expected.txt diff --git a/test/PrepareInputs/test_prepare_inputs.py b/test/GenerateInputs/test_generate_inputs.py similarity index 93% rename from test/PrepareInputs/test_prepare_inputs.py rename to test/GenerateInputs/test_generate_inputs.py index 1508faa9..a8b0a26d 100644 --- a/test/PrepareInputs/test_prepare_inputs.py +++ b/test/GenerateInputs/test_generate_inputs.py @@ -7,12 +7,12 @@ from src import runner -OUTDIR = "test/PrepareInputs/output/" -EXPDIR = "test/PrepareInputs/expected/" +OUTDIR = "test/GenerateInputs/output/" +EXPDIR = "test/GenerateInputs/expected/" algorithms = ['mincostflow', 'meo', 'omicsintegrator1', "omicsintegrator2", "domino", "pathlinker", "allpairs"] algo_exp_file = {'mincostflow': 'edges', 'meo': 'edges', 'omicsintegrator1': 'edges', 'omicsintegrator2': 'edges', 'domino': 'network', 'pathlinker': 'network', "allpairs": 'network'} -class TestPrepareInputs: +class TestGenerateInputs: def setup_class(cls): """ Create the expected output directory