Fix files with outdated cases

test/BowTieBuilder/test_btb2.py

@@ -0,0 +1,309 @@
+import sys
+from filecmp import cmp
+from pathlib import Path
+
+import pytest
+
+import spras.config as config
+
+config.init_from_file("config/config.yaml")
+
+# TODO consider refactoring to simplify the import
+# Modify the path because of the - in the directory
+SPRAS_ROOT = Path(__file__).parent.parent.parent.absolute()
+sys.path.append(str(Path(SPRAS_ROOT, 'docker-wrappers', 'BowTieBuilder')))
+from spras.btb import BowTieBuilder as BTB
+
+TEST_DIR = Path('test', 'BowTieBuilder/')
+OUT_FILE_DEFAULT = Path(TEST_DIR, 'output', 'raw-pathway.txt')
+
+
+class TestBowTieBuilder:
+    """
+    Run the BowTieBuilder algorithm with missing arguments
+    """
+    def test_btb_missing(self):
+        with pytest.raises(ValueError):
+            # No edges
+            BTB.run(
+                           targets=Path(TEST_DIR, 'input', 'target.txt'),
+                           sources=Path(TEST_DIR, 'input', 'source.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        with pytest.raises(ValueError):
+            # No source
+            BTB.run(
+                           targets=Path(TEST_DIR, 'input', 'target.txt'),
+                           edges=Path(TEST_DIR, 'input', 'edges.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        with pytest.raises(ValueError):
+            # No target
+            BTB.run(
+                           sources=Path(TEST_DIR, 'input', 'source.txt'),
+                           edges=Path(TEST_DIR, 'input', 'edges.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+
+
+    """
+    Run the BowTieBuilder algorithm with missing files
+    """
+    def test_btb_file(self):
+        with pytest.raises(ValueError):
+            BTB.run(sources=Path(TEST_DIR, 'input', 'unknown.txt'),
+                           targets=Path(TEST_DIR, 'input', 'target.txt'),
+                           edges=Path(TEST_DIR, 'input', 'edges.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+
+    """
+    Run the BowTieBuilder algorithm with bad input data
+    """
+    def test_format_error(self):
+        with pytest.raises(IndexError):
+            BTB.run(sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           edges=Path(TEST_DIR, 'input', 'bad-edges.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+
+    """
+    Run the BowTieBuilder algorithm on the example input files and check the output matches the expected output
+    """
+    def test_btb(self):
+            OUT_FILE_DEFAULT.unlink(missing_ok=True)
+            BTB.run(edges=Path(TEST_DIR, 'input', 'btb-edges.txt'),
+                            sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                            targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                            output_file=OUT_FILE_DEFAULT)
+            assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+            expected_file = Path(TEST_DIR, 'expected', 'btb-output.txt')
+
+            # Read the content of the output files and expected file into sets
+            with open(OUT_FILE_DEFAULT, 'r') as output_file:
+                output_content = set(output_file.read().splitlines())
+            with open(expected_file, 'r') as expected_output_file:
+                expected_content = set(expected_output_file.read().splitlines())
+
+            # Check if the sets are equal, regardless of the order of lines
+            assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm on the example disjoint input files and check the output matches the expected output
+    """
+    def test_disjoint(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'disjoint-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'disjoint-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'disjoint-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'disjoint-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm on the example disjoint2 input files and check the output matches the expected output
+    """
+    def test_disjoint2(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'disjoint2-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'disjoint-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'disjoint-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'disjoint-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm with a missing input file
+    """
+    def test_missing_file(self):
+        with pytest.raises(ValueError):
+            with pytest.raises(OSError):
+                BTB.run(edges=Path(TEST_DIR, 'input', 'missing.txt'),
+                            sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                            targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                            output_file=OUT_FILE_DEFAULT)
+
+
+    """
+    Run the BowTieBuilder algorithm on the example source to source input files and check the output matches the expected output
+    """
+    def test_source_to_source(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'source-to-source-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'source-to-source-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm on the example source to source input files and check the output matches the expected output
+    """
+    def test_source_to_source2(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'source-to-source2-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'source-to-source2-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm on two separate source to target paths connected by sources and check the output matches the expected output
+    """
+
+    def test_source_to_source_disjoint(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'source-to-source-disjoint-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'source-to-source-disjoint-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm on the example bidirectional input files and check the output matches the expected output
+    """
+
+    def test_bidirectional(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'bidirectional-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'bidirectional-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm on the example target to source input files and check the output matches the expected output
+    """
+
+    def test_target_to_source(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'target-to-source-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'empty-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm on the example loop network files and check the output matches the expected output
+    """
+
+    def test_loop(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'loop-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'loop-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    """
+    Run the BowTieBuilder algorithm on the weighted input files and check the output matches the expected output
+    """
+
+    def test_weighted(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'weighted-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'weighted-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'
+
+    def test_weight_one(self):
+        OUT_FILE_DEFAULT.unlink(missing_ok=True)
+        BTB.run(edges=Path(TEST_DIR, 'input', 'weight-one-edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           output_file=OUT_FILE_DEFAULT)
+        assert OUT_FILE_DEFAULT.exists(), 'Output file was not written'
+        expected_file = Path(TEST_DIR, 'expected', 'weighted-output.txt')
+
+        # Read the content of the output files and expected file into sets
+        with open(OUT_FILE_DEFAULT, 'r') as output_file:
+            output_content = set(output_file.read().splitlines())
+        with open(expected_file, 'r') as expected_output_file:
+            expected_content = set(expected_output_file.read().splitlines())
+
+        # Check if the sets are equal, regardless of the order of lines
+        assert output_content == expected_content, 'Output file does not match expected output file'

test/BowtieBuilder/test_btb.py

@@ -26,20 +26,20 @@ def test_btb_missing(self):
         with pytest.raises(ValueError):
             # No edges
             BTB.run(
-                           targets=Path(TEST_DIR, 'input', 'target.txt'),
-                           sources=Path(TEST_DIR, 'input', 'sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'target1.txt'),
+                           sources=Path(TEST_DIR, 'input', 'source1.txt'),
                            output_file=OUT_FILE_DEFAULT)
         with pytest.raises(ValueError):
             # No source
             BTB.run(
-                           targets=Path(TEST_DIR, 'input', 'target.txt'),
-                           edges=Path(TEST_DIR, 'input', 'edges.txt'),
+                           targets=Path(TEST_DIR, 'input', 'target1.txt'),
+                           edges=Path(TEST_DIR, 'input', 'edges1.txt'),
                            output_file=OUT_FILE_DEFAULT)
         with pytest.raises(ValueError):
             # No target
             BTB.run(
-                           sources=Path(TEST_DIR, 'input', 'source.txt'),
-                           edges=Path(TEST_DIR, 'input', 'edges.txt'),
+                           sources=Path(TEST_DIR, 'input', 'source1.txt'),
+                           edges=Path(TEST_DIR, 'input', 'edges1.txt'),
                            output_file=OUT_FILE_DEFAULT)
 
 
@@ -53,15 +53,15 @@ def test_btb_file(self):
                            edges=Path(TEST_DIR, 'input', 'edges.txt'),
                            output_file=OUT_FILE_DEFAULT)
 
-    # """
-    # Run the BowTieBuilder algorithm with bad input data
-    # """
-    # def test_format_error(self):
-    #     with pytest.raises(IndexError):
-    #         BTB.run(sources=Path(TEST_DIR, 'input', 'source.txt'),
-    #                        targets=Path(TEST_DIR, 'input', 'target.txt'),
-    #                        edges=Path(TEST_DIR, 'input', 'edges_bad.txt'),
-    #                        output_file=OUT_FILE_DEFAULT)
+    """
+    Run the BowTieBuilder algorithm with bad input data
+    """
+    def test_format_error(self):
+        with pytest.raises(IndexError):
+            BTB.run(sources=Path(TEST_DIR, 'input', 'btb-sources.txt'),
+                           targets=Path(TEST_DIR, 'input', 'btb-targets.txt'),
+                           edges=Path(TEST_DIR, 'input', 'bad-edges.txt'),
+                           output_file=OUT_FILE_DEFAULT)
 
     """
     Run the BowTieBuilder algorithm on the example input files and check the output matches the expected output