fix: correct flag

Author: tristan-f-r

config/config.yaml

@@ -37,7 +37,7 @@ container_registry:
 # combinations. For instance if we have the following:
 # - name: "myAlg"
 #   params:
-#         include: true
+#         include: false
 #         a: [1,2]
 #         b: [0.5,0.75]
 #
@@ -47,13 +47,13 @@ container_registry:
 algorithms:
   - name: "pathlinker"
     params:
-      include: true
+      include: false
       run1:
         k: range(100,201,100)
 
   - name: "omicsintegrator1"
     params:
-      include: true
+      include: false
       run1:
         b: [5, 6]
         w: np.linspace(0,5,2)
@@ -62,7 +62,7 @@ algorithms:
 
   - name: "omicsintegrator2"
     params:
-      include: true
+      include: false
       run1:
         b: 4
         g: 0
@@ -72,15 +72,15 @@ algorithms:
 
   - name: "meo"
     params:
-      include: true
+      include: false
       run1:
         max_path_length: 3
         local_search: "Yes"
         rand_restarts: 10
 
   - name: "mincostflow"
     params:
-      include: true
+      include: false
       run1:
         flow: 1 # The flow must be an int
         capacity: 1
@@ -91,7 +91,7 @@ algorithms:
 
   - name: "domino"
     params:
-      include: true
+      include: false
       run1:
         slice_threshold: 0.3
         module_threshold: 0.05
@@ -149,17 +149,17 @@ reconstruction_settings:
 analysis:
   # Create one summary per pathway file and a single summary table for all pathways for each dataset
   summary:
-    include: true
+    include: false
   # Create output files for each pathway that can be visualized with GraphSpace
   graphspace:
-    include: true
+    include: false
   # Create Cytoscape session file with all pathway graphs for each dataset
   cytoscape:
-    include: true
+    include: false
   # Machine learning analysis (e.g. clustering) of the pathway output files for each dataset
   ml:
     # ml analysis per dataset
-    include: true
+    include: false
     # adds ml analysis per algorithm output
     # only runs for algorithms with multiple parameter combinations chosen
     aggregate_per_algorithm: true
@@ -175,7 +175,7 @@ analysis:
   evaluation:
     # evaluation per dataset-goldstandard pair
     # evaluation will not run unless ml include is set to true
-    include: true
+    include: false
     # adds evaluation per algorithm per dataset-goldstandard pair
     # evaluation per algortihm will not run unless ml include and ml aggregate_per_algorithm are set to true
     aggregate_per_algorithm: true

spras/allpairs.py

@@ -59,8 +59,10 @@ def generate_inputs(data: Dataset, filename_map):
         # signal to `run` that the graph is directed.
         if has_direction(edges_df):
             edges_df = convert_undirected_to_directed(edges_df)
-            # we also touch a 'directed_flag.txt' file to say that this is directed
-            Path(filename_map['directed_flag']).touch()
+            # we write to a 'directed_flag.txt' file to say that this is directed
+            Path(filename_map['directed_flag']).write_text("true")
+        else:
+            Path(filename_map['directed_flag']).write_text("false")
 
         # This is pretty memory intensive. We might want to keep the interactome centralized.
         edges_df.to_csv(filename_map["network"], sep="\t", index=False,
@@ -76,7 +78,7 @@ def run(nodetypes=None, network=None, directed_flag=None, output_file=None, cont
         @param container_framework: choose the container runtime framework, currently supports "docker" or "singularity" (optional)
         @param output_file: path to the output pathway file (required)
         """
-        if not nodetypes or not network or not output_file:
+        if not nodetypes or not network or not output_file or not directed_flag:
             raise ValueError('Required All Pairs Shortest Paths arguments are missing')
 
         work_dir = '/apsp'
@@ -100,7 +102,7 @@ def run(nodetypes=None, network=None, directed_flag=None, output_file=None, cont
                    '--network', network_file,
                    '--nodes', node_file,
                    '--output', mapped_out_file]
-        if directed_flag and Path(directed_flag).exists():
+        if Path(directed_flag).read_text().strip() == "true":
             command.append("--directed")
 
         container_suffix = "allpairs:v4"

test/AllPairs/input/directed-flag-false.txt

@@ -0,0 +1 @@
+false

test/AllPairs/input/directed-flag-true.txt

@@ -0,0 +1 @@
+true

test/AllPairs/test_ap.py

@@ -48,6 +48,7 @@ def test_allpairs(self):
         AllPairs.run(
             nodetypes=str(TEST_DIR / 'input' / 'sample-in-nodetypes.txt'),
             network=str(TEST_DIR / 'input' / 'sample-in-net.txt'),
+            directed_flag=str(TEST_DIR / 'input' / 'directed-flag-false.txt'),
             output_file=str(out_path)
         )
         assert out_path.exists()
@@ -70,6 +71,7 @@ def test_allpairs_singularity(self):
         AllPairs.run(
             nodetypes=str(TEST_DIR / 'input' / 'sample-in-nodetypes.txt'),
             network=str(TEST_DIR / 'input' / 'sample-in-net.txt'),
+            directed_flag=str(TEST_DIR / 'input' / 'directed-flag-false.txt'),
             output_file=str(out_path),
             container_framework="singularity")
         assert out_path.exists()
@@ -83,6 +85,7 @@ def test_allpairs_singularity_unpacked(self):
         AllPairs.run(
             nodetypes=str(TEST_DIR / 'input/sample-in-nodetypes.txt'),
             network=str(TEST_DIR / 'input/sample-in-net.txt'),
+            directed_flag=str(TEST_DIR / 'input' / 'directed-flag-false.txt'),
             output_file=str(out_path),
             container_framework="singularity")
         config.config.unpack_singularity = False
@@ -104,6 +107,7 @@ def test_allpairs_correctness(self):
         AllPairs.run(
             nodetypes=str(TEST_DIR / 'input' / 'correctness-nodetypes.txt'),
             network=str(TEST_DIR / 'input' / 'correctness-network.txt'),
+            directed_flag=str(TEST_DIR / 'input' / 'directed-flag-false.txt'),
             output_file=str(OUT_DIR / 'correctness-out.txt')
         )
 
@@ -113,13 +117,11 @@ def test_allpairs_directed(self):
         out_path = OUT_DIR / 'directed-out.txt'
         out_path.unlink(missing_ok=True)
 
-        OUT_DIR.joinpath('directed-flag.txt').touch()
-
         AllPairs.run(
             nodetypes=str(TEST_DIR / 'input' / 'directed-nodetypes.txt'),
             network=str(TEST_DIR / 'input' / 'directed-network.txt'),
+            directed_flag=str(TEST_DIR / 'input' / 'directed-flag-true.txt'),
             output_file=str(OUT_DIR / 'directed-out.txt'),
-            directed_flag=str(OUT_DIR / 'directed-flag.txt')
         )
 
         edge_equality_test_util(out_path, EXPECTED_DIR.joinpath('directed-expected.txt'))
@@ -137,6 +139,7 @@ def test_allpairs_zero_length(self):
         AllPairs.run(
             nodetypes=TEST_DIR / 'input' / 'zero-length-nodetypes.txt',
             network=TEST_DIR / 'input' / 'zero-length-network.txt',
+            directed_flag=str(TEST_DIR / 'input' / 'directed-flag-false.txt'),
             output_file=OUT_DIR / 'zero-length-out.txt'
         )