chore: disable more pathways

:/

Author: tristan-f-r

datasets/synthetic_data/pathways.jsonc

@@ -10,11 +10,12 @@
     "Notch signaling pathway",
     "JAK/STAT signaling pathway",
     "Interleukin signaling pathway",
-    // TODO: Inspect why this pathway doesn't work well for sampling.
+    // TODO: Inspect why these pathway doesn't work well for sampling.
     // "Interferon-gamma signaling pathway",
-    "Integrin signalling pathway",
+    // "Integrin signalling pathway",
     "Insulin/IGF pathway-protein kinase B signaling cascade",
-    "Inflammation mediated by chemokine and cytokine signaling pathway",
+    // TODO: and this one
+    // "Inflammation mediated by chemokine and cytokine signaling pathway",
     "Hedgehog signaling pathway",
     "FGF signaling pathway",
     "FAS signaling pathway",

datasets/synthetic_data/scripts/sampling.py

@@ -5,6 +5,7 @@
 from tools.sample import attempt_sample
 from tools.trim import trim_data_file
 from datasets.synthetic_data.scripts.util.parser import parser
+import random
 
 synthetic_directory = Path(__file__).parent.parent.resolve()
 
@@ -63,7 +64,13 @@ def sources_and_targets(pathway_node_prizes_df: pandas.DataFrame) -> SourcesTarg
 
 
 def main():
-    pathway_name = parser().parse_args().pathway
+    arg_parser = parser()
+    arg_parser.add_argument("--seed", "The seed to use", type=int, required=False)
+    args = arg_parser.parse_args()
+    pathway_name = args.pathway
+    if args.seed is not None:
+        random.seed(args.seed)
+
     print("Reading interactome...")
     interactome_df = pandas.read_csv(
         synthetic_directory / "processed" / "interactome.tsv",