Merge pull request Reed-CompBio#169 from ntalluri/update-dataset-label

Add Dataset Label Checking

config/config.yaml

@@ -99,6 +99,7 @@ algorithms:
 # Assume that if a dataset label does not change, the lists of associated input files do not change
 datasets:
     -
+      # Labels can only contain letters, numbers, or underscores
       label: data0
       node_files: ["node-prizes.txt", "sources.txt", "targets.txt"]
       # DataLoader.py can currently only load a single edge file, which is the primary network

config/egfr.yaml

@@ -72,7 +72,7 @@ datasets:
     data_dir: input
     edge_files:
       - phosphosite-irefindex13.0-uniprot.txt
-    label: tps-egfr
+    label: tps_egfr
     node_files:
       - tps-egfr-prizes.txt
     other_files: []

spras/config.py

@@ -15,6 +15,7 @@
 import copy as copy
 import itertools as it
 import os
+import re
 
 import numpy as np
 import yaml
@@ -140,6 +141,11 @@ def process_config(self, raw_config):
         # Convert to dicts to simplify the yaml logging
         self.datasets = {dataset["label"]: dict(dataset) for dataset in raw_config["datasets"]}
 
+        for key in self.datasets:
+            pattern = r'^\w+$'
+            if not bool(re.match(pattern, key)):
+                raise ValueError(f"Dataset label \'{key}\' contains invalid values. Dataset labels can only contain letters, numbers, or underscores.")
+
         # Code snipped from Snakefile that may be useful for assigning default labels
         # dataset_labels = [dataset.get('label', f'dataset{index}') for index, dataset in enumerate(datasets)]
         # Maps from the dataset label to the dataset list index

test/test_config.py

@@ -102,3 +102,20 @@ def test_config_container_registry(self):
         test_config["container_registry"]["owner"] = ""
         config.init_global(test_config)
         assert (config.config.container_prefix == config.DEFAULT_CONTAINER_PREFIX)
+
+    def test_error_dataset_label(self):
+        test_config = get_test_config()
+        error_test_dicts = [{"label":"test$"}, {"label":"@test'"}, {"label":"[test]"}, {"label":"test-test"}, {"label":"✉"}]
+
+        for test_dict in error_test_dicts:
+            test_config["datasets"]= [test_dict]
+            with pytest.raises(ValueError): #raises error if any chars other than letters, numbers, or underscores are in dataset label
+                config.init_global(test_config)
+
+    def test_correct_dataset_label(self):
+        test_config = get_test_config()
+        correct_test_dicts = [{"label":"test"},  {"label":"123"}, {"label":"test123"}, {"label":"123test"}, {"label":"_"}, {"label":"test_test"}, {"label":"_test"}, {"label":"test_"}]
+
+        for test_dict in correct_test_dicts:
+            test_config["datasets"]= [test_dict]
+            config.init_global(test_config) # no error should be raised