fix linting

Author: PlushZ

tools/flexynesis/fetch_cbioportal_data.py

@@ -2,8 +2,10 @@
 
 import argparse
 import os
+
 from flexynesis.utils import CBioPortalData
 
+
 def main():
     parser = argparse.ArgumentParser(description="Fetch and prepare cBioPortal data for Flexynesis.")
     parser.add_argument("--study_id", required=True, help="cBioPortal study ID (e.g., 'brca_tcga')")
@@ -19,8 +21,8 @@ def main():
         raise ValueError("Clinical data ('clin') is required for splitting the dataset.")
 
     file_mapping = {
-        "clin": "data_clinical_patient.txt", # can be any with 'clinical' in file name
-        "mut": "data_mutations.txt", # any with 'mutations' in file name
+        "clin": "data_clinical_patient.txt",  # can be any with 'clinical' in file name
+        "mut": "data_mutations.txt",  # any with 'mutations' in file name
         "omics": "data_cna.txt",
         "other": None
     }
@@ -49,12 +51,11 @@ def main():
     for data_type in data_types:
         if data_type in dataset['train']:
             train_file = os.path.join(args.output_dir, f"{data_type}_train.csv")
-            dataset['train'][data_type].to_csv(train_file, index=True)  
-            print(f"Wrote training data to {train_file}")
+            dataset['train'][data_type].to_csv(train_file, index=True)
         if data_type in dataset['test']:
             test_file = os.path.join(args.output_dir, f"{data_type}_test.csv")
-            dataset['test'][data_type].to_csv(test_file, index=True) 
-            print(f"Wrote test data to {test_file}")
+            dataset['test'][data_type].to_csv(test_file, index=True)
+
 
 if __name__ == "__main__":
-    main()
+    main()

tools/flexynesis/flexynesis_cbioportal_import.xml

@@ -41,22 +41,22 @@
             <param name="data_types" value="clin,mut" />
             <param name="split_ratio" value="0.7" />
             <output_collection name="datasets" type="list">
-                <element name="clin_train">
+                <element name="clin_test">
                     <assert_contents>
                         <has_text_matching expression="PATIENT_ID"/>
                     </assert_contents>
                 </element>
-                <element name="mut_train">
+                <element name="clin_train">
                     <assert_contents>
-                        <has_text_matching expression="Hugo_Symbol"/>
+                        <has_text_matching expression="PATIENT_ID"/>
                     </assert_contents>
                 </element>
-                <element name="clin_test">
+                <element name="mut_test">
                     <assert_contents>
-                        <has_text_matching expression="PATIENT_ID"/>
+                        <has_text_matching expression="Hugo_Symbol"/>
                     </assert_contents>
                 </element>
-                <element name="mut_test">
+                <element name="mut_train">
                     <assert_contents>
                         <has_text_matching expression="Hugo_Symbol"/>
                     </assert_contents>