Add logger to spia exporter

PathwayMerger · Mar 1, 2019 · 21dfffd · 21dfffd
1 parent 4749bdb
commit 21dfffd
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 1 deletion.
diff --git a/setup.cfg b/setup.cfg
@@ -58,7 +58,7 @@ install_requires =
     bio2bel_wikipathways==0.2.2
     bio2bel_reactome==0.2.3
     pybel==0.13.1
-    pybel-tools==0.7.0
+    pybel-tools>=0.7.0
 
 # Random options
 zip_safe = false

diff --git a/src/pathme/cli.py b/src/pathme/cli.py
@@ -308,9 +308,20 @@ def export_to_spia(kegg_path, reactome_path, wikipathways_path, output):
     from pybel_tools.analysis.spia import bel_to_spia_matrices, spia_matrices_to_excel
 
     kegg_pickles = get_files_in_folder(kegg_path)
+
+    if not kegg_pickles:
+        log.warning('No KEGG files found. Please create the BEL KEGG files')
+
     reactome_pickles = get_files_in_folder(reactome_path)
+
+    if not reactome_pickles:
+        log.warning('No Reactome files found. Please create the BEL Reactome files')
+
     wp_pickles = get_files_in_folder(wikipathways_path)
 
+    if not wp_pickles:
+        log.warning('No WikiPathways files found. Please create the BEL WikiPathways files')
+
     all_pickles = kegg_pickles + reactome_pickles + wp_pickles
 
     log.info(f'A total of {len(all_pickles)} will be exported')