Add debugging and change home page text

Author: ddomingof

src/pathme_viewer/cli.py

@@ -9,9 +9,8 @@
 
 import click
 from bio2bel_chebi import Manager as ChebiManager
-from bio2bel_hgnc import Manager as HgncManager
-from pybel import union
 
+from bio2bel_hgnc import Manager as HgncManager
 from pathme.constants import (
     KEGG,
     KEGG_DIR,
@@ -28,6 +27,7 @@
     get_file_name_from_url,
     unzip_file
 )
+from pybel import union
 from .constants import DEFAULT_CACHE_CONNECTION
 from .load_db import load_kegg, load_reactome, load_wikipathways
 from .manager import Manager
@@ -55,17 +55,25 @@ def set_debug_param(debug):
 @click.group(help='PathMe')
 def main():
     """Main click method"""
-    logging.basicConfig(level=20, format="%(asctime)s - %(levelname)s - %(name)s - %(message)s")
+    logging.basicConfig(level=10, format="%(asctime)s - %(levelname)s - %(name)s - %(message)s")
 
 
 @main.command()
 @click.option('--host', default='0.0.0.0', help='Flask host. Defaults to 0.0.0.0')
 @click.option('--port', type=int, default=5000, help='Flask port. Defaults to 5000')
 @click.option('--template', help='Defaults to "../templates"')
 @click.option('--static', help='Defaults to "../static"')
-def web(host, port, template, static):
+@click.option('-v', '--verbose', is_flag=True)
+def web(host, port, template, static, verbose):
     """Run web service."""
     from .web.web import create_app
+
+    if verbose:
+        log.setLevel(logging.DEBUG)
+        log.debug('Debug mode activated')
+    else:
+        log.setLevel(logging.INFO)
+
     app = create_app(template_folder=template, static_folder=static)
     app.run(host=host, port=port)
 

src/pathme_viewer/graph_utils.py

@@ -77,6 +77,10 @@ def merge_pathways(pathways):
         add_annotation_value(graph, 'Database', pathway.resource_name)
         add_annotation_value(graph, 'PathwayID', pathway.pathway_id)
 
+        log.debug('Adding graph {} {}:with {} nodes and {} edges'.format(
+            name, resource, graph.number_of_nodes(), graph.number_of_edges())
+        )
+
         networks.append(graph)
 
     if not networks:

src/pathme_viewer/templates/pathme.html

@@ -51,8 +51,8 @@
         {{ util.flashed_messages(dismissible=True, container=False) }}
 
         <div class="jumbotron">
-            <h1>PathMe</h1>
-            <p>A tool to merge and explore the mechanistic pathway knowledge.
+            <h1>PathMe Viewer</h1>
+            <p>A web application to merge and explore the mechanistic pathway knowledge.
             </p>
         </div>
 

src/pathme_viewer/web/views.py

@@ -120,7 +120,7 @@ def get_network():
 
     graph = merge_pathways(pathways)
 
-    log.info('Exporting graph with {} nodes and {} edges'.format(graph.number_of_nodes(), graph.number_of_edges()))
+    log.info('Exporting merged graph with {} nodes and {} edges'.format(graph.number_of_nodes(), graph.number_of_edges()))
 
     return export_graph(graph, request.args.get('format'))