Fixing an issue with the security of the server by replacing all the …

README.md

@@ -76,22 +76,22 @@ Get a neuron of this search term by index of total neurons matching the search c
 ### Example 3
 
 Get a neuron (Here: The first neuron in the database) by the global index (1) from the database:
-- `python get_SWC.py --index 1`
+- `python get_swc.py --index 1`
 
 ### Example 4
 
 Get a neuron by it's known name and download as SWC file:
-- `python get_SWC.py --name cnic_001`
+- `python get_swc.py --name cnic_001`
 
 ### Example 5
 
 The following will download *all* SWC files from the region *Neocortex* to the current working directory
-- `python get_SWC.py --region neocortex`
+- `python get_swc.py --region neocortex`
 
 and the following command will just download the first ten neurons from the *Neocortex* region.
-- `python get_SWC.py --region neocortex --neurons 10`
+- `python get_swc.py --region neocortex --neurons 10`
 
 ### Example 6
 
 To download a whole *Smith* archive in SWC format from the database, use the following commmand:
-- `python get_SWC.py --archive Smith` 
+- `python get_swc.py --archive Smith` 

get_swc.py

@@ -1,43 +1,51 @@
 #!/usr/bin/env python
+import os
 from rest_wrapper.rest_wrapper import *
 import argparse
 from geometry_tools.geometry_tools import check_cylinder_intersections
 
 parser = argparse.ArgumentParser(description="Access NeuroMorpho.org v7 w/ REST API and download SWC files")
+parser.add_argument('--output', required=True, type=str, help="The output directory where the results will be written")
 parser.add_argument('--region', required=False, type=str, help="Brain region", metavar="R")
 parser.add_argument('--neurons', required=False, type=int, help="Count of neurons (-1 means all)", metavar="C")
 parser.add_argument('--name', required=False, type=str, help="Name of neuron", metavar="N")
 parser.add_argument('--index', required=False, type=int, help="Index of neuron", metavar="I")
 parser.add_argument('--archive', required=False, type=str, help="Archive name", metavar="A")
-parser.add_argument('--filters', required=False, type=str, help="One or multuple filters", metavar="[FILTER]",
-                    action='append', nargs=1)
+parser.add_argument('--filters', required=False, type=str, help="One or multuple filters", metavar="[FILTER]", action='append', nargs=1)
 parser.add_argument('--search', required=False, type=str, help="Search term", metavar="S")
 parser.add_argument('--validate', action='store_true', help="Check for cylinder intersections")
-
 args = parser.parse_args()
 
+# verify the output directory 
+if not os.path.isdir(args.output):
+   try:
+       os.mkdir(args.output)
+   except:
+       print('Please provide a valid directory. The directory [%s] does not exist' % args.output)
+       exit(0)
+
 if args.region:
     numNeurons = (args.neurons != -1 and args.neurons) or -1
     brainRegion = (args.region != -1 and args.region) or "neocortex"
-    get_swc_by_brain_region(brainRegion, numNeurons)
+    get_swc_by_brain_region(brainRegion, numNeurons, output_dir=args.output)
 elif args.archive:
     numNeurons = (args.neurons != -1 and args.neurons) or -1
     archiveName = (args.archive != -1 and args.archive) or "Smith"
-    get_swc_by_archive_name(archiveName, numNeurons)
+    get_swc_by_archive_name(archiveName, numNeurons, output_dir=args.output)
 elif args.search:
     if args.index:
-        fileName = get_swc_by_filter_rule_for_search_term(args.filters, args.search, 500, args.index)
+        fileName = get_swc_by_filter_rule_for_search_term(args.filters, args.search, 500, args.index, output_dir=args.output)
         if args.validate:
             print(check_cylinder_intersections(fileName))
     else:
-        fileName = get_swc_by_filter_rule_for_search_term(args.filters, args.search, args.neurons, -1)
+        fileName = get_swc_by_filter_rule_for_search_term(args.filters, args.search, args.neurons, -1, output_dir=args.output)
         if args.validate:
             print(check_cylinder_intersections(fileName))
 elif not (args.region or not ((args.index is not None) ^ (args.name is not None))):
     if args.index:
-        get_swc_by_neuron_index(args.index)
+        get_swc_by_neuron_index(args.index, output_dir=args.output)
     if args.name:
-        fileName = get_swc_by_neuron_name(args.name)
+        fileName = get_swc_by_neuron_name(args.name, output_dir=args.output)
         if args.validate: check_cylinder_intersections(fileName)
 else:
     parser.print_help()