--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_organism_jbrowse.py	Mon Sep 11 05:45:08 2017 -0400
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import filecmp
+import logging
+import os
+import subprocess
+import sys
+import time
+
+from webapollo import GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+def are_dir_trees_equal(dir1, dir2):
+    """
+    Compare two directories recursively. Files in each directory are
+    assumed to be equal if their names and contents are equal.
+
+    @param dir1: First directory path
+    @param dir2: Second directory path
+
+    @return: True if the directory trees are the same and
+        there were no errors while accessing the directories or files,
+        False otherwise.
+
+    # http://stackoverflow.com/questions/4187564/recursive-dircmp-compare-two-directories-to-ensure-they-have-the-same-files-and/6681395#6681395
+    """
+
+    dirs_cmp = filecmp.dircmp(dir1, dir2)
+    if len(dirs_cmp.left_only) > 0 or len(dirs_cmp.right_only) > 0 or \
+            len(dirs_cmp.funny_files) > 0:
+        print(('LEFT', dirs_cmp.left_only))
+        print(('RIGHT', dirs_cmp.right_only))
+        print(('FUNNY', dirs_cmp.funny_files))
+        return False
+    (_, mismatch, errors) = filecmp.cmpfiles(
+        dir1, dir2, dirs_cmp.common_files, shallow=False)
+    if len(mismatch) > 0 or len(errors) > 0:
+        print(mismatch)
+        print(errors)
+        return False
+    for common_dir in dirs_cmp.common_dirs:
+        new_dir1 = os.path.join(dir1, common_dir)
+        new_dir2 = os.path.join(dir2, common_dir)
+        if not are_dir_trees_equal(new_dir1, new_dir2):
+            return False
+    return True
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
+    WAAuth(parser)
+    OrgOrGuess(parser)
+    parser.add_argument('target_dir', help='Target directory')
+
+    args = parser.parse_args()
+
+    wa = WebApolloInstance(args.apollo, args.username, args.password)
+    # User must have an account
+    org_cn = GuessOrg(args, wa)
+    if isinstance(org_cn, list):
+        org_cn = org_cn[0]
+    org = wa.organisms.findOrganismByCn(org_cn)
+
+    if not os.path.exists(args.target_dir):
+        os.makedirs(args.target_dir)
+
+    if not os.path.exists(os.path.join(org['directory'], 'seq')):
+        sys.stderr.write("Missing seq directory BEFORE copy")
+        sys.exit(1)
+
+    cmd = [
+        'rsync', '-avr',
+        org['directory'].rstrip('/') + '/',
+        os.path.join(args.target_dir, 'data', '')
+    ]
+    # We run this OBSESSIVELY because my org had a hiccup where the origin
+    # (silent) cp -R failed at one point. This caused MANY HEADACHES.
+    #
+    # Our response is to run this 3 times (in case the issue is temporary),
+    # with delays in between. And ensure that we have the correct number of
+    # files / folders before and after.
+    sys.stderr.write(' '.join(cmd))
+    sys.stderr.write('\n')
+    sys.stderr.write(subprocess.check_output(cmd))
+    if not are_dir_trees_equal(
+        os.path.join(org['directory'].rstrip('/')),
+        os.path.join(args.target_dir, 'data')
+    ):
+        # Not good
+        time.sleep(5)
+        sys.stderr.write('\n')
+        sys.stderr.write(' '.join(cmd))
+        sys.stderr.write('\n')
+        sys.stderr.write(subprocess.check_output(cmd))
+        if not are_dir_trees_equal(
+            os.path.join(org['directory'].rstrip('/'), 'data'),
+            os.path.join(args.target_dir, 'data')
+        ):
+            time.sleep(5)
+            sys.stderr.write('\n')
+            sys.stderr.write(' '.join(cmd))
+            sys.stderr.write('\n')
+            sys.stderr.write(subprocess.check_output(cmd))
+            if not are_dir_trees_equal(
+                os.path.join(org['directory'].rstrip('/'), 'data'),
+                os.path.join(args.target_dir, 'data')
+            ):
+                sys.stderr.write('FAILED THREE TIMES TO COPY. SOMETHING IS WRONG WRONG WRONG.')
+                sys.exit(2)