diff fetch_organism_jbrowse.py @ 10:df0e4eb2dfa5 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"

--- a/fetch_organism_jbrowse.py	Mon Jul 29 10:09:19 2019 -0400
+++ b/fetch_organism_jbrowse.py	Mon Dec 02 05:44:41 2019 -0500
@@ -9,7 +9,13 @@
 import sys
 import time
 
-from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
+from apollo import accessible_organisms
+from apollo.util import GuessOrg, OrgOrGuess
+
+from arrow.apollo import get_apollo_instance
+
+from webapollo import UserObj, handle_credentials
+
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger(__name__)
 
@@ -52,27 +58,34 @@
 
 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')
     parser.add_argument('email', help='User Email')
 
     args = parser.parse_args()
 
-    wa = WebApolloInstance(args.apollo, args.username, args.password)
+    wa = get_apollo_instance()
     # 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)
 
     # User must have an account, if not, create it
-    gx_user = wa.users.assertOrCreateUser(args.email)
+    gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
+    handle_credentials(gx_user)
+
+    all_orgs = wa.organisms.get_organisms()
+    if 'error' in all_orgs:
+        all_orgs = []
+    all_orgs = [org['commonName'] for org in all_orgs]
+    if org_cn not in all_orgs:
+        raise Exception("Could not find organism %s" % org_cn)
 
     # User must have READ access
-
-    if not PermissionCheck(gx_user, org_cn, "READ"):
-        raise Exception("READ permissions are required for this action")
+    orgs = accessible_organisms(gx_user, [org_cn], 'READ')
+    if not orgs:
+        raise Exception("You do not have write permission on this organism")
+    org = wa.organisms.show_organism(org_cn)
 
     if not os.path.exists(args.target_dir):
         os.makedirs(args.target_dir)
@@ -94,7 +107,7 @@
     # files / folders before and after.
     sys.stderr.write(' '.join(cmd))
     sys.stderr.write('\n')
-    sys.stderr.write(subprocess.check_output(cmd))
+    sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
     if not are_dir_trees_equal(
         os.path.join(org['directory'].rstrip('/')),
         os.path.join(args.target_dir, 'data')
@@ -104,7 +117,7 @@
         sys.stderr.write('\n')
         sys.stderr.write(' '.join(cmd))
         sys.stderr.write('\n')
-        sys.stderr.write(subprocess.check_output(cmd))
+        sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
         if not are_dir_trees_equal(
             os.path.join(org['directory'].rstrip('/'), 'data'),
             os.path.join(args.target_dir, 'data')
@@ -113,7 +126,7 @@
             sys.stderr.write('\n')
             sys.stderr.write(' '.join(cmd))
             sys.stderr.write('\n')
-            sys.stderr.write(subprocess.check_output(cmd))
+            sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
             if not are_dir_trees_equal(
                 os.path.join(org['directory'].rstrip('/'), 'data'),
                 os.path.join(args.target_dir, 'data')