diff create_or_update_organism.py @ 0:b4a85d0c85b8 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_or_update_organism.py	Mon Sep 11 05:47:07 2017 -0400
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import json
+import logging
+import shutil
+import sys
+import time
+
+from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
+    WAAuth(parser)
+
+    parser.add_argument('jbrowse', help='JBrowse Data Directory')
+    parser.add_argument('email', help='User Email')
+    OrgOrGuess(parser)
+    parser.add_argument('--genus', help='Organism Genus')
+    parser.add_argument('--species', help='Organism Species')
+    parser.add_argument('--public', action='store_true', help='Make organism public')
+    parser.add_argument('--group', help='Give access to a user group')
+    parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
+
+    args = parser.parse_args()
+    wa = WebApolloInstance(args.apollo, args.username, args.password)
+
+    org_cn = GuessOrg(args, wa)
+    if isinstance(org_cn, list):
+        org_cn = org_cn[0]
+
+    # User must have an account
+    gx_user = AssertUser(wa.users.loadUsers(email=args.email))
+
+    log.info("Determining if add or update required")
+    try:
+        org = wa.organisms.findOrganismByCn(org_cn)
+    except Exception:
+        org = None
+
+    if org:
+        has_perms = False
+        old_directory = org.directory
+        for user_owned_organism in gx_user.organismPermissions:
+            if 'WRITE' in user_owned_organism['permissions']:
+                has_perms = True
+                break
+
+        if not has_perms:
+            print("Naming Conflict. You do not have permissions to access this organism. Either request permission from the owner, or choose a different name for your organism.")
+            sys.exit(2)
+
+        log.info("\tUpdating Organism")
+        data = wa.organisms.updateOrganismInfo(
+            org['id'],
+            org_cn,
+            args.jbrowse,
+            # mandatory
+            genus=args.genus,
+            species=args.species,
+            public=args.public
+        )
+        time.sleep(2)
+        if(args.remove_old_directory):
+            shutil.rmtree(old_directory)
+
+        data = [wa.organisms.findOrganismById(org['id'])]
+
+    else:
+        # New organism
+        log.info("\tAdding Organism")
+        data = wa.organisms.addOrganism(
+            org_cn,
+            args.jbrowse,
+            genus=args.genus,
+            species=args.species,
+            public=args.public
+        )
+
+        # Must sleep before we're ready to handle
+        time.sleep(2)
+        log.info("Updating permissions for %s on %s", gx_user, org_cn)
+        wa.users.updateOrganismPermission(
+            gx_user, org_cn,
+            write=True,
+            export=True,
+            read=True,
+        )
+
+        # Group access
+        if args.group:
+            group = wa.groups.loadGroupByName(name=args.group)
+            res = wa.groups.updateOrganismPermission(group, org_cn,
+                                                     administrate=False, write=True, read=True,
+                                                     export=True)
+
+    data = [o for o in data if o['commonName'] == org_cn]
+    print(json.dumps(data, indent=2))