# HG changeset patch
# User gga
# Date 1535722450 14400
# Node ID 0af4179e6758b988584e17b2923054d57682a672
# Parent  a5de2095bd0103a8546343e79a7fe5d718cace0c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2

diff -r a5de2095bd01 -r 0af4179e6758 create_account.py
--- a/create_account.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/create_account.py	Fri Aug 31 09:34:10 2018 -0400
@@ -2,17 +2,11 @@
 from __future__ import print_function
 
 import argparse
-import random
 import time
 
 from six.moves.builtins import str
 
-from webapollo import WAAuth, WebApolloInstance
-
-
-def pwgen(length):
-    chars = list('qwrtpsdfghjklzxcvbnm')
-    return ''.join(random.choice(chars) for _ in range(length))
+from webapollo import PasswordGenerator, WAAuth, WebApolloInstance
 
 
 if __name__ == '__main__':
@@ -26,7 +20,7 @@
 
     wa = WebApolloInstance(args.apollo, args.username, args.password)
 
-    password = pwgen(12)
+    password = PasswordGenerator(12)
     time.sleep(1)
     users = wa.users.loadUsers()
     user = [u for u in users
diff -r a5de2095bd01 -r 0af4179e6758 create_features_from_gff3.py
--- a/create_features_from_gff3.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/create_features_from_gff3.py	Fri Aug 31 09:34:10 2018 -0400
@@ -8,7 +8,7 @@
 
 from six.moves.builtins import str
 
-from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry
+from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger(__name__)
 
@@ -25,14 +25,15 @@
 
     wa = WebApolloInstance(args.apollo, args.username, args.password)
     # User must have an account
-    gx_user = AssertUser(wa.users.loadUsers(email=args.email))
+    gx_user = wa.users.assertOrCreateUser(args.email)
 
     # Get organism
     org_cn = GuessOrg(args, wa)
     if isinstance(org_cn, list):
         org_cn = org_cn[0]
 
-    # TODO: Check user perms on org.
+    if not PermissionCheck(gx_user, org_cn, "WRITE"):
+        raise Exception("Action not permitted")
     org = wa.organisms.findOrganismByCn(org_cn)
 
     bad_quals = ['date_creation', 'source', 'owner', 'date_last_modified', 'Name', 'ID']
diff -r a5de2095bd01 -r 0af4179e6758 create_or_update_organism.py
--- a/create_or_update_organism.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/create_or_update_organism.py	Fri Aug 31 09:34:10 2018 -0400
@@ -8,11 +8,10 @@
 import sys
 import time
 
-from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance
+from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, 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)
@@ -33,8 +32,8 @@
     if isinstance(org_cn, list):
         org_cn = org_cn[0]
 
-    # User must have an account
-    gx_user = AssertUser(wa.users.loadUsers(email=args.email))
+    # User must have an account, if not, create it
+    gx_user = wa.users.assertOrCreateUser(args.email)
 
     log.info("Determining if add or update required")
     try:
@@ -43,14 +42,9 @@
         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:
+        if not PermissionCheck(gx_user, org_cn, "WRITE"):
             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)
 
diff -r a5de2095bd01 -r 0af4179e6758 delete_features.py
--- a/delete_features.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/delete_features.py	Fri Aug 31 09:34:10 2018 -0400
@@ -5,7 +5,7 @@
 import logging
 import random
 
-from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, retry
+from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, retry
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger(__name__)
 
@@ -21,14 +21,15 @@
 
     wa = WebApolloInstance(args.apollo, args.username, args.password)
     # User must have an account
-    gx_user = AssertUser(wa.users.loadUsers(email=args.email))
+    gx_user = wa.users.assertOrCreateUser(args.email)
 
     # Get organism
     org_cn = GuessOrg(args, wa)
     if isinstance(org_cn, list):
         org_cn = org_cn[0]
 
-    # TODO: Check user perms on org.
+    if not PermissionCheck(gx_user, org_cn, "WRITE"):
+        raise Exception("Action not permitted")
     org = wa.organisms.findOrganismByCn(org_cn)
 
     sequences = wa.organisms.getSequencesForOrganism(org['id'])
diff -r a5de2095bd01 -r 0af4179e6758 delete_organism.py
--- a/delete_organism.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/delete_organism.py	Fri Aug 31 09:34:10 2018 -0400
@@ -4,7 +4,7 @@
 import argparse
 import logging
 
-from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance
+from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger(__name__)
 
@@ -19,14 +19,15 @@
 
     wa = WebApolloInstance(args.apollo, args.username, args.password)
     # User must have an account
-    gx_user = AssertUser(wa.users.loadUsers(email=args.email))
+    gx_user = wa.users.assertOrCreateUser(args.email)
 
     # Get organism
     org_cn = GuessOrg(args, wa)
     if isinstance(org_cn, list):
         org_cn = org_cn[0]
 
-    # TODO: Check user perms on org.
+    if not PermissionCheck(gx_user, org_cn, "WRITE"):
+        raise Exception("You do not have write permission on this organism")
     org = wa.organisms.findOrganismByCn(org_cn)
 
     # Call setSequence to tell apollo which organism we're working with
@@ -34,7 +35,9 @@
     # Then get a list of features.
     features = wa.annotations.getFeatures()
     # For each feature in the features
-    for feature in features['features']:
-        # We see that deleteFeatures wants a uniqueName, and so we pass
-        # is the uniquename field in the feature.
-        print(wa.annotations.deleteFeatures([feature['uniquename']]))
+    # If it exists
+    if 'features' in features:
+        for feature in features['features']:
+            # We see that deleteFeatures wants a uniqueName, and so we pass
+            # is the uniquename field in the feature.
+            print(wa.annotations.deleteFeatures([feature['uniquename']]))
diff -r a5de2095bd01 -r 0af4179e6758 delete_organism.xml
--- a/delete_organism.xml	Mon Mar 12 06:32:27 2018 -0400
+++ b/delete_organism.xml	Fri Aug 31 09:34:10 2018 -0400
@@ -16,6 +16,7 @@
         --gff "$gff_out"
         --fasta "$fasta_out"
         --json "$json_out"
+        "$__user_email__"
 
         &&
 
@@ -38,7 +39,9 @@
     <param name="ask_two" type="boolean" truevalue="yes" falsevalue="" label="Are you really, really SURE you want to do this?" help="There's NO coming back from this."/>
   </inputs>
   <outputs>
-    <data format="tabular" name="output" label="Process and Error Log"/>
+    <data format="tabular" name="output" label="Process and Error Log">
+        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
+    </data>
 
     <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
     <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
diff -r a5de2095bd01 -r 0af4179e6758 export.py
--- a/export.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/export.py	Fri Aug 31 09:34:10 2018 -0400
@@ -9,7 +9,7 @@
 
 from Bio import SeqIO
 
-from webapollo import CnOrGuess, GuessCn, WAAuth, WebApolloInstance
+from webapollo import CnOrGuess, GuessCn, PermissionCheck, WAAuth, WebApolloInstance
 
 try:
     import StringIO as io
@@ -71,15 +71,21 @@
     parser.add_argument('--gff', type=argparse.FileType('w'))
     parser.add_argument('--fasta', type=argparse.FileType('w'))
     parser.add_argument('--json', type=argparse.FileType('w'))
-
+    parser.add_argument('email', help='User Email')
     args = parser.parse_args()
 
     wa = WebApolloInstance(args.apollo, args.username, args.password)
 
     org_cn_list, seqs = GuessCn(args, wa)
 
+    # User must have an apollo account, if not, create it
+    gx_user = wa.users.assertOrCreateUser(args.email)
+
     org_data = []
     for org_cn in org_cn_list:
+        # User must have read permission on organism
+        if not PermissionCheck(gx_user, org_cn, "READ"):
+            continue
         indiv_org_data = export(org_cn, seqs)
         org_data.append(indiv_org_data)
     args.json.write(json.dumps(org_data, indent=2))
diff -r a5de2095bd01 -r 0af4179e6758 fetch_organism_jbrowse.py
--- a/fetch_organism_jbrowse.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/fetch_organism_jbrowse.py	Fri Aug 31 09:34:10 2018 -0400
@@ -9,7 +9,7 @@
 import sys
 import time
 
-from webapollo import GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance
+from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger(__name__)
 
@@ -55,6 +55,7 @@
     WAAuth(parser)
     OrgOrGuess(parser)
     parser.add_argument('target_dir', help='Target directory')
+    parser.add_argument('email', help='User Email')
 
     args = parser.parse_args()
 
@@ -65,6 +66,14 @@
         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)
+
+    # User must have READ access
+
+    if not PermissionCheck(gx_user, org_cn, "READ"):
+        raise Exception("READ permissions are required for this action")
+
     if not os.path.exists(args.target_dir):
         os.makedirs(args.target_dir)
 
diff -r a5de2095bd01 -r 0af4179e6758 list_organisms.py
--- a/list_organisms.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/list_organisms.py	Fri Aug 31 09:34:10 2018 -0400
@@ -4,7 +4,7 @@
 import argparse
 import json
 
-from webapollo import AssertUser, WAAuth, WebApolloInstance, accessible_organisms
+from webapollo import WAAuth, WebApolloInstance, accessible_organisms
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance')
@@ -14,7 +14,8 @@
 
     wa = WebApolloInstance(args.apollo, args.username, args.password)
 
-    gx_user = AssertUser(wa.users.loadUsers(email=args.email))
+    gx_user = wa.users.assertOrCreateUser(args.email)
+
     all_orgs = wa.organisms.findAllOrganisms()
 
     orgs = accessible_organisms(gx_user, all_orgs)
diff -r a5de2095bd01 -r 0af4179e6758 webapollo.py
--- a/webapollo.py	Mon Mar 12 06:32:27 2018 -0400
+++ b/webapollo.py	Fri Aug 31 09:34:10 2018 -0400
@@ -5,6 +5,7 @@
 import json
 import logging
 import os
+import random
 import time
 from abc import abstractmethod
 
@@ -478,6 +479,25 @@
         raise Exception("User is not an administrator. Permission denied")
 
 
+def PermissionCheck(user, org_cn, permission_type):
+    return any(org["organism"] == org_cn and permission_type in org["permissions"] for org in user.organismPermissions)
+
+
+def PasswordGenerator(length):
+    chars = list('qwrtpsdfghjklzxcvbnm')
+    return ''.join(random.choice(chars) for _ in range(length))
+
+
+def IsRemoteUser():
+    if 'GALAXY_WEBAPOLLO_REMOTE_USER' not in os.environ:
+        return False
+    value = os.environ['GALAXY_WEBAPOLLO_REMOTE_USER']
+    if value.lower() in ('true', 't', '1'):
+        return True
+    else:
+        return False
+
+
 class WebApolloInstance(object):
 
     def __init__(self, url, username, password):
@@ -1254,7 +1274,10 @@
         return self.request('addOrganism', data)
 
     def findAllOrganisms(self):
-        return self.request('findAllOrganisms', {})
+        orgs = self.request('findAllOrganisms', {})
+        if not isinstance(orgs, (list,)):
+            orgs = []
+        return orgs
 
     def findOrganismByCn(self, cn):
         orgs = self.findAllOrganisms()
@@ -1352,7 +1375,7 @@
         data = {'group': group.name, 'userId': user.userId}
         return self.request('removeUserFromGroup', data)
 
-    def createUser(self, email, firstName, lastName, newPassword, role="user", groups=None):
+    def createUser(self, email, firstName, lastName, newPassword, role="user", groups=None, addToHistory=False):
         data = {
             'firstName': firstName,
             'lastName': lastName,
@@ -1363,7 +1386,19 @@
             'newPassword': newPassword,
             # 'organismPermissions': [],
         }
-        return self.request('createUser', data)
+        returnData = self.request('createUser', data)
+        if addToHistory and not IsRemoteUser():
+            f = open("Apollo_credentials.txt", "w")
+            f.write('Username: %s\tPassword: %s' % (email, newPassword))
+        return returnData
+
+    def assertOrCreateUser(self, email):
+        try:
+            gx_user = AssertUser(self.loadUsers(email))
+        except Exception:
+            self.createUser(email, email, email, PasswordGenerator(12), role='user', addToHistory=True)
+            gx_user = AssertUser(self.loadUsers(email))
+        return gx_user
 
     def deleteUser(self, user):
         return self.request('deleteUser', {'userId': user.userId})
@@ -1532,11 +1567,6 @@
         os.environ['GALAXY_WEBAPOLLO_USER'],
         os.environ['GALAXY_WEBAPOLLO_PASSWORD']
     )
-    # Assert that the email exists in apollo
-    try:
-        gx_user = wa.requireUser(email)
-    except UnknownUserException:
-        return []
 
     # Key for cached data
     cacheKey = 'groups-' + email
@@ -1545,7 +1575,7 @@
     if cacheKey not in cache:
         # However if it ISN'T there, we know we're safe to fetch + put in
         # there.
-        data = _galaxy_list_groups(wa, gx_user, *args, **kwargs)
+        data = _galaxy_list_groups(wa, *args, **kwargs)
         cache[cacheKey] = data
         return data
     try:
@@ -1558,12 +1588,12 @@
     except KeyError:
         # If access fails due to eviction, we will fail over and can ensure that
         # data is inserted.
-        data = _galaxy_list_groups(wa, gx_user, *args, **kwargs)
+        data = _galaxy_list_groups(wa, *args, **kwargs)
         cache[cacheKey] = data
         return data
 
 
-def _galaxy_list_groups(wa, gx_user, *args, **kwargs):
+def _galaxy_list_groups(wa, *args, **kwargs):
     # Fetch the groups.
     group_data = []
     for group in wa.groups.loadGroups():