Mercurial > repos > gga > apollo_export

comparison webapollo.py @ 5:950fb2bf116d draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
author gga
date Fri, 31 Aug 2018 09:33:38 -0400
parents 5559e41721c3
children 0e47d146590b
comparison
equal deleted inserted replaced
4:5559e41721c3 5:950fb2bf116d
3 import argparse 3 import argparse
4 import collections 4 import collections
5 import json 5 import json
6 import logging 6 import logging
7 import os 7 import os
8 import random
8 import time 9 import time
9 from abc import abstractmethod 10 from abc import abstractmethod
10 11
11 from BCBio import GFF 12 from BCBio import GFF
12 13
476 return True 477 return True
477 else: 478 else:
478 raise Exception("User is not an administrator. Permission denied") 479 raise Exception("User is not an administrator. Permission denied")
479 480
480 481
482 def PermissionCheck(user, org_cn, permission_type):
483 return any(org["organism"] == org_cn and permission_type in org["permissions"] for org in user.organismPermissions)
484
485
486 def PasswordGenerator(length):
487 chars = list('qwrtpsdfghjklzxcvbnm')
488 return ''.join(random.choice(chars) for _ in range(length))
489
490
491 def IsRemoteUser():
492 if 'GALAXY_WEBAPOLLO_REMOTE_USER' not in os.environ:
493 return False
494 value = os.environ['GALAXY_WEBAPOLLO_REMOTE_USER']
495 if value.lower() in ('true', 't', '1'):
496 return True
497 else:
498 return False
499
500
481 class WebApolloInstance(object): 501 class WebApolloInstance(object):
482 502
483 def __init__(self, url, username, password): 503 def __init__(self, url, username, password):
484 self.apollo_url = url 504 self.apollo_url = url
485 self.username = username 505 self.username = username
1252 data['species'] = species 1272 data['species'] = species
1253 1273
1254 return self.request('addOrganism', data) 1274 return self.request('addOrganism', data)
1255 1275
1256 def findAllOrganisms(self): 1276 def findAllOrganisms(self):
1257 return self.request('findAllOrganisms', {}) 1277 orgs = self.request('findAllOrganisms', {})
1278 if not isinstance(orgs, (list,)):
1279 orgs = []
1280 return orgs
1258 1281
1259 def findOrganismByCn(self, cn): 1282 def findOrganismByCn(self, cn):
1260 orgs = self.findAllOrganisms() 1283 orgs = self.findAllOrganisms()
1261 orgs = [x for x in orgs if x['commonName'] == cn] 1284 orgs = [x for x in orgs if x['commonName'] == cn]
1262 if len(orgs) == 0: 1285 if len(orgs) == 0:
1350 1373
1351 def removeUserFromGroup(self, group, user): 1374 def removeUserFromGroup(self, group, user):
1352 data = {'group': group.name, 'userId': user.userId} 1375 data = {'group': group.name, 'userId': user.userId}
1353 return self.request('removeUserFromGroup', data) 1376 return self.request('removeUserFromGroup', data)
1354 1377
1355 def createUser(self, email, firstName, lastName, newPassword, role="user", groups=None): 1378 def createUser(self, email, firstName, lastName, newPassword, role="user", groups=None, addToHistory=False):
1356 data = { 1379 data = {
1357 'firstName': firstName, 1380 'firstName': firstName,
1358 'lastName': lastName, 1381 'lastName': lastName,
1359 'email': email, 1382 'email': email,
1360 'role': role, 1383 'role': role,
1361 'groups': [] if groups is None else groups, 1384 'groups': [] if groups is None else groups,
1362 # 'availableGroups': [], 1385 # 'availableGroups': [],
1363 'newPassword': newPassword, 1386 'newPassword': newPassword,
1364 # 'organismPermissions': [], 1387 # 'organismPermissions': [],
1365 } 1388 }
1366 return self.request('createUser', data) 1389 returnData = self.request('createUser', data)
1390 if addToHistory and not IsRemoteUser():
1391 f = open("Apollo_credentials.txt", "w")
1392 f.write('Username: %s\tPassword: %s' % (email, newPassword))
1393 return returnData
1394
1395 def assertOrCreateUser(self, email):
1396 try:
1397 gx_user = AssertUser(self.loadUsers(email))
1398 except Exception:
1399 self.createUser(email, email, email, PasswordGenerator(12), role='user', addToHistory=True)
1400 gx_user = AssertUser(self.loadUsers(email))
1401 return gx_user
1367 1402
1368 def deleteUser(self, user): 1403 def deleteUser(self, user):
1369 return self.request('deleteUser', {'userId': user.userId}) 1404 return self.request('deleteUser', {'userId': user.userId})
1370 1405
1371 def updateUser(self, user, email, firstName, lastName, newPassword): 1406 def updateUser(self, user, email, firstName, lastName, newPassword):
1530 wa = WebApolloInstance( 1565 wa = WebApolloInstance(
1531 os.environ['GALAXY_WEBAPOLLO_URL'], 1566 os.environ['GALAXY_WEBAPOLLO_URL'],
1532 os.environ['GALAXY_WEBAPOLLO_USER'], 1567 os.environ['GALAXY_WEBAPOLLO_USER'],
1533 os.environ['GALAXY_WEBAPOLLO_PASSWORD'] 1568 os.environ['GALAXY_WEBAPOLLO_PASSWORD']
1534 ) 1569 )
1535 # Assert that the email exists in apollo
1536 try:
1537 gx_user = wa.requireUser(email)
1538 except UnknownUserException:
1539 return []
1540 1570
1541 # Key for cached data 1571 # Key for cached data
1542 cacheKey = 'groups-' + email 1572 cacheKey = 'groups-' + email
1543 # We don't want to trust "if key in cache" because between asking and fetch 1573 # We don't want to trust "if key in cache" because between asking and fetch
1544 # it might through key error. 1574 # it might through key error.
1545 if cacheKey not in cache: 1575 if cacheKey not in cache:
1546 # However if it ISN'T there, we know we're safe to fetch + put in 1576 # However if it ISN'T there, we know we're safe to fetch + put in
1547 # there. 1577 # there.
1548 data = _galaxy_list_groups(wa, gx_user, *args, **kwargs) 1578 data = _galaxy_list_groups(wa, *args, **kwargs)
1549 cache[cacheKey] = data 1579 cache[cacheKey] = data
1550 return data 1580 return data
1551 try: 1581 try:
1552 # The cache key may or may not be in the cache at this point, it 1582 # The cache key may or may not be in the cache at this point, it
1553 # /likely/ is. However we take no chances that it wasn't evicted between 1583 # /likely/ is. However we take no chances that it wasn't evicted between
1556 data = cache[cacheKey] 1586 data = cache[cacheKey]
1557 return data 1587 return data
1558 except KeyError: 1588 except KeyError:
1559 # If access fails due to eviction, we will fail over and can ensure that 1589 # If access fails due to eviction, we will fail over and can ensure that
1560 # data is inserted. 1590 # data is inserted.
1561 data = _galaxy_list_groups(wa, gx_user, *args, **kwargs) 1591 data = _galaxy_list_groups(wa, *args, **kwargs)
1562 cache[cacheKey] = data 1592 cache[cacheKey] = data
1563 return data 1593 return data
1564 1594
1565 1595
1566 def _galaxy_list_groups(wa, gx_user, *args, **kwargs): 1596 def _galaxy_list_groups(wa, *args, **kwargs):
1567 # Fetch the groups. 1597 # Fetch the groups.
1568 group_data = [] 1598 group_data = []
1569 for group in wa.groups.loadGroups(): 1599 for group in wa.groups.loadGroups():
1570 # Reformat 1600 # Reformat
1571 group_data.append((group.name, group.name, False)) 1601 group_data.append((group.name, group.name, False))