vcf-miner.client

Python client for VCF-Miner

How to get started

Go to a directory of you choice and clone this repository:

git clone https://github.com/ratzeni/vcf-miner.client.git
cd vcf-miner.client

Install vcf-miner.client

python setup.py install

Examples

Connection

from vcfminerclient import VCFMinerClient
from alta.utils import a_logger, LOG_LEVELS

logger = a_logger('main',level='INFO')
conf=dict(host='http://localhost:8888',
          username='Admin',
          password='temppass',
          server_host='192.168.1.1',
          server_user='username')

client = VCFMinerClient(conf=conf, logger=logger)

2017-04-28 12:35:16|INFO    |main |Connecting to http://localhost:8888 
2017-04-28 12:35:22|INFO    |main |User Admin is authenticated

Show Auth Details

result = client.get_authentication()

{'errors': None,
 'result': {u'isAuthenticated': True,
            u'userToken': u'7c2f7227-1cfe-4815-90da-70dfa2fb6ca7:ea428c44-2f3d-4e07-9d68-b5ddadeef538'
            },
 'success': True,
 'warnings': None}

Create new User

result = client.create_user(new_username='newUser', new_password='newPassword')

{'errors': None,
 'result': ['"#Id"\t"Username"\t"NameLast"\t"NameFirst"\t"Email"\t"Phone"\t"IsLdapUser"\t"IsAllowedToLogin"\t"PersonId"\t"EmployeeId"\t"RacfId"\t"Created"\t"LastLogin"\t"PasswordSaltIfLocal"\t"PasswordHashIfLocal"',
  '"1"\t"Admin"\t""\t"Admin"\t""\t""\t"false"\t"true"\t""\t""\t""\t"2014-05-30 21:19:03.003"\t"2017-06-06 16:40:53.053"\t"5e63c61d-79a1-4c42-b14b-d7c820570a75"\t"$2a$08$wZ0xOUJw/BBqUxJwxwDhxuYRR4Gyuphmb6LOg3/oymNP8Txuowtay"',
  '"2"\t"kelaz"\t""\t"Kelaz"\t""\t""\t"false"\t"true"\t""\t""\t""\t"2017-04-19 04:25:44.044"\t"2017-04-26 19:07:29.029"\t"5e63c61d-79a1-4c42-b14b-d7c820570a75"\t"$2a$08$DLgWcx.j43k3pLUBw4DXcOn5R6Da4b2uqvguIIhttA2iQqEBLk./C"',
  '"3"\t"newUser"\t""\t"NewUser"\t""\t""\t"false"\t"true"\t""\t""\t""\t"2017-06-06 04:40:57.200"\t"2017-06-06 04:40:57.200"\t"5e63c61d-79a1-4c42-b14b-d7c820570a75"\t"$2a$08$KHiMrMLGbqNPfyqs6xd3V.l68CfVd4tUbLW7cn9mqSZg.rx5vs71K"'],
 'success': True,
 'warnings': None}

List Users

result = client.get_users()

{'errors': None,
 'result': [{u'created': u'2014-05-30T21:19:03.000+0000',
   u'email': u'',
   u'employeeId': u'',
   u'id': 1,
   u'isAllowedToLogin': True,
   u'isLdapUser': False,
   u'lastLogin': u'2017-04-28T10:41:35.000+0000',
   u'nameFirst': u'Admin',
   u'nameLast': u'',
   u'passwordHashIfLocal': u'',
   u'passwordSaltIfLocal': u'',
   u'personId': u'',
   u'phone': u'',
   u'racfId': u'',
   u'username': u'Admin'}],
 'success': True,
 'warnings': None}

Create Group

result = client.create_group('myFirstGroup')

{'errors': None,
 'result': {u'created': u'2017-04-28T10:50:26.022+0000',
  u'groupName': u'myFirstGroup',
  u'id': 1,
  u'ownerUserId': 1},
 'success': True,
 'warnings': None}

Add User to Group

result = client.add_user_to_group('Admin', 'myFirstGroup')

{'errors': None,
 'result': None,
 'success': True,
 'warnings': 'No JSON object could be decoded'}

List Groups (for user)

result = client.get_groups(username='Admin')

{'errors': None,
 'result': [{u'created': u'2017-04-28T10:50:26.000+0000',
   u'groupName': u'myFirstGroup',
   u'id': 1,
   u'ownerUserId': 1}],
 'success': True,
 'warnings': None}

List Users in Group

result = client.get_users_in_group('myFirstGroup')

{'errors': None,
 'result': [{u'created': u'2014-05-30T21:19:03.000+0000',
   u'email': u'',
   u'employeeId': u'',
   u'id': 1,
   u'isAllowedToLogin': True,
   u'isLdapUser': False,
   u'lastLogin': u'2017-04-28T10:41:35.000+0000',
   u'nameFirst': u'Admin',
   u'nameLast': u'',
   u'passwordHashIfLocal': u'',
   u'passwordSaltIfLocal': u'',
   u'personId': u'',
   u'phone': u'',
   u'racfId': u'',
   u'username': u'Admin'}],
 'success': True,
 'warnings': None}

Upload VCF

result = client.upload_vcf(vcfpath='/my/vcf/path/some.genotypes.vcf', vcfname='my_vcf')

{'errors': None,
 'result': 'File uploaded and workspace constructed : { "owner" : "Admin" , "alias" : "my_vcf" , "ready" : 1 , "_id" :  { "$oid" : "59033ffbe4b0d97b915db706"} , "key" : "w95aba91216131373b571c1f796ce0f113aa84e95"}',
 'success': True,
 'warnings': 'No JSON object could be decoded'}

Add VCF to group

result = client.add_vcf_to_group('my_vcf', groupname='myFirstGroup')

{'errors': None,
 'result': '',
 'success': True,
 'warnings': 'No JSON object could be decoded'}

List VCF in Group

result = client.get_vcf_for_group('myFirstGroup')

{'errors': None,
 'result': [{u'description': u'user=Admin,name=my_vcf,date=Fri Apr 28 13:13:31 UTC 2017',
   u'id': 1,
   u'key': u'w95aba91216131373b571c1f796ce0f113aa84e95',
   u'ownerUserId': 1,
   u'type': u'WKS'}],
 'success': True,
 'warnings': None}

Add VCF to User

result = client.add_vcf_to_user('my_vcf', username='Admin')

{'errors': None,
 'result': None,
 'success': True,
 'warnings': "VCF 'my_vcf already in User 'Admin'"}

List VCF in User

result = client.get_vcf_for_user(username="Admin")

{'errors': None,
 'result': [{u'description': u'user=Admin,name=my_vcf,date=Tue May 02 10:32:53 UTC 2017',
   u'id': 1,
   u'key': u'w5fbd4e0de94b9d4aefc9799a9c042aaec8065bf7',
   u'ownerUserId': 1,
   u'type': u'WKS'}],
 'success': True,
 'warnings': None}

Delete VCF

result = client.delete_vcf(vcfname='my_vcf')

{'errors': None,
 'result': {u'status': u'workspace= w5fbd4e0de94b9d4aefc9799a9c042aaec8065bf7 deleted'},
 'success': True,
 'warnings': None}

Remove User from Group

result = client.remove_user_from_group(username='Admin', groupname='myFirstGroup')

{'errors': None,
 'result': None,
 'success': True,
 'warnings': 'No JSON object could be decoded'}

Delete Group

result = client.delete_group(groupname='myFirstGroup')

{'errors': None,
 'result': None,
 'success': True,
 'warnings': 'No JSON object could be decoded'}