URL encoding

mcmd/client/api.py

@@ -1,23 +1,23 @@
-from urllib.parse import urljoin
+from urllib.parse import urljoin, quote
 
 from mcmd.config import config
 
 
 def endpoint(func):
     def wrapper(*args, **kwargs):
-        return urljoin(config.get('host', 'selected'), func(*args, **kwargs))
+        return urljoin(config.get('host', 'selected'), quote(func(*args, **kwargs)))
 
     return wrapper
 
 
 @endpoint
-def rest1():
-    return 'api/v1/'
+def rest1(path: str):
+    return urljoin('api/v1/', path)
 
 
 @endpoint
-def rest2():
-    return 'api/v2/'
+def rest2(path: str):
+    return urljoin('api/v2/', path)
 
 
 @endpoint

mcmd/client/auth.py

@@ -4,7 +4,6 @@
 """
 
 import json
-from urllib.parse import urljoin
 
 import requests
 from requests import HTTPError
@@ -41,7 +40,10 @@ def check_token():
         return
 
     try:
-        response = requests.get(urljoin(api.rest2(), 'sys_sec_Token?q=token=={}'.format(_token)),
+        response = requests.get(api.rest2('sys_sec_Token'),
+                                params={
+                                    'q': 'token=={}'.format(_token)
+                                },
                                 headers={'Content-Type': 'application/json', 'x-molgenis-token': _token})
         response.raise_for_status()
     except HTTPError as e:

mcmd/client/molgenis_client.py

@@ -7,8 +7,9 @@
 
 
 @request
-def get(url):
+def get(url, params=None):
     return requests.get(url,
+                        params=params,
                         headers=_get_default_headers())
 
 

mcmd/commands/add.py

@@ -132,7 +132,7 @@ def add_user(args):
     superuser = args.is_superuser
     ch_pwd = args.change_password
 
-    post(api.rest1() + 'sys_sec_User',
+    post(api.rest1('sys_sec_User'),
          data={'username': args.username,
                'password_': password,
                'changePassword': ch_pwd,
@@ -158,14 +158,18 @@ def add_package(args):
     if args.parent:
         data['parent'] = args.parent
 
-    post(api.rest1() + 'sys_md_Package', data=data)
+    post(api.rest1('sys_md_Package'), data=data)
 
 
 @command
 def add_token(args):
     io.start('Adding token %s for user %s' % (highlight(args.token), highlight(args.user)))
 
-    user = get(api.rest2() + 'sys_sec_User?attrs=id&q=username==%s' % args.user)
+    user = get(api.rest2('sys_sec_User'),
+               params={
+                   'attrs': 'id',
+                   'q': 'username=={}'.format(args.user)
+               })
     if user.json()['total'] == 0:
         raise McmdError('Unknown user %s' % args.user)
 
@@ -174,7 +178,7 @@ def add_token(args):
     data = {'User': user_id,
             'token': args.token}
 
-    post(api.rest1() + 'sys_sec_Token', data=data)
+    post(api.rest1('sys_sec_Token'), data=data)
 
 
 @command

mcmd/commands/delete.py

@@ -77,8 +77,7 @@ def _delete_entity_type_data(args):
     if args.force or (not args.force and io.confirm(
             'Are you sure you want to delete all data in entity type {}?'.format(args.resource))):
         io.start('Deleting all data from entity {}'.format(highlight(args.resource)))
-        url = urljoin(api.rest1(), args.resource)
-        client.delete(url)
+        client.delete(api.rest1(args.resource))
 
 
 def _delete_package(args):
@@ -97,16 +96,22 @@ def _delete_package_contents(args):
 
 
 def _delete_entity_types_in_package(package_id):
-    response = client.get(
-        api.rest2() + ResourceType.ENTITY_TYPE.get_entity_id() + '?attrs=id&q=package==' + package_id)
+    response = client.get(api.rest2(ResourceType.ENTITY_TYPE.get_entity_id()),
+                          params={
+                              'attrs': 'id',
+                              'q': 'package==' + package_id
+                          })
     entity_ids = [entity_type['id'] for entity_type in response.json()['items']]
     if len(entity_ids) > 0:
         _delete_rows(ResourceType.ENTITY_TYPE.get_entity_id(), entity_ids)
 
 
 def _delete_packages_in_package(package_id):
-    response = client.get(
-        api.rest2() + ResourceType.PACKAGE.get_entity_id() + '?attrs=id&q=parent==' + package_id)
+    response = client.get(api.rest2(ResourceType.PACKAGE.get_entity_id()),
+                          params={
+                              'attrs': 'id',
+                              'q': 'parent==' + package_id
+                          })
     package_ids = [entity_type['id'] for entity_type in response.json()['items']]
     if len(package_ids) > 0:
         _delete_rows(ResourceType.PACKAGE.get_entity_id(), package_ids)
@@ -120,8 +125,7 @@ def _delete_group(args):
 
 
 def _delete_rows(entity_type, rows):
-    url = '{}{}'.format(api.rest2(), entity_type)
-    client.delete_data(url, rows)
+    client.delete_data(api.rest2(entity_type), rows)
 
 
 def _get_resource_type(args):

mcmd/commands/make.py

@@ -42,7 +42,10 @@ def make(args):
 
 def _find_group(role):
     io.debug('Fetching groups')
-    groups = get(api.rest2() + 'sys_sec_Group?attrs=name')
+    groups = get(api.rest2('sys_sec_Group',
+                           params={
+                               'attrs': 'name'
+                           }))
     role = lower_kebab(role)
 
     matches = {len(group['name']): group['name'] for group in groups.json()['items'] if role.startswith(group['name'])}

mcmd/commands/set.py

@@ -65,15 +65,17 @@ def set_(args):
     entity = _get_settings_entity(args.type)
     io.start(
         'Updating {} of {} settings to {}'.format(highlight(args.setting), highlight(args.type), highlight(args.value)))
-    row = _get_row_id(entity)
-    url = '{}{}/{}/{}'.format(api.rest1(), entity, row, args.setting)
+    row = _get_first_row_id(entity)
+    url = api.rest1('{}/{}/{}'.format(entity, row, args.setting))
     put(url, json.dumps(args.value))
 
 
 def _get_settings():
-    entity = 'sys_md_EntityType'
-    query = 'q=extends==sys_set_settings&attrs=~id'
-    molgenis_settings = _quick_get(entity, query)
+    molgenis_settings = get(api.rest2('sys_md_EntityType'),
+                            params={
+                                'q': 'extends==sys_set_settings',
+                                'attrs': '~id'
+                            }).json()['items']
     return [setting['id'] for setting in molgenis_settings]
 
 
@@ -90,13 +92,9 @@ def _get_settings_entity(setting):
             raise McmdError('Setting [{}] is not a valid settings entity'.format(setting))
 
 
-def _quick_get(entity, q):
-    rest = api.rest2()
-    url = '{}{}?{}'.format(rest, entity, q)
-    return get(url).json()['items']
-
-
-def _get_row_id(entity):
-    query = 'attrs=~id'
-    settings = _quick_get(entity, query)
+def _get_first_row_id(entity):
+    settings = get(api.rest2(entity),
+                   params={
+                       'attrs': '~id'
+                   }).json()['items']
     return settings[0]['id']

mcmd/utils/principals.py

@@ -30,13 +30,20 @@ def principal_exists(principal_name, principal_type):
 
 def user_exists(username):
     log.debug('Checking if user %s exists' % username)
-    response = get(api.rest2() + 'sys_sec_User?q=username==' + username)
+    response = get(api.rest2('sys_sec_User'),
+                   params={
+                       'q': 'username==' + username
+                   })
+
     return int(response.json()['total']) > 0
 
 
 def role_exists(rolename):
     log.debug('Checking if role %s exists' % rolename)
-    response = get(api.rest2() + 'sys_sec_Role?q=name==' + rolename.upper())
+    response = get(api.rest2('sys_sec_Role'),
+                   params={
+                       'q': 'name==' + rolename.upper()
+                   })
     return int(response.json()['total']) > 0
 
 

mcmd/utils/resources.py

@@ -52,15 +52,22 @@ def detect_resource_type(resource_id, types: List[ResourceType]):
 
 def resource_exists(resource_id, resource_type):
     log.debug('Checking if %s %s exists' % (resource_type.get_label(), resource_id))
-    query = '?q={}=={}'.format(resource_type.get_identifying_attribute(), resource_id)
-    response = get(api.rest2() + resource_type.get_entity_id() + query)
+    query = '{}=={}'.format(resource_type.get_identifying_attribute(), resource_id)
+    response = get(api.rest2(resource_type.get_entity_id()),
+                   params={
+                       'q': query
+                   })
     return int(response.json()['total']) > 0
 
 
 def one_resource_exists(resources, resource_type):
     log.debug('Checking if one of [{}] exists in [{}]'.format(','.join(resources), resource_type.get_label()))
-    query = '?q={}=in=({})'.format(resource_type.get_identifying_attribute(), ','.join(resources))
-    response = get(api.rest2() + resource_type.get_entity_id() + query)
+    query = '{}=in=({})'.format(resource_type.get_identifying_attribute(), ','.join(resources))
+    response = get(api.rest2(resource_type.get_entity_id()),
+                   params={
+                       'q': query
+                   })
+
     return int(response.json()['total']) > 0