pyxetabase 3.1.0.dev21__tar.gz → 3.1.0.dev23__tar.gz

{pyxetabase-3.1.0.dev21 → pyxetabase-3.1.0.dev23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 3.1.0.dev21
+Version: 3.1.0.dev23
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-3.1.0.dev21 → pyxetabase-3.1.0.dev23}/pyxetabase/opencga_config.py

@@ -76,6 +76,35 @@ class ClientConfiguration(object):
         except requests.ConnectionError:
             raise Exception('Unreachable host "{}"'.format(self.host))
 
+    @property
+    def host(self):
+        return self._config['rest']['host']
+
+    @host.setter
+    def host(self, new_host):
+        self._config['rest']['host'] = new_host
+
+    @property
+    def tlsAllowInvalidCertificates(self):
+        if ('tlsAllowInvalidCertificates' in self._config['rest']
+                and self._config['rest']['tlsAllowInvalidCertificates'] is not None):
+            return self._config['rest']['tlsAllowInvalidCertificates']
+        else:
+            return False
+
+    @property
+    def version(self):
+        return self._config['version'] if 'version' in self._config else 'v2'
+
+    @property
+    def cookies(self):
+        if 'cookies' in self._config and self._config['cookies']:
+            python_session_fhand = open(os.path.expanduser("~/.opencga/python_session.json"), 'r')
+            session_info = json.loads(python_session_fhand.read())
+            return session_info['cookies']
+        else:
+            return None
+
     @property
     def configuration(self):
         return self._config

{pyxetabase-3.1.0.dev21 → pyxetabase-3.1.0.dev23}/pyxetabase/rest_clients/admin_client.py

@@ -147,8 +147,7 @@ class Admin(_ParentRestClient):
 
     def sync_users(self, data=None, **options):
         """
-        Synchronise a group of users from an authentication origin with a
-            group in a study from catalog.
+        [DEPRECATED] Moved to /users/sync.
         PATH: /{apiVersion}/admin/users/sync
 
         :param dict data: JSON containing the parameters. (REQUIRED)

{pyxetabase-3.1.0.dev21 → pyxetabase-3.1.0.dev23}/pyxetabase/rest_clients/file_client.py

@@ -420,7 +420,7 @@ class File(_ParentRestClient):
             MICROARRAY_EXPRESSION_TWOCHANNELS_GENEPIX DATAMATRIX_EXPRESSION
             IDLIST IDLIST_RANKED ANNOTATION_GENEVSANNOTATION OTHER_NEWICK
             OTHER_BLAST OTHER_INTERACTION OTHER_GENOTYPE OTHER_PLINK OTHER_VCF
-            OTHER_PED VCF4 CVDB VARIANT ALIGNMENT COVERAGE SEQUENCE PEDIGREE
+            OTHER_PED VCF4 VARIANT ALIGNMENT COVERAGE SEQUENCE PEDIGREE
             REFERENCE_GENOME NONE UNKNOWN']
         :param str checksum: Expected MD5 file checksum.
         :param bool resource: Boolean field indicating whether the file is a

{pyxetabase-3.1.0.dev21 → pyxetabase-3.1.0.dev23}/pyxetabase/rest_clients/meta_client.py

@@ -55,15 +55,16 @@ class Meta(_ParentRestClient):
 
         return self._get(category='meta', resource='model', **options)
 
-    def openapi(self, **options):
+    def openapi(self, url, **options):
         """
         Opencga openapi json.
         PATH: /{apiVersion}/meta/openapi
 
-        :param str environment: Environment of the app.
-        :param str host: Opencga host without environment.
+        :param str url: Opencga host with environment. (REQUIRED)
+        :param str study: Opencga study to be default in queries.
         """
 
+        options['url'] = url
         return self._get(category='meta', resource='openapi', **options)
 
     def ping(self, **options):

{pyxetabase-3.1.0.dev21 → pyxetabase-3.1.0.dev23}/pyxetabase/rest_clients/study_client.py

@@ -166,6 +166,19 @@ class Study(_ParentRestClient):
 
         return self._get(category='studies', resource='groups', query_id=study, **options)
 
+    def sync_groups(self, study, data=None, **options):
+        """
+        Associate a remote group from an authentication origin with a local
+            group in a study.
+        PATH: /{apiVersion}/studies/{study}/groups/sync
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        """
+
+        return self._post(category='studies', resource='sync', query_id=study, subcategory='groups', data=data, **options)
+
     def update_groups(self, study, data=None, **options):
         """
         Add or remove a group.
@@ -386,6 +399,21 @@ class Study(_ParentRestClient):
 
         return self._post(category='studies', resource='update', query_id=study, data=data, **options)
 
+    def sync_users(self, study, authentication_origin_id, **options):
+        """
+        Synchronize all users from the remote groups of a given authentication
+            origin.
+        PATH: /{apiVersion}/studies/{study}/users/sync
+
+        :param str authentication_origin_id: Authentication origin ID.
+            (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        """
+
+        options['authenticationOriginId'] = authentication_origin_id
+        return self._post(category='studies', resource='sync', query_id=study, subcategory='users', **options)
+
     def variable_sets(self, study, **options):
         """
         Fetch variableSets from a study.

{pyxetabase-3.1.0.dev21 → pyxetabase-3.1.0.dev23}/pyxetabase.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 3.1.0.dev21
+Version: 3.1.0.dev23
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-3.1.0.dev21 → pyxetabase-3.1.0.dev23}/setup.py

@@ -14,7 +14,7 @@ with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
 
 setup(
     name='pyxetabase',
-    version='3.1.0.dev21',
+    version='3.1.0.dev23',
     description='A REST client for OpenCGA enterprise REST web services',
     long_description=long_description,
     long_description_content_type='text/x-rst',