pyxetabase 3.1.0.dev21__py3-none-any.whl → 3.1.0.dev23__py3-none-any.whl

pyopencga/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

pyopencga/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)

pyopencga/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

pyopencga/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/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/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/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/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/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.dist-info → pyxetabase-3.1.0.dev23.dist-info}/METADATA

@@ -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.dist-info → pyxetabase-3.1.0.dev23.dist-info}/RECORD

@@ -2,18 +2,18 @@ pyopencga/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyopencga/commons.py,sha256=asnM3N7Q6JdgD6hXWmlX875HJizTLAODqs0dl3UYH-E,14307
 pyopencga/exceptions.py,sha256=GmtDcurD3d_fzaa8AEntF4-sZR4Elgg4Iz3z-UUqjYU,274
 pyopencga/opencga_client.py,sha256=gM9UzbjXwHKYRbsz3qmhS8xHuIlr13sn-VEzx6cscxk,14858
-pyopencga/opencga_config.py,sha256=hqBChooRKrkA6JmEbb6pOBTlfE_tv6_67H5WTKUXoDE,6047
+pyopencga/opencga_config.py,sha256=RK23fextK79S5wq4FaQygwuPnE4p4J9GbjY6hJ0Krxc,7009
 pyopencga/rest_response.py,sha256=Gx7utYTsXV-aciFZV4f7M2eNDQg5IlphGK_T8q_PhHE,8634
 pyopencga/retry.py,sha256=_X02bDcJmr9cWH4Bt0YfUPkYborpuStmw5WDDKczwHM,2296
 pyopencga/rest_clients/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyopencga/rest_clients/_parent_rest_clients.py,sha256=6_U1y3fwOCDDlfrdzoigkgbUZke8Msu6dW87CZPwccU,4277
-pyopencga/rest_clients/admin_client.py,sha256=dGPcDodsHQJw83ZcajZkWDxs2RmmQ4ZyFr45VMDo2bo,7000
+pyopencga/rest_clients/admin_client.py,sha256=jn34TGFeonEvsC4bEpiw7_kTkH_R47Joo3T3grz8LTs,6926
 pyopencga/rest_clients/alignment_client.py,sha256=qVce3PTZcoYj2HIOwKtHgTp-GNDMnAG6zIWcLDnnWdM,18508
 pyopencga/rest_clients/clinical_analysis_client.py,sha256=e14y-qJznmAIMsIVpdh2ynv5pXx2yjOq7r7Mq_yVSkg,69578
 pyopencga/rest_clients/cohort_client.py,sha256=6HcNiUL3WVsLfRtcitwJuxyraECJ6RExV8GvE2oQhDM,16323
 pyopencga/rest_clients/disease_panel_client.py,sha256=dD5_nzetek5Hk2sSqT1JasdNu8ohkO3yMfdY76jGU8U,18512
 pyopencga/rest_clients/family_client.py,sha256=MC8WHfzycB7WeRqb8FZEt2YLFTNrdSnky-bHwsr-6uY,18585
-pyopencga/rest_clients/file_client.py,sha256=SnFrV6Bs-_ZMoZMoGviNMK1yi2xLXnTQCjm20ovecew,33729
+pyopencga/rest_clients/file_client.py,sha256=xoUE7e1oyaVhdO-ZnLEnbyUPTgyKGYhhtqXwvhkPP90,33724
 pyopencga/rest_clients/ga4gh_client.py,sha256=iU0PvOmxTbhFS-AUD6BDp41uU1BAxWJUiiv1waioX6A,3505
 pyopencga/rest_clients/individual_client.py,sha256=jYO4nHluP-gsdX7iM43qwlP9t9QIZBPiUv8sNXMOQ1Q,23224
 pyopencga/rest_clients/job_client.py,sha256=2u1fBSFb87gRsxcsF6ySQGgnKSJLCiaczrxUQ_iAesQ,19810
@@ -21,7 +21,7 @@ pyopencga/rest_clients/meta_client.py,sha256=xVN3YcOrCmoq2Nsx2vZoA-K40phHyWWAlR-
 pyopencga/rest_clients/organization_client.py,sha256=wOv7E5kStrRt8FoqA4Xo6q0eVenf367vhfa5KZ8hQCs,9464
 pyopencga/rest_clients/project_client.py,sha256=XuajvAQB9qUGhYRpmZxA1bBkgDkgyS78w-BUepIidtI,5211
 pyopencga/rest_clients/sample_client.py,sha256=UAUDzZCfIaSKCwaIGe11ek11w_tMcxGqNaRXTYwbjMg,23620
-pyopencga/rest_clients/study_client.py,sha256=cbShzD4GtZ6kchUHdhPGfKX1YxytsJGZ8ifttzeXoCQ,20248
+pyopencga/rest_clients/study_client.py,sha256=1ba7-zOxP6ZX_YLpKkzFsfBVBZk4rwRwVoZzzaMVPDo,21490
 pyopencga/rest_clients/user_client.py,sha256=XS4FDLuPaDt9VKHlLIYixvqqLRfBEZ9pwzblUM3GDfQ,7147
 pyopencga/rest_clients/variant_client.py,sha256=qao-KWLjp04mDN3q7tQYsJzsQpxMaMvMzE8zAp8t7pg,75435
 pyopencga/rest_clients/variant_operation_client.py,sha256=HYBQOSwXKdFTDbaxZfA4hUa66yKCfwCT7r272hLdQLc,36910
@@ -30,12 +30,12 @@ pyxetabase/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyxetabase/commons.py,sha256=Okt5DgvSpZW9PUsxoLNpROb0BDrdr_zhgry4X3dQpfk,14308
 pyxetabase/exceptions.py,sha256=GmtDcurD3d_fzaa8AEntF4-sZR4Elgg4Iz3z-UUqjYU,274
 pyxetabase/opencga_client.py,sha256=V-M9i28z3A-Vgw5BnG_Ddm0MUdjQ0_XG38gohGtzavI,15386
-pyxetabase/opencga_config.py,sha256=hqBChooRKrkA6JmEbb6pOBTlfE_tv6_67H5WTKUXoDE,6047
+pyxetabase/opencga_config.py,sha256=RK23fextK79S5wq4FaQygwuPnE4p4J9GbjY6hJ0Krxc,7009
 pyxetabase/rest_response.py,sha256=TgwTI2LZFF_jV9-HSawGkF_qZ88n-dxEtIKiFcfPyDk,8635
 pyxetabase/retry.py,sha256=LjViQOaa_GkpDFkcRq9jIS183mE9t4Rq0uls9PV_mfI,2297
 pyxetabase/rest_clients/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyxetabase/rest_clients/_parent_rest_clients.py,sha256=ZL9VxTxS1cRcg-ofrE9QJXYL8mlVkbXpvFvwhofo-uI,4280
-pyxetabase/rest_clients/admin_client.py,sha256=f2q7-ZPu5Ee4LvGBV0PYh-Af_dlt6V0yAagAFI_t6Lw,7001
+pyxetabase/rest_clients/admin_client.py,sha256=WebfbQVa7CjiaNcp5MqwAkgDTqCfW-v5AgTaxmL5EF0,6927
 pyxetabase/rest_clients/alignment_client.py,sha256=srY1fmjMZCPWlbqhrD2gYVhS2zu7fgPx61tZOqQi4Wc,18509
 pyxetabase/rest_clients/clinical_analysis_client.py,sha256=j2LmLT8wg3C9srRMB2mksEVFnqN22Anb7HxZCbdF50c,69126
 pyxetabase/rest_clients/cohort_client.py,sha256=D-su-AFOziztVMI-oAcr5G2Uq_psbLV8Wt0bqZ7zZgI,16324
@@ -43,21 +43,21 @@ pyxetabase/rest_clients/cvdb_client.py,sha256=V7ny5nQEeJqsbALAe7JLyoV6b0XyYF7c9l
 pyxetabase/rest_clients/disease_panel_client.py,sha256=GAYRyAfoB_VunskXOhAzMNbsrFupb6M2QbRK3x1Y5vo,18513
 pyxetabase/rest_clients/family_client.py,sha256=n-kyjnrV09R50JxyiHjFs8rCQkOKFU0Z1O7oVYuaKxg,18586
 pyxetabase/rest_clients/federation_client.py,sha256=p5B8dRq9gj-fdgIfIPhmkT7mNU65cRFtH06kaGtmbWE,5066
-pyxetabase/rest_clients/file_client.py,sha256=fwTWnZtprYNDUBvRetLLe6PTBxW_M8LxN6OlAMGWXC4,33730
+pyxetabase/rest_clients/file_client.py,sha256=7mGziH-_IuHuhs7B2yOby3s969qHqDMNLAOpDdnE3J0,33725
 pyxetabase/rest_clients/ga4gh_client.py,sha256=fPnmiblnfpz_zcZPJblGqOFksrdiF3MUer3fv2nwQwk,3506
 pyxetabase/rest_clients/individual_client.py,sha256=C59zr_t7tTxNR7ZBeAPY6fyYl59fE7KY05MaLyXWmXw,23225
 pyxetabase/rest_clients/job_client.py,sha256=amoBW3SL56l6sAPCUB55rZhLR8DcdIIfb5ymOZ9NkLQ,19811
-pyxetabase/rest_clients/meta_client.py,sha256=zFA4QpwNuMm5sgJbF6VP6OcG4lUlSHah91ncc724bxU,2257
+pyxetabase/rest_clients/meta_client.py,sha256=uExVRfdSKiXteLYe7R3q9x3zCp9mMWWMyPDU56TtoDo,2308
 pyxetabase/rest_clients/organization_client.py,sha256=tnwUTCqJoGiKXMQLMv4ymHA16JxnR5iL2SMLaJDBRs8,9465
 pyxetabase/rest_clients/project_client.py,sha256=M8naPsj47z2ylTrJNU_JyHReKzXrB038PoEtKKrtxmc,5212
 pyxetabase/rest_clients/sample_client.py,sha256=VOsPAhw9HwaEHzzw_5gcVQ1v2xSesvzN3TO4z2opaNo,23621
-pyxetabase/rest_clients/study_client.py,sha256=hZ1GAYMrAhfjD_PqSXLwYRFpPFewxoLI_GhaSrzVyuE,20249
+pyxetabase/rest_clients/study_client.py,sha256=STtboEiGP-lQ1UptjHxk-ANd3uG6cA6U3srvOO4UQIE,21491
 pyxetabase/rest_clients/user_client.py,sha256=frA7-rMii-yoRyca_Orkj1T80OeEe-zCdWZCHKn1sio,7683
 pyxetabase/rest_clients/variant_client.py,sha256=mmBuVE0JBThJr5zsLGci5nykNcCKyfZXRKl-h3HT9PA,75436
 pyxetabase/rest_clients/variant_operation_client.py,sha256=oN7AEQzAkrmLQLbw86CODCEnR5xM6UkqrdN-9WPO_rM,36911
 pyxetabase/rest_clients/workflow_client.py,sha256=QYnyI17aNCjq-uXlguaSj78F0xupeWwmf8uYK1Y5tf4,12482
-pyxetabase-3.1.0.dev21.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
-pyxetabase-3.1.0.dev21.dist-info/METADATA,sha256=MEEiHWrd_g2oPp_s8kOCE1WwkpodGvHk5PpTEth9Eb8,5540
-pyxetabase-3.1.0.dev21.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-pyxetabase-3.1.0.dev21.dist-info/top_level.txt,sha256=0m5pDpBX-lM8QpPl7bTpTQAm4kgu2-nr-pcaEu4Tn_8,11
-pyxetabase-3.1.0.dev21.dist-info/RECORD,,
+pyxetabase-3.1.0.dev23.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+pyxetabase-3.1.0.dev23.dist-info/METADATA,sha256=tqFdL8jRI_LDEPlN6dw-CWIohbj2y0PYr5EQn0aa5Rs,5540
+pyxetabase-3.1.0.dev23.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pyxetabase-3.1.0.dev23.dist-info/top_level.txt,sha256=0m5pDpBX-lM8QpPl7bTpTQAm4kgu2-nr-pcaEu4Tn_8,11
+pyxetabase-3.1.0.dev23.dist-info/RECORD,,