pyxetabase 4.0.0.dev40__tar.gz → 4.0.0.dev69__tar.gz

{pyxetabase-4.0.0.dev40 → pyxetabase-4.0.0.dev69}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev40
+Version: 4.0.0.dev69
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev40 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/admin_client.py

@@ -54,6 +54,16 @@ class Admin(_ParentRestClient):
 
         return self._post(category='admin', resource='install', subcategory='catalog', data=data, **options)
 
+    def update_catalog_workspace(self, data=None, **options):
+        """
+        Update the OpenCGA Catalog workspace.
+        PATH: /{apiVersion}/admin/catalog/workspace/update
+
+        :param dict data: JSON containing the workspace parameters. (REQUIRED)
+        """
+
+        return self._post(category='admin', resource='update', subcategory='catalog/workspace', data=data, **options)
+
     def list_organizations(self, **options):
         """
         List current Organizations.

{pyxetabase-4.0.0.dev40 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/clinical_analysis_client.py

@@ -350,32 +350,6 @@ class ClinicalAnalysis(_ParentRestClient):
 
         return self._get(category='analysis', resource='info', subcategory='clinical/interpretation', second_query_id=interpretations, **options)
 
-    def run_interpreter_cancer_tiering(self, data=None, **options):
-        """
-        Run cancer tiering interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run
-
-        :param dict data: Cancer tiering interpretation analysis params.
-            (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/cancerTiering', data=data, **options)
-
     def run_interpreter_exomiser(self, data=None, **options):
         """
         Run exomiser interpretation analysis.
@@ -401,62 +375,31 @@ class ClinicalAnalysis(_ParentRestClient):
 
         return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/exomiser', data=data, **options)
 
-    def run_interpreter_team(self, data=None, **options):
-        """
-        Run TEAM interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/team/run
-
-        :param dict data: TEAM interpretation analysis params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/team', data=data, **options)
-
-    def run_interpreter_tiering(self, data=None, **options):
+    def rd_interpreter(self, **options):
         """
-        Run tiering interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/tiering/run
+        Rare disease interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/rd
 
-        :param dict data: Tiering interpretation analysis params. (REQUIRED)
+        :param str clinical_analysis_id: Clinical analysis ID.
+        :param str proband_id: Proband ID.
+        :param str family_id: Family ID.
+        :param str panel_ids: List of panel IDs (separated by commas).
+        :param str disorder_id: Disorder ID.
+        :param str config_file: RD interpretation configuration file
+            (otherwise the default one will be used).
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
         """
 
-        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/tiering', data=data, **options)
+        return self._get(category='analysis', resource='rd', subcategory='clinical/interpreter', **options)
 
-    def run_interpreter_zetta(self, data=None, **options):
+    def run_interpreter_rd(self, data=None, **options):
         """
-        Run Zetta interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/zetta/run
+        Run interpretation analysis for rare diseases.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/rd/run
 
-        :param dict data: Zetta interpretation analysis params. (REQUIRED)
+        :param dict data: Parameters to execute the rare disease
+            interpretation analysis. (REQUIRED)
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
         :param str job_id: Job ID. It must be a unique string within the
@@ -474,7 +417,7 @@ class ClinicalAnalysis(_ParentRestClient):
             execution, but the job will not actually run.
         """
 
-        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/zetta', data=data, **options)
+        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/rd', data=data, **options)
 
     def load(self, data=None, **options):
         """

{pyxetabase-4.0.0.dev40 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/cvdb_client.py

@@ -593,6 +593,33 @@ class CVDB(_ParentRestClient):
 
         return self._get(category='analysis', resource='query', subcategory='cvdb/analysis', **options)
 
+    def run_delete(self, data=None, **options):
+        """
+        Delete clinical analyses indexed in CVDB for a given study or a list
+            of clinical analysis IDs.
+        PATH: /{apiVersion}/analysis/cvdb/delete/run
+
+        :param dict data: Parameters: Delete clinical analyses indexed in CVDB
+            for a given study or a list of clinical analysis IDs. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        """
+
+        return self._post(category='analysis', resource='run', subcategory='cvdb/delete', data=data, **options)
+
     def aggregate_evidence(self, **options):
         """
         Calculate and fetch clinical variant evidence aggregation stats.
@@ -1145,13 +1172,12 @@ class CVDB(_ParentRestClient):
 
     def run_index(self, data=None, **options):
         """
-        Index clinical analyses of a OpenCGA project, a study or a list of
-            clinical analyses into CVDB.
+        Index clinical analyses of a study or a list of clinical analyses into
+            CVDB.
         PATH: /{apiVersion}/analysis/cvdb/index/run
 
-        :param dict data: Parameters: Index clinical analyses of a OpenCGA
-            project, a study or a list of clinical analyses into CVDB.
-            (REQUIRED)
+        :param dict data: Parameters: Index clinical analyses of a study or a
+            list of clinical analyses into CVDB. (REQUIRED)
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
         :param str job_id: Job ID. It must be a unique string within the

{pyxetabase-4.0.0.dev40 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/disease_panel_client.py

@@ -190,21 +190,14 @@ class DiseasePanel(_ParentRestClient):
         Import panels.
         PATH: /{apiVersion}/panels/import
 
+        :param str include: Fields included in the response, whole JSON path
+            must be provided.
+        :param str exclude: Fields excluded in the response, whole JSON path
+            must be provided.
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_description: Job description.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
+        :param bool include_result: Flag indicating to include the created or
+            updated document result in the response.
         :param dict data: Panel parameters.
         """
 

{pyxetabase-4.0.0.dev40 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/file_client.py

@@ -436,6 +436,18 @@ class File(_ParentRestClient):
 
         return self._post(category='files', resource='upload', **options)
 
+    def update_uri(self, data=None, **options):
+        """
+        Update URIs of files that have been manually moved in disk.
+        PATH: /{apiVersion}/files/uri/update
+
+        :param dict data: Parameters to modify. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        """
+
+        return self._post(category='files', resource='update', subcategory='uri', data=data, **options)
+
     def acl(self, files, **options):
         """
         Return the acl defined for the file or folder. If member is provided,

{pyxetabase-4.0.0.dev40 → pyxetabase-4.0.0.dev69}/pyxetabase.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev40
+Version: 4.0.0.dev69
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev40 → pyxetabase-4.0.0.dev69}/setup.py

@@ -14,7 +14,7 @@ with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
 
 setup(
     name='pyxetabase',
-    version='4.0.0.dev40',
+    version='4.0.0.dev69',
     description='A REST client for OpenCGA enterprise REST web services',
     long_description=long_description,
     long_description_content_type='text/x-rst',