pyxetabase 4.0.0.dev44__tar.gz → 4.0.0.dev45__tar.gz

{pyxetabase-4.0.0.dev44 → pyxetabase-4.0.0.dev45}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev44
+Version: 4.0.0.dev45
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev44 → pyxetabase-4.0.0.dev45}/pyxetabase/rest_clients/clinical_analysis_client.py

@@ -350,6 +350,32 @@ 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.
@@ -375,31 +401,62 @@ class ClinicalAnalysis(_ParentRestClient):
 
         return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/exomiser', data=data, **options)
 
-    def rd_interpreter(self, **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):
         """
-        Rare disease interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/rd
+        Run tiering interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/tiering/run
 
-        :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 dict data: 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._get(category='analysis', resource='rd', subcategory='clinical/interpreter', **options)
+        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/tiering', data=data, **options)
 
-    def run_interpreter_rd(self, data=None, **options):
+    def run_interpreter_zetta(self, data=None, **options):
         """
-        Run interpretation analysis for rare diseases.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/rd/run
+        Run Zetta interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/zetta/run
 
-        :param dict data: Parameters to execute the rare disease
-            interpretation analysis. (REQUIRED)
+        :param dict data: Zetta 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
@@ -417,7 +474,7 @@ class ClinicalAnalysis(_ParentRestClient):
             execution, but the job will not actually run.
         """
 
-        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/rd', data=data, **options)
+        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/zetta', data=data, **options)
 
     def load(self, data=None, **options):
         """

{pyxetabase-4.0.0.dev44 → pyxetabase-4.0.0.dev45}/pyxetabase/rest_clients/disease_panel_client.py

@@ -192,6 +192,19 @@ class DiseasePanel(_ParentRestClient):
 
         :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 dict data: Panel parameters.
         """
 

{pyxetabase-4.0.0.dev44 → pyxetabase-4.0.0.dev45}/pyxetabase.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev44
+Version: 4.0.0.dev45
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev44 → pyxetabase-4.0.0.dev45}/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.dev44',
+    version='4.0.0.dev45',
     description='A REST client for OpenCGA enterprise REST web services',
     long_description=long_description,
     long_description_content_type='text/x-rst',