pyxetabase 4.0.0.dev8__tar.gz → 4.0.0.dev10__tar.gz

{pyxetabase-4.0.0.dev8 → pyxetabase-4.0.0.dev10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev8
+Version: 4.0.0.dev10
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev8 → pyxetabase-4.0.0.dev10}/pyxetabase/rest_clients/job_client.py

@@ -265,7 +265,8 @@ class Job(_ParentRestClient):
         Execute an analysis from a custom binary.
         PATH: /{apiVersion}/jobs/tool/run
 
-        :param dict data: Workflow tool run parameters. (REQUIRED)
+        :param dict data: Container image to be executed and its requirements.
+            (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.dev8 → pyxetabase-4.0.0.dev10}/pyxetabase/rest_clients/user_tool_client.py

@@ -64,7 +64,7 @@ class UserTool(_ParentRestClient):
         :param str scope: External tool scope. Allowed types:
             [CLINICAL_INTERPRETATION, SECONDARY_ANALYSIS, RESEARCH or OTHER].
         :param str workflow_repository_name: Workflow repository name.
-        :param str docker_name: Docker name.
+        :param str container_name: Container name.
         :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
             Examples: >2018, 2017-2018, <201805.
         :param str modification_date: Modification date. Format:
@@ -133,39 +133,7 @@ class UserTool(_ParentRestClient):
         Execute an analysis from a custom binary.
         PATH: /{apiVersion}/tools/custom/run
 
-        :param dict data: Container image to be executed and its requirements.
-            (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='tools', resource='run', subcategory='custom', data=data, **options)
-
-    def run_custom(self, tool_id, data=None, **options):
-        """
-        Execute an analysis from a custom binary.
-        PATH: /{apiVersion}/tools/custom/{toolId}/run
-
         :param dict data: Custom tool run parameters. (REQUIRED)
-        :param str tool_id: Comma separated list of external tool IDs up to a
-            maximum of 100. Also admits basic regular expressions using the
-            operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search. (REQUIRED)
-        :param int version: Tool version. If not provided, the latest version
-            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
@@ -183,7 +151,7 @@ class UserTool(_ParentRestClient):
             execution, but the job will not actually run.
         """
 
-        return self._post(category='tools', resource='run', subcategory='custom', second_query_id=tool_id, data=data, **options)
+        return self._post(category='tools', resource='run', subcategory='custom', data=data, **options)
 
     def update_custom(self, tool_id, data=None, **options):
         """
@@ -236,7 +204,7 @@ class UserTool(_ParentRestClient):
         :param str scope: External tool scope. Allowed types:
             [CLINICAL_INTERPRETATION, SECONDARY_ANALYSIS, RESEARCH or OTHER].
         :param str workflow_repository_name: Workflow repository name.
-        :param str docker_name: Docker name.
+        :param str container_name: Container name.
         :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
             Examples: >2018, 2017-2018, <201805.
         :param str modification_date: Modification date. Format:
@@ -290,7 +258,7 @@ class UserTool(_ParentRestClient):
         :param str scope: External tool scope. Allowed types:
             [CLINICAL_INTERPRETATION, SECONDARY_ANALYSIS, RESEARCH or OTHER].
         :param str workflow_repository_name: Workflow repository name.
-        :param str docker_name: Docker name.
+        :param str container_name: Container name.
         :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
             Examples: >2018, 2017-2018, <201805.
         :param str modification_date: Modification date. Format:
@@ -326,18 +294,12 @@ class UserTool(_ParentRestClient):
 
         return self._post(category='tools', resource='create', subcategory='walker', data=data, **options)
 
-    def run_walker(self, tool_id, data=None, **options):
+    def run_walker(self, data=None, **options):
         """
         Execute an analysis from a custom binary.
-        PATH: /{apiVersion}/tools/walker/{toolId}/run
+        PATH: /{apiVersion}/tools/walker/run
 
         :param dict data: Variant walker params. (REQUIRED)
-        :param str tool_id: Comma separated list of external tool IDs up to a
-            maximum of 100. Also admits basic regular expressions using the
-            operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search. (REQUIRED)
-        :param int version: Tool version. If not provided, the latest version
-            will be used.
         :param str project: Project [organization@]project where project can
             be either the ID or the alias.
         :param str study: Study [[organization@]project:]study where study and
@@ -357,7 +319,7 @@ class UserTool(_ParentRestClient):
             execution, but the job will not actually run.
         """
 
-        return self._post(category='tools', resource='run', subcategory='walker', second_query_id=tool_id, data=data, **options)
+        return self._post(category='tools', resource='run', subcategory='walker', data=data, **options)
 
     def create_workflow(self, data=None, **options):
         """
@@ -389,18 +351,12 @@ class UserTool(_ParentRestClient):
 
         return self._post(category='tools', resource='import', subcategory='workflow', data=data, **options)
 
-    def run_workflow(self, tool_id, data=None, **options):
+    def run_workflow(self, data=None, **options):
         """
-        Execute a user tool of type WORKFLOW.
-        PATH: /{apiVersion}/tools/workflow/{toolId}/run
+        Run a user tool of type WORKFLOW.
+        PATH: /{apiVersion}/tools/workflow/run
 
         :param dict data: Workflow tool run parameters. (REQUIRED)
-        :param str tool_id: Comma separated list of external tool IDs up to a
-            maximum of 100. Also admits basic regular expressions using the
-            operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
-            sensitive, '~/value/i' for case insensitive search. (REQUIRED)
-        :param int version: Tool version. If not provided, the latest version
-            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
@@ -418,7 +374,7 @@ class UserTool(_ParentRestClient):
             execution, but the job will not actually run.
         """
 
-        return self._post(category='tools', resource='run', subcategory='workflow', second_query_id=tool_id, data=data, **options)
+        return self._post(category='tools', resource='run', subcategory='workflow', data=data, **options)
 
     def update_workflow(self, tool_id, data=None, **options):
         """

{pyxetabase-4.0.0.dev8 → pyxetabase-4.0.0.dev10}/pyxetabase.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev8
+Version: 4.0.0.dev10
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev8 → pyxetabase-4.0.0.dev10}/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.dev8',
+    version='4.0.0.dev10',
     description='A REST client for OpenCGA enterprise REST web services',
     long_description=long_description,
     long_description_content_type='text/x-rst',