pyxetabase 4.0.0.dev59__tar.gz → 4.0.0.dev69__tar.gz

{pyxetabase-4.0.0.dev59 → pyxetabase-4.0.0.dev69}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev59
+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.dev59 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/admin_client.py

@@ -27,7 +27,7 @@ class Admin(_ParentRestClient):
         :param str entity: Entity to be grouped by. Allowed values: ['AUDIT
             NOTE ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL
             COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS INTERPRETATION
-            VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL EXTERNAL_TOOL
+            VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL WORKFLOW
             RESOURCE'] (REQUIRED)
         :param str fields: Comma separated list of fields by which to group
             by. (REQUIRED)

{pyxetabase-4.0.0.dev59 → 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.dev59 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/job_client.py

@@ -56,12 +56,6 @@ class Job(_ParentRestClient):
             search.
         :param str tool_type: Tool type executed by the job [OPERATION,
             ANALYSIS].
-        :param str tool.minimum_requirements.queue: Queue where the job is
-            expected to be executed.
-        :param str tool.minimum_requirements.processor_type: Processor type
-            required to run the job. Allowed values: [CPU, GPU, FPGA].
-        :param str execution.queue.id: Queue id where the job has been
-            submitted to be executed.
         :param str user_id: User that created the job.
         :param str priority: Priority of the job.
         :param str status: Filter by status.
@@ -124,12 +118,6 @@ class Job(_ParentRestClient):
             search.
         :param str tool_type: Tool type executed by the job [OPERATION,
             ANALYSIS].
-        :param str tool.minimum_requirements.queue: Queue where the job is
-            expected to be executed.
-        :param str tool.minimum_requirements.processor_type: Processor type
-            required to run the job. Allowed values: [CPU, GPU, FPGA].
-        :param str execution.queue.id: Queue id where the job has been
-            submitted to be executed.
         :param str tool.external_executor.id: Id of the external executor.
             This field is only applicable for jobs executed by an external
             executor.
@@ -214,12 +202,6 @@ class Job(_ParentRestClient):
             search.
         :param str tool_type: Tool type executed by the job [OPERATION,
             ANALYSIS].
-        :param str tool.minimum_requirements.queue: Queue where the job is
-            expected to be executed.
-        :param str tool.minimum_requirements.processor_type: Processor type
-            required to run the job. Allowed values: [CPU, GPU, FPGA].
-        :param str execution.queue.id: Queue id where the job has been
-            submitted to be executed.
         :param str tool.external_executor.id: Id of the external executor.
             This field is only applicable for jobs executed by an external
             executor.
@@ -283,8 +265,7 @@ class Job(_ParentRestClient):
         Execute an analysis from a custom binary.
         PATH: /{apiVersion}/jobs/tool/run
 
-        :param dict data: Container image to be executed and its requirements.
-            (REQUIRED)
+        :param dict data: NextFlow run parameters. (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.dev59 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/study_client.py

@@ -139,8 +139,7 @@ class Study(_ParentRestClient):
         :param str resource: Resource involved. Allowed values: ['AUDIT NOTE
             ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT
             DISEASE_PANEL FAMILY CLINICAL_ANALYSIS INTERPRETATION VARIANT
-            ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL EXTERNAL_TOOL
-            RESOURCE']
+            ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL WORKFLOW RESOURCE']
         :param str resource_id: Resource ID.
         :param str resource_uuid: resource UUID.
         :param str status: Filter by status. Allowed values: ['SUCCESS ERROR']

{pyxetabase-4.0.0.dev59 → pyxetabase-4.0.0.dev69}/pyxetabase/rest_clients/workflow_client.py

@@ -118,7 +118,7 @@ class Workflow(_ParentRestClient):
         Execute a workflow analysis.
         PATH: /{apiVersion}/workflows/run
 
-        :param dict data: Workflow tool run parameters. (REQUIRED)
+        :param dict data: NextFlow run parameters. (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.dev59 → pyxetabase-4.0.0.dev69}/pyxetabase.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev59
+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.dev59 → pyxetabase-4.0.0.dev69}/pyxetabase.egg-info/SOURCES.txt

@@ -33,7 +33,6 @@ pyxetabase/rest_clients/project_client.py
 pyxetabase/rest_clients/sample_client.py
 pyxetabase/rest_clients/study_client.py
 pyxetabase/rest_clients/user_client.py
-pyxetabase/rest_clients/user_tool_client.py
 pyxetabase/rest_clients/variant_client.py
 pyxetabase/rest_clients/variant_operation_client.py
 pyxetabase/rest_clients/workflow_client.py

{pyxetabase-4.0.0.dev59 → 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.dev59',
+    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',

pyxetabase-4.0.0.dev59/pyxetabase/rest_clients/user_tool_client.py

@@ -1,471 +0,0 @@
-"""
-WARNING: AUTOGENERATED CODE
-
-    This code was generated by a tool.
-    
-    Manual changes to this file may cause unexpected behavior in your application.
-    Manual changes to this file will be overwritten if the code is regenerated.
-"""
-
-from pyxetabase.rest_clients._parent_rest_clients import _ParentRestClient
-
-
-class UserTool(_ParentRestClient):
-    """
-    This class contains methods for the 'User Tools' webservices
-    PATH: /{apiVersion}/tools
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(UserTool, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def update_acl(self, members, action, data=None, **options):
-        """
-        Update the set of user tool permissions granted for the member.
-        PATH: /{apiVersion}/tools/acl/{members}/update
-
-        :param dict data: JSON containing the parameters to update the
-            permissions. (REQUIRED)
-        :param str action: Action to be performed [ADD, SET, REMOVE or RESET].
-            Allowed values: ['SET ADD REMOVE RESET'] (REQUIRED)
-        :param str members: Comma separated list of user or group ids.
-            (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        options['action'] = action
-        return self._post(category='tools', resource='update', subcategory='acl', second_query_id=members, data=data, **options)
-
-    def aggregation_stats(self, **options):
-        """
-        Fetch user tool stats.
-        PATH: /{apiVersion}/tools/aggregationStats
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str 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.
-        :param str name: Comma separated list of external tool names 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.
-        :param str uuid: Comma separated list of external tool UUIDs up to a
-            maximum of 100.
-        :param str tags: Comma separated list of tags.
-        :param bool draft: Boolean field indicating whether the workflow is a
-            draft or not.
-        :param str internal.registration_user_id: UserId that created the
-            workflow.
-        :param str type: External tool type. Allowed types: [CUSTOM_TOOL,
-            VARIANT_WALKER or WORKFLOW].
-        :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 container_name: Container name.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :param str field: Field to apply aggregation statistics to (or a list
-            of fields separated by semicolons), e.g.:
-            studies;type;numSamples[0..10]:1;format:sum(size).
-        """
-
-        return self._get(category='tools', resource='aggregationStats', **options)
-
-    def run_custom_builder(self, data=None, **options):
-        """
-        Execute an analysis from a custom binary.
-        PATH: /{apiVersion}/tools/custom/builder/run
-
-        :param dict data: body. (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/builder', data=data, **options)
-
-    def create_custom(self, data=None, **options):
-        """
-        Register a new user tool of type CUSTOM_TOOL.
-        PATH: /{apiVersion}/tools/custom/create
-
-        :param dict data: JSON containing workflow information. (REQUIRED)
-        :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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='tools', resource='create', subcategory='custom', data=data, **options)
-
-    def run_custom_docker(self, data=None, **options):
-        """
-        Execute an analysis from a custom binary.
-        PATH: /{apiVersion}/tools/custom/run
-
-        :param dict data: Custom tool run parameters. (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 update_custom(self, tool_id, data=None, **options):
-        """
-        Update some custom user tool attributes.
-        PATH: /{apiVersion}/tools/custom/{toolId}/update
-
-        :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 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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        :param dict data: body.
-        """
-
-        return self._post(category='tools', resource='update', subcategory='custom', second_query_id=tool_id, data=data, **options)
-
-    def distinct(self, field, **options):
-        """
-        User tool distinct method.
-        PATH: /{apiVersion}/tools/distinct
-
-        :param str field: Comma separated list of fields for which to obtain
-            the distinct values. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str 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.
-        :param str name: Comma separated list of external tool names 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.
-        :param str uuid: Comma separated list of external tool UUIDs up to a
-            maximum of 100.
-        :param str tags: Comma separated list of tags.
-        :param bool draft: Boolean field indicating whether the workflow is a
-            draft or not.
-        :param str internal.registration_user_id: UserId that created the
-            workflow.
-        :param str type: External tool type. Allowed types: [CUSTOM_TOOL,
-            VARIANT_WALKER or WORKFLOW].
-        :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 container_name: Container name.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        options['field'] = field
-        return self._get(category='tools', resource='distinct', **options)
-
-    def search(self, **options):
-        """
-        User tool search method.
-        PATH: /{apiVersion}/tools/search
-
-        :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 int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param bool count: Get the total number of results matching the query.
-            Deactivated by default.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str 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.
-        :param str name: Comma separated list of external tool names 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.
-        :param str uuid: Comma separated list of external tool UUIDs up to a
-            maximum of 100.
-        :param str tags: Comma separated list of tags.
-        :param bool draft: Boolean field indicating whether the workflow is a
-            draft or not.
-        :param str internal.registration_user_id: UserId that created the
-            workflow.
-        :param str type: External tool type. Allowed types: [CUSTOM_TOOL,
-            VARIANT_WALKER or WORKFLOW].
-        :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 container_name: Container name.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='tools', resource='search', **options)
-
-    def create_walker(self, data=None, **options):
-        """
-        Register a new user tool of type VARIANT_WALKER.
-        PATH: /{apiVersion}/tools/walker/create
-
-        :param dict data: JSON containing workflow information. (REQUIRED)
-        :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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='tools', resource='create', subcategory='walker', data=data, **options)
-
-    def run_walker(self, data=None, **options):
-        """
-        Execute an analysis from a custom binary.
-        PATH: /{apiVersion}/tools/walker/run
-
-        :param dict data: Variant walker params. (REQUIRED)
-        :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
-            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='walker', data=data, **options)
-
-    def update_walker(self, tool_id, data=None, **options):
-        """
-        Update some variant walker tool attributes.
-        PATH: /{apiVersion}/tools/walker/{toolId}/update
-
-        :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 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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        :param dict data: body.
-        """
-
-        return self._post(category='tools', resource='update', subcategory='walker', second_query_id=tool_id, data=data, **options)
-
-    def create_workflow(self, data=None, **options):
-        """
-        Register a new user tool of type WORKFLOW.
-        PATH: /{apiVersion}/tools/workflow/create
-
-        :param dict data: JSON containing workflow information. (REQUIRED)
-        :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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='tools', resource='create', subcategory='workflow', data=data, **options)
-
-    def import_workflow(self, data=None, **options):
-        """
-        Import a user tool of type WORKFLOW.
-        PATH: /{apiVersion}/tools/workflow/import
-
-        :param dict data: Repository parameters. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._post(category='tools', resource='import', subcategory='workflow', data=data, **options)
-
-    def run_workflow(self, data=None, **options):
-        """
-        Run a user tool of type WORKFLOW.
-        PATH: /{apiVersion}/tools/workflow/run
-
-        :param dict data: Workflow tool run parameters. (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='workflow', data=data, **options)
-
-    def update_workflow(self, tool_id, data=None, **options):
-        """
-        Update some user tool attributes.
-        PATH: /{apiVersion}/tools/workflow/{toolId}/update
-
-        :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 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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        :param dict data: body.
-        """
-
-        return self._post(category='tools', resource='update', subcategory='workflow', second_query_id=tool_id, data=data, **options)
-
-    def acl(self, tools, **options):
-        """
-        Returns the acl of the user tools. If member is provided, it will only
-            return the acl for the member.
-        PATH: /{apiVersion}/tools/{tools}/acl
-
-        :param str tools: Comma separated of external tool ids. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str member: User or group id.
-        :param bool silent: Boolean to retrieve all possible entries that are
-            queried for, false to raise an exception whenever one of the
-            entries looked for cannot be shown for whichever reason.
-        """
-
-        return self._get(category='tools', resource='acl', query_id=tools, **options)
-
-    def delete(self, tools, **options):
-        """
-        Delete user tools.
-        PATH: /{apiVersion}/tools/{tools}/delete
-
-        :param str tools: Comma separated of external tool ids. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._delete(category='tools', resource='delete', query_id=tools, **options)
-
-    def info(self, tools, **options):
-        """
-        Get user tool information.
-        PATH: /{apiVersion}/tools/{tools}/info
-
-        :param str tools: Comma separated of external tool ids. (REQUIRED)
-        :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 version: Comma separated list of external tool versions.
-            'all' to get all the external tool versions. Not supported if
-            multiple external tool ids are provided.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='tools', resource='info', query_id=tools, **options)
-