pyxetabase 3.1.0.dev25__tar.gz → 4.0.0.dev8__tar.gz

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 3.1.0.dev25
+Version: 4.0.0.dev8
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/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 WORKFLOW
+            VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL EXTERNAL_TOOL
             RESOURCE'] (REQUIRED)
         :param str fields: Comma separated list of fields by which to group
             by. (REQUIRED)

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/pyxetabase/rest_clients/clinical_analysis_client.py

@@ -502,6 +502,85 @@ class ClinicalAnalysis(_ParentRestClient):
 
         return self._post(category='analysis', resource='load', subcategory='clinical', data=data, **options)
 
+    def run_pipeline_affy(self, data=None, **options):
+        """
+        Execute the clinical genomics pipeline that performs QC (FastQC,...),
+            mapping (BWA, Bowtie,...) , variant calling (GATK,...) and variant
+            indexing in OpenCGA storage.
+        PATH: /{apiVersion}/analysis/clinical/pipeline/affy/run
+
+        :param dict data: JSON with parameters to execute the command
+            affy-pipeline. (REQUIRED)
+        :param str study: study.
+        :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/pipeline/affy', data=data, **options)
+
+    def run_pipeline_genomics(self, data=None, **options):
+        """
+        Execute the clinical genomics pipeline that performs QC (FastQC,...),
+            mapping (BWA, Bowtie,...) , variant calling (GATK,...) and variant
+            indexing in OpenCGA storage.
+        PATH: /{apiVersion}/analysis/clinical/pipeline/genomics/run
+
+        :param dict data: JSON with parameters to execute the command
+            ngs-pipeline-genomics. (REQUIRED)
+        :param str study: study.
+        :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/pipeline/genomics', data=data, **options)
+
+    def run_pipeline_prepare(self, data=None, **options):
+        """
+        Prepare the clinical pipeline.
+        PATH: /{apiVersion}/analysis/clinical/pipeline/prepare/run
+
+        :param dict data: JSON with parameters to execute the command
+            ngs-pipeline-prepare. (REQUIRED)
+        :param str study: study.
+        :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/pipeline/prepare', data=data, **options)
+
     def aggregation_stats_rga(self, field, **options):
         """
         RGA aggregation stats.
@@ -1086,6 +1165,9 @@ class ClinicalAnalysis(_ParentRestClient):
             analysts is being updated. Allowed values: ['ADD SET REMOVE']
         :param str files_action: Action to be performed if the array of files
             is being updated. Allowed values: ['ADD SET REMOVE']
+        :param str reported_files_action: Action to be performed if the array
+            of reported files is being updated. Allowed values: ['ADD SET
+            REMOVE']
         :param str panels_action: Action to be performed if the array of
             panels is being updated. Allowed values: ['ADD SET REMOVE']
         :param str annotation_sets_action: Action to be performed if the array
@@ -1260,11 +1342,10 @@ class ClinicalAnalysis(_ParentRestClient):
             project can be either the ID or UUID.
         :param str comments_action: Action to be performed if the array of
             comments is being updated. Allowed values: ['ADD REMOVE REPLACE']
-        :param str supporting_evidences_action: Action to be performed if the
-            array of supporting evidences is being updated. Allowed values:
-            ['ADD SET REMOVE']
-        :param str files_action: Action to be performed if the array of files
-            is being updated. Allowed values: ['ADD SET REMOVE']
+        :param str signatures_action: Action to be performed if the array of
+            signatures is being updated. Allowed values: ['ADD SET REMOVE']
+        :param str references_action: Action to be performed if the array of
+            references is being updated. Allowed values: ['ADD SET REMOVE']
         :param bool include_result: Flag indicating to include the created or
             updated document result in the response.
         """

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/pyxetabase/rest_clients/file_client.py

@@ -407,11 +407,11 @@ class File(_ParentRestClient):
         :param str format: File format. Allowed values: ['VCF BCF GVCF TBI
             BIGWIG SAM BAM BAI CRAM CRAI FASTQ FASTA PED TAB_SEPARATED_VALUES
             COMMA_SEPARATED_VALUES XML PROTOCOL_BUFFER JSON AVRO PARQUET PDF
-            IMAGE PLAIN BINARY NONE UNKNOWN']
+            IMAGE PLAIN BINARY JAVASCRIPT NONE UNKNOWN']
         :param str file_format: [DEPRECATED] File format. Allowed values:
             ['VCF BCF GVCF TBI BIGWIG SAM BAM BAI CRAM CRAI FASTQ FASTA PED
             TAB_SEPARATED_VALUES COMMA_SEPARATED_VALUES XML PROTOCOL_BUFFER
-            JSON AVRO PARQUET PDF IMAGE PLAIN BINARY NONE UNKNOWN']
+            JSON AVRO PARQUET PDF IMAGE PLAIN BINARY JAVASCRIPT NONE UNKNOWN']
         :param str bioformat: File bioformat. Allowed values:
             ['MICROARRAY_EXPRESSION_ONECHANNEL_AGILENT
             MICROARRAY_EXPRESSION_ONECHANNEL_AFFYMETRIX
@@ -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 VARIANT ALIGNMENT COVERAGE SEQUENCE PEDIGREE
+            OTHER_PED VCF4 CVDB 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
@@ -557,6 +557,19 @@ class File(_ParentRestClient):
 
         return self._post(category='files', resource='annotations/update', query_id=file, subcategory='annotationSets', second_query_id=annotation_set, data=data, **options)
 
+    def update_content(self, file, data=None, **options):
+        """
+        Overwrite the content of a file.
+        PATH: /{apiVersion}/files/{file}/content/update
+
+        :param dict data: File parameters. (REQUIRED)
+        :param str file: File id or name. (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', query_id=file, subcategory='content', data=data, **options)
+
     def download(self, file, **options):
         """
         Download file.

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/pyxetabase/rest_clients/job_client.py

@@ -265,7 +265,7 @@ class Job(_ParentRestClient):
         Execute an analysis from a custom binary.
         PATH: /{apiVersion}/jobs/tool/run
 
-        :param dict data: NextFlow run parameters. (REQUIRED)
+        :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

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/pyxetabase/rest_clients/study_client.py

@@ -139,7 +139,8 @@ 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 WORKFLOW RESOURCE']
+            ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL EXTERNAL_TOOL
+            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.dev8/pyxetabase/rest_clients/user_tool_client.py

@@ -0,0 +1,493 @@
+"""
+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 docker_name: Docker 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: 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
+            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', second_query_id=tool_id, 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 docker_name: Docker 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 docker_name: Docker 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, tool_id, data=None, **options):
+        """
+        Execute an analysis from a custom binary.
+        PATH: /{apiVersion}/tools/walker/{toolId}/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
+            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', 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, tool_id, data=None, **options):
+        """
+        Execute a user tool of type WORKFLOW.
+        PATH: /{apiVersion}/tools/workflow/{toolId}/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
+            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', second_query_id=tool_id, 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)
+

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/pyxetabase/rest_clients/variant_operation_client.py

@@ -105,8 +105,7 @@ class VariantOperation(_ParentRestClient):
             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 str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
+        :param str project: project.
         :param dict data: Parameters to configure a variant annotation
             extension.
         """

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/pyxetabase/rest_clients/workflow_client.py

@@ -118,7 +118,7 @@ class Workflow(_ParentRestClient):
         Execute a workflow analysis.
         PATH: /{apiVersion}/workflows/run
 
-        :param dict data: NextFlow run parameters. (REQUIRED)
+        :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

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/pyxetabase.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 3.1.0.dev25
+Version: 4.0.0.dev8
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/pyxetabase.egg-info/SOURCES.txt

@@ -33,6 +33,7 @@ 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-3.1.0.dev25 → pyxetabase-4.0.0.dev8}/setup.py

@@ -14,7 +14,7 @@ with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
 
 setup(
     name='pyxetabase',
-    version='3.1.0.dev25',
+    version='4.0.0.dev8',
     description='A REST client for OpenCGA enterprise REST web services',
     long_description=long_description,
     long_description_content_type='text/x-rst',