pyxetabase 4.0.0.dev35__py3-none-any.whl → 4.0.0.dev74__py3-none-any.whl

pyxetabase/rest_clients/_parent_rest_clients.py

@@ -1,6 +1,7 @@
-import json
+import os
+import requests
 
-from pyxetabase.commons import execute
+from pyxetabase.commons import execute, _create_rest_url, snake_to_camel_case
 from pyxetabase.rest_response import RestResponse
 from pyxetabase.retry import retry
 
@@ -87,18 +88,23 @@ class _ParentRestClient(object):
     def _post(self, category, resource, data=None, query_id=None, subcategory=None,
               second_query_id=None, **options):
         """Queries the REST service and returns the result"""
-        if data is not None:
-            return self._rest_retry(
-                method='post', category=category, resource=resource, query_id=query_id,
-                subcategory=subcategory, second_query_id=second_query_id,
-                data=data, **options
-            )
+        # Special treatment for the "/{apiVersion}/files/upload" endpoint
+        if category == 'files' and resource == 'upload':
+            response = self._upload(category=category, resource=resource, **options)
+            return RestResponse(response)
         else:
-            return self._rest_retry(
-                method='post', category=category, resource=resource, query_id=query_id,
-                subcategory=subcategory, second_query_id=second_query_id,
-                **options
-            )
+            if data is not None:
+                return self._rest_retry(
+                    method='post', category=category, resource=resource, query_id=query_id,
+                    subcategory=subcategory, second_query_id=second_query_id,
+                    data=data, **options
+                )
+            else:
+                return self._rest_retry(
+                    method='post', category=category, resource=resource, query_id=query_id,
+                    subcategory=subcategory, second_query_id=second_query_id,
+                    **options
+                )
 
     def _delete(self, category, resource, query_id=None, subcategory=None,
                 second_query_id=None, **options):
@@ -108,3 +114,31 @@ class _ParentRestClient(object):
             subcategory=subcategory, second_query_id=second_query_id,
             **options
         )
+
+    def _upload(self, category, resource, **options):
+        """Upload files"""
+
+        # Checking that the parameter file contains the file path to upload
+        if 'file' not in options or not isinstance(options['file'], str):
+            raise ValueError('To upload a file, please specify the file path as the "file" parameter.')
+
+        # Creating URL and headers
+        url, header = _create_rest_url(host=self._cfg.host, version=self._cfg.version, sid=self.token,
+                                       category=category, resource=resource, options=options)
+
+        # Creating data
+        data = {}
+        for k, v in options.items():
+            if k == 'file':  # Param "file" is not included in data
+                continue
+            data[snake_to_camel_case(k)] = v
+
+        # Uploading
+        fpath = os.path.realpath(os.path.expanduser(options['file']))
+        with open(fpath, "rb") as f:
+            fhand = {"file": (fpath, f, "application/octet-stream")}
+            response = requests.post(url, headers=header, files=fhand, data=data or None)
+            if response.status_code != 200:
+                raise Exception(response.content)
+
+        return response.json()

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)
@@ -54,16 +54,23 @@ class Admin(_ParentRestClient):
 
         return self._post(category='admin', resource='install', subcategory='catalog', data=data, **options)
 
-    def jwt_catalog(self, data=None, **options):
+    def update_catalog_workspace(self, data=None, **options):
         """
-        Change JWT secret key.
-        PATH: /{apiVersion}/admin/catalog/jwt
+        Update the OpenCGA Catalog workspace.
+        PATH: /{apiVersion}/admin/catalog/workspace/update
 
-        :param dict data: JSON containing the parameters. (REQUIRED)
-        :param str organization: Organization id.
+        :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.
+        PATH: /{apiVersion}/admin/organizations/list
         """
 
-        return self._post(category='admin', resource='jwt', subcategory='catalog', data=data, **options)
+        return self._get(category='admin', resource='list', subcategory='organizations', **options)
 
     def fetch_resource(self, data=None, **options):
         """

pyxetabase/rest_clients/clinical_analysis_client.py

@@ -375,22 +375,27 @@ class ClinicalAnalysis(_ParentRestClient):
 
         return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/exomiser', data=data, **options)
 
-    def query_interpreter_rd(self, **options):
-        """
-        RD interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/rd/query
-
-        :param str clinical_analysis_id: Comma separated list of clinical
-            analysis IDs or names up to a maximum of 100.
+    def rd_interpreter(self, **options):
+        """
+        Rare disease interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/rd
+
+        :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.
         """
 
-        return self._get(category='analysis', resource='query', subcategory='clinical/interpreter/rd', **options)
+        return self._get(category='analysis', resource='rd', subcategory='clinical/interpreter', **options)
 
     def run_interpreter_rd(self, data=None, **options):
         """
-        Run clinical interpretation analysis for rare diseases.
+        Run interpretation analysis for rare diseases.
         PATH: /{apiVersion}/analysis/clinical/interpreter/rd/run
 
         :param dict data: Parameters to execute the rare disease
@@ -440,6 +445,88 @@ 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 [[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/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 [[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/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 [[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/pipeline/prepare', data=data, **options)
+
     def aggregation_stats_rga(self, field, **options):
         """
         RGA aggregation stats.
@@ -1024,6 +1111,9 @@ 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
@@ -1198,11 +1288,10 @@ 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/rest_clients/cohort_client.py

@@ -61,6 +61,9 @@ class Cohort(_ParentRestClient):
         :param str status: status.
         :param str internal_status: internalStatus.
         :param str annotation: Cohort annotation.
+        :param str tags: Tags. 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 acl: acl.
         :param str samples: Cohort sample IDs.
         :param str num_samples: Number of samples.
@@ -137,6 +140,9 @@ class Cohort(_ParentRestClient):
         :param str uuid: Comma separated list of cohort IDs up to a maximum of
             100.
         :param str type: Cohort type.
+        :param str tags: Tags. 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 creation_date: creationDate.
         :param str modification_date: modificationDate.
         :param bool deleted: deleted.
@@ -223,6 +229,9 @@ class Cohort(_ParentRestClient):
         :param str uuid: Comma separated list of cohort IDs up to a maximum of
             100.
         :param str type: Cohort type.
+        :param str tags: Tags. 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 creation_date: creationDate.
         :param str modification_date: modificationDate.
         :param bool deleted: deleted.
@@ -303,6 +312,8 @@ class Cohort(_ParentRestClient):
         :param str annotation_sets_action: Action to be performed if the array
             of annotationSets is being updated. Allowed values: ['ADD SET
             REMOVE']
+        :param str tags_action: Action to be performed if the array of tags 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.
         :param dict data: body.

pyxetabase/rest_clients/disease_panel_client.py

@@ -190,8 +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 bool include_result: Flag indicating to include the created or
+            updated document result in the response.
         :param dict data: Panel parameters.
         """
 

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
@@ -422,7 +422,7 @@ class File(_ParentRestClient):
             OTHER_BLAST OTHER_INTERACTION OTHER_GENOTYPE OTHER_PLINK OTHER_VCF
             OTHER_PED VCF4 CVDB VARIANT ALIGNMENT COVERAGE SEQUENCE PEDIGREE
             REFERENCE_GENOME NONE UNKNOWN']
-        :param str checksum: Expected MD5 file checksum.
+        :param str checksum: Expected SHA-256 file checksum.
         :param bool resource: Boolean field indicating whether the file is a
             resource or not.
         :param str study: Study [[organization@]project:]study where study and
@@ -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,
@@ -557,6 +569,19 @@ 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/rest_clients/job_client.py

@@ -56,6 +56,12 @@ 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.
@@ -118,6 +124,12 @@ 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.
@@ -202,6 +214,12 @@ 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.
@@ -265,7 +283,8 @@ 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: 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/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/rest_clients/user_tool_client.py

@@ -0,0 +1,471 @@
+"""
+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)
+

pyxetabase/rest_clients/variant_operation_client.py

@@ -627,33 +627,6 @@ class VariantOperation(_ParentRestClient):
 
         return self._post(category='operation', resource='secondaryIndex', subcategory='variant', data=data, **options)
 
-    def delete_variant_secondary_index(self, **options):
-        """
-        Remove a secondary index from the search engine for a specific set of
-            samples.
-        PATH: /{apiVersion}/operation/variant/secondaryIndex/delete
-
-        :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.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str samples: Samples to remove. Needs to provide all the
-            samples in the secondary index.
-        """
-
-        return self._delete(category='operation', resource='delete', subcategory='variant/secondaryIndex', **options)
-
     def setup_variant(self, data=None, **options):
         """
         Execute Variant Setup to allow using the variant engine. This setup is

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-4.0.0.dev35.dist-info → pyxetabase-4.0.0.dev74.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev35
+Version: 4.0.0.dev74
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev35.dist-info → pyxetabase-4.0.0.dev74.dist-info}/RECORD

@@ -6,30 +6,31 @@ pyxetabase/opencga_config.py,sha256=RK23fextK79S5wq4FaQygwuPnE4p4J9GbjY6hJ0Krxc,
 pyxetabase/rest_response.py,sha256=TgwTI2LZFF_jV9-HSawGkF_qZ88n-dxEtIKiFcfPyDk,8635
 pyxetabase/retry.py,sha256=LjViQOaa_GkpDFkcRq9jIS183mE9t4Rq0uls9PV_mfI,2297
 pyxetabase/rest_clients/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pyxetabase/rest_clients/_parent_rest_clients.py,sha256=ZL9VxTxS1cRcg-ofrE9QJXYL8mlVkbXpvFvwhofo-uI,4280
-pyxetabase/rest_clients/admin_client.py,sha256=WebfbQVa7CjiaNcp5MqwAkgDTqCfW-v5AgTaxmL5EF0,6927
+pyxetabase/rest_clients/_parent_rest_clients.py,sha256=OuCnmaziUCENpmpA3CzKJGEhMY_Z-7Q_rlkH75QDi7I,5854
+pyxetabase/rest_clients/admin_client.py,sha256=SzUuUBw1WNaCEOaS15UsHhn0OPgJ0WTEEoR043Z2zwM,7206
 pyxetabase/rest_clients/alignment_client.py,sha256=srY1fmjMZCPWlbqhrD2gYVhS2zu7fgPx61tZOqQi4Wc,18509
-pyxetabase/rest_clients/clinical_analysis_client.py,sha256=7JN6mg0QoKaC4yGVr5ujXymh6Dn4Ua4g-9ptb66Fi7A,65708
-pyxetabase/rest_clients/cohort_client.py,sha256=D-su-AFOziztVMI-oAcr5G2Uq_psbLV8Wt0bqZ7zZgI,16324
+pyxetabase/rest_clients/clinical_analysis_client.py,sha256=JvDSSxkdGIXP7nTX_CsxodjB6JNP8q_Df5vxW_kc6_M,70461
+pyxetabase/rest_clients/cohort_client.py,sha256=_OIKohOlZcz3kRfP-FEneLkdCDVewlbG75YrhMT0aTg,17104
 pyxetabase/rest_clients/cvdb_client.py,sha256=V7ny5nQEeJqsbALAe7JLyoV6b0XyYF7c9lsn-qK-i8o,143102
-pyxetabase/rest_clients/disease_panel_client.py,sha256=WhYn08O4CjfZN-kDZjZgiJge1cfzlGvGL2OO8zUhW_A,17721
+pyxetabase/rest_clients/disease_panel_client.py,sha256=YQIykUElEUGtOKGivnl9vNyHIrrZ_tXMnA1cvK8eE1A,18066
 pyxetabase/rest_clients/family_client.py,sha256=n-kyjnrV09R50JxyiHjFs8rCQkOKFU0Z1O7oVYuaKxg,18586
 pyxetabase/rest_clients/federation_client.py,sha256=p5B8dRq9gj-fdgIfIPhmkT7mNU65cRFtH06kaGtmbWE,5066
-pyxetabase/rest_clients/file_client.py,sha256=fwTWnZtprYNDUBvRetLLe6PTBxW_M8LxN6OlAMGWXC4,33730
+pyxetabase/rest_clients/file_client.py,sha256=pbGgpRHlxRCNWTuVnuA1U5Zm3fKpwmJye1tKXElE90g,34777
 pyxetabase/rest_clients/ga4gh_client.py,sha256=fPnmiblnfpz_zcZPJblGqOFksrdiF3MUer3fv2nwQwk,3506
 pyxetabase/rest_clients/individual_client.py,sha256=C59zr_t7tTxNR7ZBeAPY6fyYl59fE7KY05MaLyXWmXw,23225
-pyxetabase/rest_clients/job_client.py,sha256=amoBW3SL56l6sAPCUB55rZhLR8DcdIIfb5ymOZ9NkLQ,19811
+pyxetabase/rest_clients/job_client.py,sha256=oN55qQsj2C7LF4VG5tQQtyCNZNf4Y1MdmZCNiMP4Dnw,20955
 pyxetabase/rest_clients/meta_client.py,sha256=uExVRfdSKiXteLYe7R3q9x3zCp9mMWWMyPDU56TtoDo,2308
 pyxetabase/rest_clients/organization_client.py,sha256=tnwUTCqJoGiKXMQLMv4ymHA16JxnR5iL2SMLaJDBRs8,9465
 pyxetabase/rest_clients/project_client.py,sha256=M8naPsj47z2ylTrJNU_JyHReKzXrB038PoEtKKrtxmc,5212
 pyxetabase/rest_clients/sample_client.py,sha256=VOsPAhw9HwaEHzzw_5gcVQ1v2xSesvzN3TO4z2opaNo,23621
-pyxetabase/rest_clients/study_client.py,sha256=STtboEiGP-lQ1UptjHxk-ANd3uG6cA6U3srvOO4UQIE,21491
+pyxetabase/rest_clients/study_client.py,sha256=LSm6larpU5X6ceqVRmTP6yx4YMvRkNRiWZsFPs0l8Xk,21508
 pyxetabase/rest_clients/user_client.py,sha256=frA7-rMii-yoRyca_Orkj1T80OeEe-zCdWZCHKn1sio,7683
+pyxetabase/rest_clients/user_tool_client.py,sha256=QCqFpwB0B6w0likPj8y_lhQ3VXBMEgPcDlPCOui3cbI,23522
 pyxetabase/rest_clients/variant_client.py,sha256=mmBuVE0JBThJr5zsLGci5nykNcCKyfZXRKl-h3HT9PA,75436
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