pyxetabase 3.1.0.dev25__py3-none-any.whl → 4.0.0.dev29__py3-none-any.whl

pyopencga/rest_clients/variant_operation_client.py

@@ -1,746 +0,0 @@
-"""
-WARNING: AUTOGENERATED CODE
-
-    This code was generated by a tool.
-    
-    Manual changes to this file may cause unexpected behavior in your application.
-    Manual changes to this file will be overwritten if the code is regenerated.
-"""
-
-from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient
-
-
-class VariantOperation(_ParentRestClient):
-    """
-    This class contains methods for the 'Operations - Variant Storage' webservices
-    PATH: /{apiVersion}/operation
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(VariantOperation, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def configure_cellbase(self, data=None, **options):
-        """
-        Update Cellbase configuration.
-        PATH: /{apiVersion}/operation/cellbase/configure
-
-        :param str project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param bool annotation_update: Create and load variant annotations
-            into the database.
-        :param str annotation_save_id: Save a copy of the current variant
-            annotation at the database.
-        :param dict data: New cellbase configuration.
-        """
-
-        return self._post(category='operation', resource='configure', subcategory='cellbase', data=data, **options)
-
-    def aggregate_variant(self, data=None, **options):
-        """
-        Find variants where not all the samples are present, and fill the
-            empty values, excluding HOM-REF (0/0) values.
-        PATH: /{apiVersion}/operation/variant/aggregate
-
-        :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 dict data: Variant aggregate params.
-        """
-
-        return self._post(category='operation', resource='aggregate', subcategory='variant', data=data, **options)
-
-    def delete_variant_annotation(self, **options):
-        """
-        Deletes a saved copy of variant annotation.
-        PATH: /{apiVersion}/operation/variant/annotation/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 project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param str annotation_id: Annotation identifier.
-        """
-
-        return self._delete(category='operation', resource='delete', subcategory='variant/annotation', **options)
-
-    def variant_annotation_extension_configure(self, data=None, **options):
-        """
-        Install a variant annotation extension and configure the project to
-            use it.
-        PATH: /{apiVersion}/operation/variant/annotation/extension/configure
-
-        :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 dict data: Parameters to configure a variant annotation
-            extension.
-        """
-
-        return self._post(category='operation', resource='configure', subcategory='variant/annotation/extension', data=data, **options)
-
-    def index_variant_annotation(self, data=None, **options):
-        """
-        Create and load variant annotations into the database.
-        PATH: /{apiVersion}/operation/variant/annotation/index
-
-        :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 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 dict data: Variant annotation index params.
-        """
-
-        return self._post(category='operation', resource='index', subcategory='variant/annotation', data=data, **options)
-
-    def save_variant_annotation(self, data=None, **options):
-        """
-        Save a copy of the current variant annotation at the database.
-        PATH: /{apiVersion}/operation/variant/annotation/save
-
-        :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 project: Project [organization@]project where project can
-            be either the ID or the alias.
-        :param dict data: Variant annotation save params.
-        """
-
-        return self._post(category='operation', resource='save', subcategory='variant/annotation', data=data, **options)
-
-    def configure_variant(self, data=None, **options):
-        """
-        Update Variant Storage Engine configuration. Can be updated at Project
-            or Study level.
-        PATH: /{apiVersion}/operation/variant/configure
-
-        :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 dict data: Configuration params to update.
-        """
-
-        return self._post(category='operation', resource='configure', subcategory='variant', data=data, **options)
-
-    def delete_variant(self, data=None, **options):
-        """
-        Remove variant files from the variant storage.
-        PATH: /{apiVersion}/operation/variant/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 dict data: Variant delete file params.
-        """
-
-        return self._post(category='operation', resource='delete', subcategory='variant', data=data, **options)
-
-    def aggregate_variant_family(self, data=None, **options):
-        """
-        Find variants where not all the samples are present, and fill the
-            empty values.
-        PATH: /{apiVersion}/operation/variant/family/aggregate
-
-        :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 dict data: Variant aggregate family params.
-        """
-
-        return self._post(category='operation', resource='aggregate', subcategory='variant/family', data=data, **options)
-
-    def index_variant_family(self, data=None, **options):
-        """
-        DEPRECATED: integrated in index (DEPRECATED Build the family index).
-        PATH: /{apiVersion}/operation/variant/family/index
-
-        :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 dict data: Variant family index params.
-        """
-
-        return self._post(category='operation', resource='index', subcategory='variant/family', data=data, **options)
-
-    def index_variant(self, data=None, **options):
-        """
-        Index variant files into the variant storage.
-        PATH: /{apiVersion}/operation/variant/index
-
-        :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 dict data: Variant index params.
-        """
-
-        return self._post(category='operation', resource='index', subcategory='variant', data=data, **options)
-
-    def launcher_variant_index(self, data=None, **options):
-        """
-        Detect non-indexed VCF files in the study, and submit a job for
-            indexing them.
-        PATH: /{apiVersion}/operation/variant/index/launcher
-
-        :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 dict data: .
-        """
-
-        return self._post(category='operation', resource='launcher', subcategory='variant/index', data=data, **options)
-
-    def run_variant_julie(self, data=None, **options):
-        """
-        Transform VariantStats into PopulationFrequency values and updates the
-            VariantAnnotation.
-        PATH: /{apiVersion}/operation/variant/julie/run
-
-        :param dict data: Julie tool params. Specify list of cohorts from
-            multiple studies with {study}:{cohort}. (REQUIRED)
-        :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 project: project.
-        """
-
-        return self._post(category='operation', resource='run', subcategory='variant/julie', data=data, **options)
-
-    def repair_variant_metadata(self, data=None, **options):
-        """
-        Execute some repairs on Variant Storage Metadata. Advanced users only.
-        PATH: /{apiVersion}/operation/variant/metadata/repair
-
-        :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 dict data: Variant storage metadata repair params.
-        """
-
-        return self._post(category='operation', resource='repair', subcategory='variant/metadata', data=data, **options)
-
-    def synchronize_variant_metadata(self, data=None, **options):
-        """
-        Synchronize catalog with variant storage metadata.
-        PATH: /{apiVersion}/operation/variant/metadata/synchronize
-
-        :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 dict data: Variant storage metadata synchronize params.
-        """
-
-        return self._post(category='operation', resource='synchronize', subcategory='variant/metadata', data=data, **options)
-
-    def prune_variant(self, data=None, **options):
-        """
-        Prune orphan variants from studies in a project.
-        PATH: /{apiVersion}/operation/variant/prune
-
-        :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 dict data: Variant prune params. Use dry-run to just generate a
-            report with the orphan variants.
-        """
-
-        return self._post(category='operation', resource='prune', subcategory='variant', data=data, **options)
-
-    def delete_variant_sample(self, data=None, **options):
-        """
-        Remove variant samples from the variant storage.
-        PATH: /{apiVersion}/operation/variant/sample/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 dict data: Variant delete sample params.
-        """
-
-        return self._post(category='operation', resource='delete', subcategory='variant/sample', data=data, **options)
-
-    def index_variant_sample(self, data=None, **options):
-        """
-        DEPRECATED You should use the new sample index method instead.
-        PATH: /{apiVersion}/operation/variant/sample/index
-
-        :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 dict data: Variant sample index params.
-        """
-
-        return self._post(category='operation', resource='index', subcategory='variant/sample', data=data, **options)
-
-    def variant_sample_index_configure(self, data=None, **options):
-        """
-        DEPRECATED You should use the new sample index configure method.
-        PATH: /{apiVersion}/operation/variant/sample/index/configure
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool skip_rebuild: Skip sample index re-build.
-        :param dict data: New SampleIndexConfiguration.
-        """
-
-        return self._post(category='operation', resource='configure', subcategory='variant/sample/index', data=data, **options)
-
-    def delete_variant_score(self, **options):
-        """
-        Remove a variant score in the database.
-        PATH: /{apiVersion}/operation/variant/score/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 name: Unique name of the score within the study.
-        :param bool resume: Resume a previously failed remove.
-        :param bool force: Force remove of partially indexed scores.
-        """
-
-        return self._delete(category='operation', resource='delete', subcategory='variant/score', **options)
-
-    def index_variant_score(self, data=None, **options):
-        """
-        Index a variant score in the database.
-        PATH: /{apiVersion}/operation/variant/score/index
-
-        :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 dict data: Variant score index params. scoreName: Unique name
-            of the score within the study. cohort1: Cohort used to compute the
-            score. Use the cohort 'ALL' if all samples from the study where
-            used to compute the score. cohort2: Second cohort used to compute
-            the score, typically to compare against the first cohort. If only
-            one cohort was used to compute the score, leave empty.
-            inputColumns: Indicate which columns to load from the input file.
-            Provide the column position (starting in 0) for the column with the
-            score with 'SCORE=n'. Optionally, the PValue column with
-            'PVALUE=n'. The, to indicate the variant associated with the score,
-            provide either the columns ['CHROM', 'POS', 'REF', 'ALT'], or the
-            column 'VAR' containing a variant representation with format
-            'chr:start:ref:alt'. e.g.
-            'CHROM=0,POS=1,REF=3,ALT=4,SCORE=5,PVALUE=6' or
-            'VAR=0,SCORE=1,PVALUE=2'. resume: Resume a previously failed
-            indexation.
-        """
-
-        return self._post(category='operation', resource='index', subcategory='variant/score', data=data, **options)
-
-    def variant_secondary_annotation_index(self, data=None, **options):
-        """
-        Creates a secondary index using a search engine. If samples are
-            provided, sample data will be added to the secondary index. (New!).
-        PATH: /{apiVersion}/operation/variant/secondary/annotation/index
-
-        :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 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 dict data: Variant secondary annotation index params.
-        """
-
-        return self._post(category='operation', resource='index', subcategory='variant/secondary/annotation', data=data, **options)
-
-    def variant_secondary_sample_index(self, data=None, **options):
-        """
-        Build and annotate the sample index. (New!) .
-        PATH: /{apiVersion}/operation/variant/secondary/sample/index
-
-        :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 dict data: Variant sample index params.
-        """
-
-        return self._post(category='operation', resource='index', subcategory='variant/secondary/sample', data=data, **options)
-
-    def configure_variant_secondary_sample_index(self, data=None, **options):
-        """
-        Update SampleIndex configuration (New!).
-        PATH: /{apiVersion}/operation/variant/secondary/sample/index/configure
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool skip_rebuild: Skip sample index re-build.
-        :param dict data: New SampleIndexConfiguration.
-        """
-
-        return self._post(category='operation', resource='configure', subcategory='variant/secondary/sample/index', data=data, **options)
-
-    def secondary_index_variant(self, data=None, **options):
-        """
-        DEPRECATED you should use the new annotation index method instead.
-        PATH: /{apiVersion}/operation/variant/secondaryIndex
-
-        :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 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 dict data: Variant secondary annotation index params.
-        """
-
-        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
-            necessary before starting any variant operation.
-        PATH: /{apiVersion}/operation/variant/setup
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param dict data: Variant setup params.
-        """
-
-        return self._post(category='operation', resource='setup', subcategory='variant', data=data, **options)
-
-    def delete_variant_stats(self, data=None, **options):
-        """
-        Deletes the VariantStats of a cohort/s from the database.
-        PATH: /{apiVersion}/operation/variant/stats/delete
-
-        :param dict data: Variant stats delete params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='operation', resource='delete', subcategory='variant/stats', data=data, **options)
-
-    def index_variant_stats(self, data=None, **options):
-        """
-        Compute variant stats for any cohort and any set of variants and index
-            the result in the variant storage database.
-        PATH: /{apiVersion}/operation/variant/stats/index
-
-        :param dict data: Variant stats params. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        """
-
-        return self._post(category='operation', resource='index', subcategory='variant/stats', data=data, **options)
-
-    def delete_variant_study(self, data=None, **options):
-        """
-        Remove whole study from the variant storage.
-        PATH: /{apiVersion}/operation/variant/study/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 dict data: Variant delete study params.
-        """
-
-        return self._post(category='operation', resource='delete', subcategory='variant/study', data=data, **options)
-