pyxetabase 4.0.0.dev0__py3-none-any.whl → 4.0.0.dev1__py3-none-any.whl

pyopencga/rest_clients/clinical_analysis_client.py

@@ -1,1279 +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 ClinicalAnalysis(_ParentRestClient):
-    """
-    This class contains methods for the 'Analysis - Clinical' webservices
-    PATH: /{apiVersion}/analysis/clinical
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(ClinicalAnalysis, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def update_acl(self, members, action, data=None, **options):
-        """
-        Update the set of permissions granted for the member.
-        PATH: /{apiVersion}/analysis/clinical/acl/{members}/update
-
-        :param dict data: JSON containing the parameters to add ACLs.
-            (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.
-        :param bool propagate: Propagate permissions to related families,
-            individuals, samples and files.
-        """
-
-        options['action'] = action
-        return self._post(category='analysis', resource='update', subcategory='clinical/acl', second_query_id=members, data=data, **options)
-
-    def aggregation_stats(self, **options):
-        """
-        Fetch catalog clinical analysis aggregation stats.
-        PATH: /{apiVersion}/analysis/clinical/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 Clinical Analysis 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 uuid: Comma separated list of Clinical Analysis UUIDs up to
-            a maximum of 100.
-        :param str type: Clinical Analysis type.
-        :param str disorder: Clinical Analysis disorder. 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 files: Clinical Analysis files.
-        :param str sample: Sample associated to the proband or any member of a
-            family.
-        :param str individual: Proband or any member of a family.
-        :param str proband: Clinical Analysis proband.
-        :param str proband_samples: Clinical Analysis proband samples.
-        :param str family: Clinical Analysis family.
-        :param str family_members: Clinical Analysis family members.
-        :param str family_member_samples: Clinical Analysis family members
-            samples.
-        :param str panels: Clinical Analysis panels.
-        :param bool locked: Locked Clinical Analyses.
-        :param str analyst_id: Clinical Analysis analyst id.
-        :param str priority: Clinical Analysis priority.
-        :param str flags: Clinical Analysis flags.
-        :param str creation_date: Clinical Analysis Creation date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Clinical Analysis Modification date.
-            Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str due_date: Clinical Analysis due date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str quality_control_summary: Clinical Analysis quality control
-            summary.
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :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='analysis', resource='aggregationStats', subcategory='clinical', **options)
-
-    def load_annotation_sets(self, variable_set_id, path, data=None, **options):
-        """
-        Load annotation sets from a TSV file.
-        PATH: /{apiVersion}/analysis/clinical/annotationSets/load
-
-        :param str path: Path where the TSV file is located in OpenCGA or
-            where it should be located. (REQUIRED)
-        :param str variable_set_id: Variable set ID or name. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool parents: Flag indicating whether to create parent
-            directories if they don't exist (only when TSV file was not
-            previously associated).
-        :param str annotation_set_id: Annotation set id. If not provided,
-            variableSetId will be used.
-        :param dict data: JSON containing the 'content' of the TSV file if
-            this has not yet been registered into OpenCGA.
-        """
-
-        options['variableSetId'] = variable_set_id
-        options['path'] = path
-        return self._post(category='analysis', resource='load', subcategory='clinical/annotationSets', data=data, **options)
-
-    def update_clinical_configuration(self, data=None, **options):
-        """
-        Update Clinical Analysis configuration.
-        PATH: /{apiVersion}/analysis/clinical/clinical/configuration/update
-
-        :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='analysis', resource='update', subcategory='clinical/clinical/configuration', data=data, **options)
-
-    def create(self, data=None, **options):
-        """
-        Create a new clinical analysis.
-        PATH: /{apiVersion}/analysis/clinical/create
-
-        :param dict data: JSON containing clinical analysis 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 skip_create_default_interpretation: Flag to skip creating
-            and initialise an empty default primary interpretation (Id will be
-            '{clinicalAnalysisId}.1'). This flag is only considered if no
-            Interpretation object is passed.
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='analysis', resource='create', subcategory='clinical', data=data, **options)
-
-    def distinct(self, field, **options):
-        """
-        Clinical Analysis distinct method.
-        PATH: /{apiVersion}/analysis/clinical/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 Clinical Analysis 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 uuid: Comma separated list of Clinical Analysis UUIDs up to
-            a maximum of 100.
-        :param str type: Clinical Analysis type.
-        :param str disorder: Clinical Analysis disorder. 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 files: Clinical Analysis files.
-        :param str sample: Sample associated to the proband or any member of a
-            family.
-        :param str individual: Proband or any member of a family.
-        :param str proband: Clinical Analysis proband.
-        :param str proband_samples: Clinical Analysis proband samples.
-        :param str family: Clinical Analysis family.
-        :param str family_members: Clinical Analysis family members.
-        :param str family_member_samples: Clinical Analysis family members
-            samples.
-        :param str panels: Clinical Analysis panels.
-        :param bool locked: Locked Clinical Analyses.
-        :param str analyst_id: Clinical Analysis analyst id.
-        :param str priority: Clinical Analysis priority.
-        :param str flags: Clinical Analysis flags.
-        :param str creation_date: Clinical Analysis Creation date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Clinical Analysis Modification date.
-            Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str due_date: Clinical Analysis due date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str quality_control_summary: Clinical Analysis quality control
-            summary.
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        options['field'] = field
-        return self._get(category='analysis', resource='distinct', subcategory='clinical', **options)
-
-    def aggregation_stats_interpretation(self, **options):
-        """
-        Fetch catalog interpretation aggregation stats.
-        PATH: /{apiVersion}/analysis/clinical/interpretation/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 Interpretation 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 uuid: Comma separated list of Interpretation UUIDs up to a
-            maximum of 100.
-        :param str name: Comma separated list of Interpretation names up to a
-            maximum of 100.
-        :param str clinical_analysis_id: Clinical Analysis id.
-        :param str analyst_id: Analyst ID.
-        :param str method_name: Interpretation method name. 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 panels: Interpretation panels.
-        :param str primary_findings: Interpretation primary findings.
-        :param str secondary_findings: Interpretation secondary findings.
-        :param str creation_date: Interpretation Creation date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Interpretation Modification date.
-            Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str release: Release when it was created.
-        :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='analysis', resource='aggregationStats', subcategory='clinical/interpretation', **options)
-
-    def distinct_interpretation(self, field, **options):
-        """
-        Interpretation distinct method.
-        PATH: /{apiVersion}/analysis/clinical/interpretation/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 Interpretation 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 uuid: Comma separated list of Interpretation UUIDs up to a
-            maximum of 100.
-        :param str name: Comma separated list of Interpretation names up to a
-            maximum of 100.
-        :param str clinical_analysis_id: Clinical Analysis id.
-        :param str analyst_id: Analyst ID.
-        :param str method_name: Interpretation method name. 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 panels: Interpretation panels.
-        :param str primary_findings: Interpretation primary findings.
-        :param str secondary_findings: Interpretation secondary findings.
-        :param str creation_date: Interpretation Creation date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Interpretation Modification date.
-            Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str release: Release when it was created.
-        """
-
-        options['field'] = field
-        return self._get(category='analysis', resource='distinct', subcategory='clinical/interpretation', **options)
-
-    def search_interpretation(self, **options):
-        """
-        Search clinical interpretations.
-        PATH: /{apiVersion}/analysis/clinical/interpretation/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 sort: Sort the results.
-        :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 Interpretation 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 uuid: Comma separated list of Interpretation UUIDs up to a
-            maximum of 100.
-        :param str name: Comma separated list of Interpretation names up to a
-            maximum of 100.
-        :param str clinical_analysis_id: Clinical Analysis id.
-        :param str analyst_id: Analyst ID.
-        :param str method_name: Interpretation method name. 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 panels: Interpretation panels.
-        :param str primary_findings: Interpretation primary findings.
-        :param str secondary_findings: Interpretation secondary findings.
-        :param str creation_date: Interpretation Creation date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Interpretation Modification date.
-            Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str release: Release when it was created.
-        """
-
-        return self._get(category='analysis', resource='search', subcategory='clinical/interpretation', **options)
-
-    def info_interpretation(self, interpretations, **options):
-        """
-        Clinical interpretation information.
-        PATH: /{apiVersion}/analysis/clinical/interpretation/{interpretations}/info
-
-        :param str interpretations: Comma separated list of clinical
-            interpretation IDs  up to a maximum of 100. (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 interpretation versions.
-            'all' to get all the interpretation versions. Not supported if
-            multiple interpretation ids are provided.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='analysis', resource='info', subcategory='clinical/interpretation', second_query_id=interpretations, **options)
-
-    def run_interpreter_cancer_tiering(self, data=None, **options):
-        """
-        Run cancer tiering interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run
-
-        :param dict data: Cancer tiering interpretation analysis 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='analysis', resource='run', subcategory='clinical/interpreter/cancerTiering', data=data, **options)
-
-    def run_interpreter_exomiser(self, data=None, **options):
-        """
-        Run exomiser interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/exomiser/run
-
-        :param dict data: Exomiser interpretation analysis 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='analysis', resource='run', subcategory='clinical/interpreter/exomiser', data=data, **options)
-
-    def run_interpreter_team(self, data=None, **options):
-        """
-        Run TEAM interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/team/run
-
-        :param dict data: TEAM interpretation analysis 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='analysis', resource='run', subcategory='clinical/interpreter/team', data=data, **options)
-
-    def run_interpreter_tiering(self, data=None, **options):
-        """
-        Run tiering interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/tiering/run
-
-        :param dict data: Tiering interpretation analysis 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='analysis', resource='run', subcategory='clinical/interpreter/tiering', data=data, **options)
-
-    def run_interpreter_zetta(self, data=None, **options):
-        """
-        Run Zetta interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/zetta/run
-
-        :param dict data: Zetta interpretation analysis 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='analysis', resource='run', subcategory='clinical/interpreter/zetta', data=data, **options)
-
-    def load(self, data=None, **options):
-        """
-        Load clinical analyses from a file.
-        PATH: /{apiVersion}/analysis/clinical/load
-
-        :param dict data: Parameters to load clinical analysis in OpenCGA
-            catalog from a file. (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='load', subcategory='clinical', data=data, **options)
-
-    def aggregation_stats_rga(self, field, **options):
-        """
-        RGA aggregation stats.
-        PATH: /{apiVersion}/analysis/clinical/rga/aggregationStats
-
-        :param str field: List of fields separated by semicolons, e.g.:
-            clinicalSignificances;type. For nested fields use >>, e.g.:
-            type>>clinicalSignificances;knockoutType. (REQUIRED)
-        :param int limit: Number of results to be returned.
-        :param int skip: Number of results to skip.
-        :param str sample_id: Filter by sample id.
-        :param str individual_id: Filter by individual id.
-        :param str sex: Filter by sex.
-        :param str phenotypes: Filter by phenotypes.
-        :param str disorders: Filter by disorders.
-        :param str num_parents: Filter by the number of parents registered.
-        :param str gene_id: Filter by gene id.
-        :param str gene_name: Filter by gene name.
-        :param str chromosome: Filter by chromosome.
-        :param str start: Filter by start position.
-        :param str end: Filter by end position.
-        :param str transcript_id: Filter by transcript id.
-        :param str variants: Filter by variant id.
-        :param str db_snps: Filter by DB_SNP id.
-        :param str knockout_type: Filter by knockout type.
-        :param str filter: Filter by filter (PASS, NOT_PASS).
-        :param str type: Filter by variant type.
-        :param str clinical_significance: Filter by clinical significance.
-        :param str population_frequency: Filter by population frequency.
-        :param str consequence_type: Filter by consequence type.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        options['field'] = field
-        return self._get(category='analysis', resource='aggregationStats', subcategory='clinical/rga', **options)
-
-    def query_rga_gene(self, **options):
-        """
-        Query gene RGA.
-        PATH: /{apiVersion}/analysis/clinical/rga/gene/query
-
-        :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 include_individual: Include only the comma separated list
-            of individuals to the response.
-        :param int skip_individual: Number of individuals to skip.
-        :param int limit_individual: Limit number of individuals returned
-            (default: 1000).
-        :param str sample_id: Filter by sample id.
-        :param str individual_id: Filter by individual id.
-        :param str sex: Filter by sex.
-        :param str phenotypes: Filter by phenotypes.
-        :param str disorders: Filter by disorders.
-        :param str num_parents: Filter by the number of parents registered.
-        :param str gene_id: Filter by gene id.
-        :param str gene_name: Filter by gene name.
-        :param str chromosome: Filter by chromosome.
-        :param str start: Filter by start position.
-        :param str end: Filter by end position.
-        :param str transcript_id: Filter by transcript id.
-        :param str variants: Filter by variant id.
-        :param str db_snps: Filter by DB_SNP id.
-        :param str knockout_type: Filter by knockout type.
-        :param str filter: Filter by filter (PASS, NOT_PASS).
-        :param str type: Filter by variant type.
-        :param str clinical_significance: Filter by clinical significance.
-        :param str population_frequency: Filter by population frequency.
-        :param str consequence_type: Filter by consequence type.
-        :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/rga/gene', **options)
-
-    def summary_rga_gene(self, **options):
-        """
-        RGA gene summary stats.
-        PATH: /{apiVersion}/analysis/clinical/rga/gene/summary
-
-        :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 sample_id: Filter by sample id.
-        :param str individual_id: Filter by individual id.
-        :param str sex: Filter by sex.
-        :param str phenotypes: Filter by phenotypes.
-        :param str disorders: Filter by disorders.
-        :param str num_parents: Filter by the number of parents registered.
-        :param str gene_id: Filter by gene id.
-        :param str gene_name: Filter by gene name.
-        :param str chromosome: Filter by chromosome.
-        :param str start: Filter by start position.
-        :param str end: Filter by end position.
-        :param str transcript_id: Filter by transcript id.
-        :param str variants: Filter by variant id.
-        :param str db_snps: Filter by DB_SNP id.
-        :param str knockout_type: Filter by knockout type.
-        :param str filter: Filter by filter (PASS, NOT_PASS).
-        :param str type: Filter by variant type.
-        :param str clinical_significance: Filter by clinical significance.
-        :param str population_frequency: Filter by population frequency.
-        :param str consequence_type: Filter by consequence type.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._get(category='analysis', resource='summary', subcategory='clinical/rga/gene', **options)
-
-    def run_rga_index(self, data=None, **options):
-        """
-        Generate Recessive Gene Analysis secondary index.
-        PATH: /{apiVersion}/analysis/clinical/rga/index/run
-
-        :param dict data: Recessive Gene Analysis index 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.
-        :param bool auxiliar_index: Index auxiliar collection to improve
-            performance assuming RGA is completely indexed.
-        """
-
-        return self._post(category='analysis', resource='run', subcategory='clinical/rga/index', data=data, **options)
-
-    def query_rga_individual(self, **options):
-        """
-        Query individual RGA.
-        PATH: /{apiVersion}/analysis/clinical/rga/individual/query
-
-        :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 sample_id: Filter by sample id.
-        :param str individual_id: Filter by individual id.
-        :param str sex: Filter by sex.
-        :param str phenotypes: Filter by phenotypes.
-        :param str disorders: Filter by disorders.
-        :param str num_parents: Filter by the number of parents registered.
-        :param str gene_id: Filter by gene id.
-        :param str gene_name: Filter by gene name.
-        :param str chromosome: Filter by chromosome.
-        :param str start: Filter by start position.
-        :param str end: Filter by end position.
-        :param str transcript_id: Filter by transcript id.
-        :param str variants: Filter by variant id.
-        :param str db_snps: Filter by DB_SNP id.
-        :param str knockout_type: Filter by knockout type.
-        :param str filter: Filter by filter (PASS, NOT_PASS).
-        :param str type: Filter by variant type.
-        :param str clinical_significance: Filter by clinical significance.
-        :param str population_frequency: Filter by population frequency.
-        :param str consequence_type: Filter by consequence type.
-        :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/rga/individual', **options)
-
-    def summary_rga_individual(self, **options):
-        """
-        RGA individual summary stats.
-        PATH: /{apiVersion}/analysis/clinical/rga/individual/summary
-
-        :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 sample_id: Filter by sample id.
-        :param str individual_id: Filter by individual id.
-        :param str sex: Filter by sex.
-        :param str phenotypes: Filter by phenotypes.
-        :param str disorders: Filter by disorders.
-        :param str num_parents: Filter by the number of parents registered.
-        :param str gene_id: Filter by gene id.
-        :param str gene_name: Filter by gene name.
-        :param str chromosome: Filter by chromosome.
-        :param str start: Filter by start position.
-        :param str end: Filter by end position.
-        :param str transcript_id: Filter by transcript id.
-        :param str variants: Filter by variant id.
-        :param str db_snps: Filter by DB_SNP id.
-        :param str knockout_type: Filter by knockout type.
-        :param str filter: Filter by filter (PASS, NOT_PASS).
-        :param str type: Filter by variant type.
-        :param str clinical_significance: Filter by clinical significance.
-        :param str population_frequency: Filter by population frequency.
-        :param str consequence_type: Filter by consequence type.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._get(category='analysis', resource='summary', subcategory='clinical/rga/individual', **options)
-
-    def query_rga_variant(self, **options):
-        """
-        Query variant RGA.
-        PATH: /{apiVersion}/analysis/clinical/rga/variant/query
-
-        :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 include_individual: Include only the comma separated list
-            of individuals to the response.
-        :param int skip_individual: Number of individuals to skip.
-        :param int limit_individual: Limit number of individuals returned
-            (default: 1000).
-        :param str sample_id: Filter by sample id.
-        :param str individual_id: Filter by individual id.
-        :param str sex: Filter by sex.
-        :param str phenotypes: Filter by phenotypes.
-        :param str disorders: Filter by disorders.
-        :param str num_parents: Filter by the number of parents registered.
-        :param str gene_id: Filter by gene id.
-        :param str gene_name: Filter by gene name.
-        :param str chromosome: Filter by chromosome.
-        :param str start: Filter by start position.
-        :param str end: Filter by end position.
-        :param str transcript_id: Filter by transcript id.
-        :param str variants: Filter by variant id.
-        :param str db_snps: Filter by DB_SNP id.
-        :param str knockout_type: Filter by knockout type.
-        :param str filter: Filter by filter (PASS, NOT_PASS).
-        :param str type: Filter by variant type.
-        :param str clinical_significance: Filter by clinical significance.
-        :param str population_frequency: Filter by population frequency.
-        :param str consequence_type: Filter by consequence type.
-        :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/rga/variant', **options)
-
-    def summary_rga_variant(self, **options):
-        """
-        RGA variant summary stats.
-        PATH: /{apiVersion}/analysis/clinical/rga/variant/summary
-
-        :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 sample_id: Filter by sample id.
-        :param str individual_id: Filter by individual id.
-        :param str sex: Filter by sex.
-        :param str phenotypes: Filter by phenotypes.
-        :param str disorders: Filter by disorders.
-        :param str num_parents: Filter by the number of parents registered.
-        :param str gene_id: Filter by gene id.
-        :param str gene_name: Filter by gene name.
-        :param str chromosome: Filter by chromosome.
-        :param str start: Filter by start position.
-        :param str end: Filter by end position.
-        :param str transcript_id: Filter by transcript id.
-        :param str variants: Filter by variant id.
-        :param str db_snps: Filter by DB_SNP id.
-        :param str knockout_type: Filter by knockout type.
-        :param str filter: Filter by filter (PASS, NOT_PASS).
-        :param str type: Filter by variant type.
-        :param str clinical_significance: Filter by clinical significance.
-        :param str population_frequency: Filter by population frequency.
-        :param str consequence_type: Filter by consequence type.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._get(category='analysis', resource='summary', subcategory='clinical/rga/variant', **options)
-
-    def search(self, **options):
-        """
-        Clinical analysis search.
-        PATH: /{apiVersion}/analysis/clinical/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 bool flatten_annotations: Flatten the annotations?.
-        :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 Clinical Analysis 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 uuid: Comma separated list of Clinical Analysis UUIDs up to
-            a maximum of 100.
-        :param str type: Clinical Analysis type.
-        :param str disorder: Clinical Analysis disorder. 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 files: Clinical Analysis files.
-        :param str sample: Sample associated to the proband or any member of a
-            family.
-        :param str individual: Proband or any member of a family.
-        :param str proband: Clinical Analysis proband.
-        :param str proband_samples: Clinical Analysis proband samples.
-        :param str family: Clinical Analysis family.
-        :param str family_members: Clinical Analysis family members.
-        :param str family_member_samples: Clinical Analysis family members
-            samples.
-        :param str panels: Clinical Analysis panels.
-        :param bool locked: Locked Clinical Analyses.
-        :param str analyst_id: Clinical Analysis analyst id.
-        :param str priority: Clinical Analysis priority.
-        :param str flags: Clinical Analysis flags.
-        :param str creation_date: Clinical Analysis Creation date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Clinical Analysis Modification date.
-            Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str due_date: Clinical Analysis due date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str quality_control_summary: Clinical Analysis quality control
-            summary.
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='analysis', resource='search', subcategory='clinical', **options)
-
-    def query_variant(self, **options):
-        """
-        Fetch clinical variants.
-        PATH: /{apiVersion}/analysis/clinical/variant/query
-
-        :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 bool approximate_count: Get an approximate count, instead of an
-            exact total count. Reduces execution time.
-        :param int approximate_count_sampling_size: Sampling size to get the
-            approximate count. Larger values increase accuracy but also
-            increase execution time.
-        :param str saved_filter: Use a saved filter at User level.
-        :param str include_interpretation: Interpretation ID to include the
-            fields related to this interpretation.
-        :param str id: List of variant IDs in the format chrom:start:ref:alt,
-            e.g. 19:7177679:C:T.
-        :param str region: List of regions, these can be just a single
-            chromosome name or regions in the format chr:start-end, e.g.:
-            2,3:100000-200000.
-        :param str type: List of types, accepted values are SNV, MNV, INDEL,
-            SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION,
-            DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g.
-            SNV,INDEL.
-        :param str study: Filter variants from the given studies, these can be
-            either the numeric ID or the alias with the format
-            organization@project:study.
-        :param str file: Filter variants from the files specified. This will
-            set includeFile parameter when not provided.
-        :param str filter: Specify the FILTER for any of the files. If 'file'
-            filter is provided, will match the file and the filter. e.g.:
-            PASS,LowGQX.
-        :param str qual: Specify the QUAL for any of the files. If 'file'
-            filter is provided, will match the file and the qual. e.g.: >123.4.
-        :param str file_data: Filter by file data (i.e. FILTER, QUAL and INFO
-            columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file
-            is specified, will use all files from 'file' filter. e.g. AN>200 or
-            file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined.
-            e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP.
-        :param str sample: Filter variants by sample genotype. This will
-            automatically set 'includeSample' parameter when not provided. This
-            filter accepts multiple 3 forms: 1) List of samples: Samples that
-            contain the main variant. Accepts AND ';' and OR ',' operators. 
-            e.g. HG0097,HG0098 . 2) List of samples with genotypes:
-            {sample}:{gt1},{gt2}. Accepts AND ';' and OR ',' operators.  e.g.
-            HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will
-            also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice
-            versa. When filtering by multi-allelic genotypes, any secondary
-            allele will match, regardless of its position e.g. 1/2 will match
-            with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted:
-            HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS  e.g.
-            HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation
-            mode: {sample}:{segregation}. Only one sample accepted.Accepted
-            segregation modes: [ autosomalDominant, autosomalRecessive,
-            XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo,
-            deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case
-            insensitive. e.g. HG0097:DeNovo Sample must have parents defined
-            and indexed. .
-        :param str sample_data: Filter by any SampleData field from samples.
-            [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will
-            use all samples from 'sample' or 'genotype' filter. e.g. DP>200 or
-            HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined.
-            e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10.
-        :param str sample_annotation: Selects some samples using metadata
-            information from Catalog. e.g.
-            age>20;phenotype=hpo:123,hpo:456;name=smith.
-        :param str cohort: Select variants with calculated stats for the
-            selected cohorts.
-        :param str cohort_stats_ref: Reference Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_alt: Alternate Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_maf: Minor Allele Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_mgf: Minor Genotype Frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
-        :param str cohort_stats_pass: Filter PASS frequency:
-            [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
-        :param str missing_alleles: Number of missing alleles:
-            [{study:}]{cohort}[<|>|<=|>=]{number}.
-        :param str missing_genotypes: Number of missing genotypes:
-            [{study:}]{cohort}[<|>|<=|>=]{number}.
-        :param str score: Filter by variant score:
-            [{study:}]{score}[<|>|<=|>=]{number}.
-        :param str family: Filter variants where any of the samples from the
-            given family contains the variant (HET or HOM_ALT).
-        :param str family_disorder: Specify the disorder to use for the family
-            segregation.
-        :param str family_segregation: Filter by segregation mode from a given
-            family. Accepted values: [ autosomalDominant, autosomalRecessive,
-            XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo,
-            deNovoStrict, mendelianError, compoundHeterozygous ].
-        :param str family_members: Sub set of the members of a given family.
-        :param str family_proband: Specify the proband child to use for the
-            family segregation.
-        :param str gene: List of genes, most gene IDs are accepted (HGNC,
-            Ensembl gene, ...). This is an alias to 'xref' parameter.
-        :param str ct: List of SO consequence types, e.g.
-            missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts
-            aliases 'loss_of_function' and 'protein_altering'.
-        :param str xref: List of any external reference, these can be genes,
-            proteins or variants. Accepted IDs include HGNC, Ensembl genes,
-            dbSNP, ClinVar, HPO, Cosmic, HGVS ...
-        :param str biotype: List of biotypes, e.g. protein_coding.
-        :param str protein_substitution: Protein substitution scores include
-            SIFT and PolyPhen. You can query using the score
-            {protein_score}[<|>|<=|>=]{number} or the description
-            {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant.
-        :param str conservation: Filter by conservation score:
-            {conservation_score}[<|>|<=|>=]{number} e.g.
-            phastCons>0.5,phylop<0.1,gerp>0.1.
-        :param str population_frequency_alt: Alternate Population Frequency:
-            {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
-        :param str population_frequency_ref: Reference Population Frequency:
-            {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
-        :param str population_frequency_maf: Population minor allele
-            frequency: {study}:{population}[<|>|<=|>=]{number}. e.g.
-            1000G:ALL<0.01.
-        :param str transcript_flag: List of transcript flags. e.g. canonical,
-            CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc,
-            TSO500.
-        :param str gene_trait_id: List of gene trait association id. e.g.
-            'umls:C0007222' , 'OMIM:269600'.
-        :param str go: List of GO (Gene Ontology) terms. e.g. 'GO:0002020'.
-        :param str expression: List of tissues of interest. e.g. 'lung'.
-        :param str protein_keyword: List of Uniprot protein variant annotation
-            keywords.
-        :param str drug: List of drug names.
-        :param str functional_score: Functional score:
-            {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
-            cadd_raw<=0.3.
-        :param str clinical: Clinical source: clinvar, cosmic.
-        :param str clinical_significance: Clinical significance: benign,
-            likely_benign, likely_pathogenic, pathogenic.
-        :param bool clinical_confirmed_status: Clinical confirmed status.
-        :param str custom_annotation: Custom annotation:
-            {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}.
-        :param str panel: Filter by genes from the given disease panel.
-        :param str panel_mode_of_inheritance: Filter genes from specific
-            panels that match certain mode of inheritance. Accepted values : [
-            autosomalDominant, autosomalRecessive, XLinkedDominant,
-            XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError,
-            compoundHeterozygous ].
-        :param str panel_confidence: Filter genes from specific panels that
-            match certain confidence. Accepted values : [ high, medium, low,
-            rejected ].
-        :param str panel_role_in_cancer: Filter genes from specific panels
-            that match certain role in cancer. Accepted values : [ both,
-            oncogene, tumorSuppressorGene, fusion ].
-        :param str panel_feature_type: Filter elements from specific panels by
-            type. Accepted values : [ gene, region, str, variant ].
-        :param bool panel_intersection: Intersect panel genes and regions with
-            given genes and regions from que input query. This will prevent
-            returning variants from regions out of the panel.
-        :param str source: Select the variant data source from where to fetch
-            the data. Accepted values are 'variant_index' (default) and
-            'secondary_sample_index'. When selecting a secondary_index, the
-            data will be retrieved exclusively from that secondary index, and
-            the 'include/exclude' parameters will be ignored. If the given
-            query can not be fully resolved using the secondary index, an
-            exception will be raised. As the returned variants will only
-            contain data from the secondary_index, some data might be missing
-            or be partial.
-        :param str trait: List of traits, based on ClinVar, HPO, COSMIC, i.e.:
-            IDs, histologies, descriptions,...
-        """
-
-        return self._get(category='analysis', resource='query', subcategory='clinical/variant', **options)
-
-    def acl(self, clinical_analyses, **options):
-        """
-        Returns the acl of the clinical analyses. If member is provided, it
-            will only return the acl for the member.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/acl
-
-        :param str clinical_analyses: Comma separated list of clinical
-            analysis IDs or names up to a maximum of 100. (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='analysis', resource='acl', subcategory='clinical', second_query_id=clinical_analyses, **options)
-
-    def delete(self, clinical_analyses, **options):
-        """
-        Delete clinical analyses.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/delete
-
-        :param str clinical_analyses: Comma separated list of clinical
-            analysis IDs or names up to a maximum of 100. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool force: Force deletion if the ClinicalAnalysis contains
-            interpretations or is locked.
-        """
-
-        return self._delete(category='analysis', resource='delete', subcategory='clinical', second_query_id=clinical_analyses, **options)
-
-    def update(self, clinical_analyses, data=None, **options):
-        """
-        Update clinical analysis attributes.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/update
-
-        :param dict data: JSON containing clinical analysis information.
-            (REQUIRED)
-        :param str clinical_analyses: Comma separated list of clinical
-            analysis 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 comments_action: Action to be performed if the array of
-            comments is being updated. Allowed values: ['ADD REMOVE REPLACE']
-        :param str flags_action: Action to be performed if the array of flags
-            is being updated. Allowed values: ['ADD SET REMOVE']
-        :param str analysts_action: Action to be performed if the array of
-            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 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
-            of annotationSets 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.
-        """
-
-        return self._post(category='analysis', resource='update', subcategory='clinical', second_query_id=clinical_analyses, data=data, **options)
-
-    def update_annotation_sets_annotations(self, clinical_analysis, annotation_set, data=None, **options):
-        """
-        Update annotations from an annotationSet.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/annotationSets/{annotationSet}/annotations/update
-
-        :param str annotation_set: AnnotationSet ID to be updated. (REQUIRED)
-        :param str clinical_analysis: Clinical analysis ID. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str action: Action to be performed: ADD to add new annotations;
-            REPLACE to replace the value of an already existing annotation; SET
-            to set the new list of annotations removing any possible old
-            annotations; REMOVE to remove some annotations; RESET to set some
-            annotations to the default value configured in the corresponding
-            variables of the VariableSet if any. Allowed values: ['ADD SET
-            REMOVE RESET REPLACE']
-        :param dict data: Json containing the map of annotations when the
-            action is ADD, SET or REPLACE, a json with only the key 'remove'
-            containing the comma separated variables to be removed as a value
-            when the action is REMOVE or a json with only the key 'reset'
-            containing the comma separated variables that will be set to the
-            default value when the action is RESET.
-        """
-
-        return self._post(category='analysis/clinical', resource='annotations/update', query_id=clinical_analysis, subcategory='annotationSets', second_query_id=annotation_set, data=data, **options)
-
-    def info(self, clinical_analysis, **options):
-        """
-        Clinical analysis info.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/info
-
-        :param str clinical_analysis: Comma separated list of clinical
-            analysis IDs or names up to a maximum of 100. (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 bool flatten_annotations: Flatten the annotations?.
-        :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 clinical versions. 'all'
-            to get all the clinical versions. Not supported if multiple
-            clinical ids are provided.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='analysis', resource='info', subcategory='clinical', second_query_id=clinical_analysis, **options)
-
-    def create_interpretation(self, clinical_analysis, data=None, **options):
-        """
-        Create a new Interpretation.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create
-
-        :param dict data: JSON containing clinical interpretation information.
-            (REQUIRED)
-        :param str clinical_analysis: Clinical analysis ID. (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: [[organization@]project:]study id.
-        :param str set_as: Set interpretation as. Allowed values: ['PRIMARY
-            SECONDARY']
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='analysis/clinical', resource='create', query_id=clinical_analysis, subcategory='interpretation', data=data, **options)
-
-    def clear_interpretation(self, clinical_analysis, interpretations, **options):
-        """
-        Clear the fields of the main interpretation of the Clinical Analysis.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/clear
-
-        :param str clinical_analysis: Clinical analysis ID. (REQUIRED)
-        :param str interpretations: Interpretation IDs of the Clinical
-            Analysis. (REQUIRED)
-        :param str study: [[organization@]project:]study ID.
-        """
-
-        return self._post(category='analysis/clinical', resource='clear', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretations, **options)
-
-    def delete_interpretation(self, clinical_analysis, interpretations, **options):
-        """
-        Delete interpretation.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/delete
-
-        :param str interpretations: Interpretation IDs of the Clinical
-            Analysis. (REQUIRED)
-        :param str clinical_analysis: Clinical analysis ID. (REQUIRED)
-        :param str study: [[organization@]project:]study ID.
-        :param str set_as_primary: Interpretation id to set as primary from
-            the list of secondaries in case of deleting the actual primary one.
-        """
-
-        return self._delete(category='analysis/clinical', resource='delete', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretations, **options)
-
-    def revert_interpretation(self, clinical_analysis, interpretation, version, **options):
-        """
-        Revert to a previous interpretation version.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/revert
-
-        :param int version: Version to revert to. (REQUIRED)
-        :param str interpretation: Interpretation ID. (REQUIRED)
-        :param str clinical_analysis: Clinical analysis ID. (REQUIRED)
-        :param str study: [[organization@]project:]study ID.
-        """
-
-        options['version'] = version
-        return self._post(category='analysis/clinical', resource='revert', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretation, **options)
-
-    def update_interpretation(self, clinical_analysis, interpretation, data=None, **options):
-        """
-        Update interpretation fields.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update
-
-        :param dict data: JSON containing clinical interpretation information.
-            (REQUIRED)
-        :param str interpretation: Interpretation ID. (REQUIRED)
-        :param str clinical_analysis: Clinical analysis ID. (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: [[organization@]project:]study ID.
-        :param str primary_findings_action: Action to be performed if the
-            array of primary findings is being updated. Allowed values: ['ADD
-            SET REMOVE REPLACE']
-        :param str methods_action: Action to be performed if the array of
-            methods is being updated. Allowed values: ['ADD SET REMOVE']
-        :param str secondary_findings_action: Action to be performed if the
-            array of secondary findings is being updated. Allowed values: ['ADD
-            SET REMOVE REPLACE']
-        :param str comments_action: Action to be performed if the array of
-            comments is being updated. To REMOVE or REPLACE, the date will need
-            to be provided to identify the comment. Allowed values: ['ADD
-            REMOVE REPLACE']
-        :param str panels_action: Action to be performed if the array of
-            panels is being updated. Allowed values: ['ADD SET REMOVE']
-        :param str set_as: Set interpretation as. Allowed values: ['PRIMARY
-            SECONDARY']
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='analysis/clinical', resource='update', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretation, data=data, **options)
-
-    def update_report(self, clinical_analysis, data=None, **options):
-        """
-        Update clinical analysis report.
-        PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/report/update
-
-        :param dict data: JSON containing clinical report information.
-            (REQUIRED)
-        :param str clinical_analysis: Clinical analysis ID. (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 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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='analysis/clinical', resource='update', query_id=clinical_analysis, subcategory='report', data=data, **options)
-