pyxetabase 4.0.0.dev56__py3-none-any.whl

pyxetabase/rest_clients/clinical_analysis_client.py

@@ -0,0 +1,1216 @@
+"""
+WARNING: AUTOGENERATED CODE
+
+    This code was generated by a tool.
+    
+    Manual changes to this file may cause unexpected behavior in your application.
+    Manual changes to this file will be overwritten if the code is regenerated.
+"""
+
+from pyxetabase.rest_clients._parent_rest_clients import _ParentRestClient
+
+
+class 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_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 rd_interpreter(self, **options):
+        """
+        Rare disease interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/rd
+
+        :param str clinical_analysis_id: Clinical analysis ID.
+        :param str proband_id: Proband ID.
+        :param str family_id: Family ID.
+        :param str panel_ids: List of panel IDs (separated by commas).
+        :param str disorder_id: Disorder ID.
+        :param str config_file: RD interpretation configuration file
+            (otherwise the default one will be used).
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        """
+
+        return self._get(category='analysis', resource='rd', subcategory='clinical/interpreter', **options)
+
+    def run_interpreter_rd(self, data=None, **options):
+        """
+        Run interpretation analysis for rare diseases.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/rd/run
+
+        :param dict data: Parameters to execute the rare disease
+            interpretation analysis. (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/rd', 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 trait: List of traits, based on ClinVar, HPO, COSMIC, i.e.:
+            IDs, histologies, descriptions,...
+        :param str ci_status_id: Clinical interpretation status ID (or list of
+            IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
+            CLOSED.
+        """
+
+        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)
+