pyxetabase 4.0.0.dev0__py3-none-any.whl → 4.0.0.dev2__py3-none-any.whl

pyopencga/rest_clients/sample_client.py

@@ -1,446 +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 Sample(_ParentRestClient):
-    """
-    This class contains methods for the 'Samples' webservices
-    PATH: /{apiVersion}/samples
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Sample, 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}/samples/acl/{members}/update
-
-        :param dict data: JSON containing the parameters to update the
-            permissions. If propagate flag is set to true, it will propagate
-            the permissions defined to the individuals that are associated to
-            the matching samples. (REQUIRED)
-        :param str action: Action to be performed [ADD, SET, REMOVE or RESET].
-            Allowed values: ['SET ADD REMOVE RESET'] (REQUIRED)
-        :param str members: Comma separated list of user or group ids.
-            (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        options['action'] = action
-        return self._post(category='samples', resource='update', subcategory='acl', second_query_id=members, data=data, **options)
-
-    def aggregation_stats(self, **options):
-        """
-        Fetch catalog sample stats.
-        PATH: /{apiVersion}/samples/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 sample 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 sample UUIDs up to a maximum of
-            100.
-        :param bool somatic: Somatic sample.
-        :param str individual_id: Individual ID or UUID.
-        :param str file_ids: Comma separated list of file IDs, paths or UUIDs.
-        :param str cohort_ids: Comma separated list of cohort IDs.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param str processing_product: Processing product.
-        :param str processing_preparation_method: Processing preparation
-            method.
-        :param str processing_extraction_method: Processing extraction method.
-        :param str processing_lab_sample_id: Processing lab sample id.
-        :param str collection_from: Collection from.
-        :param str collection_type: Collection type.
-        :param str collection_method: Collection method.
-        :param str phenotypes: Comma separated list of phenotype ids or names.
-            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 annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str internal_rga_status: Index status of the sample for the
-            Recessive Gene Analysis. Allowed values: ['NOT_INDEXED INDEXED
-            INVALID_PERMISSIONS INVALID_METADATA INVALID']
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :param str stats_id: Sample variant stats Id. If this field is not
-            provided and the user filters by other stats fields, it will
-            automatically be set to ALL.
-        :param str stats_variant_count: Sample variant stats VariantCount.
-        :param str stats_chromosome_count: Sample variant stats
-            ChromosomeCount.
-        :param str stats_type_count: Sample variant stats TypeCount.
-        :param str stats_genotype_count: Sample variant stats GenotypeCount.
-        :param str stats_ti_tv_ratio: Sample variant stats TiTvRatio.
-        :param str stats_quality_avg: Sample variant stats QualityAvg.
-        :param str stats_quality_std_dev: Sample variant stats QualityStdDev.
-        :param str stats_heterozygosity_rate: Sample variant stats
-            HeterozygosityRate.
-        :param str stats_depth_count: Sample variant stats DepthCount.
-        :param str stats_biotype_count: Sample variant stats BiotypeCount.
-        :param str stats_clinical_significance_count: Sample variant stats
-            ClinicalSignificanceCount.
-        :param str stats_consequence_type_count: Sample variant stats
-            ConsequenceTypeCount.
-        :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='samples', resource='aggregationStats', **options)
-
-    def load_annotation_sets(self, variable_set_id, path, data=None, **options):
-        """
-        Load annotation sets from a TSV file.
-        PATH: /{apiVersion}/samples/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='samples', resource='load', subcategory='annotationSets', data=data, **options)
-
-    def create(self, data=None, **options):
-        """
-        Create sample.
-        PATH: /{apiVersion}/samples/create
-
-        :param dict data: JSON containing sample information. (REQUIRED)
-        :param str include: Fields included in the response, whole JSON path
-            must be provided.
-        :param str exclude: Fields excluded in the response, whole JSON path
-            must be provided.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='samples', resource='create', data=data, **options)
-
-    def distinct(self, field, **options):
-        """
-        Sample distinct method.
-        PATH: /{apiVersion}/samples/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 sample 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 sample UUIDs up to a maximum of
-            100.
-        :param bool somatic: Somatic sample.
-        :param str individual_id: Individual ID or UUID.
-        :param str file_ids: Comma separated list of file IDs, paths or UUIDs.
-        :param str cohort_ids: Comma separated list of cohort IDs.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param str processing_product: Processing product.
-        :param str processing_preparation_method: Processing preparation
-            method.
-        :param str processing_extraction_method: Processing extraction method.
-        :param str processing_lab_sample_id: Processing lab sample id.
-        :param str collection_from: Collection from.
-        :param str collection_type: Collection type.
-        :param str collection_method: Collection method.
-        :param str phenotypes: Comma separated list of phenotype ids or names.
-            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 annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str internal_rga_status: Index status of the sample for the
-            Recessive Gene Analysis. Allowed values: ['NOT_INDEXED INDEXED
-            INVALID_PERMISSIONS INVALID_METADATA INVALID']
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :param str stats_id: Sample variant stats Id. If this field is not
-            provided and the user filters by other stats fields, it will
-            automatically be set to ALL.
-        :param str stats_variant_count: Sample variant stats VariantCount.
-        :param str stats_chromosome_count: Sample variant stats
-            ChromosomeCount.
-        :param str stats_type_count: Sample variant stats TypeCount.
-        :param str stats_genotype_count: Sample variant stats GenotypeCount.
-        :param str stats_ti_tv_ratio: Sample variant stats TiTvRatio.
-        :param str stats_quality_avg: Sample variant stats QualityAvg.
-        :param str stats_quality_std_dev: Sample variant stats QualityStdDev.
-        :param str stats_heterozygosity_rate: Sample variant stats
-            HeterozygosityRate.
-        :param str stats_depth_count: Sample variant stats DepthCount.
-        :param str stats_biotype_count: Sample variant stats BiotypeCount.
-        :param str stats_clinical_significance_count: Sample variant stats
-            ClinicalSignificanceCount.
-        :param str stats_consequence_type_count: Sample variant stats
-            ConsequenceTypeCount.
-        """
-
-        options['field'] = field
-        return self._get(category='samples', resource='distinct', **options)
-
-    def load(self, file, **options):
-        """
-        Load samples from a ped file [EXPERIMENTAL].
-        PATH: /{apiVersion}/samples/load
-
-        :param str file: file. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str variable_set: variableSet.
-        """
-
-        options['file'] = file
-        return self._get(category='samples', resource='load', **options)
-
-    def search(self, **options):
-        """
-        Sample search method.
-        PATH: /{apiVersion}/samples/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 include_individual: Include Individual object as an
-            attribute.
-        :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 sample 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 sample UUIDs up to a maximum of
-            100.
-        :param bool somatic: Somatic sample.
-        :param str individual_id: Individual ID or UUID.
-        :param str file_ids: Comma separated list of file IDs, paths or UUIDs.
-        :param str cohort_ids: Comma separated list of cohort IDs.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param str processing_product: Processing product.
-        :param str processing_preparation_method: Processing preparation
-            method.
-        :param str processing_extraction_method: Processing extraction method.
-        :param str processing_lab_sample_id: Processing lab sample id.
-        :param str collection_from: Collection from.
-        :param str collection_type: Collection type.
-        :param str collection_method: Collection method.
-        :param str phenotypes: Comma separated list of phenotype ids or names.
-            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 annotation: Annotation filters. Example:
-            age>30;gender=FEMALE. For more information, please visit
-            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
-        :param str acl: Filter entries for which a user has the provided
-            permissions. Format: acl={user}:{permissions}. Example:
-            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which
-            user john has both WRITE and WRITE_ANNOTATIONS permissions. Only
-            study owners or administrators can query by this field. .
-        :param str internal_rga_status: Index status of the sample for the
-            Recessive Gene Analysis. Allowed values: ['NOT_INDEXED INDEXED
-            INVALID_PERMISSIONS INVALID_METADATA INVALID']
-        :param str release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :param str stats_id: Sample variant stats Id. If this field is not
-            provided and the user filters by other stats fields, it will
-            automatically be set to ALL.
-        :param str stats_variant_count: Sample variant stats VariantCount.
-        :param str stats_chromosome_count: Sample variant stats
-            ChromosomeCount.
-        :param str stats_type_count: Sample variant stats TypeCount.
-        :param str stats_genotype_count: Sample variant stats GenotypeCount.
-        :param str stats_ti_tv_ratio: Sample variant stats TiTvRatio.
-        :param str stats_quality_avg: Sample variant stats QualityAvg.
-        :param str stats_quality_std_dev: Sample variant stats QualityStdDev.
-        :param str stats_heterozygosity_rate: Sample variant stats
-            HeterozygosityRate.
-        :param str stats_depth_count: Sample variant stats DepthCount.
-        :param str stats_biotype_count: Sample variant stats BiotypeCount.
-        :param str stats_clinical_significance_count: Sample variant stats
-            ClinicalSignificanceCount.
-        :param str stats_consequence_type_count: Sample variant stats
-            ConsequenceTypeCount.
-        """
-
-        return self._get(category='samples', resource='search', **options)
-
-    def acl(self, samples, **options):
-        """
-        Returns the acl of the samples. If member is provided, it will only
-            return the acl for the member.
-        PATH: /{apiVersion}/samples/{samples}/acl
-
-        :param str samples: Comma separated list sample IDs or UUIDs 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='samples', resource='acl', query_id=samples, **options)
-
-    def delete(self, samples, **options):
-        """
-        Delete samples.
-        PATH: /{apiVersion}/samples/{samples}/delete
-
-        :param str samples: Comma separated list sample IDs or UUIDs up to a
-            maximum of 100. (REQUIRED)
-        :param bool force: Force the deletion of samples even if they are
-            associated to files, individuals or cohorts.
-        :param str empty_files_action: Action to be performed over files that
-            were associated only to the sample to be deleted. Possible actions
-            are NONE, TRASH, DELETE.
-        :param bool delete_empty_cohorts: Boolean indicating if the cohorts
-            associated only to the sample to be deleted should be also deleted.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._delete(category='samples', resource='delete', query_id=samples, **options)
-
-    def info(self, samples, **options):
-        """
-        Get sample information.
-        PATH: /{apiVersion}/samples/{samples}/info
-
-        :param str samples: Comma separated list sample IDs or UUIDs 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 include_individual: Include Individual object as an
-            attribute.
-        :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 sample versions. 'all' to
-            get all the sample versions. Not supported if multiple sample ids
-            are provided.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='samples', resource='info', query_id=samples, **options)
-
-    def update(self, samples, data=None, **options):
-        """
-        Update some sample attributes.
-        PATH: /{apiVersion}/samples/{samples}/update
-
-        :param str samples: Comma separated list sample IDs or UUIDs 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 annotation_sets_action: Action to be performed if the array
-            of annotationSets is being updated. Allowed values: ['ADD SET
-            REMOVE']
-        :param str phenotypes_action: Action to be performed if the array of
-            phenotypes is being updated [SET, ADD, REMOVE]. Allowed values:
-            ['ADD SET REMOVE']
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        :param dict data: body.
-        """
-
-        return self._post(category='samples', resource='update', query_id=samples, data=data, **options)
-
-    def update_annotation_sets_annotations(self, sample, annotation_set, data=None, **options):
-        """
-        Update annotations from an annotationSet.
-        PATH: /{apiVersion}/samples/{sample}/annotationSets/{annotationSet}/annotations/update
-
-        :param str annotation_set: AnnotationSet ID to be updated. (REQUIRED)
-        :param str sample: Sample 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='samples', resource='annotations/update', query_id=sample, subcategory='annotationSets', second_query_id=annotation_set, data=data, **options)
-