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

pyopencga/rest_clients/ga4gh_client.py

@@ -1,86 +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 GA4GH(_ParentRestClient):
-    """
-    This class contains methods for the 'GA4GH' webservices
-    PATH: /{apiVersion}/ga4gh
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(GA4GH, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def search_reads(self, **options):
-        """
-        Description.
-        PATH: /{apiVersion}/ga4gh/reads/search
-        """
-
-        return self._post(category='ga4gh', resource='search', subcategory='reads', **options)
-
-    def fetch_reads(self, study, file, **options):
-        """
-        Fetch alignment files using HTSget protocol.
-        PATH: /{apiVersion}/ga4gh/reads/{study}/{file}
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID. (REQUIRED)
-        :param str file: File id, name or path. (REQUIRED)
-        :param str reference_name: Reference sequence name (Example: 'chr1',
-            '1' or 'chrX'.
-        :param int start: The start position of the range on the reference,
-            0-based, inclusive.
-        :param int end: The end position of the range on the reference,
-            0-based, exclusive.
-        :param str reference_genome: Reference genome.
-        """
-
-        return self._get(category='ga4gh/reads', query_id=study, second_query_id=file, **options)
-
-    def responses(self, chrom, pos, allele, beacon, **options):
-        """
-        Beacon webservice.
-        PATH: /{apiVersion}/ga4gh/responses
-
-        :param str beacon: Beacon IDs. If specified, only beacons with the
-            given IDs are queried. Responses from all the supported beacons are
-            obtained otherwise. Format: [id1,id2]. (REQUIRED)
-        :param str allele: Any string of nucleotides A,C,T,G or D, I for
-            deletion and insertion, respectively. Note: For compatibility with
-            conventions set by some of the existing beacons, DEL and INS
-            identifiers are also accepted. (REQUIRED)
-        :param int pos: Coordinate within a chromosome. Position is a number
-            and is 0-based. (REQUIRED)
-        :param str chrom: Chromosome ID. Accepted values: 1-22, X, Y, MT.
-            Note: For compatibility with conventions set by some of the
-            existing beacons, an arbitrary prefix is accepted as well (e.g.
-            chr1 is equivalent to chrom1 and 1). (REQUIRED)
-        :param str ref: Genome ID. If not specified, all the genomes supported
-            by the given beacons are queried. Note: For compatibility with
-            conventions set by some of the existing beacons, both GRC or HG
-            notation are accepted, case insensitive.
-        """
-
-        options['chrom'] = chrom
-        options['pos'] = pos
-        options['allele'] = allele
-        options['beacon'] = beacon
-        return self._get(category='ga4gh', resource='responses', **options)
-
-    def search_variants(self, **options):
-        """
-        Description.
-        PATH: /{apiVersion}/ga4gh/variants/search
-        """
-
-        return self._post(category='ga4gh', resource='search', subcategory='variants', **options)
-

pyopencga/rest_clients/individual_client.py

@@ -1,435 +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 Individual(_ParentRestClient):
-    """
-    This class contains methods for the 'Individuals' webservices
-    PATH: /{apiVersion}/individuals
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Individual, 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}/individuals/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 samples that are associated to the
-            matching individuals. (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 individual permissions to related
-            samples.
-        """
-
-        options['action'] = action
-        return self._post(category='individuals', resource='update', subcategory='acl', second_query_id=members, data=data, **options)
-
-    def aggregation_stats(self, **options):
-        """
-        Fetch catalog individual stats.
-        PATH: /{apiVersion}/individuals/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 individual 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 individual UUIDs up to a maximum
-            of 100.
-        :param str name: Comma separated list individual names up to a maximum
-            of 100. Also admits basic regular expressions using the operator
-            '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive,
-            '~/value/i' for case insensitive search.
-        :param str father: Father ID, name or UUID.
-        :param str mother: Mother ID, name or UUID.
-        :param str samples: Sample ID, name or UUID.
-        :param str family_ids: Comma separated list of family ids the
-            individuals may belong to.
-        :param str sex: Individual sex.
-        :param str date_of_birth: Individual date of birth.
-        :param str ethnicity: Individual ethnicity. 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 disorders: Comma separated list of disorder 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 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 population_name: Population 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 population_subpopulation: Subpopulation 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 karyotypic_sex: Individual karyotypic sex.
-        :param str life_status: Individual life status.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :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 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 release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        :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='individuals', resource='aggregationStats', **options)
-
-    def load_annotation_sets(self, variable_set_id, path, data=None, **options):
-        """
-        Load annotation sets from a TSV file.
-        PATH: /{apiVersion}/individuals/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='individuals', resource='load', subcategory='annotationSets', data=data, **options)
-
-    def create(self, data=None, **options):
-        """
-        Create individual.
-        PATH: /{apiVersion}/individuals/create
-
-        :param dict data: JSON containing individual 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 str samples: Comma separated list of sample ids to be
-            associated to the created individual.
-        :param bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='individuals', resource='create', data=data, **options)
-
-    def distinct(self, field, **options):
-        """
-        Individual distinct method.
-        PATH: /{apiVersion}/individuals/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 individual 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 individual UUIDs up to a maximum
-            of 100.
-        :param str name: Comma separated list individual names up to a maximum
-            of 100. Also admits basic regular expressions using the operator
-            '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive,
-            '~/value/i' for case insensitive search.
-        :param str family_ids: Comma separated list of family ids the
-            individuals may belong to.
-        :param str father: Father ID, name or UUID.
-        :param str mother: Mother ID, name or UUID.
-        :param str samples: Sample ID, name or UUID.
-        :param str sex: Individual sex.
-        :param str ethnicity: Individual ethnicity. 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 date_of_birth: Individual date of birth.
-        :param str disorders: Comma separated list of disorder 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 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 population_name: Population 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 population_subpopulation: Subpopulation 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 karyotypic_sex: Individual karyotypic sex.
-        :param str life_status: Individual life status.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :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 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 release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        """
-
-        options['field'] = field
-        return self._get(category='individuals', resource='distinct', **options)
-
-    def search(self, **options):
-        """
-        Search for individuals.
-        PATH: /{apiVersion}/individuals/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 individual 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 individual UUIDs up to a maximum
-            of 100.
-        :param str name: Comma separated list individual names up to a maximum
-            of 100. Also admits basic regular expressions using the operator
-            '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive,
-            '~/value/i' for case insensitive search.
-        :param str father: Father ID, name or UUID.
-        :param str mother: Mother ID, name or UUID.
-        :param str samples: Sample ID, name or UUID.
-        :param str family_ids: Comma separated list of family ids the
-            individuals may belong to.
-        :param str sex: Individual sex.
-        :param str date_of_birth: Individual date of birth.
-        :param str ethnicity: Individual ethnicity. 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 disorders: Comma separated list of disorder 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 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 population_name: Population 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 population_subpopulation: Subpopulation 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 karyotypic_sex: Individual karyotypic sex.
-        :param str life_status: Individual life status.
-        :param str internal_status: Filter by internal status.
-        :param str status: Filter by status.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        :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 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 release: Release when it was created.
-        :param int snapshot: Snapshot value (Latest version of the entry in
-            the specified release).
-        """
-
-        return self._get(category='individuals', resource='search', **options)
-
-    def acl(self, individuals, **options):
-        """
-        Return the acl of the individual. If member is provided, it will only
-            return the acl for the member.
-        PATH: /{apiVersion}/individuals/{individuals}/acl
-
-        :param str individuals: Comma separated list of individual IDs, names
-            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='individuals', resource='acl', query_id=individuals, **options)
-
-    def delete(self, individuals, **options):
-        """
-        Delete existing individuals.
-        PATH: /{apiVersion}/individuals/{individuals}/delete
-
-        :param str individuals: Comma separated list of individual ids.
-            (REQUIRED)
-        :param bool force: Force the deletion of individuals that already
-            belong to families.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._delete(category='individuals', resource='delete', query_id=individuals, **options)
-
-    def info(self, individuals, **options):
-        """
-        Get individual information.
-        PATH: /{apiVersion}/individuals/{individuals}/info
-
-        :param str individuals: Comma separated list of individual IDs, names
-            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 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 individual versions. 'all'
-            to get all the individual versions. Not supported if multiple
-            individual ids are provided.
-        :param bool deleted: Boolean to retrieve deleted individuals.
-        """
-
-        return self._get(category='individuals', resource='info', query_id=individuals, **options)
-
-    def update(self, individuals, data=None, **options):
-        """
-        Update some individual attributes.
-        PATH: /{apiVersion}/individuals/{individuals}/update
-
-        :param str individuals: Comma separated list of individual 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 samples_action: Action to be performed if the array of
-            samples 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 str disorders_action: Action to be performed if the array of
-            disorders is being updated [SET, ADD, REMOVE]. 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.
-        :param dict data: body.
-        """
-
-        return self._post(category='individuals', resource='update', query_id=individuals, data=data, **options)
-
-    def update_annotation_sets_annotations(self, individual, annotation_set, data=None, **options):
-        """
-        Update annotations from an annotationSet.
-        PATH: /{apiVersion}/individuals/{individual}/annotationSets/{annotationSet}/annotations/update
-
-        :param str annotation_set: AnnotationSet ID to be updated. (REQUIRED)
-        :param str individual: Individual ID, name or UUID. (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='individuals', resource='annotations/update', query_id=individual, subcategory='annotationSets', second_query_id=annotation_set, data=data, **options)
-
-    def relatives(self, individual, **options):
-        """
-        Get individual relatives.
-        PATH: /{apiVersion}/individuals/{individual}/relatives
-
-        :param str individual: Individual ID, name or UUID. (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 int degree: Pedigree degree.
-        """
-
-        return self._get(category='individuals', resource='relatives', query_id=individual, **options)
-