diff --git a/gemmapy/sdk/api/default_api.py b/gemmapy/sdk/api/default_api.py index 6f8fa14..7a0a25d 100644 --- a/gemmapy/sdk/api/default_api.py +++ b/gemmapy/sdk/api/default_api.py @@ -5370,6 +5370,8 @@ def get_result_set(self, result_set, **kwargs): # noqa: E501 :param float threshold: :param int offset: :param int limit: + :param bool include_factor_values_in_contrasts: Include complete factor values in contrasts instead of only populating `factorValueId` and `secondFactorValueId`. In 2.9.0, this will default to false. + :param bool include_taxon_in_genes: Include complete taxon in genes instead of only populating `taxonId`. When this is set to true, a `taxa` collection will be included in `DifferentialExpressionAnalysisResultSetValueObject`. In 2.9.0, this will default to false. :return: PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject If the method is called asynchronously, returns the request thread. @@ -5407,12 +5409,14 @@ def get_result_set_with_http_info(self, result_set, **kwargs): # noqa: E501 :param float threshold: :param int offset: :param int limit: + :param bool include_factor_values_in_contrasts: Include complete factor values in contrasts instead of only populating `factorValueId` and `secondFactorValueId`. In 2.9.0, this will default to false. + :param bool include_taxon_in_genes: Include complete taxon in genes instead of only populating `taxonId`. When this is set to true, a `taxa` collection will be included in `DifferentialExpressionAnalysisResultSetValueObject`. In 2.9.0, this will default to false. :return: PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject If the method is called asynchronously, returns the request thread. """ - all_params = ['result_set', 'threshold', 'offset', 'limit'] # noqa: E501 + all_params = ['result_set', 'threshold', 'offset', 'limit', 'include_factor_values_in_contrasts', 'include_taxon_in_genes'] # noqa: E501 all_params.append('async_req') all_params.append('_return_http_data_only') all_params.append('_preload_content') @@ -5447,6 +5451,10 @@ def get_result_set_with_http_info(self, result_set, **kwargs): # noqa: E501 query_params.append(('offset', params['offset'])) # noqa: E501 if 'limit' in params: query_params.append(('limit', params['limit'])) # noqa: E501 + if 'include_factor_values_in_contrasts' in params: + query_params.append(('includeFactorValuesInContrasts', params['include_factor_values_in_contrasts'])) # noqa: E501 + if 'include_taxon_in_genes' in params: + query_params.append(('includeTaxonInGenes', params['include_taxon_in_genes'])) # noqa: E501 header_params = {} diff --git a/gemmapy/sdk/api_client.py b/gemmapy/sdk/api_client.py index 48b8b2b..46051a2 100644 --- a/gemmapy/sdk/api_client.py +++ b/gemmapy/sdk/api_client.py @@ -73,7 +73,7 @@ def __init__(self, configuration=None, header_name=None, header_value=None, self.default_headers[header_name] = header_value self.cookie = cookie # Set default User-Agent. - self.user_agent = 'gemmapy/1.0.5' + self.user_agent = 'gemmapy/1.0.6' def __del__(self): self.pool.close() diff --git a/gemmapy/sdk/models/audit_event_value_object.py b/gemmapy/sdk/models/audit_event_value_object.py index d09e810..83ad1a9 100644 --- a/gemmapy/sdk/models/audit_event_value_object.py +++ b/gemmapy/sdk/models/audit_event_value_object.py @@ -34,8 +34,8 @@ class AuditEventValueObject(object): 'action': 'str', 'note': 'str', 'detail': 'str', - 'event_type_name': 'str', - 'action_name': 'str' + 'action_name': 'str', + 'event_type_name': 'str' } attribute_map = { @@ -45,11 +45,11 @@ class AuditEventValueObject(object): 'action': 'action', 'note': 'note', 'detail': 'detail', - 'event_type_name': 'eventTypeName', - 'action_name': 'actionName' + 'action_name': 'actionName', + 'event_type_name': 'eventTypeName' } - def __init__(self, id=None, performer=None, _date=None, action=None, note=None, detail=None, event_type_name=None, action_name=None): # noqa: E501 + def __init__(self, id=None, performer=None, _date=None, action=None, note=None, detail=None, action_name=None, event_type_name=None): # noqa: E501 """AuditEventValueObject - a model defined in Swagger""" # noqa: E501 self._id = None self._performer = None @@ -57,8 +57,8 @@ def __init__(self, id=None, performer=None, _date=None, action=None, note=None, self._action = None self._note = None self._detail = None - self._event_type_name = None self._action_name = None + self._event_type_name = None self.discriminator = None if id is not None: self.id = id @@ -72,10 +72,10 @@ def __init__(self, id=None, performer=None, _date=None, action=None, note=None, self.note = note if detail is not None: self.detail = detail - if event_type_name is not None: - self.event_type_name = event_type_name if action_name is not None: self.action_name = action_name + if event_type_name is not None: + self.event_type_name = event_type_name @property def id(self): @@ -210,46 +210,46 @@ def detail(self, detail): self._detail = detail @property - def event_type_name(self): - """Gets the event_type_name of this AuditEventValueObject. # noqa: E501 + def action_name(self): + """Gets the action_name of this AuditEventValueObject. # noqa: E501 - :return: The event_type_name of this AuditEventValueObject. # noqa: E501 + :return: The action_name of this AuditEventValueObject. # noqa: E501 :rtype: str """ - return self._event_type_name + return self._action_name - @event_type_name.setter - def event_type_name(self, event_type_name): - """Sets the event_type_name of this AuditEventValueObject. + @action_name.setter + def action_name(self, action_name): + """Sets the action_name of this AuditEventValueObject. - :param event_type_name: The event_type_name of this AuditEventValueObject. # noqa: E501 + :param action_name: The action_name of this AuditEventValueObject. # noqa: E501 :type: str """ - self._event_type_name = event_type_name + self._action_name = action_name @property - def action_name(self): - """Gets the action_name of this AuditEventValueObject. # noqa: E501 + def event_type_name(self): + """Gets the event_type_name of this AuditEventValueObject. # noqa: E501 - :return: The action_name of this AuditEventValueObject. # noqa: E501 + :return: The event_type_name of this AuditEventValueObject. # noqa: E501 :rtype: str """ - return self._action_name + return self._event_type_name - @action_name.setter - def action_name(self, action_name): - """Sets the action_name of this AuditEventValueObject. + @event_type_name.setter + def event_type_name(self, event_type_name): + """Sets the event_type_name of this AuditEventValueObject. - :param action_name: The action_name of this AuditEventValueObject. # noqa: E501 + :param event_type_name: The event_type_name of this AuditEventValueObject. # noqa: E501 :type: str """ - self._action_name = action_name + self._event_type_name = event_type_name def to_dict(self): """Returns the model properties as a dict""" diff --git a/gemmapy/sdk/models/contrast_result_value_object.py b/gemmapy/sdk/models/contrast_result_value_object.py index 75911c1..8c90b7a 100644 --- a/gemmapy/sdk/models/contrast_result_value_object.py +++ b/gemmapy/sdk/models/contrast_result_value_object.py @@ -170,6 +170,7 @@ def log_fold_change(self, log_fold_change): def factor_value_id(self): """Gets the factor_value_id of this ContrastResultValueObject. # noqa: E501 + This property is mutually exclusive with `factorValue`. # noqa: E501 :return: The factor_value_id of this ContrastResultValueObject. # noqa: E501 :rtype: int @@ -180,6 +181,7 @@ def factor_value_id(self): def factor_value_id(self, factor_value_id): """Sets the factor_value_id of this ContrastResultValueObject. + This property is mutually exclusive with `factorValue`. # noqa: E501 :param factor_value_id: The factor_value_id of this ContrastResultValueObject. # noqa: E501 :type: int @@ -212,6 +214,7 @@ def factor_value(self, factor_value): def second_factor_value_id(self): """Gets the second_factor_value_id of this ContrastResultValueObject. # noqa: E501 + This property is mutually exclusive with `secondFactorValue`. # noqa: E501 :return: The second_factor_value_id of this ContrastResultValueObject. # noqa: E501 :rtype: int @@ -222,6 +225,7 @@ def second_factor_value_id(self): def second_factor_value_id(self, second_factor_value_id): """Sets the second_factor_value_id of this ContrastResultValueObject. + This property is mutually exclusive with `secondFactorValue`. # noqa: E501 :param second_factor_value_id: The second_factor_value_id of this ContrastResultValueObject. # noqa: E501 :type: int diff --git a/gemmapy/sdk/models/diff_ex_result_set_summary_value_object.py b/gemmapy/sdk/models/diff_ex_result_set_summary_value_object.py index db699df..600b0e4 100644 --- a/gemmapy/sdk/models/diff_ex_result_set_summary_value_object.py +++ b/gemmapy/sdk/models/diff_ex_result_set_summary_value_object.py @@ -38,9 +38,9 @@ class DiffExResultSetSummaryValueObject(object): 'number_of_diff_expressed_probes': 'int', 'upregulated_count': 'int', 'downregulated_count': 'int', + 'number_of_upregulated_probes': 'int', 'number_of_downregulated_probes': 'int', - 'qvalue': 'float', - 'number_of_upregulated_probes': 'int' + 'qvalue': 'float' } attribute_map = { @@ -54,12 +54,12 @@ class DiffExResultSetSummaryValueObject(object): 'number_of_diff_expressed_probes': 'numberOfDiffExpressedProbes', 'upregulated_count': 'upregulatedCount', 'downregulated_count': 'downregulatedCount', + 'number_of_upregulated_probes': 'numberOfUpregulatedProbes', 'number_of_downregulated_probes': 'numberOfDownregulatedProbes', - 'qvalue': 'qvalue', - 'number_of_upregulated_probes': 'numberOfUpregulatedProbes' + 'qvalue': 'qvalue' } - def __init__(self, id=None, array_designs_used=None, baseline_group=None, experimental_factors=None, number_of_genes_analyzed=None, number_of_probes_analyzed=None, threshold=None, number_of_diff_expressed_probes=None, upregulated_count=None, downregulated_count=None, number_of_downregulated_probes=None, qvalue=None, number_of_upregulated_probes=None): # noqa: E501 + def __init__(self, id=None, array_designs_used=None, baseline_group=None, experimental_factors=None, number_of_genes_analyzed=None, number_of_probes_analyzed=None, threshold=None, number_of_diff_expressed_probes=None, upregulated_count=None, downregulated_count=None, number_of_upregulated_probes=None, number_of_downregulated_probes=None, qvalue=None): # noqa: E501 """DiffExResultSetSummaryValueObject - a model defined in Swagger""" # noqa: E501 self._id = None self._array_designs_used = None @@ -71,9 +71,9 @@ def __init__(self, id=None, array_designs_used=None, baseline_group=None, experi self._number_of_diff_expressed_probes = None self._upregulated_count = None self._downregulated_count = None + self._number_of_upregulated_probes = None self._number_of_downregulated_probes = None self._qvalue = None - self._number_of_upregulated_probes = None self.discriminator = None if id is not None: self.id = id @@ -95,12 +95,12 @@ def __init__(self, id=None, array_designs_used=None, baseline_group=None, experi self.upregulated_count = upregulated_count if downregulated_count is not None: self.downregulated_count = downregulated_count + if number_of_upregulated_probes is not None: + self.number_of_upregulated_probes = number_of_upregulated_probes if number_of_downregulated_probes is not None: self.number_of_downregulated_probes = number_of_downregulated_probes if qvalue is not None: self.qvalue = qvalue - if number_of_upregulated_probes is not None: - self.number_of_upregulated_probes = number_of_upregulated_probes @property def id(self): @@ -312,6 +312,27 @@ def downregulated_count(self, downregulated_count): self._downregulated_count = downregulated_count + @property + def number_of_upregulated_probes(self): + """Gets the number_of_upregulated_probes of this DiffExResultSetSummaryValueObject. # noqa: E501 + + + :return: The number_of_upregulated_probes of this DiffExResultSetSummaryValueObject. # noqa: E501 + :rtype: int + """ + return self._number_of_upregulated_probes + + @number_of_upregulated_probes.setter + def number_of_upregulated_probes(self, number_of_upregulated_probes): + """Sets the number_of_upregulated_probes of this DiffExResultSetSummaryValueObject. + + + :param number_of_upregulated_probes: The number_of_upregulated_probes of this DiffExResultSetSummaryValueObject. # noqa: E501 + :type: int + """ + + self._number_of_upregulated_probes = number_of_upregulated_probes + @property def number_of_downregulated_probes(self): """Gets the number_of_downregulated_probes of this DiffExResultSetSummaryValueObject. # noqa: E501 @@ -354,27 +375,6 @@ def qvalue(self, qvalue): self._qvalue = qvalue - @property - def number_of_upregulated_probes(self): - """Gets the number_of_upregulated_probes of this DiffExResultSetSummaryValueObject. # noqa: E501 - - - :return: The number_of_upregulated_probes of this DiffExResultSetSummaryValueObject. # noqa: E501 - :rtype: int - """ - return self._number_of_upregulated_probes - - @number_of_upregulated_probes.setter - def number_of_upregulated_probes(self, number_of_upregulated_probes): - """Sets the number_of_upregulated_probes of this DiffExResultSetSummaryValueObject. - - - :param number_of_upregulated_probes: The number_of_upregulated_probes of this DiffExResultSetSummaryValueObject. # noqa: E501 - :type: int - """ - - self._number_of_upregulated_probes = number_of_upregulated_probes - def to_dict(self): """Returns the model properties as a dict""" result = {} diff --git a/gemmapy/sdk/models/differential_expression_analysis_result_set_value_object.py b/gemmapy/sdk/models/differential_expression_analysis_result_set_value_object.py index 451bc77..68d472b 100644 --- a/gemmapy/sdk/models/differential_expression_analysis_result_set_value_object.py +++ b/gemmapy/sdk/models/differential_expression_analysis_result_set_value_object.py @@ -33,6 +33,7 @@ class DifferentialExpressionAnalysisResultSetValueObject(object): 'experimental_factors': 'list[ExperimentalFactorValueObject]', 'baseline_group': 'FactorValueBasicValueObject', 'second_baseline_group': 'FactorValueBasicValueObject', + 'taxa': 'list[TaxonValueObject]', 'results': 'list[DifferentialExpressionAnalysisResultValueObject]' } @@ -42,16 +43,18 @@ class DifferentialExpressionAnalysisResultSetValueObject(object): 'experimental_factors': 'experimentalFactors', 'baseline_group': 'baselineGroup', 'second_baseline_group': 'secondBaselineGroup', + 'taxa': 'taxa', 'results': 'results' } - def __init__(self, id=None, analysis=None, experimental_factors=None, baseline_group=None, second_baseline_group=None, results=None): # noqa: E501 + def __init__(self, id=None, analysis=None, experimental_factors=None, baseline_group=None, second_baseline_group=None, taxa=None, results=None): # noqa: E501 """DifferentialExpressionAnalysisResultSetValueObject - a model defined in Swagger""" # noqa: E501 self._id = None self._analysis = None self._experimental_factors = None self._baseline_group = None self._second_baseline_group = None + self._taxa = None self._results = None self.discriminator = None if id is not None: @@ -64,6 +67,8 @@ def __init__(self, id=None, analysis=None, experimental_factors=None, baseline_g self.baseline_group = baseline_group if second_baseline_group is not None: self.second_baseline_group = second_baseline_group + if taxa is not None: + self.taxa = taxa if results is not None: self.results = results @@ -172,6 +177,27 @@ def second_baseline_group(self, second_baseline_group): self._second_baseline_group = second_baseline_group + @property + def taxa(self): + """Gets the taxa of this DifferentialExpressionAnalysisResultSetValueObject. # noqa: E501 + + + :return: The taxa of this DifferentialExpressionAnalysisResultSetValueObject. # noqa: E501 + :rtype: list[TaxonValueObject] + """ + return self._taxa + + @taxa.setter + def taxa(self, taxa): + """Sets the taxa of this DifferentialExpressionAnalysisResultSetValueObject. + + + :param taxa: The taxa of this DifferentialExpressionAnalysisResultSetValueObject. # noqa: E501 + :type: list[TaxonValueObject] + """ + + self._taxa = taxa + @property def results(self): """Gets the results of this DifferentialExpressionAnalysisResultSetValueObject. # noqa: E501 diff --git a/gemmapy/sdk/models/differential_expression_analysis_value_object.py b/gemmapy/sdk/models/differential_expression_analysis_value_object.py index eb467cb..e2f4d76 100644 --- a/gemmapy/sdk/models/differential_expression_analysis_value_object.py +++ b/gemmapy/sdk/models/differential_expression_analysis_value_object.py @@ -300,6 +300,7 @@ def subset_factor_value(self, subset_factor_value): def subset_factor_value_id(self): """Gets the subset_factor_value_id of this DifferentialExpressionAnalysisValueObject. # noqa: E501 + This property is mutually exclusive with `subsetFactorValue`. # noqa: E501 :return: The subset_factor_value_id of this DifferentialExpressionAnalysisValueObject. # noqa: E501 :rtype: int @@ -310,6 +311,7 @@ def subset_factor_value_id(self): def subset_factor_value_id(self, subset_factor_value_id): """Sets the subset_factor_value_id of this DifferentialExpressionAnalysisValueObject. + This property is mutually exclusive with `subsetFactorValue`. # noqa: E501 :param subset_factor_value_id: The subset_factor_value_id of this DifferentialExpressionAnalysisValueObject. # noqa: E501 :type: int @@ -388,6 +390,7 @@ def factor_values_used_by_experimental_factor_id(self, factor_values_used_by_exp def is_subset(self): """Gets the is_subset of this DifferentialExpressionAnalysisValueObject. # noqa: E501 + Indicate if this analysis is a subset of another experiment. if this is set, additional fields relevant to the subset will be populated. # noqa: E501 :return: The is_subset of this DifferentialExpressionAnalysisValueObject. # noqa: E501 :rtype: bool @@ -398,6 +401,7 @@ def is_subset(self): def is_subset(self, is_subset): """Sets the is_subset of this DifferentialExpressionAnalysisValueObject. + Indicate if this analysis is a subset of another experiment. if this is set, additional fields relevant to the subset will be populated. # noqa: E501 :param is_subset: The is_subset of this DifferentialExpressionAnalysisValueObject. # noqa: E501 :type: bool diff --git a/gemmapy/sdk/models/expression_experiment_value_object.py b/gemmapy/sdk/models/expression_experiment_value_object.py index be6d07c..e80a0fa 100644 --- a/gemmapy/sdk/models/expression_experiment_value_object.py +++ b/gemmapy/sdk/models/expression_experiment_value_object.py @@ -51,8 +51,8 @@ class ExpressionExperimentValueObject(object): 'short_name': 'str', 'source': 'str', 'technology_type': 'str', - 'bio_assay_count': 'int', 'taxon_id': 'int', + 'bio_assay_count': 'int', 'trouble_details': 'str', 'number_of_array_designs': 'int', 'number_of_processed_expression_vectors': 'int', @@ -83,15 +83,15 @@ class ExpressionExperimentValueObject(object): 'short_name': 'shortName', 'source': 'source', 'technology_type': 'technologyType', - 'bio_assay_count': 'bioAssayCount', 'taxon_id': 'taxonId', + 'bio_assay_count': 'bioAssayCount', 'trouble_details': 'troubleDetails', 'number_of_array_designs': 'numberOfArrayDesigns', 'number_of_processed_expression_vectors': 'numberOfProcessedExpressionVectors', 'taxon': 'taxon' } - def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_event=None, needs_attention=None, last_needs_attention_event=None, curation_note=None, last_note_update_event=None, number_of_bio_assays=None, description=None, name=None, accession=None, batch_confound=None, batch_effect=None, batch_effect_statistics=None, external_database=None, external_database_uri=None, external_uri=None, geeq=None, metadata=None, short_name=None, source=None, technology_type=None, bio_assay_count=None, taxon_id=None, trouble_details=None, number_of_array_designs=None, number_of_processed_expression_vectors=None, taxon=None): # noqa: E501 + def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_event=None, needs_attention=None, last_needs_attention_event=None, curation_note=None, last_note_update_event=None, number_of_bio_assays=None, description=None, name=None, accession=None, batch_confound=None, batch_effect=None, batch_effect_statistics=None, external_database=None, external_database_uri=None, external_uri=None, geeq=None, metadata=None, short_name=None, source=None, technology_type=None, taxon_id=None, bio_assay_count=None, trouble_details=None, number_of_array_designs=None, number_of_processed_expression_vectors=None, taxon=None): # noqa: E501 """ExpressionExperimentValueObject - a model defined in Swagger""" # noqa: E501 self._id = None self._last_updated = None @@ -116,8 +116,8 @@ def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_even self._short_name = None self._source = None self._technology_type = None - self._bio_assay_count = None self._taxon_id = None + self._bio_assay_count = None self._trouble_details = None self._number_of_array_designs = None self._number_of_processed_expression_vectors = None @@ -169,10 +169,10 @@ def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_even self.source = source if technology_type is not None: self.technology_type = technology_type - if bio_assay_count is not None: - self.bio_assay_count = bio_assay_count if taxon_id is not None: self.taxon_id = taxon_id + if bio_assay_count is not None: + self.bio_assay_count = bio_assay_count if trouble_details is not None: self.trouble_details = trouble_details if number_of_array_designs is not None: @@ -672,46 +672,46 @@ def technology_type(self, technology_type): self._technology_type = technology_type @property - def bio_assay_count(self): - """Gets the bio_assay_count of this ExpressionExperimentValueObject. # noqa: E501 + def taxon_id(self): + """Gets the taxon_id of this ExpressionExperimentValueObject. # noqa: E501 - :return: The bio_assay_count of this ExpressionExperimentValueObject. # noqa: E501 + :return: The taxon_id of this ExpressionExperimentValueObject. # noqa: E501 :rtype: int """ - return self._bio_assay_count + return self._taxon_id - @bio_assay_count.setter - def bio_assay_count(self, bio_assay_count): - """Sets the bio_assay_count of this ExpressionExperimentValueObject. + @taxon_id.setter + def taxon_id(self, taxon_id): + """Sets the taxon_id of this ExpressionExperimentValueObject. - :param bio_assay_count: The bio_assay_count of this ExpressionExperimentValueObject. # noqa: E501 + :param taxon_id: The taxon_id of this ExpressionExperimentValueObject. # noqa: E501 :type: int """ - self._bio_assay_count = bio_assay_count + self._taxon_id = taxon_id @property - def taxon_id(self): - """Gets the taxon_id of this ExpressionExperimentValueObject. # noqa: E501 + def bio_assay_count(self): + """Gets the bio_assay_count of this ExpressionExperimentValueObject. # noqa: E501 - :return: The taxon_id of this ExpressionExperimentValueObject. # noqa: E501 + :return: The bio_assay_count of this ExpressionExperimentValueObject. # noqa: E501 :rtype: int """ - return self._taxon_id + return self._bio_assay_count - @taxon_id.setter - def taxon_id(self, taxon_id): - """Sets the taxon_id of this ExpressionExperimentValueObject. + @bio_assay_count.setter + def bio_assay_count(self, bio_assay_count): + """Sets the bio_assay_count of this ExpressionExperimentValueObject. - :param taxon_id: The taxon_id of this ExpressionExperimentValueObject. # noqa: E501 + :param bio_assay_count: The bio_assay_count of this ExpressionExperimentValueObject. # noqa: E501 :type: int """ - self._taxon_id = taxon_id + self._bio_assay_count = bio_assay_count @property def trouble_details(self): diff --git a/gemmapy/sdk/models/expression_experiment_with_search_result_value_object.py b/gemmapy/sdk/models/expression_experiment_with_search_result_value_object.py index 3ad520a..6182b39 100644 --- a/gemmapy/sdk/models/expression_experiment_with_search_result_value_object.py +++ b/gemmapy/sdk/models/expression_experiment_with_search_result_value_object.py @@ -52,8 +52,8 @@ class ExpressionExperimentWithSearchResultValueObject(object): 'source': 'str', 'technology_type': 'str', 'search_result': 'SearchResultValueObjectExpressionExperimentValueObject', - 'bio_assay_count': 'int', 'taxon_id': 'int', + 'bio_assay_count': 'int', 'trouble_details': 'str', 'number_of_array_designs': 'int', 'number_of_processed_expression_vectors': 'int', @@ -85,15 +85,15 @@ class ExpressionExperimentWithSearchResultValueObject(object): 'source': 'source', 'technology_type': 'technologyType', 'search_result': 'searchResult', - 'bio_assay_count': 'bioAssayCount', 'taxon_id': 'taxonId', + 'bio_assay_count': 'bioAssayCount', 'trouble_details': 'troubleDetails', 'number_of_array_designs': 'numberOfArrayDesigns', 'number_of_processed_expression_vectors': 'numberOfProcessedExpressionVectors', 'taxon': 'taxon' } - def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_event=None, needs_attention=None, last_needs_attention_event=None, curation_note=None, last_note_update_event=None, number_of_bio_assays=None, description=None, name=None, accession=None, batch_confound=None, batch_effect=None, batch_effect_statistics=None, external_database=None, external_database_uri=None, external_uri=None, geeq=None, metadata=None, short_name=None, source=None, technology_type=None, search_result=None, bio_assay_count=None, taxon_id=None, trouble_details=None, number_of_array_designs=None, number_of_processed_expression_vectors=None, taxon=None): # noqa: E501 + def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_event=None, needs_attention=None, last_needs_attention_event=None, curation_note=None, last_note_update_event=None, number_of_bio_assays=None, description=None, name=None, accession=None, batch_confound=None, batch_effect=None, batch_effect_statistics=None, external_database=None, external_database_uri=None, external_uri=None, geeq=None, metadata=None, short_name=None, source=None, technology_type=None, search_result=None, taxon_id=None, bio_assay_count=None, trouble_details=None, number_of_array_designs=None, number_of_processed_expression_vectors=None, taxon=None): # noqa: E501 """ExpressionExperimentWithSearchResultValueObject - a model defined in Swagger""" # noqa: E501 self._id = None self._last_updated = None @@ -119,8 +119,8 @@ def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_even self._source = None self._technology_type = None self._search_result = None - self._bio_assay_count = None self._taxon_id = None + self._bio_assay_count = None self._trouble_details = None self._number_of_array_designs = None self._number_of_processed_expression_vectors = None @@ -174,10 +174,10 @@ def __init__(self, id=None, last_updated=None, troubled=None, last_troubled_even self.technology_type = technology_type if search_result is not None: self.search_result = search_result - if bio_assay_count is not None: - self.bio_assay_count = bio_assay_count if taxon_id is not None: self.taxon_id = taxon_id + if bio_assay_count is not None: + self.bio_assay_count = bio_assay_count if trouble_details is not None: self.trouble_details = trouble_details if number_of_array_designs is not None: @@ -698,46 +698,46 @@ def search_result(self, search_result): self._search_result = search_result @property - def bio_assay_count(self): - """Gets the bio_assay_count of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 + def taxon_id(self): + """Gets the taxon_id of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 - :return: The bio_assay_count of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 + :return: The taxon_id of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 :rtype: int """ - return self._bio_assay_count + return self._taxon_id - @bio_assay_count.setter - def bio_assay_count(self, bio_assay_count): - """Sets the bio_assay_count of this ExpressionExperimentWithSearchResultValueObject. + @taxon_id.setter + def taxon_id(self, taxon_id): + """Sets the taxon_id of this ExpressionExperimentWithSearchResultValueObject. - :param bio_assay_count: The bio_assay_count of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 + :param taxon_id: The taxon_id of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 :type: int """ - self._bio_assay_count = bio_assay_count + self._taxon_id = taxon_id @property - def taxon_id(self): - """Gets the taxon_id of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 + def bio_assay_count(self): + """Gets the bio_assay_count of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 - :return: The taxon_id of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 + :return: The bio_assay_count of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 :rtype: int """ - return self._taxon_id + return self._bio_assay_count - @taxon_id.setter - def taxon_id(self, taxon_id): - """Sets the taxon_id of this ExpressionExperimentWithSearchResultValueObject. + @bio_assay_count.setter + def bio_assay_count(self, bio_assay_count): + """Sets the bio_assay_count of this ExpressionExperimentWithSearchResultValueObject. - :param taxon_id: The taxon_id of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 + :param bio_assay_count: The bio_assay_count of this ExpressionExperimentWithSearchResultValueObject. # noqa: E501 :type: int """ - self._taxon_id = taxon_id + self._bio_assay_count = bio_assay_count @property def trouble_details(self): diff --git a/gemmapy/sdk/models/factor_value_basic_value_object.py b/gemmapy/sdk/models/factor_value_basic_value_object.py index fad1f89..2ac2a3e 100644 --- a/gemmapy/sdk/models/factor_value_basic_value_object.py +++ b/gemmapy/sdk/models/factor_value_basic_value_object.py @@ -32,11 +32,11 @@ class FactorValueBasicValueObject(object): 'ontology_id': 'str', 'experimental_factor_id': 'int', 'experimental_factor_category': 'CharacteristicValueObject', - 'measurement': 'MeasurementValueObject', 'characteristics': 'list[CharacteristicValueObject]', 'statements': 'list[StatementValueObject]', 'summary': 'str', - 'value': 'str' + 'value': 'str', + 'is_measurement': 'bool' } attribute_map = { @@ -44,24 +44,24 @@ class FactorValueBasicValueObject(object): 'ontology_id': 'ontologyId', 'experimental_factor_id': 'experimentalFactorId', 'experimental_factor_category': 'experimentalFactorCategory', - 'measurement': 'measurement', 'characteristics': 'characteristics', 'statements': 'statements', 'summary': 'summary', - 'value': 'value' + 'value': 'value', + 'is_measurement': 'isMeasurement' } - def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, experimental_factor_category=None, measurement=None, characteristics=None, statements=None, summary=None, value=None): # noqa: E501 + def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, experimental_factor_category=None, characteristics=None, statements=None, summary=None, value=None, is_measurement=None): # noqa: E501 """FactorValueBasicValueObject - a model defined in Swagger""" # noqa: E501 self._id = None self._ontology_id = None self._experimental_factor_id = None self._experimental_factor_category = None - self._measurement = None self._characteristics = None self._statements = None self._summary = None self._value = None + self._is_measurement = None self.discriminator = None if id is not None: self.id = id @@ -71,8 +71,6 @@ def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, exper self.experimental_factor_id = experimental_factor_id if experimental_factor_category is not None: self.experimental_factor_category = experimental_factor_category - if measurement is not None: - self.measurement = measurement if characteristics is not None: self.characteristics = characteristics if statements is not None: @@ -81,6 +79,8 @@ def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, exper self.summary = summary if value is not None: self.value = value + if is_measurement is not None: + self.is_measurement = is_measurement @property def id(self): @@ -166,27 +166,6 @@ def experimental_factor_category(self, experimental_factor_category): self._experimental_factor_category = experimental_factor_category - @property - def measurement(self): - """Gets the measurement of this FactorValueBasicValueObject. # noqa: E501 - - - :return: The measurement of this FactorValueBasicValueObject. # noqa: E501 - :rtype: MeasurementValueObject - """ - return self._measurement - - @measurement.setter - def measurement(self, measurement): - """Sets the measurement of this FactorValueBasicValueObject. - - - :param measurement: The measurement of this FactorValueBasicValueObject. # noqa: E501 - :type: MeasurementValueObject - """ - - self._measurement = measurement - @property def characteristics(self): """Gets the characteristics of this FactorValueBasicValueObject. # noqa: E501 @@ -273,6 +252,29 @@ def value(self, value): self._value = value + @property + def is_measurement(self): + """Gets the is_measurement of this FactorValueBasicValueObject. # noqa: E501 + + Indicate if this factor value represents a measurement. When this is true, the `measurement` field will be populated. # noqa: E501 + + :return: The is_measurement of this FactorValueBasicValueObject. # noqa: E501 + :rtype: bool + """ + return self._is_measurement + + @is_measurement.setter + def is_measurement(self, is_measurement): + """Sets the is_measurement of this FactorValueBasicValueObject. + + Indicate if this factor value represents a measurement. When this is true, the `measurement` field will be populated. # noqa: E501 + + :param is_measurement: The is_measurement of this FactorValueBasicValueObject. # noqa: E501 + :type: bool + """ + + self._is_measurement = is_measurement + def to_dict(self): """Returns the model properties as a dict""" result = {} diff --git a/gemmapy/sdk/models/factor_value_value_object.py b/gemmapy/sdk/models/factor_value_value_object.py index c83e713..9e2d166 100644 --- a/gemmapy/sdk/models/factor_value_value_object.py +++ b/gemmapy/sdk/models/factor_value_value_object.py @@ -38,8 +38,8 @@ class FactorValueValueObject(object): 'factor_id': 'int', 'category': 'str', 'category_uri': 'str', - 'factor_value': 'str', 'description': 'str', + 'factor_value': 'str', 'is_measurement': 'bool', 'measurement': 'MeasurementValueObject' } @@ -55,13 +55,13 @@ class FactorValueValueObject(object): 'factor_id': 'factorId', 'category': 'category', 'category_uri': 'categoryUri', - 'factor_value': 'factorValue', 'description': 'description', + 'factor_value': 'factorValue', 'is_measurement': 'isMeasurement', 'measurement': 'measurement' } - def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, experimental_factor_category=None, characteristics=None, statements=None, summary=None, factor_id=None, category=None, category_uri=None, factor_value=None, description=None, is_measurement=None, measurement=None): # noqa: E501 + def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, experimental_factor_category=None, characteristics=None, statements=None, summary=None, factor_id=None, category=None, category_uri=None, description=None, factor_value=None, is_measurement=None, measurement=None): # noqa: E501 """FactorValueValueObject - a model defined in Swagger""" # noqa: E501 self._id = None self._ontology_id = None @@ -73,8 +73,8 @@ def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, exper self._factor_id = None self._category = None self._category_uri = None - self._factor_value = None self._description = None + self._factor_value = None self._is_measurement = None self._measurement = None self.discriminator = None @@ -98,10 +98,10 @@ def __init__(self, id=None, ontology_id=None, experimental_factor_id=None, exper self.category = category if category_uri is not None: self.category_uri = category_uri - if factor_value is not None: - self.factor_value = factor_value if description is not None: self.description = description + if factor_value is not None: + self.factor_value = factor_value if is_measurement is not None: self.is_measurement = is_measurement if measurement is not None: @@ -324,56 +324,56 @@ def category_uri(self, category_uri): self._category_uri = category_uri @property - def factor_value(self): - """Gets the factor_value of this FactorValueValueObject. # noqa: E501 + def description(self): + """Gets the description of this FactorValueValueObject. # noqa: E501 Use `summary` if you need a human-readable representation of this factor value or lookup the `characteristics` bag. # noqa: E501 - :return: The factor_value of this FactorValueValueObject. # noqa: E501 + :return: The description of this FactorValueValueObject. # noqa: E501 :rtype: str """ - return self._factor_value + return self._description - @factor_value.setter - def factor_value(self, factor_value): - """Sets the factor_value of this FactorValueValueObject. + @description.setter + def description(self, description): + """Sets the description of this FactorValueValueObject. Use `summary` if you need a human-readable representation of this factor value or lookup the `characteristics` bag. # noqa: E501 - :param factor_value: The factor_value of this FactorValueValueObject. # noqa: E501 + :param description: The description of this FactorValueValueObject. # noqa: E501 :type: str """ - self._factor_value = factor_value + self._description = description @property - def description(self): - """Gets the description of this FactorValueValueObject. # noqa: E501 + def factor_value(self): + """Gets the factor_value of this FactorValueValueObject. # noqa: E501 - This property is never filled nor used; use `summary` if you need a human-readable representation of this factor value. # noqa: E501 + Use `summary` if you need a human-readable representation of this factor value or lookup the `characteristics` bag. # noqa: E501 - :return: The description of this FactorValueValueObject. # noqa: E501 + :return: The factor_value of this FactorValueValueObject. # noqa: E501 :rtype: str """ - return self._description + return self._factor_value - @description.setter - def description(self, description): - """Sets the description of this FactorValueValueObject. + @factor_value.setter + def factor_value(self, factor_value): + """Sets the factor_value of this FactorValueValueObject. - This property is never filled nor used; use `summary` if you need a human-readable representation of this factor value. # noqa: E501 + Use `summary` if you need a human-readable representation of this factor value or lookup the `characteristics` bag. # noqa: E501 - :param description: The description of this FactorValueValueObject. # noqa: E501 + :param factor_value: The factor_value of this FactorValueValueObject. # noqa: E501 :type: str """ - self._description = description + self._factor_value = factor_value @property def is_measurement(self): """Gets the is_measurement of this FactorValueValueObject. # noqa: E501 - Check if a `measurement` key exists instead. # noqa: E501 + Indicate if this factor value represents a measurement. When this is true, the `measurement` field will be populated. # noqa: E501 :return: The is_measurement of this FactorValueValueObject. # noqa: E501 :rtype: bool @@ -384,7 +384,7 @@ def is_measurement(self): def is_measurement(self, is_measurement): """Sets the is_measurement of this FactorValueValueObject. - Check if a `measurement` key exists instead. # noqa: E501 + Indicate if this factor value represents a measurement. When this is true, the `measurement` field will be populated. # noqa: E501 :param is_measurement: The is_measurement of this FactorValueValueObject. # noqa: E501 :type: bool diff --git a/gemmapy/sdk/models/gene_value_object.py b/gemmapy/sdk/models/gene_value_object.py index 24a63e6..24bd9dc 100644 --- a/gemmapy/sdk/models/gene_value_object.py +++ b/gemmapy/sdk/models/gene_value_object.py @@ -36,7 +36,8 @@ class GeneValueObject(object): 'accessions': 'list[DatabaseEntryValueObject]', 'official_name': 'str', 'official_symbol': 'str', - 'taxon': 'TaxonValueObject' + 'taxon': 'TaxonValueObject', + 'taxon_id': 'int' } attribute_map = { @@ -48,10 +49,11 @@ class GeneValueObject(object): 'accessions': 'accessions', 'official_name': 'officialName', 'official_symbol': 'officialSymbol', - 'taxon': 'taxon' + 'taxon': 'taxon', + 'taxon_id': 'taxonId' } - def __init__(self, id=None, aliases=None, multifunctionality_rank=None, ncbi_id=None, ensembl_id=None, accessions=None, official_name=None, official_symbol=None, taxon=None): # noqa: E501 + def __init__(self, id=None, aliases=None, multifunctionality_rank=None, ncbi_id=None, ensembl_id=None, accessions=None, official_name=None, official_symbol=None, taxon=None, taxon_id=None): # noqa: E501 """GeneValueObject - a model defined in Swagger""" # noqa: E501 self._id = None self._aliases = None @@ -62,6 +64,7 @@ def __init__(self, id=None, aliases=None, multifunctionality_rank=None, ncbi_id= self._official_name = None self._official_symbol = None self._taxon = None + self._taxon_id = None self.discriminator = None if id is not None: self.id = id @@ -81,6 +84,8 @@ def __init__(self, id=None, aliases=None, multifunctionality_rank=None, ncbi_id= self.official_symbol = official_symbol if taxon is not None: self.taxon = taxon + if taxon_id is not None: + self.taxon_id = taxon_id @property def id(self): @@ -271,6 +276,29 @@ def taxon(self, taxon): self._taxon = taxon + @property + def taxon_id(self): + """Gets the taxon_id of this GeneValueObject. # noqa: E501 + + This property is mutually exclusive with `taxon`. # noqa: E501 + + :return: The taxon_id of this GeneValueObject. # noqa: E501 + :rtype: int + """ + return self._taxon_id + + @taxon_id.setter + def taxon_id(self, taxon_id): + """Sets the taxon_id of this GeneValueObject. + + This property is mutually exclusive with `taxon`. # noqa: E501 + + :param taxon_id: The taxon_id of this GeneValueObject. # noqa: E501 + :type: int + """ + + self._taxon_id = taxon_id + def to_dict(self): """Returns the model properties as a dict""" result = {} diff --git a/sdk-gen/openapi.yaml b/sdk-gen/openapi.yaml index e3e9c24..b0be4e2 100644 --- a/sdk-gen/openapi.yaml +++ b/sdk-gen/openapi.yaml @@ -72,6 +72,22 @@ paths: type: integer description: Limit the number of results retrieved. format: int32 + - name: includeFactorValuesInContrasts + in: query + description: "Include complete factor values in contrasts instead of only\ + \ populating `factorValueId` and `secondFactorValueId`. In 2.9.0, this will\ + \ default to false." + schema: + type: boolean + default: true + - name: includeTaxonInGenes + in: query + description: "Include complete taxon in genes instead of only populating `taxonId`.\ + \ When this is set to true, a `taxa` collection will be included in `DifferentialExpressionAnalysisResultSetValueObject`.\ + \ In 2.9.0, this will default to false." + schema: + type: boolean + default: true responses: default: content: @@ -2397,16 +2413,16 @@ paths: items: type: string enum: - - ubic.gemma.model.blacklist.BlacklistedEntity - - ubic.gemma.model.genome.biosequence.BioSequence - - ubic.gemma.model.expression.arrayDesign.ArrayDesign - - ubic.gemma.model.expression.experiment.ExpressionExperiment - - ubic.gemma.model.genome.Gene - - ubic.gemma.model.analysis.expression.ExpressionExperimentSet - ubic.gemma.model.common.description.BibliographicReference + - ubic.gemma.model.expression.designElement.CompositeSequence - ubic.gemma.model.genome.gene.GeneSet - ubic.gemma.model.association.phenotype.PhenotypeAssociation - - ubic.gemma.model.expression.designElement.CompositeSequence + - ubic.gemma.model.expression.experiment.ExpressionExperiment + - ubic.gemma.model.analysis.expression.ExpressionExperimentSet + - ubic.gemma.model.genome.biosequence.BioSequence + - ubic.gemma.model.genome.Gene + - ubic.gemma.model.blacklist.BlacklistedEntity + - ubic.gemma.model.expression.arrayDesign.ArrayDesign - name: limit in: query description: Maximum number of search results to return; capped at 2000 unless @@ -3192,11 +3208,13 @@ components: format: double factorValueId: type: integer + description: This property is mutually exclusive with `factorValue`. format: int64 factorValue: $ref: '#/components/schemas/FactorValueBasicValueObject' secondFactorValueId: type: integer + description: This property is mutually exclusive with `secondFactorValue`. format: int64 secondFactorValue: $ref: '#/components/schemas/FactorValueBasicValueObject' @@ -3248,15 +3266,15 @@ components: downregulatedCount: type: integer format: int32 + numberOfUpregulatedProbes: + type: integer + format: int32 numberOfDownregulatedProbes: type: integer format: int32 qvalue: type: number format: double - numberOfUpregulatedProbes: - type: integer - format: int32 DifferentialExpressionAnalysisResultSetValueObject: type: object properties: @@ -3273,6 +3291,11 @@ components: $ref: '#/components/schemas/FactorValueBasicValueObject' secondBaselineGroup: $ref: '#/components/schemas/FactorValueBasicValueObject' + taxa: + uniqueItems: true + type: array + items: + $ref: '#/components/schemas/TaxonValueObject' results: type: array items: @@ -3341,6 +3364,7 @@ components: $ref: '#/components/schemas/FactorValueValueObject' subsetFactorValueId: type: integer + description: This property is mutually exclusive with `subsetFactorValue`. format: int64 sourceExperiment: type: integer @@ -3360,6 +3384,8 @@ components: $ref: '#/components/schemas/FactorValueValueObject' isSubset: type: boolean + description: "Indicate if this analysis is a subset of another experiment.\ + \ if this is set, additional fields relevant to the subset will be populated." ExperimentalFactorValueObject: type: object properties: @@ -3425,8 +3451,6 @@ components: format: int64 experimentalFactorCategory: $ref: '#/components/schemas/CharacteristicValueObject' - measurement: - $ref: '#/components/schemas/MeasurementValueObject' characteristics: type: array items: @@ -3442,6 +3466,10 @@ components: description: Use `summary` if you need a human-readable representation of this factor value or lookup the `characteristics` bag. deprecated: true + isMeasurement: + type: boolean + description: "Indicate if this factor value represents a measurement. When\ + \ this is true, the `measurement` field will be populated." FactorValueValueObject: type: object properties: @@ -3478,20 +3506,20 @@ components: type: string description: Use experimentalFactorCategory.categoryUri instead. deprecated: true - factorValue: + description: type: string description: Use `summary` if you need a human-readable representation of this factor value or lookup the `characteristics` bag. deprecated: true - description: + factorValue: type: string - description: This property is never filled nor used; use `summary` if you - need a human-readable representation of this factor value. + description: Use `summary` if you need a human-readable representation of + this factor value or lookup the `characteristics` bag. deprecated: true isMeasurement: type: boolean - description: Check if a `measurement` key exists instead. - deprecated: true + description: "Indicate if this factor value represents a measurement. When\ + \ this is true, the `measurement` field will be populated." measurement: $ref: '#/components/schemas/MeasurementValueObject' GeneValueObject: @@ -3524,6 +3552,10 @@ components: type: string taxon: $ref: '#/components/schemas/TaxonValueObject' + taxonId: + type: integer + description: This property is mutually exclusive with `taxon`. + format: int64 MeasurementValueObject: type: object properties: @@ -3553,6 +3585,7 @@ components: - CHARARRAY - BOOLEANARRAY - STRINGARRAY + description: This property exists only if this factor value is a measurement PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject: type: object properties: @@ -3620,6 +3653,7 @@ components: format: int32 externalDatabase: $ref: '#/components/schemas/ExternalDatabaseValueObject' + description: This property is mutually exclusive with `taxonId`. BuildInfoValueObject: type: object properties: @@ -4024,10 +4058,10 @@ components: type: string detail: type: string - eventTypeName: - type: string actionName: type: string + eventTypeName: + type: string ExpressionExperimentValueObject: type: object properties: @@ -4090,12 +4124,12 @@ components: type: string technologyType: type: string - bioAssayCount: - type: integer - format: int32 taxonId: type: integer format: int64 + bioAssayCount: + type: integer + format: int32 troubleDetails: type: string numberOfArrayDesigns: @@ -6375,12 +6409,12 @@ components: type: string searchResult: $ref: '#/components/schemas/SearchResultValueObjectExpressionExperimentValueObject' - bioAssayCount: - type: integer - format: int32 taxonId: type: integer format: int64 + bioAssayCount: + type: integer + format: int32 troubleDetails: type: string numberOfArrayDesigns: @@ -6475,7 +6509,7 @@ components: \ the exact phrase \"alpha beta gamma\". \ \ |\n| Field | `shortName:GSE00001` \ \ | Results with short name GSE00001.
List of supported\ - \ fields

ubic.gemma.model.expression.experiment.ExpressionExperiment

ubic.gemma.model.genome.gene.GeneSet

ubic.gemma.model.expression.designElement.CompositeSequence

ubic.gemma.model.expression.arrayDesign.ArrayDesign

ubic.gemma.model.genome.Gene

ubic.gemma.model.genome.biosequence.BioSequence

\ + \ fields

ubic.gemma.model.genome.gene.GeneSet

ubic.gemma.model.expression.experiment.ExpressionExperiment

ubic.gemma.model.expression.designElement.CompositeSequence

ubic.gemma.model.expression.arrayDesign.ArrayDesign

ubic.gemma.model.genome.Gene

ubic.gemma.model.genome.biosequence.BioSequence

\ \ |\n| Prefix | `alpha*` | Results must start with\ \ \"alpha\". \ \ |\n| Wildcard | `BRCA?` \ @@ -6493,6 +6527,33 @@ components: externalDocs: url: https://lucene.apache.org/core/3_6_2/queryparsersyntax.html x-gemma-searchable-properties: + ubic.gemma.model.genome.gene.GeneSet: + - description + - name + - characteristics.value + - characteristics.valueUri + - literatureSources.abstractText + - literatureSources.authorList + - literatureSources.fullTextUri + - literatureSources.name + - literatureSources.title + - sourceAccession.accession + - literatureSources.chemicals.name + - literatureSources.chemicals.registryNumber + - literatureSources.keywords.term + - literatureSources.meshTerms.term + - literatureSources.pubAccession.accession + - members.gene.ensemblId + - members.gene.name + - members.gene.ncbiGeneId + - members.gene.officialName + - members.gene.officialSymbol + - members.gene.accessions.accession + - members.gene.aliases.alias + - members.gene.products.name + - members.gene.products.ncbiGi + - members.gene.products.previousNcbiId + - members.gene.products.accessions.accession ubic.gemma.model.expression.experiment.ExpressionExperiment: - description - name @@ -6538,33 +6599,6 @@ components: - experimentalDesign.experimentalFactors.factorValues.characteristics.secondObjectUri - experimentalDesign.experimentalFactors.factorValues.characteristics.value - experimentalDesign.experimentalFactors.factorValues.characteristics.valueUri - ubic.gemma.model.genome.gene.GeneSet: - - description - - name - - characteristics.value - - characteristics.valueUri - - literatureSources.abstractText - - literatureSources.authorList - - literatureSources.fullTextUri - - literatureSources.name - - literatureSources.title - - sourceAccession.accession - - literatureSources.chemicals.name - - literatureSources.chemicals.registryNumber - - literatureSources.keywords.term - - literatureSources.meshTerms.term - - literatureSources.pubAccession.accession - - members.gene.ensemblId - - members.gene.name - - members.gene.ncbiGeneId - - members.gene.officialName - - members.gene.officialSymbol - - members.gene.accessions.accession - - members.gene.aliases.alias - - members.gene.products.name - - members.gene.products.ncbiGi - - members.gene.products.previousNcbiId - - members.gene.products.accessions.accession ubic.gemma.model.expression.designElement.CompositeSequence: - description - name @@ -8354,16 +8388,16 @@ components: items: type: string enum: - - ubic.gemma.model.blacklist.BlacklistedEntity - - ubic.gemma.model.genome.biosequence.BioSequence - - ubic.gemma.model.expression.arrayDesign.ArrayDesign - - ubic.gemma.model.expression.experiment.ExpressionExperiment - - ubic.gemma.model.genome.Gene - - ubic.gemma.model.analysis.expression.ExpressionExperimentSet - ubic.gemma.model.common.description.BibliographicReference + - ubic.gemma.model.expression.designElement.CompositeSequence - ubic.gemma.model.genome.gene.GeneSet - ubic.gemma.model.association.phenotype.PhenotypeAssociation - - ubic.gemma.model.expression.designElement.CompositeSequence + - ubic.gemma.model.expression.experiment.ExpressionExperiment + - ubic.gemma.model.analysis.expression.ExpressionExperimentSet + - ubic.gemma.model.genome.biosequence.BioSequence + - ubic.gemma.model.genome.Gene + - ubic.gemma.model.blacklist.BlacklistedEntity + - ubic.gemma.model.expression.arrayDesign.ArrayDesign ResponseDataObjectListTaxonValueObject: type: object properties: