Index

_

__enter__() (obj_tables.core.Model method) __exit__() (obj_tables.core.Model method) __new__() (obj_tables.core.ModelMeta static method) __setattr__() (obj_tables.core.Model method) __str__() (obj_tables.core.InvalidAttribute method) (obj_tables.core.InvalidModel method) (obj_tables.core.InvalidObject method) (obj_tables.core.InvalidObjectSet method) (obj_tables.core.Model method) (obj_tables.migrate.DataSchemaMigration method) (obj_tables.migrate.GitRepo method) (obj_tables.migrate.MigrationSpec method) (obj_tables.migrate.Migrator method) (obj_tables.migrate.SchemaChanges method) (obj_tables.sci.refs.Identifier method) _ALLOWED_ATTRS (obj_tables.migrate.MigrationSpec attribute) _alphabet (obj_tables.bio.seq.SeqAttribute attribute) _ATTRIBUTES (obj_tables.migrate.SchemaChanges attribute) _CHANGES_FILE_ATTRS (obj_tables.migrate.SchemaChanges attribute)

_CHANGES_LISTS (obj_tables.migrate.MigrationSpec attribute) _comments (obj_tables.core.Model attribute) _compiled_expression (obj_tables.math.expression.ParsedExpression attribute) _compiled_expression_with_units (obj_tables.math.expression.ParsedExpression attribute) _compiled_namespace (obj_tables.math.expression.ParsedExpression attribute) _compiled_namespace_with_units (obj_tables.math.expression.ParsedExpression attribute) _data_frames (obj_tables.io.PandasWriter attribute) _doc_metadata (obj_tables.io.ReaderBase attribute) _index_dicts (obj_tables.core.Manager attribute) _migrated_copy_attr_name (obj_tables.migrate.Migrator attribute) _model_metadata (obj_tables.io.ReaderBase attribute) _new_instances (obj_tables.core.Manager attribute) _obj_tables_tokens (obj_tables.math.expression.ParsedExpression attribute) _objs (obj_tables.math.expression.ParsedExpression attribute) _parsed_expression (obj_tables.math.expression.Expression attribute) _prepared (obj_tables.migrate.MigrationSpec attribute) _py_tokens (obj_tables.math.expression.ParsedExpression attribute) _REQUIRED_ATTRS (obj_tables.migrate.MigrationSpec attribute) _reverse_index (obj_tables.core.Manager attribute) _source (obj_tables.core.Model attribute)

A

abs_module_path (obj_tables.migrate.SchemaModule attribute) AbstractModel (class in obj_tables.abstract) AbstractModel.Meta (class in obj_tables.abstract) AbstractModelMeta (class in obj_tables.abstract) activate() (obj_tables.migrate.VirtualEnvUtil method) add() (obj_tables.core.RelatedManager method) add_file() (obj_tables.migrate.GitRepo method) add_metadata_to_file() (in module obj_tables.utils) all() (obj_tables.core.Manager method) all_schema_changes_files() (obj_tables.migrate.SchemaChanges static method) all_schema_changes_with_commits() (obj_tables.migrate.SchemaChanges static method) api (in module obj_tables.web_service) App (class in obj_tables.__main__) App.Meta (class in obj_tables.__main__) append (obj_tables.core.ModelMerge attribute) append() (obj_tables.core.ManyToManyRelatedManager method) (obj_tables.core.ManyToOneRelatedManager method) (obj_tables.core.OneToManyRelatedManager method) (obj_tables.core.RelatedManager method) are_attr_paths_equal() (obj_tables.core.Model class method) are_related_attributes_serializable() (obj_tables.core.Model class method) arguments (obj_tables.__main__.BaseController.Meta attribute) (obj_tables.__main__.ConvertController.Meta attribute) (obj_tables.__main__.DiffController.Meta attribute) (obj_tables.__main__.GenTemplateController.Meta attribute) (obj_tables.__main__.InitSchemaController.Meta attribute) (obj_tables.__main__.NormalizeController.Meta attribute) (obj_tables.__main__.ValidateController.Meta attribute) (obj_tables.__main__.VizSchemaController.Meta attribute) (obj_tables.migrate.CementControllers.DataSchemaMigrationConfigController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateFileController.Meta attribute) (obj_tables.migrate.CementControllers.SchemaChangesTemplateController.Meta attribute)

ArrayAttribute (class in obj_tables.math.numeric) ast_eq() (obj_tables.math.expression.LinearParsedExpressionValidator static method) attr (obj_tables.core.LocalAttribute attribute) (obj_tables.math.expression.ParsedExpression attribute) Attribute (class in obj_tables.core) attribute (obj_tables.core.InvalidAttribute attribute) (obj_tables.core.RelatedManager attribute) attribute_order (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) attribute_seq (obj_tables.core.ModelSource attribute) attributes (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.InvalidModel attribute) (obj_tables.core.InvalidObject attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) automated_migrate() (obj_tables.migrate.DataSchemaMigration method)

B

base_controller (obj_tables.__main__.App.Meta attribute) BaseController (class in obj_tables.__main__) BaseController.Meta (class in obj_tables.__main__) BaseRelatedAttribute (class in obj_tables.core)

bcforms (obj_tables.chem.core.ChemicalStructureFormat attribute) BooleanAttribute (class in obj_tables.core) bpforms (obj_tables.chem.core.ChemicalStructureFormat attribute) branch (obj_tables.migrate.GitRepo attribute) (obj_tables.utils.RepoMetadata attribute)

C

cell (obj_tables.core.TableFormat attribute) cell_dialect (obj_tables.core.ManyToManyAttribute attribute) (obj_tables.core.OneToManyAttribute attribute) (obj_tables.core.ToManyAttribute attribute) CellDialect (class in obj_tables.core) CementControllers (class in obj_tables.migrate) CementControllers.DataSchemaMigrationConfigController (class in obj_tables.migrate) CementControllers.DataSchemaMigrationConfigController.Meta (class in obj_tables.migrate) CementControllers.MigrateController (class in obj_tables.migrate) CementControllers.MigrateController.Meta (class in obj_tables.migrate) CementControllers.MigrateFileController (class in obj_tables.migrate) CementControllers.MigrateFileController.Meta (class in obj_tables.migrate) CementControllers.SchemaChangesTemplateController (class in obj_tables.migrate) CementControllers.SchemaChangesTemplateController.Meta (class in obj_tables.migrate) CHECK_SAME_RELATED_ATTRIBUTE_NAME (obj_tables.core.ModelMeta attribute) checkout_commit() (obj_tables.migrate.GitRepo method) ChemicalFormulaAttribute (class in obj_tables.chem.core) ChemicalStructure (class in obj_tables.chem.core) ChemicalStructureAttribute (class in obj_tables.chem.core) ChemicalStructureFormat (class in obj_tables.chem.core) children (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) choices (obj_tables.sci.units.QuantityAttribute attribute) (obj_tables.sci.units.UnitAttribute attribute) clean() (obj_tables.core.Attribute method) (obj_tables.core.BooleanAttribute method) (obj_tables.core.DateAttribute method) (obj_tables.core.DateTimeAttribute method) (obj_tables.core.EnumAttribute method) (obj_tables.core.FloatAttribute method) (obj_tables.core.IntegerAttribute method) (obj_tables.core.ListAttribute method) (obj_tables.core.LocalPathAttribute method) (obj_tables.core.Model method) (obj_tables.core.RangeAttribute method) (obj_tables.core.StringAttribute method) (obj_tables.core.TimeAttribute method) (obj_tables.core.Validator method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method)

clean_up() (obj_tables.migrate.DataSchemaMigration method) clear() (obj_tables.core.RelatedManager method) clear_new_instances() (obj_tables.core.Manager method) clone_repo_from_url() (obj_tables.migrate.GitRepo method) cls (obj_tables.core.LocalAttribute attribute) (obj_tables.core.Manager attribute) code() (obj_tables.math.expression.ObjTablesToken property) COLLECTIONS_ATTRS (obj_tables.migrate.Migrator attribute) column (obj_tables.core.TableFormat attribute) commit_changes() (obj_tables.migrate.GitRepo method) commit_DAG (obj_tables.migrate.GitRepo attribute) commit_hash (obj_tables.migrate.SchemaChanges attribute) commits_as_graph() (obj_tables.migrate.GitRepo method) commits_in_dependency_consistent_seq() (obj_tables.migrate.GitRepo method) compartment (obj_tables.chem.core.ReactionParticipant attribute) compartments (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer attribute) Convert (class in obj_tables.web_service) convert() (in module obj_tables.io) ConvertController (class in obj_tables.__main__) ConvertController.Meta (class in obj_tables.__main__) copy() (obj_tables.core.Model method) (obj_tables.migrate.GitRepo method) copy_value() (obj_tables.core.Attribute method) (obj_tables.core.LiteralAttribute method) (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method) create() (obj_tables.core.RelatedManager method) create_model_manager() (obj_tables.core.ModelMeta method) create_template() (in module obj_tables.io) create_worksheet_style() (obj_tables.io.WorkbookWriter static method) csv (obj_tables.core.CellDialect attribute) CUSTOM_IO_CLASSES_FILE (obj_tables.migrate.DataSchemaMigration attribute) cut() (obj_tables.core.ManyToManyRelatedManager method) (obj_tables.core.ManyToOneRelatedManager method) (obj_tables.core.Model method) (obj_tables.core.OneToManyRelatedManager method) cut_relations() (obj_tables.core.Model method)

D

data_config_file_basename (obj_tables.migrate.DataSchemaMigration attribute) data_git_repo (obj_tables.migrate.DataSchemaMigration attribute) data_repo_location (obj_tables.migrate.DataSchemaMigration attribute) data_repo_metadata() (obj_tables.utils.DataFileMetadata property) DataFileMetadata (class in obj_tables.utils) DataRepoMetadata (class in obj_tables.utils) DataRepoMetadata.Meta (class in obj_tables.utils) DataSchemaMigration (class in obj_tables.migrate) DateAttribute (class in obj_tables.core) DateTimeAttribute (class in obj_tables.core) deactivate() (obj_tables.migrate.VirtualEnvUtil method) default (obj_tables.bio.seq.FeatureLocAttribute attribute) (obj_tables.bio.seq.SeqAttribute attribute) (obj_tables.core.Attribute attribute) (obj_tables.core.BooleanAttribute attribute) (obj_tables.core.DateAttribute attribute) (obj_tables.core.DateTimeAttribute attribute) (obj_tables.core.FloatAttribute attribute) (obj_tables.core.IntegerAttribute attribute) (obj_tables.core.StringAttribute attribute) (obj_tables.core.TimeAttribute attribute) (obj_tables.math.numeric.ArrayAttribute attribute) (obj_tables.math.numeric.TableAttribute attribute) (obj_tables.math.symbolic.SymbolicBasicAttribute attribute) (obj_tables.math.symbolic.SymbolicExprAttribute attribute) (obj_tables.math.symbolic.SymbolicSymbolAttribute attribute) default_cleaned_value (obj_tables.core.Attribute attribute) (obj_tables.core.BooleanAttribute attribute) (obj_tables.core.DateAttribute attribute) (obj_tables.core.DateTimeAttribute attribute) (obj_tables.core.FloatAttribute attribute) (obj_tables.core.IntegerAttribute attribute) (obj_tables.core.StringAttribute attribute) (obj_tables.core.TimeAttribute attribute) DEFAULT_INDENT (obj_tables.core.Model attribute) DEFAULT_IO_CLASSES (obj_tables.migrate.Migrator attribute) DEFAULT_MAX_DEPTH (obj_tables.core.Model attribute) del_temp_dirs() (obj_tables.migrate.GitRepo method) deleted_models (obj_tables.migrate.Migrator attribute) description (obj_tables.__main__.BaseController.Meta attribute) (obj_tables.__main__.ConvertController.Meta attribute) (obj_tables.__main__.DiffController.Meta attribute) (obj_tables.__main__.GenTemplateController.Meta attribute) (obj_tables.__main__.InitSchemaController.Meta attribute) (obj_tables.__main__.NormalizeController.Meta attribute) (obj_tables.__main__.ValidateController.Meta attribute) (obj_tables.__main__.VizSchemaController.Meta attribute) (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Attribute attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.migrate.CementControllers.DataSchemaMigrationConfigController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateFileController.Meta attribute) (obj_tables.migrate.CementControllers.SchemaChangesTemplateController.Meta attribute) (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute)

deserialize() (obj_tables.bio.seq.FeatureLocAttribute method) (obj_tables.bio.seq.FreqPosMatrixAttribute method) (obj_tables.bio.seq.SeqAttribute method) (obj_tables.chem.core.ChemicalFormulaAttribute method) (obj_tables.chem.core.ChemicalStructure method) (obj_tables.chem.core.ChemicalStructureAttribute method) (obj_tables.chem.core.ReactionEquation method) (obj_tables.chem.core.ReactionEquationAttribute method) (obj_tables.core.Attribute method) (obj_tables.core.LiteralAttribute method) (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.Model class method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.core.RelatedAttribute method) (obj_tables.grammar.ToManyGrammarAttribute method) (obj_tables.math.expression.Expression class method) (obj_tables.math.expression.ManyToOneExpressionAttribute method) (obj_tables.math.expression.OneToOneExpressionAttribute method) (obj_tables.math.numeric.ArrayAttribute method) (obj_tables.math.numeric.TableAttribute method) (obj_tables.math.symbolic.SymbolicBasicAttribute method) (obj_tables.sci.refs.DoisAttribute method) (obj_tables.sci.refs.IdentifierAttribute method) (obj_tables.sci.refs.IdentifiersAttribute method) (obj_tables.sci.refs.PubMedIdsAttribute method) deserialize_from_cell() (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.core.ToManyAttribute method) destroy() (obj_tables.migrate.VirtualEnvUtil method) destroyed() (obj_tables.migrate.VirtualEnvUtil method) Diff (class in obj_tables.web_service) diff_workbooks() (in module obj_tables.utils) DiffController (class in obj_tables.__main__) DiffController.Meta (class in obj_tables.__main__) difference() (obj_tables.core.Model method) difference_update() (obj_tables.core.RelatedManager method) directory (obj_tables.migrate.SchemaModule attribute) discard() (obj_tables.core.RelatedManager method) DnaSeqAttribute (class in obj_tables.bio.seq) DOC_METADATA_PATTERN (obj_tables.io.WorkbookReader attribute) DoiAttribute (class in obj_tables.sci.refs) DoisAttribute (class in obj_tables.sci.refs)

E

EmailAttribute (class in obj_tables.core) EMPTY_SUBDIR (obj_tables.migrate.GitRepo attribute) endpoint (obj_tables.web_service.Convert attribute) (obj_tables.web_service.Diff attribute) (obj_tables.web_service.GenTemplate attribute) (obj_tables.web_service.InitSchema attribute) (obj_tables.web_service.Normalize attribute) (obj_tables.web_service.Validate attribute) (obj_tables.web_service.VizSchema attribute) enum_class (obj_tables.core.EnumAttribute attribute) EnumAttribute (class in obj_tables.core) errors (obj_tables.math.expression.ParsedExpression attribute) eval() (obj_tables.math.expression.ParsedExpression method) existing_defs (obj_tables.migrate.Migrator attribute) existing_schema (obj_tables.migrate.Migrator attribute) expected_migrated_files() (obj_tables.migrate.MigrationSpec method) Expression (class in obj_tables.math.expression)

expression (obj_tables.math.expression.LinearParsedExpressionValidator attribute) (obj_tables.math.expression.ParsedExpression attribute) Expression.Meta (class in obj_tables.math.expression) expression_is_linear (obj_tables.math.expression.Expression.Meta attribute), [1] expression_term_model (obj_tables.math.expression.ExpressionExpressionTermMeta attribute), [1] expression_term_models (obj_tables.math.expression.Expression.Meta attribute), [1] expression_term_token_pattern (obj_tables.math.expression.ExpressionTermMeta attribute), [1] expression_term_units (obj_tables.math.expression.ExpressionTermMeta attribute), [1] expression_term_value (obj_tables.math.expression.ExpressionStaticTermMeta attribute), [1] expression_type (obj_tables.math.expression.Expression.Meta attribute), [1] expression_unit_registry (obj_tables.math.expression.Expression.Meta attribute), [1] expression_valid_functions (obj_tables.math.expression.Expression.Meta attribute), [1] ExpressionDynamicTermMeta (class in obj_tables.math.expression) ExpressionExpressionTermMeta (class in obj_tables.math.expression) ExpressionStaticTermMeta (class in obj_tables.math.expression) ExpressionTermMeta (class in obj_tables.math.expression) extend() (obj_tables.core.RelatedManager method)

F

FeatureLocAttribute (class in obj_tables.bio.seq) file (obj_tables.chem.core.ReactionEquation attribute) final_schema_branch (obj_tables.migrate.MigrationSpec attribute) final_schema_git_metadata (obj_tables.migrate.MigrationSpec attribute) final_schema_hash (obj_tables.migrate.MigrationSpec attribute) final_schema_url (obj_tables.migrate.MigrationSpec attribute) find_file() (obj_tables.migrate.SchemaChanges static method) find_schema_modules() (obj_tables.migrate.Utils static method) fixtures_dir() (obj_tables.migrate.GitRepo method) flags (obj_tables.core.RegexAttribute attribute) FloatAttribute (class in obj_tables.core) format_doc_metadata() (in module obj_tables.io) FreqPosMatrixAttribute (class in obj_tables.bio.seq) from_builtin() (obj_tables.bio.seq.FeatureLocAttribute method) (obj_tables.bio.seq.FreqPosMatrixAttribute method) (obj_tables.bio.seq.SeqAttribute method) (obj_tables.chem.core.ChemicalFormulaAttribute method) (obj_tables.chem.core.ChemicalStructureAttribute method) (obj_tables.chem.core.ReactionEquationAttribute method) (obj_tables.core.Attribute method) (obj_tables.core.DateAttribute method) (obj_tables.core.DateTimeAttribute method) (obj_tables.core.EnumAttribute method) (obj_tables.core.IntegerAttribute method) (obj_tables.core.ListAttribute method) (obj_tables.core.LiteralAttribute method) (obj_tables.core.LocalPathAttribute method) (obj_tables.core.RangeAttribute method) (obj_tables.core.RelatedAttribute method) (obj_tables.core.TimeAttribute method) (obj_tables.math.numeric.ArrayAttribute method) (obj_tables.math.numeric.TableAttribute method) (obj_tables.math.symbolic.SymbolicBasicAttribute method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.refs.DoisAttribute method) (obj_tables.sci.refs.IdentifierAttribute method) (obj_tables.sci.refs.IdentifiersAttribute method) (obj_tables.sci.refs.PubMedIdsAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method)

from_dict() (obj_tables.chem.core.ChemicalStructure method) (obj_tables.core.Model static method) (obj_tables.sci.refs.Identifier method) from_str() (obj_tables.sci.refs.Identifier method) frozen_columns (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) full_migrate() (obj_tables.migrate.Migrator method) FUNC_PATTERN (obj_tables.math.expression.ParsedExpression attribute)

G

gbl() (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer method) gbl_part() (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer method) gbl_parts() (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer method) GC_PERIOD (obj_tables.core.Manager attribute) gen_merge_map() (obj_tables.core.Model method) gen_serialized_val_obj_map() (obj_tables.core.Model method) gen_transformer() (obj_tables.grammar.ToManyGrammarAttribute class method) generate_filename() (obj_tables.migrate.SchemaChanges method) generate_instance() (obj_tables.migrate.SchemaChanges static method) generate_migration_spec() (obj_tables.migrate.DataSchemaMigration method) GenTemplate (class in obj_tables.web_service) GenTemplateController (class in obj_tables.__main__) GenTemplateController.Meta (class in obj_tables.__main__) get() (obj_tables.core.Manager method) (obj_tables.core.RelatedManager method) get_all_related() (obj_tables.core.Model static method) get_attr_index() (obj_tables.core.Model class method) get_attr_order() (in module obj_tables.utils) get_attribute_by_name() (in module obj_tables.utils) get_attrs() (in module obj_tables.utils) (obj_tables.core.Model class method) get_attrs_by_val() (obj_tables.core.Model method) get_children() (obj_tables.core.Model method) get_cls_and_model() (obj_tables.math.expression.LinearParsedExpressionValidator method) get_commit() (obj_tables.migrate.GitRepo method) get_commits() (obj_tables.migrate.GitRepo method) get_component_by_id() (in module obj_tables.utils) get_data_file_git_commit_hash() (obj_tables.migrate.DataSchemaMigration method) get_date_timestamp() (obj_tables.migrate.SchemaChanges static method) get_default() (obj_tables.core.Attribute method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method) get_default_cleaned_value() (obj_tables.core.Attribute method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method) get_dependents() (obj_tables.migrate.GitRepo method) get_empty_literal_attrs() (obj_tables.core.Model method) get_empty_related_attrs() (obj_tables.core.Model method) get_fields() (in module obj_tables.io) get_hash() (obj_tables.migrate.GitRepo static method) (obj_tables.migrate.SchemaChanges method) get_immediate_children() (obj_tables.core.Model method) get_init_value() (obj_tables.core.Attribute method) (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.OneToManyAttribute method) get_literal_attrs() (obj_tables.core.Model class method) get_manager() (obj_tables.core.Model class method) get_metadata() (obj_tables.migrate.GitRepo method) get_migrations_config() (obj_tables.migrate.MigrationSpec static method) get_model() (in module obj_tables.core) (in module obj_tables.web_service) get_model_errors_by_model() (obj_tables.core.InvalidObjectSet method) get_model_sheet_name() (obj_tables.io.WorkbookReader class method) get_models() (in module obj_tables.core) (in module obj_tables.utils) get_name() (obj_tables.migrate.DataSchemaMigration method) get_name_static() (obj_tables.migrate.DataSchemaMigration static method) get_nested_attr() (obj_tables.core.Model class method) get_nested_attr_val() (obj_tables.core.Model method) get_non_empty_literal_attrs() (obj_tables.core.Model method) get_non_empty_related_attrs() (obj_tables.core.Model method) get_none_value() (obj_tables.core.Attribute method)

get_obj_units() (in module obj_tables.sci.units) get_object_errors_by_model() (obj_tables.core.InvalidObjectSet method) get_one() (obj_tables.core.Manager method) (obj_tables.core.RelatedManager method) get_or_create() (obj_tables.core.RelatedManager method) get_or_create_model_obj() (obj_tables.grammar.ToManyGrammarTransformer method) get_ordered_attributes() (in module obj_tables.io) get_path() (obj_tables.migrate.SchemaModule method) get_possible_model_sheet_names() (obj_tables.io.WorkbookReader class method) get_primary_attribute() (obj_tables.core.Model method) get_reader() (obj_tables.io.Reader static method) get_related() (obj_tables.core.Model method) get_related_attrs() (obj_tables.core.Model class method) get_related_default() (obj_tables.core.RelatedAttribute method) get_related_errors() (in module obj_tables.utils) get_related_init_value() (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.RelatedAttribute method) get_related_models() (in module obj_tables.utils) get_schema() (in module obj_tables.utils) get_schema_models() (in module obj_tables.__main__) get_schema_package() (obj_tables.migrate.DataSchemaMigration method) get_sort_key() (obj_tables.core.Model class method) get_source() (obj_tables.core.Model method) get_str() (obj_tables.math.expression.ParsedExpression method) get_temp_dir() (obj_tables.migrate.GitRepo method) get_url() (obj_tables.sci.refs.DoiAttribute static method) (obj_tables.sci.refs.Identifier method) (obj_tables.sci.refs.PubMedIdAttribute static method) get_writer() (obj_tables.io.Writer static method) get_xlsx_validation() (obj_tables.chem.core.ChemicalFormulaAttribute method) (obj_tables.chem.core.ChemicalStructureAttribute method) (obj_tables.chem.core.ReactionEquationAttribute method) (obj_tables.core.Attribute method) (obj_tables.core.BooleanAttribute method) (obj_tables.core.DateAttribute method) (obj_tables.core.DateTimeAttribute method) (obj_tables.core.EnumAttribute method) (obj_tables.core.FloatAttribute method) (obj_tables.core.IntegerAttribute method) (obj_tables.core.ListAttribute method) (obj_tables.core.LocalPathAttribute method) (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.core.PositiveFloatAttribute method) (obj_tables.core.PositiveIntegerAttribute method) (obj_tables.core.RangeAttribute method) (obj_tables.core.StringAttribute method) (obj_tables.core.TimeAttribute method) (obj_tables.math.expression.ManyToOneExpressionAttribute method) (obj_tables.math.expression.OneToOneExpressionAttribute method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.refs.DoisAttribute method) (obj_tables.sci.refs.IdentifierAttribute method) (obj_tables.sci.refs.IdentifiersAttribute method) (obj_tables.sci.refs.PubMedIdsAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method) git_hash_map (obj_tables.migrate.GitRepo attribute) git_repos (obj_tables.migrate.DataSchemaMigration attribute) GitRepo (class in obj_tables.migrate) grammar (obj_tables.grammar.ToManyGrammarAttribute attribute), [1] grammar_path (obj_tables.grammar.ToManyGrammarAttribute attribute) group_objects_by_model() (in module obj_tables.utils)

H

handlers (obj_tables.__main__.App.Meta attribute) has_attr_vals() (obj_tables.core.Model method) hash_prefix() (obj_tables.migrate.GitRepo static method) hash_prefix_from_sc_file() (obj_tables.migrate.SchemaChanges static method) head_commit() (obj_tables.migrate.GitRepo method) header_row_col_names() (obj_tables.io.WorkbookReader class method) help (obj_tables.__main__.BaseController.Meta attribute) (obj_tables.__main__.ConvertController.Meta attribute) (obj_tables.__main__.DiffController.Meta attribute) (obj_tables.__main__.GenTemplateController.Meta attribute) (obj_tables.__main__.InitSchemaController.Meta attribute) (obj_tables.__main__.NormalizeController.Meta attribute) (obj_tables.__main__.ValidateController.Meta attribute) (obj_tables.__main__.VizSchemaController.Meta attribute) (obj_tables.migrate.CementControllers.DataSchemaMigrationConfigController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateFileController.Meta attribute) (obj_tables.migrate.CementControllers.SchemaChangesTemplateController.Meta attribute)

I

id (obj_tables.sci.refs.Identifier attribute) Identifier (class in obj_tables.sci.refs) IdentifierAttribute (class in obj_tables.sci.refs) IdentifiersAttribute (class in obj_tables.sci.refs) IdMatch (class in obj_tables.math.expression) import_custom_IO_classes() (obj_tables.migrate.DataSchemaMigration method) import_migration_wrapper() (obj_tables.migrate.MigrationWrapper static method) import_module_for_migration() (obj_tables.migrate.SchemaModule method) in_package() (obj_tables.migrate.SchemaModule method) inchi (obj_tables.chem.core.ChemicalStructureFormat attribute) index() (obj_tables.core.RelatedManager method) indexed_attrs_tuples (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) inheritance (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) init_attribute_order() (obj_tables.core.ModelMeta method) init_attributes() (obj_tables.core.ModelMeta method) init_inheritance() (obj_tables.core.ModelMeta method) init_ordering() (obj_tables.core.ModelMeta method) init_primary_attribute() (obj_tables.core.ModelMeta method) init_related_attributes() (obj_tables.core.ModelMeta method) init_schema() (in module obj_tables.utils) init_value (obj_tables.core.Attribute attribute)

init_verbose_names() (obj_tables.core.ModelMeta method) InitSchema (class in obj_tables.web_service) InitSchemaController (class in obj_tables.__main__) InitSchemaController.Meta (class in obj_tables.__main__) insert_all_new() (obj_tables.core.Manager method) install_from_pip_spec() (obj_tables.migrate.VirtualEnvUtil method) IntegerAttribute (class in obj_tables.core) intersection_update() (obj_tables.core.RelatedManager method) invalid_models (obj_tables.core.InvalidObjectSet attribute) invalid_objects (obj_tables.core.InvalidObjectSet attribute) InvalidAttribute (class in obj_tables.core) InvalidModel (class in obj_tables.core) InvalidObject (class in obj_tables.core) InvalidObjectSet (class in obj_tables.core) io_classes (obj_tables.migrate.DataSchemaMigration attribute) (obj_tables.migrate.MigrationSpec attribute) (obj_tables.migrate.Migrator attribute) IoWarning is_equal() (obj_tables.chem.core.ReactionEquation method) (obj_tables.chem.core.ReactionParticipant method) (obj_tables.core.Model method) (obj_tables.core.Range method) is_installed() (obj_tables.migrate.VirtualEnvUtil method) is_linear (obj_tables.math.expression.LinearParsedExpressionValidator attribute) is_prepared() (obj_tables.migrate.MigrationSpec method) is_primary (obj_tables.core.LocalAttribute attribute) is_related (obj_tables.core.LocalAttribute attribute) is_related_to_many (obj_tables.core.LocalAttribute attribute) is_serializable() (obj_tables.core.Model class method)

J

join (obj_tables.core.ModelMerge attribute) join_separated_list() (in module obj_tables.core)

json (obj_tables.core.CellDialect attribute) JsonReader (class in obj_tables.io) JsonWriter (class in obj_tables.io)

L

label (obj_tables.__main__.App.Meta attribute) (obj_tables.__main__.BaseController.Meta attribute) (obj_tables.__main__.ConvertController.Meta attribute) (obj_tables.__main__.DiffController.Meta attribute) (obj_tables.__main__.GenTemplateController.Meta attribute) (obj_tables.__main__.InitSchemaController.Meta attribute) (obj_tables.__main__.NormalizeController.Meta attribute) (obj_tables.__main__.ValidateController.Meta attribute) (obj_tables.__main__.VizSchemaController.Meta attribute) (obj_tables.migrate.CementControllers.DataSchemaMigrationConfigController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateFileController.Meta attribute) (obj_tables.migrate.CementControllers.SchemaChangesTemplateController.Meta attribute) latest_hash() (obj_tables.migrate.GitRepo method) lcl() (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer method) lcl_part() (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer method) lcl_parts() (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer method) legal_token (obj_tables.math.expression.ParsedExpression attribute) legal_token_name (obj_tables.math.expression.ParsedExpression attribute) LEGAL_TOKENS (obj_tables.math.expression.ParsedExpression attribute) LEGAL_TOKENS_NAMES (obj_tables.math.expression.ParsedExpression attribute) LexMatch (class in obj_tables.math.expression) lin_coeffs (obj_tables.math.expression.ParsedExpression attribute)

LinearParsedExpressionValidator (class in obj_tables.math.expression) LinearParsedExpressionValidator.DistributeMult (class in obj_tables.math.expression) LinearParsedExpressionValidator.DistributeSub (class in obj_tables.math.expression) LinearParsedExpressionValidator.MoveCoeffsToLeft (class in obj_tables.math.expression) LinearParsedExpressionValidator.MultiplyNums (class in obj_tables.math.expression) LinearParsedExpressionValidator.RemoveUnaryOps (class in obj_tables.math.expression) link_model() (obj_tables.io.WorkbookReader method) ListAttribute (class in obj_tables.core) LiteralAttribute (class in obj_tables.core) load() (obj_tables.migrate.MigrationSpec class method) (obj_tables.migrate.SchemaChanges static method) load_config_file() (obj_tables.migrate.DataSchemaMigration static method) load_transformations() (obj_tables.migrate.SchemaChanges method) loaded_schema_changes (obj_tables.migrate.DataSchemaMigration attribute) local_attributes (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute) (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) LocalAttribute (class in obj_tables.core) LocalPathAttribute (class in obj_tables.core) location (obj_tables.core.InvalidAttribute attribute) LongStringAttribute (class in obj_tables.core)

M

main() (in module obj_tables.__main__) make_data_schema_migration_conf_file_cmd() (obj_tables.migrate.DataSchemaMigration static method) make_expression_obj() (obj_tables.math.expression.Expression static method) make_metadata_objects() (obj_tables.io.WriterBase method) make_migration_config_file() (obj_tables.migrate.DataSchemaMigration static method) make_obj() (obj_tables.math.expression.Expression class method) make_template() (obj_tables.migrate.SchemaChanges method) make_template_command() (obj_tables.migrate.SchemaChanges static method) Manager (class in obj_tables.core) ManyToManyAttribute (class in obj_tables.core) ManyToManyRelatedManager (class in obj_tables.core) ManyToOneAttribute (class in obj_tables.core) ManyToOneExpressionAttribute (class in obj_tables.math.expression) ManyToOneRelatedManager (class in obj_tables.core) match_string() (obj_tables.math.expression.IdMatch property) math_func_id (obj_tables.math.expression.ObjTablesTokenCodes attribute) max (obj_tables.core.FloatAttribute attribute) (obj_tables.core.IntegerAttribute attribute) max_length (obj_tables.bio.seq.SeqAttribute attribute) (obj_tables.core.StringAttribute attribute) (obj_tables.math.numeric.ArrayAttribute attribute) max_related (obj_tables.core.LocalAttribute attribute) (obj_tables.core.RelatedAttribute attribute) max_related_rev (obj_tables.core.LocalAttribute attribute) (obj_tables.core.RelatedAttribute attribute) mediatypes() (obj_tables.web_service.Convert method) (obj_tables.web_service.Diff method) (obj_tables.web_service.GenTemplate method) (obj_tables.web_service.InitSchema method) (obj_tables.web_service.Normalize method) (obj_tables.web_service.Validate method) (obj_tables.web_service.VizSchema method) merge (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) merge() (obj_tables.core.Attribute method) (obj_tables.core.FloatAttribute method) (obj_tables.core.LiteralAttribute method) (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.Model method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) merge_attrs() (obj_tables.core.Model method) (obj_tables.math.expression.Expression method) merge_doc_metadata() (obj_tables.io.WorkbookReader method) message (obj_tables.math.expression.ParsedExpressionError attribute) (obj_tables.migrate.MigratorError attribute) messages (obj_tables.core.InvalidAttribute attribute) methods (obj_tables.web_service.Convert attribute) (obj_tables.web_service.Diff attribute) (obj_tables.web_service.GenTemplate attribute) (obj_tables.web_service.InitSchema attribute) (obj_tables.web_service.Normalize attribute) (obj_tables.web_service.Validate attribute) (obj_tables.web_service.VizSchema attribute)

migrate() (obj_tables.migrate.Migrator method) migrate_files() (obj_tables.migrate.DataSchemaMigration static method) migrate_from_config() (obj_tables.migrate.MigrationController static method) migrate_from_spec() (obj_tables.migrate.MigrationController static method) migrate_in_place (obj_tables.migrate.MigrationSpec attribute) migrate_over_schema_sequence() (obj_tables.migrate.MigrationController static method) migrate_suffix (obj_tables.migrate.MigrationSpec attribute) MIGRATE_SUFFIX (obj_tables.migrate.Migrator attribute) MIGRATED_COPY_ATTR_PREFIX (obj_tables.migrate.Migrator attribute) migrated_defs (obj_tables.migrate.Migrator attribute) migrated_schema (obj_tables.migrate.Migrator attribute) MigrateWarning migration_config_data (obj_tables.migrate.DataSchemaMigration attribute) migration_specs (obj_tables.migrate.DataSchemaMigration attribute) MigrationController (class in obj_tables.migrate) migrations_config_file (obj_tables.migrate.MigrationSpec attribute) migrations_dir() (obj_tables.migrate.GitRepo method) MigrationSpec (class in obj_tables.migrate) MigrationWrapper (class in obj_tables.migrate) Migrator (class in obj_tables.migrate) MigratorError min (obj_tables.core.FloatAttribute attribute) (obj_tables.core.IntegerAttribute attribute) min_length (obj_tables.bio.seq.SeqAttribute attribute) (obj_tables.core.StringAttribute attribute) (obj_tables.math.numeric.ArrayAttribute attribute) min_related (obj_tables.core.LocalAttribute attribute) (obj_tables.core.RelatedAttribute attribute) min_related_rev (obj_tables.core.LocalAttribute attribute) (obj_tables.core.RelatedAttribute attribute) Model (class in obj_tables.core) model (obj_tables.core.InvalidModel attribute) model() (obj_tables.math.expression.ObjTablesToken property) Model.Meta (class in obj_tables.core) model_cls (obj_tables.math.expression.ParsedExpression attribute) model_id() (obj_tables.math.expression.ObjTablesToken property) MODEL_METADATA_PATTERN (obj_tables.io.WorkbookReader attribute) model_type() (obj_tables.math.expression.IdMatch property) (obj_tables.math.expression.ObjTablesToken property) MODEL_TYPE_DISAMBIG_PATTERN (obj_tables.math.expression.ParsedExpression attribute) ModelMerge (class in obj_tables.core) ModelMeta (class in obj_tables.core) MODELS (obj_tables.io.ReaderBase attribute), [1] (obj_tables.io.WriterBase attribute), [1] models_map (obj_tables.migrate.Migrator attribute) ModelSource (class in obj_tables.core) modify_migrated_models() (obj_tables.migrate.MigrationWrapper method) module_name (obj_tables.migrate.SchemaModule attribute) module_path (obj_tables.migrate.SchemaModule attribute) modules (obj_tables.migrate.Migrator attribute) MODULES (obj_tables.migrate.SchemaModule attribute) multiple_cells (obj_tables.core.TableFormat attribute) MultiSeparatedValuesReader (class in obj_tables.io) MultiSeparatedValuesWriter (class in obj_tables.io) MUNGED_MODEL_NAME_SUFFIX (obj_tables.migrate.SchemaModule attribute)

N

name (obj_tables.core.Attribute attribute) (obj_tables.core.LocalAttribute attribute) (obj_tables.migrate.MigrationSpec attribute) (obj_tables.migrate.VirtualEnvUtil attribute) namespace (obj_tables.sci.onto.OntoTermAttribute attribute) (obj_tables.sci.refs.Identifier attribute) nan (obj_tables.core.FloatAttribute attribute) next_id (obj_tables.math.expression.LinearParsedExpressionValidator attribute) none (obj_tables.chem.core.ReactionEquationAttribute attribute) (obj_tables.core.DateAttribute attribute) (obj_tables.core.DateTimeAttribute attribute) (obj_tables.core.EnumAttribute attribute) (obj_tables.core.IntegerAttribute attribute) (obj_tables.core.RegexAttribute attribute) (obj_tables.core.StringAttribute attribute) (obj_tables.core.TimeAttribute attribute) (obj_tables.sci.onto.OntoTermAttribute attribute) (obj_tables.sci.uncertainty.UncertainFloatAttribute attribute) (obj_tables.sci.units.QuantityAttribute attribute) (obj_tables.sci.units.UnitAttribute attribute)

none_value (obj_tables.core.Attribute attribute) Normalize (class in obj_tables.web_service) normalize() (obj_tables.core.Model method) normalize_attr_tuples() (obj_tables.core.ModelMeta method) normalize_tuple_of_tuples_of_attribute_names() (obj_tables.core.ModelMeta static method) NormalizeController (class in obj_tables.__main__) NormalizeController.Meta (class in obj_tables.__main__) num_ops_since_gc (obj_tables.core.Manager attribute) num_py_tokens() (obj_tables.math.expression.LexMatch property) number (obj_tables.math.expression.ObjTablesTokenCodes attribute) NumericAttribute (class in obj_tables.core)

O

obj_id (obj_tables.math.expression.ObjTablesTokenCodes attribute) obj_tables (module) obj_tables.__main__ (module) obj_tables._version (module) obj_tables.abstract (module) obj_tables.bio (module) obj_tables.bio.seq (module) obj_tables.chem (module) obj_tables.chem.core (module) obj_tables.core (module) obj_tables.grammar (module) obj_tables.io (module) obj_tables.math (module) obj_tables.math.expression (module) obj_tables.math.numeric (module) obj_tables.math.symbolic (module) obj_tables.migrate (module) obj_tables.sci (module) obj_tables.sci.onto (module) obj_tables.sci.refs (module) obj_tables.sci.uncertainty (module) obj_tables.sci.units (module) obj_tables.utils (module) obj_tables.web_service (module)

obj_tables_tokens() (obj_tables.math.expression.LexMatch property) object (obj_tables.core.InvalidObject attribute) (obj_tables.core.RelatedManager attribute) objects (obj_tables.abstract.AbstractModel attribute) (obj_tables.grammar.ToManyGrammarTransformer attribute) (obj_tables.utils.DataRepoMetadata attribute) (obj_tables.utils.RepoMetadata attribute) (obj_tables.utils.SchemaRepoMetadata attribute) ObjTablesToken (class in obj_tables.math.expression) ObjTablesTokenCodes (class in obj_tables.math.expression) ObjTablesWarning OneToManyAttribute (class in obj_tables.core) OneToManyRelatedManager (class in obj_tables.core) OneToOneAttribute (class in obj_tables.core) OneToOneExpressionAttribute (class in obj_tables.math.expression) ontology (obj_tables.sci.onto.OntoTermAttribute attribute) OntoTermAttribute (class in obj_tables.sci.onto) op (obj_tables.math.expression.ObjTablesTokenCodes attribute) opaque_ids (obj_tables.math.expression.LinearParsedExpressionValidator attribute) ordering (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) other (obj_tables.math.expression.ObjTablesTokenCodes attribute)

P

package_name (obj_tables.migrate.SchemaModule attribute) PandasWriter (class in obj_tables.io) parse_module_path() (obj_tables.migrate.SchemaModule static method) parse_worksheet_heading_metadata() (obj_tables.io.WorkbookReader class method) PARSED_EXPR (obj_tables.migrate.Migrator attribute) parsed_expression (obj_tables.math.expression.LinearParsedExpressionValidator attribute) ParsedExpression (class in obj_tables.math.expression) ParsedExpressionError parser (obj_tables.chem.core.ReactionEquation attribute) (obj_tables.grammar.ToManyGrammarAttribute attribute) path_name (obj_tables.core.ModelSource attribute) path_of_migrated_file() (obj_tables.migrate.Migrator static method) pattern (obj_tables.core.RegexAttribute attribute) PATTERN (obj_tables.sci.refs.DoisAttribute attribute) pformat() (obj_tables.core.Model method) pop() (obj_tables.core.RelatedManager method) PositiveFloatAttribute (class in obj_tables.core) PositiveIntegerAttribute (class in obj_tables.core) post() (obj_tables.web_service.Convert method) (obj_tables.web_service.Diff method) (obj_tables.web_service.GenTemplate method) (obj_tables.web_service.InitSchema method) (obj_tables.web_service.Normalize method) (obj_tables.web_service.Validate method) (obj_tables.web_service.VizSchema method)

pprint() (obj_tables.core.Model method) PrefixMiddleware (class in obj_tables.web_service) prepare() (obj_tables.migrate.DataSchemaMigration method) (obj_tables.migrate.MigrationSpec method) (obj_tables.migrate.Migrator method) prepare_existing_models() (obj_tables.migrate.MigrationWrapper method) primary (obj_tables.core.Attribute attribute) primary_attribute (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) primary_class (obj_tables.core.LocalAttribute attribute) (obj_tables.core.RelatedAttribute attribute) primary_name (obj_tables.core.LocalAttribute attribute) ProteinSeqAttribute (class in obj_tables.bio.seq) PubMedIdAttribute (class in obj_tables.sci.refs) PubMedIdsAttribute (class in obj_tables.sci.refs)

Q

QuantityAttribute (class in obj_tables.sci.units)

R

rand_schema_name() (in module obj_tables.utils) randomize_object_graph() (in module obj_tables.utils) Range (class in obj_tables.core) RangeAttribute (class in obj_tables.core) ReactionEquation (class in obj_tables.chem.core) ReactionEquation.ParseTreeTransformer (class in obj_tables.chem.core) ReactionEquationAttribute (class in obj_tables.chem.core) ReactionParticipant (class in obj_tables.chem.core) read_existing_file() (obj_tables.migrate.Migrator method) read_metadata_from_file() (in module obj_tables.utils) read_model() (obj_tables.io.WorkbookReader method) read_sheet() (obj_tables.io.WorkbookReader method) read_workbook() (in module obj_tables.web_service) read_worksheet_metadata() (obj_tables.io.WorkbookReader class method) Reader (class in obj_tables.io) ReaderBase (class in obj_tables.io) record_git_repo() (obj_tables.migrate.DataSchemaMigration method) recreate_whitespace() (obj_tables.math.expression.ParsedExpression method) RegexAttribute (class in obj_tables.core) registry (obj_tables.sci.units.QuantityAttribute attribute) (obj_tables.sci.units.UnitAttribute attribute) related (obj_tables.core.InvalidAttribute attribute) (obj_tables.core.RelatedManager attribute) related_attributes (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) related_class (obj_tables.core.LocalAttribute attribute) (obj_tables.core.RelatedAttribute attribute) related_default (obj_tables.core.RelatedAttribute attribute) related_init_value (obj_tables.core.RelatedAttribute attribute) related_manager (obj_tables.core.ManyToManyAttribute attribute) (obj_tables.core.ManyToOneAttribute attribute) (obj_tables.core.OneToManyAttribute attribute) related_name (obj_tables.core.LocalAttribute attribute) (obj_tables.core.RelatedAttribute attribute) related_objects (obj_tables.math.expression.ParsedExpression attribute) related_type (obj_tables.core.RelatedAttribute attribute)

related_validate() (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.core.RelatedAttribute method) RelatedAttribute (class in obj_tables.core) RelatedManager (class in obj_tables.core) remove() (obj_tables.core.ManyToManyRelatedManager method) (obj_tables.core.ManyToOneRelatedManager method) (obj_tables.core.OneToManyRelatedManager method) renamed_attributes (obj_tables.migrate.Migrator attribute) (obj_tables.migrate.SchemaChanges attribute) renamed_attributes_map (obj_tables.migrate.Migrator attribute) renamed_models (obj_tables.migrate.Migrator attribute) (obj_tables.migrate.SchemaChanges attribute) repo (obj_tables.migrate.GitRepo attribute) repo_dir (obj_tables.migrate.GitRepo attribute) repo_name() (obj_tables.migrate.GitRepo method) repo_url (obj_tables.migrate.GitRepo attribute) RepoMetadata (class in obj_tables.utils) RepoMetadata.Meta (class in obj_tables.utils) reset() (obj_tables.core.Manager method) revision (obj_tables.utils.RepoMetadata attribute) RnaSeqAttribute (class in obj_tables.bio.seq) row (obj_tables.core.ModelSource attribute) (obj_tables.core.TableFormat attribute) run() (obj_tables.core.Validator method) (obj_tables.io.JsonReader method) (obj_tables.io.JsonWriter method) (obj_tables.io.MultiSeparatedValuesReader method) (obj_tables.io.MultiSeparatedValuesWriter method) (obj_tables.io.PandasWriter method) (obj_tables.io.Reader method) (obj_tables.io.ReaderBase method) (obj_tables.io.WorkbookReader method) (obj_tables.io.WorkbookWriter method) (obj_tables.io.Writer method) (obj_tables.io.WriterBase method) (obj_tables.migrate.Migrator method) (obj_tables.migrate.SchemaModule method)

S

save_in_workbook() (in module obj_tables.web_service) save_out_workbook() (in module obj_tables.web_service) save_schema() (in module obj_tables.web_service) SCALAR_ATTRS (obj_tables.migrate.Migrator attribute) schema_changes_file (obj_tables.migrate.SchemaChanges attribute) schema_changes_for_data_file() (obj_tables.migrate.DataSchemaMigration method) schema_files (obj_tables.migrate.MigrationSpec attribute) schema_git_repo (obj_tables.migrate.DataSchemaMigration attribute) schema_repo (obj_tables.migrate.SchemaChanges attribute) schema_repo_metadata() (obj_tables.utils.DataFileMetadata property) SchemaChanges (class in obj_tables.migrate) SchemaModule (class in obj_tables.migrate) SchemaRepoMetadata (class in obj_tables.utils) SchemaRepoMetadata.Meta (class in obj_tables.utils) SchemaWarning secondary_class (obj_tables.core.LocalAttribute attribute) secondary_name (obj_tables.core.LocalAttribute attribute) separator (obj_tables.core.ListAttribute attribute) seq_of_renamed_attributes (obj_tables.migrate.MigrationSpec attribute) seq_of_renamed_models (obj_tables.migrate.MigrationSpec attribute) seq_of_transformations (obj_tables.migrate.MigrationSpec attribute) SeqAttribute (class in obj_tables.bio.seq) serialize() (obj_tables.bio.seq.FeatureLocAttribute method) (obj_tables.bio.seq.FreqPosMatrixAttribute method) (obj_tables.bio.seq.SeqAttribute method) (obj_tables.chem.core.ChemicalFormulaAttribute method) (obj_tables.chem.core.ChemicalStructure method) (obj_tables.chem.core.ChemicalStructureAttribute method) (obj_tables.chem.core.ReactionEquation method) (obj_tables.chem.core.ReactionEquationAttribute method) (obj_tables.chem.core.ReactionParticipant method) (obj_tables.core.Attribute method) (obj_tables.core.DateAttribute method) (obj_tables.core.DateTimeAttribute method) (obj_tables.core.EnumAttribute method) (obj_tables.core.FloatAttribute method) (obj_tables.core.IntegerAttribute method) (obj_tables.core.ListAttribute method) (obj_tables.core.LiteralAttribute method) (obj_tables.core.LocalPathAttribute method) (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.Model method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.core.RangeAttribute method) (obj_tables.core.RelatedAttribute method) (obj_tables.core.StringAttribute method) (obj_tables.core.TimeAttribute method) (obj_tables.grammar.ToManyGrammarAttribute method) (obj_tables.math.expression.Expression method) (obj_tables.math.expression.ManyToOneExpressionAttribute method) (obj_tables.math.expression.OneToOneExpressionAttribute method) (obj_tables.math.numeric.ArrayAttribute method) (obj_tables.math.numeric.TableAttribute method) (obj_tables.math.symbolic.SymbolicBasicAttribute method) (obj_tables.math.symbolic.SymbolicExprAttribute method) (obj_tables.math.symbolic.SymbolicSymbolAttribute method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.refs.DoisAttribute method) (obj_tables.sci.refs.IdentifierAttribute method) (obj_tables.sci.refs.IdentifiersAttribute method) (obj_tables.sci.refs.PubMedIdsAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method)

serialize_to_cell() (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.core.ToManyAttribute method) serialized_format() (obj_tables.chem.core.ChemicalStructure property) serialized_value() (obj_tables.chem.core.ChemicalStructure property) set_git_repo_metadata_from_path() (in module obj_tables.utils) set_location_and_value() (obj_tables.core.InvalidAttribute method) set_nested_attr_val() (obj_tables.core.Model method) set_related_value() (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.core.RelatedAttribute method) set_source() (obj_tables.core.Model method) set_value() (obj_tables.core.Attribute method) (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) sheet_name (obj_tables.core.ModelSource attribute) SlugAttribute (class in obj_tables.core) smiles (obj_tables.chem.core.ChemicalStructureFormat attribute) sort() (obj_tables.core.Model class method) source_report() (in module obj_tables.utils) species (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer attribute) (obj_tables.chem.core.ReactionParticipant attribute) species_cls (obj_tables.chem.core.ReactionEquationAttribute attribute) split_separated_list() (in module obj_tables.core) stacked_on (obj_tables.__main__.ConvertController.Meta attribute) (obj_tables.__main__.DiffController.Meta attribute) (obj_tables.__main__.GenTemplateController.Meta attribute) (obj_tables.__main__.InitSchemaController.Meta attribute) (obj_tables.__main__.NormalizeController.Meta attribute) (obj_tables.__main__.ValidateController.Meta attribute) (obj_tables.__main__.VizSchemaController.Meta attribute) (obj_tables.migrate.CementControllers.DataSchemaMigrationConfigController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateFileController.Meta attribute) (obj_tables.migrate.CementControllers.SchemaChangesTemplateController.Meta attribute) stacked_type (obj_tables.__main__.ConvertController.Meta attribute) (obj_tables.__main__.DiffController.Meta attribute) (obj_tables.__main__.GenTemplateController.Meta attribute) (obj_tables.__main__.InitSchemaController.Meta attribute) (obj_tables.__main__.NormalizeController.Meta attribute) (obj_tables.__main__.ValidateController.Meta attribute) (obj_tables.__main__.VizSchemaController.Meta attribute) (obj_tables.migrate.CementControllers.DataSchemaMigrationConfigController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateController.Meta attribute) (obj_tables.migrate.CementControllers.MigrateFileController.Meta attribute) (obj_tables.migrate.CementControllers.SchemaChangesTemplateController.Meta attribute) standardize() (obj_tables.migrate.MigrationSpec method) start() (obj_tables.chem.core.ReactionEquation.ParseTreeTransformer method) (obj_tables.grammar.ToManyGrammarTransformer method) stoichiometry (obj_tables.chem.core.ReactionParticipant attribute) StringAttribute (class in obj_tables.core) SymbolicBasicAttribute (class in obj_tables.math.symbolic) SymbolicExprAttribute (class in obj_tables.math.symbolic) SymbolicSymbolAttribute (class in obj_tables.math.symbolic) symmetric_difference_update() (obj_tables.core.RelatedManager method) sympy_type (obj_tables.math.symbolic.SymbolicBasicAttribute attribute)

T

table_format (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) table_id (obj_tables.core.ModelSource attribute) TableAttribute (class in obj_tables.math.numeric) TableFormat (class in obj_tables.core) temp_dirs (obj_tables.migrate.GitRepo attribute) terms (obj_tables.sci.onto.OntoTermAttribute attribute) test_eval() (obj_tables.math.expression.ParsedExpression method) test_migration() (obj_tables.migrate.DataSchemaMigration method) TimeAttribute (class in obj_tables.core) to_builtin() (obj_tables.bio.seq.FeatureLocAttribute method) (obj_tables.bio.seq.FreqPosMatrixAttribute method) (obj_tables.bio.seq.SeqAttribute method) (obj_tables.chem.core.ChemicalFormulaAttribute method) (obj_tables.chem.core.ChemicalStructureAttribute method) (obj_tables.chem.core.ReactionEquationAttribute method) (obj_tables.core.Attribute method) (obj_tables.core.DateAttribute method) (obj_tables.core.DateTimeAttribute method) (obj_tables.core.EnumAttribute method) (obj_tables.core.IntegerAttribute method) (obj_tables.core.ListAttribute method) (obj_tables.core.LiteralAttribute method) (obj_tables.core.LocalPathAttribute method) (obj_tables.core.RangeAttribute method) (obj_tables.core.RelatedAttribute method) (obj_tables.core.TimeAttribute method) (obj_tables.math.numeric.ArrayAttribute method) (obj_tables.math.numeric.TableAttribute method) (obj_tables.math.symbolic.SymbolicBasicAttribute method) (obj_tables.math.symbolic.SymbolicExprAttribute method) (obj_tables.math.symbolic.SymbolicSymbolAttribute method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.refs.DoisAttribute method) (obj_tables.sci.refs.IdentifierAttribute method) (obj_tables.sci.refs.IdentifiersAttribute method) (obj_tables.sci.refs.PubMedIdsAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method)

to_dict() (obj_tables.chem.core.ChemicalStructure method) (obj_tables.chem.core.ReactionEquation method) (obj_tables.chem.core.ReactionParticipant method) (obj_tables.core.Model static method) (obj_tables.sci.refs.Identifier method) to_pandas() (in module obj_tables.utils) to_str() (obj_tables.sci.refs.Identifier method) token_pattern() (obj_tables.math.expression.IdMatch property) token_string() (obj_tables.math.expression.ObjTablesToken property) tokenize() (obj_tables.math.expression.ParsedExpression method) ToManyAttribute (class in obj_tables.core) ToManyGrammarAttribute (class in obj_tables.grammar) ToManyGrammarTransformer (class in obj_tables.grammar) transformations (obj_tables.migrate.Migrator attribute) (obj_tables.migrate.SchemaChanges attribute) transformations_file (obj_tables.migrate.SchemaChanges attribute) Transformer (obj_tables.grammar.ToManyGrammarAttribute attribute) tree (obj_tables.math.expression.LinearParsedExpressionValidator attribute) tsv (obj_tables.core.CellDialect attribute) type (obj_tables.core.Attribute attribute) (obj_tables.core.ListAttribute attribute) (obj_tables.core.LocalAttribute attribute) (obj_tables.core.RangeAttribute attribute)

U

UncertainFloatAttribute (class in obj_tables.sci.uncertainty) unique (obj_tables.core.Attribute attribute) unique_case_insensitive (obj_tables.core.Attribute attribute) unique_together (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute)

unit_registry (obj_tables.math.expression.ParsedExpression attribute) UnitAttribute (class in obj_tables.sci.units) update() (obj_tables.core.RelatedManager method) upsert() (obj_tables.core.Manager method) upsert_all() (obj_tables.core.Manager method) url (obj_tables.utils.RepoMetadata attribute) UrlAttribute (class in obj_tables.core) Utils (class in obj_tables.migrate)

V

valid_functions (obj_tables.math.expression.ParsedExpression attribute) VALID_NOTE_TYPES (obj_tables.math.expression.LinearParsedExpressionValidator attribute) VALID_PYTHON_ID_PREFIX (obj_tables.math.expression.LinearParsedExpressionValidator attribute) Validate (class in obj_tables.web_service) validate() (obj_tables.bio.seq.FeatureLocAttribute method) (obj_tables.bio.seq.FreqPosMatrixAttribute method) (obj_tables.bio.seq.SeqAttribute method) (obj_tables.chem.core.ChemicalFormulaAttribute method) (obj_tables.chem.core.ChemicalStructureAttribute method) (obj_tables.chem.core.ReactionEquationAttribute method) (obj_tables.core.Attribute method) (obj_tables.core.BooleanAttribute method) (obj_tables.core.DateAttribute method) (obj_tables.core.DateTimeAttribute method) (obj_tables.core.EmailAttribute method) (obj_tables.core.EnumAttribute method) (obj_tables.core.FloatAttribute method) (obj_tables.core.IntegerAttribute method) (obj_tables.core.ListAttribute method) (obj_tables.core.LiteralAttribute method) (obj_tables.core.LocalPathAttribute method) (obj_tables.core.ManyToManyAttribute method) (obj_tables.core.ManyToOneAttribute method) (obj_tables.core.Model method) (obj_tables.core.OneToManyAttribute method) (obj_tables.core.OneToOneAttribute method) (obj_tables.core.PositiveFloatAttribute method) (obj_tables.core.PositiveIntegerAttribute method) (obj_tables.core.RangeAttribute method) (obj_tables.core.RegexAttribute method) (obj_tables.core.StringAttribute method) (obj_tables.core.TimeAttribute method) (obj_tables.core.UrlAttribute method) (obj_tables.core.Validator method) (obj_tables.math.expression.Expression class method) (obj_tables.math.expression.LinearParsedExpressionValidator method) (obj_tables.math.numeric.ArrayAttribute method) (obj_tables.math.numeric.TableAttribute method) (obj_tables.math.symbolic.SymbolicBasicAttribute method) (obj_tables.migrate.DataSchemaMigration method) (obj_tables.migrate.MigrationSpec method) (obj_tables.migrate.SchemaChanges static method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.refs.DoisAttribute method) (obj_tables.sci.refs.IdentifierAttribute method) (obj_tables.sci.refs.IdentifiersAttribute method) (obj_tables.sci.refs.PubMedIdsAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method) validate_attr_tuples() (obj_tables.core.ModelMeta class method)

validate_attribute_inheritance() (obj_tables.core.ModelMeta class method) validate_attributes() (obj_tables.core.ModelMeta class method) validate_meta() (obj_tables.core.ModelMeta class method) validate_primary_attribute() (obj_tables.core.ModelMeta class method) validate_related_attributes() (obj_tables.core.Model class method) (obj_tables.core.ModelMeta class method) validate_unique() (obj_tables.bio.seq.FeatureLocAttribute method) (obj_tables.bio.seq.SeqAttribute method) (obj_tables.chem.core.ChemicalFormulaAttribute method) (obj_tables.chem.core.ChemicalStructureAttribute method) (obj_tables.chem.core.ReactionEquationAttribute method) (obj_tables.core.Attribute method) (obj_tables.core.Model class method) (obj_tables.math.numeric.ArrayAttribute method) (obj_tables.math.numeric.TableAttribute method) (obj_tables.math.symbolic.SymbolicBasicAttribute method) ValidateController (class in obj_tables.__main__) ValidateController.Meta (class in obj_tables.__main__) Validator (class in obj_tables.core) value (obj_tables.core.InvalidAttribute attribute) value() (obj_tables.chem.core.ChemicalStructure property) value_equal() (obj_tables.core.Attribute method) (obj_tables.core.FloatAttribute method) (obj_tables.core.RangeAttribute method) (obj_tables.sci.onto.OntoTermAttribute method) (obj_tables.sci.uncertainty.UncertainFloatAttribute method) (obj_tables.sci.units.QuantityAttribute method) (obj_tables.sci.units.UnitAttribute method) verbose_name (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Attribute attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) verbose_name_plural (obj_tables.abstract.AbstractModel.Meta attribute) (obj_tables.core.Model.Meta attribute), [1] (obj_tables.utils.DataRepoMetadata.Meta attribute) (obj_tables.utils.RepoMetadata.Meta attribute) (obj_tables.utils.SchemaRepoMetadata.Meta attribute) verbose_related_name (obj_tables.core.RelatedAttribute attribute) verify_schemas() (obj_tables.migrate.DataSchemaMigration method) VirtualEnvUtil (class in obj_tables.migrate) visit_BinOp() (obj_tables.math.expression.LinearParsedExpressionValidator.DistributeMult method) (obj_tables.math.expression.LinearParsedExpressionValidator.DistributeSub method) (obj_tables.math.expression.LinearParsedExpressionValidator.MoveCoeffsToLeft method) (obj_tables.math.expression.LinearParsedExpressionValidator.MultiplyNums method) visit_UnaryOp() (obj_tables.math.expression.LinearParsedExpressionValidator.RemoveUnaryOps method) viz_schema() (in module obj_tables.utils) VizSchema (class in obj_tables.web_service) VizSchemaController (class in obj_tables.__main__) VizSchemaController.Meta (class in obj_tables.__main__)

W

WorkbookReader (class in obj_tables.io) WorkbookWriter (class in obj_tables.io) write_migrated_file() (obj_tables.migrate.Migrator method) write_model() (obj_tables.io.WorkbookWriter method) write_schema() (obj_tables.io.WorkbookWriter method)

write_sheet() (obj_tables.io.PandasWriter method) (obj_tables.io.WorkbookWriter method) write_toc() (obj_tables.io.WorkbookWriter method) Writer (class in obj_tables.io) WriterBase (class in obj_tables.io)

X

xlsx_col_name() (in module obj_tables.core)