Index

A

add_constraint() (intermine.query.Query method) add_join() (intermine.query.Query method) add_path_description() (intermine.query.Query method) add_sort_order() (intermine.query.Query method) add_tags() (intermine.lists.list.List method) (intermine.lists.listmanager.ListManager method) add_view() (intermine.query.Query method)

append() (intermine.lists.list.List method) (intermine.model.Path method) (intermine.pathfeatures.SortOrderList method) as_logic() (intermine.model.CodelessNode method) (intermine.model.ConstraintNode method) (intermine.model.ConstraintTree method) ASC (intermine.pathfeatures.SortOrder attribute) Attribute (class in intermine.model) attributes (intermine.model.Class attribute)

B

BinaryConstraint (class in intermine.constraints)

C

calculate_enrichment() (intermine.lists.list.List method) check_return_status() (intermine.results.JSONIterator method) check_syntax() (intermine.constraints.LogicParser method) child_type (intermine.constraints.Constraint attribute) (intermine.pathfeatures.Join attribute) (intermine.pathfeatures.PathDescription attribute) (intermine.pathfeatures.PathFeature attribute) children() (intermine.query.Query method) Class (class in intermine.model) clear() (intermine.pathfeatures.SortOrderList method) clear_view() (intermine.query.Query method) clone() (intermine.query.Query method) (intermine.results.InterMineURLOpener method) coded_constraints (intermine.query.Query attribute) CodedConstraint (class in intermine.constraints) CodelessNode (class in intermine.model) Collection (class in intermine.model) collections (intermine.model.Class attribute)

Column (class in intermine.model) column() (intermine.model.Model method) (intermine.query.Query method) ComposedClass (class in intermine.model) Constraint (class in intermine.constraints) CONSTRAINT_CLASSES (intermine.constraints.ConstraintFactory attribute) (intermine.constraints.TemplateConstraintFactory attribute) ConstraintError ConstraintFactory (class in intermine.constraints) ConstraintNode (class in intermine.model) constraints (intermine.query.Query attribute) ConstraintTree (class in intermine.model) count (intermine.lists.list.List attribute) count() (intermine.query.Query method) (intermine.query.Template method) create_list() (intermine.lists.listmanager.ListManager method)

D

date_created (intermine.lists.list.List attribute) decode_binary() (in module intermine.results) DEFAULT_DESCRIPTION (intermine.lists.listmanager.ListManager attribute) DEFAULT_LIST_NAME (intermine.lists.listmanager.ListManager attribute) del_name() (intermine.lists.list.List method) delete() (intermine.idresolution.Job method) (intermine.lists.list.List method) (intermine.results.InterMineURLOpener method) delete_lists() (intermine.lists.listmanager.ListManager method)

delete_temporary_lists() (intermine.lists.listmanager.ListManager method) deregister() (intermine.webservice.Service method) DESC (intermine.pathfeatures.SortOrder attribute) description (intermine.lists.list.List attribute) DIFFERENCE_PATH (intermine.lists.listmanager.ListManager attribute) DIRECTIONS (intermine.pathfeatures.SortOrder attribute)

E

editable_constraints (intermine.query.Template attribute) EmptyLogicError encode_dict() (in module intermine.results) encode_headers() (in module intermine.results) encode_str() (in module intermine.results)

end (intermine.model.Path attribute) end_class (intermine.model.Path attribute) EnrichmentLine (class in intermine.results) ensure_str() (in module intermine.webservice)

F

fetch_results() (intermine.idresolution.Job method) fetch_status() (intermine.idresolution.Job method) Field (class in intermine.model) field_dict (intermine.model.ComposedClass attribute) fields (intermine.model.Class attribute)

fieldtype (intermine.model.Attribute attribute) (intermine.model.Collection attribute) (intermine.model.Field attribute) (intermine.model.Reference attribute) first() (intermine.query.Query method) FlatFileIterator (class in intermine.results) flush() (intermine.webservice.Service method) from_xml() (intermine.query.Query class method)

G

get_adjusted_template() (intermine.query.Template method) get_all_list_names() (intermine.lists.listmanager.ListManager method) get_all_lists() (intermine.lists.listmanager.ListManager method) get_class() (intermine.model.Model method) (intermine.model.Path method) get_codes() (intermine.constraints.CodedConstraint method) (intermine.constraints.LogicGroup method) get_constraint() (intermine.constraints.LogicParser method) (intermine.query.Query method) get_default_sort_order() (intermine.query.Query method) get_deregistration_token() (intermine.webservice.Service method) get_field() (intermine.model.Class method) get_json() (in module intermine.idresolution) get_list() (intermine.lists.listmanager.ListManager method) get_list_append_uri() (intermine.query.Query method) get_list_count() (intermine.lists.listmanager.ListManager method) get_list_upload_uri() (intermine.query.Query method) get_logic() (intermine.query.Query method) get_name() (intermine.lists.list.List method)

get_next_code() (intermine.constraints.ConstraintFactory method) get_next_row_from_connection() (intermine.results.JSONIterator method) get_priority() (intermine.constraints.LogicParser method) get_results() (intermine.webservice.Service method) get_results_list() (intermine.query.Query method) (intermine.query.Template method) get_results_path() (intermine.query.Query method) (intermine.query.Template method) get_row_list() (intermine.query.Query method) (intermine.query.Template method) get_sort_order() (intermine.query.Query method) get_subclass_dict() (intermine.query.Query method) get_switchable_status() (intermine.constraints.TemplateConstraint method) get_tags() (intermine.lists.listmanager.ListManager method) get_template() (intermine.webservice.Service method) get_unused_list_name() (intermine.lists.listmanager.ListManager method) getData() (in module intermine.registry) getInfo() (in module intermine.registry) getMines() (in module intermine.registry)

H

has_id (intermine.model.ComposedClass attribute) has_key() (intermine.results.ResultRow method) headers() (intermine.results.InterMineURLOpener method) http_error_400() (intermine.results.InterMineURLOpener method) http_error_401() (intermine.results.InterMineURLOpener method)

http_error_403() (intermine.results.InterMineURLOpener method) http_error_404() (intermine.results.InterMineURLOpener method) http_error_500() (intermine.results.InterMineURLOpener method) http_error_default() (intermine.results.InterMineURLOpener method)

I

id (intermine.results.ResultObject attribute) IDS_PATH (intermine.webservice.Service attribute) in_() (intermine.model.Column method) infix_to_postfix() (intermine.constraints.LogicParser method) INITIAL_BACKOFF (intermine.idresolution.Job attribute) INITIAL_DECAY (intermine.idresolution.Job attribute) INNER (intermine.pathfeatures.Join attribute) intermine (module) intermine.constraints (module) intermine.decorators (module) intermine.errors (module) intermine.idresolution (module) intermine.lists (module) intermine.lists.list (module) intermine.lists.listmanager (module) intermine.model (module) intermine.pathfeatures (module) intermine.query (module)

intermine.registry (module) intermine.results (module) intermine.util (module) intermine.webservice (module) InterMineURLOpener (class in intermine.results) intersect() (intermine.lists.listmanager.ListManager method) INTERSECTION_PATH (intermine.lists.listmanager.ListManager attribute) is_attribute() (intermine.model.Path method) is_authorized (intermine.lists.list.List attribute) is_class() (intermine.model.Path method) is_empty() (intermine.pathfeatures.SortOrderList method) is_reference() (intermine.model.Path method) isa() (intermine.model.Class method) IsaConstraint (class in intermine.constraints) items() (intermine.results.ResultRow method) iteritems() (intermine.results.ResultRow method) iterkeys() (intermine.results.ResultRow method) itervalues() (intermine.results.ResultRow method)

J

Job (class in intermine.idresolution) Join (class in intermine.pathfeatures) JSON (intermine.results.InterMineURLOpener attribute)

JSON_FORMATS (intermine.results.ResultIterator attribute) JSONIterator (class in intermine.results)

K

keys() (intermine.results.ResultRow method) (intermine.webservice.Registry method)

L

l() (intermine.lists.listmanager.ListManager method) LEADING_OP_PATTERN (intermine.query.Query attribute) LEGAL_OPS (intermine.constraints.LogicGroup attribute) List (class in intermine.lists.list) LIST_APPENDING_PATH (intermine.webservice.Service attribute) LIST_CREATION_PATH (intermine.webservice.Service attribute) LIST_ENRICHMENT_PATH (intermine.webservice.Service attribute) list_manager() (intermine.webservice.Service method) LIST_MANAGER_METHODS (intermine.webservice.Service attribute) LIST_PATH (intermine.webservice.Service attribute) LIST_RENAME_PATH (intermine.webservice.Service attribute) LIST_TAG_PATH (intermine.webservice.Service attribute)

list_type (intermine.lists.list.List attribute) ListConstraint (class in intermine.constraints) ListManager (class in intermine.lists.listmanager) ListServiceError load_query() (intermine.webservice.Service method) LOG (intermine.lists.list.List attribute) (intermine.lists.listmanager.ListManager attribute) (intermine.model.Model attribute) (intermine.results.JSONIterator attribute) LOGIC_SPLIT_PATTERN (intermine.query.Query attribute) LogicGroup (class in intermine.constraints) LogicNode (class in intermine.constraints) LogicParseError LogicParser (class in intermine.constraints) LoopConstraint (class in intermine.constraints)

M

make_constraint() (intermine.constraints.ConstraintFactory method) make_list_constraint() (intermine.lists.list.List method) (intermine.query.Query method) make_list_names() (intermine.lists.listmanager.ListManager method) make_path() (intermine.model.Model method) MAX_BACKOFF (intermine.idresolution.Job attribute) MINES_PATH (intermine.webservice.Registry attribute)

Model (class in intermine.model) model (intermine.webservice.Service attribute) MODEL_PATH (intermine.webservice.Service attribute) ModelError ModelParseError MultiConstraint (class in intermine.constraints)

N

name (intermine.lists.list.List attribute) (intermine.model.ComposedClass attribute) new_query() (intermine.webservice.Service method)

next() (intermine.pathfeatures.SortOrderList method) (intermine.results.FlatFileIterator method) (intermine.results.JSONIterator method) (intermine.results.ResultIterator method) NUMERIC_TYPES (intermine.model.Model attribute)

O

one() (intermine.query.Query method) open() (intermine.results.InterMineURLOpener method) openAnything() (in module intermine.util) OPS (intermine.constraints.BinaryConstraint attribute) (intermine.constraints.CodedConstraint attribute) (intermine.constraints.IsaConstraint attribute) (intermine.constraints.ListConstraint attribute) ops (intermine.constraints.LogicParser attribute) OPS (intermine.constraints.LoopConstraint attribute) (intermine.constraints.MultiConstraint attribute) (intermine.constraints.RangeConstraint attribute) (intermine.constraints.TernaryConstraint attribute) (intermine.constraints.UnaryConstraint attribute)

OPTIONAL_OFF (intermine.constraints.TemplateConstraint attribute) OPTIONAL_ON (intermine.constraints.TemplateConstraint attribute) ORPHANED_OP_PATTERN (intermine.query.Query attribute) OUTER (intermine.pathfeatures.Join attribute) outerjoin() (intermine.query.Query method)

P

parent_classes (intermine.model.ComposedClass attribute) parents (intermine.model.ComposedClass attribute) parse() (intermine.constraints.LogicParser method) parse_header() (intermine.results.JSONIterator method) parse_list_upload_response() (intermine.lists.listmanager.ListManager method) parse_model() (intermine.model.Model method) parse_path_string() (intermine.model.Model method) PARSED_FORMATS (intermine.results.ResultIterator attribute) Path (class in intermine.model) PathDescription (class in intermine.pathfeatures)

PathFeature (class in intermine.pathfeatures) PathParseError PLAIN_TEXT (intermine.results.InterMineURLOpener attribute) poll() (intermine.idresolution.Job method) post_content() (intermine.results.InterMineURLOpener method) post_plain_text() (intermine.results.InterMineURLOpener method) postfix_to_tree() (intermine.constraints.LogicParser method) prefix() (intermine.model.Path method) prefix_path() (intermine.query.Query method) prepare_url() (intermine.results.InterMineURLOpener method)

Q

Query (class in intermine.query) QUERY_LIST_APPEND_PATH (intermine.webservice.Service attribute) QUERY_LIST_UPLOAD_PATH (intermine.webservice.Service attribute)

QUERY_PATH (intermine.webservice.Service attribute) QueryError QueryParseError

R

RangeConstraint (class in intermine.constraints) read() (intermine.results.InterMineURLOpener method) ReadableException Reference (class in intermine.model) references (intermine.model.Class attribute) refresh_lists() (intermine.lists.listmanager.ListManager method) register() (intermine.webservice.Service method) Registry (class in intermine.webservice) release (intermine.webservice.Service attribute) RELEASE_PATH (intermine.webservice.Service attribute) remove_tags() (intermine.lists.list.List method) (intermine.lists.listmanager.ListManager method) REQUIRED (intermine.constraints.TemplateConstraint attribute)

required (intermine.constraints.TemplateConstraint attribute) requires_version() (in module intermine.decorators) resolve_ids() (intermine.webservice.Service method) resolve_service_path() (intermine.webservice.Service method) ResultError ResultIterator (class in intermine.results) ResultObject (class in intermine.results) ResultRow (class in intermine.results) results() (intermine.query.Query method) (intermine.query.Template method) root (intermine.model.Path attribute) ROW_FORMATS (intermine.results.ResultIterator attribute) rows() (intermine.query.Query method) (intermine.query.Template method)

S

safe_dict() (intermine.lists.listmanager.ListManager static method) safe_key() (in module intermine.lists.listmanager) SAVEDQUERY_PATH (intermine.webservice.Service attribute) SCHEME (intermine.webservice.Service attribute) search() (intermine.webservice.Service method) SEARCH_PATH (intermine.webservice.Service attribute) select() (intermine.model.Column method) (intermine.query.Query method) (intermine.webservice.Service method) separate_arg_sets() (intermine.constraints.TemplateConstraint method) SERIALISED_OPS (intermine.constraints.LoopConstraint attribute) Service (class in intermine.webservice) SERVICE_RESOLUTION_PATH (intermine.webservice.Service attribute) ServiceError set_logic() (intermine.query.Query method) set_name() (intermine.lists.list.List method)

size (intermine.lists.list.List attribute) SO_SPLIT_PATTERN (intermine.query.Query attribute) SortOrder (class in intermine.pathfeatures) SortOrderList (class in intermine.pathfeatures) status (intermine.lists.list.List attribute) STRING_FORMATS (intermine.results.ResultIterator attribute) SubClassConstraint (class in intermine.constraints) subtract() (intermine.lists.listmanager.ListManager method) SUBTRACTION_PATH (intermine.lists.listmanager.ListManager attribute) summarise() (intermine.query.Query method) switch_off() (intermine.constraints.TemplateConstraint method) switch_on() (intermine.constraints.TemplateConstraint method) switched_off (intermine.constraints.TemplateConstraint attribute)

T

TableResultRow (class in intermine.results) tags (intermine.lists.list.List attribute) Template (class in intermine.query) TemplateBinaryConstraint (class in intermine.constraints) TemplateConstraint (class in intermine.constraints) TemplateConstraintFactory (class in intermine.constraints) TemplateIsaConstraint (class in intermine.constraints) TemplateListConstraint (class in intermine.constraints) TemplateLoopConstraint (class in intermine.constraints) TemplateMultiConstraint (class in intermine.constraints) TEMPLATEQUERY_PATH (intermine.webservice.Service attribute) TemplateRangeConstraint (class in intermine.constraints) templates (intermine.webservice.Service attribute) TEMPLATES_PATH (intermine.webservice.Service attribute) TemplateSubClassConstraint (class in intermine.constraints) TemplateTernaryConstraint (class in intermine.constraints)

TemplateUnaryConstraint (class in intermine.constraints) TernaryConstraint (class in intermine.constraints) title (intermine.lists.list.List attribute) to_ancestry() (intermine.model.Model method) to_classes() (intermine.model.Model method) to_d() (intermine.results.ResultRow method) to_dict() (intermine.constraints.BinaryConstraint method) (intermine.constraints.CodedConstraint method) (intermine.constraints.ListConstraint method) (intermine.constraints.LoopConstraint method) (intermine.constraints.MultiConstraint method) (intermine.constraints.SubClassConstraint method) (intermine.constraints.TernaryConstraint method) (intermine.pathfeatures.Join method) (intermine.pathfeatures.PathDescription method) (intermine.pathfeatures.PathFeature method) to_formatted_xml() (intermine.query.Query method) to_l() (intermine.results.ResultRow method) (intermine.results.TableResultRow method) to_Node() (intermine.query.Query method) to_query() (intermine.lists.list.List method) (intermine.query.Query method) to_query_params() (intermine.query.Query method) (intermine.query.Template method) to_string() (intermine.constraints.BinaryConstraint method) (intermine.constraints.CodedConstraint method) (intermine.constraints.ListConstraint method) (intermine.constraints.LoopConstraint method) (intermine.constraints.MultiConstraint method) (intermine.constraints.SubClassConstraint method) (intermine.constraints.TemplateBinaryConstraint method) (intermine.constraints.TemplateConstraint method) (intermine.constraints.TemplateIsaConstraint method) (intermine.constraints.TemplateListConstraint method) (intermine.constraints.TemplateLoopConstraint method) (intermine.constraints.TemplateMultiConstraint method) (intermine.constraints.TemplateRangeConstraint method) (intermine.constraints.TemplateSubClassConstraint method) (intermine.constraints.TemplateTernaryConstraint method) (intermine.constraints.TemplateUnaryConstraint method) (intermine.constraints.TernaryConstraint method) (intermine.pathfeatures.PathFeature method) (intermine.pathfeatures.SortOrder method) to_xml() (intermine.query.Query method) TRAILING_OP_PATTERN (intermine.query.Query attribute)

U

UnaryConstraint (class in intermine.constraints) UnimplementedError union() (intermine.lists.listmanager.ListManager method) UNION_PATH (intermine.lists.listmanager.ListManager attribute)

update_tags() (intermine.lists.list.List method) USER_AGENT (intermine.results.InterMineURLOpener attribute) USERS_PATH (intermine.webservice.Service attribute)

V

valid_join_styles (intermine.pathfeatures.Join attribute) validate_logic() (intermine.query.Query method) validate_path() (intermine.model.Model method) validate_sort_order() (intermine.query.Query method) values() (intermine.results.ResultRow method) verify() (intermine.query.Query method) verify_constraint_paths() (intermine.query.Query method)

verify_join_paths() (intermine.query.Query method) verify_pd_paths() (intermine.query.Query method) verify_views() (intermine.query.Query method) version (intermine.webservice.Service attribute) VERSION_PATH (intermine.webservice.Service attribute) vivify() (intermine.model.Model method)

W

WebserviceError where() (intermine.model.Column method) (intermine.query.Query method)

widgets (intermine.webservice.Service attribute) WIDGETS_PATH (intermine.webservice.Service attribute)

X

xor() (intermine.lists.listmanager.ListManager method)