Index

_

__init__() (crate_anon.anonymise.altermethod.AlterMethod method) (crate_anon.anonymise.config.Config method) (crate_anon.anonymise.config.DatabaseSafeConfig method) (crate_anon.anonymise.dbholder.DatabaseHolder method) (crate_anon.anonymise.dd.DataDictionary method) (crate_anon.anonymise.ddr.DataDictionaryRow method) (crate_anon.anonymise.fetch_wordlists.NameInfo method) (crate_anon.anonymise.fetch_wordlists.UsForenameInfo method) (crate_anon.anonymise.fetch_wordlists.UsSurname1990Info method) (crate_anon.anonymise.fetch_wordlists.UsSurname2010Info method) (crate_anon.anonymise.make_demo_database.BlobDoc method) (crate_anon.anonymise.make_demo_database.FilenameDoc method) (crate_anon.anonymise.make_demo_database.Note method) (crate_anon.anonymise.make_demo_database.Patient method) (crate_anon.anonymise.models.OptOutMpid method) (crate_anon.anonymise.models.OptOutPid method) (crate_anon.anonymise.models.PatientInfo method) (crate_anon.anonymise.models.TridRecord method) (crate_anon.anonymise.patient.Patient method) (crate_anon.anonymise.scrub.NonspecificScrubber method) (crate_anon.anonymise.scrub.PersonalizedScrubber method) (crate_anon.anonymise.scrub.ScrubberBase method) (crate_anon.anonymise.scrub.WordList method) (crate_anon.anonymise.test_anonymisation.FieldInfo method) (crate_anon.common.extendedconfigparser.ConfigSection method) (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) (crate_anon.common.sql.ColumnId method) (crate_anon.common.sql.JoinInfo method) (crate_anon.common.sql.SchemaId method) (crate_anon.common.sql.TableId method) (crate_anon.common.sql.TransactionSizeLimiter method) (crate_anon.common.sql.ViewMaker method) (crate_anon.common.sql.WhereCondition method) (crate_anon.crateweb.consent.forms.ClinicianSubmitContactRequestForm method) (crate_anon.crateweb.consent.forms.ResearcherSubmitContactRequestForm method) (crate_anon.crateweb.consent.forms.SuperuserSubmitContactRequestForm method) (crate_anon.crateweb.consent.forms.TeamRepAdminForm method) (crate_anon.crateweb.consent.models.ClinicianInfoHolder method) (crate_anon.crateweb.consent.models.ContactRequest method) (crate_anon.crateweb.consent.models.DummyObjectCollection method) (crate_anon.crateweb.core.utils.JavascriptBranchNode method) (crate_anon.crateweb.core.utils.JavascriptLeafNode method) (crate_anon.crateweb.core.utils.JavascriptTree method) (crate_anon.crateweb.core.utils.JavascriptTreeNode method) (crate_anon.crateweb.extra.admin.ReadOnlyChangeList method) (crate_anon.crateweb.extra.pdf.CratePdfPlan method) (crate_anon.crateweb.research.forms.ClinicianAllTextFromPidForm method) (crate_anon.crateweb.research.forms.DatabasePickerForm method) (crate_anon.crateweb.research.forms.FieldPickerInfo method) (crate_anon.crateweb.research.forms.PidLookupForm method) (crate_anon.crateweb.research.forms.QueryBuilderForm method) (crate_anon.crateweb.research.forms.RidLookupForm method) (crate_anon.crateweb.research.forms.SQLHelperDrugTypeForm method) (crate_anon.crateweb.research.forms.SQLHelperFindAnywhereForm method) (crate_anon.crateweb.research.forms.SQLHelperTextAnywhereForm method) (crate_anon.crateweb.research.html_functions.HtmlElementCounter method) (crate_anon.crateweb.research.models.PatientExplorer method) (crate_anon.crateweb.research.models.PatientMultiQuery method) (crate_anon.crateweb.research.models.Query method) (crate_anon.crateweb.research.models.TableQueryArgs method) (crate_anon.crateweb.research.research_db_info.ColumnInfo method) (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase method) (crate_anon.crateweb.research.sql_writer.SelectElement method) (crate_anon.crateweb.research.views.NlpSourceResult method) (crate_anon.linkage.fuzzy_id_match.Comparison method) (crate_anon.linkage.fuzzy_id_match.DirectComparison method) (crate_anon.linkage.fuzzy_id_match.FullPartialNoMatchComparison method) (crate_anon.linkage.fuzzy_id_match.FuzzyIdFreq method) (crate_anon.linkage.fuzzy_id_match.IdFreq method) (crate_anon.linkage.fuzzy_id_match.MatchConfig method) (crate_anon.linkage.fuzzy_id_match.MatchNoMatchComparison method) (crate_anon.linkage.fuzzy_id_match.MatchResult method) (crate_anon.linkage.fuzzy_id_match.NameFrequencyInfo method) (crate_anon.linkage.fuzzy_id_match.Person method) (crate_anon.linkage.fuzzy_id_match.PostcodeFrequencyInfo method) (crate_anon.linkage.fuzzy_id_match.TemporalIdentifier method) (crate_anon.linkage.fuzzy_id_match.TestCondition method) (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method) (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) (crate_anon.nlp_manager.cloud_config.CloudConfig method) (crate_anon.nlp_manager.cloud_parser.Cloud method) (crate_anon.nlp_manager.cloud_request.CloudRequest method) (crate_anon.nlp_manager.cloud_request.CloudRequestListProcessors method) (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method) (crate_anon.nlp_manager.cloud_run_info.CloudRunInfo method) (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) (crate_anon.nlp_manager.models.NlpRecord method) (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) (crate_anon.nlp_manager.nlp_manager.DbInfo method) (crate_anon.nlp_manager.output_user_config.OutputUserConfig method) (crate_anon.nlp_manager.parse_biochemistry.Creatinine method) (crate_anon.nlp_manager.parse_biochemistry.Crp method) (crate_anon.nlp_manager.parse_biochemistry.Glucose method) (crate_anon.nlp_manager.parse_biochemistry.HbA1c method) (crate_anon.nlp_manager.parse_biochemistry.HDLCholesterol method) (crate_anon.nlp_manager.parse_biochemistry.LDLCholesterol method) (crate_anon.nlp_manager.parse_biochemistry.Lithium method) (crate_anon.nlp_manager.parse_biochemistry.Potassium method) (crate_anon.nlp_manager.parse_biochemistry.Sodium method) (crate_anon.nlp_manager.parse_biochemistry.TotalCholesterol method) (crate_anon.nlp_manager.parse_biochemistry.Triglycerides method) (crate_anon.nlp_manager.parse_biochemistry.Tsh method) (crate_anon.nlp_manager.parse_biochemistry.Urea method) (crate_anon.nlp_manager.parse_clinical.Bmi method) (crate_anon.nlp_manager.parse_clinical.Bp method) (crate_anon.nlp_manager.parse_clinical.Height method) (crate_anon.nlp_manager.parse_clinical.Weight method) (crate_anon.nlp_manager.parse_cognitive.Ace method) (crate_anon.nlp_manager.parse_cognitive.MiniAce method) (crate_anon.nlp_manager.parse_cognitive.Mmse method) (crate_anon.nlp_manager.parse_cognitive.Moca method) (crate_anon.nlp_manager.parse_gate.Gate method) (crate_anon.nlp_manager.parse_haematology.Basophils method) (crate_anon.nlp_manager.parse_haematology.Eosinophils method) (crate_anon.nlp_manager.parse_haematology.Esr method) (crate_anon.nlp_manager.parse_haematology.Haematocrit method) (crate_anon.nlp_manager.parse_haematology.Haemoglobin method) (crate_anon.nlp_manager.parse_haematology.Lymphocytes method) (crate_anon.nlp_manager.parse_haematology.Monocytes method) (crate_anon.nlp_manager.parse_haematology.Neutrophils method) (crate_anon.nlp_manager.parse_haematology.Platelets method) (crate_anon.nlp_manager.parse_haematology.RBC method) (crate_anon.nlp_manager.parse_haematology.Wbc method) (crate_anon.nlp_manager.parse_haematology.WbcBase method) (crate_anon.nlp_manager.parse_medex.Medex method) (crate_anon.nlp_manager.parse_medex.PseudoTempDir method) (crate_anon.nlp_manager.prepare_umls_for_bioyodie.UmlsBioyodieConversionConfig method) (crate_anon.nlp_manager.regex_parser.NumeratorOutOfDenominatorParser method) (crate_anon.nlp_manager.regex_parser.NumericalResultParser method) (crate_anon.nlp_manager.regex_parser.SimpleNumericalResultParser method) (crate_anon.nlp_manager.regex_parser.ValidatorBase method) (crate_anon.nlp_webserver.models.DocProcRequest method) (crate_anon.nlp_webserver.models.Document method) (crate_anon.nlp_webserver.security.Credentials method) (crate_anon.nlp_webserver.server_processor.ServerProcessor method) (crate_anon.nlp_webserver.views.NlprpProcessRequest method) (crate_anon.nlp_webserver.views.NlpWebViews method) (crate_anon.preprocess.ddhint.DDHint method) (crate_anon.preprocess.postcodes.BUA method) (crate_anon.preprocess.postcodes.BUASD method) (crate_anon.preprocess.postcodes.CASWard method) (crate_anon.preprocess.postcodes.CCG method) (crate_anon.preprocess.postcodes.Country method) (crate_anon.preprocess.postcodes.County2019 method) (crate_anon.preprocess.postcodes.EER method) (crate_anon.preprocess.postcodes.GOR method) (crate_anon.preprocess.postcodes.IMDLookupEN method) (crate_anon.preprocess.postcodes.IMDLookupSC method) (crate_anon.preprocess.postcodes.IMDLookupWA method) (crate_anon.preprocess.postcodes.LAD method) (crate_anon.preprocess.postcodes.LAU method) (crate_anon.preprocess.postcodes.LEP method) (crate_anon.preprocess.postcodes.LSOA2011 method) (crate_anon.preprocess.postcodes.MSOA2011 method) (crate_anon.preprocess.postcodes.NationalPark method) (crate_anon.preprocess.postcodes.OAClassification method) (crate_anon.preprocess.postcodes.Parish method) (crate_anon.preprocess.postcodes.PCT2019 method) (crate_anon.preprocess.postcodes.PFA method) (crate_anon.preprocess.postcodes.Postcode method) (crate_anon.preprocess.postcodes.SSR method) (crate_anon.preprocess.postcodes.TTWA method) (crate_anon.preprocess.postcodes.Ward2019 method) (crate_anon.preprocess.postcodes.WestminsterConstituency method) (crate_anon.preprocess.preprocess_pcmis.PcmisConfigOptions method) (crate_anon.preprocess.rio_view_func.RioViewConfigOptions method)

A

about() (in module crate_anon.crateweb.core.views) AbstractContactRequestForm (class in crate_anon.crateweb.consent.forms) Ace (class in crate_anon.nlp_manager.parse_cognitive) AceValidator (class in crate_anon.nlp_manager.parse_cognitive) activate() (crate_anon.crateweb.research.models.Highlight method) (crate_anon.crateweb.research.models.PatientExplorer method) (crate_anon.crateweb.research.models.Query method) add() (crate_anon.anonymise.models.OptOutMpid class method) (crate_anon.anonymise.models.OptOutPid class method) add_arguments() (crate_anon.crateweb.consent.management.commands.email_rdbm.Command method) (crate_anon.crateweb.consent.management.commands.fetch_optouts.Command method) (crate_anon.crateweb.consent.management.commands.lookup_consent.Command method) (crate_anon.crateweb.consent.management.commands.lookup_patient.Command method) (crate_anon.crateweb.core.management.commands.runcpserver.Command method) add_bulk_source_index_request() (crate_anon.preprocess.ddhint.DDHint method) add_child() (crate_anon.crateweb.core.utils.JavascriptBranchNode method) (crate_anon.crateweb.core.utils.JavascriptTree method) add_columns() (in module crate_anon.common.sql) add_file() (crate_anon.anonymise.scrub.WordList method) add_file_timestamp_to_url_query() (in module crate_anon.crateweb.research.archive_backend) add_from() (crate_anon.common.sql.ViewMaker method) add_geography_to_view() (in module crate_anon.preprocess.preprocess_pcmis) add_index_only() (in module crate_anon.preprocess.rio_view_func) add_indexes() (in module crate_anon.common.sql) add_lines_after_trigger() (in module crate_anon.nlp_manager.build_medex_itself) add_lines_if_not_in() (in module crate_anon.nlp_manager.build_medex_itself) add_output_column() (crate_anon.crateweb.research.models.PatientMultiQuery method) add_patient_condition() (crate_anon.crateweb.research.models.PatientMultiQuery method) add_postcode_geography_view() (in module crate_anon.preprocess.preprocess_rio) add_processor_to_request() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method) add_select() (crate_anon.common.sql.ViewMaker method) add_source_index_request() (crate_anon.preprocess.ddhint.DDHint method) add_src_hash() (crate_anon.anonymise.ddr.DataDictionaryRow property) add_text() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method) add_to_select() (in module crate_anon.crateweb.research.sql_writer) add_user() (in module crate_anon.nlp_webserver.manage_users) add_value() (crate_anon.anonymise.scrub.PersonalizedScrubber method) add_where() (crate_anon.common.sql.ViewMaker method) add_word() (crate_anon.anonymise.scrub.WordList method) AddHighlightForm (class in crate_anon.crateweb.research.forms) addition_only() (crate_anon.anonymise.ddr.DataDictionaryRow property) AddOnlyModelAdmin (class in crate_anon.crateweb.extra.admin) AddQueryForm (class in crate_anon.crateweb.research.forms) all_crate_python_processors_nlprp_processor_info() (in module crate_anon.nlp_manager.all_processors) all_full_queries() (crate_anon.crateweb.research.models.PatientMultiQuery property) all_parser_classes() (in module crate_anon.nlp_manager.all_processors) all_queries() (crate_anon.crateweb.research.models.PatientExplorer method) (crate_anon.crateweb.research.models.PatientMultiQuery method) all_queries_specific_patients() (crate_anon.crateweb.research.models.PatientMultiQuery method) all_tablemaker_classes() (in module crate_anon.nlp_manager.all_processors)

all_text_from_pid() (in module crate_anon.crateweb.research.views) all_text_from_pid_with_db() (in module crate_anon.crateweb.research.views) AllStaffReadOnlyModelAdmin (class in crate_anon.crateweb.extra.admin) alter() (crate_anon.anonymise.altermethod.AlterMethod method) alter_method() (crate_anon.anonymise.ddr.DataDictionaryRow property) alter_methods() (crate_anon.anonymise.ddr.DataDictionaryRow property) AlterMethod (class in crate_anon.anonymise.altermethod) ALTERMETHOD (class in crate_anon.anonymise.constants) anonymise() (in module crate_anon.anonymise.anonymise) archive_attachment() (in module crate_anon.crateweb.research.views) archive_attachment_url() (in module crate_anon.crateweb.research.archive_backend) archive_misconfigured_response() (in module crate_anon.crateweb.research.archive_backend) archive_root_url() (in module crate_anon.crateweb.research.archive_backend) archive_static() (in module crate_anon.crateweb.research.views) archive_static_url() (in module crate_anon.crateweb.research.archive_backend) archive_template() (in module crate_anon.crateweb.research.views) archive_template_url() (in module crate_anon.crateweb.research.archive_backend) ArchiveAttachmentAudit (class in crate_anon.crateweb.research.models) ArchiveAttachmentAudit.DoesNotExist ArchiveAttachmentAudit.MultipleObjectsReturned ArchiveAttachmentAuditMgrAdmin (class in crate_anon.crateweb.core.admin) ArchiveContextKeys (class in crate_anon.crateweb.research.archive_backend) ArchiveTemplateAudit (class in crate_anon.crateweb.research.models) ArchiveTemplateAudit.DoesNotExist ArchiveTemplateAudit.MultipleObjectsReturned ArchiveTemplateAuditMgrAdmin (class in crate_anon.crateweb.core.admin) as_ordered_dict() (crate_anon.crateweb.research.models.Highlight static method) as_text() (crate_anon.anonymise.altermethod.AlterMethod property) assemble_units() (in module crate_anon.nlp_manager.regex_units) assert_correct() (crate_anon.linkage.fuzzy_id_match.TestCondition method) assert_freq_info() (crate_anon.anonymise.fetch_wordlists.NameInfo method) assert_has_frequency_info() (crate_anon.linkage.fuzzy_id_match.FuzzyIdFreq method) (crate_anon.linkage.fuzzy_id_match.IdFreq method) assert_valid_as_candidate() (crate_anon.linkage.fuzzy_id_match.Person method) assert_valid_as_proband() (crate_anon.linkage.fuzzy_id_match.Person method) assert_view_has_same_num_rows() (in module crate_anon.common.sql) at_start_wb() (in module crate_anon.nlp_manager.regex_func) at_wb_start_end() (in module crate_anon.nlp_manager.regex_func) audit() (crate_anon.crateweb.research.models.PatientExplorer method) (crate_anon.crateweb.research.models.Query method) audit_archive_attachment() (in module crate_anon.crateweb.research.archive_backend) audit_archive_template() (in module crate_anon.crateweb.research.archive_backend) auto_delete_emailattachment_files_on_change() (in module crate_anon.crateweb.consent.models) auto_delete_emailattachment_files_on_delete() (in module crate_anon.crateweb.consent.models) auto_delete_leaflet_files_on_change() (in module crate_anon.crateweb.consent.models) auto_delete_leaflet_files_on_delete() (in module crate_anon.crateweb.consent.models) auto_delete_letter_files_on_change() (in module crate_anon.crateweb.consent.models) auto_delete_letter_files_on_delete() (in module crate_anon.crateweb.consent.models) auto_delete_study_files_on_change() (in module crate_anon.crateweb.consent.models) auto_delete_study_files_on_delete() (in module crate_anon.crateweb.consent.models)

B

baseline_log_odds_same_person() (crate_anon.linkage.fuzzy_id_match.MatchConfig property) BaseNlpParser (class in crate_anon.nlp_manager.base_nlp_parser) basetype() (crate_anon.crateweb.research.research_db_info.ColumnInfo property) Basophils (class in crate_anon.nlp_manager.parse_haematology) BasophilsValidator (class in crate_anon.nlp_manager.parse_haematology) bayes_compare() (in module crate_anon.linkage.fuzzy_id_match) being_scrubbed() (crate_anon.anonymise.ddr.DataDictionaryRow property) BlankHighlightForm (class in crate_anon.crateweb.research.forms) BlankQueryForm (class in crate_anon.crateweb.research.forms) BlobDoc (class in crate_anon.anonymise.make_demo_database)

Bmi (class in crate_anon.nlp_manager.parse_clinical) BmiValidator (class in crate_anon.nlp_manager.parse_clinical) Bp (class in crate_anon.nlp_manager.parse_clinical) BpValidator (class in crate_anon.nlp_manager.parse_clinical) BUA (class in crate_anon.preprocess.postcodes) BUASD (class in crate_anon.preprocess.postcodes) build() (crate_anon.anonymise.scrub.WordList method) build_regex() (crate_anon.anonymise.scrub.NonspecificScrubber method) build_regexes() (crate_anon.anonymise.scrub.PersonalizedScrubber method) bulk_hash() (in module crate_anon.linkage.bulk_hash)

C

cache_load() (in module crate_anon.linkage.fuzzy_id_match) cache_save() (in module crate_anon.linkage.fuzzy_id_match) cached_funcs() (crate_anon.anonymise.dd.DataDictionary method) calc_approaches_in_past_year() (crate_anon.crateweb.consent.models.ContactRequest method) can_communicate_directly() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase method) cancel_request() (in module crate_anon.nlp_manager.nlp_manager) CASWard (class in crate_anon.preprocess.postcodes) CCG (class in crate_anon.preprocess.postcodes) change_password() (in module crate_anon.nlp_webserver.manage_users) charity_report() (in module crate_anon.crateweb.consent.views) CharityPaymentRecord (class in crate_anon.crateweb.consent.models) CharityPaymentRecord.DoesNotExist CharityPaymentRecord.MultipleObjectsReturned CharityPaymentRecordMgrAdmin (class in crate_anon.crateweb.core.admin) check_against_source_db() (crate_anon.anonymise.dd.DataDictionary method) check_if_ready() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method) check_password() (in module crate_anon.nlp_webserver.security) check_prohibited_fieldnames() (crate_anon.anonymise.ddr.DataDictionaryRow method) check_token() (crate_anon.nlp_webserver.views.NlpWebViews method) check_valid() (crate_anon.anonymise.config.Config method) (crate_anon.anonymise.dd.DataDictionary method) (crate_anon.anonymise.ddr.DataDictionaryRow method) cherrypy() (in module crate_anon.nlp_webserver.wsgi_launchers) classname() (crate_anon.nlp_manager.base_nlp_parser.TableMaker class method) clean() (crate_anon.crateweb.consent.forms.AbstractContactRequestForm method) (crate_anon.crateweb.core.admin.ConsentModeAdminForm method) (crate_anon.crateweb.core.admin.PatientResponseAdminForm method) (crate_anon.crateweb.research.forms.QueryBuilderForm method) (crate_anon.crateweb.research.forms.SQLHelperFindAnywhereForm method) clear_cache() (crate_anon.anonymise.scrub.PersonalizedScrubber method) (crate_anon.anonymise.scrub.WordList method) clear_caches() (crate_anon.anonymise.dd.DataDictionary method) clear_output_columns() (crate_anon.crateweb.research.models.PatientMultiQuery method) clear_patient_conditions() (crate_anon.crateweb.research.models.PatientMultiQuery method) cli_lookup_consent() (in module crate_anon.crateweb.consent.management.commands.lookup_consent) cli_lookup_patient() (in module crate_anon.crateweb.consent.management.commands.lookup_patient) ClinicalDatabaseType (class in crate_anon.crateweb.config.constants) clinician_address_components() (crate_anon.crateweb.consent.models.PatientLookupBase method) clinician_address_components_str() (crate_anon.crateweb.consent.models.PatientLookupBase method) clinician_initiated_contact_request() (in module crate_anon.crateweb.consent.views) clinician_name_address_str() (crate_anon.crateweb.consent.models.PatientLookupBase method) clinician_pack() (in module crate_anon.crateweb.consent.views) clinician_response_view() (in module crate_anon.crateweb.consent.views) clinician_salutation() (crate_anon.crateweb.consent.models.PatientLookupBase method) clinician_title_forename_surname() (crate_anon.crateweb.consent.models.PatientLookupBase method) ClinicianAllTextFromPidForm (class in crate_anon.crateweb.research.forms) ClinicianInfoHolder (class in crate_anon.crateweb.consent.models) ClinicianRespondedListFilter (class in crate_anon.crateweb.core.admin) ClinicianResponse (class in crate_anon.crateweb.consent.models) ClinicianResponse.DoesNotExist ClinicianResponse.MultipleObjectsReturned ClinicianResponseDevAdmin (class in crate_anon.crateweb.core.admin) ClinicianResponseForm (class in crate_anon.crateweb.consent.forms) ClinicianSubmitContactRequestForm (class in crate_anon.crateweb.consent.forms) Cloud (class in crate_anon.nlp_manager.cloud_parser) CloudConfig (class in crate_anon.nlp_manager.cloud_config) CloudNlpConfigKeys (class in crate_anon.nlp_manager.constants) CloudRequest (class in crate_anon.nlp_manager.cloud_request) CloudRequestListProcessors (class in crate_anon.nlp_manager.cloud_request) CloudRequestProcess (class in crate_anon.nlp_manager.cloud_request) CloudRequestQueueManagement (class in crate_anon.nlp_manager.cloud_request) CloudRunInfo (class in crate_anon.nlp_manager.cloud_run_info) coin() (in module crate_anon.anonymise.make_demo_database) colinfolist() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase property) collapsible_div_contentdiv() (crate_anon.crateweb.research.html_functions.HtmlElementCounter method) coltype_length_if_text() (in module crate_anon.common.sql) column() (crate_anon.common.sql.ColumnId property) column_id() (crate_anon.common.sql.SchemaId method) (crate_anon.common.sql.TableId method) (crate_anon.common.sql.WhereCondition property) (crate_anon.crateweb.research.research_db_info.ColumnInfo property) column_present() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase method) ColumnId (class in crate_anon.common.sql) ColumnInfo (class in crate_anon.crateweb.research.research_db_info) columns_to_table_column_hierarchy() (in module crate_anon.common.sql) Command (class in crate_anon.crateweb.consent.management.commands.email_rdbm) (class in crate_anon.crateweb.consent.management.commands.fetch_optouts) (class in crate_anon.crateweb.consent.management.commands.lookup_consent) (class in crate_anon.crateweb.consent.management.commands.lookup_patient) (class in crate_anon.crateweb.consent.management.commands.populate) (class in crate_anon.crateweb.consent.management.commands.resubmit_unprocessed_tasks) (class in crate_anon.crateweb.consent.management.commands.test_email) (class in crate_anon.crateweb.core.management.commands.runcpserver) commit() (crate_anon.common.sql.TransactionSizeLimiter method) (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) commit_admindb() (in module crate_anon.anonymise.anonymise) commit_all() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) commit_and_announce() (in module crate_anon.preprocess.postcodes) commit_dest_db() (crate_anon.anonymise.config.Config method) commit_destdb() (in module crate_anon.anonymise.anonymise) common_context() (in module crate_anon.crateweb.core.context_processors) common_find_text() (in module crate_anon.crateweb.research.views) common_tense() (in module crate_anon.nlp_manager.regex_parser) compare_probands_to_sample() (in module crate_anon.linkage.fuzzy_id_match) compare_probands_to_sample_from_csv() (in module crate_anon.linkage.fuzzy_id_match) Comparison (class in crate_anon.linkage.fuzzy_id_match) comparison() (crate_anon.linkage.fuzzy_id_match.FuzzyIdFreq method) (crate_anon.linkage.fuzzy_id_match.IdFreq method) compile_blob_mysql() (in module crate_anon.anonymise.make_demo_database) compile_regex() (in module crate_anon.nlp_manager.regex_func) compile_regex_dict() (in module crate_anon.nlp_manager.regex_func) Config (class in crate_anon.anonymise.config) configfail() (in module crate_anon.common.extendedconfigparser) ConfigSection (class in crate_anon.common.extendedconfigparser) ConsentAppConfig (class in crate_anon.crateweb.config.apps) ConsentMode (class in crate_anon.crateweb.consent.models) ConsentMode.DoesNotExist ConsentMode.MultipleObjectsReturned ConsentModeAdminForm (class in crate_anon.crateweb.core.admin) ConsentModeDevAdmin (class in crate_anon.crateweb.core.admin) ConsentModeInline (class in crate_anon.crateweb.core.admin) ConsentModeMgrAdmin (class in crate_anon.crateweb.core.admin) consider_withdrawal() (crate_anon.crateweb.consent.models.ConsentMode method) constant() (crate_anon.anonymise.ddr.DataDictionaryRow property) contactable() (crate_anon.crateweb.consent.models.ClinicianInfoHolder method) ContactRequest (class in crate_anon.crateweb.consent.models) ContactRequest.DoesNotExist ContactRequest.MultipleObjectsReturned ContactRequestDevAdmin (class in crate_anon.crateweb.core.admin) ContactRequestMgrAdmin (class in crate_anon.crateweb.core.admin) ContactRequestResAdmin (class in crate_anon.crateweb.core.admin) contains() (crate_anon.anonymise.scrub.WordList method) contains_patient_info() (crate_anon.anonymise.ddr.DataDictionaryRow property) contains_vital_patient_info() (crate_anon.anonymise.ddr.DataDictionaryRow property) convert_date() (in module crate_anon.preprocess.postcodes) convert_float() (in module crate_anon.preprocess.postcodes) convert_int() (in module crate_anon.preprocess.postcodes) copy() (crate_anon.linkage.fuzzy_id_match.Person method) CoreAppConfig (class in crate_anon.crateweb.config.apps) count_rows() (in module crate_anon.anonymise.anonymise) Country (class in crate_anon.preprocess.postcodes) County2019 (class in crate_anon.preprocess.postcodes) crate_anon.anonymise.__init__ module crate_anon.anonymise.altermethod module crate_anon.anonymise.anonregex module crate_anon.anonymise.anonymise module crate_anon.anonymise.anonymise_cli module crate_anon.anonymise.config module crate_anon.anonymise.config_singleton module crate_anon.anonymise.constants module crate_anon.anonymise.dbholder module crate_anon.anonymise.dd module crate_anon.anonymise.ddr module crate_anon.anonymise.eponyms module crate_anon.anonymise.fetch_wordlists module crate_anon.anonymise.launch_multiprocess_anonymiser module crate_anon.anonymise.make_demo_database module crate_anon.anonymise.models module crate_anon.anonymise.patient module crate_anon.anonymise.scrub module crate_anon.anonymise.test_anonymisation module crate_anon.anonymise.test_extract_text module crate_anon.common.__init__ module crate_anon.common.bugfix_flashtext module crate_anon.common.constants module crate_anon.common.dockerfunc module crate_anon.common.exceptions module crate_anon.common.extendedconfigparser module crate_anon.common.file_io module crate_anon.common.formatting module crate_anon.common.memsize module crate_anon.common.parallel module crate_anon.common.profiling module crate_anon.common.sql module crate_anon.common.stringfunc module crate_anon.crateweb.__init__ module crate_anon.crateweb.config.__init__ module crate_anon.crateweb.config.apps module crate_anon.crateweb.config.constants module crate_anon.crateweb.config.settings module crate_anon.crateweb.config.urls module crate_anon.crateweb.config.wsgi module crate_anon.crateweb.consent.__init__ module crate_anon.crateweb.consent.celery module crate_anon.crateweb.consent.forms module crate_anon.crateweb.consent.lookup module crate_anon.crateweb.consent.lookup_crs module crate_anon.crateweb.consent.lookup_dummy module crate_anon.crateweb.consent.lookup_rio module crate_anon.crateweb.consent.management.__init__ module crate_anon.crateweb.consent.management.commands.__init__ module crate_anon.crateweb.consent.management.commands.email_rdbm module crate_anon.crateweb.consent.management.commands.fetch_optouts module crate_anon.crateweb.consent.management.commands.lookup_consent module crate_anon.crateweb.consent.management.commands.lookup_patient module crate_anon.crateweb.consent.management.commands.populate module crate_anon.crateweb.consent.management.commands.resubmit_unprocessed_tasks module crate_anon.crateweb.consent.management.commands.test_email module crate_anon.crateweb.consent.migrations.0001_initial module crate_anon.crateweb.consent.migrations.0002_auto_20160621_1511 module crate_anon.crateweb.consent.migrations.0003_auto_20160628_1301 module crate_anon.crateweb.consent.migrations.0004_auto_20160703_1530 module crate_anon.crateweb.consent.migrations.0005_auto_20170203_1348 module crate_anon.crateweb.consent.migrations.0006_auto_20170206_1617 module crate_anon.crateweb.consent.migrations.0007_auto_20170228_1052 module crate_anon.crateweb.consent.migrations.0008_auto_20170507_1218 module crate_anon.crateweb.consent.migrations.0009_auto_20180629_1132 module crate_anon.crateweb.consent.migrations.0010_auto_20180629_1238 module crate_anon.crateweb.consent.migrations.0011_auto_20181022_0801 module crate_anon.crateweb.consent.migrations.0012_auto_20181102_1335 module crate_anon.crateweb.consent.migrations.0013_auto_20181223_1124 module crate_anon.crateweb.consent.migrations.0014_contactrequest_rdbm_to_contact_pt module crate_anon.crateweb.consent.migrations.0015_auto_20190104_1255 module crate_anon.crateweb.consent.migrations.0016_auto_20190212_1118 module crate_anon.crateweb.consent.migrations.__init__ module crate_anon.crateweb.consent.models module crate_anon.crateweb.consent.storage module crate_anon.crateweb.consent.tasks module crate_anon.crateweb.consent.teamlookup module crate_anon.crateweb.consent.teamlookup_dummy module crate_anon.crateweb.consent.teamlookup_rio module crate_anon.crateweb.consent.utils module crate_anon.crateweb.consent.views module

crate_anon.crateweb.core.__init__ module crate_anon.crateweb.core.admin module crate_anon.crateweb.core.auth_views module crate_anon.crateweb.core.constants module crate_anon.crateweb.core.context_processors module crate_anon.crateweb.core.management.__init__ module crate_anon.crateweb.core.management.commands.__init__ module crate_anon.crateweb.core.management.commands.runcpserver module crate_anon.crateweb.core.middleware module crate_anon.crateweb.core.utils module crate_anon.crateweb.core.views module crate_anon.crateweb.extra.__init__ module crate_anon.crateweb.extra.admin module crate_anon.crateweb.extra.pdf module crate_anon.crateweb.extra.salutation module crate_anon.crateweb.manage module crate_anon.crateweb.research.__init__ module crate_anon.crateweb.research.archive_backend module crate_anon.crateweb.research.archive_func module crate_anon.crateweb.research.forms module crate_anon.crateweb.research.html_functions module crate_anon.crateweb.research.migrations.0001_initial module crate_anon.crateweb.research.migrations.0002_auto_20170203_1348 module crate_anon.crateweb.research.migrations.0003_patientexplorer_patientexploreraudit module crate_anon.crateweb.research.migrations.0004_auto_20170212_0137 module crate_anon.crateweb.research.migrations.0005_query_sql_hash module crate_anon.crateweb.research.migrations.0006_patientexplorer_pmq_hash module crate_anon.crateweb.research.migrations.0007_sitewidequery module crate_anon.crateweb.research.migrations.0008_query_display module crate_anon.crateweb.research.migrations.0009_query_no_null module crate_anon.crateweb.research.migrations.0010_query_last_run module crate_anon.crateweb.research.migrations.0011_auto_20190521_2109 module crate_anon.crateweb.research.migrations.0012_archiveattachmentaudit_archivetemplateaudit module crate_anon.crateweb.research.migrations.__init__ module crate_anon.crateweb.research.models module crate_anon.crateweb.research.research_db_info module crate_anon.crateweb.research.sql_writer module crate_anon.crateweb.research.tests module crate_anon.crateweb.research.views module crate_anon.crateweb.specimen_secret_local_settings.__init__ module crate_anon.crateweb.specimen_secret_local_settings.crateweb_local_settings module crate_anon.crateweb.userprofile.__init__ module crate_anon.crateweb.userprofile.forms module crate_anon.crateweb.userprofile.migrations.0001_initial module crate_anon.crateweb.userprofile.migrations.0002_userprofile_sql_scratchpad module crate_anon.crateweb.userprofile.migrations.0003_auto_20160628_1301 module crate_anon.crateweb.userprofile.migrations.0004_userprofile_patients_per_page module crate_anon.crateweb.userprofile.migrations.0005_userprofile_patient_multiquery_scratchpad module crate_anon.crateweb.userprofile.migrations.0006_auto_20170212_0137 module crate_anon.crateweb.userprofile.migrations.0007_auto_20170507_1218 module crate_anon.crateweb.userprofile.migrations.__init__ module crate_anon.crateweb.userprofile.models module crate_anon.crateweb.userprofile.views module crate_anon.linkage.__init__ module crate_anon.linkage.bulk_hash module crate_anon.linkage.fuzzy_id_match module crate_anon.nlp_manager.__init__ module crate_anon.nlp_manager.all_processors module crate_anon.nlp_manager.base_nlp_parser module crate_anon.nlp_manager.build_gate_java_interface module crate_anon.nlp_manager.build_medex_itself module crate_anon.nlp_manager.build_medex_java_interface module crate_anon.nlp_manager.cloud_config module crate_anon.nlp_manager.cloud_parser module crate_anon.nlp_manager.cloud_request module crate_anon.nlp_manager.cloud_run_info module crate_anon.nlp_manager.constants module crate_anon.nlp_manager.input_field_config module crate_anon.nlp_manager.launch_multiprocess_nlp module crate_anon.nlp_manager.models module crate_anon.nlp_manager.nlp_definition module crate_anon.nlp_manager.nlp_manager module crate_anon.nlp_manager.number module crate_anon.nlp_manager.output_user_config module crate_anon.nlp_manager.parse_biochemistry module crate_anon.nlp_manager.parse_clinical module crate_anon.nlp_manager.parse_cognitive module crate_anon.nlp_manager.parse_gate module crate_anon.nlp_manager.parse_haematology module crate_anon.nlp_manager.parse_medex module crate_anon.nlp_manager.prepare_umls_for_bioyodie module crate_anon.nlp_manager.regex_func module crate_anon.nlp_manager.regex_numbers module crate_anon.nlp_manager.regex_parser module crate_anon.nlp_manager.regex_test module crate_anon.nlp_manager.regex_units module crate_anon.nlp_manager.run_gate_annie_demo module crate_anon.nlp_manager.run_gate_kcl_kconnect_demo module crate_anon.nlp_manager.run_gate_kcl_lewy_demo module crate_anon.nlp_manager.run_gate_kcl_pharmacotherapy_demo module crate_anon.nlp_manager.show_crate_gate_pipeline_options module crate_anon.nlp_manager.show_crate_medex_pipeline_options module crate_anon.nlp_manager.test_all_regex module crate_anon.nlp_webserver.__init__ module crate_anon.nlp_webserver.constants module crate_anon.nlp_webserver.initialize_db module crate_anon.nlp_webserver.manage_users module crate_anon.nlp_webserver.models module crate_anon.nlp_webserver.print_demos module crate_anon.nlp_webserver.procs module crate_anon.nlp_webserver.security module crate_anon.nlp_webserver.server_processor module crate_anon.nlp_webserver.settings module crate_anon.nlp_webserver.tasks module crate_anon.nlp_webserver.views module crate_anon.nlp_webserver.wsgi_app module crate_anon.nlp_webserver.wsgi_launchers module crate_anon.preprocess.__init__ module crate_anon.preprocess.ddhint module crate_anon.preprocess.postcodes module crate_anon.preprocess.preprocess_pcmis module crate_anon.preprocess.preprocess_rio module crate_anon.preprocess.rio_constants module crate_anon.preprocess.rio_ddgen module crate_anon.preprocess.rio_pk module crate_anon.preprocess.rio_view_func module crate_anon.preprocess.rio_views module crate_anon.tools.__init__ module crate_anon.tools.celery_status module crate_anon.tools.email_rdbm module crate_anon.tools.launch_celery module crate_anon.tools.launch_cherrypy_server module crate_anon.tools.launch_docs module crate_anon.tools.launch_flower module crate_anon.tools.launch_nlp_webserver_celery module crate_anon.tools.launch_nlp_webserver_flower module crate_anon.tools.launch_nlp_webserver_gunicorn module crate_anon.tools.print_crateweb_demo_config module crate_anon.tools.to_base64 module crate_anon.tools.winservice module CrateDir (class in crate_anon.common.constants) CratePdfPlan (class in crate_anon.crateweb.extra.pdf) create() (crate_anon.crateweb.consent.models.ClinicianResponse class method) (crate_anon.crateweb.consent.models.ContactRequest class method) (crate_anon.crateweb.consent.models.EmailAttachment class method) (crate_anon.crateweb.consent.models.Letter class method) (crate_anon.crateweb.consent.models.PatientResponse class method) create_clinician_email() (crate_anon.crateweb.consent.models.Email class method) create_clinician_initiated_cr_email() (crate_anon.crateweb.consent.models.Email class method) create_consent_confirmation_to_patient() (crate_anon.crateweb.consent.models.Letter class method) create_error_response() (crate_anon.nlp_webserver.views.NlpWebViews method) create_indexes() (crate_anon.preprocess.ddhint.DDHint method) (in module crate_anon.anonymise.anonymise) create_pcmis_views() (in module crate_anon.preprocess.preprocess_pcmis) create_rdbm_email() (crate_anon.crateweb.consent.models.Email class method) create_rdbm_text_email() (crate_anon.crateweb.consent.models.Email class method) create_request_to_patient() (crate_anon.crateweb.consent.models.Letter class method) create_researcher_approval() (crate_anon.crateweb.consent.models.Letter class method) create_researcher_approval_email() (crate_anon.crateweb.consent.models.Email class method) create_researcher_withdrawal() (crate_anon.crateweb.consent.models.Letter class method) create_researcher_withdrawal_email() (crate_anon.crateweb.consent.models.Email class method) create_response() (crate_anon.nlp_webserver.views.NlpWebViews method) create_rio_views() (in module crate_anon.preprocess.preprocess_rio) create_view() (crate_anon.common.sql.ViewMaker method) (in module crate_anon.common.sql) Creatinine (class in crate_anon.nlp_manager.parse_biochemistry) CreatinineValidator (class in crate_anon.nlp_manager.parse_biochemistry) Credentials (class in crate_anon.nlp_webserver.security) Crp (class in crate_anon.nlp_manager.parse_biochemistry) CrpValidator (class in crate_anon.nlp_manager.parse_biochemistry) current() (crate_anon.crateweb.consent.models.ClinicianInfoHolder method) CustomFileSystemStorage (class in crate_anon.crateweb.consent.storage)

D

d_description() (crate_anon.linkage.fuzzy_id_match.Comparison property) (crate_anon.linkage.fuzzy_id_match.DirectComparison property) (crate_anon.linkage.fuzzy_id_match.FailureComparison property) (crate_anon.linkage.fuzzy_id_match.FullPartialNoMatchComparison property) (crate_anon.linkage.fuzzy_id_match.MatchNoMatchComparison property) data_filename() (crate_anon.nlp_manager.cloud_config.CloudConfig property) data_finder_excel() (crate_anon.crateweb.research.models.PatientExplorer property) database_schema_part() (crate_anon.common.sql.TableId method) DatabaseConfigKeys (class in crate_anon.nlp_manager.constants) DatabaseHolder (class in crate_anon.anonymise.dbholder) DatabasePickerForm (class in crate_anon.crateweb.research.forms) DatabaseSafeConfig (class in crate_anon.anonymise.config) DataDictionary (class in crate_anon.anonymise.dd) DataDictionaryRow (class in crate_anon.anonymise.ddr) datetime_iso_for_filename() (in module crate_anon.crateweb.research.views) days_since_discharge() (crate_anon.crateweb.consent.models.PatientLookupBase method) days_to_years() (in module crate_anon.crateweb.consent.utils) db() (crate_anon.common.sql.ColumnId property) (crate_anon.common.sql.SchemaId property) (crate_anon.common.sql.TableId property) DbInfo (class in crate_anon.nlp_manager.nlp_manager) dbs_with_secret_map() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo property) DDHint (class in crate_anon.preprocess.ddhint) deactivate() (crate_anon.crateweb.research.models.Highlight method) debug_cache_hits() (crate_anon.anonymise.dd.DataDictionary method) debug_delete_something() (crate_anon.linkage.fuzzy_id_match.Person method) debug_mutate_something() (crate_anon.linkage.fuzzy_id_match.Person method) debug_query() (in module crate_anon.crateweb.research.models) decide() (crate_anon.crateweb.consent.models.ContactRequest method) DECISION (class in crate_anon.anonymise.constants) Decision (class in crate_anon.crateweb.consent.models) decision() (crate_anon.anonymise.ddr.DataDictionaryRow property) decision_form_to_pt_re_study() (in module crate_anon.crateweb.consent.views) decision_valid() (crate_anon.crateweb.consent.models.Decision method) decrypt_password() (in module crate_anon.nlp_webserver.security) defines_primary_pids() (crate_anon.anonymise.ddr.DataDictionaryRow property) delete_all_from_queue() (crate_anon.nlp_manager.cloud_request.CloudRequestQueueManagement method) delete_all_progress_records() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) delete_dest_record() (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) delete_dest_records() (crate_anon.nlp_manager.cloud_run_info.CloudRunInfo method) delete_dest_rows_with_no_src_row() (in module crate_anon.anonymise.anonymise) delete_from_queue() (crate_anon.nlp_manager.cloud_request.CloudRequestQueueManagement method) (crate_anon.nlp_webserver.views.NlpWebViews method) delete_if_permitted() (crate_anon.crateweb.research.models.PatientExplorer method) (crate_anon.crateweb.research.models.Query method) delete_progress_records_where_srcpk_not() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) delete_where_no_source() (in module crate_anon.nlp_manager.nlp_manager) delete_where_srcpk_not() (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) delimit_sql_identifier() (in module crate_anon.crateweb.research.archive_func) demo_config() (in module crate_anon.nlp_webserver.print_demos) demo_nlp_config() (in module crate_anon.nlp_manager.nlp_definition) demo_processors() (in module crate_anon.nlp_webserver.print_demos) describe_sqla_col() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser static method) dest_dbname() (crate_anon.nlp_manager.base_nlp_parser.TableMaker property) dest_dialect() (crate_anon.anonymise.config.Config property) dest_engine() (crate_anon.nlp_manager.base_nlp_parser.TableMaker property) dest_metadata() (crate_anon.nlp_manager.base_nlp_parser.TableMaker property) dest_session() (crate_anon.nlp_manager.base_nlp_parser.TableMaker property) dest_signature() (crate_anon.anonymise.ddr.DataDictionaryRow property)

dest_sqla_coltype() (crate_anon.anonymise.ddr.DataDictionaryRow property) dest_sqla_column() (crate_anon.anonymise.ddr.DataDictionaryRow property) dest_tablename() (crate_anon.nlp_manager.output_user_config.OutputUserConfig property) dest_tables_columns() (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) (crate_anon.nlp_manager.cloud_parser.Cloud method) (crate_anon.nlp_manager.parse_clinical.Bp method) (crate_anon.nlp_manager.parse_gate.Gate method) (crate_anon.nlp_manager.parse_medex.Medex method) (crate_anon.nlp_manager.regex_parser.NumeratorOutOfDenominatorParser method) (crate_anon.nlp_manager.regex_parser.NumericalResultParser method) (crate_anon.nlp_manager.regex_parser.ValidatorBase method) dest_tables_indexes() (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) (crate_anon.nlp_manager.cloud_parser.Cloud method) (crate_anon.nlp_manager.parse_gate.Gate method) (crate_anon.nlp_manager.parse_medex.Medex method) destdb() (crate_anon.nlp_manager.base_nlp_parser.TableMaker property) destfields() (crate_anon.nlp_manager.output_user_config.OutputUserConfig property) detailed_test() (crate_anon.nlp_manager.regex_parser.NumericalResultParser method) DevAdminSite (class in crate_anon.crateweb.core.admin) dictfetchall() (crate_anon.crateweb.research.models.Query method) DirectComparison (class in crate_anon.linkage.fuzzy_id_match) do_cprofile() (in module crate_anon.common.profiling) do_cprofile_raw() (in module crate_anon.common.profiling) DockerConstants (class in crate_anon.common.constants) DocProcRequest (class in crate_anon.nlp_webserver.models) Document (class in crate_anon.nlp_webserver.models) does_table_fail_minimum_fields() (crate_anon.anonymise.config.DatabaseSafeConfig method) does_text_contain_word_chars() (in module crate_anon.common.stringfunc) download_privatestorage() (in module crate_anon.crateweb.consent.views) draft_approval_email() (in module crate_anon.crateweb.consent.views) draft_approval_letter() (in module crate_anon.crateweb.consent.views) draft_clinician_email() (in module crate_anon.crateweb.consent.views) draft_confirm_traffic_light_letter() (in module crate_anon.crateweb.consent.views) draft_first_traffic_light_letter() (in module crate_anon.crateweb.consent.views) draft_letter_clinician_to_pt_re_study() (in module crate_anon.crateweb.consent.views) draft_traffic_light_decision_form() (in module crate_anon.crateweb.consent.views) draft_withdrawal_email() (in module crate_anon.crateweb.consent.views) draft_withdrawal_letter() (in module crate_anon.crateweb.consent.views) drop_columns() (in module crate_anon.common.sql) drop_for_clindocs_table() (in module crate_anon.preprocess.preprocess_rio) drop_for_master_patient_table() (in module crate_anon.preprocess.preprocess_rio) drop_for_nonpatient_table() (in module crate_anon.preprocess.preprocess_rio) drop_for_patient_table() (in module crate_anon.preprocess.preprocess_rio) drop_for_progress_notes() (in module crate_anon.preprocess.preprocess_rio) drop_indexes() (crate_anon.preprocess.ddhint.DDHint method) (in module crate_anon.common.sql) drop_pcmis_views() (in module crate_anon.preprocess.preprocess_pcmis) drop_remake() (in module crate_anon.anonymise.anonymise) (in module crate_anon.nlp_manager.nlp_manager) drop_rio_views() (in module crate_anon.preprocess.preprocess_rio) drop_view() (crate_anon.common.sql.ViewMaker method) (in module crate_anon.common.sql) drugmatch() (in module crate_anon.crateweb.research.views) dumb_make_identifier() (in module crate_anon.common.sql) DummyObjectCollection (class in crate_anon.crateweb.consent.models) DummyPatientSourceInfo (class in crate_anon.crateweb.consent.models) DummyPatientSourceInfo.DoesNotExist DummyPatientSourceInfo.MultipleObjectsReturned DummyPatientSourceInfoDevAdmin (class in crate_anon.crateweb.core.admin)

E

edit_display() (in module crate_anon.crateweb.research.views) edit_profile() (in module crate_anon.crateweb.userprofile.views) EditOnceOnlyModelAdmin (class in crate_anon.crateweb.extra.admin) EditOnlyModelAdmin (class in crate_anon.crateweb.extra.admin) EER (class in crate_anon.preprocess.postcodes) eligible_for_query_builder() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase property) Email (class in crate_anon.crateweb.consent.models) Email.DoesNotExist Email.MultipleObjectsReturned email_css() (in module crate_anon.crateweb.consent.utils) email_rdbm() (in module crate_anon.crateweb.manage) EmailAttachment (class in crate_anon.crateweb.consent.models) EmailAttachment.DoesNotExist EmailAttachment.MultipleObjectsReturned EmailDevAdmin (class in crate_anon.crateweb.core.admin) EmailMgrAdmin (class in crate_anon.crateweb.core.admin) EmailResAdmin (class in crate_anon.crateweb.core.admin) EmailSentListFilter (class in crate_anon.crateweb.core.admin) EmailTransmission (class in crate_anon.crateweb.consent.models) EmailTransmission.DoesNotExist EmailTransmission.MultipleObjectsReturned embedded_attachment_html() (in module crate_anon.crateweb.research.archive_func) encrypt_master_pid() (crate_anon.anonymise.config.Config method) encrypt_password() (in module crate_anon.nlp_webserver.security) encrypt_primary_pid() (crate_anon.anonymise.config.Config method) ensure_columns_present() (in module crate_anon.common.sql) ensure_rid() (crate_anon.anonymise.models.PatientInfo method)

ensure_trid() (crate_anon.anonymise.models.PatientInfo method) EnumColours (class in crate_anon.anonymise.make_demo_database) EnvVar (class in crate_anon.common.constants) Eosinophils (class in crate_anon.nlp_manager.parse_haematology) EosinophilsValidator (class in crate_anon.nlp_manager.parse_haematology) EponymInfo (class in crate_anon.anonymise.eponyms) escape_literal_for_regex_giving_charlist() (in module crate_anon.anonymise.anonregex) escape_literal_string_for_regex() (in module crate_anon.anonymise.anonregex) (in module crate_anon.crateweb.research.html_functions) escape_percent_for_python_dbapi() (in module crate_anon.common.sql) escape_percent_in_literal() (in module crate_anon.common.sql) escape_quote_in_literal() (in module crate_anon.common.sql) escape_sql_string_literal() (in module crate_anon.common.sql) escape_sql_string_or_int_literal() (in module crate_anon.common.sql) Esr (class in crate_anon.nlp_manager.parse_haematology) EsrValidator (class in crate_anon.nlp_manager.parse_haematology) estimate_count_patients() (in module crate_anon.anonymise.anonymise) examples_for_paper() (in module crate_anon.anonymise.anonregex) exclusion_report() (in module crate_anon.crateweb.consent.views) exclusion_values() (crate_anon.anonymise.ddr.DataDictionaryRow property) execute() (in module crate_anon.common.sql) exists() (crate_anon.crateweb.consent.models.EmailAttachment method) ExtendedBase (class in crate_anon.preprocess.postcodes) ExtendedConfigParser (class in crate_anon.common.extendedconfigparser) ExtendedUserMgrAdmin (class in crate_anon.crateweb.core.admin) extract_text_extension_permissible() (crate_anon.anonymise.config.Config method) extracting_text_altermethods() (crate_anon.anonymise.ddr.DataDictionaryRow property)

F

f_score() (in module crate_anon.nlp_manager.regex_test) factor_micromolar_from_mg_per_dl() (in module crate_anon.nlp_manager.regex_units) factor_millimolar_from_mg_per_dl() (in module crate_anon.nlp_manager.regex_units) FailureComparison (class in crate_anon.linkage.fuzzy_id_match) fetch_english_words() (in module crate_anon.anonymise.fetch_wordlists) fetch_eponyms() (in module crate_anon.anonymise.fetch_wordlists) fetch_from_queue() (crate_anon.nlp_webserver.views.NlpWebViews method) fetch_optouts() (in module crate_anon.crateweb.consent.management.commands.fetch_optouts) fetch_us_forenames() (in module crate_anon.anonymise.fetch_wordlists) fetch_us_surnames() (in module crate_anon.anonymise.fetch_wordlists) FieldInfo (class in crate_anon.anonymise.test_anonymisation) fieldname_is_pid() (in module crate_anon.anonymise.anonymise) FieldPickerInfo (class in crate_anon.crateweb.research.forms) FilenameDoc (class in crate_anon.anonymise.make_demo_database) filter_files() (in module crate_anon.anonymise.fetch_wordlists) filter_studies_for_researcher() (crate_anon.crateweb.consent.models.Study static method) finalize_a() (crate_anon.crateweb.consent.models.ClinicianResponse method) finalize_b() (crate_anon.crateweb.consent.models.ClinicianResponse method) finalize_clinician_response_in_background() (in module crate_anon.crateweb.consent.views) first_dbinfo() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo property) first_dbinfo_with_secret_map() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo property) float_or_na_for_us_surnames() (in module crate_anon.anonymise.fetch_wordlists) float_validator() (in module crate_anon.crateweb.research.forms)

forename_freq() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) forename_metaphone_freq() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) forename_surname() (in module crate_anon.crateweb.extra.salutation) form (crate_anon.crateweb.core.admin.ConsentModeMgrAdmin attribute) (crate_anon.crateweb.core.admin.PatientResponseMgrAdmin attribute) (crate_anon.crateweb.core.admin.TeamRepMgrAdmin attribute) format_sql_for_print() (in module crate_anon.common.sql) freq_p() (crate_anon.anonymise.fetch_wordlists.NameInfo property) frequency_and_timex() (crate_anon.nlp_manager.parse_medex.Medex static method) frequency_rules_line() (in module crate_anon.nlp_manager.build_medex_itself) friendly_name() (crate_anon.nlp_manager.base_nlp_parser.TableMaker property) friendly_name_with_section() (crate_anon.nlp_manager.base_nlp_parser.TableMaker property) from_file() (crate_anon.anonymise.ddr.DataDictionaryRow property) from_hashed_csv() (crate_anon.linkage.fuzzy_id_match.Person class method) from_plaintext_csv() (crate_anon.linkage.fuzzy_id_match.Person class method) from_schema_tag() (crate_anon.common.sql.SchemaId class method) from_str() (crate_anon.linkage.fuzzy_id_match.TemporalIdentifier class method) from_table() (crate_anon.crateweb.research.sql_writer.SelectElement method) from_table_str() (crate_anon.crateweb.research.sql_writer.SelectElement method) FullPartialNoMatchComparison (class in crate_anon.linkage.fuzzy_id_match) fully_matches() (crate_anon.linkage.fuzzy_id_match.FuzzyIdFreq method) fully_or_partially_matches() (crate_anon.linkage.fuzzy_id_match.FuzzyIdFreq method) fully_qualified_classname() (crate_anon.nlp_manager.base_nlp_parser.TableMaker class method) FuzzyIdFreq (class in crate_anon.linkage.fuzzy_id_match)

G

Gate (class in crate_anon.nlp_manager.parse_gate) gate_api_error() (in module crate_anon.nlp_webserver.tasks) GateApiKeys (class in crate_anon.nlp_manager.constants) GateFieldNames (class in crate_anon.nlp_manager.constants) GateResultKeys (class in crate_anon.nlp_manager.constants) gen_all_values_for_patient() (in module crate_anon.anonymise.patient) gen_data_finder_queries() (crate_anon.crateweb.research.models.PatientMultiQuery method) gen_descendants() (crate_anon.crateweb.core.utils.JavascriptTreeNode method) gen_display_rows() (crate_anon.crateweb.research.models.Query method) gen_excel_row_elements() (in module crate_anon.crateweb.research.models) gen_index_row_sets_by_table() (in module crate_anon.anonymise.anonymise) gen_integers_from_file() (in module crate_anon.common.file_io) gen_ints() (in module crate_anon.common.extendedconfigparser) gen_lines() (in module crate_anon.common.extendedconfigparser) gen_monster_queries() (crate_anon.crateweb.research.models.PatientMultiQuery method) gen_name_from_name_info() (in module crate_anon.anonymise.fetch_wordlists) gen_name_info_via_min_length() (in module crate_anon.anonymise.fetch_wordlists) gen_nonpatient_tables_with_int_pk() (in module crate_anon.anonymise.anonymise) gen_nonpatient_tables_without_int_pk() (in module crate_anon.anonymise.anonymise) gen_opt_out_pids_from_database() (in module crate_anon.anonymise.anonymise) gen_opt_out_pids_from_file() (in module crate_anon.anonymise.anonymise) gen_opt_out_pids_mpids() (in module crate_anon.crateweb.consent.lookup) gen_opt_out_pids_mpids_rio_cpft_datamart() (in module crate_anon.crateweb.consent.lookup_rio) gen_opt_out_pids_mpids_rio_generic() (in module crate_anon.crateweb.consent.lookup_rio) gen_opt_out_pids_mpids_rio_raw() (in module crate_anon.crateweb.consent.lookup_rio) gen_optout_rids() (in module crate_anon.anonymise.anonymise) gen_patient_ids() (in module crate_anon.anonymise.anonymise) gen_pks() (in module crate_anon.anonymise.anonymise) gen_rows() (crate_anon.crateweb.research.models.Query method) (in module crate_anon.anonymise.anonymise) gen_src_pks() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) gen_sufficiently_frequent_names() (in module crate_anon.anonymise.fetch_wordlists) gen_text() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) gen_text_metadataobj() (crate_anon.nlp_webserver.views.NlprpProcessRequest method) gen_text_metadatastr() (crate_anon.nlp_webserver.views.NlprpProcessRequest method) gen_us_forename_info() (in module crate_anon.anonymise.fetch_wordlists) gen_us_forename_info_by_sex() (in module crate_anon.anonymise.fetch_wordlists) gen_us_surname_1990_info() (in module crate_anon.anonymise.fetch_wordlists) gen_us_surname_2010_info() (in module crate_anon.anonymise.fetch_wordlists) gen_valid_words_from_words() (in module crate_anon.anonymise.fetch_wordlists) gen_words() (in module crate_anon.common.extendedconfigparser) gen_words_from_file() (in module crate_anon.common.file_io) generate_encryption_key() (in module crate_anon.nlp_webserver.security) generate_random_nhs() (in module crate_anon.crateweb.consent.views) generic_error() (in module crate_anon.crateweb.research.views) GenericLookupClassMeta (class in crate_anon.preprocess.postcodes) GenericLookupClassType (class in crate_anon.preprocess.postcodes) get_abs_url() (crate_anon.crateweb.consent.models.ClinicianResponse method) get_abs_url_maybe() (crate_anon.crateweb.consent.models.ClinicianResponse method) get_abs_url_no() (crate_anon.crateweb.consent.models.ClinicianResponse method) get_abs_url_path() (crate_anon.crateweb.consent.models.ClinicianResponse method) get_abs_url_yes() (crate_anon.crateweb.consent.models.ClinicianResponse method) get_active_highlights() (crate_anon.crateweb.research.models.Highlight static method) get_active_pe_id_or_none() (crate_anon.crateweb.research.models.PatientExplorer static method) get_active_pe_or_none() (crate_anon.crateweb.research.models.PatientExplorer static method) get_active_query_id_or_none() (crate_anon.crateweb.research.models.Query static method) get_active_query_or_none() (crate_anon.crateweb.research.models.Query static method) get_address_components() (crate_anon.crateweb.userprofile.models.UserProfile method) get_all_pes() (in module crate_anon.crateweb.research.views) get_all_queries() (in module crate_anon.crateweb.research.views) get_all_sitewide_queries() (in module crate_anon.crateweb.research.views) get_all_subclasses() (in module crate_anon.nlp_manager.all_processors) get_anon_fragments_from_string() (in module crate_anon.anonymise.anonregex) get_approval_email_html() (crate_anon.crateweb.consent.models.ContactRequest method) get_approval_letter_html() (crate_anon.crateweb.consent.models.ContactRequest method) get_archive_attachment_filepath() (in module crate_anon.crateweb.research.archive_backend) get_archive_static_filepath() (in module crate_anon.crateweb.research.archive_backend) get_archive_template_filepath() (in module crate_anon.crateweb.research.archive_backend) get_auth_credentials() (in module crate_anon.nlp_webserver.security) get_bool() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) get_changelist() (crate_anon.crateweb.extra.admin.AddOnlyModelAdmin method) (crate_anon.crateweb.extra.admin.ReadOnlyModelAdmin method) get_clinician_email_html() (crate_anon.crateweb.consent.models.ContactRequest method) get_clinician_initiated_email_html() (crate_anon.crateweb.consent.models.ContactRequest method) get_clinician_involvement() (crate_anon.crateweb.consent.models.ContactRequest static method) get_clinician_pack_pdf() (crate_anon.crateweb.consent.models.ContactRequest method) get_cloud_config() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) get_cloud_config_or_raise() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) get_code_regex_elements() (in module crate_anon.anonymise.anonregex) get_coltype_parts() (crate_anon.nlp_manager.cloud_parser.Cloud static method) get_column_names() (crate_anon.crateweb.research.models.Query method) (in module crate_anon.common.sql) get_columns() (crate_anon.nlp_manager.output_user_config.OutputUserConfig method) get_common_querydict() (crate_anon.crateweb.consent.models.ClinicianResponse method) get_compiled_regex_results() (in module crate_anon.nlp_manager.regex_test) get_config_section() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) get_confirm_traffic_to_patient_letter_html() (crate_anon.crateweb.consent.models.ConsentMode method) get_consent_mode() (in module crate_anon.crateweb.consent.views) get_contact_request() (in module crate_anon.crateweb.consent.views) get_copy_columns() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) get_copy_indexes() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) get_core_columns_for_dest() (crate_anon.nlp_manager.input_field_config.InputFieldConfig static method) get_core_indexes_for_dest() (crate_anon.nlp_manager.input_field_config.InputFieldConfig static method) get_count() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) get_database() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) get_date_regex_elements() (in module crate_anon.anonymise.anonregex) get_dbinfo_by_name() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_dbinfo_by_schema_id() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_decision_form_to_pt_re_study() (crate_anon.crateweb.consent.models.ContactRequest method) get_default_database_name() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_default_date_column() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_default_date_field() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase method) get_default_gate_home() (in module crate_anon.nlp_manager.prepare_umls_for_bioyodie) get_default_java_home() (in module crate_anon.nlp_manager.prepare_umls_for_bioyodie) get_default_schema_name() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_dest_sqla_table() (crate_anon.anonymise.dd.DataDictionary method) get_dest_table_for_src_db_table() (crate_anon.anonymise.dd.DataDictionary method) get_dest_tables() (crate_anon.anonymise.dd.DataDictionary method) get_dest_tables_for_src_db_table() (crate_anon.anonymise.dd.DataDictionary method) get_dest_tables_with_patient_info() (crate_anon.anonymise.dd.DataDictionary method) get_destdb_engine_outside_transaction() (crate_anon.anonymise.config.Config method) get_digit_string_from_vaguely_numeric_string() (in module crate_anon.common.stringfunc) get_display_column_names() (crate_anon.crateweb.research.models.Query method) get_display_indexes() (crate_anon.crateweb.research.models.Query method) get_display_list() (crate_anon.crateweb.research.models.Query method) get_display_rows() (crate_anon.crateweb.research.models.Query method) get_docids() (in module crate_anon.anonymise.test_anonymisation) get_domain_from_email() (in module crate_anon.crateweb.consent.utils) get_dummy_teams() (in module crate_anon.crateweb.consent.teamlookup_dummy) get_elements_code() (crate_anon.anonymise.scrub.PersonalizedScrubber method) get_elements_date() (crate_anon.anonymise.scrub.PersonalizedScrubber method) get_elements_numeric() (crate_anon.anonymise.scrub.PersonalizedScrubber method) get_elements_phrase() (crate_anon.anonymise.scrub.PersonalizedScrubber method) get_elements_words() (crate_anon.anonymise.scrub.PersonalizedScrubber method) get_env_dict() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) get_excel() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_executed_cursor() (crate_anon.crateweb.research.models.PatientExplorer static method) (crate_anon.crateweb.research.models.Query method) get_executed_researchdb_cursor() (in module crate_anon.crateweb.research.models) get_executed_researchdb_cursor_qmark_placeholders() (in module crate_anon.crateweb.research.models) get_extra_hasher() (crate_anon.anonymise.config.Config method) (in module crate_anon.anonymise.config) get_fieldnames_for_src_table() (crate_anon.anonymise.dd.DataDictionary method) get_fields() (crate_anon.crateweb.extra.admin.AddOnlyModelAdmin method) get_first_from_table() (in module crate_anon.common.sql) get_first_traffic_light_letter_html() (crate_anon.crateweb.consent.models.PatientLookup method) get_forename_surname() (crate_anon.crateweb.userprofile.models.UserProfile method) get_formatted_sql() (crate_anon.crateweb.research.models.QueryBase method) get_friendly_date() (in module crate_anon.crateweb.core.utils) get_gate_results() (in module crate_anon.nlp_webserver.tasks) get_hash() (crate_anon.anonymise.scrub.NonspecificScrubber method) (crate_anon.anonymise.scrub.PersonalizedScrubber method) (crate_anon.anonymise.scrub.ScrubberBase method) (crate_anon.anonymise.scrub.WordList method) get_highlight_descriptions() (in module crate_anon.crateweb.research.views) get_id_numbers_as_str() (crate_anon.crateweb.consent.models.PatientLookupBase method) get_identical_pes() (in module crate_anon.crateweb.research.views) get_identical_queries() (in module crate_anon.crateweb.research.views) get_index_names() (in module crate_anon.common.sql) get_index_request_dict() (crate_anon.common.sql.ViewMaker method) get_initial_surname_tuple_from_string() (in module crate_anon.crateweb.extra.salutation) get_int_default_if_failure() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) get_int_list() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) get_int_pk_ddr() (crate_anon.anonymise.dd.DataDictionary method) get_int_pk_name() (crate_anon.anonymise.dd.DataDictionary method) get_int_positive_raise_if_no_default() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) get_int_raise_if_no_default() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) get_involves_lack_of_capacity() (crate_anon.crateweb.consent.models.Study method) get_join_info() (in module crate_anon.crateweb.research.sql_writer) get_latest_consent_mode_from_rio_cpft_datamart() (in module crate_anon.crateweb.consent.lookup_rio) get_latest_consent_mode_from_rio_generic() (in module crate_anon.crateweb.consent.lookup_rio) get_latest_consent_mode_from_rio_raw() (in module crate_anon.crateweb.consent.lookup_rio) get_latest_patient_lookup() (crate_anon.crateweb.consent.models.ConsentMode method) get_lead_researcher_name_address() (crate_anon.crateweb.consent.models.Study method) get_lead_researcher_salutation() (crate_anon.crateweb.consent.models.Study method) get_letter_clinician_to_pt_re_study() (crate_anon.crateweb.consent.models.ContactRequest method) get_linked_mrid_column() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_local_processors() (crate_anon.nlp_manager.cloud_run_info.CloudRunInfo method) get_lookup_tables() (crate_anon.common.sql.ViewMaker method)

get_mandatory_scrubber_sigs() (crate_anon.anonymise.dd.DataDictionary method) get_metaphone() (in module crate_anon.linkage.fuzzy_id_match) get_mgr_admin_url() (crate_anon.crateweb.consent.models.ContactRequest method) get_mmsys_configfile_text() (in module crate_anon.nlp_manager.prepare_umls_for_bioyodie) get_mpid() (in module crate_anon.crateweb.research.models) get_mpid_name() (crate_anon.anonymise.dd.DataDictionary method) get_mrid_column_from_schema() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_mrid_column_from_table() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_nlp_config_filename_or_exit() (in module crate_anon.nlp_manager.nlp_definition) get_nlp_parser_class() (in module crate_anon.nlp_manager.all_processors) get_nlp_values() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method) get_nlp_values_gate() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess static method) get_nlp_values_internal() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess static method) get_number_of_length_n_regex_elements() (in module crate_anon.anonymise.anonregex) get_optout_defining_fields() (crate_anon.anonymise.dd.DataDictionary method) get_or_create() (crate_anon.crateweb.consent.models.ConsentMode class method) get_or_none() (crate_anon.crateweb.consent.models.ConsentMode class method) get_original_sql() (crate_anon.crateweb.research.models.QueryBase method) get_patient_id_query() (crate_anon.crateweb.research.models.PatientExplorer method) get_patient_lookup() (in module crate_anon.crateweb.consent.views) get_patient_mrids() (crate_anon.crateweb.research.models.PatientExplorer method) get_patient_regex_string() (crate_anon.anonymise.scrub.PersonalizedScrubber method) get_patient_src_tables_with_active_dest() (crate_anon.anonymise.dd.DataDictionary method) get_patientnum_anontext() (in module crate_anon.anonymise.test_anonymisation) get_patientnum_rawtext() (in module crate_anon.anonymise.test_anonymisation) get_patients_per_page() (in module crate_anon.crateweb.userprofile.models) get_pcmis_dd_settings() (in module crate_anon.preprocess.preprocess_pcmis) get_pcmis_views() (in module crate_anon.preprocess.preprocess_pcmis) get_pdf_from_html_with_django_settings() (in module crate_anon.crateweb.extra.pdf) get_per_page() (in module crate_anon.crateweb.userprofile.models) get_permission_date() (crate_anon.crateweb.consent.models.ContactRequest method) get_phrase_regex_elements() (in module crate_anon.anonymise.anonregex) get_pid() (in module crate_anon.crateweb.research.models) get_pid_lookup() (in module crate_anon.crateweb.research.models) get_pid_name() (crate_anon.anonymise.dd.DataDictionary method) get_pid_subset_from_field() (in module crate_anon.anonymise.anonymise) get_pids_from_field_limits() (in module crate_anon.anonymise.anonymise) get_pids_from_file() (in module crate_anon.anonymise.anonymise) get_pids_from_limits() (in module crate_anon.anonymise.anonymise) get_pids_from_list() (in module crate_anon.anonymise.anonymise) get_pids_query_field_limits() (in module crate_anon.anonymise.anonymise) get_pk_ddr() (crate_anon.anonymise.dd.DataDictionary method) get_plain_eponyms() (in module crate_anon.anonymise.eponyms) get_postcode_sector() (in module crate_anon.linkage.fuzzy_id_match) get_processor() (crate_anon.nlp_webserver.server_processor.ServerProcessor class method) get_processor_from_id() (crate_anon.nlp_webserver.server_processor.ServerProcessor class method) get_processor_nlprp() (crate_anon.nlp_webserver.server_processor.ServerProcessor class method) get_progress_record() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) get_pt_age_years() (crate_anon.crateweb.consent.models.PatientLookupBase method) get_pyvalue_list() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) get_queryset() (crate_anon.crateweb.core.admin.ConsentModeMgrAdmin method) (crate_anon.crateweb.core.admin.ContactRequestResAdmin method) (crate_anon.crateweb.core.admin.EmailMgrAdmin method) (crate_anon.crateweb.core.admin.EmailResAdmin method) (crate_anon.crateweb.core.admin.LetterMgrAdmin method) (crate_anon.crateweb.core.admin.LetterResAdmin method) (crate_anon.crateweb.core.admin.PatientResponseMgrAdmin method) (crate_anon.crateweb.core.admin.StudyResAdmin method) get_queryset_possible_contact_studies() (crate_anon.crateweb.consent.models.Study static method) get_raw_info() (crate_anon.anonymise.scrub.PersonalizedScrubber method) get_readonly_fields() (crate_anon.crateweb.extra.admin.AddOnlyModelAdmin method) get_regex_dict_match() (in module crate_anon.nlp_manager.regex_func) get_regex_from_elements() (in module crate_anon.anonymise.anonregex) get_regex_from_highlights() (in module crate_anon.crateweb.research.html_functions) get_regex_str_for_debugging() (crate_anon.nlp_manager.regex_parser.NumericalResultParser method) get_regex_string_from_elements() (in module crate_anon.anonymise.anonregex) get_remote_processors() (crate_anon.nlp_manager.cloud_request.CloudRequestListProcessors method) (crate_anon.nlp_manager.cloud_run_info.CloudRunInfo method) get_requested_processors() (crate_anon.nlp_manager.cloud_run_info.CloudRunInfo method) get_response_explanation() (crate_anon.crateweb.consent.models.ClinicianResponse method) get_rid_column() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_rio_dd_settings() (in module crate_anon.preprocess.rio_ddgen) get_rio_patient_id_col() (in module crate_anon.preprocess.preprocess_rio) get_rio_teams_rcep_crate() (in module crate_anon.crateweb.consent.teamlookup_rio) get_rio_views() (in module crate_anon.preprocess.preprocess_rio) get_rowcount() (crate_anon.crateweb.research.models.Query method) get_rows() (crate_anon.crateweb.research.models.Query method) get_rows_for_dest_table() (crate_anon.anonymise.dd.DataDictionary method) get_rows_for_src_table() (crate_anon.anonymise.dd.DataDictionary method) get_safe_colour() (crate_anon.crateweb.research.models.Highlight method) get_salutation() (crate_anon.crateweb.userprofile.models.UserProfile method) get_schema_infodictlist() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase method) get_scrub_from_db_table_pairs() (crate_anon.anonymise.dd.DataDictionary method) get_scrub_from_rows() (crate_anon.anonymise.dd.DataDictionary method) get_scrub_method() (crate_anon.anonymise.scrub.PersonalizedScrubber static method) get_source_databases() (crate_anon.anonymise.dd.DataDictionary method) get_spec_match_regex() (in module crate_anon.common.stringfunc) get_sql() (crate_anon.common.sql.ViewMaker method) get_sql_args_for_django() (crate_anon.crateweb.research.models.Query method) get_sqlatype() (in module crate_anon.anonymise.config) get_src_db_tablepairs() (crate_anon.anonymise.dd.DataDictionary method) get_src_db_tablepairs_w_int_pk() (crate_anon.anonymise.dd.DataDictionary method) get_src_db_tablepairs_w_pt_info() (crate_anon.anonymise.dd.DataDictionary method) get_src_dbs_tables_for_dest_table() (crate_anon.anonymise.dd.DataDictionary method) get_src_dbs_tables_with_no_pt_info_int_pk() (crate_anon.anonymise.dd.DataDictionary method) get_src_dbs_tables_with_no_pt_info_no_pk() (crate_anon.anonymise.dd.DataDictionary method) get_src_dialect() (crate_anon.anonymise.config.Config method) get_src_tables() (crate_anon.anonymise.dd.DataDictionary method) get_src_tables_with_active_dest() (crate_anon.anonymise.dd.DataDictionary method) get_src_tables_with_patient_info() (crate_anon.anonymise.dd.DataDictionary method) get_str() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) get_str_list() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) get_string_regex_elements() (in module crate_anon.anonymise.anonregex) get_suppressed_tables() (crate_anon.preprocess.ddhint.DDHint method) get_table() (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) get_table_names() (in module crate_anon.common.sql) get_tablenames() (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) get_text_start_end() (crate_anon.nlp_manager.parse_medex.Medex static method) get_title_forename_surname() (crate_anon.crateweb.userprofile.models.UserProfile method) get_tp_regex_string() (crate_anon.anonymise.scrub.PersonalizedScrubber method) get_traffic_light_decision_form() (crate_anon.crateweb.consent.models.PatientLookupBase method) get_transation_limiter() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) get_trid() (crate_anon.anonymise.models.TridRecord class method) get_trid_column() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_tsv() (crate_anon.anonymise.dd.DataDictionary method) (crate_anon.anonymise.ddr.DataDictionaryRow method) (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) get_uk_postcode_regex_elements() (in module crate_anon.anonymise.anonregex) get_uk_postcode_regex_string() (in module crate_anon.anonymise.anonregex) get_unprocessed() (crate_anon.crateweb.consent.models.ConsentMode static method) (crate_anon.crateweb.consent.models.ContactRequest static method) (crate_anon.crateweb.consent.models.PatientResponse static method) get_users() (in module crate_anon.nlp_webserver.manage_users) get_valid_pid_subset() (in module crate_anon.anonymise.anonymise) get_variablename_regexstrlist() (crate_anon.nlp_manager.parse_biochemistry.CreatinineValidator class method) (crate_anon.nlp_manager.parse_biochemistry.CrpValidator class method) (crate_anon.nlp_manager.parse_biochemistry.GlucoseValidator class method) (crate_anon.nlp_manager.parse_biochemistry.HbA1cValidator class method) (crate_anon.nlp_manager.parse_biochemistry.HDLCholesterolValidator class method) (crate_anon.nlp_manager.parse_biochemistry.LDLCholesterolValidator class method) (crate_anon.nlp_manager.parse_biochemistry.LithiumValidator class method) (crate_anon.nlp_manager.parse_biochemistry.PotassiumValidator class method) (crate_anon.nlp_manager.parse_biochemistry.SodiumValidator class method) (crate_anon.nlp_manager.parse_biochemistry.TotalCholesterolValidator class method) (crate_anon.nlp_manager.parse_biochemistry.TriglyceridesValidator class method) (crate_anon.nlp_manager.parse_biochemistry.TshValidator class method) (crate_anon.nlp_manager.parse_biochemistry.UreaValidator class method) (crate_anon.nlp_manager.parse_clinical.BmiValidator class method) (crate_anon.nlp_manager.parse_clinical.BpValidator class method) (crate_anon.nlp_manager.parse_clinical.HeightValidator class method) (crate_anon.nlp_manager.parse_clinical.WeightValidator class method) (crate_anon.nlp_manager.parse_cognitive.AceValidator class method) (crate_anon.nlp_manager.parse_cognitive.MiniAceValidator class method) (crate_anon.nlp_manager.parse_cognitive.MmseValidator class method) (crate_anon.nlp_manager.parse_cognitive.MocaValidator class method) (crate_anon.nlp_manager.parse_haematology.BasophilsValidator class method) (crate_anon.nlp_manager.parse_haematology.EosinophilsValidator class method) (crate_anon.nlp_manager.parse_haematology.EsrValidator class method) (crate_anon.nlp_manager.parse_haematology.HaematocritValidator class method) (crate_anon.nlp_manager.parse_haematology.HaemoglobinValidator class method) (crate_anon.nlp_manager.parse_haematology.LymphocytesValidator class method) (crate_anon.nlp_manager.parse_haematology.MonocytesValidator class method) (crate_anon.nlp_manager.parse_haematology.NeutrophilsValidator class method) (crate_anon.nlp_manager.parse_haematology.PlateletsValidator class method) (crate_anon.nlp_manager.parse_haematology.RBCValidator class method) (crate_anon.nlp_manager.parse_haematology.WbcValidator class method) (crate_anon.nlp_manager.regex_parser.ValidatorBase class method) get_view_names() (in module crate_anon.common.sql) get_withdrawal_email_html() (crate_anon.crateweb.consent.models.ContactRequest method) get_withdrawal_letter_html() (crate_anon.crateweb.consent.models.ContactRequest method) get_word_alternatives() (in module crate_anon.anonymise.config) get_xlsx_binary() (crate_anon.crateweb.research.models.PatientExplorer method) get_zipped_tsv_binary() (crate_anon.crateweb.research.models.PatientExplorer method) getsize() (in module crate_anon.common.memsize) Glucose (class in crate_anon.nlp_manager.parse_biochemistry) GlucoseValidator (class in crate_anon.nlp_manager.parse_biochemistry) GOR (class in crate_anon.preprocess.postcodes) gp_address_components() (crate_anon.crateweb.consent.models.PatientLookupBase method) gp_address_components_str() (crate_anon.crateweb.consent.models.PatientLookupBase method) gp_name_address_str() (crate_anon.crateweb.consent.models.PatientLookupBase method) gp_title_forename_surname() (crate_anon.crateweb.consent.models.PatientLookupBase method) guess_mimetype() (in module crate_anon.crateweb.core.utils)

H

hack_django_pyodbc_azure_cursorwrapper() (in module crate_anon.crateweb.research.models) Haematocrit (class in crate_anon.nlp_manager.parse_haematology) HaematocritValidator (class in crate_anon.nlp_manager.parse_haematology) Haemoglobin (class in crate_anon.nlp_manager.parse_haematology) HaemoglobinValidator (class in crate_anon.nlp_manager.parse_haematology) handle() (crate_anon.crateweb.consent.management.commands.email_rdbm.Command method) (crate_anon.crateweb.consent.management.commands.fetch_optouts.Command method) (crate_anon.crateweb.consent.management.commands.lookup_consent.Command method) (crate_anon.crateweb.consent.management.commands.lookup_patient.Command method) (crate_anon.crateweb.consent.management.commands.populate.Command method) (crate_anon.crateweb.consent.management.commands.resubmit_unprocessed_tasks.Command method) (crate_anon.crateweb.consent.management.commands.test_email.Command method) (crate_anon.crateweb.core.management.commands.runcpserver.Command method) handle_nlprp_request() (crate_anon.nlp_webserver.views.NlpWebViews method) has_active_destination() (crate_anon.anonymise.dd.DataDictionary method) has_add_permission() (crate_anon.crateweb.extra.admin.EditOnceOnlyModelAdmin method) (crate_anon.crateweb.extra.admin.EditOnlyModelAdmin method) (crate_anon.crateweb.extra.admin.ReadOnlyModelAdmin method) has_been_sent() (crate_anon.crateweb.consent.models.Email method) has_change_permission() (crate_anon.crateweb.core.admin.ContactRequestResAdmin method) (crate_anon.crateweb.core.admin.EmailResAdmin method) (crate_anon.crateweb.core.admin.LetterResAdmin method) (crate_anon.crateweb.core.admin.PatientResponseMgrAdmin method) (crate_anon.crateweb.extra.admin.AllStaffReadOnlyModelAdmin method) has_delete_permission() (crate_anon.crateweb.extra.admin.AddOnlyModelAdmin method) (crate_anon.crateweb.extra.admin.EditOnceOnlyModelAdmin method) (crate_anon.crateweb.extra.admin.EditOnlyModelAdmin method) (crate_anon.crateweb.extra.admin.ReadOnlyModelAdmin method) has_dob() (crate_anon.linkage.fuzzy_id_match.Person method) has_first_name() (crate_anon.linkage.fuzzy_id_match.Person method) has_module_permission() (crate_anon.crateweb.core.admin.ContactRequestResAdmin method) (crate_anon.crateweb.core.admin.EmailResAdmin method) (crate_anon.crateweb.core.admin.LetterResAdmin method) (crate_anon.crateweb.extra.admin.AllStaffReadOnlyModelAdmin method) has_mrid() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase property)

has_output_columns() (crate_anon.crateweb.research.models.PatientExplorer property) (crate_anon.crateweb.research.models.PatientMultiQuery property) has_patient_id_query() (crate_anon.crateweb.research.models.PatientExplorer property) (crate_anon.crateweb.research.models.PatientMultiQuery property) has_table_and_column() (crate_anon.common.sql.ColumnId property) hash() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) hash64() (crate_anon.crateweb.research.models.PatientMultiQuery property) hash_identity_file() (in module crate_anon.linkage.fuzzy_id_match) hash_object() (crate_anon.anonymise.config.Config method) hash_password() (in module crate_anon.nlp_webserver.security) hashed() (crate_anon.linkage.fuzzy_id_match.Person method) hashed_csv_dict() (crate_anon.linkage.fuzzy_id_match.Person method) HbA1c (class in crate_anon.nlp_manager.parse_biochemistry) hba1c_mmol_per_mol_from_percent() (in module crate_anon.nlp_manager.parse_biochemistry) HbA1cValidator (class in crate_anon.nlp_manager.parse_biochemistry) HDLCholesterol (class in crate_anon.nlp_manager.parse_biochemistry) HDLCholesterolValidator (class in crate_anon.nlp_manager.parse_biochemistry) Height (class in crate_anon.nlp_manager.parse_clinical) HeightValidator (class in crate_anon.nlp_manager.parse_clinical) HelpUrl (class in crate_anon.common.constants) Highlight (class in crate_anon.crateweb.research.models) Highlight.DoesNotExist Highlight.MultipleObjectsReturned highlight_activate() (in module crate_anon.crateweb.research.views) highlight_deactivate() (in module crate_anon.crateweb.research.views) highlight_delete() (in module crate_anon.crateweb.research.views) highlight_edit_select() (in module crate_anon.crateweb.research.views) highlight_text() (in module crate_anon.crateweb.research.html_functions) home() (in module crate_anon.crateweb.core.views) html() (crate_anon.crateweb.core.utils.JavascriptBranchNode method) (crate_anon.crateweb.core.utils.JavascriptLeafNode method) (crate_anon.crateweb.core.utils.JavascriptTree method) (crate_anon.crateweb.core.utils.JavascriptTreeNode method) html_form_date_to_python() (in module crate_anon.crateweb.research.forms) html_summary() (crate_anon.crateweb.consent.models.Study property) HtmlElementCounter (class in crate_anon.crateweb.research.html_functions)

I

identical_record_exists_by_hash() (in module crate_anon.anonymise.anonymise) identical_record_exists_by_pk() (in module crate_anon.anonymise.anonymise) identifier() (crate_anon.common.sql.SchemaId method) (crate_anon.common.sql.TableId method) IdFreq (class in crate_anon.linkage.fuzzy_id_match) IMDLookupEN (class in crate_anon.preprocess.postcodes) IMDLookupSC (class in crate_anon.preprocess.postcodes) IMDLookupWA (class in crate_anon.preprocess.postcodes) inclusion_values() (crate_anon.anonymise.ddr.DataDictionaryRow property) INDEX (class in crate_anon.anonymise.constants) index() (crate_anon.nlp_webserver.views.NlpWebViews method) indexes() (crate_anon.nlp_manager.output_user_config.OutputUserConfig property) init_row_counts() (crate_anon.anonymise.config.Config method) inner_main() (in module crate_anon.anonymise.anonymise_cli) (in module crate_anon.nlp_manager.nlp_manager) (in module crate_anon.tools.launch_celery) InputFieldConfig (class in crate_anon.nlp_manager.input_field_config) InputFieldConfigKeys (class in crate_anon.nlp_manager.constants) inputfieldconfigs() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) int_or_none() (crate_anon.nlp_manager.parse_medex.Medex static method)

int_validator() (in module crate_anon.crateweb.research.forms) internal_error() (in module crate_anon.nlp_webserver.tasks) is_clinician() (in module crate_anon.crateweb.core.utils) is_consent_mode_unknown() (crate_anon.crateweb.consent.models.ContactRequest method) is_developer() (in module crate_anon.crateweb.core.utils) is_extra_form() (crate_anon.crateweb.consent.models.ContactRequest method) is_field_denied() (crate_anon.anonymise.config.DatabaseSafeConfig method) is_my_job_by_hash() (in module crate_anon.common.parallel) is_my_job_by_hash_prehashed() (in module crate_anon.common.parallel) is_my_job_by_int() (in module crate_anon.common.parallel) is_pk_integer() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method) is_sql_column_type_textual() (in module crate_anon.common.sql) is_superuser() (in module crate_anon.crateweb.core.utils) is_table_denied() (crate_anon.anonymise.config.DatabaseSafeConfig method) is_tabular() (crate_anon.nlp_manager.cloud_parser.Cloud method) is_unchanged() (crate_anon.anonymise.patient.Patient method) is_under_15() (crate_anon.crateweb.consent.models.PatientLookupBase method) is_under_16() (crate_anon.crateweb.consent.models.PatientLookupBase method) is_valid() (crate_anon.common.sql.ColumnId property) is_valid_postcode() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) (crate_anon.linkage.fuzzy_id_match.PostcodeFrequencyInfo method)

J

javascript_quoted_string_from_html() (in module crate_anon.crateweb.core.utils) JavascriptBranchNode (class in crate_anon.crateweb.core.utils) JavascriptLeafNode (class in crate_anon.crateweb.core.utils) JavascriptTree (class in crate_anon.crateweb.core.utils) JavascriptTreeNode (class in crate_anon.crateweb.core.utils)

JoinInfo (class in crate_anon.common.sql) js_action_dict_key_value() (crate_anon.crateweb.core.utils.JavascriptLeafNode method) js_data() (crate_anon.crateweb.core.utils.JavascriptTree method) js_str_html() (crate_anon.crateweb.core.utils.JavascriptTree method) json_compact() (in module crate_anon.crateweb.research.archive_func)

K

KeywordProcessorFixed (class in crate_anon.common.bugfix_flashtext)

kg_from_st_lb_oz() (in module crate_anon.nlp_manager.regex_units)

L

LAD (class in crate_anon.preprocess.postcodes) latest_date() (in module crate_anon.crateweb.consent.utils) LAU (class in crate_anon.preprocess.postcodes) launch_archive() (in module crate_anon.crateweb.research.views) LDLCholesterol (class in crate_anon.nlp_manager.parse_biochemistry) LDLCholesterolValidator (class in crate_anon.nlp_manager.parse_biochemistry) Leaflet (class in crate_anon.crateweb.consent.models) Leaflet.DoesNotExist Leaflet.MultipleObjectsReturned leaflet_upload_to() (in module crate_anon.crateweb.consent.models) LeafletMgrAdmin (class in crate_anon.crateweb.core.admin) LeafletResAdmin (class in crate_anon.crateweb.core.admin) learning_alternative_regex_groups() (in module crate_anon.nlp_manager.regex_parser) LEP (class in crate_anon.preprocess.postcodes) Letter (class in crate_anon.crateweb.consent.models) Letter.DoesNotExist Letter.MultipleObjectsReturned LetterDevAdmin (class in crate_anon.crateweb.core.admin) LetterMgrAdmin (class in crate_anon.crateweb.core.admin) LetterResAdmin (class in crate_anon.crateweb.core.admin) LetterSendingStatusFilter (class in crate_anon.crateweb.core.admin) lex_freq() (in module crate_anon.nlp_manager.build_medex_itself) lex_route() (in module crate_anon.nlp_manager.build_medex_itself) list_processors() (crate_anon.nlp_webserver.views.NlpWebViews method) Lithium (class in crate_anon.nlp_manager.parse_biochemistry)

LithiumValidator (class in crate_anon.nlp_manager.parse_biochemistry) load_dd() (crate_anon.anonymise.config.Config method) local_structure_help() (in module crate_anon.crateweb.research.views) log_odds_same() (crate_anon.linkage.fuzzy_id_match.Person method) log_odds_same_hashed() (crate_anon.linkage.fuzzy_id_match.TestCondition method) log_odds_same_plaintext() (crate_anon.linkage.fuzzy_id_match.TestCondition method) login_view() (in module crate_anon.crateweb.core.auth_views) logout_view() (in module crate_anon.crateweb.core.auth_views) logtag() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) lookup_consent() (in module crate_anon.crateweb.consent.lookup) lookup_cpft_crs() (in module crate_anon.crateweb.consent.lookup_crs) lookup_cpft_rio_crate_preprocessed() (in module crate_anon.crateweb.consent.lookup_rio) lookup_cpft_rio_generic() (in module crate_anon.crateweb.consent.lookup_rio) lookup_cpft_rio_rcep() (in module crate_anon.crateweb.consent.lookup_rio) lookup_dummy_clinical() (in module crate_anon.crateweb.consent.lookup_dummy) lookup_from_fragment() (in module crate_anon.preprocess.rio_view_func) lookup_from_fragment_first_row() (in module crate_anon.preprocess.rio_view_func) lookup_from_fragment_first_row_outer_apply() (in module crate_anon.preprocess.rio_view_func) lookup_patient() (in module crate_anon.crateweb.consent.lookup) lookups() (crate_anon.crateweb.core.admin.ClinicianRespondedListFilter method) (crate_anon.crateweb.core.admin.EmailSentListFilter method) (crate_anon.crateweb.core.admin.LetterSendingStatusFilter method) lower_case_words_from_file() (in module crate_anon.anonymise.scrub) LSOA2011 (class in crate_anon.preprocess.postcodes) Lymphocytes (class in crate_anon.nlp_manager.parse_haematology) LymphocytesValidator (class in crate_anon.nlp_manager.parse_haematology)

M

m_from_ft_in() (in module crate_anon.nlp_manager.regex_units) m_from_m_cm() (in module crate_anon.nlp_manager.regex_units) main() (in module crate_anon.anonymise.anonymise_cli) (in module crate_anon.anonymise.fetch_wordlists) (in module crate_anon.anonymise.launch_multiprocess_anonymiser) (in module crate_anon.anonymise.make_demo_database) (in module crate_anon.anonymise.test_anonymisation) (in module crate_anon.anonymise.test_extract_text) (in module crate_anon.crateweb.consent.management.commands.fetch_optouts) (in module crate_anon.crateweb.consent.management.commands.lookup_consent) (in module crate_anon.crateweb.consent.management.commands.lookup_patient) (in module crate_anon.crateweb.core.management.commands.runcpserver) (in module crate_anon.crateweb.manage) (in module crate_anon.linkage.bulk_hash) (in module crate_anon.linkage.fuzzy_id_match) (in module crate_anon.nlp_manager.build_gate_java_interface) (in module crate_anon.nlp_manager.build_medex_itself) (in module crate_anon.nlp_manager.build_medex_java_interface) (in module crate_anon.nlp_manager.launch_multiprocess_nlp) (in module crate_anon.nlp_manager.nlp_manager) (in module crate_anon.nlp_manager.prepare_umls_for_bioyodie) (in module crate_anon.nlp_manager.run_gate_annie_demo) (in module crate_anon.nlp_manager.run_gate_kcl_kconnect_demo) (in module crate_anon.nlp_manager.run_gate_kcl_lewy_demo) (in module crate_anon.nlp_manager.run_gate_kcl_pharmacotherapy_demo) (in module crate_anon.nlp_manager.show_crate_gate_pipeline_options) (in module crate_anon.nlp_manager.show_crate_medex_pipeline_options) (in module crate_anon.nlp_webserver.initialize_db) (in module crate_anon.nlp_webserver.manage_users) (in module crate_anon.nlp_webserver.print_demos) (in module crate_anon.preprocess.postcodes) (in module crate_anon.preprocess.preprocess_pcmis) (in module crate_anon.preprocess.preprocess_rio) (in module crate_anon.tools.celery_status) (in module crate_anon.tools.email_rdbm) (in module crate_anon.tools.launch_celery) (in module crate_anon.tools.launch_cherrypy_server) (in module crate_anon.tools.launch_docs) (in module crate_anon.tools.launch_flower) (in module crate_anon.tools.launch_nlp_webserver_celery) (in module crate_anon.tools.launch_nlp_webserver_flower) (in module crate_anon.tools.launch_nlp_webserver_gunicorn) (in module crate_anon.tools.print_crateweb_demo_config) (in module crate_anon.tools.winservice) make_collapsible_sql_query() (in module crate_anon.crateweb.research.html_functions) make_cpft_email_address() (in module crate_anon.crateweb.consent.utils) make_deletion_data() (in module crate_anon.linkage.fuzzy_id_match) make_dummy_objects() (in module crate_anon.crateweb.consent.models) make_excel() (crate_anon.crateweb.research.models.Query method) make_forename_surname_email_address() (in module crate_anon.crateweb.consent.utils) make_highlight_replacement_regex() (in module crate_anon.crateweb.research.html_functions) make_identifier() (in module crate_anon.common.sql) make_nlp_parser() (in module crate_anon.nlp_manager.all_processors) make_nlp_parser_unconfigured() (in module crate_anon.nlp_manager.all_processors) make_pdf_on_disk_from_html_with_django_settings() (in module crate_anon.crateweb.extra.pdf) make_query() (crate_anon.crateweb.research.models.PatientMultiQuery method) make_result_element() (in module crate_anon.crateweb.research.html_functions) make_string_literal() (in module crate_anon.common.sql) make_tables() (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) make_tsv() (crate_anon.crateweb.research.models.Query method) make_typo_data() (in module crate_anon.linkage.fuzzy_id_match) make_unique_id() (in module crate_anon.nlp_webserver.models) make_url() (crate_anon.common.constants.HelpUrl static method) make_wbc_regex() (crate_anon.nlp_manager.parse_haematology.WbcBase static method) mandatory_scrubbers_unfulfilled() (crate_anon.anonymise.patient.Patient property) manual_patient_id_query() (crate_anon.crateweb.research.models.PatientMultiQuery property) ManualPeQueryForm (class in crate_anon.crateweb.research.forms) mark_audited() (crate_anon.crateweb.research.models.PatientExplorer method) (crate_anon.crateweb.research.models.Query method) mark_deleted() (crate_anon.crateweb.research.models.PatientExplorer method) (crate_anon.crateweb.research.models.Query method) mark_sent() (crate_anon.crateweb.consent.models.Letter method) master_pid() (crate_anon.anonymise.ddr.DataDictionaryRow property) MatchConfig (class in crate_anon.linkage.fuzzy_id_match) matches() (crate_anon.linkage.fuzzy_id_match.IdFreq method) (crate_anon.linkage.fuzzy_id_match.TemporalIdentifier method) matches_fielddef() (crate_anon.anonymise.ddr.DataDictionaryRow method) (in module crate_anon.common.sql) matches_hashed() (crate_anon.linkage.fuzzy_id_match.TestCondition method) matches_plaintext() (crate_anon.linkage.fuzzy_id_match.TestCondition method) matches_tabledef() (crate_anon.anonymise.ddr.DataDictionaryRow method) (in module crate_anon.common.sql) MatchNoMatchComparison (class in crate_anon.linkage.fuzzy_id_match) MatchResult (class in crate_anon.linkage.fuzzy_id_match) mean_across_genders() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) Medex (class in crate_anon.nlp_manager.parse_medex) metadata() (crate_anon.anonymise.dbholder.DatabaseHolder property) metaphone_frequency() (crate_anon.linkage.fuzzy_id_match.NameFrequencyInfo method) MgrAdminSite (class in crate_anon.crateweb.core.admin) micromolar_from_mg_per_dl() (in module crate_anon.nlp_manager.regex_units) Migration (class in crate_anon.crateweb.consent.migrations.0001_initial) (class in crate_anon.crateweb.consent.migrations.0002_auto_20160621_1511) (class in crate_anon.crateweb.consent.migrations.0003_auto_20160628_1301) (class in crate_anon.crateweb.consent.migrations.0004_auto_20160703_1530) (class in crate_anon.crateweb.consent.migrations.0005_auto_20170203_1348) (class in crate_anon.crateweb.consent.migrations.0006_auto_20170206_1617) (class in crate_anon.crateweb.consent.migrations.0007_auto_20170228_1052) (class in crate_anon.crateweb.consent.migrations.0008_auto_20170507_1218) (class in crate_anon.crateweb.consent.migrations.0009_auto_20180629_1132) (class in crate_anon.crateweb.consent.migrations.0010_auto_20180629_1238) (class in crate_anon.crateweb.consent.migrations.0011_auto_20181022_0801) (class in crate_anon.crateweb.consent.migrations.0012_auto_20181102_1335) (class in crate_anon.crateweb.consent.migrations.0013_auto_20181223_1124) (class in crate_anon.crateweb.consent.migrations.0014_contactrequest_rdbm_to_contact_pt) (class in crate_anon.crateweb.consent.migrations.0015_auto_20190104_1255) (class in crate_anon.crateweb.consent.migrations.0016_auto_20190212_1118) (class in crate_anon.crateweb.research.migrations.0001_initial) (class in crate_anon.crateweb.research.migrations.0002_auto_20170203_1348) (class in crate_anon.crateweb.research.migrations.0003_patientexplorer_patientexploreraudit) (class in crate_anon.crateweb.research.migrations.0004_auto_20170212_0137) (class in crate_anon.crateweb.research.migrations.0005_query_sql_hash) (class in crate_anon.crateweb.research.migrations.0006_patientexplorer_pmq_hash) (class in crate_anon.crateweb.research.migrations.0007_sitewidequery) (class in crate_anon.crateweb.research.migrations.0008_query_display) (class in crate_anon.crateweb.research.migrations.0009_query_no_null) (class in crate_anon.crateweb.research.migrations.0010_query_last_run) (class in crate_anon.crateweb.research.migrations.0011_auto_20190521_2109) (class in crate_anon.crateweb.research.migrations.0012_archiveattachmentaudit_archivetemplateaudit) (class in crate_anon.crateweb.userprofile.migrations.0001_initial) (class in crate_anon.crateweb.userprofile.migrations.0002_userprofile_sql_scratchpad) (class in crate_anon.crateweb.userprofile.migrations.0003_auto_20160628_1301) (class in crate_anon.crateweb.userprofile.migrations.0004_userprofile_patients_per_page) (class in crate_anon.crateweb.userprofile.migrations.0005_userprofile_patient_multiquery_scratchpad) (class in crate_anon.crateweb.userprofile.migrations.0006_auto_20170212_0137) (class in crate_anon.crateweb.userprofile.migrations.0007_auto_20170507_1218) millimolar_from_mg_per_dl() (in module crate_anon.nlp_manager.regex_units) MiniAce (class in crate_anon.nlp_manager.parse_cognitive) MiniAceValidator (class in crate_anon.nlp_manager.parse_cognitive) Missing (class in crate_anon.crateweb.core.management.commands.runcpserver) Mmse (class in crate_anon.nlp_manager.parse_cognitive) MmseValidator (class in crate_anon.nlp_manager.parse_cognitive) Moca (class in crate_anon.nlp_manager.parse_cognitive) MocaValidator (class in crate_anon.nlp_manager.parse_cognitive) mockup() (crate_anon.crateweb.consent.models.ContactRequest method) model (crate_anon.crateweb.core.admin.ArchiveAttachmentAuditMgrAdmin attribute) (crate_anon.crateweb.core.admin.ArchiveTemplateAuditMgrAdmin attribute) (crate_anon.crateweb.core.admin.ConsentModeInline attribute) (crate_anon.crateweb.core.admin.EmailDevAdmin attribute) (crate_anon.crateweb.core.admin.PatientExplorerAuditMgrAdmin attribute) (crate_anon.crateweb.core.admin.QueryMgrAdmin attribute) (crate_anon.crateweb.core.admin.StudyInline attribute) (crate_anon.crateweb.core.admin.UserProfileInline attribute) module crate_anon.anonymise.__init__ crate_anon.anonymise.altermethod crate_anon.anonymise.anonregex crate_anon.anonymise.anonymise crate_anon.anonymise.anonymise_cli crate_anon.anonymise.config crate_anon.anonymise.config_singleton crate_anon.anonymise.constants crate_anon.anonymise.dbholder crate_anon.anonymise.dd crate_anon.anonymise.ddr crate_anon.anonymise.eponyms crate_anon.anonymise.fetch_wordlists crate_anon.anonymise.launch_multiprocess_anonymiser crate_anon.anonymise.make_demo_database crate_anon.anonymise.models crate_anon.anonymise.patient crate_anon.anonymise.scrub crate_anon.anonymise.test_anonymisation crate_anon.anonymise.test_extract_text crate_anon.common.__init__ crate_anon.common.bugfix_flashtext crate_anon.common.constants crate_anon.common.dockerfunc crate_anon.common.exceptions crate_anon.common.extendedconfigparser crate_anon.common.file_io crate_anon.common.formatting crate_anon.common.memsize crate_anon.common.parallel crate_anon.common.profiling crate_anon.common.sql crate_anon.common.stringfunc crate_anon.crateweb.__init__ crate_anon.crateweb.config.__init__ crate_anon.crateweb.config.apps crate_anon.crateweb.config.constants crate_anon.crateweb.config.settings crate_anon.crateweb.config.urls crate_anon.crateweb.config.wsgi crate_anon.crateweb.consent.__init__ crate_anon.crateweb.consent.celery crate_anon.crateweb.consent.forms crate_anon.crateweb.consent.lookup crate_anon.crateweb.consent.lookup_crs crate_anon.crateweb.consent.lookup_dummy crate_anon.crateweb.consent.lookup_rio crate_anon.crateweb.consent.management.__init__ crate_anon.crateweb.consent.management.commands.__init__ crate_anon.crateweb.consent.management.commands.email_rdbm crate_anon.crateweb.consent.management.commands.fetch_optouts crate_anon.crateweb.consent.management.commands.lookup_consent crate_anon.crateweb.consent.management.commands.lookup_patient crate_anon.crateweb.consent.management.commands.populate crate_anon.crateweb.consent.management.commands.resubmit_unprocessed_tasks crate_anon.crateweb.consent.management.commands.test_email crate_anon.crateweb.consent.migrations.0001_initial crate_anon.crateweb.consent.migrations.0002_auto_20160621_1511 crate_anon.crateweb.consent.migrations.0003_auto_20160628_1301 crate_anon.crateweb.consent.migrations.0004_auto_20160703_1530 crate_anon.crateweb.consent.migrations.0005_auto_20170203_1348 crate_anon.crateweb.consent.migrations.0006_auto_20170206_1617 crate_anon.crateweb.consent.migrations.0007_auto_20170228_1052 crate_anon.crateweb.consent.migrations.0008_auto_20170507_1218 crate_anon.crateweb.consent.migrations.0009_auto_20180629_1132 crate_anon.crateweb.consent.migrations.0010_auto_20180629_1238 crate_anon.crateweb.consent.migrations.0011_auto_20181022_0801 crate_anon.crateweb.consent.migrations.0012_auto_20181102_1335 crate_anon.crateweb.consent.migrations.0013_auto_20181223_1124 crate_anon.crateweb.consent.migrations.0014_contactrequest_rdbm_to_contact_pt crate_anon.crateweb.consent.migrations.0015_auto_20190104_1255 crate_anon.crateweb.consent.migrations.0016_auto_20190212_1118 crate_anon.crateweb.consent.migrations.__init__ crate_anon.crateweb.consent.models crate_anon.crateweb.consent.storage crate_anon.crateweb.consent.tasks crate_anon.crateweb.consent.teamlookup crate_anon.crateweb.consent.teamlookup_dummy crate_anon.crateweb.consent.teamlookup_rio crate_anon.crateweb.consent.utils crate_anon.crateweb.consent.views crate_anon.crateweb.core.__init__ crate_anon.crateweb.core.admin crate_anon.crateweb.core.auth_views crate_anon.crateweb.core.constants crate_anon.crateweb.core.context_processors crate_anon.crateweb.core.management.__init__ crate_anon.crateweb.core.management.commands.__init__ crate_anon.crateweb.core.management.commands.runcpserver crate_anon.crateweb.core.middleware crate_anon.crateweb.core.utils crate_anon.crateweb.core.views crate_anon.crateweb.extra.__init__ crate_anon.crateweb.extra.admin crate_anon.crateweb.extra.pdf crate_anon.crateweb.extra.salutation crate_anon.crateweb.manage crate_anon.crateweb.research.__init__ crate_anon.crateweb.research.archive_backend crate_anon.crateweb.research.archive_func crate_anon.crateweb.research.forms crate_anon.crateweb.research.html_functions crate_anon.crateweb.research.migrations.0001_initial crate_anon.crateweb.research.migrations.0002_auto_20170203_1348 crate_anon.crateweb.research.migrations.0003_patientexplorer_patientexploreraudit crate_anon.crateweb.research.migrations.0004_auto_20170212_0137 crate_anon.crateweb.research.migrations.0005_query_sql_hash crate_anon.crateweb.research.migrations.0006_patientexplorer_pmq_hash crate_anon.crateweb.research.migrations.0007_sitewidequery crate_anon.crateweb.research.migrations.0008_query_display crate_anon.crateweb.research.migrations.0009_query_no_null crate_anon.crateweb.research.migrations.0010_query_last_run crate_anon.crateweb.research.migrations.0011_auto_20190521_2109 crate_anon.crateweb.research.migrations.0012_archiveattachmentaudit_archivetemplateaudit crate_anon.crateweb.research.migrations.__init__ crate_anon.crateweb.research.models crate_anon.crateweb.research.research_db_info crate_anon.crateweb.research.sql_writer crate_anon.crateweb.research.tests crate_anon.crateweb.research.views crate_anon.crateweb.specimen_secret_local_settings.__init__ crate_anon.crateweb.specimen_secret_local_settings.crateweb_local_settings crate_anon.crateweb.userprofile.__init__ crate_anon.crateweb.userprofile.forms crate_anon.crateweb.userprofile.migrations.0001_initial crate_anon.crateweb.userprofile.migrations.0002_userprofile_sql_scratchpad crate_anon.crateweb.userprofile.migrations.0003_auto_20160628_1301 crate_anon.crateweb.userprofile.migrations.0004_userprofile_patients_per_page crate_anon.crateweb.userprofile.migrations.0005_userprofile_patient_multiquery_scratchpad crate_anon.crateweb.userprofile.migrations.0006_auto_20170212_0137 crate_anon.crateweb.userprofile.migrations.0007_auto_20170507_1218 crate_anon.crateweb.userprofile.migrations.__init__ crate_anon.crateweb.userprofile.models crate_anon.crateweb.userprofile.views crate_anon.linkage.__init__ crate_anon.linkage.bulk_hash crate_anon.linkage.fuzzy_id_match crate_anon.nlp_manager.__init__ crate_anon.nlp_manager.all_processors crate_anon.nlp_manager.base_nlp_parser crate_anon.nlp_manager.build_gate_java_interface crate_anon.nlp_manager.build_medex_itself crate_anon.nlp_manager.build_medex_java_interface crate_anon.nlp_manager.cloud_config crate_anon.nlp_manager.cloud_parser crate_anon.nlp_manager.cloud_request crate_anon.nlp_manager.cloud_run_info crate_anon.nlp_manager.constants crate_anon.nlp_manager.input_field_config crate_anon.nlp_manager.launch_multiprocess_nlp crate_anon.nlp_manager.models crate_anon.nlp_manager.nlp_definition crate_anon.nlp_manager.nlp_manager crate_anon.nlp_manager.number crate_anon.nlp_manager.output_user_config crate_anon.nlp_manager.parse_biochemistry crate_anon.nlp_manager.parse_clinical crate_anon.nlp_manager.parse_cognitive crate_anon.nlp_manager.parse_gate crate_anon.nlp_manager.parse_haematology crate_anon.nlp_manager.parse_medex crate_anon.nlp_manager.prepare_umls_for_bioyodie crate_anon.nlp_manager.regex_func crate_anon.nlp_manager.regex_numbers crate_anon.nlp_manager.regex_parser crate_anon.nlp_manager.regex_test crate_anon.nlp_manager.regex_units crate_anon.nlp_manager.run_gate_annie_demo crate_anon.nlp_manager.run_gate_kcl_kconnect_demo crate_anon.nlp_manager.run_gate_kcl_lewy_demo crate_anon.nlp_manager.run_gate_kcl_pharmacotherapy_demo crate_anon.nlp_manager.show_crate_gate_pipeline_options crate_anon.nlp_manager.show_crate_medex_pipeline_options crate_anon.nlp_manager.test_all_regex crate_anon.nlp_webserver.__init__ crate_anon.nlp_webserver.constants crate_anon.nlp_webserver.initialize_db crate_anon.nlp_webserver.manage_users crate_anon.nlp_webserver.models crate_anon.nlp_webserver.print_demos crate_anon.nlp_webserver.procs crate_anon.nlp_webserver.security crate_anon.nlp_webserver.server_processor crate_anon.nlp_webserver.settings crate_anon.nlp_webserver.tasks crate_anon.nlp_webserver.views crate_anon.nlp_webserver.wsgi_app crate_anon.nlp_webserver.wsgi_launchers crate_anon.preprocess.__init__ crate_anon.preprocess.ddhint crate_anon.preprocess.postcodes crate_anon.preprocess.preprocess_pcmis crate_anon.preprocess.preprocess_rio crate_anon.preprocess.rio_constants crate_anon.preprocess.rio_ddgen crate_anon.preprocess.rio_pk crate_anon.preprocess.rio_view_func crate_anon.preprocess.rio_views crate_anon.tools.__init__ crate_anon.tools.celery_status crate_anon.tools.email_rdbm crate_anon.tools.launch_celery crate_anon.tools.launch_cherrypy_server crate_anon.tools.launch_docs crate_anon.tools.launch_flower crate_anon.tools.launch_nlp_webserver_celery crate_anon.tools.launch_nlp_webserver_flower crate_anon.tools.launch_nlp_webserver_gunicorn crate_anon.tools.print_crateweb_demo_config crate_anon.tools.to_base64 crate_anon.tools.winservice

Monocytes (class in crate_anon.nlp_manager.parse_haematology) MonocytesValidator (class in crate_anon.nlp_manager.parse_haematology) MPID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute) mpid() (crate_anon.anonymise.patient.Patient property) MRID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute) mrid() (crate_anon.anonymise.patient.Patient property) MSOA2011 (class in crate_anon.preprocess.postcodes) mutate_name() (in module crate_anon.linkage.fuzzy_id_match) mutate_postcode() (in module crate_anon.linkage.fuzzy_id_match)

N

n_middle_names() (crate_anon.linkage.fuzzy_id_match.Person method) n_postcodes() (crate_anon.linkage.fuzzy_id_match.Person method) name() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) name_frequency() (crate_anon.linkage.fuzzy_id_match.NameFrequencyInfo method) NameFrequencyInfo (class in crate_anon.linkage.fuzzy_id_match) NameInfo (class in crate_anon.anonymise.fetch_wordlists) NationalPark (class in crate_anon.preprocess.postcodes) Neutrophils (class in crate_anon.nlp_manager.parse_haematology) NeutrophilsValidator (class in crate_anon.nlp_manager.parse_haematology) new_trid() (crate_anon.anonymise.models.TridRecord class method) next() (crate_anon.crateweb.research.html_functions.HtmlElementCounter method) nlp_source_url() (in module crate_anon.crateweb.research.archive_func) NlpConfigPrefixes (class in crate_anon.nlp_manager.constants) nlpdef_name() (crate_anon.nlp_manager.base_nlp_parser.TableMaker property) NlpDefConfigKeys (class in crate_anon.nlp_manager.constants) NlpDefinition (class in crate_anon.nlp_manager.nlp_definition) NlpDefValues (class in crate_anon.nlp_manager.constants) NlpOutputConfigKeys (class in crate_anon.nlp_manager.constants) NlpRecord (class in crate_anon.nlp_manager.models) nlprp_description() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser class method) nlprp_is_default_version() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser class method) nlprp_local_processors() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) nlprp_local_processors_json() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) nlprp_name() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser class method) (crate_anon.nlp_manager.parse_gate.Gate method)

nlprp_processor_dict() (in module crate_anon.nlp_webserver.tasks) nlprp_processor_info() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method) nlprp_processor_info_json() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method) nlprp_schema_info() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method) (crate_anon.nlp_manager.parse_gate.Gate method) nlprp_title() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser class method) nlprp_version() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser class method) NlprpProcessRequest (class in crate_anon.nlp_webserver.views) NlpSourceResult (class in crate_anon.crateweb.research.views) NlpWebViews (class in crate_anon.nlp_webserver.views) no_query_selected() (in module crate_anon.crateweb.research.views) noncloud_processors() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) NonspecificScrubber (class in crate_anon.anonymise.scrub) Note (class in crate_anon.anonymise.make_demo_database) notify() (crate_anon.common.sql.TransactionSizeLimiter method) notify_dest_db_transaction() (crate_anon.anonymise.config.Config method) notify_rdbm_of_bad_progress() (crate_anon.crateweb.consent.models.ContactRequest method) notify_rdbm_of_good_progress() (crate_anon.crateweb.consent.models.ContactRequest method) notify_rdbm_of_work() (crate_anon.crateweb.consent.models.ConsentMode method) (crate_anon.crateweb.consent.models.ContactRequest method) notify_src_bytes_read() (crate_anon.anonymise.config.Config method) notify_transaction() (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) now() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) null_literals() (crate_anon.nlp_manager.output_user_config.OutputUserConfig property) NumeratorOutOfDenominatorParser (class in crate_anon.nlp_manager.regex_parser) NumericalResultParser (class in crate_anon.nlp_manager.regex_parser)

O

OAClassification (class in crate_anon.preprocess.postcodes) offender_description() (crate_anon.anonymise.ddr.DataDictionaryRow property) ok_to_run() (crate_anon.crateweb.research.models.PatientMultiQuery property) opt_bool() (crate_anon.common.extendedconfigparser.ConfigSection method) opt_int() (crate_anon.common.extendedconfigparser.ConfigSection method) opt_int_positive() (crate_anon.common.extendedconfigparser.ConfigSection method) opt_multiline() (crate_anon.common.extendedconfigparser.ConfigSection method) opt_multiline_csv_pairs() (crate_anon.common.extendedconfigparser.ConfigSection method) opt_multiline_int() (crate_anon.common.extendedconfigparser.ConfigSection method) opt_out_info() (crate_anon.anonymise.ddr.DataDictionaryRow property) opt_pyvalue_list() (crate_anon.common.extendedconfigparser.ConfigSection method) opt_str() (crate_anon.common.extendedconfigparser.ConfigSection method) opt_strlist() (crate_anon.common.extendedconfigparser.ConfigSection method) opting_out() (crate_anon.anonymise.models.OptOutMpid class method) (crate_anon.anonymise.models.OptOutPid class method)

opting_out_mpid() (in module crate_anon.anonymise.anonymise) opting_out_pid() (in module crate_anon.anonymise.anonymise) OPTIONAL_POC (in module crate_anon.nlp_manager.regex_parser) OPTIONAL_RESULTS_IGNORABLES (in module crate_anon.nlp_manager.regex_parser) OptOutMpid (class in crate_anon.anonymise.models) OptOutPid (class in crate_anon.anonymise.models) other_section() (crate_anon.common.extendedconfigparser.ConfigSection method) out_of() (in module crate_anon.nlp_manager.regex_units) out_of_anything() (in module crate_anon.nlp_manager.regex_units) output_cols_html() (crate_anon.crateweb.research.models.PatientMultiQuery property) output_columns() (crate_anon.crateweb.research.models.PatientMultiQuery property) OutputUserConfig (class in crate_anon.nlp_manager.output_user_config) overall_progress() (crate_anon.anonymise.config.Config method) overflow_div() (crate_anon.crateweb.research.html_functions.HtmlElementCounter method) (in module crate_anon.crateweb.research.html_functions) overlaps() (crate_anon.linkage.fuzzy_id_match.TemporalIdentifier method)

P

p_d_given_h() (crate_anon.linkage.fuzzy_id_match.Comparison property) (crate_anon.linkage.fuzzy_id_match.DirectComparison property) (crate_anon.linkage.fuzzy_id_match.FailureComparison property) (crate_anon.linkage.fuzzy_id_match.FullPartialNoMatchComparison property) (crate_anon.linkage.fuzzy_id_match.MatchNoMatchComparison property) p_d_given_not_h() (crate_anon.linkage.fuzzy_id_match.Comparison property) (crate_anon.linkage.fuzzy_id_match.DirectComparison property) (crate_anon.linkage.fuzzy_id_match.FailureComparison property) (crate_anon.linkage.fuzzy_id_match.FullPartialNoMatchComparison property) (crate_anon.linkage.fuzzy_id_match.MatchNoMatchComparison property) p_middle_name_present() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) paginate() (in module crate_anon.crateweb.core.utils) Parish (class in crate_anon.preprocess.postcodes) parse() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method) (crate_anon.nlp_manager.parse_clinical.Bp method) (crate_anon.nlp_manager.parse_clinical.Height method) (crate_anon.nlp_manager.parse_clinical.Weight method) (crate_anon.nlp_manager.parse_gate.Gate method) (crate_anon.nlp_manager.parse_medex.Medex method) (crate_anon.nlp_manager.regex_parser.NumeratorOutOfDenominatorParser method) (crate_anon.nlp_manager.regex_parser.NumericalResultParser method) (crate_anon.nlp_manager.regex_parser.SimpleNumericalResultParser method) (crate_anon.nlp_manager.regex_parser.ValidatorBase method) parse_command() (crate_anon.nlp_webserver.views.NlpWebViews method) parse_privileged_sql() (in module crate_anon.crateweb.research.views) parser() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) parser_add_from_tables() (in module crate_anon.common.sql) parser_add_result_column() (in module crate_anon.common.sql) partially_matches() (crate_anon.linkage.fuzzy_id_match.FuzzyIdFreq method) password_change() (in module crate_anon.crateweb.core.auth_views) Patient (class in crate_anon.anonymise.make_demo_database) (class in crate_anon.anonymise.patient) patient_conditions() (crate_anon.crateweb.research.models.PatientMultiQuery property) patient_id_query() (crate_anon.crateweb.research.models.PatientMultiQuery method) patient_processing_fn() (in module crate_anon.anonymise.anonymise) patient_template_html() (in module crate_anon.crateweb.research.archive_func) PatientExplorer (class in crate_anon.crateweb.research.models) PatientExplorer.DoesNotExist PatientExplorer.MultipleObjectsReturned PatientExplorerAudit (class in crate_anon.crateweb.research.models) PatientExplorerAudit.DoesNotExist PatientExplorerAudit.MultipleObjectsReturned PatientExplorerAuditMgrAdmin (class in crate_anon.crateweb.core.admin) PatientFieldPythonTypes (class in crate_anon.crateweb.research.research_db_info) PatientInfo (class in crate_anon.anonymise.models) PatientLookup (class in crate_anon.crateweb.consent.models) PatientLookup.DoesNotExist PatientLookup.MultipleObjectsReturned PatientLookupBase (class in crate_anon.crateweb.consent.models) PatientLookupDevAdmin (class in crate_anon.crateweb.core.admin) PatientMultiQuery (class in crate_anon.crateweb.research.models) PatientResponse (class in crate_anon.crateweb.consent.models) PatientResponse.DoesNotExist PatientResponse.MultipleObjectsReturned PatientResponseAdminForm (class in crate_anon.crateweb.core.admin) PatientResponseDevAdmin (class in crate_anon.crateweb.core.admin) PatientResponseMgrAdmin (class in crate_anon.crateweb.core.admin) PcmisConfigOptions (class in crate_anon.preprocess.preprocess_pcmis) PCT2019 (class in crate_anon.preprocess.postcodes) pdf_css() (in module crate_anon.crateweb.consent.utils) pe_activate() (in module crate_anon.crateweb.research.views) pe_build() (in module crate_anon.crateweb.research.views) pe_choose() (in module crate_anon.crateweb.research.views) pe_data_finder_excel() (in module crate_anon.crateweb.research.views) pe_data_finder_results() (in module crate_anon.crateweb.research.views) pe_delete() (in module crate_anon.crateweb.research.views) pe_edit() (in module crate_anon.crateweb.research.views) pe_excel() (in module crate_anon.crateweb.research.views) pe_monster_results() (in module crate_anon.crateweb.research.views) pe_one_table() (in module crate_anon.crateweb.research.views) pe_results() (in module crate_anon.crateweb.research.views) pe_submit() (in module crate_anon.crateweb.research.views) pe_table_browser() (in module crate_anon.crateweb.research.views) pe_tsv_zip() (in module crate_anon.crateweb.research.views) per() (in module crate_anon.nlp_manager.regex_units) Person (class in crate_anon.linkage.fuzzy_id_match) person_matches() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) PersonalizedScrubber (class in crate_anon.anonymise.scrub) PFA (class in crate_anon.preprocess.postcodes) PID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute) pid() (crate_anon.anonymise.patient.Patient property) pid_rid_lookup() (in module crate_anon.crateweb.research.views) pid_rid_lookup_with_db() (in module crate_anon.crateweb.research.views) PidLookup (class in crate_anon.crateweb.research.models) pidlookup() (in module crate_anon.crateweb.research.views) PidLookup.DoesNotExist PidLookup.MultipleObjectsReturned

pidlookup_with_db() (in module crate_anon.crateweb.research.views) PidLookupForm (class in crate_anon.crateweb.research.forms) pk() (crate_anon.anonymise.ddr.DataDictionaryRow property) plaintext_csv_columns() (crate_anon.linkage.fuzzy_id_match.Person method) plaintext_csv_dict() (crate_anon.linkage.fuzzy_id_match.Person method) Platelets (class in crate_anon.nlp_manager.parse_haematology) PlateletsValidator (class in crate_anon.nlp_manager.parse_haematology) populate() (crate_anon.crateweb.consent.models.Leaflet static method) populate_generic_lookup_table() (in module crate_anon.preprocess.postcodes) populate_postcode_table() (in module crate_anon.preprocess.postcodes) possible_processor_names() (in module crate_anon.nlp_manager.all_processors) possible_processor_table() (in module crate_anon.nlp_manager.all_processors) Postcode (class in crate_anon.preprocess.postcodes) postcode_sector_freq() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) postcode_sector_frequency() (crate_anon.linkage.fuzzy_id_match.PostcodeFrequencyInfo method) postcode_sector_population() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) (crate_anon.linkage.fuzzy_id_match.PostcodeFrequencyInfo method) postcode_unit_freq() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) postcode_unit_frequency() (crate_anon.linkage.fuzzy_id_match.PostcodeFrequencyInfo method) postcode_unit_population() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) (crate_anon.linkage.fuzzy_id_match.PostcodeFrequencyInfo method) PostcodeFrequencyInfo (class in crate_anon.linkage.fuzzy_id_match) posterior_log_odds() (crate_anon.linkage.fuzzy_id_match.Comparison method) (crate_anon.linkage.fuzzy_id_match.FailureComparison method) (crate_anon.linkage.fuzzy_id_match.FullPartialNoMatchComparison method) Potassium (class in crate_anon.nlp_manager.parse_biochemistry) PotassiumValidator (class in crate_anon.nlp_manager.parse_biochemistry) power() (in module crate_anon.nlp_manager.regex_units) pre() (in module crate_anon.crateweb.research.html_functions) prepare_umls_for_bioyodie() (in module crate_anon.nlp_manager.prepare_umls_for_bioyodie) prepare_umls_for_bioyodie_meta() (in module crate_anon.nlp_manager.prepare_umls_for_bioyodie) prettified_chunks() (crate_anon.crateweb.research.models.SitewideQuery property) prettify_sql_and_args() (in module crate_anon.crateweb.research.html_functions) prettify_sql_html() (in module crate_anon.crateweb.research.html_functions) primary_pid() (crate_anon.anonymise.ddr.DataDictionaryRow property) print_cloud_processors() (in module crate_anon.nlp_manager.nlp_manager) print_compiled_regex_results() (in module crate_anon.nlp_manager.regex_test) print_info() (crate_anon.nlp_manager.base_nlp_parser.TableMaker class method) (crate_anon.nlp_manager.parse_clinical.Bp class method) (crate_anon.nlp_manager.parse_gate.Gate class method) (crate_anon.nlp_manager.parse_medex.Medex class method) (crate_anon.nlp_manager.regex_parser.NumeratorOutOfDenominatorParser method) (crate_anon.nlp_manager.regex_parser.NumericalResultParser method) (crate_anon.nlp_manager.regex_parser.ValidatorBase method) print_record_counts() (in module crate_anon.common.formatting) process() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method) process_all() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method) process_all_tables() (in module crate_anon.preprocess.preprocess_pcmis) (in module crate_anon.preprocess.preprocess_rio) process_change() (crate_anon.crateweb.consent.models.ConsentMode method) process_clindocs_table() (in module crate_anon.preprocess.preprocess_rio) process_cloud_nlp() (in module crate_anon.nlp_manager.nlp_manager) process_cloud_now() (in module crate_anon.nlp_manager.nlp_manager) process_doc() (in module crate_anon.anonymise.test_anonymisation) process_master_patient_table() (in module crate_anon.preprocess.preprocess_rio) process_nlp() (in module crate_anon.nlp_manager.nlp_manager) process_nlp_gate() (in module crate_anon.nlp_webserver.tasks) process_nlp_internal() (in module crate_anon.nlp_webserver.tasks) process_nlp_text_immediate() (in module crate_anon.nlp_webserver.tasks) process_nonpatient_table() (in module crate_anon.preprocess.preprocess_rio) process_nonpatient_tables() (in module crate_anon.anonymise.anonymise) process_now() (crate_anon.nlp_webserver.views.NlpWebViews method) process_patient_table() (in module crate_anon.preprocess.preprocess_rio) process_patient_tables() (in module crate_anon.anonymise.anonymise) process_progress_notes() (in module crate_anon.preprocess.preprocess_rio) process_request() (crate_anon.crateweb.consent.models.ContactRequest method) process_request_main() (crate_anon.crateweb.consent.models.ContactRequest method) process_response() (crate_anon.crateweb.consent.models.PatientResponse method) process_table() (in module crate_anon.anonymise.anonymise) (in module crate_anon.preprocess.preprocess_pcmis) (in module crate_anon.preprocess.preprocess_rio) processor_ids() (crate_anon.nlp_webserver.views.NlprpProcessRequest method) processor_ids_jsonstr() (crate_anon.nlp_webserver.views.NlprpProcessRequest method) ProcessorConfigKeys (class in crate_anon.nlp_manager.constants) processors() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) progdb() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) progressdb_engine() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) progressdb_metadata() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) progressdb_session() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) PseudoTempDir (class in crate_anon.nlp_manager.parse_medex) pt_address_components() (crate_anon.crateweb.consent.models.PatientLookupBase method) pt_address_components_str() (crate_anon.crateweb.consent.models.PatientLookupBase method) pt_conditions_html() (crate_anon.crateweb.research.models.PatientMultiQuery property) pt_forename_surname() (crate_anon.crateweb.consent.models.PatientLookupBase method) pt_name_address_components() (crate_anon.crateweb.consent.models.PatientLookupBase method) pt_salutation() (crate_anon.crateweb.consent.models.PatientLookupBase method) pt_title_forename_surname() (crate_anon.crateweb.consent.models.PatientLookupBase method) put_in_queue() (crate_anon.nlp_webserver.views.NlpWebViews method)

Q

Query (class in crate_anon.crateweb.research.models) Query.DoesNotExist Query.MultipleObjectsReturned query_activate() (in module crate_anon.crateweb.research.views) query_add_sitewide() (in module crate_anon.crateweb.research.views) query_build() (in module crate_anon.crateweb.research.views) query_context() (in module crate_anon.crateweb.research.views) query_count() (in module crate_anon.crateweb.research.views) query_count_current() (in module crate_anon.crateweb.research.views) query_delete() (in module crate_anon.crateweb.research.views) query_edit_select() (in module crate_anon.crateweb.research.views) query_excel() (in module crate_anon.crateweb.research.views) query_results() (in module crate_anon.crateweb.research.views)

query_results_recordwise() (in module crate_anon.crateweb.research.views) query_submit() (in module crate_anon.crateweb.research.views) query_tsv() (in module crate_anon.crateweb.research.views) QueryAudit (class in crate_anon.crateweb.research.models) QueryAudit.DoesNotExist QueryAudit.MultipleObjectsReturned QueryBase (class in crate_anon.crateweb.research.models) querybuilder_type() (crate_anon.crateweb.research.research_db_info.ColumnInfo property) QueryBuilderForm (class in crate_anon.crateweb.research.forms) QueryMgrAdmin (class in crate_anon.crateweb.core.admin) queryset() (crate_anon.crateweb.core.admin.ClinicianRespondedListFilter method) (crate_anon.crateweb.core.admin.EmailSentListFilter method) (crate_anon.crateweb.core.admin.LetterSendingStatusFilter method)

R

raise_missing() (crate_anon.common.extendedconfigparser.ExtendedConfigParser static method) RBC (class in crate_anon.nlp_manager.parse_haematology) RBCValidator (class in crate_anon.nlp_manager.parse_haematology) read_config_and_replace_values() (in module crate_anon.nlp_manager.prepare_umls_for_bioyodie) read_from_file() (crate_anon.anonymise.dd.DataDictionary method) read_from_source_databases() (crate_anon.anonymise.dd.DataDictionary method) read_people() (in module crate_anon.linkage.fuzzy_id_match) read_people_2() (in module crate_anon.linkage.fuzzy_id_match) read_static_file_contents() (in module crate_anon.crateweb.consent.utils) ReadOnlyChangeList (class in crate_anon.crateweb.extra.admin) ReadOnlyModelAdmin (class in crate_anon.crateweb.extra.admin) record_lookup_table() (crate_anon.common.sql.ViewMaker method) record_lookup_table_keyfield() (crate_anon.common.sql.ViewMaker method) record_lookup_table_keyfields() (crate_anon.common.sql.ViewMaker method) reduce_to_alphanumeric() (in module crate_anon.common.stringfunc) refresh_from_primary_clinical_record() (crate_anon.crateweb.consent.models.ConsentMode class method) remove_scrub_from_alter_methods() (crate_anon.anonymise.ddr.DataDictionaryRow method) remove_whitespace() (in module crate_anon.common.stringfunc) renames() (crate_anon.nlp_manager.output_user_config.OutputUserConfig property) render_bad_pe() (in module crate_anon.crateweb.research.views) render_bad_query() (in module crate_anon.crateweb.research.views) render_bad_query_id() (in module crate_anon.crateweb.research.views) render_email_html_to_string() (in module crate_anon.crateweb.consent.utils) render_lookup() (in module crate_anon.crateweb.research.views) render_missing_pe() (in module crate_anon.crateweb.research.views) render_missing_query() (in module crate_anon.crateweb.research.views) render_pdf_html_to_string() (in module crate_anon.crateweb.consent.utils) render_resultcount() (in module crate_anon.crateweb.research.views) render_resultset() (in module crate_anon.crateweb.research.views) render_resultset_recordwise() (in module crate_anon.crateweb.research.views) reparse_select() (in module crate_anon.crateweb.research.sql_writer) replace_in_file() (in module crate_anon.nlp_manager.build_medex_itself) replace_keywords() (crate_anon.common.bugfix_flashtext.KeywordProcessorFixed method) replacement_sqlserver_pyodbc_cursorwrapper_fetchone() (in module crate_anon.crateweb.research.models) report_exception() (in module crate_anon.common.exceptions) request_by_address_components() (crate_anon.crateweb.consent.models.ContactRequest method) request_index() (crate_anon.common.sql.ViewMaker method) require_absent() (crate_anon.common.extendedconfigparser.ConfigSection method) require_external_tool() (in module crate_anon.nlp_manager.prepare_umls_for_bioyodie)

require_option_to_be_absent() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) require_section() (crate_anon.common.extendedconfigparser.ExtendedConfigParser method) required() (crate_anon.anonymise.ddr.DataDictionaryRow property) required_scrubber() (crate_anon.anonymise.ddr.DataDictionaryRow property) ResearchAppConfig (class in crate_anon.crateweb.config.apps) ResearchDatabaseInfo (class in crate_anon.crateweb.research.research_db_info) researchdb_schemas() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo property) ResearchDbInfoKeys (class in crate_anon.crateweb.config.constants) ResearcherAdminSite (class in crate_anon.crateweb.core.admin) ResearcherSubmitContactRequestForm (class in crate_anon.crateweb.consent.forms) resend() (crate_anon.crateweb.consent.models.Email method) RestrictAdminMiddleware (class in crate_anon.crateweb.core.middleware) resultset_html_table() (in module crate_anon.crateweb.research.views) retrieve_nlp_data() (in module crate_anon.nlp_manager.nlp_manager) RID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute) rid() (crate_anon.anonymise.patient.Patient property) ridlookup() (in module crate_anon.crateweb.research.views) ridlookup_with_db() (in module crate_anon.crateweb.research.views) RidLookupForm (class in crate_anon.crateweb.research.forms) rio_add_audit_info() (in module crate_anon.preprocess.rio_view_func) rio_add_bay_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_carespell_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_consultant_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_diagnosis_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_gp_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_gp_lookup_with_practice() (in module crate_anon.preprocess.rio_view_func) rio_add_gp_practice_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_ims_event_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_location_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_org_contact_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_team_lookup() (in module crate_anon.preprocess.rio_view_func) rio_add_user_lookup() (in module crate_anon.preprocess.rio_view_func) rio_amend_standard_noncore() (in module crate_anon.preprocess.rio_view_func) rio_noncore_yn() (in module crate_anon.preprocess.rio_view_func) RioViewConfigOptions (class in crate_anon.preprocess.rio_view_func) rm_user() (in module crate_anon.nlp_webserver.manage_users) runcpserver() (in module crate_anon.crateweb.core.management.commands.runcpserver) (in module crate_anon.crateweb.manage) runserver() (in module crate_anon.crateweb.manage)

S

safe_path() (in module crate_anon.crateweb.research.archive_backend) salutation() (in module crate_anon.crateweb.extra.salutation) salutation_default_title() (in module crate_anon.crateweb.extra.salutation) save() (crate_anon.crateweb.consent.models.ConsentMode method) (crate_anon.crateweb.research.models.PatientExplorer method) (crate_anon.crateweb.research.models.PidLookup method) (crate_anon.crateweb.research.models.Query method) (crate_anon.crateweb.research.models.SitewideQuery method) save_display() (in module crate_anon.crateweb.research.views) save_model() (crate_anon.crateweb.core.admin.ConsentModeMgrAdmin method) (crate_anon.crateweb.core.admin.PatientResponseMgrAdmin method) (crate_anon.crateweb.extra.admin.ReadOnlyModelAdmin method) save_people_from_db() (in module crate_anon.linkage.fuzzy_id_match) schema() (crate_anon.common.sql.ColumnId property) (crate_anon.common.sql.SchemaId property) (crate_anon.common.sql.TableId property) schema_id() (crate_anon.common.sql.ColumnId property) (crate_anon.common.sql.TableId property) schema_identifier() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase property) schema_infodictlist() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase property) schema_tag() (crate_anon.common.sql.SchemaId property) SchemaId (class in crate_anon.common.sql) scrub() (crate_anon.anonymise.patient.Patient method) (crate_anon.anonymise.scrub.NonspecificScrubber method) (crate_anon.anonymise.scrub.PersonalizedScrubber method) (crate_anon.anonymise.scrub.ScrubberBase method) (crate_anon.anonymise.scrub.WordList method) scrubber_hash() (crate_anon.anonymise.patient.Patient property) ScrubberBase (class in crate_anon.anonymise.scrub) SCRUBMETHOD (class in crate_anon.anonymise.constants) SCRUBSRC (class in crate_anon.anonymise.constants) SelectElement (class in crate_anon.crateweb.research.sql_writer) selftest() (in module crate_anon.linkage.fuzzy_id_match) semantic_rule_engine_line() (in module crate_anon.nlp_manager.build_medex_itself) send() (crate_anon.crateweb.consent.models.Email method) send_cloud_requests() (in module crate_anon.nlp_manager.nlp_manager) send_process_request() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method) serve_html_or_pdf() (in module crate_anon.crateweb.extra.pdf) serve_pdf_from_html() (in module crate_anon.crateweb.extra.pdf) ServerProcessor (class in crate_anon.nlp_webserver.server_processor) set_display_list() (crate_anon.crateweb.research.models.Query method) set_distinct() (in module crate_anon.common.sql) set_distinct_within_parsed() (in module crate_anon.common.sql) set_echo() (crate_anon.anonymise.config.Config method) (crate_anon.nlp_manager.nlp_definition.NlpDefinition method) set_formatted_sql() (crate_anon.crateweb.research.models.QueryBase method) set_from_clinician_info_holder() (crate_anon.crateweb.consent.models.PatientLookup method) set_from_dict() (crate_anon.anonymise.ddr.DataDictionaryRow method) set_from_src_db_info() (crate_anon.anonymise.ddr.DataDictionaryRow method) set_from_text() (crate_anon.anonymise.altermethod.AlterMethod method) set_gp_name_components() (crate_anon.crateweb.consent.models.PatientLookupBase method) set_http_response_status() (crate_anon.nlp_webserver.views.NlpWebViews method) set_mpid() (crate_anon.anonymise.models.PatientInfo method) (crate_anon.anonymise.patient.Patient method) set_node_id() (crate_anon.crateweb.core.utils.JavascriptTreeNode method) set_override_query() (crate_anon.crateweb.research.models.PatientMultiQuery method) set_parser() (crate_anon.nlp_webserver.server_processor.ServerProcessor method) set_print_not_execute() (in module crate_anon.common.sql) set_procinfo_if_correct() (crate_anon.nlp_manager.cloud_parser.Cloud method) set_queue_id() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method) set_rate_limit() (crate_anon.nlp_manager.cloud_request.CloudRequest class method) set_scrubber_info() (crate_anon.anonymise.models.PatientInfo method) set_src_sqla_coltype() (crate_anon.anonymise.ddr.DataDictionaryRow method) set_tablename() (crate_anon.nlp_manager.regex_parser.NumericalResultParser method) (crate_anon.nlp_manager.regex_parser.ValidatorBase method) SettingsKeys (class in crate_anon.crateweb.core.constants) setup_opt_out() (in module crate_anon.anonymise.anonymise) show_cloud_queue() (in module crate_anon.nlp_manager.nlp_manager) show_dest_counts() (in module crate_anon.anonymise.anonymise) (in module crate_anon.nlp_manager.nlp_manager) show_docs() (in module crate_anon.preprocess.postcodes) show_queue() (crate_anon.nlp_manager.cloud_request.CloudRequestQueueManagement method) (crate_anon.nlp_webserver.views.NlpWebViews method) show_sitewide_queries() (in module crate_anon.crateweb.research.views) show_source_counts() (in module crate_anon.anonymise.anonymise) (in module crate_anon.nlp_manager.nlp_manager) simple_lookup_join() (in module crate_anon.preprocess.rio_view_func) simple_view_expr() (in module crate_anon.preprocess.rio_view_func) simple_view_where() (in module crate_anon.preprocess.rio_view_func) SimpleNumericalResultParser (class in crate_anon.nlp_manager.regex_parser) single_record_html_table() (in module crate_anon.crateweb.research.views)

single_research_db() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo property) single_research_db_with_secret_map() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo property) SingleNhsNumberForm (class in crate_anon.crateweb.consent.forms) SingleResearchDatabase (class in crate_anon.crateweb.research.research_db_info) site_absolute_url() (in module crate_anon.crateweb.core.utils) sitewide_query_delete() (in module crate_anon.crateweb.research.views) sitewide_query_process() (in module crate_anon.crateweb.research.views) SitewideQuery (class in crate_anon.crateweb.research.models) SitewideQuery.DoesNotExist SitewideQuery.MultipleObjectsReturned size() (crate_anon.crateweb.consent.models.EmailAttachment method) skip_row_by_value() (crate_anon.anonymise.ddr.DataDictionaryRow method) skip_row_if_extract_text_fails() (crate_anon.anonymise.ddr.DataDictionaryRow property) Sodium (class in crate_anon.nlp_manager.parse_biochemistry) SodiumValidator (class in crate_anon.nlp_manager.parse_biochemistry) sort() (crate_anon.anonymise.dd.DataDictionary method) source_db_names() (crate_anon.anonymise.config.Config property) source_info() (in module crate_anon.crateweb.research.views) source_session() (crate_anon.nlp_manager.input_field_config.InputFieldConfig property) split_db_schema_table() (in module crate_anon.common.sql) split_db_schema_table_column() (in module crate_anon.common.sql) sql() (crate_anon.common.sql.WhereCondition method) sql_chunks() (crate_anon.crateweb.research.models.SitewideQuery property) sql_fragment_cast_to_int() (in module crate_anon.common.sql) sql_select_column() (crate_anon.crateweb.research.sql_writer.SelectElement method) sql_select_from() (crate_anon.crateweb.research.sql_writer.SelectElement method) sqlhelper_drug_type() (in module crate_anon.crateweb.research.views) sqlhelper_drug_type_with_db() (in module crate_anon.crateweb.research.views) sqlhelper_text_anywhere() (in module crate_anon.crateweb.research.views) sqlhelper_text_anywhere_with_db() (in module crate_anon.crateweb.research.views) SQLHelperDrugTypeForm (class in crate_anon.crateweb.research.forms) SQLHelperFindAnywhereForm (class in crate_anon.crateweb.research.forms) SQLHelperTextAnywhereForm (class in crate_anon.crateweb.research.forms) src_db_lowercase() (crate_anon.anonymise.ddr.DataDictionaryRow property) src_field_lowercase() (crate_anon.anonymise.ddr.DataDictionaryRow property) src_flags() (crate_anon.anonymise.ddr.DataDictionaryRow property) src_signature() (crate_anon.anonymise.ddr.DataDictionaryRow property) src_sqla_coltype() (crate_anon.anonymise.ddr.DataDictionaryRow property) src_table_lowercase() (crate_anon.anonymise.ddr.DataDictionaryRow property) srcdatetimefield() (crate_anon.nlp_manager.input_field_config.InputFieldConfig property) srcdb() (crate_anon.nlp_manager.input_field_config.InputFieldConfig property) srcfield() (crate_anon.nlp_manager.input_field_config.InputFieldConfig property) SRCFLAG (class in crate_anon.anonymise.constants) srcpkfield() (crate_anon.nlp_manager.input_field_config.InputFieldConfig property) srctable() (crate_anon.nlp_manager.input_field_config.InputFieldConfig property) SSR (class in crate_anon.preprocess.postcodes) standard_rio_code_lookup() (in module crate_anon.preprocess.rio_view_func) standard_rio_code_lookup_with_national_code() (in module crate_anon.preprocess.rio_view_func) standardize_name() (in module crate_anon.linkage.fuzzy_id_match) standardize_postcode() (in module crate_anon.linkage.fuzzy_id_match) start_server() (in module crate_anon.crateweb.core.management.commands.runcpserver) start_task_session() (in module crate_anon.nlp_webserver.tasks) stop() (crate_anon.crateweb.consent.models.ContactRequest method) store_clinician_details() (crate_anon.crateweb.consent.models.ContactRequest method) str_or_none() (crate_anon.nlp_manager.parse_medex.Medex static method) str_to_coltype_general() (crate_anon.nlp_manager.cloud_parser.Cloud static method) string_time_now() (in module crate_anon.crateweb.core.utils) structure_excel() (in module crate_anon.crateweb.research.views) structure_table_long() (in module crate_anon.crateweb.research.views) structure_table_paginated() (in module crate_anon.crateweb.research.views) structure_tree() (in module crate_anon.crateweb.research.views) structure_tsv() (in module crate_anon.crateweb.research.views) Study (class in crate_anon.crateweb.consent.models) Study.DoesNotExist Study.MultipleObjectsReturned study_details() (in module crate_anon.crateweb.consent.views) study_details_upload_to() (in module crate_anon.crateweb.consent.models) study_form() (in module crate_anon.crateweb.consent.views) study_form_upload_to() (in module crate_anon.crateweb.consent.models) study_pack() (in module crate_anon.crateweb.consent.views) StudyInline (class in crate_anon.crateweb.core.admin) StudyMgrAdmin (class in crate_anon.crateweb.core.admin) StudyResAdmin (class in crate_anon.crateweb.core.admin) submit_contact_request() (in module crate_anon.crateweb.consent.views) summary_html() (crate_anon.crateweb.research.models.PatientExplorer property) (crate_anon.crateweb.research.models.PatientMultiQuery method) SuperuserSubmitContactRequestForm (class in crate_anon.crateweb.consent.forms) suppress_table() (crate_anon.preprocess.ddhint.DDHint method) suppress_tables() (crate_anon.preprocess.ddhint.DDHint method) surname_freq() (crate_anon.linkage.fuzzy_id_match.MatchConfig method) surname_metaphone_freq() (crate_anon.linkage.fuzzy_id_match.MatchConfig method)

T

table() (crate_anon.common.sql.ColumnId property) (crate_anon.common.sql.TableId property) table_contains() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) table_id() (crate_anon.common.sql.ColumnId property) (crate_anon.common.sql.SchemaId method) (crate_anon.common.sql.WhereCondition property) (crate_anon.crateweb.research.research_db_info.ColumnInfo property) table_is_rio_type() (in module crate_anon.preprocess.preprocess_rio) table_names() (crate_anon.anonymise.dbholder.DatabaseHolder property) table_part() (crate_anon.common.sql.TableId method) table_str() (crate_anon.common.sql.WhereCondition method) TableId (class in crate_anon.common.sql) TableMaker (class in crate_anon.nlp_manager.base_nlp_parser) TableQueryArgs (class in crate_anon.crateweb.research.models) tables() (crate_anon.nlp_manager.base_nlp_parser.TableMaker method) tables_containing_field() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) tag() (crate_anon.crateweb.research.html_functions.HtmlElementCounter method) talks_to_world() (crate_anon.crateweb.research.research_db_info.SingleResearchDatabase property) team_choices() (crate_anon.crateweb.consent.models.TeamInfo class method) TeamInfo (class in crate_anon.crateweb.consent.models) TeamRep (class in crate_anon.crateweb.consent.models) TeamRep.DoesNotExist TeamRep.MultipleObjectsReturned TeamRepAdminForm (class in crate_anon.crateweb.consent.forms) TeamRepMgrAdmin (class in crate_anon.crateweb.core.admin) teams() (crate_anon.crateweb.consent.models.TeamInfo static method) template_html() (in module crate_anon.crateweb.research.archive_func) TemporalIdentifier (class in crate_anon.linkage.fuzzy_id_match) temporary_tablename() (crate_anon.nlp_manager.nlp_definition.NlpDefinition property) terminate() (in module crate_anon.nlp_manager.build_medex_itself) test() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method) (crate_anon.nlp_manager.parse_biochemistry.Creatinine method) (crate_anon.nlp_manager.parse_biochemistry.Crp method) (crate_anon.nlp_manager.parse_biochemistry.Glucose method) (crate_anon.nlp_manager.parse_biochemistry.HbA1c method) (crate_anon.nlp_manager.parse_biochemistry.HDLCholesterol method) (crate_anon.nlp_manager.parse_biochemistry.LDLCholesterol method) (crate_anon.nlp_manager.parse_biochemistry.Lithium method) (crate_anon.nlp_manager.parse_biochemistry.Potassium method) (crate_anon.nlp_manager.parse_biochemistry.Sodium method) (crate_anon.nlp_manager.parse_biochemistry.TotalCholesterol method) (crate_anon.nlp_manager.parse_biochemistry.Triglycerides method) (crate_anon.nlp_manager.parse_biochemistry.Tsh method) (crate_anon.nlp_manager.parse_biochemistry.Urea method) (crate_anon.nlp_manager.parse_clinical.Bmi method) (crate_anon.nlp_manager.parse_clinical.Bp method) (crate_anon.nlp_manager.parse_clinical.Height method) (crate_anon.nlp_manager.parse_clinical.Weight method) (crate_anon.nlp_manager.parse_cognitive.Ace method) (crate_anon.nlp_manager.parse_cognitive.AceValidator method) (crate_anon.nlp_manager.parse_cognitive.MiniAce method) (crate_anon.nlp_manager.parse_cognitive.Mmse method) (crate_anon.nlp_manager.parse_cognitive.Moca method) (crate_anon.nlp_manager.parse_gate.Gate method) (crate_anon.nlp_manager.parse_haematology.Basophils method) (crate_anon.nlp_manager.parse_haematology.Eosinophils method) (crate_anon.nlp_manager.parse_haematology.Esr method) (crate_anon.nlp_manager.parse_haematology.Haematocrit method) (crate_anon.nlp_manager.parse_haematology.Haemoglobin method) (crate_anon.nlp_manager.parse_haematology.Lymphocytes method) (crate_anon.nlp_manager.parse_haematology.Monocytes method) (crate_anon.nlp_manager.parse_haematology.Neutrophils method) (crate_anon.nlp_manager.parse_haematology.Platelets method) (crate_anon.nlp_manager.parse_haematology.RBC method) (crate_anon.nlp_manager.parse_haematology.Wbc method) (crate_anon.nlp_manager.parse_medex.Medex method) (crate_anon.nlp_manager.regex_parser.ValidatorBase method)

test_all() (in module crate_anon.nlp_manager.parse_biochemistry) (in module crate_anon.nlp_manager.parse_clinical) (in module crate_anon.nlp_manager.parse_cognitive) (in module crate_anon.nlp_manager.parse_haematology) (in module crate_anon.nlp_manager.regex_parser) (in module crate_anon.nlp_manager.regex_units) test_all_processors() (in module crate_anon.nlp_manager.all_processors) test_all_regex_nlp() (in module crate_anon.nlp_manager.test_all_regex) test_anon() (in module crate_anon.anonymise.test_anonymisation) test_base_regexes() (in module crate_anon.nlp_manager.regex_parser) test_bp_parser() (crate_anon.nlp_manager.parse_clinical.Bp method) test_consent_lookup() (in module crate_anon.crateweb.consent.views) test_email_rdbm() (in module crate_anon.crateweb.consent.views) test_nlp_stdin() (in module crate_anon.nlp_manager.nlp_manager) test_numerator_denominator_parser() (crate_anon.nlp_manager.regex_parser.NumeratorOutOfDenominatorParser method) test_numerical_parser() (crate_anon.nlp_manager.regex_parser.NumericalResultParser method) test_parser() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method) test_patient_lookup() (in module crate_anon.crateweb.consent.views) test_text_regex() (in module crate_anon.nlp_manager.regex_test) test_unit_regexes() (in module crate_anon.nlp_manager.regex_units) test_validator() (crate_anon.nlp_manager.regex_parser.ValidatorBase method) TestAnonRegexes (class in crate_anon.anonymise.anonregex) TestCondition (class in crate_anon.linkage.fuzzy_id_match) TestTemporalIdentifier (class in crate_anon.linkage.fuzzy_id_match) text_columns() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method) textfinder_sql() (in module crate_anon.crateweb.research.views) textmatch() (in module crate_anon.crateweb.research.views) TextProcessingFailed times_ten_to_power() (in module crate_anon.nlp_manager.regex_numbers) title_forename_surname() (in module crate_anon.crateweb.extra.salutation) to_date() (in module crate_anon.crateweb.consent.utils) to_float() (in module crate_anon.nlp_manager.number) to_json_str() (in module crate_anon.nlp_manager.cloud_request) to_pos_float() (in module crate_anon.nlp_manager.number) toggle_distinct() (in module crate_anon.common.sql) TotalCholesterol (class in crate_anon.nlp_manager.parse_biochemistry) TotalCholesterolValidator (class in crate_anon.nlp_manager.parse_biochemistry) TransactionSizeLimiter (class in crate_anon.common.sql) translate_sql_qmark_to_percent() (in module crate_anon.common.sql) tree_id() (crate_anon.crateweb.core.utils.JavascriptTree property) TRID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute) trid() (crate_anon.anonymise.patient.Patient property) TridRecord (class in crate_anon.anonymise.models) Triglycerides (class in crate_anon.nlp_manager.parse_biochemistry) TriglyceridesValidator (class in crate_anon.nlp_manager.parse_biochemistry) Tsh (class in crate_anon.nlp_manager.parse_biochemistry) TshValidator (class in crate_anon.nlp_manager.parse_biochemistry) TTWA (class in crate_anon.preprocess.postcodes)

U

UmlsBioyodieConversionConfig (class in crate_anon.nlp_manager.prepare_umls_for_bioyodie) unique_identifier() (crate_anon.nlp_manager.cloud_parser.Cloud class method) unit_tests() (in module crate_anon.common.sql) (in module crate_anon.crateweb.research.sql_writer) units_by_dimension() (in module crate_anon.nlp_manager.regex_units) units_times() (in module crate_anon.nlp_manager.regex_units) update_metadata() (crate_anon.anonymise.dbholder.DatabaseHolder method) uprint() (in module crate_anon.common.stringfunc) Urea (class in crate_anon.nlp_manager.parse_biochemistry) UreaValidator (class in crate_anon.nlp_manager.parse_biochemistry) url() (crate_anon.crateweb.consent.storage.CustomFileSystemStorage method) url_with_querystring() (in module crate_anon.crateweb.core.utils) UrlKeys (class in crate_anon.crateweb.config.constants)

UrlNames (class in crate_anon.crateweb.config.constants) user_saved_so_create_profile() (in module crate_anon.crateweb.userprofile.models) UserProfile (class in crate_anon.crateweb.userprofile.models) UserProfile.DoesNotExist UserProfile.MultipleObjectsReturned UserProfileAppConfig (class in crate_anon.crateweb.config.apps) UserProfileForm (class in crate_anon.crateweb.userprofile.forms) UserProfileInline (class in crate_anon.crateweb.core.admin) uses_database_level() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo class method) UsForenameInfo (class in crate_anon.anonymise.fetch_wordlists) using_fulltext_index() (crate_anon.anonymise.ddr.DataDictionaryRow property) UsSurname1990Info (class in crate_anon.anonymise.fetch_wordlists) UsSurname2010Info (class in crate_anon.anonymise.fetch_wordlists) utf8len() (in module crate_anon.nlp_manager.cloud_request)

V

validate_1() (in module crate_anon.linkage.fuzzy_id_match) validate_2_fetch_cdl() (in module crate_anon.linkage.fuzzy_id_match) validate_2_fetch_rio() (in module crate_anon.linkage.fuzzy_id_match) validate_blank_form() (in module crate_anon.crateweb.research.views) validate_decision() (crate_anon.crateweb.consent.models.Decision method) validate_email_request() (in module crate_anon.crateweb.consent.views) validate_letter_request() (in module crate_anon.crateweb.consent.views) validate_researcher_email_domain() (in module crate_anon.crateweb.consent.utils) ValidatorBase (class in crate_anon.nlp_manager.regex_parser) values_from_row() (in module crate_anon.preprocess.postcodes) view_email_attachment() (in module crate_anon.crateweb.consent.views)

view_email_html() (in module crate_anon.crateweb.consent.views) view_formatting_dict() (in module crate_anon.preprocess.rio_view_func) view_leaflet() (in module crate_anon.crateweb.consent.views) view_letter() (in module crate_anon.crateweb.consent.views) ViewMaker (class in crate_anon.common.sql) visibility_button() (in module crate_anon.crateweb.research.html_functions) visibility_contentdiv() (in module crate_anon.crateweb.research.html_functions) visibility_div_contentdiv() (crate_anon.crateweb.research.html_functions.HtmlElementCounter method) visibility_div_spanbutton() (crate_anon.crateweb.research.html_functions.HtmlElementCounter method) visibility_div_with_divbutton() (crate_anon.crateweb.research.html_functions.HtmlElementCounter method) (in module crate_anon.crateweb.research.html_functions)

W

waitress() (in module crate_anon.nlp_webserver.wsgi_launchers) Ward2019 (class in crate_anon.preprocess.postcodes) warn_if_not_within_docker_dir() (in module crate_anon.common.dockerfunc) Wbc (class in crate_anon.nlp_manager.parse_haematology) WbcBase (class in crate_anon.nlp_manager.parse_haematology) WbcValidator (class in crate_anon.nlp_manager.parse_haematology) Weight (class in crate_anon.nlp_manager.parse_clinical) WeightValidator (class in crate_anon.nlp_manager.parse_clinical) WestminsterConstituency (class in crate_anon.preprocess.postcodes) where_allergies_current() (in module crate_anon.preprocess.rio_view_func)

where_clindocs_current() (in module crate_anon.preprocess.rio_view_func) where_not_deleted_flag() (in module crate_anon.preprocess.rio_view_func) where_patient_clause() (crate_anon.crateweb.research.models.PatientMultiQuery method) where_prognotes_current() (in module crate_anon.preprocess.rio_view_func) WhereCondition (class in crate_anon.common.sql) wipe_and_recreate_destination_db() (in module crate_anon.anonymise.anonymise) wipe_destination_data_for_opt_out_patients() (in module crate_anon.anonymise.anonymise) with_new_identifier() (crate_anon.linkage.fuzzy_id_match.TemporalIdentifier method) withdraw_consent() (crate_anon.crateweb.consent.models.ContactRequest method) WordList (class in crate_anon.anonymise.scrub) write_words_to_file() (in module crate_anon.anonymise.fetch_wordlists)