CRATE
stable
Contents:
1. Overview
2. Package elements in brief
3. Reference publications
4. Installing CRATE
5. Preprocessing tools
6. Anonymisation
7. Natural language processing (NLP)
8. Configuring the CRATE web interface
9. Using the CRATE web interface
10. Ancillary tools
11. FAQs and troubleshooting
12. Linkage tools
13. Additional notes
14. Automatic documentation of source code
15. Index of CRATE commands
16. Licences
17. Change log/history
18. Things to do
19. Abbreviations
20. Glossary
CRATE
»
Index
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Index
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_
__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.dd.DDTableSummary method)
(crate_anon.anonymise.dd.ScrubSourceFieldInfo 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.NonspecificReplacer method)
(crate_anon.anonymise.scrub.NonspecificScrubber method)
(crate_anon.anonymise.scrub.PersonalizedScrubber method)
(crate_anon.anonymise.scrub.Replacer 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.IndexCreationInfo 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.comparison.AdjustLogOddsComparison method)
(crate_anon.linkage.comparison.Comparison method)
(crate_anon.linkage.comparison.DirectComparison method)
(crate_anon.linkage.comparison.FullPartialNoMatchComparison method)
(crate_anon.linkage.comparison.MatchNoMatchComparison method)
(crate_anon.linkage.frequencies.BasicNameFreqInfo method)
(crate_anon.linkage.frequencies.NameFrequencyInfo method)
(crate_anon.linkage.frequencies.PostcodeFrequencyInfo method)
(crate_anon.linkage.identifiers.BasicName method)
(crate_anon.linkage.identifiers.ComparisonInfo method)
(crate_anon.linkage.identifiers.DateOfBirth method)
(crate_anon.linkage.identifiers.DummyLetterIdentifier method)
(crate_anon.linkage.identifiers.DummyLetterTemporalIdentifier method)
(crate_anon.linkage.identifiers.Forename method)
(crate_anon.linkage.identifiers.Gender method)
(crate_anon.linkage.identifiers.Identifier method)
(crate_anon.linkage.identifiers.IdentifierFourState method)
(crate_anon.linkage.identifiers.IdentifierThreeState method)
(crate_anon.linkage.identifiers.IdentifierTwoState method)
(crate_anon.linkage.identifiers.PerfectID method)
(crate_anon.linkage.identifiers.Postcode method)
(crate_anon.linkage.identifiers.Surname method)
(crate_anon.linkage.identifiers.SurnameFragment method)
(crate_anon.linkage.identifiers.TemporalIDHolder method)
(crate_anon.linkage.matchconfig.MatchConfig method)
(crate_anon.linkage.matchresult.MatchResult method)
(crate_anon.linkage.people.People method)
(crate_anon.linkage.person.Person method)
(crate_anon.linkage.person_io.PersonWriter method)
(crate_anon.linkage.tests.fuzzy_id_match_tests.FuzzyLinkageTests method)
(crate_anon.linkage.tests.fuzzy_id_match_tests.TestCondition method)
(crate_anon.linkage.validation.entropy_names.ValidationNameFreqInfo method)
(crate_anon.linkage.validation.validate_fuzzy_linkage.CPFTValidationExtras method)
(crate_anon.linkage.validation.validate_fuzzy_linkage.PostcodeInfo 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_request_sender.CloudRequestSender 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.Albumin method)
(crate_anon.nlp_manager.parse_biochemistry.AlkPhos method)
(crate_anon.nlp_manager.parse_biochemistry.ALT method)
(crate_anon.nlp_manager.parse_biochemistry.Bilirubin method)
(crate_anon.nlp_manager.parse_biochemistry.Creatinine method)
(crate_anon.nlp_manager.parse_biochemistry.Crp method)
(crate_anon.nlp_manager.parse_biochemistry.GammaGT 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.parse_substance_misuse.AlcoholUnits 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_manager.regex_read_codes.ReadCode method)
(crate_anon.nlp_manager.tests.cloud_request_sender_tests.TestCloudRequestSender 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)
(crate_anon.preprocess.systmone_ddgen.ScrubSrcAlterMethodInfo method)
(crate_anon.preprocess.systmone_ddgen.SystmOneSRESpecRow 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)
actions (crate_anon.crateweb.core.admin.EmailResAdmin attribute)
(crate_anon.crateweb.extra.admin.AddOnlyModelAdmin attribute)
(crate_anon.crateweb.extra.admin.EditOnceOnlyModelAdmin attribute)
(crate_anon.crateweb.extra.admin.EditOnlyModelAdmin attribute)
(crate_anon.crateweb.extra.admin.ReadOnlyModelAdmin attribute)
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_alter_method() (crate_anon.preprocess.systmone_ddgen.ScrubSrcAlterMethodInfo 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.consent.management.commands.make_ethics_pack.Command method)
(crate_anon.crateweb.core.management.commands.runcpserver.Command method)
add_basic_options() (in module crate_anon.linkage.fuzzy_id_match)
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_comparison_options() (in module crate_anon.linkage.fuzzy_id_match)
add_config_options() (in module crate_anon.linkage.fuzzy_id_match)
add_error_probabilities() (in module crate_anon.linkage.fuzzy_id_match)
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_hasher_options() (in module crate_anon.linkage.fuzzy_id_match)
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_matching_rules() (in module crate_anon.linkage.fuzzy_id_match)
add_output_column() (crate_anon.crateweb.research.models.PatientMultiQuery method)
add_patient_condition() (crate_anon.crateweb.research.models.PatientMultiQuery method)
add_people() (crate_anon.linkage.people.People method)
add_person() (crate_anon.linkage.people.People method)
add_postcode_geography_view() (in module crate_anon.preprocess.preprocess_rio)
(in module crate_anon.preprocess.preprocess_systmone)
add_select() (crate_anon.common.sql.ViewMaker method)
add_source_index_request() (crate_anon.preprocess.ddhint.DDHint method)
add_src_flag() (crate_anon.preprocess.systmone_ddgen.ScrubSrcAlterMethodInfo method)
add_src_hash (crate_anon.anonymise.ddr.DataDictionaryRow property)
add_subparsers() (in module crate_anon.linkage.fuzzy_id_match)
add_testpatient_view() (in module crate_anon.preprocess.preprocess_systmone)
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)
AdjustLogOddsComparison (class in crate_anon.linkage.comparison)
age_years() (in module crate_anon.linkage.helpers)
Albumin (class in crate_anon.nlp_manager.parse_biochemistry)
AlbuminValidator (class in crate_anon.nlp_manager.parse_biochemistry)
AlcoholUnits (class in crate_anon.nlp_manager.parse_substance_misuse)
AlcoholUnitsValidator (class in crate_anon.nlp_manager.parse_substance_misuse)
AlkPhos (class in crate_anon.nlp_manager.parse_biochemistry)
AlkPhosValidator (class in crate_anon.nlp_manager.parse_biochemistry)
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_local_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)
AllowlistSerializer (class in crate_anon.crateweb.anonymise_api.serializers)
AllStaffReadOnlyModelAdmin (class in crate_anon.crateweb.extra.admin)
ALT (class in crate_anon.nlp_manager.parse_biochemistry)
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)
AlterMethodType (class in crate_anon.anonymise.constants)
ALTValidator (class in crate_anon.nlp_manager.parse_biochemistry)
anchor() (in module crate_anon.common.regex_helpers)
annotate_systmone_dd_row() (in module crate_anon.preprocess.systmone_ddgen)
AnonRegexTests2 (class in crate_anon.anonymise.tests.anonregex_tests)
AnonymisationTests (class in crate_anon.crateweb.anonymise_api.tests)
anonymise() (in module crate_anon.anonymise.anonymise)
AnonymiseDatabaseSafeConfigDefaults (class in crate_anon.anonymise.constants)
AnonymiseDatabaseSafeConfigKeys (class in crate_anon.anonymise.constants)
any_read_code_of() (in module crate_anon.nlp_manager.regex_read_codes)
ApiConfig (class in crate_anon.crateweb.config.apps)
ApiKeys (class in crate_anon.crateweb.anonymise_api.constants)
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_dict() (crate_anon.linkage.frequencies.BasicNameFreqInfo method)
(crate_anon.linkage.identifiers.BasicName method)
(crate_anon.linkage.identifiers.DateOfBirth method)
(crate_anon.linkage.identifiers.DummyLetterTemporalIdentifier method)
(crate_anon.linkage.identifiers.Gender method)
(crate_anon.linkage.identifiers.Identifier method)
(crate_anon.linkage.identifiers.PerfectID method)
(crate_anon.linkage.identifiers.Postcode method)
(crate_anon.linkage.identifiers.Surname method)
(crate_anon.linkage.identifiers.TemporalIDHolder method)
(crate_anon.linkage.person.Person method)
as_ordered_dict() (crate_anon.crateweb.research.models.Highlight static method)
as_row() (crate_anon.anonymise.ddr.DataDictionaryRow method)
as_text (crate_anon.anonymise.altermethod.AlterMethod property)
assemble_units() (in module crate_anon.nlp_manager.regex_units)
assert_alphabetical() (in module crate_anon.common.regex_helpers)
assert_freq_info() (crate_anon.anonymise.fetch_wordlists.NameInfo method)
assert_text_regex() (in module crate_anon.nlp_manager.tests.regex_test_helperfunc)
assert_view_has_same_num_rows() (in module crate_anon.common.sql)
at_start_wb() (in module crate_anon.common.regex_helpers)
at_wb_start_end() (in module crate_anon.common.regex_helpers)
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
BaseNlpParser (class in crate_anon.nlp_manager.base_nlp_parser)
basetype (crate_anon.crateweb.research.research_db_info.ColumnInfo property)
BasicName (class in crate_anon.linkage.identifiers)
BasicNameFreqInfo (class in crate_anon.linkage.frequencies)
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.comparison)
being_scrubbed (crate_anon.anonymise.ddr.DataDictionaryRow property)
Bilirubin (class in crate_anon.nlp_manager.parse_biochemistry)
BilirubinValidator (class in crate_anon.nlp_manager.parse_biochemistry)
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
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)
CertainComparison (class in crate_anon.linkage.comparison)
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_comparison_as_expected() (crate_anon.linkage.tests.fuzzy_id_match_tests.TestCondition 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_replacement_text_all_dates() (crate_anon.anonymise.scrub.NonspecificScrubber 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)
cli_make_ethics_pack() (in module crate_anon.crateweb.consent.management.commands.make_ethics_pack)
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)
CloudRequestProcessTests (class in crate_anon.nlp_manager.tests.cloud_request_process_tests)
CloudRequestQueueManagement (class in crate_anon.nlp_manager.cloud_request)
CloudRequestSender (class in crate_anon.nlp_manager.cloud_request_sender)
CloudRequestSender.State (class in crate_anon.nlp_manager.cloud_request_sender)
CloudRequestSenderTests (class in crate_anon.nlp_manager.tests.cloud_request_sender_tests)
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)
(crate_anon.common.sql.IndexCreationInfo attribute)
column_id (crate_anon.common.sql.WhereCondition property)
(crate_anon.crateweb.research.research_db_info.ColumnInfo property)
column_id() (crate_anon.common.sql.SchemaId method)
(crate_anon.common.sql.TableId method)
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.make_ethics_pack)
(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.ensuresuperuser)
(class in crate_anon.crateweb.core.management.commands.runcpserver)
Commands (class in crate_anon.linkage.fuzzy_id_match)
comment() (crate_anon.preprocess.systmone_ddgen.SystmOneSRESpecRow method)
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_files() (in module crate_anon.linkage.fuzzy_id_match)
Comparison (class in crate_anon.linkage.comparison)
comparison() (crate_anon.linkage.identifiers.Identifier method)
(crate_anon.linkage.identifiers.IdentifierFourState method)
(crate_anon.linkage.identifiers.IdentifierThreeState method)
(crate_anon.linkage.identifiers.IdentifierTwoState method)
(crate_anon.linkage.identifiers.PerfectID method)
(crate_anon.linkage.identifiers.Surname method)
(crate_anon.linkage.identifiers.TemporalIDHolder method)
comparison_relevant() (crate_anon.linkage.identifiers.Identifier method)
ComparisonInfo (class in crate_anon.linkage.identifiers)
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)
component_regex_strings() (crate_anon.nlp_manager.regex_read_codes.ReadCode method)
compress_docstring() (in module crate_anon.common.stringfunc)
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_patient_scrub_src_info (crate_anon.anonymise.ddr.DataDictionaryRow property)
contains_scrub_src (crate_anon.anonymise.ddr.DataDictionaryRow property)
contains_third_party_info (crate_anon.anonymise.ddr.DataDictionaryRow property)
contains_third_party_info_directly (crate_anon.anonymise.ddr.DataDictionaryRow property)
contains_vital_patient_info (crate_anon.anonymise.ddr.DataDictionaryRow property)
contextual_columnname() (in module crate_anon.preprocess.systmone_ddgen)
contextual_tablename() (in module crate_anon.preprocess.systmone_ddgen)
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.people.People method)
(crate_anon.linkage.person.Person method)
core_columnname() (in module crate_anon.preprocess.systmone_ddgen)
core_tablename() (in module crate_anon.preprocess.systmone_ddgen)
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)
CPFTAddressCol (class in crate_anon.preprocess.systmone_ddgen)
CPFTGenericCol (class in crate_anon.preprocess.systmone_ddgen)
CPFTOtherCol (class in crate_anon.preprocess.systmone_ddgen)
CPFTPatientCol (class in crate_anon.preprocess.systmone_ddgen)
CPFTTable (class in crate_anon.preprocess.systmone_ddgen)
CPFTValidationExtras (class in crate_anon.linkage.validation.validate_fuzzy_linkage)
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.check_text_extractor
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.demo_config
module
crate_anon.anonymise.draft_dd
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.show_counts
module
crate_anon.anonymise.summarize_dd
module
crate_anon.anonymise.test_anonymisation
module
crate_anon.anonymise.test_extract_text
module
crate_anon.anonymise.tests.anonregex_tests
module
crate_anon.anonymise.tests.scrub_tests
module
crate_anon.common.__init__
module
crate_anon.common.argparse_assist
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.inputfunc
module
crate_anon.common.logfunc
module
crate_anon.common.memsize
module
crate_anon.common.parallel
module
crate_anon.common.profiling
module
crate_anon.common.regex_helpers
module
crate_anon.common.spreadsheet
module
crate_anon.common.sql
module
crate_anon.common.stringfunc
module
crate_anon.common.tests.regex_helper_tests
module
crate_anon.common.tests.spreadsheet_tests
module
crate_anon.common.tests.sql_tests
module
crate_anon.common.tests.stringfunc_tests
module
crate_anon.crateweb.__init__
module
crate_anon.crateweb.anonymise_api.__init__
module
crate_anon.crateweb.anonymise_api.constants
module
crate_anon.crateweb.anonymise_api.serializers
module
crate_anon.crateweb.anonymise_api.tests
module
crate_anon.crateweb.anonymise_api.urls
module
crate_anon.crateweb.anonymise_api.views
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.test_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.make_ethics_pack
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.0017_replace_nullbooleanfield
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.ensuresuperuser
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.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.comparison
module
crate_anon.linkage.constants
module
crate_anon.linkage.frequencies
module
crate_anon.linkage.fuzzy_id_match
module
crate_anon.linkage.helpers
module
crate_anon.linkage.identifiers
module
crate_anon.linkage.matchconfig
module
crate_anon.linkage.matchresult
module
crate_anon.linkage.people
module
crate_anon.linkage.person
module
crate_anon.linkage.person_io
module
crate_anon.linkage.tests.fuzzy_id_match_tests
module
crate_anon.linkage.validation.entropy_names
module
crate_anon.linkage.validation.other_examples_for_paper
module
crate_anon.linkage.validation.test_01_make_inputs
module
crate_anon.linkage.validation.test_03_figure_3_stepwise_illustration
module
crate_anon.linkage.validation.test_04_verbose_comparison
module
crate_anon.linkage.validation.test_hash_speed
module
crate_anon.linkage.validation.validate_fuzzy_linkage
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_request_sender
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.parse_substance_misuse
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_read_codes
module
crate_anon.nlp_manager.regex_units
module
crate_anon.nlp_manager.run_crate_nlp_demo
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.tests.__init__
module
crate_anon.nlp_manager.tests.all_processors_tests
module
crate_anon.nlp_manager.tests.cloud_request_process_tests
module
crate_anon.nlp_manager.tests.cloud_request_sender_tests
module
crate_anon.nlp_manager.tests.nlp_parser_tests
module
crate_anon.nlp_manager.tests.parse_biochemistry_tests
module
crate_anon.nlp_manager.tests.parse_clinical_tests
module
crate_anon.nlp_manager.tests.parse_cognitive_tests
module
crate_anon.nlp_manager.tests.parse_haematology_tests
module
crate_anon.nlp_manager.tests.parse_substance_misuse_tests
module
crate_anon.nlp_manager.tests.regex_numbers_tests
module
crate_anon.nlp_manager.tests.regex_parser_tests
module
crate_anon.nlp_manager.tests.regex_read_codes_tests
module
crate_anon.nlp_manager.tests.regex_test_helperfunc
module
crate_anon.nlp_manager.tests.regex_units_tests
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.tests.settings_tests
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.constants
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.preprocess_systmone
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.preprocess.systmone_ddgen
module
crate_anon.preprocess.tests.systmone_ddgen_tests
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
CrateCommand (class in crate_anon.common.constants)
CratePath (class in crate_anon.common.constants)
CratePdfPlan (class in crate_anon.crateweb.extra.pdf)
CrateS1ViewCol (class in crate_anon.preprocess.systmone_ddgen)
CrateView (class in crate_anon.preprocess.systmone_ddgen)
CratewebService (class in crate_anon.tools.winservice)
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_from_file() (crate_anon.anonymise.dd.DataDictionary class 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.comparison.AdjustLogOddsComparison property)
(crate_anon.linkage.comparison.CertainComparison property)
(crate_anon.linkage.comparison.Comparison property)
(crate_anon.linkage.comparison.DirectComparison property)
(crate_anon.linkage.comparison.FullPartialNoMatchComparison property)
(crate_anon.linkage.comparison.ImpossibleComparison property)
(crate_anon.linkage.comparison.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)
DateOfBirth (class in crate_anon.linkage.identifiers)
DateRegexNames (class in crate_anon.anonymise.anonregex)
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)
DDTableSummary (class in crate_anon.anonymise.dd)
deactivate() (crate_anon.crateweb.research.models.Highlight method)
debug_cache_hits() (crate_anon.anonymise.dd.DataDictionary method)
debug_compare() (crate_anon.linkage.person.Person method)
debug_comparison_report() (crate_anon.linkage.person.Person method)
debug_delete_something() (crate_anon.linkage.person.Person method)
debug_gen_identifiers() (crate_anon.linkage.person.Person method)
debug_is_valid_postcode() (crate_anon.linkage.frequencies.PostcodeFrequencyInfo method)
debug_mutate_something() (crate_anon.linkage.person.Person method)
debug_postcode_sector_population() (crate_anon.linkage.frequencies.PostcodeFrequencyInfo method)
(crate_anon.linkage.matchconfig.MatchConfig method)
debug_postcode_unit_population() (crate_anon.linkage.frequencies.PostcodeFrequencyInfo method)
(crate_anon.linkage.matchconfig.MatchConfig 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)
(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_info_theory_bayes_cancer() (in module crate_anon.linkage.validation.entropy_names)
demo_nlp_config() (in module crate_anon.nlp_manager.nlp_definition)
demo_processors() (in module crate_anon.nlp_webserver.print_demos)
DenylistSerializer (class in crate_anon.crateweb.anonymise_api.serializers)
describe_sqla_col() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser static method)
description() (crate_anon.preprocess.systmone_ddgen.SystmOneSRESpecRow method)
dest_dbname (crate_anon.nlp_manager.base_nlp_parser.TableMaker property)
dest_dialect (crate_anon.anonymise.config.Config property)
(crate_anon.anonymise.dd.DataDictionary property)
(crate_anon.anonymise.ddr.DataDictionaryRow property)
dest_dialect_name (crate_anon.anonymise.config.Config property)
(crate_anon.anonymise.dd.DataDictionary property)
(crate_anon.anonymise.ddr.DataDictionaryRow 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_should_be_encrypted_pid_type (crate_anon.anonymise.ddr.DataDictionaryRow 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)
(crate_anon.nlp_manager.tests.nlp_parser_tests.FruitParser 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)
detailed_test_multiple() (crate_anon.nlp_manager.regex_parser.NumericalResultParser method)
DevAdminSite (class in crate_anon.crateweb.core.admin)
dict_from_str() (in module crate_anon.linkage.helpers)
dictfetchall() (crate_anon.crateweb.research.models.Query method)
DirectComparison (class in crate_anon.linkage.comparison)
DjangoRichHelpFormatter (class in crate_anon.crateweb.manage)
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_dd() (in module crate_anon.anonymise.draft_dd)
draft_first_traffic_light_letter() (in module crate_anon.crateweb.consent.views)
draft_from_source_databases() (crate_anon.anonymise.dd.DataDictionary method)
draft_letter_clinician_to_pt_re_study() (in module crate_anon.crateweb.consent.views)
draft_researcher_cover_letter() (in module crate_anon.crateweb.consent.views)
draft_traffic_light_decision_form() (in module crate_anon.crateweb.consent.views)
draft_traffic_light_decision_form_generic() (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)
DummyLetterIdentifier (class in crate_anon.linkage.identifiers)
DummyLetterTemporalIdentifier (class in crate_anon.linkage.identifiers)
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)
DummyTemporalIdentifierTests (class in crate_anon.linkage.tests.fuzzy_id_match_tests)
DuplicateIDError
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_has_freq_info_if_id_present() (crate_anon.linkage.identifiers.BasicName method)
(crate_anon.linkage.identifiers.DateOfBirth method)
(crate_anon.linkage.identifiers.DummyLetterTemporalIdentifier method)
(crate_anon.linkage.identifiers.Gender method)
(crate_anon.linkage.identifiers.Identifier method)
(crate_anon.linkage.identifiers.PerfectID method)
(crate_anon.linkage.identifiers.Postcode method)
(crate_anon.linkage.identifiers.Surname method)
(crate_anon.linkage.identifiers.TemporalIDHolder method)
ensure_no_source_type_mismatch() (in module crate_anon.anonymise.dd)
ensure_rid() (crate_anon.anonymise.models.PatientInfo method)
ensure_trid() (crate_anon.anonymise.models.PatientInfo method)
ensure_valid_as_candidate() (crate_anon.linkage.person.Person method)
ensure_valid_as_proband() (crate_anon.linkage.person.Person method)
ensure_valid_as_probands() (crate_anon.linkage.people.People method)
ensure_valid_as_sample() (crate_anon.linkage.people.People method)
entropy() (in module crate_anon.linkage.validation.entropy_names)
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)
eq() (in module crate_anon.preprocess.systmone_ddgen)
eq_re() (in module crate_anon.preprocess.systmone_ddgen)
escape_literal_for_regex_allowing_flexible_whitespace() (in module crate_anon.common.regex_helpers)
escape_literal_for_regex_giving_charlist() (in module crate_anon.common.regex_helpers)
escape_literal_string_for_regex() (in module crate_anon.common.regex_helpers)
(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.tests.anonregex_tests)
exceeds_primary_threshold() (crate_anon.linkage.matchconfig.MatchConfig method)
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.tests.regex_test_helperfunc)
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)
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_gutenberg_word_freq() (in module crate_anon.anonymise.fetch_wordlists)
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)
filter_words_by_freq() (in module crate_anon.anonymise.fetch_wordlists)
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)
first_n_characters_required() (in module crate_anon.common.regex_helpers)
first_two_char_frequency() (crate_anon.linkage.frequencies.NameFrequencyInfo method)
float_or_na_for_us_surnames() (in module crate_anon.anonymise.fetch_wordlists)
float_validator() (in module crate_anon.crateweb.research.forms)
Forename (class in crate_anon.linkage.identifiers)
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_dict() (crate_anon.linkage.frequencies.BasicNameFreqInfo class method)
(crate_anon.linkage.identifiers.DateOfBirth class method)
(crate_anon.linkage.identifiers.Forename class method)
(crate_anon.linkage.identifiers.Gender class method)
(crate_anon.linkage.identifiers.Identifier class method)
(crate_anon.linkage.identifiers.Postcode class method)
(crate_anon.linkage.identifiers.Surname class method)
from_file (crate_anon.anonymise.ddr.DataDictionaryRow property)
from_json_dict() (crate_anon.linkage.person.Person class method)
from_json_str() (crate_anon.linkage.person.Person class method)
from_plaintext_csv() (crate_anon.linkage.person.Person class method)
from_plaintext_str() (crate_anon.linkage.identifiers.DateOfBirth class method)
(crate_anon.linkage.identifiers.Forename class method)
(crate_anon.linkage.identifiers.Gender class method)
(crate_anon.linkage.identifiers.Identifier class method)
(crate_anon.linkage.identifiers.Postcode class method)
(crate_anon.linkage.identifiers.Surname class method)
from_schema_tag() (crate_anon.common.sql.SchemaId class method)
from_table() (crate_anon.crateweb.research.sql_writer.SelectElement method)
from_table_str() (crate_anon.crateweb.research.sql_writer.SelectElement method)
FruitParser (class in crate_anon.nlp_manager.tests.nlp_parser_tests)
FullPartialNoMatchComparison (class in crate_anon.linkage.comparison)
fully_matches() (crate_anon.linkage.identifiers.BasicName method)
(crate_anon.linkage.identifiers.DateOfBirth method)
(crate_anon.linkage.identifiers.DummyLetterTemporalIdentifier method)
(crate_anon.linkage.identifiers.Gender method)
(crate_anon.linkage.identifiers.IdentifierTwoState method)
(crate_anon.linkage.identifiers.PerfectID method)
(crate_anon.linkage.identifiers.Postcode method)
(crate_anon.linkage.identifiers.Surname method)
fully_qualified_classname() (crate_anon.nlp_manager.base_nlp_parser.TableMaker class method)
FuzzyDefaults (class in crate_anon.linkage.constants)
FuzzyLinkageTests (class in crate_anon.linkage.tests.fuzzy_id_match_tests)
G
GammaGT (class in crate_anon.nlp_manager.parse_biochemistry)
GammaGTValidator (class in crate_anon.nlp_manager.parse_biochemistry)
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_best_comparisons() (in module crate_anon.linkage.identifiers)
gen_chunks_from_files() (in module crate_anon.common.inputfunc)
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_dummy_data() (in module crate_anon.linkage.validation.test_hash_speed)
gen_excel_row_elements() (in module crate_anon.crateweb.research.models)
gen_gender_weighted_frequencies() (in module crate_anon.linkage.validation.entropy_names)
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_lines_from_binary_files_with_maxfiles() (in module crate_anon.anonymise.fetch_wordlists)
gen_monster_queries() (crate_anon.crateweb.research.models.PatientMultiQuery method)
gen_mutual_info_name_probabilities() (in module crate_anon.linkage.validation.entropy_names)
gen_name_frequency_tuples() (in module crate_anon.linkage.validation.entropy_names)
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_person_from_file() (in module crate_anon.linkage.person_io)
gen_pks() (in module crate_anon.anonymise.anonymise)
gen_rows() (crate_anon.crateweb.research.models.Query method)
(in module crate_anon.anonymise.anonymise)
gen_rows_from_csv() (in module crate_anon.common.spreadsheet)
gen_rows_from_ods() (in module crate_anon.common.spreadsheet)
gen_rows_from_spreadsheet() (in module crate_anon.common.spreadsheet)
gen_rows_from_tsv() (in module crate_anon.common.spreadsheet)
gen_rows_from_xlsx() (in module crate_anon.common.spreadsheet)
gen_shortlist() (crate_anon.linkage.people.People method)
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_word_freq_tuples_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)
gen_words_from_gutenberg_ids() (in module crate_anon.anonymise.fetch_wordlists)
Gender (class in crate_anon.linkage.identifiers)
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_anonymised() (crate_anon.crateweb.anonymise_api.serializers.ScrubSerializer method)
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_cfg_from_args() (in module crate_anon.linkage.fuzzy_id_match)
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.tests.regex_test_helperfunc)
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_schema_name() (crate_anon.crateweb.research.research_db_info.ResearchDatabaseInfo method)
get_demo_csv() (in module crate_anon.linkage.fuzzy_id_match)
get_demo_people() (in module crate_anon.linkage.fuzzy_id_match)
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_all() (crate_anon.anonymise.dd.DataDictionary method)
get_dest_tables_for_src_db_table() (crate_anon.anonymise.dd.DataDictionary method)
get_dest_tables_included() (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_docstring() (in module crate_anon.common.stringfunc)
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_phrase_unless_numeric() (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_first_two_char() (in module crate_anon.linkage.helpers)
get_forename_freq_info() (crate_anon.linkage.matchconfig.MatchConfig method)
get_forename_surname() (crate_anon.crateweb.userprofile.models.UserProfile method)
get_formatted_sql() (crate_anon.crateweb.research.models.QueryBase method)
get_frequencies() (in module crate_anon.linkage.validation.entropy_names)
get_friendly_date() (in module crate_anon.crateweb.core.utils)
get_gate_results() (in module crate_anon.nlp_webserver.tasks)
get_generic_date_regex_elements() (in module crate_anon.anonymise.anonregex)
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_flag() (in module crate_anon.preprocess.systmone_ddgen)
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.helpers)
get_mgr_admin_url() (crate_anon.crateweb.consent.models.ContactRequest method)
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_names_for_metaphone() (crate_anon.linkage.frequencies.NameFrequencyInfo 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_perfect_match() (crate_anon.linkage.people.People method)
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.helpers)
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_processors() (in module crate_anon.nlp_manager.run_crate_nlp_demo)
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_dict_search() (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_replacer() (crate_anon.anonymise.scrub.NonspecificScrubber 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_alter_details() (in module crate_anon.preprocess.systmone_ddgen)
get_scrub_from_db_table_pairs() (crate_anon.anonymise.dd.DataDictionary method)
get_scrub_from_rows() (crate_anon.anonymise.dd.DataDictionary method)
get_scrub_from_rows_as_fieldinfo() (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_no_pt_info() (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_summary_info_all_tables() (crate_anon.anonymise.dd.DataDictionary method)
get_summary_info_for_table() (crate_anon.anonymise.dd.DataDictionary method)
get_suppressed_tables() (crate_anon.preprocess.ddhint.DDHint method)
get_surname_freq_info() (crate_anon.linkage.matchconfig.MatchConfig 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_tables_w_no_pt_info() (crate_anon.anonymise.dd.DataDictionary method)
get_tables_w_scrub_src() (crate_anon.anonymise.dd.DataDictionary 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.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_unique_match() (crate_anon.linkage.people.People method)
get_unique_match_detailed() (crate_anon.linkage.people.People method)
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.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)
getdictprob() (in module crate_anon.linkage.helpers)
getdictval() (in module crate_anon.linkage.helpers)
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.make_ethics_pack.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.ensuresuperuser.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.person.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_special_alter_method (crate_anon.anonymise.ddr.DataDictionaryRow 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)
HashConfigKeys (class in crate_anon.anonymise.constants)
hashed() (crate_anon.linkage.identifiers.Identifier method)
(crate_anon.linkage.people.People method)
(crate_anon.linkage.person.Person method)
HashTests (class in crate_anon.anonymise.tests.scrub_tests)
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)
header_row() (crate_anon.anonymise.ddr.DataDictionaryRow class method)
Height (class in crate_anon.nlp_manager.parse_clinical)
HeightValidator (class in crate_anon.nlp_manager.parse_clinical)
help_v2_compare() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
help_v2_fetch() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
help_v2_hash() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
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)
HomeView (class in crate_anon.crateweb.anonymise_api.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 (class in crate_anon.linkage.identifiers)
identifier() (crate_anon.common.sql.SchemaId method)
(crate_anon.common.sql.TableId method)
IdentifierFourState (class in crate_anon.linkage.identifiers)
IdentifierThreeState (class in crate_anon.linkage.identifiers)
IdentifierTwoState (class in crate_anon.linkage.identifiers)
identity() (in module crate_anon.linkage.helpers)
IMDLookupEN (class in crate_anon.preprocess.postcodes)
IMDLookupSC (class in crate_anon.preprocess.postcodes)
IMDLookupWA (class in crate_anon.preprocess.postcodes)
ImpossibleComparison (class in crate_anon.linkage.comparison)
include (crate_anon.anonymise.ddr.DataDictionaryRow property)
include() (crate_anon.preprocess.systmone_ddgen.ScrubSrcAlterMethodInfo method)
inclusion_values (crate_anon.anonymise.ddr.DataDictionaryRow property)
index() (crate_anon.nlp_webserver.views.NlpWebViews method)
index_name (crate_anon.common.sql.IndexCreationInfo attribute)
IndexCreationInfo (class in crate_anon.common.sql)
indexes (crate_anon.nlp_manager.output_user_config.OutputUserConfig property)
IndexType (class in crate_anon.anonymise.constants)
inf_bits_from_p() (in module crate_anon.linkage.validation.entropy_names)
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_a_date() (crate_anon.anonymise.scrub.NonspecificReplacer static method)
is_clinician() (in module crate_anon.crateweb.core.utils)
is_cloud_processor() (crate_anon.nlp_manager.base_nlp_parser.TableMaker class method)
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_free_text() (in module crate_anon.preprocess.systmone_ddgen)
is_hashed() (crate_anon.linkage.person.Person method)
is_in() (in module crate_anon.preprocess.systmone_ddgen)
is_in_re() (in module crate_anon.preprocess.systmone_ddgen)
is_master_patient_table() (in module crate_anon.preprocess.systmone_ddgen)
is_mpid() (in module crate_anon.preprocess.systmone_ddgen)
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_nfa_postcode() (in module crate_anon.linkage.helpers)
is_ok_nhs_number() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
is_other_system_id() (in module crate_anon.preprocess.systmone_ddgen)
is_pair_in() (in module crate_anon.preprocess.systmone_ddgen)
is_pair_in_re() (in module crate_anon.preprocess.systmone_ddgen)
is_pid() (in module crate_anon.preprocess.systmone_ddgen)
is_pk() (in module crate_anon.preprocess.systmone_ddgen)
is_pk_integer() (crate_anon.nlp_manager.input_field_config.InputFieldConfig method)
is_plaintext() (crate_anon.linkage.person.Person method)
is_pseudopostcode() (in module crate_anon.linkage.helpers)
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_isoformat_blurred_date() (in module crate_anon.linkage.helpers)
is_valid_isoformat_date() (in module crate_anon.linkage.helpers)
is_valid_postcode() (crate_anon.linkage.matchconfig.MatchConfig method)
isoformat_date_or_none() (in module crate_anon.linkage.helpers)
isoformat_optional_date_str() (in module crate_anon.linkage.helpers)
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)
last_imd() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
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)
linked_table_core (crate_anon.preprocess.systmone_ddgen.SystmOneSRESpecRow property)
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)
ln() (in module crate_anon.linkage.helpers)
load_dd() (crate_anon.anonymise.config.Config method)
local_structure_help() (in module crate_anon.crateweb.research.views)
log_likelihood_ratio_from_p() (in module crate_anon.linkage.helpers)
log_odds_same() (crate_anon.linkage.person.Person method)
log_odds_same_hashed() (crate_anon.linkage.tests.fuzzy_id_match_tests.TestCondition method)
log_odds_same_plaintext() (crate_anon.linkage.tests.fuzzy_id_match_tests.TestCondition method)
log_posterior_odds_from_pdh_pdnh() (in module crate_anon.linkage.helpers)
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_phrase_lines_from_file() (in module crate_anon.anonymise.scrub)
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.check_text_extractor)
(in module crate_anon.anonymise.demo_config)
(in module crate_anon.anonymise.draft_dd)
(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.show_counts)
(in module crate_anon.anonymise.summarize_dd)
(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.linkage.validation.entropy_names)
(in module crate_anon.linkage.validation.test_03_figure_3_stepwise_illustration)
(in module crate_anon.linkage.validation.test_04_verbose_comparison)
(in module crate_anon.linkage.validation.test_hash_speed)
(in module crate_anon.linkage.validation.validate_fuzzy_linkage)
(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.run_crate_nlp_demo)
(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.preprocess.preprocess_systmone)
(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.validation.validate_fuzzy_linkage)
make_dest_datatype_explicit() (crate_anon.anonymise.ddr.DataDictionaryRow method)
make_dest_datatypes_explicit() (crate_anon.anonymise.dd.DataDictionary method)
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_safe_for_spreadsheet() (in module crate_anon.common.spreadsheet)
make_simple_numeric_regex() (in module crate_anon.nlp_manager.regex_parser)
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_twocol_table() (in module crate_anon.common.stringfunc)
make_typo_data() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
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)
make_wsgi_app() (in module crate_anon.nlp_webserver.wsgi_app)
mandatory_scrubbers_unfulfilled (crate_anon.anonymise.patient.Patient property)
mangle_unicode_to_ascii() (in module crate_anon.linkage.helpers)
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.matchconfig)
matches_fielddef() (crate_anon.anonymise.ddr.DataDictionaryRow method)
(in module crate_anon.common.sql)
matches_hashed() (crate_anon.linkage.tests.fuzzy_id_match_tests.TestCondition method)
matches_plaintext() (crate_anon.linkage.tests.fuzzy_id_match_tests.TestCondition method)
matches_tabledef() (crate_anon.anonymise.ddr.DataDictionaryRow method)
(in module crate_anon.common.sql)
MatchNoMatchComparison (class in crate_anon.linkage.comparison)
MatchResult (class in crate_anon.linkage.matchresult)
mebibytes() (in module crate_anon.common.constants)
Medex (class in crate_anon.nlp_manager.parse_medex)
media (crate_anon.crateweb.consent.forms.AbstractContactRequestForm property)
(crate_anon.crateweb.consent.forms.ClinicianResponseForm property)
(crate_anon.crateweb.consent.forms.ClinicianSubmitContactRequestForm property)
(crate_anon.crateweb.consent.forms.ResearcherSubmitContactRequestForm property)
(crate_anon.crateweb.consent.forms.SingleNhsNumberForm property)
(crate_anon.crateweb.consent.forms.SuperuserSubmitContactRequestForm property)
(crate_anon.crateweb.consent.forms.TeamRepAdminForm property)
(crate_anon.crateweb.core.admin.ConsentModeAdminForm property)
(crate_anon.crateweb.core.admin.PatientResponseAdminForm property)
(crate_anon.crateweb.research.forms.AddHighlightForm property)
(crate_anon.crateweb.research.forms.AddQueryForm property)
(crate_anon.crateweb.research.forms.BlankHighlightForm property)
(crate_anon.crateweb.research.forms.BlankQueryForm property)
(crate_anon.crateweb.research.forms.ClinicianAllTextFromPidForm property)
(crate_anon.crateweb.research.forms.DatabasePickerForm property)
(crate_anon.crateweb.research.forms.ManualPeQueryForm property)
(crate_anon.crateweb.research.forms.PidLookupForm property)
(crate_anon.crateweb.research.forms.QueryBuilderForm property)
(crate_anon.crateweb.research.forms.RidLookupForm property)
(crate_anon.crateweb.research.forms.SQLHelperDrugTypeForm property)
(crate_anon.crateweb.research.forms.SQLHelperFindAnywhereForm property)
(crate_anon.crateweb.research.forms.SQLHelperTextAnywhereForm property)
(crate_anon.crateweb.userprofile.forms.UserProfileForm property)
metadata (crate_anon.anonymise.dbholder.DatabaseHolder property)
metaphone_frequency() (crate_anon.linkage.frequencies.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.consent.migrations.0017_replace_nullbooleanfield)
(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)
mk_blurry_dates() (in module crate_anon.linkage.helpers)
mk_developer_debug_request() (in module crate_anon.crateweb.consent.management.commands.make_ethics_pack)
mk_dummy_match_config() (in module crate_anon.linkage.matchconfig)
mk_test_config() (in module crate_anon.linkage.tests.fuzzy_id_match_tests)
mkdir_for_filename() (in module crate_anon.linkage.helpers)
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)
modify_dd_for_systmone() (in module crate_anon.preprocess.systmone_ddgen)
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.check_text_extractor
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.demo_config
crate_anon.anonymise.draft_dd
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.show_counts
crate_anon.anonymise.summarize_dd
crate_anon.anonymise.test_anonymisation
crate_anon.anonymise.test_extract_text
crate_anon.anonymise.tests.anonregex_tests
crate_anon.anonymise.tests.scrub_tests
crate_anon.common.__init__
crate_anon.common.argparse_assist
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.inputfunc
crate_anon.common.logfunc
crate_anon.common.memsize
crate_anon.common.parallel
crate_anon.common.profiling
crate_anon.common.regex_helpers
crate_anon.common.spreadsheet
crate_anon.common.sql
crate_anon.common.stringfunc
crate_anon.common.tests.regex_helper_tests
crate_anon.common.tests.spreadsheet_tests
crate_anon.common.tests.sql_tests
crate_anon.common.tests.stringfunc_tests
crate_anon.crateweb.__init__
crate_anon.crateweb.anonymise_api.__init__
crate_anon.crateweb.anonymise_api.constants
crate_anon.crateweb.anonymise_api.serializers
crate_anon.crateweb.anonymise_api.tests
crate_anon.crateweb.anonymise_api.urls
crate_anon.crateweb.anonymise_api.views
crate_anon.crateweb.config.__init__
crate_anon.crateweb.config.apps
crate_anon.crateweb.config.constants
crate_anon.crateweb.config.settings
crate_anon.crateweb.config.test_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.make_ethics_pack
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.0017_replace_nullbooleanfield
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.ensuresuperuser
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.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.comparison
crate_anon.linkage.constants
crate_anon.linkage.frequencies
crate_anon.linkage.fuzzy_id_match
crate_anon.linkage.helpers
crate_anon.linkage.identifiers
crate_anon.linkage.matchconfig
crate_anon.linkage.matchresult
crate_anon.linkage.people
crate_anon.linkage.person
crate_anon.linkage.person_io
crate_anon.linkage.tests.fuzzy_id_match_tests
crate_anon.linkage.validation.entropy_names
crate_anon.linkage.validation.other_examples_for_paper
crate_anon.linkage.validation.test_01_make_inputs
crate_anon.linkage.validation.test_03_figure_3_stepwise_illustration
crate_anon.linkage.validation.test_04_verbose_comparison
crate_anon.linkage.validation.test_hash_speed
crate_anon.linkage.validation.validate_fuzzy_linkage
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_request_sender
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.parse_substance_misuse
crate_anon.nlp_manager.regex_func
crate_anon.nlp_manager.regex_numbers
crate_anon.nlp_manager.regex_parser
crate_anon.nlp_manager.regex_read_codes
crate_anon.nlp_manager.regex_units
crate_anon.nlp_manager.run_crate_nlp_demo
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.tests.__init__
crate_anon.nlp_manager.tests.all_processors_tests
crate_anon.nlp_manager.tests.cloud_request_process_tests
crate_anon.nlp_manager.tests.cloud_request_sender_tests
crate_anon.nlp_manager.tests.nlp_parser_tests
crate_anon.nlp_manager.tests.parse_biochemistry_tests
crate_anon.nlp_manager.tests.parse_clinical_tests
crate_anon.nlp_manager.tests.parse_cognitive_tests
crate_anon.nlp_manager.tests.parse_haematology_tests
crate_anon.nlp_manager.tests.parse_substance_misuse_tests
crate_anon.nlp_manager.tests.regex_numbers_tests
crate_anon.nlp_manager.tests.regex_parser_tests
crate_anon.nlp_manager.tests.regex_read_codes_tests
crate_anon.nlp_manager.tests.regex_test_helperfunc
crate_anon.nlp_manager.tests.regex_units_tests
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.tests.settings_tests
crate_anon.nlp_webserver.views
crate_anon.nlp_webserver.wsgi_app
crate_anon.nlp_webserver.wsgi_launchers
crate_anon.preprocess.__init__
crate_anon.preprocess.constants
crate_anon.preprocess.ddhint
crate_anon.preprocess.postcodes
crate_anon.preprocess.preprocess_pcmis
crate_anon.preprocess.preprocess_rio
crate_anon.preprocess.preprocess_systmone
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.preprocess.systmone_ddgen
crate_anon.preprocess.tests.systmone_ddgen_tests
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.anonymise.patient.Patient property)
MPID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute)
mrid (crate_anon.anonymise.patient.Patient property)
MRID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute)
MSOA2011 (class in crate_anon.preprocess.postcodes)
MultipleComparisonTestBase (class in crate_anon.linkage.tests.fuzzy_id_match_tests)
mutate_name() (in module crate_anon.linkage.helpers)
mutate_postcode() (in module crate_anon.linkage.helpers)
mutual_info() (in module crate_anon.linkage.validation.entropy_names)
N
n_definers (crate_anon.anonymise.dd.DataDictionary property)
n_forenames() (crate_anon.linkage.person.Person method)
n_postcodes() (crate_anon.linkage.person.Person method)
n_rows (crate_anon.anonymise.dd.DataDictionary property)
name (crate_anon.nlp_manager.nlp_definition.NlpDefinition property)
name_frequency() (crate_anon.linkage.frequencies.NameFrequencyInfo method)
name_frequency_info() (crate_anon.linkage.frequencies.NameFrequencyInfo method)
named_capture_group() (in module crate_anon.common.regex_helpers)
NameFrequencyInfo (class in crate_anon.linkage.frequencies)
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)
NlpParserProcessTests (class in crate_anon.nlp_manager.tests.nlp_parser_tests)
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)
NlprpDocgenSettingsTests (class in crate_anon.nlp_webserver.tests.settings_tests)
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)
noncapture_group() (in module crate_anon.common.regex_helpers)
noncloud_processors (crate_anon.nlp_manager.nlp_definition.NlpDefinition property)
NonspecificReplacer (class in crate_anon.anonymise.scrub)
NonspecificScrubber (class in crate_anon.anonymise.scrub)
NonspecificScrubberTests (class in crate_anon.anonymise.tests.scrub_tests)
not_just_at_start() (in module crate_anon.preprocess.systmone_ddgen)
not_null (crate_anon.anonymise.ddr.DataDictionaryRow property)
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)
omit() (crate_anon.preprocess.systmone_ddgen.ScrubSrcAlterMethodInfo method)
omit_rows_by_filter() (crate_anon.anonymise.dd.DataDictionary method)
open_even_if_zipped() (in module crate_anon.linkage.helpers)
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_int() (in module crate_anon.linkage.helpers)
optional_named_capture_group() (in module crate_anon.common.regex_helpers)
optional_noncapture_group() (in module crate_anon.common.regex_helpers)
OptOutMpid (class in crate_anon.anonymise.models)
OptOutPid (class in crate_anon.anonymise.models)
OrderedMultipleComparisonTests (class in crate_anon.linkage.tests.fuzzy_id_match_tests)
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.identifiers.Identifier method)
P
p_d_given_h (crate_anon.linkage.comparison.AdjustLogOddsComparison property)
(crate_anon.linkage.comparison.CertainComparison property)
(crate_anon.linkage.comparison.Comparison property)
(crate_anon.linkage.comparison.DirectComparison property)
(crate_anon.linkage.comparison.FullPartialNoMatchComparison property)
(crate_anon.linkage.comparison.ImpossibleComparison property)
(crate_anon.linkage.comparison.MatchNoMatchComparison property)
p_d_given_not_h (crate_anon.linkage.comparison.AdjustLogOddsComparison property)
(crate_anon.linkage.comparison.CertainComparison property)
(crate_anon.linkage.comparison.Comparison property)
(crate_anon.linkage.comparison.DirectComparison property)
(crate_anon.linkage.comparison.FullPartialNoMatchComparison property)
(crate_anon.linkage.comparison.ImpossibleComparison property)
(crate_anon.linkage.comparison.MatchNoMatchComparison property)
p_en (crate_anon.linkage.identifiers.BasicName property)
p_from_inf() (in module crate_anon.linkage.validation.entropy_names)
p_log2_p_over_q() (in module crate_anon.linkage.validation.entropy_names)
p_log2p() (in module crate_anon.linkage.validation.entropy_names)
p_n (crate_anon.linkage.identifiers.BasicName property)
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.parse_substance_misuse.AlcoholUnits 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_manager.tests.nlp_parser_tests.FruitParser method)
parse_alcohol_none() (crate_anon.nlp_manager.parse_substance_misuse.AlcoholUnits method)
parse_alcohol_units() (crate_anon.nlp_manager.parse_substance_misuse.AlcoholUnits method)
parse_command() (crate_anon.nlp_webserver.views.NlpWebViews method)
parse_date() (crate_anon.anonymise.scrub.NonspecificReplacer static 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)
partial_calcs() (in module crate_anon.linkage.validation.entropy_names)
partially_matches() (crate_anon.linkage.identifiers.BasicName method)
(crate_anon.linkage.identifiers.DateOfBirth method)
(crate_anon.linkage.identifiers.IdentifierThreeState method)
(crate_anon.linkage.identifiers.Postcode method)
(crate_anon.linkage.identifiers.Surname method)
partially_matches_second() (crate_anon.linkage.identifiers.BasicName method)
(crate_anon.linkage.identifiers.IdentifierFourState method)
(crate_anon.linkage.identifiers.Surname 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)
People (class in crate_anon.linkage.people)
per() (in module crate_anon.nlp_manager.regex_units)
PerfectID (class in crate_anon.linkage.identifiers)
Person (class in crate_anon.linkage.person)
PersonalizedScrubber (class in crate_anon.anonymise.scrub)
PersonalizedScrubberTests (class in crate_anon.anonymise.tests.scrub_tests)
PersonWriter (class in crate_anon.linkage.person_io)
PFA (class in crate_anon.preprocess.postcodes)
pid (crate_anon.anonymise.patient.Patient property)
PID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute)
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)
plain_or_hashed_txt() (crate_anon.linkage.person.Person static method)
plaintext_csv_columns() (crate_anon.linkage.person.Person class method)
plaintext_csv_dict() (crate_anon.linkage.person.Person method)
plaintext_str_core() (crate_anon.linkage.identifiers.BasicName method)
(crate_anon.linkage.identifiers.DateOfBirth method)
(crate_anon.linkage.identifiers.DummyLetterTemporalIdentifier method)
(crate_anon.linkage.identifiers.Gender method)
(crate_anon.linkage.identifiers.Identifier method)
(crate_anon.linkage.identifiers.PerfectID method)
(crate_anon.linkage.identifiers.Postcode method)
(crate_anon.linkage.identifiers.Surname method)
(crate_anon.linkage.identifiers.SurnameFragment method)
(crate_anon.linkage.identifiers.TemporalIDHolder 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_local_processor_names() (in module crate_anon.nlp_manager.all_processors)
possible_local_processor_names_without_external_tools() (in module crate_anon.nlp_manager.all_processors)
possible_processor_names_including_cloud() (in module crate_anon.nlp_manager.all_processors)
possible_processor_table() (in module crate_anon.nlp_manager.all_processors)
Postcode (class in crate_anon.linkage.identifiers)
(class in crate_anon.preprocess.postcodes)
postcode_temporal_identifiers() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
postcode_unit_sector_freq() (crate_anon.linkage.matchconfig.MatchConfig method)
postcode_unit_sector_frequency() (crate_anon.linkage.frequencies.PostcodeFrequencyInfo method)
PostcodeFrequencyInfo (class in crate_anon.linkage.frequencies)
PostcodeInfo (class in crate_anon.linkage.validation.validate_fuzzy_linkage)
posterior_log_odds() (crate_anon.linkage.comparison.AdjustLogOddsComparison method)
(crate_anon.linkage.comparison.CertainComparison method)
(crate_anon.linkage.comparison.Comparison method)
(crate_anon.linkage.comparison.DirectComparison method)
(crate_anon.linkage.comparison.FullPartialNoMatchComparison method)
(crate_anon.linkage.comparison.ImpossibleComparison 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)
preprocess_systmone() (in module crate_anon.preprocess.preprocess_systmone)
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.tests.regex_test_helperfunc)
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_generic_table_column() (in module crate_anon.preprocess.systmone_ddgen)
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_proband_chunk() (in module crate_anon.linkage.fuzzy_id_match)
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)
process_text() (in module crate_anon.nlp_manager.run_crate_nlp_demo)
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)
QueryColnames (class in crate_anon.linkage.validation.validate_fuzzy_linkage)
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)
RawDescriptionArgumentDefaultsRichHelpFormatter (class in crate_anon.common.argparse_assist)
RBC (class in crate_anon.nlp_manager.parse_haematology)
RBCValidator (class in crate_anon.nlp_manager.parse_haematology)
read_from_file() (crate_anon.anonymise.dd.DataDictionary method)
read_people() (in module crate_anon.linkage.fuzzy_id_match)
read_people_alternate_groups() (in module crate_anon.linkage.fuzzy_id_match)
read_static_file_contents() (in module crate_anon.crateweb.consent.utils)
read_systmone_sre_spec() (in module crate_anon.preprocess.systmone_ddgen)
ReadCode (class in crate_anon.nlp_manager.regex_read_codes)
ReadCodes (class in crate_anon.nlp_manager.regex_read_codes)
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)
RecordNotPrintable
RecordsPerRequestExceeded
reduce_to_alphanumeric() (in module crate_anon.common.stringfunc)
refresh_from_primary_clinical_record() (crate_anon.crateweb.consent.models.ConsentMode class method)
regex_components_from_read_codes() (in module crate_anon.nlp_manager.regex_read_codes)
regex_or() (in module crate_anon.common.regex_helpers)
regex_str() (crate_anon.nlp_manager.regex_read_codes.ReadCode method)
RegexHelperTests (class in crate_anon.common.tests.regex_helper_tests)
relative_entropy_kl_divergence() (in module crate_anon.linkage.validation.entropy_names)
relevant_for_nlp() (in module crate_anon.common.stringfunc)
remove_none_values_from_spreadsheet() (in module crate_anon.common.spreadsheet)
remove_redundant_whitespace() (in module crate_anon.linkage.helpers)
remove_rows_by_filter() (crate_anon.anonymise.dd.DataDictionary method)
remove_rows_by_modifying_filter() (crate_anon.anonymise.dd.DataDictionary 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() (crate_anon.anonymise.scrub.NonspecificReplacer method)
(crate_anon.anonymise.scrub.Replacer method)
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)
Replacer (class in crate_anon.anonymise.scrub)
report_exception() (in module crate_anon.common.exceptions)
report_processor_errors() (in module crate_anon.nlp_manager.cloud_request)
request_by_address_components() (crate_anon.crateweb.consent.models.ContactRequest method)
request_index() (crate_anon.common.sql.ViewMaker method)
RequestTooLong
require_absent() (crate_anon.common.extendedconfigparser.ConfigSection method)
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.anonymise.patient.Patient property)
RID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute)
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)
run_tests_nlp_and_validator_classes() (in module crate_anon.nlp_manager.tests.regex_test_helperfunc)
runcpserver() (in module crate_anon.crateweb.core.management.commands.runcpserver)
(in module crate_anon.crateweb.manage)
runserver() (in module crate_anon.crateweb.manage)
S
S1AddressCol (class in crate_anon.preprocess.systmone_ddgen)
S1ContactCol (class in crate_anon.preprocess.systmone_ddgen)
S1GenericCol (class in crate_anon.preprocess.systmone_ddgen)
S1HospNumCol (class in crate_anon.preprocess.systmone_ddgen)
S1PatientCol (class in crate_anon.preprocess.systmone_ddgen)
S1RelCol (class in crate_anon.preprocess.systmone_ddgen)
S1Table (class in crate_anon.preprocess.systmone_ddgen)
safe_path() (in module crate_anon.crateweb.research.archive_backend)
safe_upper() (in module crate_anon.linkage.helpers)
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_html_response_as_pdf() (in module crate_anon.crateweb.consent.management.commands.make_ethics_pack)
save_model() (crate_anon.crateweb.core.admin.ConsentModeMgrAdmin method)
(crate_anon.crateweb.core.admin.PatientResponseMgrAdmin method)
(crate_anon.crateweb.extra.admin.ReadOnlyModelAdmin method)
save_pdf_response() (in module crate_anon.crateweb.consent.management.commands.make_ethics_pack)
save_people_from_db() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
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)
ScrubberTestCase (class in crate_anon.anonymise.tests.scrub_tests)
ScrubMethod (class in crate_anon.anonymise.constants)
ScrubSerializer (class in crate_anon.crateweb.anonymise_api.serializers)
ScrubSourceFieldInfo (class in crate_anon.anonymise.dd)
ScrubSrc (class in crate_anon.anonymise.constants)
ScrubSrcAlterMethodInfo (class in crate_anon.preprocess.systmone_ddgen)
ScrubView (class in crate_anon.crateweb.anonymise_api.views)
SelectElement (class in crate_anon.crateweb.research.sql_writer)
semantic_rule_engine_line() (in module crate_anon.nlp_manager.build_medex_itself)
send() (crate_anon.crateweb.consent.models.Email method)
send_process_request() (crate_anon.nlp_manager.cloud_request.CloudRequestProcess method)
send_requests() (crate_anon.nlp_manager.cloud_request_sender.CloudRequestSender method)
serializer_class (crate_anon.crateweb.anonymise_api.views.ScrubView attribute)
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)
service() (crate_anon.tools.winservice.CratewebService method)
set_alter_methods_directly() (crate_anon.anonymise.ddr.DataDictionaryRow method)
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_gender() (crate_anon.linkage.identifiers.BasicName method)
(crate_anon.linkage.identifiers.Surname 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_pseudo_postcode_info() (crate_anon.linkage.validation.validate_fuzzy_linkage.CPFTValidationExtras 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() (crate_anon.anonymise.tests.scrub_tests.NonspecificScrubberTests method)
(crate_anon.anonymise.tests.scrub_tests.PersonalizedScrubberTests method)
(crate_anon.anonymise.tests.scrub_tests.ScrubberTestCase method)
(crate_anon.anonymise.tests.scrub_tests.WordListTests method)
(crate_anon.crateweb.anonymise_api.tests.AnonymisationTests method)
(crate_anon.nlp_manager.tests.cloud_request_process_tests.CloudRequestProcessTests method)
(crate_anon.nlp_manager.tests.cloud_request_sender_tests.CloudRequestSenderTests method)
(crate_anon.nlp_manager.tests.nlp_parser_tests.NlpParserProcessTests method)
setup_opt_out() (in module crate_anon.anonymise.anonymise)
should_be_fulltext_indexed() (in module crate_anon.preprocess.systmone_ddgen)
show_cloud_queue() (in module crate_anon.nlp_manager.nlp_manager)
show_dest_counts() (in module crate_anon.anonymise.show_counts)
(in module crate_anon.nlp_manager.nlp_manager)
show_docs() (in module crate_anon.preprocess.postcodes)
show_info_theory_calcs() (in module crate_anon.linkage.validation.entropy_names)
show_partial_match_frequencies() (in module crate_anon.linkage.validation.entropy_names)
show_queue() (crate_anon.nlp_manager.cloud_request.CloudRequestQueueManagement method)
(crate_anon.nlp_webserver.views.NlpWebViews method)
show_record_counts() (in module crate_anon.anonymise.show_counts)
show_sitewide_queries() (in module crate_anon.crateweb.research.views)
show_source_counts() (in module crate_anon.anonymise.show_counts)
(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)
simplify_punctuation_whitespace() (in module crate_anon.linkage.helpers)
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)
(crate_anon.linkage.people.People method)
skip_row_by_value() (crate_anon.anonymise.ddr.DataDictionaryRow method)
skip_row_if_extract_text_fails (crate_anon.anonymise.ddr.DataDictionaryRow property)
skip_spreadsheet_row() (in module crate_anon.common.spreadsheet)
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)
sort_asc_best_to_worst() (crate_anon.linkage.identifiers.ComparisonInfo static 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)
SpecificSerializer (class in crate_anon.crateweb.anonymise_api.serializers)
speedtest() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
split_db_schema_table() (in module crate_anon.common.sql)
split_db_schema_table_column() (in module crate_anon.common.sql)
SpreadsheetFileExtensions (class in crate_anon.common.spreadsheet)
SpreadsheetTests (class in crate_anon.common.tests.spreadsheet_tests)
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)
SqlTests (class in crate_anon.common.tests.sql_tests)
src_db_lowercase (crate_anon.anonymise.ddr.DataDictionaryRow property)
src_dialect (crate_anon.anonymise.ddr.DataDictionaryRow property)
src_field_lowercase (crate_anon.anonymise.ddr.DataDictionaryRow property)
src_flags (crate_anon.anonymise.ddr.DataDictionaryRow property)
src_is_textual (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)
src_textlength (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.helpers)
standardize_perfect_id_key() (in module crate_anon.linkage.helpers)
standardize_perfect_id_value() (in module crate_anon.linkage.helpers)
standardize_postcode() (in module crate_anon.linkage.helpers)
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)
StringFuncTests (class in crate_anon.common.tests.stringfunc_tests)
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)
summarize_dd() (in module crate_anon.anonymise.summarize_dd)
summary_html (crate_anon.crateweb.research.models.PatientExplorer property)
summary_html() (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 (class in crate_anon.linkage.identifiers)
surname_alternative_fragments() (in module crate_anon.linkage.helpers)
SurnameFragment (class in crate_anon.linkage.identifiers)
Switches (class in crate_anon.linkage.constants)
SystmOneContext (class in crate_anon.preprocess.systmone_ddgen)
SystmOneDDGenTests (class in crate_anon.preprocess.tests.systmone_ddgen_tests)
SystmOneSRESpecRow (class in crate_anon.preprocess.systmone_ddgen)
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.WhereCondition property)
(crate_anon.crateweb.research.research_db_info.ColumnInfo property)
table_id() (crate_anon.common.sql.SchemaId method)
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)
tablename_core (crate_anon.preprocess.systmone_ddgen.SystmOneSRESpecRow property)
tablename_prefix() (in module crate_anon.preprocess.systmone_ddgen)
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)
tcmatch() (in module crate_anon.preprocess.systmone_ddgen)
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)
TemporalIDHolder (class in crate_anon.linkage.identifiers)
temporary_tablename (crate_anon.nlp_manager.nlp_definition.NlpDefinition property)
terminate() (in module crate_anon.nlp_manager.build_medex_itself)
(in module crate_anon.preprocess.systmone_ddgen)
test() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method)
(crate_anon.nlp_manager.parse_biochemistry.Albumin method)
(crate_anon.nlp_manager.parse_biochemistry.AlkPhos method)
(crate_anon.nlp_manager.parse_biochemistry.ALT method)
(crate_anon.nlp_manager.parse_biochemistry.Bilirubin method)
(crate_anon.nlp_manager.parse_biochemistry.Creatinine method)
(crate_anon.nlp_manager.parse_biochemistry.Crp method)
(crate_anon.nlp_manager.parse_biochemistry.GammaGT 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.parse_substance_misuse.AlcoholUnits method)
(crate_anon.nlp_manager.regex_parser.ValidatorBase method)
(crate_anon.nlp_manager.tests.nlp_parser_tests.FruitParser method)
test_all_biochemistry() (crate_anon.nlp_manager.tests.parse_biochemistry_tests.TestBiochemistry static method)
test_all_clinical() (crate_anon.nlp_manager.tests.parse_clinical_tests.TestClinical static method)
test_all_cognitive() (crate_anon.nlp_manager.tests.parse_cognitive_tests.TestCognitive static method)
test_all_dates_in_supported_formats_blurred() (crate_anon.anonymise.tests.scrub_tests.NonspecificScrubberTests method)
test_all_dates_scrubbed() (crate_anon.anonymise.tests.scrub_tests.NonspecificScrubberTests method)
test_all_haematology() (crate_anon.nlp_manager.tests.parse_haematology_tests.TestHaematology static method)
test_all_processors() (crate_anon.nlp_manager.tests.all_processors_tests.TestNlpProcessors static method)
test_all_substance_misuse() (crate_anon.nlp_manager.tests.parse_substance_misuse_tests.TestSubstanceMisuse static method)
test_anon() (in module crate_anon.anonymise.test_anonymisation)
test_bp_parser() (crate_anon.nlp_manager.parse_clinical.Bp method)
test_consent_lookup() (in module crate_anon.crateweb.consent.views)
test_email_addresses() (crate_anon.anonymise.tests.anonregex_tests.AnonRegexTests2 method)
test_email_addresses_scrubbed() (crate_anon.anonymise.tests.scrub_tests.NonspecificScrubberTests method)
test_email_rdbm() (in module crate_anon.crateweb.consent.views)
test_exact_match() (crate_anon.linkage.tests.fuzzy_id_match_tests.FuzzyLinkageTests method)
test_excluded_tables() (crate_anon.preprocess.tests.systmone_ddgen_tests.SystmOneDDGenTests method)
test_hash_speed() (in module crate_anon.linkage.validation.test_hash_speed)
test_identifier_transformations() (crate_anon.linkage.tests.fuzzy_id_match_tests.FuzzyLinkageTests method)
test_nlp_stdin() (in module crate_anon.nlp_manager.nlp_manager)
test_non_dates_scrubbed() (crate_anon.anonymise.tests.scrub_tests.NonspecificScrubberTests method)
test_numerator_denominator_parser() (crate_anon.nlp_manager.regex_parser.NumeratorOutOfDenominatorParser method)
test_numerical_parser() (crate_anon.nlp_manager.regex_parser.NumericalResultParser method)
test_order_correct_with_duplicate_names_1() (crate_anon.linkage.tests.fuzzy_id_match_tests.OrderedMultipleComparisonTests method)
test_order_correct_with_duplicate_names_2() (crate_anon.linkage.tests.fuzzy_id_match_tests.OrderedMultipleComparisonTests method)
test_parser() (crate_anon.nlp_manager.base_nlp_parser.BaseNlpParser method)
test_patient_lookup() (in module crate_anon.crateweb.consent.views)
test_raises_for_unsupported_date_formats() (crate_anon.anonymise.tests.scrub_tests.NonspecificScrubberTests method)
test_shortlist() (crate_anon.linkage.tests.fuzzy_id_match_tests.FuzzyLinkageTests method)
test_str_int_hash_equivalent() (crate_anon.anonymise.tests.scrub_tests.HashTests method)
test_uk_postcodes() (crate_anon.anonymise.tests.anonregex_tests.AnonRegexTests2 method)
test_unit_regexes() (crate_anon.nlp_manager.tests.regex_units_tests.TestUnitRegexes static method)
test_validator() (crate_anon.nlp_manager.regex_parser.ValidatorBase method)
test_with_incomparable_identifiers() (crate_anon.linkage.tests.fuzzy_id_match_tests.UnorderedMultipleComparisonTests method)
test_write_values() (crate_anon.common.tests.spreadsheet_tests.SpreadsheetTests method)
TestAnonRegexes (class in crate_anon.anonymise.tests.anonregex_tests)
TestBiochemistry (class in crate_anon.nlp_manager.tests.parse_biochemistry_tests)
TestClinical (class in crate_anon.nlp_manager.tests.parse_clinical_tests)
TestCloudRequestSender (class in crate_anon.nlp_manager.tests.cloud_request_sender_tests)
TestCognitive (class in crate_anon.nlp_manager.tests.parse_cognitive_tests)
TestCondition (class in crate_anon.linkage.tests.fuzzy_id_match_tests)
TestHaematology (class in crate_anon.nlp_manager.tests.parse_haematology_tests)
TestNlpProcessors (class in crate_anon.nlp_manager.tests.all_processors_tests)
TestNumberRegexes (class in crate_anon.nlp_manager.tests.regex_numbers_tests)
TestParserRegexes (class in crate_anon.nlp_manager.tests.regex_parser_tests)
TestReadCodeRegexes (class in crate_anon.nlp_manager.tests.regex_read_codes_tests)
TestSubstanceMisuse (class in crate_anon.nlp_manager.tests.parse_substance_misuse_tests)
TestUnitRegexes (class in crate_anon.nlp_manager.tests.regex_units_tests)
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
third_party_pid (crate_anon.anonymise.ddr.DataDictionaryRow property)
tidy_draft() (crate_anon.anonymise.dd.DataDictionary method)
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.anonymise.patient.Patient property)
TRID (crate_anon.crateweb.research.research_db_info.PatientFieldPythonTypes attribute)
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)
trim_docstring() (in module crate_anon.common.stringfunc)
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
unique (crate_anon.common.sql.IndexCreationInfo attribute)
unit_tests() (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)
UnorderedMultipleComparisonTests (class in crate_anon.linkage.tests.fuzzy_id_match_tests)
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_cloud_processors (crate_anon.nlp_manager.nlp_definition.NlpDefinition property)
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
v2_hashed() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
v2_outhashed() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
v2_outplain() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
v2_plaintext() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
validate_1() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
validate_2_fetch_cdl() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
validate_2_fetch_pcmis() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
validate_2_fetch_rio() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
validate_2_fetch_systmone() (in module crate_anon.linkage.validation.validate_fuzzy_linkage)
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_prob() (in module crate_anon.linkage.helpers)
validate_researcher_email_domain() (in module crate_anon.crateweb.consent.utils)
validate_uncertain_prob() (in module crate_anon.linkage.helpers)
ValidationNameFreqInfo (class in crate_anon.linkage.validation.entropy_names)
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_identifier_long() (in module crate_anon.anonymise.ddr)
warn_if_llr_order_unexpected() (crate_anon.linkage.identifiers.IdentifierTwoState method)
warn_if_not_within_docker_dir() (in module crate_anon.common.dockerfunc)
warn_once() (in module crate_anon.common.logfunc)
warn_or_fail_if_default_key() (in module crate_anon.linkage.fuzzy_id_match)
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)
weighted_mean() (crate_anon.linkage.frequencies.BasicNameFreqInfo static method)
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)
withdraw_consent() (crate_anon.crateweb.consent.models.ContactRequest method)
WordList (class in crate_anon.anonymise.scrub)
WordListTests (class in crate_anon.anonymise.tests.scrub_tests)
write() (crate_anon.anonymise.dd.DataDictionary method)
(crate_anon.linkage.person_io.PersonWriter method)
write_csv() (in module crate_anon.common.spreadsheet)
write_ods() (in module crate_anon.common.spreadsheet)
write_people() (in module crate_anon.linkage.person_io)
write_spreadsheet() (in module crate_anon.common.spreadsheet)
write_tsv() (in module crate_anon.common.spreadsheet)
write_words_to_file() (in module crate_anon.anonymise.fetch_wordlists)
write_xlsx() (in module crate_anon.common.spreadsheet)
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