Index

A

add_visit() (OpenSpecimenAPIconnector.os_core.visit.visit method) (OpenSpecimenAPIconnector.os_util.visit_util.visit_util method) add_visit_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) add_visit_speci() (OpenSpecimenAPIconnector.os_util.visit_util.visit_util method) add_visit_specimen() (OpenSpecimenAPIconnector.os_core.visit.visit method) aggregator (class in OpenSpecimenAPIconnector.os_util.aggregated_fields) assign_role() (OpenSpecimenAPIconnector.os_core.users.users method) (OpenSpecimenAPIconnector.os_util.users_util.user_util method) assign_user_role_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) ausgabe() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) (OpenSpecimenAPIconnector.os_core.collection_protocol_event.collection_protocol_event method) (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) (OpenSpecimenAPIconnector.os_core.csv_bulk.csv_bulk method) (OpenSpecimenAPIconnector.os_core.institute.institutes method) (OpenSpecimenAPIconnector.os_core.participant.participant method) (OpenSpecimenAPIconnector.os_core.query.query method) (OpenSpecimenAPIconnector.os_core.site.sites method) (OpenSpecimenAPIconnector.os_core.specimen.specimen method) (OpenSpecimenAPIconnector.os_core.users.users method) (OpenSpecimenAPIconnector.os_core.visit.visit method)

B

bbmri_connector (class in OpenSpecimenAPIconnector.mg_util.OpenSpecimenBBMRImapping) bbmri_mapping (class in OpenSpecimenAPIconnector.mg_core.mappings) biobank_extension() (OpenSpecimenAPIconnector.mg_core.mappings.bbmri_mapping method)

biobank_map() (OpenSpecimenAPIconnector.mg_core.mappings.bbmri_mapping method) bulk_import() (OpenSpecimenAPIconnector.os_util.bulk_operations.bulk_operations method) bulk_operations (class in OpenSpecimenAPIconnector.os_util.bulk_operations)

C

change_password() (OpenSpecimenAPIconnector.os_core.users.users method) (OpenSpecimenAPIconnector.os_util.users_util.user_util method) change_user_pw_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) check_login() (OpenSpecimenAPIconnector.config.config method) check_specimen() (OpenSpecimenAPIconnector.os_core.specimen.specimen method) collection_map() (OpenSpecimenAPIconnector.mg_core.mappings.bbmri_mapping method) collection_protocol (class in OpenSpecimenAPIconnector.os_core.collection_protocol) collection_protocol_event (class in OpenSpecimenAPIconnector.os_core.collection_protocol_event) collection_protocol_registration (class in OpenSpecimenAPIconnector.os_core.collection_protocol_registration) collection_protocol_util (class in OpenSpecimenAPIconnector.os_util.collection_protocol_util) config (class in OpenSpecimenAPIconnector.config) container (class in OpenSpecimenAPIconnector.os_core.container) container_util (class in OpenSpecimenAPIconnector.os_util.container_util) cp_search_url_gen() (OpenSpecimenAPIconnector.os_core.url.url_gen method) cpevent_util (class in OpenSpecimenAPIconnector.os_util.cpevent_util) cpr_util (class in OpenSpecimenAPIconnector.os_util.cpr_util) create_aql() (OpenSpecimenAPIconnector.os_util.query_util.query_util method) create_bulk_import_job() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) create_collection_protocol() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) create_container() (OpenSpecimenAPIconnector.os_core.container.container method) (OpenSpecimenAPIconnector.os_util.container_util.container_util method) create_container_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) create_cp() (OpenSpecimenAPIconnector.os_util.collection_protocol_util.collection_protocol_util method) create_cp_event_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method)

create_CP_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) create_csv_export_job() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) create_event() (OpenSpecimenAPIconnector.os_core.collection_protocol_event.collection_protocol_event method) (OpenSpecimenAPIconnector.os_util.cpevent_util.cpevent_util method) create_export_job() (OpenSpecimenAPIconnector.os_core.csv_export.CSV_exporter method) create_extension() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) create_institute() (OpenSpecimenAPIconnector.os_core.institute.institutes method) (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) (OpenSpecimenAPIconnector.os_util.institute_util.institutes_util method) create_participant() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) create_participant_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) create_registration() (OpenSpecimenAPIconnector.os_util.cpr_util.cpr_util method) create_site() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) create_sites() (OpenSpecimenAPIconnector.os_core.site.sites method) (OpenSpecimenAPIconnector.os_util.site_util.site_util method) create_specimen() (OpenSpecimenAPIconnector.os_core.specimen.specimen method) (OpenSpecimenAPIconnector.os_util.specimen_util.specimen_util method) create_specimen_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) create_user() (OpenSpecimenAPIconnector.os_core.users.users method) (OpenSpecimenAPIconnector.os_util.users_util.user_util method) create_user_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) csv_bulk (class in OpenSpecimenAPIconnector.os_core.csv_bulk) csv_export() (OpenSpecimenAPIconnector.os_util.csv_exp_util.csv_exporter method) CSV_exporter (class in OpenSpecimenAPIconnector.os_core.csv_export) csv_exporter (class in OpenSpecimenAPIconnector.os_util.csv_exp_util)

D

delete_collection_protocol() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) delete_consent() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) delete_event() (OpenSpecimenAPIconnector.os_core.collection_protocol_event.collection_protocol_event method) delete_institute() (OpenSpecimenAPIconnector.os_core.institute.institutes method) delete_participant() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) delete_request() (OpenSpecimenAPIconnector.os_core.req_util.OS_request_gen method) delete_sites() (OpenSpecimenAPIconnector.os_core.site.sites method)

delete_specimen() (OpenSpecimenAPIconnector.os_core.specimen.specimen method) delete_specimens() (OpenSpecimenAPIconnector.os_core.url.url_gen method) (OpenSpecimenAPIconnector.os_util.specimen_util.specimen_util method) delete_user() (OpenSpecimenAPIconnector.os_core.users.users method) delete_visit() (OpenSpecimenAPIconnector.os_core.visit.visit method) disable_container() (OpenSpecimenAPIconnector.os_core.container.container method) download_consent_form() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method)

E

execute() (OpenSpecimenAPIconnector.mg_util.OpenSpecimenBBMRImapping.bbmri_connector method) execute_aql() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) (OpenSpecimenAPIconnector.os_core.query.query method)

execute_query() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) (OpenSpecimenAPIconnector.os_core.query.query method) (OpenSpecimenAPIconnector.os_util.query_util.query_util method) extract_age_fields() (OpenSpecimenAPIconnector.os_util.aggregated_fields.aggregator method)

G

get_all_collection_protocols() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) get_all_containers() (OpenSpecimenAPIconnector.os_core.container.container method) get_all_events() (OpenSpecimenAPIconnector.os_core.collection_protocol_event.collection_protocol_event method) get_all_institutes() (OpenSpecimenAPIconnector.os_core.institute.institutes method) get_all_sites() (OpenSpecimenAPIconnector.os_core.site.sites method) get_all_users() (OpenSpecimenAPIconnector.os_core.users.users method) get_auth() (OpenSpecimenAPIconnector.config.config method) get_collection_protocol() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) get_conf_obj() (OpenSpecimenAPIconnector.config.config method) get_consents() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) get_container() (OpenSpecimenAPIconnector.os_core.container.container method) get_cp_pandas_template() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) get_event() (OpenSpecimenAPIconnector.os_core.collection_protocol_event.collection_protocol_event method) get_institute() (OpenSpecimenAPIconnector.os_core.institute.institutes method) get_job_output() (OpenSpecimenAPIconnector.os_core.csv_export.CSV_exporter method) get_job_status() (OpenSpecimenAPIconnector.os_core.csv_bulk.csv_bulk method) get_participant() (OpenSpecimenAPIconnector.os_core.participant.participant method)

get_participant_matches() (OpenSpecimenAPIconnector.os_core.participant.participant method) get_participants() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) (OpenSpecimenAPIconnector.os_util.cpr_util.cpr_util method) get_registration() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) get_registrations() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) (OpenSpecimenAPIconnector.os_util.cpr_util.cpr_util method) get_request() (OpenSpecimenAPIconnector.os_core.req_util.OS_request_gen method) get_roles() (OpenSpecimenAPIconnector.os_core.users.users method) get_site() (OpenSpecimenAPIconnector.os_core.site.sites method) get_specimen() (OpenSpecimenAPIconnector.os_core.specimen.specimen method) get_template() (OpenSpecimenAPIconnector.os_core.csv_bulk.csv_bulk method) get_url() (OpenSpecimenAPIconnector.config.config method) get_user() (OpenSpecimenAPIconnector.os_core.users.users method) get_visit() (OpenSpecimenAPIconnector.os_core.visit.visit method) get_visit_namespr() (OpenSpecimenAPIconnector.os_core.visit.visit method) get_visits_cpr() (OpenSpecimenAPIconnector.os_core.visit.visit method)

H

head_request() (OpenSpecimenAPIconnector.os_core.req_util.OS_request_gen method)

I

institutes (class in OpenSpecimenAPIconnector.os_core.institute)

institutes_util (class in OpenSpecimenAPIconnector.os_util.institute_util)

J

job_report() (OpenSpecimenAPIconnector.os_core.csv_bulk.csv_bulk method)

Json_factory (class in OpenSpecimenAPIconnector.os_core.jsons)

M

mark_as_mandatory() (OpenSpecimenAPIconnector.os_core.mandatory.mark_mandatory method) mark_mandatory (class in OpenSpecimenAPIconnector.os_core.mandatory) merge_colelction_protocols() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) merge_cps() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) (OpenSpecimenAPIconnector.os_util.collection_protocol_util.collection_protocol_util method) merge_participants() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) module OpenSpecimenAPIconnector OpenSpecimenAPIconnector.config OpenSpecimenAPIconnector.mg_core OpenSpecimenAPIconnector.mg_core.mappings OpenSpecimenAPIconnector.mg_util OpenSpecimenAPIconnector.mg_util.OpenSpecimenBBMRImapping OpenSpecimenAPIconnector.os_core OpenSpecimenAPIconnector.os_core.collection_protocol OpenSpecimenAPIconnector.os_core.collection_protocol_event OpenSpecimenAPIconnector.os_core.collection_protocol_registration OpenSpecimenAPIconnector.os_core.container OpenSpecimenAPIconnector.os_core.csv_bulk OpenSpecimenAPIconnector.os_core.csv_export OpenSpecimenAPIconnector.os_core.institute OpenSpecimenAPIconnector.os_core.jsons OpenSpecimenAPIconnector.os_core.mandatory OpenSpecimenAPIconnector.os_core.participant OpenSpecimenAPIconnector.os_core.query OpenSpecimenAPIconnector.os_core.req_util OpenSpecimenAPIconnector.os_core.site OpenSpecimenAPIconnector.os_core.specimen OpenSpecimenAPIconnector.os_core.url OpenSpecimenAPIconnector.os_core.users OpenSpecimenAPIconnector.os_core.visit OpenSpecimenAPIconnector.os_util OpenSpecimenAPIconnector.os_util.aggregated_fields OpenSpecimenAPIconnector.os_util.bulk_operations OpenSpecimenAPIconnector.os_util.collection_protocol_util OpenSpecimenAPIconnector.os_util.container_util OpenSpecimenAPIconnector.os_util.cpevent_util OpenSpecimenAPIconnector.os_util.cpr_util OpenSpecimenAPIconnector.os_util.csv_exp_util OpenSpecimenAPIconnector.os_util.institute_util OpenSpecimenAPIconnector.os_util.query_util OpenSpecimenAPIconnector.os_util.site_util OpenSpecimenAPIconnector.os_util.specimen_util OpenSpecimenAPIconnector.os_util.users_util OpenSpecimenAPIconnector.os_util.visit_util

O

OpenSpecimenAPIconnector module OpenSpecimenAPIconnector.config module OpenSpecimenAPIconnector.mg_core module OpenSpecimenAPIconnector.mg_core.mappings module OpenSpecimenAPIconnector.mg_util module OpenSpecimenAPIconnector.mg_util.OpenSpecimenBBMRImapping module OpenSpecimenAPIconnector.os_core module OpenSpecimenAPIconnector.os_core.collection_protocol module OpenSpecimenAPIconnector.os_core.collection_protocol_event module OpenSpecimenAPIconnector.os_core.collection_protocol_registration module OpenSpecimenAPIconnector.os_core.container module OpenSpecimenAPIconnector.os_core.csv_bulk module OpenSpecimenAPIconnector.os_core.csv_export module OpenSpecimenAPIconnector.os_core.institute module OpenSpecimenAPIconnector.os_core.jsons module OpenSpecimenAPIconnector.os_core.mandatory module OpenSpecimenAPIconnector.os_core.participant module OpenSpecimenAPIconnector.os_core.query module OpenSpecimenAPIconnector.os_core.req_util module

OpenSpecimenAPIconnector.os_core.site module OpenSpecimenAPIconnector.os_core.specimen module OpenSpecimenAPIconnector.os_core.url module OpenSpecimenAPIconnector.os_core.users module OpenSpecimenAPIconnector.os_core.visit module OpenSpecimenAPIconnector.os_util module OpenSpecimenAPIconnector.os_util.aggregated_fields module OpenSpecimenAPIconnector.os_util.bulk_operations module OpenSpecimenAPIconnector.os_util.collection_protocol_util module OpenSpecimenAPIconnector.os_util.container_util module OpenSpecimenAPIconnector.os_util.cpevent_util module OpenSpecimenAPIconnector.os_util.cpr_util module OpenSpecimenAPIconnector.os_util.csv_exp_util module OpenSpecimenAPIconnector.os_util.institute_util module OpenSpecimenAPIconnector.os_util.query_util module OpenSpecimenAPIconnector.os_util.site_util module OpenSpecimenAPIconnector.os_util.specimen_util module OpenSpecimenAPIconnector.os_util.users_util module OpenSpecimenAPIconnector.os_util.visit_util module OS_request_gen (class in OpenSpecimenAPIconnector.os_core.req_util)

P

participant (class in OpenSpecimenAPIconnector.os_core.participant) person_extension() (OpenSpecimenAPIconnector.mg_core.mappings.bbmri_mapping method)

person_map() (OpenSpecimenAPIconnector.mg_core.mappings.bbmri_mapping method) post_request() (OpenSpecimenAPIconnector.os_core.req_util.OS_request_gen method) put_request() (OpenSpecimenAPIconnector.os_core.req_util.OS_request_gen method)

Q

query (class in OpenSpecimenAPIconnector.os_core.query)

query_url_gen() (OpenSpecimenAPIconnector.os_core.url.url_gen method) query_util (class in OpenSpecimenAPIconnector.os_util.query_util)

R

register_to_cp() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method) (OpenSpecimenAPIconnector.os_util.cpr_util.cpr_util method)

run_aggregation() (OpenSpecimenAPIconnector.os_util.aggregated_fields.aggregator method) run_upload() (OpenSpecimenAPIconnector.os_core.csv_bulk.csv_bulk method)

S

search_collection_protocols() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) search_cps() (OpenSpecimenAPIconnector.os_util.collection_protocol_util.collection_protocol_util method) search_institutes() (OpenSpecimenAPIconnector.os_core.institute.institutes method) search_query() (OpenSpecimenAPIconnector.os_core.query.query method) (OpenSpecimenAPIconnector.os_util.query_util.query_util method) search_sites() (OpenSpecimenAPIconnector.os_core.site.sites method) (OpenSpecimenAPIconnector.os_util.site_util.site_util method) search_specimen() (OpenSpecimenAPIconnector.os_core.url.url_gen method) search_specimens() (OpenSpecimenAPIconnector.os_core.specimen.specimen method) (OpenSpecimenAPIconnector.os_util.specimen_util.specimen_util method) search_visit_cprid() (OpenSpecimenAPIconnector.os_core.url.url_gen method) (OpenSpecimenAPIconnector.os_util.visit_util.visit_util method)

search_visit_name_spr() (OpenSpecimenAPIconnector.os_core.url.url_gen method) search_visit_namespr() (OpenSpecimenAPIconnector.os_util.visit_util.visit_util method) set_auth() (OpenSpecimenAPIconnector.config.config method) set_base_url() (OpenSpecimenAPIconnector.config.config method) set_login() (OpenSpecimenAPIconnector.config.config method) site_search_url_gen() (OpenSpecimenAPIconnector.os_core.url.url_gen method) site_util (class in OpenSpecimenAPIconnector.os_util.site_util) sites (class in OpenSpecimenAPIconnector.os_core.site) specimen (class in OpenSpecimenAPIconnector.os_core.specimen) specimen_util (class in OpenSpecimenAPIconnector.os_util.specimen_util) storage_location_json() (OpenSpecimenAPIconnector.os_core.jsons.Json_factory method)

U

update_collection_protocol() (OpenSpecimenAPIconnector.os_core.collection_protocol.collection_protocol method) update_container() (OpenSpecimenAPIconnector.os_core.container.container method) (OpenSpecimenAPIconnector.os_util.container_util.container_util method) update_cp() (OpenSpecimenAPIconnector.os_util.collection_protocol_util.collection_protocol_util method) update_event() (OpenSpecimenAPIconnector.os_core.collection_protocol_event.collection_protocol_event method) (OpenSpecimenAPIconnector.os_util.cpevent_util.cpevent_util method) update_institute() (OpenSpecimenAPIconnector.os_core.institute.institutes method) update_participant() (OpenSpecimenAPIconnector.os_core.collection_protocol_registration.collection_protocol_registration method) update_registration() (OpenSpecimenAPIconnector.os_util.cpr_util.cpr_util method) update_site() (OpenSpecimenAPIconnector.os_core.site.sites method) update_sites() (OpenSpecimenAPIconnector.os_util.site_util.site_util method)

update_specimen() (OpenSpecimenAPIconnector.os_core.specimen.specimen method) (OpenSpecimenAPIconnector.os_util.specimen_util.specimen_util method) update_user() (OpenSpecimenAPIconnector.os_core.users.users method) (OpenSpecimenAPIconnector.os_util.users_util.user_util method) update_visit() (OpenSpecimenAPIconnector.os_core.visit.visit method) (OpenSpecimenAPIconnector.os_util.visit_util.visit_util method) upload_csv() (OpenSpecimenAPIconnector.os_core.csv_bulk.csv_bulk method) url_gen (class in OpenSpecimenAPIconnector.os_core.url) user_name() (OpenSpecimenAPIconnector.os_core.req_util.OS_request_gen method) user_util (class in OpenSpecimenAPIconnector.os_util.users_util) users (class in OpenSpecimenAPIconnector.os_core.users)

V

visit (class in OpenSpecimenAPIconnector.os_core.visit)

visit_util (class in OpenSpecimenAPIconnector.os_util.visit_util)