# GNUmed database system bootstrapping config file #------------------------------------------------- # license: GPL v2 or later # author: Karsten address@hidden #---------------------------------- [revision control] file = /home/ncq/Projekte/cvs2git/vcs-mirror/gnumed/gnumed/server/bootstrap/update_db-v18_v19.conf version = 1.0 #---------------------------------- [installation] interactive = no keep temp files = no description = $description$ This will update an existing GNUmed version 18 database to the version 19 schema. It does not do any harm to the data contained within. The existing database will be cloned first. The copy is then modified. The original database remains unchanged. ************************************************************ * Before upgrading your existing v18 database to the * * v19 schema it is very advisable to make sure you * * have created - using the 1.3 client against the v18 * * database -- an organization and a unit thereof to * * serve as your praxis and praxis location. During the * * very first start of the 1.4 client you will be asked * * which organization/unit represents your praxis/location. * ************************************************************ $description$ bundles = $bundles$ v18_fixups-pre_v19 v18-v19-static v18-v19-dynamic v19-fixups $bundles$ #---------------------------------- [bundle v18_fixups-pre_v19] database alias = gnumed_v19 minimum postgresql version = 9.1 schema base directory = ../sql/v17-v18/fixups/ schema = $schema$ v18-role-permissions-fixup.sql v18-cfg-depreciated_placeholders-fixup.sql v18-cfg-report_query-fixup.sql v18-dem-v_message_inbox-fixup.sql v18-clin-keyword_expansion-data-fixup.sql v18-clin-soapU_check-fixup.sql v18-clin-results_review_change-fixup.sql v18-ref-Epworth_Sleepiness_Scale_1997-fixup.sql v18-ref-bacterial_conjunctivitis_score-fixup.sql v18-ref-Bird_PMR_1979-fixup.sql v18-ref-DEGAM_HWI_2012-fixup.sql v18-ref-MELD_score-fixup.sql v18-ref-recalls_template-fixup.sql v18-i18n-french_translations.sql v18-bill-bill_item-fixup.sql v18-ref-paperwork_templates-fixup.sql $schema$ #---------------------------------- [bundle v18-v19-static] database alias = gnumed_v19 minimum postgresql version = 9.1 schema base directory = ../sql/v18-v19/static/ schema = $schema$ v19-ref-paperwork_templates-static.sql v19-ref-atc-static.sql v19-dem-lnk_org_unit2comm-static.sql v19-dem-praxis_branch-static.sql v19-clin-hospital_stay-static.sql v19-clin-procedure-static.sql $schema$ #---------------------------------- [bundle v18-v19-dynamic] database alias = gnumed_v19 minimum postgresql version = 9.1 schema base directory = ../sql/v18-v19/dynamic/ schema = $schema$ v19-gm-schema_revision_handling.sql v19-notifications-dynamic.sql v19-blobs-delete_document.sql v19-dem-v_staff.sql v19-dem-v_persons.sql v19-dem-v_org_unit_comms.sql v19-dem-organization-dynamic.sql v19-dem-praxis_branch-dynamic.sql v19-dem-provider_inbox-dynamic.sql v19-clin-hospital_stay-dynamic.sql v19-clin-procedure-dynamic.sql v19-clin-encounter-dynamic.sql v19-clin-episode-dynamic.sql v19-clin-v_substance_intakes.sql v19-clin-get_hints_for_patient.sql v19-clin-v_narrative.sql v19-clin-v_hospital_stays_journal.sql v19-clin-v_procedures_journal.sql v19-clin-v_emr_journal.sql v19-clin-v_emr_tree.sql v19-clin-test_type-dynamic.sql v19-clin-v_narrative4search.sql v19-GKV_formatierte_KVK_Daten.sql v19-GKV_formatierte_KVK_Daten-Gruenes_Rezept.sql v19-GKV_Stempel.sql v19-ref-billable-dynamic.sql v19-ref-paperwork_templates.sql v19-ref-auto_hint-dynamic.sql v19-ref-AUDIT_alcohol.sql v19-ref-v_atc.sql v19-cfg-report_query.sql v19-audit-grants.sql v19-release_notes-dynamic.sql $schema$ #---------------------------------- [bundle v19-fixups] database alias = gnumed_v19 minimum postgresql version = 9.1 schema base directory = ../sql/v18-v19/fixups/ schema = $schema$ v19-dem-lnk_org_unit2ext_id-fixup.sql v19-dem-org-fixup.sql v19-clin-encounter-fixup.sql $schema$ #---------------------------------- [bundle v19-test_data] database alias = gnumed_v19 minimum postgresql version = 9.1 schema base directory = ../sql/test-data/ schema = $schema$ $schema$ #---------------------------------- [database gnumed_v19] name = gnumed_v19 override name by = GM_CORE_DB drop target database = 1 target version = v19 transfer users = 1 template database = gnumed_v18 template version = v18 server alias = local host notification disable = 1 audit disable = 0 audit trail parent table = audit.audit_trail audit trail table prefix = log_ audit fields table = audit.audit_fields schema base directory = ../sql/v18-v19/ schema = $schema$ $schema$ superuser schema = $superuser schema$ $superuser schema$ script base directory = ../sql/v18-v19/python/ data import scripts = $data import scripts$ v19_v18-import-form-templates.py v19-import-form-templates.py $data import scripts$ upgrade plausibility checks = $upgrade plausibility checks$ identities::::select count(1) from dem.identity select count(1) from dem.identity names::::select count(1) from dem.names select count(1) from dem.names addresses::::select count(1) from dem.address select count(1) from dem.address episodes::::select count(1) from clin.episode select count(1) from clin.episode denormalized episodes::::select count(1) from clin.v_pat_episodes select count(1) from clin.v_pat_episodes encounters::::select count(1) from clin.encounter select count(1) from clin.v_pat_encounters issues::::select count(1) from clin.health_issue select count(1) from clin.health_issue issues view::::select count(1) from clin.v_health_issues select count(1) from clin.v_health_issues procedures::::select count(1) from clin.procedure select count(1) from clin.procedure documents::::select count(1) from blobs.doc_med select count(1) from blobs.doc_med document pages::::select count(1) from blobs.doc_obj select count(1) from blobs.doc_obj allergies::::select count(1) from clin.allergy select count(1) from clin.allergy clinical items::::select count(1) from clin.clin_root_item select count(1) from clin.clin_root_item communication channels::::select count(1) from dem.lnk_identity2comm select count(1) from dem.lnk_identity2comm test results::::select count(1) from clin.test_result select count(1) from clin.test_result unmatched test results::::select count(1) from clin.incoming_data_unmatched select count(1) from clin.incoming_data_unmatched unmatchable test results::::select count(1) from clin.incoming_data_unmatchable select count(1) from clin.incoming_data_unmatchable denormalized test results::::select count(1) from clin.v_test_results select count(1) from clin.v_test_results allergy states::::select count(1) from clin.allergy_state select count(1) from clin.allergy_state waiting list entries::::select count(1) from clin.waiting_list select count(1) from clin.waiting_list messages::::select count(1) + 1 from dem.message_inbox select count(1) from dem.message_inbox test orgs::::select count(1) from clin.test_org select count(1) from clin.test_org branded drug component intakes::::select count(1) from clin.substance_intake where fk_drug_component is not null select count(1) from clin.substance_intake where fk_drug_component is not null substance intakes::::select count(1) from clin.substance_intake where fk_drug_component is null select count(1) from clin.substance_intake where fk_drug_component is null vaccines::::select count(1) from clin.vaccine select count(1) from clin.vaccine vaccines (must have indications)::::select 0 select count(1) from clin.v_vaccines where indications is NULL vaccinations::::select count(1) from clin.vaccination select count(1) from clin.vaccination requests on results::::select count(1) from clin.test_result where fk_request is not NULL select count(1) from clin.test_result where fk_request is not NULL clinical code links (total) - internal consistency::::select True select ((select count(1) from clin.lnk_code2item_root) = (select ((select count(1) from clin.lnk_code2procedure) + (select count(1) from clin.lnk_code2rfe) + (select count(1) from clin.lnk_code2aoe) + (select count(1) from clin.lnk_code2episode) + (select count(1) from clin.lnk_code2h_issue) + (select count(1) from clin.lnk_code2narrative)))) automatic hints::::select count(1) + 1 from ref.auto_hint select count(1) from ref.auto_hint raw keyword expansions::::select count(1) + 2 from ref.keyword_expansion select count(1) from ref.keyword_expansion mapped keyword expansions::::select count(1) + 2 from ref.v_keyword_expansions select count(1) from ref.v_keyword_expansions at least one org unit (thereby org)::::select 1 select case when count(1) > 0 then 1 else 0 end from dem.org_unit $upgrade plausibility checks$ #organisations::::select count(1) from dem.org # select count(1) from dem.org #data sources::::select count(1) from ref.data_source # select count(1) from ref.data_source #ATC codes::::select count(1) from (select distinct on (code, term, fk_data_source) 1 from ref.atc) as uniq_atc # select count(1) from ref.atc #ATC vs generic codes - internal consistency::::select 0 # select code, term, fk_data_source from ref.atc except select code, term, fk_data_source from ref.generic_coding_system #LOINC codes::::select count(1) from ref.loinc # select count(1) from ref.loinc #LOINC vs generic codes - internal consistency::::select 0 # select code, term, fk_data_source from ref.loinc except select code, term, fk_data_source from ref.generic_coding_system #generic codes (total) - internal consistency::::select True # select ((select count(1) from ref.coding_system_root) = (select ((select count(1) from ref.atc) + (select count(1) from ref.loinc)))) #---------------------------------- [server local host] name = port = 5432 template database = template1 super user alias = postgres schema base directory = ../sql/v18-v19/ schema = $schema$ $schema$ #---------------------------------- [user GNUmed owner] name = gm-dbo password = gm-dbpass [user postgres] name = postgres password = postgrespassword #---------------------------------- # these really shouldn't be changed #---------------------------------- [GnuMed defaults] database owner alias = GNUmed owner groups = $groups$ $groups$ #----------------------------------