BHBC-1115

database/src/migrations/20210225205948_biohub_release.ts

@@ -5,6 +5,8 @@ import path from 'path';
 const DB_USER_API_PASS = process.env.DB_USER_API_PASS;
 const DB_USER_API = process.env.DB_USER_API;
 
+const DB_RELEASE = 'release.0.17';
+
 /**
  * Apply biohub release changes.
  *
@@ -13,62 +15,54 @@ const DB_USER_API = process.env.DB_USER_API;
  * @return {*}  {Promise<void>}
  */
 export async function up(knex: Knex): Promise<void> {
-  const create_spatial_extensions = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'create_spatial_extensions.psql')
-  );
-  const biohub_ddl = fs.readFileSync(path.join(__dirname, 'release.0.16', 'biohub.sql'));
+  const create_spatial_extensions = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'create_spatial_extensions.psql'));
+  const biohub_ddl = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'biohub.sql'));
   const populate_user_identity_source = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_user_identity_source.sql')
-  );
-  const api_set_context = fs.readFileSync(path.join(__dirname, 'release.0.16', 'api_set_context.sql'));
-  const tr_audit_trigger = fs.readFileSync(path.join(__dirname, 'release.0.16', 'tr_audit_trigger.sql'));
-  const project_audit_triggers = fs.readFileSync(path.join(__dirname, 'release.0.16', 'project_audit_triggers.sql'));
-  const api_get_context_user_id = fs.readFileSync(path.join(__dirname, 'release.0.16', 'api_get_context_user_id.sql'));
-  const tr_journal_trigger = fs.readFileSync(path.join(__dirname, 'release.0.16', 'tr_journal_trigger.sql'));
-  const project_journal_triggers = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'project_journal_triggers.sql')
+    path.join(__dirname, DB_RELEASE, 'populate_user_identity_source.sql')
   );
-  const tr_project_funding_source = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'tr_project_funding_source.sql')
-  );
-  const api_delete_project = fs.readFileSync(path.join(__dirname, 'release.0.16', 'api_delete_project.sql'));
+  const api_set_context = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'api_set_context.sql'));
+  const tr_audit_trigger = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'tr_audit_trigger.sql'));
+  const project_audit_triggers = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'project_audit_triggers.sql'));
+  const api_get_context_user_id = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'api_get_context_user_id.sql'));
+  const tr_journal_trigger = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'tr_journal_trigger.sql'));
+  const project_journal_triggers = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'project_journal_triggers.sql'));
+  const tr_project_funding_source = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'tr_project_funding_source.sql'));
+  const api_delete_project = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'api_delete_project.sql'));
 
-  const populate_first_nations = fs.readFileSync(path.join(__dirname, 'release.0.16', 'populate_first_nations.sql'));
+  const populate_first_nations = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'populate_first_nations.sql'));
   const populate_climate_change_initiatives = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_climate_change_initiatives.sql')
+    path.join(__dirname, DB_RELEASE, 'populate_climate_change_initiatives.sql')
   );
   const populate_management_action_type = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_management_action_type.sql')
+    path.join(__dirname, DB_RELEASE, 'populate_management_action_type.sql')
   );
-  const populate_funding_source = fs.readFileSync(path.join(__dirname, 'release.0.16', 'populate_funding_source.sql'));
+  const populate_funding_source = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'populate_funding_source.sql'));
   const populate_investment_action_category = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_investment_action_category.sql')
+    path.join(__dirname, DB_RELEASE, 'populate_investment_action_category.sql')
   );
-  const populate_project_type = fs.readFileSync(path.join(__dirname, 'release.0.16', 'populate_project_type.sql'));
-  const populate_activity = fs.readFileSync(path.join(__dirname, 'release.0.16', 'populate_activity.sql'));
+  const populate_project_type = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'populate_project_type.sql'));
+  const populate_activity = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'populate_activity.sql'));
   const populate_iucn_classifications = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_iucn_classifications.sql')
+    path.join(__dirname, DB_RELEASE, 'populate_iucn_classifications.sql')
   );
-  const populate_project_role = fs.readFileSync(path.join(__dirname, 'release.0.16', 'populate_project_role.sql'));
-  const populate_system_role = fs.readFileSync(path.join(__dirname, 'release.0.16', 'populate_system_role.sql'));
+  const populate_project_role = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'populate_project_role.sql'));
+  const populate_system_role = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'populate_system_role.sql'));
   const populate_administrative_activity_type = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_administrative_activity_type.sql')
+    path.join(__dirname, DB_RELEASE, 'populate_administrative_activity_type.sql')
   );
   const populate_administrative_activity_status_type = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_administrative_activity_status_type.sql')
-  );
-  const populate_proprietor_type = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_proprietor_type.sql')
+    path.join(__dirname, DB_RELEASE, 'populate_administrative_activity_status_type.sql')
   );
+  const populate_proprietor_type = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'populate_proprietor_type.sql'));
   const populate_wldtaxonomic_units = fs.readFileSync(
-    path.join(__dirname, 'release.0.16', 'populate_wldtaxonomic_units.sql')
+    path.join(__dirname, DB_RELEASE, 'populate_wldtaxonomic_units.sql')
   );
-  const tr_survey_proprietor = fs.readFileSync(path.join(__dirname, 'release.0.16', 'tr_survey_proprietor.sql'));
-  const tr_project = fs.readFileSync(path.join(__dirname, 'release.0.16', 'tr_project.sql'));
-  const tr_survey = fs.readFileSync(path.join(__dirname, 'release.0.16', 'tr_survey.sql'));
-  const tr_permit = fs.readFileSync(path.join(__dirname, 'release.0.16', 'tr_permit.sql'));
+  const tr_survey_proprietor = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'tr_survey_proprietor.sql'));
+  const tr_project = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'tr_project.sql'));
+  const tr_survey = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'tr_survey.sql'));
+  const tr_permit = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'tr_permit.sql'));
 
-  const project_dapi_views = fs.readFileSync(path.join(__dirname, 'release.0.16', 'project_dapi_views.sql'));
+  const project_dapi_views = fs.readFileSync(path.join(__dirname, DB_RELEASE, 'project_dapi_views.sql'));
 
   await knex.raw(`
     -- set up spatial extensions

database/src/migrations/release.0.16/api_delete_project.sql → database/src/migrations/release.0.17/api_delete_project.sql

@@ -17,8 +17,13 @@ $$
 --                  2021-04-19  initial release
 -- *******************************************************************
 declare
-
+  __count integer := 0;
 begin
+  select count(*) into __count from survey_publish_history where s_id in (select id from survey where p_id = __project_id);
+  if (__count > 0) then
+    raise exception 'Project cannot be deleted as associated published data exists.';  
+  end if;
+
   delete from survey_proprietor where s_id in (select id from survey where p_id = __project_id);
   delete from survey_attachment where s_id in (select id from survey where p_id = __project_id);
   delete from study_species where s_id in (select id from survey where p_id = __project_id);
@@ -35,6 +40,9 @@ begin
   delete from project_first_nation where p_id = __project_id;
   delete from project_participation where p_id = __project_id;
   delete from project where id = __project_id;
-
+
+exception
+  when others THEN
+    raise;    
 end;
 $$;

database/src/migrations/release.0.16/biohub.sql → database/src/migrations/release.0.17/biohub.sql

@@ -2,7 +2,7 @@
 -- ER/Studio Data Architect SQL Code Generation
 -- Project :      BioHub.DM1
 --
--- Date Created : Tuesday, May 18, 2021 10:47:16
+-- Date Created : Thursday, June 03, 2021 12:01:34
 -- Target DBMS : PostgreSQL 10.x-12.x
 --
 
@@ -652,7 +652,15 @@ COMMENT ON COLUMN permit.update_user IS 'The id of the user who updated the reco
 ;
 COMMENT ON COLUMN permit.revision_count IS 'Revision count used for concurrency control.'
 ;
-COMMENT ON TABLE permit IS 'Provides a record of scientific permits.'
+COMMENT ON TABLE permit IS 'Provides a record of scientific permits. Note that permits are first class objects in the data model and do not require an association to either a project or survey. Additionally:
+- Association to a survey or project implies that sampling was conducted related to the permit 
+- No association to a survey or project implies that sampling was not conducted related to the permit
+- Permits that are associated with a project should eventually be related to a survey
+- Permits can be associated with one or zero projects
+- Permits can only be associated with one survey
+- Permits that have no association with a project or survey require values for coordinator first name, last name, email address and agency name
+
+NOTE: there are conceptual problems with associating permits to projects early instead of at the survey level and these should be addressed in subsequent versions of the application.'
 ;
 
 -- 
@@ -783,7 +791,7 @@ CREATE TABLE project_attachment(
     file_name         varchar(300),
     title             varchar(300),
     description       varchar(250),
-    key               varchar(300)      NOT NULL,
+    key               varchar(1000)     NOT NULL,
     file_size         integer,
     create_date       timestamptz(6)    DEFAULT now() NOT NULL,
     create_user       integer           NOT NULL,
@@ -1318,7 +1326,7 @@ COMMENT ON COLUMN study_species.update_user IS 'The id of the user who updated t
 ;
 COMMENT ON COLUMN study_species.revision_count IS 'Revision count used for concurrency control.'
 ;
-COMMENT ON TABLE study_species IS 'The study species for the project and survey.'
+COMMENT ON TABLE study_species IS 'The study species for the survey.'
 ;
 
 -- 
@@ -1397,7 +1405,7 @@ CREATE TABLE survey_attachment(
     file_name         varchar(300),
     title             varchar(300),
     description       varchar(250),
-    key               varchar(300)      NOT NULL,
+    key               varchar(1000)     NOT NULL,
     file_size         integer,
     create_date       timestamptz(6)    DEFAULT now() NOT NULL,
     create_user       integer           NOT NULL,
@@ -1475,6 +1483,56 @@ COMMENT ON COLUMN survey_funding_source.revision_count IS 'Revision count used f
 COMMENT ON TABLE survey_funding_source IS 'A associative entity that joins surveys and funding source details.'
 ;
 
+-- 
+-- TABLE: survey_occurrence 
+--
+
+CREATE TABLE survey_occurrence(
+    id                integer                     GENERATED ALWAYS AS IDENTITY (START WITH 1 INCREMENT BY 1),
+    s_id              integer                     NOT NULL,
+    associatedtaxa    varchar(3000)               NOT NULL,
+    lifestage         varchar(3000)               NOT NULL,
+    data              json,
+    geometry          geometry(geometry, 3005),
+    geography         geography(geometry),
+    create_date       timestamptz(6)              DEFAULT now() NOT NULL,
+    create_user       integer                     NOT NULL,
+    update_date       timestamptz(6),
+    update_user       integer,
+    revision_count    integer                     DEFAULT 0 NOT NULL,
+    CONSTRAINT "PK169" PRIMARY KEY (id)
+)
+;
+
+
+
+COMMENT ON COLUMN survey_occurrence.id IS 'System generated surrogate primary key identifier.'
+;
+COMMENT ON COLUMN survey_occurrence.s_id IS 'System generated surrogate primary key identifier.'
+;
+COMMENT ON COLUMN survey_occurrence.associatedtaxa IS 'A string representation of the value provided for the given Darwin Core term.'
+;
+COMMENT ON COLUMN survey_occurrence.lifestage IS 'A string representation of the value provided for the given Darwin Core term.'
+;
+COMMENT ON COLUMN survey_occurrence.data IS 'The json data associated with the record.'
+;
+COMMENT ON COLUMN survey_occurrence.geometry IS 'The containing geometry of the record.'
+;
+COMMENT ON COLUMN survey_occurrence.geography IS 'The containing geography of the record.'
+;
+COMMENT ON COLUMN survey_occurrence.create_date IS 'The datetime the record was created.'
+;
+COMMENT ON COLUMN survey_occurrence.create_user IS 'The id of the user who created the record as identified in the system user table.'
+;
+COMMENT ON COLUMN survey_occurrence.update_date IS 'The datetime the record was updated.'
+;
+COMMENT ON COLUMN survey_occurrence.update_user IS 'The id of the user who updated the record as identified in the system user table.'
+;
+COMMENT ON COLUMN survey_occurrence.revision_count IS 'Revision count used for concurrency control.'
+;
+COMMENT ON TABLE survey_occurrence IS 'Occurrence records associated with a survey.'
+;
+
 -- 
 -- TABLE: survey_proprietor 
 --
@@ -1525,6 +1583,47 @@ COMMENT ON COLUMN survey_proprietor.revision_count IS 'Revision count used for c
 COMMENT ON TABLE survey_proprietor IS 'Intersection table associating surveys to proprietary types and associated meta data.'
 ;
 
+-- 
+-- TABLE: survey_publish_history 
+--
+
+CREATE TABLE survey_publish_history(
+    id                integer           GENERATED ALWAYS AS IDENTITY (START WITH 1 INCREMENT BY 1),
+    s_id              integer           NOT NULL,
+    publish_date      date              NOT NULL,
+    key               varchar(1000),
+    create_date       timestamptz(6)    DEFAULT now() NOT NULL,
+    create_user       integer           NOT NULL,
+    update_date       timestamptz(6),
+    update_user       integer,
+    revision_count    integer           DEFAULT 0 NOT NULL,
+    CONSTRAINT "PK165" PRIMARY KEY (id)
+)
+;
+
+
+
+COMMENT ON COLUMN survey_publish_history.id IS 'System generated surrogate primary key identifier.'
+;
+COMMENT ON COLUMN survey_publish_history.s_id IS 'System generated surrogate primary key identifier.'
+;
+COMMENT ON COLUMN survey_publish_history.publish_date IS 'The date that the survey version was published.'
+;
+COMMENT ON COLUMN survey_publish_history.key IS 'The identifying key to the file in the storage system.'
+;
+COMMENT ON COLUMN survey_publish_history.create_date IS 'The datetime the record was created.'
+;
+COMMENT ON COLUMN survey_publish_history.create_user IS 'The id of the user who created the record as identified in the system user table.'
+;
+COMMENT ON COLUMN survey_publish_history.update_date IS 'The datetime the record was updated.'
+;
+COMMENT ON COLUMN survey_publish_history.update_user IS 'The id of the user who updated the record as identified in the system user table.'
+;
+COMMENT ON COLUMN survey_publish_history.revision_count IS 'Revision count used for concurrency control.'
+;
+COMMENT ON TABLE survey_publish_history IS 'Provides a historical listing of published dates and pointers to raw data versions.'
+;
+
 -- 
 -- TABLE: system_constant 
 --
@@ -2239,6 +2338,12 @@ CREATE INDEX "Ref7487" ON survey_funding_source(pfs_id)
 CREATE INDEX "Ref15388" ON survey_funding_source(s_id)
 ;
 -- 
+-- INDEX: "Ref15396" 
+--
+
+CREATE INDEX "Ref15396" ON survey_occurrence(s_id)
+;
+-- 
 -- INDEX: "Ref15983" 
 --
 
@@ -2257,6 +2362,12 @@ CREATE INDEX "Ref15384" ON survey_proprietor(s_id)
 CREATE INDEX "Ref12785" ON survey_proprietor(fn_id)
 ;
 -- 
+-- INDEX: "Ref15395" 
+--
+
+CREATE INDEX "Ref15395" ON survey_publish_history(s_id)
+;
+-- 
 -- INDEX: sc_uk1 
 --
 
@@ -2580,6 +2691,16 @@ ALTER TABLE survey_funding_source ADD CONSTRAINT "Refsurvey88"
 ;
 
 
+-- 
+-- TABLE: survey_occurrence 
+--
+
+ALTER TABLE survey_occurrence ADD CONSTRAINT "Refsurvey96" 
+    FOREIGN KEY (s_id)
+    REFERENCES survey(id)
+;
+
+
 -- 
 -- TABLE: survey_proprietor 
 --
@@ -2600,6 +2721,16 @@ ALTER TABLE survey_proprietor ADD CONSTRAINT "Reffirst_nations85"
 ;
 
 
+-- 
+-- TABLE: survey_publish_history 
+--
+
+ALTER TABLE survey_publish_history ADD CONSTRAINT "Refsurvey95" 
+    FOREIGN KEY (s_id)
+    REFERENCES survey(id)
+;
+
+
 -- 
 -- TABLE: system_user 
 --