BHBC-2018

database/src/migrations/20221210145800_SIMS.1.4.0.ts

@@ -0,0 +1,39 @@
+import { Knex } from 'knex';
+
+const DB_SCHEMA = process.env.DB_SCHEMA;
+const DB_SCHEMA_DAPI_V1 = process.env.DB_SCHEMA_DAPI_V1;
+
+/**
+ *
+ *
+ * @export
+ * @param {Knex} knex
+ * @return {*}  {Promise<void>}
+ */
+export async function up(knex: Knex): Promise<void> {
+  await knex.raw(`
+    set search_path=${DB_SCHEMA};
+
+    alter table survey_attachment add column security_review_timestamp timestamptz(6);
+    comment on column survey_attachment.security_review_timestamp is 'The datetime that the security review for the artifact was completed.';
+
+    alter table survey_report_attachment add column security_review_timestamp timestamptz(6);
+    comment on column survey_report_attachment.security_review_timestamp is 'The datetime that the security review for the artifact was completed.';
+
+    alter table project_attachment add column security_review_timestamp timestamptz(6);
+    comment on column project_attachment.security_review_timestamp is 'The datetime that the security review for the artifact was completed.';
+
+    alter table project_report_attachment add column security_review_timestamp timestamptz(6);
+    comment on column project_report_attachment.security_review_timestamp is 'The datetime that the security review for the artifact was completed.';
+
+    SET SEARCH_PATH = ${DB_SCHEMA_DAPI_V1};
+    create or replace view survey_attachment as select * from ${DB_SCHEMA}.survey_attachment;
+    create or replace view survey_report_attachment as select * from ${DB_SCHEMA}.survey_report_attachment;
+    create or replace view project_attachment as select * from ${DB_SCHEMA}.project_attachment;
+    create or replace view project_report_attachment as select * from ${DB_SCHEMA}.project_report_attachment;
+  `);
+}
+
+export async function down(knex: Knex): Promise<void> {
+  await knex.raw(``);
+}

database/src/migrations/smoke_tests/smoketest_release.1.4.0.sql

@@ -0,0 +1,243 @@
+-- run as db super user
+\c biohub
+set role postgres;
+set search_path=biohub;
+
+do $$
+declare
+  _count integer = 0;
+  _system_user system_user%rowtype;
+  _system_user_id system_user.system_user_id%type;
+begin
+  select * into _system_user from system_user where user_identifier = 'myIDIR';
+  if _system_user.system_user_id is not null then
+    delete from permit where system_user_id = _system_user.system_user_id;
+    delete from administrative_activity where reported_system_user_id = _system_user.system_user_id;
+    delete from administrative_activity where assigned_system_user_id = _system_user.system_user_id;
+    delete from system_user_role where system_user_id = _system_user.system_user_id;
+    delete from system_user where system_user_id = _system_user.system_user_id;
+  end if;
+
+  insert into system_user (user_identity_source_id, user_identifier, record_effective_date) values ((select user_identity_source_id from user_identity_source where name = 'IDIR' and record_end_date is null), 'myIDIR', now()) returning system_user_id into _system_user_id;
+  insert into system_user_role (system_user_id, system_role_id) values (_system_user_id, (select system_role_id from system_role where name =  'System Administrator'));
+
+  select count(1) into _count from system_user;
+  assert _count > 1, 'FAIL system_user';
+  select count(1) into _count from audit_log;
+  assert _count > 1, 'FAIL audit_log';
+
+  -- drop security context for subsequent roles to instantiate
+  drop table biohub_context_temp;
+
+  raise notice 'smoketest_release(1): PASS';
+end
+$$;
+
+set role biohub_api;
+set search_path to biohub_dapi_v1, biohub, public, topology;
+do $$
+declare
+  _project_id project.project_id%type;
+  _survey_id survey.survey_id%type;
+  _count integer = 0;
+  _system_user_id system_user.system_user_id%type;
+  _study_species_id study_species.study_species_id%type;
+  _occurrence_submission_id occurrence_submission.occurrence_submission_id%type;
+  _submission_status_id submission_status.submission_status_id%type;
+  _survey_status_query text := 'select project_id, survey_id, survey_status from survey_status';
+  _survey_status_rec survey_status%rowtype;
+  _geography project.geography%type;
+  _project_funding_source_id project_funding_source.project_funding_source_id%type;
+  _project_report_attachment_id project_report_attachment.project_report_attachment_id%type;
+  _survey_report_attachment_id survey_report_attachment.survey_report_attachment_id%type;
+  _permit_id permit.permit_id%type;
+begin
+  -- set security context
+  select api_set_context('myIDIR', 'IDIR') into _system_user_id;
+  --select api_set_context('biohub_api', 'DATABASE') into _system_user_id;
+
+  select st_GeomFromEWKT('SRID=4326;POLYGON((-123.920288 48.592142,-123.667603 48.645205,-123.539886 48.536204,-123.583832 48.46978,-123.728027 48.460674,-123.868103 48.467959,-123.940887 48.5262,-123.920288 48.592142), (-103.920288 38.592142,-103.667603 38.645205,-103.539886 38.536204,-103.583832 38.46978,-103.728027 38.460674,-103.868103 38.467959,-103.940887 38.5262,-103.920288 38.592142))') into _geography;
+
+  insert into project (project_type_id
+    , name
+    , objectives
+    , start_date
+    , end_date
+    , coordinator_first_name
+    , coordinator_last_name
+    , coordinator_email_address
+    , coordinator_agency_name
+    , coordinator_public
+    , geography
+    ) values ((select project_type_id from project_type where name = 'Wildlife')
+    , 'project 10'
+    , 'my objectives'
+    , now()
+    , now()+interval '1 day'
+    , 'coordinator_first_name'
+    , 'coordinator_last_name'
+    , '[email protected]'
+    , 'coordinator_agency_name'
+    , TRUE
+    , _geography
+    ) returning project_id into _project_id;
+
+  insert into stakeholder_partnership (project_id, name) values (_project_id, 'test');
+  insert into project_activity (project_id, activity_id) values (_project_id, (select activity_id from activity where name = 'Monitoring'));
+  insert into project_climate_initiative (project_id, climate_change_initiative_id) values (_project_id, (select climate_change_initiative_id from climate_change_initiative where name = 'Monitoring'));
+  insert into project_management_actions (project_id, management_action_type_id) values (_project_id, (select management_action_type_id from management_action_type where name = 'Recovery Action'));
+  insert into project_funding_source (project_id, investment_action_category_id, funding_amount, funding_start_date, funding_end_date, funding_source_project_id) values (_project_id, (select investment_action_category_id from investment_action_category where name = 'Action 1'), '$1,000.00', now(), now(), 'test') returning project_funding_source_id into _project_funding_source_id;
+  --insert into project_funding_source (project_id, investment_action_category_id, funding_amount, funding_start_date, funding_end_date) values (_project_id, 43, '$1,000.00', now(), now());
+  insert into project_iucn_action_classification (project_id, iucn_conservation_action_level_3_subclassification_id) values (_project_id, (select iucn_conservation_action_level_3_subclassification_id from iucn_conservation_action_level_3_subclassification where name = 'Primary Education'));
+  insert into project_attachment (project_id, file_name, title, key, file_size, file_type, security_review_timestamp) values (_project_id, 'test_filename.txt', 'test filename', 'projects/'||_project_id::text, 10000, 'video', now());
+  insert into project_report_attachment (project_id, file_name, title, key, file_size, year, description, security_review_timestamp) values (_project_id, 'test_filename.txt', 'test filename', 'projects/'||_project_id::text, 10000, '2021', 'example abstract', now()) returning project_report_attachment_id into _project_report_attachment_id;
+  insert into project_report_author (project_report_attachment_id, first_name, last_name) values (_project_report_attachment_id, 'john', 'doe');
+  insert into project_report_author (project_report_attachment_id, first_name, last_name) values (_project_report_attachment_id, 'bob', 'dole');
+  insert into project_first_nation (project_id, first_nations_id) values (_project_id, (select first_nations_id from first_nations where name = 'Kitselas Nation'));
+  insert into project_participation (project_id, system_user_id, project_role_id) values (_project_id, _system_user_id, (select project_role_id from project_role where name = 'Editor'));
+
+  select count(1) into _count from stakeholder_partnership;
+  assert _count = 1, 'FAIL stakeholder_partnership';
+  select count(1) into _count from project_activity;
+  assert _count = 1, 'FAIL project_activity';
+  select count(1) into _count from project_climate_initiative;
+  assert _count = 1, 'FAIL project_climate_initiative';
+  select count(1) into _count from project_management_actions;
+  assert _count = 1, 'FAIL project_management_actions';
+  select count(1) into _count from project_funding_source;
+  assert _count = 1, 'FAIL project_funding_source';
+  select count(1) into _count from project_iucn_action_classification;
+  assert _count = 1, 'FAIL project_iucn_action_classification';
+  select count(1) into _count from project_attachment;
+  assert _count = 1, 'FAIL project_attachment';
+  select count(1) into _count from project_attachment;
+  assert _count = 1, 'FAIL project_attachment';
+  select count(1) into _count from project_report_attachment;
+  assert _count = 1, 'FAIL project_report_attachment';
+  select count(1) into _count from project_report_author;
+  assert _count = 2, 'FAIL project_report_author';
+  select count(1) into _count from project_first_nation;
+  assert _count = 1, 'FAIL project_first_nation';
+  select count(1) into _count from project_participation;
+  assert _count = 1, 'FAIL project_participation';
+
+  -- surveys
+  insert into survey (project_id
+    , name
+    , additional_details
+    , location_name
+    , location_description
+    , start_date
+    , lead_first_name
+    , lead_last_name
+    , geography
+    , ecological_season_id
+    , intended_outcome_id)
+  values (_project_id
+    , 'survey name'
+    , 'survey objectives'
+    , 'survey location name'
+    , 'survey location description'
+    , now()
+    , 'lead first'
+    , 'lead last'
+    , _geography
+    , (select ecological_season_id from ecological_season where name = 'Growing')
+    , (select intended_outcome_id from intended_outcome where name = 'Survival')    
+    ) returning survey_id into _survey_id;
+
+  insert into survey_proprietor (survey_id, first_nations_id, proprietor_type_id, rationale,disa_required)
+    values (_survey_id, (select first_nations_id from first_nations where name = 'Squamish Nation'), (select proprietor_type_id from proprietor_type where name = 'First Nations Land'), 'proprietor rationale', true);  
+  insert into survey_attachment (survey_id, file_name, title, key, file_size, file_type, security_review_timestamp) values (_survey_id, 'test_filename.txt', 'test filename', 'projects/'||_project_id::text||'/surveys/'||_survey_id::text, 10000, 'video', now());
+  insert into survey_report_attachment (survey_id, file_name, title, key, file_size, year, description, security_review_timestamp) values (_survey_id, 'test_filename.txt', 'test filename', 'projects/'||_survey_id::text, 10000, '2021', 'example abstract', now()) returning survey_report_attachment_id into _survey_report_attachment_id;
+  insert into survey_report_author (survey_report_attachment_id, first_name, last_name) values (_survey_report_attachment_id, 'john', 'doe');
+  insert into survey_report_author (survey_report_attachment_id, first_name, last_name) values (_survey_report_attachment_id, 'bob', 'dole');
+  insert into study_species (survey_id, wldtaxonomic_units_id, is_focal) values (_survey_id, (select wldtaxonomic_units_id from wldtaxonomic_units where CODE = 'AMARALB'), true);
+  insert into survey_funding_source (survey_id, project_funding_source_id) values (_survey_id, _project_funding_source_id);
+  insert into survey_vantage(survey_id, vantage_id) values (_survey_id, (select vantage_id from vantage where name = 'Aerial'));
+  insert into permit (survey_id, number, type) values (_survey_id, '8377262', 'permit type') returning permit_id into _permit_id;
+  insert into permit (survey_id, number, type) values (_survey_id, '8377261', 'permit type') returning permit_id into _permit_id;
+
+
+  select count(1) into _count from survey;
+  assert _count = 1, 'FAIL survey';
+  select count(1) into _count from survey_proprietor;
+  assert _count = 1, 'FAIL survey_proprietor';
+  select count(1) into _count from survey_attachment where survey_id = _survey_id;
+  assert _count = 1, 'FAIL survey_attachment';  
+  select count(1) into _count from survey_report_attachment;
+  assert _count = 1, 'FAIL survey_report_attachment';    
+  select count(1) into _count from survey_report_author;
+  assert _count = 2, 'FAIL survey_report_author';  
+  select count(1) into _count from study_species;
+  assert _count = 1, 'FAIL study_species';  
+  select count(1) into _count from survey_funding_source;
+  assert _count = 1, 'FAIL survey_funding_source';  
+  select count(1) into _count from survey_vantage;
+  assert _count = 1, 'FAIL survey_vantage';
+  select count(1) into _count from permit;
+  assert _count = 2, 'FAIL permit';
+
+  -- occurrence
+  -- occurrence submission 1
+  insert into occurrence_submission (survey_id, source, event_timestamp) values (_survey_id, 'BIOHUB BATCH', now()-interval '1 day') returning occurrence_submission_id into _occurrence_submission_id;
+  select count(1) into _count from occurrence_submission;
+  assert _count = 1, 'FAIL occurrence_submission';
+  insert into occurrence (occurrence_submission_id, taxonid, lifestage, eventdate, sex) values (_occurrence_submission_id, 'M-ALAL', 'Adult', now()-interval '10 day', 'male');
+  select count(1) into _count from occurrence;
+  assert _count = 1, 'FAIL occurrence';
+  insert into submission_status (occurrence_submission_id, submission_status_type_id, event_timestamp) values (_occurrence_submission_id, (select submission_status_type_id from submission_status_type where name = 'Submitted'), now()-interval '1 day') returning submission_status_id into _submission_status_id;
+  -- transpose comments on next three lines to test deletion of published surveys by system administrator
+  insert into submission_status (occurrence_submission_id, submission_status_type_id, event_timestamp) values (_occurrence_submission_id, (select submission_status_type_id from submission_status_type where name = 'Awaiting Curration'), now()-interval '1 day') returning submission_status_id into _submission_status_id;
+  insert into submission_status (occurrence_submission_id, submission_status_type_id, event_timestamp) values (_occurrence_submission_id, (select submission_status_type_id from submission_status_type where name = 'Published'), now()-interval '1 day') returning submission_status_id into _submission_status_id;
+  --insert into system_user_role (system_user_id, system_role_id) values (_system_user_id, (select system_role_id from system_role where name = 'System Administrator'));
+
+  -- occurrence submission 2
+  insert into occurrence_submission (survey_id, source, event_timestamp) values (_survey_id, 'BIOHUB BATCH', now()) returning occurrence_submission_id into _occurrence_submission_id;
+  select count(1) into _count from occurrence_submission;
+  assert _count = 2, 'FAIL occurrence_submission';
+  insert into occurrence (occurrence_submission_id, taxonid, lifestage, eventdate, sex) values (_occurrence_submission_id, 'M-ALAL', 'Adult', now()-interval '5 day', 'female');
+  select count(1) into _count from occurrence;
+  assert _count = 2, 'FAIL occurrence';
+  insert into submission_status (occurrence_submission_id, submission_status_type_id, event_timestamp) values (_occurrence_submission_id, (select submission_status_type_id from submission_status_type where name = 'Submitted'), now()) returning submission_status_id into _submission_status_id;
+  insert into submission_status (occurrence_submission_id, submission_status_type_id, event_timestamp) values (_occurrence_submission_id, (select submission_status_type_id from submission_status_type where name = 'Rejected'), now()) returning submission_status_id into _submission_status_id;
+  insert into submission_message (submission_status_id, submission_message_type_id, event_timestamp, message) values (_submission_status_id, (select submission_message_type_id from submission_message_type where name = 'Missing Required Field'), now(), 'Some required field was not supplied.');
+  select count(1) into _count from submission_status;
+  assert _count = 5, 'FAIL submission_status';
+  select count(1) into _count from submission_message;
+  assert _count = 1, 'FAIL submission_message';  
+
+--  raise notice 'survey status (project_id, survey_id, survey_status):';
+--  for _survey_status_rec in execute _survey_status_query loop
+--    raise notice 'survey status results are % % % %', _survey_status_rec.project_id, _survey_status_rec.survey_id,  _survey_status_rec.occurrence_id, _survey_status_rec.survey_status;
+--  end loop;
+
+  -- test ancillary data
+  delete from webform_draft;
+  insert into webform_draft (system_user_id, name, data) values ((select system_user_id from system_user limit 1), 'my draft name', '{ "customer": "John Doe", "items": {"product": "Beer","qty": 6}}');
+  select count(1) into _count from webform_draft;
+  assert _count = 1, 'FAIL webform_draft';
+
+  -- work ledger
+  delete from administrative_activity;
+  insert into administrative_activity (reported_system_user_id
+    , administrative_activity_type_id
+    , administrative_activity_status_type_id
+    , description
+    , data)
+    values (_system_user_id
+    , (select administrative_activity_type_id from administrative_activity_type where name = 'System Access')
+    , (select administrative_activity_status_type_id from administrative_activity_status_type where name = 'Pending')
+    , 'my activity'
+    , '{ "customer": "John Doe", "items": {"product": "Beer","qty": 6}}')
+  ;
+  select count(1) into _count from administrative_activity;
+  assert _count = 1, 'FAIL administrative_activity';
+
+  -- delete project
+  raise notice 'deleting data.';
+  call api_delete_project(_project_id);
+
+  raise notice 'smoketest_release(2): PASS';
+end
+$$;