Spi migrate users ups into test spi

spi/src/index.ts

@@ -49,6 +49,9 @@ async function main() {
     // STEP 6. Transforms SPI Design Components into SIMS Sampling Sites
     await transformSampleSites(connection);
 
+    //STEP 7.  Transforms SPI Survey Areas into SIMS Survey Locations
+    await transformSampleSites(connection);
+
     // Commit the transactions
     connection.commit();
 

spi/src/transformations/project.ts

@@ -29,24 +29,65 @@ export const transformProjects = async (connection: IDBConnection): Promise<void
             SELECT 
                 p.spi_project_id, 
                 pp.person_id, 
-                b.project_id
+                b.project_id, 
+                CONCAT(pp.first_given_name, ' ', pp.surname) AS full_name,
+                spp.email_address
             FROM 
                 public.spi_projects p
-            INNER JOIN 
-                biohub.project b ON p.spi_project_id = b.spi_project_id
-            INNER JOIN 
-                spi_persons pp ON pp.spi_project_id = p.spi_project_id
+            INNER JOIN biohub.project b 
+                ON p.spi_project_id = b.spi_project_id
+            INNER JOIN spi_persons pp 
+                ON pp.spi_project_id = p.spi_project_id
+            LEFT JOIN public.spi_secure_persons spp 
+                ON spp.first_name = pp.first_given_name
+                AND spp.last_name = pp.surname
         )
     INSERT INTO
         biohub.project_participation (project_id, system_user_id, project_role_id, create_user)
     SELECT DISTINCT
         w_mapping.project_id,
-        (SELECT biohub_user_id FROM public.migrate_spi_user_deduplication WHERE w_mapping.person_id = ANY (spi_person_ids)),
-        (SELECT project_role_id FROM biohub.project_role WHERE name = 'Collaborator'),
-        (SELECT system_user_id FROM biohub.system_user WHERE user_identifier = 'spi')
+
+        COALESCE (
+        (SELECT biohub_user_id 
+         FROM public.migrate_spi_user_deduplication 
+         WHERE w_mapping.person_id = ANY (spi_person_ids)
+        ), 
+        (SELECT system_user_id 
+         FROM biohub.system_user 
+         WHERE user_identifier = 'spi')
+        ) AS system_user_id,
+
+        CASE 
+        WHEN p.coordinator IS NOT NULL AND w_mapping.full_name LIKE '%' || TRIM(BOTH ', ' FROM p.coordinator) || '%' AND spp.email_address LIKE '%@gov.bc.ca%' THEN 
+            (SELECT project_role_id FROM biohub.project_role WHERE name = 'Coordinator')
+        WHEN NOT EXISTS (
+            SELECT 1 
+            FROM biohub.project_participation 
+            WHERE project_id = w_mapping.project_id 
+              AND project_role_id = (SELECT project_role_id FROM biohub.project_role WHERE name = 'Coordinator')
+        ) THEN (SELECT project_role_id FROM biohub.project_role WHERE name = 'Coordinator'), (SELECT system_user_id FROM biohub.system_user WHERE user_identifier = 'spi')
+         ----- double check that when the not exists is doing what we want it to do (assign spi as coordinator when coordinator is undefined)
+        WHEN spp.email_address LIKE '%@gov.bc.ca%'  
+            AND NOT EXISTS (
+             SELECT 1 
+             FROM biohub.project_participation 
+             WHERE project_id = w_mapping.project_id 
+               AND project_role_id = (SELECT project_role_id FROM biohub.project_role WHERE name = 'Coordinator')
+         ) THEN 
+            (SELECT project_role_id FROM biohub.project_role WHERE name = 'Collaborator')
+        ELSE 
+            (SELECT project_role_id FROM biohub.project_role WHERE name = 'Observer')
+        END AS project_role_id,
+
+        (SELECT system_user_id FROM biohub.system_user WHERE user_identifier = 'spi') AS create_user
+
     FROM 
         w_mapping
-    ON CONFLICT DO NOTHING;
+    JOIN public.spi_projects p 
+        ON p.spi_project_id = w_mapping.spi_project_id
+    JOIN public.spi_secure_persons spp
+        ON spp.first_name = pp.first_given_name
+        AND spp.last_name = pp.surname;
   `;
 
   await connection.sql(sql);

spi/src/transformations/sampling_period.ts

@@ -0,0 +1,70 @@
+import SQL from 'sql-template-strings';
+import { IDBConnection } from '../db';
+
+export const transformSampleVisits = async (connection: IDBConnection): Promise<void> => {
+  const transformSampleVisitsSql = SQL`
+    set search_path = biohub,public;
+
+------ transforming design component visits into sampling periods --- 
+    INSERT INTO biohub.survey_sample_period (create_date, survey_sample_method_id, start_date, end_date, start_time, end_time)
+    SELECT 
+        sdcv.when_created, 
+        ssm.survey_sample_method_id,
+        DATE(sdcv.visit_date) AS start_date,
+        DATE(COALESCE(sdcv.visit_end_date, sdcv.visit_date)) AS end_date,
+        CASE 
+            WHEN sdcv.start_time = '0000' THEN NULL
+            ELSE TO_TIMESTAMP(LPAD(sdcv.start_time, 4, '0'), 'HH24MI')::time
+        END AS start_time,
+        CASE 
+            WHEN sdcv.end_time = '0000' THEN NULL
+            ELSE TO_TIMESTAMP(LPAD(sdcv.end_time, 4, '0'), 'HH24MI')::time
+        END AS end_time
+    FROM 
+        public.spi_design_component_visits sdcv
+    JOIN 
+        public.migrate_spi_sample_design_component msd
+        ON sdcv.design_component_id = msd.design_component_id
+    JOIN 
+        biohub.survey_sample_method ssm
+        ON msd.survey_sample_site_id = ssm.survey_sample_site_id
+    GROUP BY 
+        sdcv.design_component_visit_id, 
+        sdcv.when_created, 
+        sdcv.start_time, 
+        sdcv.end_time, 
+        ssm.survey_sample_method_id;
+
+    -- possibility to create another temporary table that houses the design component visit id and the survey sample period id
+    -- ensures that we can properly attribute spi_wildlife_observations to the appropriate sampling period to get dates 
+
+    -- setting up the table -- 
+    CREATE TABLE IF NOT EXISTS public.migrate_spi_sample_period_visit (
+    design_component_visit_id INT,
+    survey_sample_period_id INT,
+    PRIMARY KEY (design_component_visit_id, survey_sample_period_id));
+
+    -- inserting component visit id and survey sample period id into the table -- 
+    INSERT INTO public.migrate_spi_sample_period_visit (design_component_visit_id, survey_sample_period_id)
+    SELECT
+        sdcv.design_component_visit_id,
+        ssp.survey_sample_period_id
+    FROM 
+        public.spi_design_component_visits sdcv
+    JOIN 
+        public.migrate_spi_sample_design_component msd
+        ON sdcv.design_component_id = msd.design_component_id
+    JOIN 
+        biohub.survey_sample_method ssm
+        ON msd.survey_sample_site_id = ssm.survey_sample_site_id
+    JOIN
+        biohub.survey_sample_period ssp
+        ON ssp.survey_sample_method_id = ssm.survey_sample_method_id
+    GROUP BY 
+        sdcv.design_component_visit_id, ssp.survey_sample_period_id;
+    `;
+
+  await connection.sql(transformSampleVisitsSql);
+
+  console.log('Successfully transformed design component visits');
+};

spi/src/transformations/study-area.ts

@@ -0,0 +1,58 @@
+import SQL from 'sql-template-strings';
+import { IDBConnection } from '../db';
+
+export const transformStudyAreas = async (connection: IDBConnection): Promise<void> => {
+  console.log('Transforming Study Area');
+
+  const sql = SQL`
+    -------------------------------------------------------------------------------------------------
+    -- Transforms SPI Study Areas into SIMS Survey Locations 
+
+    WITH w_survey_points AS (
+        SELECT 
+            bs.survey_id, 
+            sa.study_area_name,
+            sa.study_area_description,
+            igd.geo,
+            ST_ConvexHull(ST_Collect(ST_SetSRID(ST_MakePoint(wso.longitude, wso.latitude), 4326))) AS convex_hull,
+            COUNT(wso.wlo_id) AS so_count
+        FROM biohub.survey bs
+        JOIN public.spi_survey_study_areas ssa
+            ON bs.spi_survey_id = ssa.survey_id
+        JOIN public.spi_study_areas sa
+            ON ssa.study_area_id = sa.study_area_id
+        JOIN public.spi_document_references sdr
+            ON sa.study_area_id = sdr.study_area_id
+        LEFT JOIN public.imported_geo_data igd
+            ON sdr.document_reference_id = igd.spi_document_reference
+        LEFT JOIN public.spi_wildlife_observations wso
+            ON bs.spi_survey_id = wso.survey_id
+        WHERE sa.study_area_id IS NOT NULL 
+        AND wso.longitude IS NOT NULL 
+        AND wso.latitude IS NOT NULL
+        GROUP BY bs.survey_id, sa.study_area_name, sa.study_area_description, igd.geo
+    ),
+    buffered_geographies AS (
+        SELECT 
+            sp.survey_id,
+            sp.study_area_name,
+            sp.study_area_description,
+            sp.convex_hull,
+            sp.geo,
+            sp.so_count,
+            (0.2 * sqrt(ST_Area(sp.convex_hull)) + 0.05 * pow((ST_Area(sp.convex_hull) / sp.so_count), 0.75)) AS buffer_value
+        FROM w_survey_points sp
+    )
+    INSERT INTO biohub.survey_location (survey_id, name, description, geography)
+    SELECT 
+        bg.survey_id, 
+        bg.study_area_name, 
+        bg.study_area_description, 
+        COALESCE(sp.geo, ST_Buffer(bg.convex_hull, bg.buffer_value)) AS geography
+    FROM buffered_geographies bg;
+  `;
+
+  await connection.sql(sql);
+
+  console.log('Successfully transformed study areas');
+};

spi/src/transformations/survey.ts

@@ -21,7 +21,12 @@ export const transformSurveys = async (connection: IDBConnection): Promise<void>
             WHEN ss.end_date < ss.start_date THEN ss.start_date
             ELSE ss.end_date
         END AS end_date,
-        (SELECT survey_progress_id FROM biohub.survey_progress WHERE name = 'In progress'),
+        CASE
+            WHEN ss.end_date < now() THEN (SELECT survey_progress_id FROM biohub.survey_progress WHERE name = 'Completed')
+            WHEN ss.start_date > now() THEN (SELECT survey_progress_id FROM biohub.survey_progress WHERE name = 'Planning')
+            WHEN now() BETWEEN ss.start_date AND ss.end_date THEN (SELECT survey_progress_id FROM biohub.survey_progress WHERE name = 'In progress')
+            ELSE (SELECT survey_progress_id FROM biohub.survey_progress WHERE name = 'In progress')
+        END AS progress_id,
         'Start: ' || ss.start_date || '. End: ' || ss.end_date
     FROM 
         public.spi_surveys ss

spi/src/transformations/user.ts

@@ -29,39 +29,54 @@ export const transformUsers = async (connection: IDBConnection): Promise<void> =
     -------------------------------------------------------------------------------------------------
     -- Turn deduplicated users into SIMS users
     -------------------------------------------------------------------------------------------------
+    WITH w_existing_users AS (
+        SELECT 
+            system_user_id,
+            family_name,
+            given_name
+        FROM biohub.system_user
+    )
     INSERT INTO biohub.system_user (
-      user_identity_source_id,
-      user_identifier,
-      record_effective_date,
-      display_name,
-      given_name,
-      family_name,
-      notes,
-      email
+        user_identity_source_id,
+        user_identifier,
+        record_effective_date,
+        display_name,
+        given_name,
+        family_name,
+        notes,
+        email
     )
     SELECT 
-      (SELECT user_identity_source_id FROM biohub.user_identity_source WHERE name = 'UNVERIFIED'),
-      'spi-' || id,
-      now(),
-      display_name,
-      given_name,
-      family_name,
-      'Migrated from SPI as user' || id,
-      'default'
+        (SELECT user_identity_source_id FROM biohub.user_identity_source WHERE name = 'UNVERIFIED'),
+        'spi-' || md.id,
+        now(),
+        md.display_name,
+        md.given_name,
+        md.family_name,
+        'Migrated from SPI as user ' || md.id,
+        COALESCE(spp.email_address, 'default') AS email
     FROM 
-      migrate_spi_user_deduplication;
+        migrate_spi_user_deduplication md
+    LEFT JOIN 
+        public.spi_secure_persons spp ON spp.first_name = md.given_name AND spp.last_name = md.family_name
+    LEFT JOIN 
+        w_existing_users eu ON eu.given_name = md.given_name AND eu.family_name = md.family_name
+    WHERE eu.system_user_id IS NULL;
 
     -------------------------------------------------------------------------------------------------
     -- Update deduplicated users table with the system_user_id
     -------------------------------------------------------------------------------------------------
-    UPDATE 
-      migrate_spi_user_deduplication AS m
-    SET 
-      biohub_user_id = su.system_user_id
-    FROM 
-      biohub.system_user AS su
-    WHERE 
-      su.user_identifier = 'spi-' || m.id;
+    UPDATE migrate_spi_user_deduplication AS m
+    SET biohub_user_id = su.system_user_id
+    FROM biohub.system_user AS su
+    WHERE su.user_identifier = 'spi-' || m.id;
+
+    -- For existing users
+    UPDATE migrate_spi_user_deduplication AS m
+    SET biohub_user_id = eu.system_user_id
+    FROM w_existing_users eu
+    WHERE eu.given_name = m.given_name
+    AND eu.family_name = m.family_name;
   `;
 
   await connection.sql(sql);