Tweaks and another query for DBS

queries/TAT-WOW-project/DBS/find_dbs_samples.sql

@@ -1,5 +1,5 @@
 -- All samples that have had a GbS submission, and have been sequenced using a relevant primer panel
-SELECT DISTINCT ewh_sample_id
+SELECT DISTINCT ewh_sample_id, sample_uuid_bin, sample_uuid, sample_friendly_name
 FROM
 (
 SELECT  DISTINCT s.id AS ewh_sample_id,
@@ -24,6 +24,8 @@ JOIN mlwhd_mlwarehouse_proddata.iseq_flowcell iseq_flowcell USING (id_sample_tmp
 
 -- Beware! If a new primer panel is used in the lab, this list will need to be updated.
 WHERE iseq_flowcell.primer_panel IN ('PFA_GRC1_v1.0', 'PFA_GRC2_v1.0', 'PFA_Spec', 'PVIV_GRC_1.0')
+
+ORDER BY sample_friendly_name
 ;
 -- 4,301
 -- most recent vivax ones are from Feb 2021 - is this expected?

queries/TAT-WOW-project/DBS/find_stock_plates.sql

@@ -34,6 +34,8 @@ FROM
 
 JOIN mlwhd_mlwarehouse_proddata.sample mlwh_sample ON mlwh_sample.uuid_sample_lims = relevant_samples.sample_uuid
 JOIN mlwhd_mlwarehouse_proddata.stock_resource sr USING (id_sample_tmp)
+
+ORDER BY relevant_samples.sample_friendly_name
 ;
 
 -- distinct stock plate barcodes (52):

queries/TAT-WOW-project/DBS/timestamp_1_study_set_up.sql

@@ -0,0 +1,59 @@
+-- study name and timestamp concatenated, so get one row per sample
+SELECT  relevant_samples.ewh_sample_id
+        ,relevant_samples.sample_uuid_bin
+        ,relevant_samples.sample_uuid
+        ,relevant_samples.sample_friendly_name
+        ,GROUP_CONCAT(DISTINCT(sub.friendly_name)) AS study_friendly_names
+        ,GROUP_CONCAT(DISTINCT(studies.created)) AS studies_set_up
+FROM
+(
+  -- All samples that have had a GbS submission, and have been sequenced using a relevant primer panel
+  SELECT DISTINCT ewh_sample_id, sample_uuid_bin, sample_uuid, sample_friendly_name
+  FROM
+  (
+  SELECT  DISTINCT s.id AS ewh_sample_id,
+          s.uuid AS sample_uuid_bin,
+          insert(insert(insert(insert(lower(hex(s.uuid)),9,0,'-'),14,0,'-'),19,0,'-'),24,0,'-') AS sample_uuid,
+          s.friendly_name AS sample_friendly_name
+    FROM metadata m
+    JOIN events e ON e.id = m.event_id
+    JOIN event_types et ON et.id = e.event_type_id
+    JOIN roles r ON r.event_id = e.id
+    JOIN role_types rt ON r.role_type_id = rt.id
+    JOIN subjects s ON s.id = r.subject_id
+    WHERE m.created_at BETWEEN '2022-05-10' AND '2022-11-01'
+      AND et.`key` = 'order_made'
+      AND m.`key` = 'submission_template'
+      AND m.value = 'Limber-Htp - GBS'
+      AND rt.`key` = 'sample'
+  ) as gbs_samples
+
+  JOIN mlwhd_mlwarehouse_proddata.sample mlwh_sample ON mlwh_sample.uuid_sample_lims = gbs_samples.sample_uuid
+  JOIN mlwhd_mlwarehouse_proddata.iseq_flowcell iseq_flowcell USING (id_sample_tmp)
+
+  WHERE iseq_flowcell.primer_panel IN ('PFA_GRC1_v1.0', 'PFA_GRC2_v1.0', 'PFA_Spec', 'PVIV_GRC_1.0')
+) AS relevant_samples
+
+-- Find all order_made events for the relevant samples (1,837 rows, 54 distinct events)
+LEFT JOIN roles r_sample ON r_sample.subject_id = relevant_samples.ewh_sample_id
+LEFT JOIN events e ON e.id = r_sample.event_id
+LEFT JOIN event_types et ON et.id = e.event_type_id
+
+-- Find any 'study' subjects associated with these events
+LEFT JOIN roles r ON r.event_id = e.id
+LEFT JOIN role_types rt ON rt.id = r.role_type_id
+LEFT JOIN subjects sub ON r.subject_id = sub.id
+
+-- Join to MLWH study table to get timestamp of Study creation in Sequencescape
+LEFT JOIN mlwhd_mlwarehouse_proddata.study studies ON insert(insert(insert(insert(lower(hex(sub.uuid)),9,0,'-'),14,0,'-'),19,0,'-'),24,0,'-') = studies.uuid_study_lims
+
+WHERE et.`key` = 'order_made'
+  AND rt.`key` = 'study'
+
+GROUP BY relevant_samples.ewh_sample_id
+        ,relevant_samples.sample_uuid_bin
+        ,relevant_samples.sample_uuid
+        ,relevant_samples.sample_friendly_name
+
+ORDER BY relevant_samples.sample_friendly_name
+;