Additional queries used

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

@@ -0,0 +1,37 @@
+-- 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)
+
+-- 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?
+-- SSR says "we get so few samples for vivax they are waiting a while. The panel is still good and used."
+-- To find primer panel values, you can:
+  -- go to the bulk submission page in Sequencescape UI
+  -- select "Limber-Htp - GBS" as the submission template
+  -- look at the values in the 'primer panel' dropdown
+  -- an SSR can tell you which ones in the list are relevant

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

@@ -0,0 +1,46 @@
+SELECT  relevant_samples.ewh_sample_id
+        ,relevant_samples.sample_uuid_bin
+        ,relevant_samples.sample_uuid
+        ,relevant_samples.sample_friendly_name
+        ,sr.labware_human_barcode
+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
+
+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):
+-- 'DN889383T','DN906212B','DN901114D','DN906213C','DN889403G','DN889402F','DN906214D','DN873164E','DN889381R','DN873165F','DN873163D','DN889382S','DN833219F','DN833224C','DN833218E','DN824038B','DN824034U','DN824040S','DN824036W','DN824037A','DN824039C','DN906215E','DN890237C','DN906216F','DN901115E','DN946556T','DN906217G','DN903543F','DN944685T','DN944686U','DN944687V','DN944689A','DN944690Q','DN944688W','DN944691R','SQPP-2639-H','SQPP-106-M','SQPP-2634-C','SQPP-2635-D','SQPP-2636-E','DN946555S','DN946553Q','DN946554R','SQPP-101-H','SQPP-102-I','SQPP-104-K','SQPP-103-J','SQPP-105-L','SQPP-2637-F','SQPP-2643-D','SQPP-2638-G','SQPP-2645-F',
+-- stock plate barcodes match up nicely to those from WIP spreadsheet.
+-- In the WIP, if the "pre-extracted plate" column is filled out, these barcodes map to that column, otherwise they map to the "stock plate" column.
+-- All above barcodes are found in the WIP, either in "GbS" or "GbS Complete" tabs.
+-- From spot-checking, it looks like any barcodes in the WIP that are *not* in the above list are because of the time window looked at in the query.

queries/TAT-WOW-project/DBS-X/list_events.sql

@@ -0,0 +1,12 @@
+SELECT distinct s.friendly_name, et.key et_key, et.description, e.created_at, m.key m_key, m.value m_value
+    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 
+      s.friendly_name = '6543STDY10459601'
+      AND rt.`key` = 'sample'
+      and m.key != 'witnessed_by'
+	order by e.created_at

queries/TAT-WOW-project/DBS-X/metadata_keys.sql

@@ -0,0 +1 @@
+select distinct `key` from metadata;