Copied LCMB-ISC directory.

queries/TAT-WOW-project/LCMB-ISC-X/find_lcmb_isc_samples_performance_analysis.sql

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+-- Making the base sample query as a view would help with readability in the other queries.
+
+
+-- Version 1 - 529 samples, 14 seconds
+--
+SELECT subject_uuid
+FROM
+(
+  (
+    SELECT DISTINCT(fev.subject_uuid)
+    FROM metadata m
+    JOIN flat_events_view fev ON m.event_id = fev.wh_event_id
+    WHERE m.`key` = 'order_type' AND m.value = 'LCMB'
+      AND m.created_at > '2022-05-10'
+      AND fev.role_type = 'sample'
+  )
+  UNION ALL
+  (
+    SELECT DISTINCT(fev.subject_uuid)
+    FROM metadata m
+    JOIN flat_events_view fev ON m.event_id = fev.wh_event_id
+    WHERE m.`key` = 'order_type' AND m.value = 'ReISC'
+      AND m.created_at > '2022-05-10'
+      AND fev.role_type = 'sample'
+  )
+) AS all_lcmb_reisc_samples
+GROUP BY subject_uuid
+HAVING Count(*) > 1
+;
+
+
+-- Version 2 - not using flat_events_view - 529 samples, 11 seconds
+--
+SELECT id
+FROM
+(
+  (
+    SELECT DISTINCT(s.id)
+    FROM metadata m
+    JOIN events e ON e.id = m.event_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.`key` = 'order_type' AND m.value = 'LCMB'
+      AND m.created_at > '2022-05-10'
+      AND rt.`key` = 'sample'
+  )
+  UNION ALL
+  (
+    SELECT DISTINCT(s.id)
+    FROM metadata m
+    JOIN events e ON e.id = m.event_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.`key` = 'order_type' AND m.value = 'ReISC'
+      AND m.created_at > '2022-05-10'
+      AND rt.`key` = 'sample'
+  )
+) AS all_lcmb_reisc_samples
+GROUP BY id
+HAVING Count(*) > 1
+;
+
+
+-- Version 3 - querying both order_types in one - 529 samples, 6 seconds! :)
+--
+SELECT all_lcmb_reisc_samples_by_pipeline.sample_id
+FROM
+(
+  SELECT DISTINCT s.id AS sample_id, m.value AS pipeline
+  FROM metadata m
+  JOIN events e ON e.id = m.event_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.`key` = 'order_type' AND m.value IN ('LCMB', 'ReISC')
+    AND m.created_at > '2022-05-10'
+    AND rt.`key` = 'sample'
+) AS all_lcmb_reisc_samples_by_pipeline
+GROUP BY all_lcmb_reisc_samples_by_pipeline.sample_id
+HAVING Count(*) > 1
+;
+
+-- Version 4 - including event type filter - 529 samples, 2 seconds! :)
+--
+  SELECT all_lcmb_reisc_samples_by_pipeline.sample_id
+  FROM
+  (
+    SELECT DISTINCT s.id AS sample_id, m.value AS pipeline
+    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.`key` = 'order_type' AND m.value IN ('LCMB', 'ReISC')
+      AND m.created_at > '2022-05-10'
+      AND rt.`key` = 'sample'
+      AND et.`key` = 'order_made'
+  ) AS all_lcmb_reisc_samples_by_pipeline
+  GROUP BY all_lcmb_reisc_samples_by_pipeline.sample_id
+  HAVING Count(*) > 1
+;
+
+-- Version 5 - including more useful information - 529 samples, still 2ish seconds
+--
+SELECT 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,
+                  m.value AS pipeline
+  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.`key` = 'order_type' AND m.value IN ('LCMB', 'ReISC')
+    AND m.created_at > '2022-05-10'
+    AND rt.`key` = 'sample'
+    AND et.`key` = 'order_made'
+) AS all_lcmb_reisc_samples_by_pipeline
+
+GROUP BY all_lcmb_reisc_samples_by_pipeline.ewh_sample_id
+HAVING Count(*) > 1
+;

queries/TAT-WOW-project/LCMB-ISC-X/find_stock_plate.sql

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+-- stock plate info in Events WH seems sketchy
+-- Following route seems much more reliable:
+-- Events WH sample uuid --> MLWH sample --> MLWH stock_resource
+-- This retrieves the stock plate barcode from when the sample manifest was uploaded
+-- Finds 8 distinct stock plates
+
+SELECT  -- SQL_NO_CACHE
+        relevant_samples.ewh_sample_id
+        ,relevant_samples.sample_uuid_bin
+        ,relevant_samples.sample_uuid
+        ,relevant_samples.sample_friendly_name
+        ,sr.labware_human_barcode
+FROM
+(
+  -- Relevant (529) samples for LCMB-ISC pipeline
+  SELECT 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, m.value AS pipeline
+    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.`key` = 'order_type' AND m.value IN ('LCMB', 'ReISC')
+      AND m.created_at > '2022-05-10'
+      AND rt.`key` = 'sample'
+      AND et.`key` = 'order_made'
+  ) AS all_lcmb_reisc_samples_by_pipeline
+  GROUP BY all_lcmb_reisc_samples_by_pipeline.ewh_sample_id
+  HAVING Count(*) > 1
+) 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)
+;

queries/TAT-WOW-project/LCMB-ISC-X/find_studies_and_projects.sql

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+-- 2 separate queries, as each one individually takes ~2-3 seconds, but if I try to make them in a readable way into a combined query, it takes much longer.
+-- They can be joined in their entirety using UNION or JOIN, but it is probably cleaner to keep them as two separate queries and join using Tableau.
+-- If one sample is associated with multiple studies or projects, these appear as multiple rows.
+-- Doesn't filter events here by 'LCMB' or 'ReISC' (in the outer query), so we could theoretically find orders for the same samples to other pipelines.
+-- At time of writing, adding a metadata filter for 'LCMB' or 'ReISC' made the query slower and didn't change the results, so I left it out.
+
+-- Sample and study info
+SELECT  -- SQL_NO_CACHE
+        DISTINCT
+        relevant_samples.ewh_sample_id
+        ,relevant_samples.sample_uuid_bin
+        ,relevant_samples.sample_uuid
+        ,relevant_samples.sample_friendly_name
+        ,sub.id AS ewh_study_id
+        ,sub.uuid AS study_uuid_bin
+        ,insert(insert(insert(insert(lower(hex(sub.uuid)),9,0,'-'),14,0,'-'),19,0,'-'),24,0,'-') AS study_uuid
+        ,sub.friendly_name AS study_friendly_name
+FROM
+(
+  -- Relevant (529) samples for LCMB-ISC pipeline
+  SELECT 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, m.value AS pipeline
+    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.`key` = 'order_type' AND m.value IN ('LCMB', 'ReISC')
+      AND m.created_at > '2022-05-10'
+      AND rt.`key` = 'sample'
+      AND et.`key` = 'order_made'
+  ) AS all_lcmb_reisc_samples_by_pipeline
+  GROUP BY all_lcmb_reisc_samples_by_pipeline.ewh_sample_id
+  HAVING Count(*) > 1
+) 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
+
+WHERE et.`key` = 'order_made'
+  AND rt.`key` = 'study'
+;
+
+
+-- Sample and project info
+SELECT  -- SQL_NO_CACHE
+        DISTINCT
+        relevant_samples.ewh_sample_id
+        ,relevant_samples.sample_uuid_bin
+        ,relevant_samples.sample_uuid
+        ,relevant_samples.sample_friendly_name
+        ,sub.id AS ewh_project_id
+        ,sub.uuid AS project_uuid_bin
+        ,insert(insert(insert(insert(lower(hex(sub.uuid)),9,0,'-'),14,0,'-'),19,0,'-'),24,0,'-') AS project_uuid
+        ,sub.friendly_name AS project_friendly_name
+FROM
+(
+  -- Relevant (529) samples for LCMB-ISC pipeline
+  SELECT 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, m.value AS pipeline
+    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.`key` = 'order_type' AND m.value IN ('LCMB', 'ReISC')
+      AND m.created_at > '2022-05-10'
+      AND rt.`key` = 'sample'
+      AND et.`key` = 'order_made'
+  ) AS all_lcmb_reisc_samples_by_pipeline
+  GROUP BY all_lcmb_reisc_samples_by_pipeline.ewh_sample_id
+  HAVING Count(*) > 1
+) 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 'project' 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
+
+WHERE et.`key` = 'order_made'
+  AND rt.`key` = 'project'
+;
+
+
+
+
+-- Concatenating studies, so there's 1 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
+FROM
+(
+  -- Relevant (529) samples for LCMB-ISC pipeline
+  SELECT 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, m.value AS pipeline
+    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.`key` = 'order_type' AND m.value IN ('LCMB', 'ReISC')
+      AND m.created_at > '2022-05-10'
+      AND rt.`key` = 'sample'
+      AND et.`key` = 'order_made'
+  ) AS all_lcmb_reisc_samples_by_pipeline
+  GROUP BY all_lcmb_reisc_samples_by_pipeline.ewh_sample_id
+  HAVING Count(*) > 1
+) 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
+
+WHERE et.`key` = 'order_made'
+  AND rt.`key` = 'study'
+
+GROUP BY relevant_samples.ewh_sample_id
+;

queries/TAT-WOW-project/LCMB-ISC-X/find_submissions.sql

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+-- 'submission' here means when the customer asks for a batch of work to be completed
+-- this happens via the RT system, via the SSRs
+-- here we're using sample manifest upload to SS as a proxy
+
+SELECT  ewh_sample_id
+        ,sample_uuid_bin
+        ,sample_uuid
+        ,sample_friendly_name
+        ,e.id AS manifest_event_id
+        ,e.occured_at AS 'samples_created_by_manifest'
+FROM
+(
+  SELECT 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, m.value AS pipeline
+    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.`key` = 'order_type' AND m.value IN ('LCMB', 'ReISC')
+      AND m.created_at > '2022-05-10'
+      AND rt.`key` = 'sample'
+      AND et.`key` = 'order_made'
+  ) AS all_lcmb_reisc_samples_by_pipeline
+  GROUP BY all_lcmb_reisc_samples_by_pipeline.ewh_sample_id
+  HAVING Count(*) > 1
+) AS relevant_samples
+
+JOIN roles r ON r.subject_id = relevant_samples.ewh_sample_id
+JOIN events e ON e.id = r.event_id
+JOIN event_types et ON et.id = e.event_type_id
+
+WHERE et.`key` = 'sample_manifest.updated'
+;