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[DSM] PEPPER-853 sm id fix #2636

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merged 7 commits into from
Aug 4, 2023
Merged

[DSM] PEPPER-853 sm id fix #2636

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af54a7b
PEPPER-853 added a check for the number of scrolls and uss to not be …
pegahtah Jul 28, 2023
ae8bc14
Merge branch 'develop' into PEPPER-853_zeroSmIdFix
pegahtah Jul 28, 2023
45efeed
Merge branch 'develop' into PEPPER-853_zeroSmIdFix
pegahtah Aug 3, 2023
d8dbc9e
I simplified the query to first check the numbers entered
pegahtah Aug 3, 2023
1153ed8
Merge remote-tracking branch 'origin/develop' into PEPPER-853_zeroSmI…
pegahtah Aug 3, 2023
28de7a8
PEPPER-853 changes to consider NULL as 0 too
pegahtah Aug 3, 2023
d2147dd
Merge branch 'develop' into PEPPER-853_zeroSmIdFix
pegahtah Aug 4, 2023
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3 changes: 2 additions & 1 deletion ...r-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/dao/mercury/MercurySampleDao.java
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Expand Up @@ -28,6 +28,7 @@ public class MercurySampleDao implements Dao<MercurySampleDto> {
+ "LEFT JOIN ddp_onc_history_detail oD on (mr.medical_record_id = oD.medical_record_id AND NOT oD.deleted <=> 1) "
+ "LEFT JOIN ddp_tissue t on (oD.onc_history_detail_id = t.onc_history_detail_id AND NOT t.deleted <=> 1) "
+ "WHERE oD.tissue_received IS NOT NULL AND p.ddp_participant_id = ? AND ddp.instance_name = ? "
+ "AND (IFNULL(t.uss_count, 0) <> 0 OR IFNULL(t.scrolls_count, 0) <> 0) "
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Just avoiding the ones that are both 0 or both null should do the trick.

+ "AND IFNULL(t.uss_count, 0) = (SELECT count(*) from sm_id sm "
+ "left join sm_id_type smtype on (sm.sm_id_type_id = smtype.sm_id_type_id) "
+ "where smtype.sm_id_type = \"uss\" and sm.tissue_id = t.tissue_id and NOT sm.deleted <=> 1 "
Expand All @@ -40,7 +41,7 @@ public class MercurySampleDao implements Dao<MercurySampleDto> {
+ "From ddp_mercury_sequencing where ddp_participant_id = ? group by (tissue_id) ) as table2 "
+ "on table2.seqt = table1.tissue_id "
+ "LEFT JOIN (select order_id, mercury_sequencing_id, order_status, order_date, mercury_pdo_id "
+ "FROM ddp_mercury_sequencing WHERE ddp_participant_id = ?) as table3 ON(table3.mercury_sequencing_id = table2.ms_id)";
+ "FROM ddp_mercury_sequencing WHERE ddp_participant_id = ?) as table3 ON(table3.mercury_sequencing_id = table2.ms_id) ";
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Is this change intentional?

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Yeah I like to have an extra space at the end in case we need to concat the query with some other condition



public static String SQL_GET_ELIGIBLE_SAMPLES =
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