PEPPER-853 added a check for the number of scrolls and uss to not be …

…zero
broadinstitute · Jul 28, 2023 · af54a7b · af54a7b
1 parent 91ec798
commit af54a7b
Showing 1 changed file with 13 additions and 4 deletions.
diff --git a/...r-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/dao/mercury/MercurySampleDao.java b/...r-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/dao/mercury/MercurySampleDao.java
@@ -20,27 +20,36 @@
 public class MercurySampleDao implements Dao<MercurySampleDto> {
     public static String SQL_GET_ELIGIBLE_TISSUES =
             "SELECT * FROM ("
-                    + "SELECT collaborator_sample_id, t.sent_gp, oD.date_px, oD.tissue_received, t.tissue_id "
+                    + "SELECT collaborator_sample_id, t.sent_gp, oD.date_px, oD.tissue_received, t.tissue_id, "
+                    + " (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 "
+                    + "   and sm.received_date is not null) as count_of_uss, "
+                    + " (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 = \"scrolls\" and sm.tissue_id = t.tissue_id and NOT sm.deleted <=> 1 "
+                    + "   and sm.received_date is not null) as count_of_scrolls "
                     + "FROM ddp_participant as p "
                     + "LEFT JOIN ddp_instance as ddp on (ddp.ddp_instance_id = p.ddp_instance_id) "
                     + "LEFT JOIN ddp_institution inst on (inst.participant_id = p.participant_id) "
                     + "LEFT JOIN ddp_medical_record mr on (mr.institution_id = inst.institution_id AND NOT mr.deleted <=> 1) "
                     + "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) = (SELECT count(*) from sm_id sm "
+                    + "AND  IFNULL(t.uss_count, -1) = (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 "
                     + "and sm.received_date is not null) "
-                    + "AND IFNULL(t.scrolls_count, 0) = (SELECT count(*) from sm_id sm "
+                    + "AND IFNULL(t.scrolls_count, -1) = (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 = \"scrolls\" and sm.tissue_id = t.tissue_id and NOT sm.deleted <=> 1 "
                     + "and sm.received_date is not null) ) as table1 "
                     + "left join (select max(mercury_sequencing_id) AS ms_id, tissue_id as seqt "
                     + "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) "
+                    + " WHERE (table1.count_of_scrolls != 0 OR table1.count_of_uss != 0) ";
 
 
     public static String SQL_GET_ELIGIBLE_SAMPLES =