From b788614bc2c8344aec26f74c3edfd7865eb698e5 Mon Sep 17 00:00:00 2001 From: jallentxbiomed Date: Mon, 3 Nov 2025 09:08:24 -0600 Subject: [PATCH 1/4] Added admit ID to Sequencer and unique index to caseid --- snprc_ehr/resources/etls/SndEventData.xml | 2 +- .../study/datasets/datasets_metadata.xml | 5 +++++ .../src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java | 3 ++- .../snprc_ehr/query/SNPRC_EHRTriggerHelper.java | 11 ++--------- 4 files changed, 10 insertions(+), 11 deletions(-) diff --git a/snprc_ehr/resources/etls/SndEventData.xml b/snprc_ehr/resources/etls/SndEventData.xml index 28e8dd9cb..df82e7ef2 100644 --- a/snprc_ehr/resources/etls/SndEventData.xml +++ b/snprc_ehr/resources/etls/SndEventData.xml @@ -6,7 +6,7 @@ Copy to target - + diff --git a/snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml b/snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml index 40dadbc39..4ae7cb675 100644 --- a/snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -394,6 +394,11 @@ varchar + + + caseid + + Cases diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java b/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java index 47b489813..bca1eb4d5 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java @@ -30,7 +30,8 @@ public enum SNPRC_EHRSequencer { - ANIMALID("org.labkey.snprc_ehr.domain.AnimalId", 100); + ANIMALID("org.labkey.snprc_ehr.domain.AnimalId", 100), + ADMITID("org.labkey.snprc_ehr.domain.AdmitId", 270000); // "last value assigned" is stored in the table - not the same as CAMP which is the "next value to assign" // new sequences are added here // example: diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/query/SNPRC_EHRTriggerHelper.java b/snprc_ehr/src/org/labkey/snprc_ehr/query/SNPRC_EHRTriggerHelper.java index 1efec61c1..e47b46555 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/query/SNPRC_EHRTriggerHelper.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/query/SNPRC_EHRTriggerHelper.java @@ -40,6 +40,7 @@ import org.labkey.api.security.UserManager; import org.labkey.api.util.PageFlowUtil; import org.labkey.snprc_ehr.SNPRC_EHRSchema; +import org.labkey.snprc_ehr.SNPRC_EHRSequencer; import java.sql.ResultSet; import java.sql.SQLException; @@ -222,15 +223,7 @@ public Integer getNextDietCode() */ public Integer getNextCaseId() { - DbSchema dbStudySchema = SNPRC_EHRSchema.getInstance().getStudySchema(); - SQLFragment sql = new SQLFragment("SELECT MAX(c.caseid) AS MAX_CODE FROM "); - sql.append(getTableInfo("study", "cases"), "c"); - SqlSelector sqlSelector = new SqlSelector(dbStudySchema, sql); - - Integer caseId = sqlSelector.getObject(Integer.class); - - // if table has been truncated - reseed the caseid at 1 - return (caseId == null) ? 1 : caseId + 1; + return SNPRC_EHRSequencer.ADMITID.getNext(getContainer(), getUser()); } public Map getExtraContext() From 5e265b6953d1293934b124a952cabb2fd62ff3ac Mon Sep 17 00:00:00 2001 From: jallentxbiomed Date: Tue, 4 Nov 2025 10:54:17 -0600 Subject: [PATCH 2/4] removed snd etl value change --- snprc_ehr/resources/etls/SndEventData.xml | 2 +- snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/snprc_ehr/resources/etls/SndEventData.xml b/snprc_ehr/resources/etls/SndEventData.xml index df82e7ef2..28e8dd9cb 100644 --- a/snprc_ehr/resources/etls/SndEventData.xml +++ b/snprc_ehr/resources/etls/SndEventData.xml @@ -6,7 +6,7 @@ Copy to target - + diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java b/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java index bca1eb4d5..d315252b7 100644 --- a/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java +++ b/snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRSequencer.java @@ -31,7 +31,7 @@ public enum SNPRC_EHRSequencer { ANIMALID("org.labkey.snprc_ehr.domain.AnimalId", 100), - ADMITID("org.labkey.snprc_ehr.domain.AdmitId", 270000); + ADMITID("org.labkey.snprc_ehr.domain.AdmitId", 300000); // "last value assigned" is stored in the table - not the same as CAMP which is the "next value to assign" // new sequences are added here // example: From 6023dd643e901b07a5d1b4f1bf2d860d741a4af3 Mon Sep 17 00:00:00 2001 From: jallentxbiomed Date: Tue, 4 Nov 2025 13:32:49 -0600 Subject: [PATCH 3/4] remove ActiveVets query --- snprc_ehr/resources/queries/snprc_ehr/ActiveVets.sql | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 snprc_ehr/resources/queries/snprc_ehr/ActiveVets.sql diff --git a/snprc_ehr/resources/queries/snprc_ehr/ActiveVets.sql b/snprc_ehr/resources/queries/snprc_ehr/ActiveVets.sql deleted file mode 100644 index f9539b1fe..000000000 --- a/snprc_ehr/resources/queries/snprc_ehr/ActiveVets.sql +++ /dev/null @@ -1,12 +0,0 @@ -/******************************************************** -Active Vet Query for Grok. - -Restricted to Active flagged vets only -Excludes vetId 2 which is (see paper records) - -srr 07.30.2019 -********************************************************/ -select vv.displayName as VetName -from snprc_ehr.validVets vv -where vv.status = 'A' -and vv.vetId <> 2 \ No newline at end of file From 921a08907acaf89939de975b2f50977ac6a6b1ff Mon Sep 17 00:00:00 2001 From: jallentxbiomed Date: Wed, 12 Nov 2025 12:09:01 -0600 Subject: [PATCH 4/4] added scale to species --- .../referenceStudy/study/datasets/datasets_metadata.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml b/snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml index 4ae7cb675..806d12694 100644 --- a/snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -1503,6 +1503,7 @@ varchar false Species code (3 char) + 10 integer