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CNDE-2094: quick fix #253

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merged 2 commits into from
Mar 13, 2025
Merged

CNDE-2094: quick fix #253

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900084b
This attribute is needed for Event Metric even though it is not used …
johneipe Mar 13, 2025
6ffdd54
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johneipe Mar 13, 2025
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25 changes: 20 additions & 5 deletions ..._strep_pneumo_datamart_postprocessing.sql → ..._strep_pneumo_datamart_postprocessing.sql
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
CREATE PROCEDURE [dbo].[sp_bmird_strep_pneumo_datamart_postprocessing]
CREATE or ALTER PROCEDURE [dbo].[sp_bmird_strep_pneumo_datamart_postprocessing]
@phc_uids nvarchar(max),
@debug bit = 'false'
AS
Expand All @@ -9,7 +9,7 @@ BEGIN
DECLARE @Proc_Step_no FLOAT = 0;
DECLARE @Proc_Step_Name VARCHAR(200) = '';
DECLARE @batch_id bigint;
SET @batch_id = cast((format(getdate(), 'yyMMddHHmmss')) as bigint);
SET @batch_id = cast((format(getdate(), 'yyMMddHHmmssffff')) as bigint);
DECLARE @Dataflow_Name VARCHAR(200) = 'BMIRD_STREP_PNEUMO Post-Processing Event';
DECLARE @Package_Name VARCHAR(200) = 'sp_bmird_strep_pneumo_datamart_postprocessing';

Expand Down Expand Up @@ -874,7 +874,16 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
SELECT
INVESTIGATION_KEY,
STRING_AGG(TYPES_OF_INFECTIONS_, ',') WITHIN GROUP (ORDER BY TYPES_OF_INFECTIONS_ DESC)
AS TYPE_INFECTION_OTHERS_CONCAT
AS TYPE_INFECTION_OTHERS_CONCAT,
'No' as TYPE_INFECTION_BACTEREMIA,
'No' as TYPE_INFECTION_PNEUMONIA,
'No' as TYPE_INFECTION_MENINGITIS,
'No' as TYPE_INFECTION_EMPYEMA,
'No' as TYPE_INFECTION_CELLULITIS,
'No' as TYPE_INFECTION_PERITONITIS,
'No' as TYPE_INFECTION_PERICARDITIS,
'No' as TYPE_INFECTION_PUERPERAL_SEP,
'No' as TYPE_INFECTION_SEP_ARTHRITIS
into #TYPE_INFECTION_INFO_OTHERS
FROM #DM_BMD118
WHERE _mark_ = 0
Expand Down Expand Up @@ -1022,7 +1031,13 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
SELECT
INVESTIGATION_KEY,
STRING_AGG(STERILE_SITE_, ',') WITHIN GROUP (ORDER BY STERILE_SITE_ DESC)
AS STERILE_SITE_OTHERS_CONCAT
AS STERILE_SITE_OTHERS_CONCAT,
'No' as STERILE_SITE_BLOOD,
'No' as STERILE_SITE_CEREBRAL_SF,
'No' as STERILE_SITE_PLEURAL_FLUID,
'No' as STERILE_SITE_PERITONEAL_FLUID,
'No' as STERILE_SITE_PERICARDIAL_FLUID,
'No' as STERILE_SITE_JOINT_FLUID
into #STEP_STERILE_SITE_INFO_OTHERS
FROM #DM_BMD122
WHERE _mark_ = 0
Expand Down Expand Up @@ -1584,4 +1599,4 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
RETURN -1 ;

END CATCH
END;
END;
3 changes: 3 additions & 0 deletions ...ice/src/main/java/gov/cdc/etldatapipeline/investigation/repository/model/dto/Contact.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,9 @@ public class Contact {
@Column(name="ctt_inv_assigned_dt")
private String cttInvAssignedDt;

@Column(name="jurisdiction_cd")
private String jurisdictionCd;

@Column(name="ctt_jurisdiction_nm")
private String cttJurisdictionNm;

Expand Down
1 change: 1 addition & 0 deletions ...va/gov/cdc/etldatapipeline/investigation/repository/model/reporting/ContactReporting.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ public class ContactReporting {
private String localId;
private Long namedDuringInterviewUid;
private Long programJurisdictionOid;
private String jurisdictionCd;
private String recordStatusCd;
private String recordStatusTime;
private String subjectEntityEpiLinkId;
Expand Down
49 changes: 32 additions & 17 deletions ...esources/db/rdb_modern/routines/140-sp_bmird_strep_pneumo_datamart_postprocessing-001.sql
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
CREATE PROCEDURE [dbo].[sp_bmird_strep_pneumo_datamart_postprocessing]
CREATE or ALTER PROCEDURE [dbo].[sp_bmird_strep_pneumo_datamart_postprocessing]
@phc_uids nvarchar(max),
@debug bit = 'false'
AS
Expand All @@ -9,7 +9,7 @@ BEGIN
DECLARE @Proc_Step_no FLOAT = 0;
DECLARE @Proc_Step_Name VARCHAR(200) = '';
DECLARE @batch_id bigint;
SET @batch_id = cast((format(getdate(), 'yyMMddHHmmss')) as bigint);
SET @batch_id = cast((format(getdate(), 'yyMMddHHmmssffff')) as bigint);
DECLARE @Dataflow_Name VARCHAR(200) = 'BMIRD_STREP_PNEUMO Post-Processing Event';
DECLARE @Package_Name VARCHAR(200) = 'sp_bmird_strep_pneumo_datamart_postprocessing';

Expand Down Expand Up @@ -142,9 +142,9 @@ BEGIN
END as PATIENT_ADDRESS
into #BMIRD_PATIENT1
from #INVKEYS BC
left join dbo.D_PATIENT as P with (nolock)
left join dbo.D_PATIENT as P with (nolock)
on BC.PATIENT_KEY = P.PATIENT_key
left join dbo.CONDITION as C with (nolock)
left join dbo.CONDITION as C with (nolock)
on C.CONDITION_KEY = BC.CONDITION_KEY
AND P.PATIENT_KEY <> 1
;
Expand Down Expand Up @@ -189,9 +189,9 @@ BEGIN
from #BMIRD_PATIENT1 as bpa
left join dbo.v_nrt_inv_keys_attrs_mapping as inv
on bpa.investigation_key = inv.investigation_key
left join dbo.INVESTIGATION i with (nolock)
left join dbo.INVESTIGATION i with (nolock)
on i.INVESTIGATION_KEY = bpa.INVESTIGATION_KEY and i.INVESTIGATION_KEY <> 1
left join dbo.EVENT_METRIC em with (nolock)
left join dbo.EVENT_METRIC em with (nolock)
on em.event_uid = i.CASE_UID
left outer join dbo.D_ORGANIZATION o with (nolock)
on inv.ADT_HSPTL_KEY = o.ORGANIZATION_KEY and o.ORGANIZATION_KEY <> 1
Expand Down Expand Up @@ -300,7 +300,7 @@ Step 7: Merge the tables so that both <= 8 and > 8 results are included
1 as SORT_ORDER
into #ANTIMICRO1A
FROM #BMIRD_PATIENT1 bc
INNER JOIN dbo.ANTIMICROBIAL a with (nolock)
INNER JOIN dbo.ANTIMICROBIAL a with (nolock)
ON bc.ANTIMICROBIAL_GRP_KEY = a.ANTIMICROBIAL_GRP_KEY
WHERE a.ANTIMICROBIAL_GRP_KEY <> 1 AND a.ANTIMICROBIAL_AGENT_TESTED_IND = 'PENICILLIN'
ORDER BY INVESTIGATION_KEY, SORT_ORDER;
Expand Down Expand Up @@ -546,7 +546,7 @@ Step 5: Merge the tables so that both <= 8 and > 8 results are included
a.UNDERLYING_CONDITION_NM as UNDERLYING_CONDITION_
into #BMD127
FROM #BMIRD_PATIENT1 bc
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
on bc.BMIRD_MULTI_VAL_GRP_KEY = a.BMIRD_MULTI_VAL_GRP_KEY
WHERE a.UNDERLYING_CONDITION_NM IS NOT NULL
ORDER BY bc.INVESTIGATION_KEY, a.UNDERLYING_CONDITION_NM;
Expand Down Expand Up @@ -653,7 +653,7 @@ Step 4: Merge the new table with the BMIRD_ANTIMICRO table
a.NON_STERILE_SITE AS NON_STERILE_SITE_
into #DM_BMD125
FROM #BMIRD_PATIENT1 bc
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
on bc.BMIRD_MULTI_VAL_GRP_KEY = a.BMIRD_MULTI_VAL_GRP_KEY
WHERE A.NON_STERILE_SITE IS NOT NULL
ORDER BY bc.INVESTIGATION_KEY, a.NON_STERILE_SITE;
Expand All @@ -664,7 +664,7 @@ Step 4: Merge the new table with the BMIRD_ANTIMICRO table
a.STREP_PNEUMO_1_CULTURE_SITES AS ADD_CULTURE_1_SITE_
into #DM_BMD142
FROM #BMIRD_PATIENT1 bc
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
on bc.BMIRD_MULTI_VAL_GRP_KEY = a.BMIRD_MULTI_VAL_GRP_KEY
WHERE A.STREP_PNEUMO_1_CULTURE_SITES IS NOT NULL
ORDER BY bc.INVESTIGATION_KEY, a.STREP_PNEUMO_1_CULTURE_SITES;
Expand All @@ -674,7 +674,7 @@ Step 4: Merge the new table with the BMIRD_ANTIMICRO table
a.STREP_PNEUMO_2_CULTURE_SITES AS ADD_CULTURE_2_SITE_
into #DM_BMD144
FROM #BMIRD_PATIENT1 bc
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
on bc.BMIRD_MULTI_VAL_GRP_KEY = a.BMIRD_MULTI_VAL_GRP_KEY
WHERE A.STREP_PNEUMO_2_CULTURE_SITES IS NOT NULL
ORDER BY bc.INVESTIGATION_KEY, a.STREP_PNEUMO_2_CULTURE_SITES;
Expand Down Expand Up @@ -791,7 +791,7 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
distinct bc.INVESTIGATION_KEY,
a.TYPES_OF_INFECTIONS AS TYPES_OF_INFECTIONS_
from #BMIRD_PATIENT1 bc
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
on bc.BMIRD_MULTI_VAL_GRP_KEY = a.BMIRD_MULTI_VAL_GRP_KEY
)
SELECT
Expand Down Expand Up @@ -874,7 +874,16 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
SELECT
INVESTIGATION_KEY,
STRING_AGG(TYPES_OF_INFECTIONS_, ',') WITHIN GROUP (ORDER BY TYPES_OF_INFECTIONS_ DESC)
AS TYPE_INFECTION_OTHERS_CONCAT
AS TYPE_INFECTION_OTHERS_CONCAT,
'No' as TYPE_INFECTION_BACTEREMIA,
'No' as TYPE_INFECTION_PNEUMONIA,
'No' as TYPE_INFECTION_MENINGITIS,
'No' as TYPE_INFECTION_EMPYEMA,
'No' as TYPE_INFECTION_CELLULITIS,
'No' as TYPE_INFECTION_PERITONITIS,
'No' as TYPE_INFECTION_PERICARDITIS,
'No' as TYPE_INFECTION_PUERPERAL_SEP,
'No' as TYPE_INFECTION_SEP_ARTHRITIS
into #TYPE_INFECTION_INFO_OTHERS
FROM #DM_BMD118
WHERE _mark_ = 0
Expand Down Expand Up @@ -948,7 +957,7 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
distinct bc.INVESTIGATION_KEY,
a.STERILE_SITE AS STERILE_SITE_
FROM #BMIRD_PATIENT1 bc
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
INNER JOIN dbo.BMIRD_MULTI_VALUE_FIELD a with (nolock)
ON bc.BMIRD_MULTI_VAL_GRP_KEY = a.BMIRD_MULTI_VAL_GRP_KEY
)
SELECT
Expand Down Expand Up @@ -1022,7 +1031,13 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
SELECT
INVESTIGATION_KEY,
STRING_AGG(STERILE_SITE_, ',') WITHIN GROUP (ORDER BY STERILE_SITE_ DESC)
AS STERILE_SITE_OTHERS_CONCAT
AS STERILE_SITE_OTHERS_CONCAT,
'No' as STERILE_SITE_BLOOD,
'No' as STERILE_SITE_CEREBRAL_SF,
'No' as STERILE_SITE_PLEURAL_FLUID,
'No' as STERILE_SITE_PERITONEAL_FLUID,
'No' as STERILE_SITE_PERICARDIAL_FLUID,
'No' as STERILE_SITE_JOINT_FLUID
into #STEP_STERILE_SITE_INFO_OTHERS
FROM #DM_BMD122
WHERE _mark_ = 0
Expand Down Expand Up @@ -1511,7 +1526,7 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
,src.CULTURE_SEROTYPE
,src.OTHSEROTYPE
FROM #BMIRD_ANTIMICRO_6 src
LEFT JOIN dbo.BMIRD_STREP_PNEUMO_DATAMART tgt
LEFT JOIN dbo.BMIRD_STREP_PNEUMO_DATAMART tgt
on src.INVESTIGATION_KEY = tgt.INVESTIGATION_KEY
WHERE tgt.INVESTIGATION_KEY IS NULL;

Expand Down Expand Up @@ -1584,4 +1599,4 @@ Step 5: Merge the new table with the BMIRD_ANTIMICRO table
RETURN -1 ;

END CATCH
END;
END;