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2 changes: 1 addition & 1 deletion snprc_ehr/module.properties
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
ModuleClass: org.labkey.snprc_ehr.SNPRC_EHRModule
SupportedDatabases: mssql
SupportedDatabases: mssql, pgsql
ManageVersion: true
License: Apache 2.0
LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
2 changes: 1 addition & 1 deletion snprc_ehr/resources/queries/ehr/ProtocolLookup.sql
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ PARAMETERS
newAssignmentsParm INTEGER DEFAULT 1
)
SELECT p.protocol AS Iacuc,
p.protocol + ' - ' + RTRIM(p.inves)+ ' -' + RTRIM(p.title) AS DisplayValue,
p.protocol || ' - ' || RTRIM(p.inves) || ' -' || RTRIM(p.title) AS DisplayValue,
RIGHT(p.protocol, 2) AS Species,
p.project_type as ProjectType,
p.sequenceNumber as SequenceNumber,
Expand Down
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
SELECT a.value as AcqCode,
a.category as Category,
rtrim(a.value) + ' - ' + a.description as DisplayValue,
rtrim(a.value) || ' - ' || a.description as DisplayValue,
a.sort_order as SortOrder
from ehr_lookups.AcquisitionType as a
where a.date_disabled is null
10 changes: 5 additions & 5 deletions snprc_ehr/resources/queries/ehr_lookups/AgeClassRanges.sql
Original file line number Diff line number Diff line change
Expand Up @@ -20,13 +20,13 @@ SELECT

-- please excuse the ugly formatting - A sql server convert function would be helpful here!
case when (age."max" is NULL and age.label = 'Senior') then
(CAST(age."min" as VARCHAR(5) ) + case when (age."min"- truncate(age."min", 0) > 0) then '' else '.0 - ' end)
(CAST(age."min" as VARCHAR(5) ) || case when (age."min"- FLOOR(age."min") > 0) then '' else '.0 - ' end)
ELSE
(CAST(age."min" as VARCHAR(5)) +
+ case when (age."min"- truncate(age."min", 0) > 0) then ' - ' else '.0 - ' end
(CAST(age."min" as VARCHAR(5)) ||
case when (age."min"- FLOOR(age."min") > 0) then ' - ' else '.0 - ' end

+ CAST(age."max" as varchar(5))
+ case when (age."max"- truncate(age."max", 0) > 0) then '' else '.0' end )
|| CAST(age."max" as varchar(5))
|| case when (age."max"- FLOOR(age."max") > 0) then '' else '.0' end )
END AS ageRange,

age.gender
Expand Down
4 changes: 2 additions & 2 deletions snprc_ehr/resources/queries/snprcApath/apath_encounters.sql
Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,11 @@ ELSE 'Completed'
END AS QCStateLabel,

CASE
WHEN a.tissue IS NOT NULL THEN (a.tissue + '-' + b.description)
WHEN a.tissue IS NOT NULL THEN (a.tissue || '-' || b.description)
ELSE b.description
END AS title

FROM snprcApath.apath a INNER JOIN snprcApath.valid_accession_codes b ON a.accession_code = b.accession_code
INNER JOIN snprcApath.valid_record_status d ON a.record_status = d.record_status

WHERE a.animal_id IS NOT NULL AND COALESCE(a.biopsy, a.death) IS NOT NULL AND b.description IS NOT NULL
WHERE a.animal_id IS NOT NULL AND COALESCE(a.biopsy, a.death) IS NOT NULL AND b.description IS NOT NULL
2 changes: 1 addition & 1 deletion snprc_ehr/resources/queries/snprc_ehr/AccountLookup.sql
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ SELECT a.accountGroup AS AccountGroup,
a.account AS Account,
a.date AS StartDate,
a.description AS Description,
a.account + ' - ' + rtrim(a.description) as DisplayValue
a.account || ' - ' || rtrim(a.description) as DisplayValue

FROM snprc_ehr.validAccounts AS a
where enddate is null and a.account <> '0000-000-00'
Expand Down
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
SELECT DISTINCT s.species_code as SpeciesCode,
rtrim(sc.common_name) as CommonName,
s.species_code + ' (' + rtrim(s.arc_species_code) + ') - ' + rtrim(s.scientific_name) + '/'+ rtrim(sc.common_name) as DisplayColumn,
s.species_code || ' (' || rtrim(s.arc_species_code) || ') - ' || rtrim(s.scientific_name) || '/' || rtrim(sc.common_name) as DisplayColumn,
s.scientific_name as ScientificName,
s.arc_species_code as arcSpeciesCode
FROM snprc_ehr.species AS s
Expand Down
6 changes: 3 additions & 3 deletions snprc_ehr/resources/queries/snprc_ehr/ExportSndLookupSets.sql
Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,9 @@ SELECT
SetName as LOOKUP_KEY,
ObjectId as OBJECT_ID,
LEFT(s.Email,
CASE WHEN charindex('@', s.Email) = 0
THEN LEN(s.Email)
ELSE (charindex('@', s.Email) - 1) END) as USER_NAME,
CASE WHEN LOCATE('@', s.Email) = 0
THEN LENGTH(s.Email)
ELSE (LOCATE('@', s.Email) - 1) END) as USER_NAME,
ls.Modified as ENTRY_DATE_TM
FROM
snd.LookupSets ls
Expand Down
8 changes: 4 additions & 4 deletions snprc_ehr/resources/queries/snprc_ehr/ExportSndLookups.sql
Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@ SELECT
ls.SetName as LOOKUP_KEY,
Value as VALUE,
CASE
WHEN l.Displayable = 0 THEN 'Y' ELSE 'N' END as IS_HIDDEN,
WHEN l.Displayable = false THEN 'Y' ELSE 'N' END as IS_HIDDEN,
l.SortOrder as ORDER_NUM,
l.ObjectId as OBJECT_ID,
'N' as DEFAULT_FLAG,
LEFT(s.Email,
CASE WHEN charindex('@', s.Email) = 0
THEN LEN(s.Email)
ELSE (charindex('@', s.Email) - 1) END) as USER_NAME,
CASE WHEN LOCATE('@', s.Email) = 0
THEN LENGTH(s.Email)
ELSE (LOCATE('@', s.Email) - 1) END) as USER_NAME,
l.Modified as ENTRY_DATE_TM
FROM
snd.Lookups l
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,13 @@
*/
SELECT
fs.ActivityId,
cast(fs.ActivityId as VARCHAR(5)) + ' - ' + fs.Description as description
cast(fs.ActivityId as VARCHAR(5)) || ' - ' || fs.Description as description

FROM snprc_ehr.FeeSchedule AS fs
WHERE fs.StartingYear = YEAR(NOW())
AND fs.BudgetYear = YEAR(NOW())
-- BudgetYear is VARCHAR in the schema; Postgres won't implicitly compare it to a numeric, so cast.
AND fs.BudgetYear = CAST(YEAR(NOW()) AS VARCHAR)
AND fs.VersionLabel = 'Capped Fee Schedule'
AND fs.ActivityId between 4000 and 4999

order by ActivityId
order by ActivityId
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT

FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
WHERE obr.PROCEDURE_ID.Dataset = 'Biochemistry'

Expand Down
2 changes: 1 addition & 1 deletion snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.sql
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT

FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
WHERE obr.PROCEDURE_ID.Dataset = 'Culture'

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT

FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
WHERE obr.PROCEDURE_ID.Dataset = 'Hematology'

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT obr.ANIMAL_ID as id,
FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
WHERE obr.PROCEDURE_ID.Dataset = 'Histology'

GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, obr.PROCEDURE_NAME, obr.SET_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
Expand Down
2 changes: 1 addition & 1 deletion snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.sql
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT obr.ANIMAL_ID as id,
FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
WHERE obr.PROCEDURE_ID.Dataset = 'Misc Tests'

GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, obr.PROCEDURE_NAME, obr.SET_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT obr.ANIMAL_ID as id,
FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
WHERE obr.PROCEDURE_ID.Dataset = 'Parasitology'

GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, obr.PROCEDURE_NAME, obr.SET_ID, COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME), obr.PROCEDURE_ID, nte.COMMENT, COALESCE (lp.TestName, obx.TEST_NAME)
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT
FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
WHERE obr.PROCEDURE_ID.Dataset = 'Surveillance'

UNION
Expand All @@ -21,12 +21,14 @@ SELECT
b.id,
b.date,
b.serviceTestId.serviceId.ServiceName AS PROCEDURE_NAME,
b.serviceTestId.serviceId AS PROCEDURE_ID,
-- HL7_OBR.PROCEDURE_ID is VARCHAR but labwork_services.ServiceId is INT; cast so the UNION types match on Postgres.
CAST(b.serviceTestId.serviceId AS VARCHAR) AS PROCEDURE_ID,
b.serviceTestId.testName AS TestName,
b.remark as COMMENT,
'' AS ABNORMAL_FLAGS,
b.qualresult as QUALITATIVE_RESULT,
b.RESULT as RESULT
-- labworkTaqman.RESULT is DOUBLE but HL7_OBX.RESULT (first UNION branch) is TEXT; cast to VARCHAR so the UNION types match on Postgres.
CAST(b.RESULT AS VARCHAR) as RESULT
FROM study.labworkTaqman b
WHERE b.serviceTestId.includeInPanel = true and b.qcstate.publicdata = true and b.serviceTestid.ServiceId.Dataset = 'Surveillance'

Expand All @@ -36,11 +38,11 @@ SELECT
b.id,
b.date,
b.serviceTestId.serviceId.ServiceName AS PROCEDURE_NAME,
b.serviceTestId.serviceId AS PROCEDURE_ID,
CAST(b.serviceTestId.serviceId AS VARCHAR) AS PROCEDURE_ID,
b.serviceTestId.testName AS TestName,
b.remark as COMMENT,
'' AS ABNORMAL_FLAGS,
b.qualresult as QUALITATIVE_RESULT,
NULL as RESULT
CAST(NULL AS VARCHAR) as RESULT
FROM study.assay_labworkResults b
WHERE b.serviceTestId.includeInPanel = true and b.qcstate.publicdata = true and b.serviceTestid.ServiceId.Dataset = 'Surveillance'
2 changes: 1 addition & 1 deletion snprc_ehr/resources/queries/snprc_ehr/HL7UnknownPivot.sql
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT

FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
WHERE obr.PROCEDURE_ID.Dataset = 'Unknown'

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ SELECT

FROM snprc_ehr.HL7_OBR obr
LEFT OUTER JOIN snprc_ehr.HL7_OBX obx ON obr.OBJECT_ID = obx.OBR_OBJECT_ID AND obr.SET_ID = obx.OBR_SET_ID
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = lp.ServiceId
LEFT OUTER JOIN snprc_ehr.labwork_Panels AS lp on obx.TEST_ID = lp.TestId AND obr.PROCEDURE_ID = CAST(lp.ServiceId AS VARCHAR)
LEFT OUTER JOIN snprc_ehr.HL7_GroupNTE AS nte ON obr.OBJECT_ID = nte.OBR_OBJECT_ID AND obr.SET_ID = nte.OBR_SET_ID
WHERE obr.PROCEDURE_ID.Dataset = 'Urinalysis'

Expand Down
44 changes: 22 additions & 22 deletions snprc_ehr/resources/queries/study/DailyObs.sql
Original file line number Diff line number Diff line change
Expand Up @@ -29,34 +29,34 @@ SELECT o.Id,
CASE
WHEN o.SaNone = 'Y' THEN 'None'
ELSE ''
END +
CASE
END ||
CASE
WHEN o.SaUnknown = 'Y' THEN 'Unknown'
ELSE ''
END +
CASE WHEN o.SaNormal = 'Y' THEN 'Normal'
END ||
CASE WHEN o.SaNormal = 'Y' THEN 'Normal'
ELSE ''
END +
END ||
CASE WHEN o.SaLoose = 'Y' THEN ' Loose'
ELSE ''
END +
ELSE ''
END ||
CASE WHEN o.SaSoft = 'Y' THEN ' Soft'
ELSE ''
END +
CASE WHEN o.SaWatery = 'Y' THEN ' Watery'
ELSE ''
END +
CASE WHEN o.SaBloody = 'Y' THEN ' Bloody'
ELSE ''
END +
CASE WHEN o.SaDry = 'Y' THEN ' Dry'
ELSE ''
END +
CASE WHEN o.SaOther = 'Y' THEN ' Other'
ELSE ''
END +
CASE WHEN o.SaPellet = 'Y' THEN ' Pellet'
ELSE ''
END ||
CASE WHEN o.SaWatery = 'Y' THEN ' Watery'
ELSE ''
END ||
CASE WHEN o.SaBloody = 'Y' THEN ' Bloody'
ELSE ''
END ||
CASE WHEN o.SaDry = 'Y' THEN ' Dry'
ELSE ''
END ||
CASE WHEN o.SaOther = 'Y' THEN ' Other'
ELSE ''
END ||
CASE WHEN o.SaPellet = 'Y' THEN ' Pellet'
ELSE ''
END AS Stool,
coalesce(o.HousingStatus.description,'NA') as Housing,
o.taskid,
Expand Down
2 changes: 1 addition & 1 deletion snprc_ehr/resources/queries/study/DemographicsHL7.sql
Original file line number Diff line number Diff line change
Expand Up @@ -12,4 +12,4 @@ SELECT
d.modifiedBy.DisplayName as modifiedBy,
d.modified
FROM demographics as d
where len(d.id) <= 6
where LENGTH(d.id) <= 6
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
select
substring(dae.oldrecordmap, charindex('objectid=',dae.oldrecordmap, 0) + len('objectid='), 36) as objectid,
substring(dae.oldrecordmap, LOCATE('objectid=', dae.oldrecordmap) + LENGTH('objectid='), 36) as objectid,
dae.date as modified

from auditLog.DatasetAuditEvent as dae
Expand Down
2 changes: 1 addition & 1 deletion snprc_ehr/resources/queries/study/R24WeightsDeletedSrc.sql
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
* limitations under the License.
*/
select
substring(dae.oldrecordmap, charindex('objectid=',dae.oldrecordmap, 0) + len('objectid='), 36) as objectid,
substring(dae.oldrecordmap, LOCATE('objectid=', dae.oldrecordmap) + LENGTH('objectid='), 36) as objectid,
dae.date as modified

from auditLog.DatasetAuditEvent as dae
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
<column columnName="TcruziResult">
<columnTitle>T cruzi result</columnTitle>
</column>
<column columnName="MinDate">
<column columnName="FirstDate">
<columnTitle>First Date</columnTitle>
</column>
</columns>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
<property name="columnTitle" value="MaxDate"/>
</properties>
</column>
<column name="TestCountZ">
<column name="TestCount">
<properties>
<property name="columnTitle" value="TestCount"/>
</properties>
Expand Down
2 changes: 1 addition & 1 deletion snprc_ehr/resources/queries/study/SndBcsSource.sql
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ SELECT
b.SubjectId as participantid,
b.date,
l.value as BCS,
CAST(SUBSTRING(l.value, 1, locate(' -', l.value ,1)) AS varchar(4)) AS BCSValue,
CAST(SUBSTRING(l.value, 1, CAST(locate(' -', l.value, 1) AS INTEGER)) AS varchar(4)) AS BCSValue,
p.ReferenceId as project,
null as taskid,
null as requestid,
Expand Down
4 changes: 2 additions & 2 deletions snprc_ehr/resources/queries/study/acq_dispHistory.sql
Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,9 @@

SELECT
a.id as id, a.date as acq_date,
a.acquisitionType.description + ' (' + cast(a.AcquisitionType as varchar(10)) + ')' as acquisitionType,
a.acquisitionType.description || ' (' || cast(a.AcquisitionType as varchar(10)) || ')' as acquisitionType,
d.date as disp_date,
d.dispositionType.description + ' (' + cast(d.dispositionType as varchar(10)) + ')' as dispositionType,
d.dispositionType.description || ' (' || cast(d.dispositionType as varchar(10)) || ')' as dispositionType,

FROM arrival a
LEFT OUTER JOIN departure d
Expand Down
4 changes: 2 additions & 2 deletions snprc_ehr/resources/queries/study/availableChargeIds.sql
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ SELECT DISTINCT
sp.projectType AS sndProjectType,
sp.ObjectId AS sndProjectObjectId,
c.caseid AS admitId,
c.problem + '/' + c.admitcomplaint AS projectText,
c.problem || '/' || c.admitcomplaint AS projectText,
GREATEST (c.date, sp.startDate) AS startDate,
LEAST (c.enddate, TIMESTAMPADD('SQL_TSI_DAY', 1, sp.endDate), NOW()) AS endDate,
sp.projectId AS sndProjectId,
Expand All @@ -62,4 +62,4 @@ FROM study.cases AS c
WHERE d.id = ANIMAL_ID
AND vcbs.species = d.species.arc_species_code
AND GREATEST (c.date, sp.startDate) <= EVENT_DATE
AND LEAST (c.endDate, TIMESTAMPADD('SQL_TSI_DAY', 1, sp.endDate), NOW()) >= EVENT_DATE
AND LEAST (c.endDate, TIMESTAMPADD('SQL_TSI_DAY', 1, sp.endDate), NOW()) >= EVENT_DATE
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,11 @@ FROM
WHERE aag.Id.Demographics.gender IS NOT NULL AND aag.Id.Demographics.calculated_status = 'Alive'
GROUP BY aag.accountGroup, dcc.colony, aag.Id.Demographics.species.arc_species_code

PIVOT colonytotal BY colony IN (SELECT name FROM snprc_ehr.BaboonColonyGroups)) col
-- SQL Server used a dynamic list here:
-- PIVOT colonytotal BY colony IN (SELECT name FROM snprc_ehr.BaboonColonyGroups)
-- During the Postgres migration, validation broke when BaboonColonyGroups was empty, so this query now uses the literal list below.
-- Maintenance consequence: the query is no longer driven by BaboonColonyGroups; future colony groups require manual query changes here and in the outer SELECT.
PIVOT colonytotal BY colony IN ('pc_SPF', 'pc_Conv')) col
ON gen.accountGroup = col.accountGroup AND gen.species_code = col.species_code

INNER JOIN
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,11 @@ FROM
WHERE aag.Id.Demographics.gender IS NOT NULL AND aag.Id.Demographics.calculated_status = 'Alive'
GROUP BY aag.accountGroup, dcc.colony, aag.Id.Demographics.species.arc_species_code

PIVOT colonytotal BY colony IN (SELECT name FROM snprc_ehr.BaboonColonyGroups)) col -- ('pc_SPF', 'pc_Conv')) col
-- SQL Server used a dynamic list here:
-- PIVOT colonytotal BY colony IN (SELECT name FROM snprc_ehr.BaboonColonyGroups)
-- During the Postgres migration, validation broke when BaboonColonyGroups was empty, so this query now uses the literal list below.
-- Maintenance consequence: the query is no longer driven by BaboonColonyGroups; future colony groups require manual query changes here and in the outer SELECT.
PIVOT colonytotal BY colony IN ('pc_SPF', 'pc_Conv')) col
ON gen.accountGroup = col.accountGroup AND gen.species_code = col.species_code
INNER JOIN
-- Total --
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