Skip to content

26.7 fb orchardfile #735

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
NIRC-IT wants to merge 2 commits into
base: release26.7-SNAPSHOT
Choose a base branch
from
+14 −12
Open

26.7 fb orchardfile #735

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
6754388
Updated orchard file generator module and sql to reduce duplicates, f…
NIRC-IT Jul 29, 2026
db9d3d1
Updated orchard file generator module and sql to reduce duplicates, f…
NIRC-IT Jul 29, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 6 additions & 7 deletions nirc_ehr/resources/queries/study/orchardData.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,16 +3,15 @@
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
SELECT DISTINCT
d.Id,
d.gender,
d.birth,
d.species.scientific_name as species,
pa.protocol.title as protocol,
InitCap(pa.protocol.InvestigatorId.LastName) || ', ' || InitCap(pa.protocol.InvestigatorId.FirstName) as PI,
InitCap(pa.protocol.AuthorId.LastName) || ', ' || InitCap(pa.protocol.AuthorId.FirstName) as Vet,
dlh.cage.cage as cage,
dlp.protocol.title as protocol,
InitCap(dlp.protocol.InvestigatorId.LastName) || ', ' || InitCap(dlp.protocol.InvestigatorId.FirstName) as PI,
InitCap(dlp.protocol.AuthorId.LastName) || ', ' || InitCap(dlp.protocol.AuthorId.FirstName) as Vet,
d.Id.lastHousing.cage.cage as cage,
d.calculated_status as alive
FROM demographics d
LEFT JOIN demographicsLastHousing dlh ON d.Id = dlh.Id
LEFT JOIN protocolAssignment pa ON d.Id = pa.Id AND pa.endDate is null
LEFT JOIN demographicsLastProtocol dlp ON d.Id = dlp.Id
13 changes: 8 additions & 5 deletions nirc_ehr/src/org/labkey/nirc_ehr/NIRCOrchardFileGenerator.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -130,19 +130,22 @@ public void run()
else if (Objects.equals(rs.getString("gender"), "3"))
sb.append("M");
else sb.append("U");
sb.append("||NHP|"); //could change if more species
sb.append(rs.getString("cage"));
sb.append("||NHP|"); //build out if other than non-human primate
sb.append(rs.getString("cage") == null ? "" : rs.getString("cage"));
sb.append("^New Iberia^LA^70506|||||||||||");
sb.append(rs.getString("species")).append("|");
sb.append(rs.getString("protocol")).append("|||||||");
if (Objects.equals(rs.getString("alive"),"Shipped"))
sb.append("OFFSITE").append("|||||||");
else
sb.append(rs.getString("protocol") == null ? "" : rs.getString("protocol")).append("|||||||");
if (Objects.equals(rs.getString("alive"), "Alive"))
sb.append("N");
else
sb.append("Y");
sb.append(System.lineSeparator());
sb.append("ZCP|Veterinarian|").append(rs.getString("Vet")).append("|");
sb.append("ZCP|Veterinarian|").append(rs.getString("Vet") == null ? "" : rs.getString("Vet")).append("|");
sb.append(System.lineSeparator());
sb.append("PD1||||").append(rs.getString("PI")).append("|");
sb.append("PD1||||").append(rs.getString("PI") == null ? "" : rs.getString("PI")).append("|");
sb.append(System.lineSeparator());
});

Expand Down