[bot] Merge 26.5 to develop

snd/history.md

@@ -0,0 +1,30 @@
+# snd module history
+
+**TL;DR:** the `snd` module's full commit history travels with it on every migration. **File-level** history and blame work everywhere — GitHub, IntelliJ, and any tool that follows renames (Sourcetree, GitKraken, Fork, GitLens, `git log --follow`, etc.). **Directory-level** history (`git log -- snd/` or GitHub's directory tree view) only shows commits since the most recent migration — for older directory-level browsing, open the corresponding repo from the table below.
+
+## Why directory-level history is limited
+
+Each migration changed the path of the module — first from a repo root into a subdirectory, then between subdirectories. Git's rename detection is per-file, not per-directory, so a directory-level log starts fresh at each move even though every individual file's history remains intact.
+
+## Where prior history lives
+
+| Repository                                                                                                       | History active          | Notes                                                                    |
+|------------------------------------------------------------------------------------------------------------------|-------------------------|--------------------------------------------------------------------------|
+| [LabKey/snd](https://github.com/LabKey/snd)                                                                      | until 2025-02-24        | Original standalone repo. Now archived.                                  |
+| [LabKey/ehrModules/snd](https://github.com/LabKey/ehrModules/tree/fc811d93c1a99ee46e219508da17041a9bcfb2d4/snd)  | 2025-02-24 → 2026-05-05 | Rehomed via `LabKey/ehrModules` commit `76b86bc5` ("Rehome snd module"). |
+| [LabKey/snprcEHRModules/snd](https://github.com/LabKey/snprcEHRModules/tree/develop/snd)                         | 2026-05-05 → present    | Current home. Rehomed from `LabKey/ehrModules`.                          |
+
+## Browsing history
+
+### File-level (works everywhere)
+
+Any Git tool that follows renames will show full history back to the module's origin:
+
+- **GitHub**: open any individual file, then click *History* or *Blame*. GitHub follows renames automatically across migrations.
+- **IntelliJ**: right-click a file → *Git → Show History* (or *Annotate* for blame).
+- **Other tools** (Sourcetree, GitKraken, Fork, GitLens, etc.): use the file's history or blame view — these tools follow renames by default.
+- **CLI**: `git log --follow -- <path/to/file>`.
+
+### Directory-level (use the table above)
+
+There is no built-in equivalent to `--follow` for directories. To see directory-level history from before a migration, open the corresponding repo from the table above for the date range you care about and browse the module directory there.

snd/resources/queries/snd/DeletedLookupSets.sql

@@ -1,5 +1,5 @@
 select
-    substring(qae.oldrecordmap, charindex('objectid=',qae.oldrecordmap, 0) + len('objectid='), 36) as objectid,
+    substring(qae.oldrecordmap, locate('objectid=', qae.oldrecordmap) + length('objectid='), 36) as objectid,
     qae.date as modified
 
 from auditLog.QueryUpdateAuditEvent as qae

snd/resources/queries/snd/DeletedLookups.sql

@@ -1,5 +1,5 @@
 select
-    substring(qae.oldrecordmap, charindex('objectid=',qae.oldrecordmap, 0) + len('objectid='), 36) as objectid,
+    substring(qae.oldrecordmap, locate('objectid=', qae.oldrecordmap) + length('objectid='), 36) as objectid,
     qae.date as modified
 
 from auditLog.QueryUpdateAuditEvent as qae

snd/resources/schemas/dbscripts/postgresql/snd-0.000-25.000.sql

@@ -316,9 +316,16 @@ CREATE INDEX IDX_SND_EVENTSCACHE_CONTAINER ON snd.EventsCache(Container);
 -- Creation date: 9/22/2017
 -- Description:  Table valued function to return hierarchical view of a superPkg
 -- ==========================================================================================
--- NOTE: ROW_NUMBER() OVER (...) cannot be used in the recursive term of WITH RECURSIVE in
--- PostgreSQL. The TreePath is computed using SortOrder directly, which preserves ordering
--- semantics while remaining compatible with PostgreSQL's recursive CTE restrictions.
+-- NOTE: PostgreSQL forbids window functions in the recursive term of WITH RECURSIVE. We
+-- pre-compute per-parent ordinals (ROW_NUMBER PARTITION BY ParentSuperPkgId) in a
+-- non-recursive CTE that is materialized once, then join to it in both the anchor and
+-- recursive members. This produces a stable per-parent TreePath segment and avoids the
+-- collisions and 3-char truncation that result from formatting raw SortOrder values.
+-- This differs from the SQL Server twin (sqlserver/snd-0.000-25.000.sql), which uses an
+-- unpartitioned ROW_NUMBER OVER (ORDER BY SortOrder); the partitioned form is preferred
+-- and the MSSQL function should eventually be aligned. NULLS FIRST is used so a NULL
+-- SortOrder sorts first within a parent, matching MSSQL's default NULL-ordering and the
+-- prior PG behavior (COALESCE(SortOrder, 0)).
 -- ==========================================================================================
 CREATE FUNCTION snd.fGetSuperPkg(_pkgId INT)
 RETURNS TABLE (
@@ -337,14 +344,26 @@ RETURNS TABLE (
     Level           INTEGER
 )
 LANGUAGE sql AS $$
-    WITH RECURSIVE CTE1 (TopLevelPkgId, SuperPkgId, ParentSuperPkgId, PkgId, TreePath, SuperPkgPath, SortOrder, Required, Description, Narrative, Active, Repeatable, Level) AS (
+    WITH RECURSIVE
+    ordered_super_pkgs AS (
+        SELECT sp.SuperPkgId,
+               sp.ParentSuperPkgId,
+               sp.PkgId,
+               sp.SuperPkgPath,
+               sp.SortOrder,
+               sp.Required,
+               ROW_NUMBER() OVER (PARTITION BY sp.ParentSuperPkgId
+                                  ORDER BY sp.SortOrder NULLS FIRST, sp.SuperPkgId) AS Ordinal
+        FROM   snd.SuperPkgs sp
+    ),
+    CTE1 (TopLevelPkgId, SuperPkgId, ParentSuperPkgId, PkgId, TreePath, SuperPkgPath, SortOrder, Required, Description, Narrative, Active, Repeatable, Level) AS (
 
         -- anchor member
         SELECT _pkgId::INTEGER                                                         AS TopLevelPkgId,
                sp.SuperPkgId,
                sp.ParentSuperPkgId,
                sp.PkgId,
-               RIGHT(REPEAT(' ', 3) || COALESCE(sp.SortOrder, 0)::VARCHAR, 3)         AS TreePath,
+               LPAD(sp.Ordinal::TEXT, 6, '0')                                          AS TreePath,
                sp.SuperPkgPath,
                sp.SortOrder,
                sp.Required,
@@ -353,7 +372,7 @@ LANGUAGE sql AS $$
                p.Active,
                p.Repeatable,
                1                                                                       AS Level
-        FROM   snd.SuperPkgs sp
+        FROM   ordered_super_pkgs sp
                    INNER JOIN snd.Pkgs p ON sp.PkgId = p.PkgId
         WHERE  sp.PkgId = _pkgId
           AND  sp.ParentSuperPkgId IS NULL
@@ -365,7 +384,7 @@ LANGUAGE sql AS $$
                sp.SuperPkgId,
                c.SuperPkgId                                                            AS ParentSuperPkgId,
                sp.PkgId,
-               c.TreePath || '/' || RIGHT(REPEAT(' ', 3) || COALESCE(sp.SortOrder, 0)::VARCHAR, 3) AS TreePath,
+               c.TreePath || '/' || LPAD(sp.Ordinal::TEXT, 6, '0')                     AS TreePath,
                sp.SuperPkgPath,
                sp.SortOrder,
                sp.Required,
@@ -374,7 +393,7 @@ LANGUAGE sql AS $$
                p.Active,
                p.Repeatable,
                c.Level + 1                                                             AS Level
-        FROM   snd.SuperPkgs AS sp
+        FROM   ordered_super_pkgs AS sp
                    INNER JOIN CTE1 AS c ON
                            sp.ParentSuperPkgId = c.SuperPkgId
                        OR  sp.ParentSuperPkgId IN (
@@ -407,6 +426,12 @@ $$;
 -- Description:  Returns the list of ProjectItems for a Project/Revision along with
 --               sub packages for each ProjectItem
 -- ==========================================================================================
+-- See note on fGetSuperPkg above re: pre-computed ordinals. The anchor uses an ordinal
+-- ordered by (ProjectItemId, SuperPkgId), which matches the MSSQL anchor's ROW_NUMBER.
+-- The recursive sub-tree uses per-parent ordinals over (SortOrder NULLS FIRST,
+-- SuperPkgId) -- partitioned by ParentSuperPkgId, unlike MSSQL's unpartitioned form;
+-- NULLS FIRST matches MSSQL's default NULL-ordering.
+-- ==========================================================================================
 CREATE FUNCTION snd.fGetProjectItems(_projectId INT, _revisionNum INT)
 RETURNS TABLE (
     ProjectId       INTEGER,
@@ -421,27 +446,46 @@ RETURNS TABLE (
     Description     VARCHAR
 )
 LANGUAGE sql AS $$
-    WITH RECURSIVE CTE1 (ProjectId, RevisionNum, ProjectItemId, ParentObjectId, ParentSuperPkgId, SuperPkgId, PkgId, ProjectActive, Active, TreePath, Level, Description) AS (
+    WITH RECURSIVE
+    ordered_project_items AS (
+        SELECT pi.ProjectItemId,
+               pi.ParentObjectId,
+               pi.SuperPkgId,
+               pi.Active                                                              AS ItemActive,
+               p.Active                                                               AS ProjectActive,
+               ROW_NUMBER() OVER (ORDER BY pi.ProjectItemId, pi.SuperPkgId)           AS Ordinal
+        FROM   snd.ProjectItems pi
+                   INNER JOIN snd.Projects p ON pi.ParentObjectId = p.ObjectId
+        WHERE  p.ProjectId = _projectId
+          AND  p.RevisionNum = _revisionNum
+    ),
+    ordered_super_pkgs AS (
+        SELECT sp.SuperPkgId,
+               sp.ParentSuperPkgId,
+               sp.PkgId,
+               sp.SortOrder,
+               ROW_NUMBER() OVER (PARTITION BY sp.ParentSuperPkgId
+                                  ORDER BY sp.SortOrder NULLS FIRST, sp.SuperPkgId) AS Ordinal
+        FROM   snd.SuperPkgs sp
+    ),
+    CTE1 (ProjectId, RevisionNum, ProjectItemId, ParentObjectId, ParentSuperPkgId, SuperPkgId, PkgId, ProjectActive, Active, TreePath, Level, Description) AS (
 
         -- anchor member
         SELECT _projectId::INTEGER                                                          AS ProjectId,
                _revisionNum::INTEGER                                                        AS RevisionNum,
-               pi.ProjectItemId,
-               pi.ParentObjectId,
+               opi.ProjectItemId,
+               opi.ParentObjectId,
                sp.ParentSuperPkgId,
                sp.SuperPkgId,
                sp.PkgId,
-               p.Active                                                                     AS ProjectActive,
-               pi.Active,
-               RIGHT(REPEAT(' ', 3) || COALESCE(sp.SuperPkgId, 0)::VARCHAR, 3)             AS TreePath,
+               opi.ProjectActive,
+               opi.ItemActive                                                               AS Active,
+               LPAD(opi.Ordinal::TEXT, 6, '0')                                              AS TreePath,
                1                                                                            AS Level,
                pkg.Description
-        FROM   snd.ProjectItems AS pi
-                   INNER JOIN snd.Projects AS p  ON pi.ParentObjectId = p.ObjectId
-                   INNER JOIN snd.SuperPkgs AS sp ON pi.SuperPkgId = sp.SuperPkgId
+        FROM   ordered_project_items AS opi
+                   INNER JOIN snd.SuperPkgs AS sp ON opi.SuperPkgId = sp.SuperPkgId
                    INNER JOIN snd.Pkgs pkg        ON sp.PkgId = pkg.PkgId
-        WHERE  p.ProjectId = _projectId
-          AND  p.RevisionNum = _revisionNum
 
         UNION ALL
 
@@ -455,10 +499,10 @@ LANGUAGE sql AS $$
                sp.PkgId,
                c.ProjectActive,
                c.Active,
-               c.TreePath || '/' || RIGHT(REPEAT(' ', 3) || COALESCE(sp.SortOrder, 0)::VARCHAR, 3) AS TreePath,
-               c.Level + 1                                                                 AS Level,
+               c.TreePath || '/' || LPAD(sp.Ordinal::TEXT, 6, '0')                          AS TreePath,
+               c.Level + 1                                                                  AS Level,
                pkg.Description
-        FROM   snd.SuperPkgs AS sp
+        FROM   ordered_super_pkgs AS sp
                    INNER JOIN snd.Pkgs AS pkg ON sp.PkgId = pkg.PkgId
                    INNER JOIN CTE1 AS c ON
                            sp.ParentSuperPkgId = c.SuperPkgId

snd/src/org/labkey/snd/SNDManager.java

@@ -1549,20 +1549,14 @@ public void createProject(Container c, User u, Project project, BatchValidationE
         }
     }
 
-    /**
-     * Used in reviseProject to update a project
-     */
-
     //TODO: Use QUS to update columns - pass Project.objectId
-    // Note: EndDate is the only field that's updated with this
-    private void updateProjectField(Container c, User u, int id, int rev, String field, Object value)
+    private void updateProjectEndDate(Container c, User u, int id, int rev, Object endDate)
     {
         UserSchema schema = getSndUserSchema(c, u);
 
         SQLFragment sql = new SQLFragment("UPDATE " + SNDSchema.getInstance().getTableInfoProjects());
-        sql.append(" SET " + field + " = ?");
-        sql.append(" WHERE ProjectId = ? AND RevisionNum = ?");
-        sql.add(value).add(id).add(rev);
+        sql.append(" SET EndDate = ? WHERE ProjectId = ? AND RevisionNum = ?");
+        sql.add(endDate).add(id).add(rev);
 
         new SqlExecutor(schema.getDbSchema().getScope()).execute(sql);
     }
@@ -1578,8 +1572,8 @@ public void reviseProject(Container c, User u, Project project, BatchValidationE
             UserSchema schema = getSndUserSchema(c, u);
             List<Map<String, Object>> updatedProjectItems = new ArrayList<>();
 
-            updateProjectField(c, u, project.getProjectId(), project.getRevisionNum(), "EndDate",
-                    project.getEndDateRevised() == null ? null : project.getEndDateRevised());
+            updateProjectEndDate(c, u, project.getProjectId(), project.getRevisionNum(),
+                    project.getEndDateRevised());
 
             if (project.isCopyRevisedPkgs())
             {

snprc_ehr/resources/source_queries/create_v_charge_account.sql

@@ -24,6 +24,7 @@ ALTER VIEW [labkey_etl].[v_charge_account] AS
   -- 11/11/2016  added modified, modifiedby, created, and createdby columns tjh
   -- 10/22/2019  removed distinct clause from valid_charge_by_species join tjh
   -- 02/15/2020  Added fallback for missing created & createdBy columns tjh
+  -- 04/23/2026  Removed join on species table and added OUTER APPLY ja
   -- ==========================================================================================
 
 
@@ -47,7 +48,12 @@ ALTER VIEW [labkey_etl].[v_charge_account] AS
     ca.timestamp                     AS timestamp
   FROM dbo.charge_account AS ca
     LEFT OUTER JOIN dbo.TAC_COLUMNS AS tc ON tc.object_id = ca.object_id
-	LEFT OUTER JOIN dbo.valid_charge_by_species AS vcs ON ca.charge_id = vcs.charge_id
+    OUTER APPLY (
+      SELECT TOP 1 vcs2.charge_id, vcs2.arc_species_code
+      FROM dbo.valid_charge_by_species vcs2
+      WHERE vcs2.charge_id = ca.charge_id
+      ORDER BY vcs2.arc_species_code
+    ) vcs
     LEFT OUTER JOIN dbo.prd_cost_account AS pca on pca.account_id = ca.account_id