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[bot] Merge 25.7 to 25.11 #270

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Merged
github-actions merged 2 commits into from
Jun 19, 2026
+17 −5
Merged

[bot] Merge 25.7 to 25.11 #270

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a5c7c3d
DisplayPeptideGroupInformationAction revert containerId check from pr…
cnathe Jun 16, 2026
9ed38d8
Merge 25.7 to 25.11
labkey-teamcity Jun 19, 2026
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2 changes: 1 addition & 1 deletion pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -443,7 +443,7 @@ public ModelAndView getView(PeptideAndGroupForm form, BindException errors) thro
pg = PepDBManager.getPeptideGroupByID(peptideGroupId);
}
catch (NumberFormatException ignored) {}
if (pg == null || !getContainer().getId().equalsIgnoreCase(pg.getContainerId()))
if (pg == null)
{
throw new NotFoundException();
}
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10 changes: 6 additions & 4 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBManager.java
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Expand Up @@ -295,10 +295,12 @@ public static Peptides[] getParentPeptides(Peptides p) throws SQLException

public static Peptides[] getHyphanatedParents(Peptides p) throws SQLException
{
String sql = "select * from "+schema.getTableInfoPeptides()+" where peptides.protein_cat_id = ? " +
" and peptides.peptide_sequence LIKE '%"+p.getPeptide_sequence()+"%' " +
" and child = false";
Peptides[] peptides = new SqlSelector(schema.getSchema(), sql, new Object[]{p.getProtein_cat_id()}).getArray(Peptides.class);
// GitHub Kanban #1929: parameterize the LIKE clause for the stored peptide_sequence
SQLFragment sql = new SQLFragment("select * from "+schema.getTableInfoPeptides()+" where peptides.protein_cat_id = ? ", p.getProtein_cat_id());
sql.append(" and peptides.peptide_sequence LIKE ? ");
sql.add("%" + schema.getSchema().getSqlDialect().encodeLikeOpSearchString(p.getPeptide_sequence()) + "%");
sql.append(" and child = false");
Peptides[] peptides = new SqlSelector(schema.getSchema(), sql).getArray(Peptides.class);
return peptides;
}

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10 changes: 10 additions & 0 deletions pepdb/test/src/org/labkey/test/tests/pepdb/PepDBModuleTest.java
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Expand Up @@ -31,6 +31,7 @@
import org.labkey.test.TestTimeoutException;
import org.labkey.test.WebTestHelper;
import org.labkey.test.categories.CustomModules;
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.LogMethod;
import org.labkey.test.util.PostgresOnlyTest;

Expand Down Expand Up @@ -180,6 +181,15 @@ public void testSteps() throws Exception

clickAndWait(Locator.css("a.labkey-button > span"));

// Verify peptide group detail page
clickAndWait(Locator.linkWithText("List Peptide Groups"));
clickAndWait(Locator.linkWithText("gagptegprac"));
assertTextPresentInThisOrder(
"Group Information from peptide_group table for group : gagptegprac",
"There are (16) peptides in the 'gagptegprac' peptide group."
);
DataRegionTable pepTable = new DataRegionTable("group_peptides", getDriver());
assertEquals("Peptide table for group does not have expected number of rows", 16, pepTable.getDataRowCount());

/*
*
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