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Handle bad peptide_group_id values more gracefully - #212

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labkey-jeckels merged 1 commit into
release25.3-SNAPSHOTfrom
25.3_fb_pepDbCrawlerFailure
Mar 3, 2025
Merged

Handle bad peptide_group_id values more gracefully#212
labkey-jeckels merged 1 commit into
release25.3-SNAPSHOTfrom
25.3_fb_pepDbCrawlerFailure

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Rationale

The crawler found a place where we return a 500 error for bad IDs on the URL

ERROR ExceptionUtil            2025-03-02T19:49:29,387    http-nio-8111-exec-10 : Unhandled exception: For input string: "">'>'"</script><img src="x" onerror="alert('8(')">"
java.lang.NumberFormatException: For input string: "">'>'"</script><img src="x" onerror="alert('8(')">"
	at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67) ~[?:?]
	at java.base/java.lang.Integer.parseInt(Integer.java:654) ~[?:?]
	at java.base/java.lang.Integer.parseInt(Integer.java:786) ~[?:?]
	at org.scharp.atlas.pepdb.PepDBController$DisplayPeptideGroupInformationAction.getView(PepDBController.java:445) ~[pepdb-25.3-SNAPSHOT.jar:?]
	at org.scharp.atlas.pepdb.PepDBController$DisplayPeptideGroupInformationAction.getView(PepDBController.java:438) ~[pepdb-25.3-SNAPSHOT.jar:?]
	at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:75) ~[api-25.3-SNAPSHOT.jar:?]

Changes

  • Switch to a NotFoundException

@labkey-tchad labkey-tchad left a comment

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This looks like a minor change to this action's behavior (blocking cross-folder peptide references) but I presume that is intended.

@labkey-jeckels
labkey-jeckels merged commit f923709 into release25.3-SNAPSHOT Mar 3, 2025
@labkey-jeckels
labkey-jeckels deleted the 25.3_fb_pepDbCrawlerFailure branch March 3, 2025 22:03
cnathe added a commit that referenced this pull request Jun 16, 2026
…evious PR (#269)

#### Rationale
Related PR made an update for a crawler issue but added an extra
containerId check that doesn't apply in this case. Also convert one
pepdb manager method to use SQLFragment.

#### Related Pull Requests
* #212
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2 participants