Fix DOCTYPE is disallowed error in NCBI taxonomy parsing#623
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vagisha wants to merge 1 commit intorelease26.3-SNAPSHOTfrom
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Fix DOCTYPE is disallowed error in NCBI taxonomy parsing#623vagisha wants to merge 1 commit intorelease26.3-SNAPSHOTfrom
vagisha wants to merge 1 commit intorelease26.3-SNAPSHOTfrom
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…tils.getScientificNames threw PxException on NCBI eSummary lookup because the response begins with a <!DOCTYPE> declaration that XmlBeansUtil.DOCUMENT_BUILDER_FACTORY rejects. Switch to the new DOCUMENT_BUILDER_FACTORY_ALLOWING_DOCTYPE. - Added unit test
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| private static Map<Integer, String> parseScientificNames(InputStream in) | ||
| throws ParserConfigurationException, SAXException, IOException | ||
| { | ||
| Document doc = getDocumentBuilder().parse(in); |
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We may need to suppress this as a false positive if it's still showing up post-merge.
labkey-jeckels
approved these changes
Apr 8, 2026
| private static Map<Integer, String> parseScientificNames(InputStream in) | ||
| throws ParserConfigurationException, SAXException, IOException | ||
| { | ||
| Document doc = getDocumentBuilder().parse(in); |
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We may need to suppress this as a false positive if it's still showing up post-merge.
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labkey-jeckels
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Apr 9, 2026
#### Rationale `XmlBeansUtil.DOCUMENT_BUILDER_FACTORY` sets `disallow-doctype-decl=true` for XXE protection, which causes parsers to fail on any XML with a `<!DOCTYPE>` declaration. This is a problem for the Panorama Public code that parses NCBI's `esummary.fcgi` response that begins with `<!DOCTYPE eSummaryResult PUBLIC ... esummary-v1.dtd>` #### Related Pull Requests - LabKey/MacCossLabModules#605 - LabKey/MacCossLabModules#623 #### Changes - Added `DOCUMENT_BUILDER_FACTORY_ALLOWING_DOCTYPE` to `XmlBeansUtil`, mirroring the existing `SAX_PARSER_FACTORY_ALLOWING_DOCTYPE`. The DOCTYPE declaration is permitted, but every other XXE mitigation stays in place. - Extracted a private `documentBuilderFactory(boolean allowDocType)` helper, mirroring the existing `saxParserFactory(boolean)` helper.
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Rationale
NcbiUtils.getScientificNamesthrows an exception on NCBI eSummary lookup because the response begins with a <!DOCTYPE> declaration thatXmlBeansUtil.DOCUMENT_BUILDER_FACTORYrejects. The exception:SAXParseException: DOCTYPE is disallowed when the feature "http://apache.org/xml/features/disallow-doctype-decl" set to trueRelated Pull Requests
Changes
XmlBeansUtil.DOCUMENT_BUILDER_FACTORY_ALLOWING_DOCTYPE