Restore JBrowse link in References table for ChIP-seq datasets - #223
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bgajria wants to merge 1 commit into
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Restore JBrowse link in References table for ChIP-seq datasets#223bgajria wants to merge 1 commit into
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ChIPSeq.getDefaultLinkCategory now returns CHIP Seq, wiring it to the datasetLinks.xml category link template of the same name. This requires the companion EbrcModelCommon fix (getDefaultLinkCategory hook plus load-time macro substitution in DatasetPresenterSetLoader) to actually take effect and produce a working, fully-substituted URL. Root cause: this mechanism worked in 2020 (ref 42010) via a type/subtype selector on the link template plus dedicated tuning-table substitution logic. A 2025 migration converted the whole datasetLinks.xml selector scheme to category-based matching, but nothing ever set the corresponding categoryOverride on any of the 58 ChIPSeq-injected presenters across all 8 sites, so the category template has sat unused since. Fixes the missing View/Download this Data Set in the Genome Browser link, e.g. on ncraOR74A_Ncrassa_Klocko_2023_chipSeq_RSRC (DS_5ff37d322c).
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Companion PR (required together): VEuPathDB/EbrcModelCommon#134 |
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Summary
ChIPSeq.javaoverrides the newDatasetInjector.getDefaultLinkCategory()hook (see companion EbrcModelCommon PR) to returnCHIP Seq, wiring every ChIP-seq presenter that uses this injector (58 across all 8 sites — FungiDB, PiroplasmaDB, HostDB, TrichDB, PlasmoDB, ToxoDB, TriTrypDB, VectorBase) to the existing<link category="CHIP Seq">template inModel/config/datasetLinks.xml.Root cause
This mechanism worked in 2020 (ref 42010) via a type/subtype selector on the link template plus dedicated tuning-table substitution logic. A 2025 migration converted the whole
datasetLinks.xmlselector scheme to category-based matching, but nothing ever set the correspondingcategoryOverrideon any ChIP-seq presenter, so the category template has sat unused since — the "View/Download this Data Set in the Genome Browser" link silently disappeared from every ChIP-seq dataset's References table. Confirmed via full git history trace, not a guess.Example:
ncraOR74A_Ncrassa_Klocko_2023_chipSeq_RSRC(DS_5ff37d322c).Known, accepted side effect
One dataset (
tgonME49_Sullivan_m6A_WebService_RSRC, ToxoDB) already has its own hand-curated JBrowse-style link pointing at a different sibling track. After this fix it will show a second, auto-generated link pointing at its own track — not a literal duplicate, but a double entry. No other such case found across all 8 sites. Left as-is; flagging for a possible manual cleanup decision separately.Test plan
bld ApiCommonModel/Modelbuilds cleanDatasetPresentertuning table is rebuilt on a dev instance🤖 Generated with Claude Code