Fix GeneEdaSubsetPlugin to insert gene IDs as separate rows #17
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Fix GeneEdaSubsetPlugin to insert gene IDs as separate rows #17
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…returns a JSON array The EDA tabular endpoint returns gene IDs as a JSON array in a single cell (e.g. ["PBANKA_1349800","PF3D7_1335900"]), but the code was trying to insert the whole array string as a single VARCHAR(30) value. Changed convertToTmpTableRow to convertToTmpTableRows (returning List<Object[]>) so each gene ID in the array becomes its own row in the temporary table. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
ryanrdoherty
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Mar 11, 2026
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Approved, but curious how/why you are allowing the VEUPATHDB_GENE_ID variable to be either a single ID or array of IDs. Seems like it would be better to have separate variables for ID vs IDs so clients know how to handle the data up front without examining it.
Edit: I see- EDA itself groups the values because there is more than one value per entity ID. Not a fan but I guess it's what we have to work with now..
The EDA can return multiple IDs for the same gene (canonical + aliases), all of which resolve to the same gene via apidbtuning.geneid. This caused duplicate transcript rows in the WDK cache table. Fixed by adding DISTINCT to the gene-transcript join SQL. Also added _seenGeneIds deduplication in GeneEdaSubsetPlugin to reduce unnecessary temp table insertions. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Rod malaria phenotype (plasmodb) has multiple organisms so the eda returns genes from multiple orgs as JSON array
The EDA tabular endpoint returns gene IDs as a JSON array in a single cell (e.g. ["PBANKA_1349800","PF3D7_1335900"]), but the code was trying to insert the whole array string as a single VARCHAR(30) value. Changed convertToTmpTableRow to convertToTmpTableRows (returning List<Object[]>) so each gene ID in the array becomes its own row in the temporary table.
Tested on my dev site. Other eda searches working too