Issues

• Bug backlog: fix plan

  lanl/text-fetch#34 · Filter by author wshlavacek opened on Oct 3, 2026
  1

• New bioRxiv/medRxiv DOI prefix 10.64898 puts files in a subdirectory that tarballs skip

  area:outputarea:sourcesbugimpact:data-loss
  lanl/text-fetch#32 · Filter by author wshlavacek opened on Oct 2, 2026

• arXiv request errors are reported as zero results and never retried

  area:sourcesbugimpact:api-etiquette
  lanl/text-fetch#31 · Filter by author wshlavacek opened on Oct 2, 2026

• Extra API calls and quadratic writes in Europe PMC lookups, workspace saves and checkpoints

  area:sourcesarea:workspaceenhancementimpact:performance
  lanl/text-fetch#29 · Filter by author wshlavacek opened on Oct 2, 2026

• pdf batch --no-tei runs GROBID twice per PDF and the second pass drops --ocr

  area:pdfbugimpact:wrong-output
  lanl/text-fetch#28 · Filter by author wshlavacek opened on Oct 2, 2026

• arXiv PDF URL is wrong for solv-int IDs (split on the first v)

  area:sourcesbugimpact:data-loss
  lanl/text-fetch#27 · Filter by author wshlavacek opened on Oct 2, 2026

• Non-PMC articles are saved as PMCarxiv:... and old-style arXiv IDs fail to save

  area:outputarea:sourcesbugimpact:data-loss
  lanl/text-fetch#26 · Filter by author wshlavacek opened on Oct 2, 2026

• Expansion settings in the config are ignored, and confirming a dry run repeats the expansion

  area:cliarea:expansionbugimpact:wrong-output
  lanl/text-fetch#25 · Filter by author wshlavacek opened on Oct 2, 2026

• workspace clear keeps date markers and the checkpoint, so refills fetch nothing older

  area:workspacebugimpact:data-loss
  lanl/text-fetch#23 · Filter by author wshlavacek opened on Oct 2, 2026

• --update date marker advances after failed searches and fully skipped runs

  area:workspacebugimpact:data-loss
  lanl/text-fetch#22 · Filter by author wshlavacek opened on Oct 2, 2026

• --update date filters: arXiv query rejected, Europe PMC filter dropped, publication date used instead of index date

  area:sourcesarea:workspacebugimpact:data-loss
  lanl/text-fetch#21 · Filter by author wshlavacek opened on Oct 2, 2026

• Adding provenance to a tarball fails across filesystems and when compression doesn't match the name

  area:outputbugimpact:crash
  lanl/text-fetch#20 · Filter by author wshlavacek opened on Oct 2, 2026

• Checkpoint is cleared when papers failed, and all sources in a workspace share one file

  area:resumebugimpact:performance
  lanl/text-fetch#19 · Filter by author wshlavacek opened on Oct 2, 2026

• --tarball-only deletes the raw XML even when the tarball wasn't created

  area:cliarea:outputbugimpact:data-loss
  lanl/text-fetch#18 · Filter by author wshlavacek opened on Oct 2, 2026

• europepmc source of fetch never passes the email, so it downloads nothing

  area:cliarea:fetchbugimpact:data-loss
  lanl/text-fetch#17 · Filter by author wshlavacek opened on Oct 2, 2026

• tarball create --include-incomplete drops the incomplete files unless validation is off

  area:cliarea:outputbugimpact:data-loss
  lanl/text-fetch#15 · Filter by author wshlavacek opened on Oct 2, 2026

• workspace update skips workspaces built by fetch, and Europe PMC updates download nothing

  area:cliarea:workspacebugimpact:data-loss
  lanl/text-fetch#14 · Filter by author wshlavacek opened on Oct 2, 2026

• JATS validator counts reference titles as the article title, so empty articles validate as VALID

  area:outputbugimpact:data-loss
  lanl/text-fetch#13 · Filter by author wshlavacek opened on Oct 2, 2026

• An interrupted save truncates doi_index.json, and the next run silently starts with an empty index

  area:workspacebugimpact:data-loss
  lanl/text-fetch#12 · Filter by author wshlavacek opened on Oct 2, 2026
  1

• PMC source ignores max_results and silently stops at 10,000 PMIDs

  area:fetcharea:sourcesbugimpact:data-loss
  lanl/text-fetch#11 · Filter by author wshlavacek opened on Oct 2, 2026

• --resume and --update are ignored for expansion fetches, and the checkpoint is overwritten

  area:expansionarea:resumebugimpact:performance
  lanl/text-fetch#10 · Filter by author wshlavacek opened on Oct 2, 2026

• fetch --dry-run without an expansion flag runs a full download

  area:cliarea:fetchbugimpact:api-etiquette
  lanl/text-fetch#9 · Filter by author wshlavacek opened on Oct 2, 2026

• bioRxiv/medRxiv sources ignore the query and download every preprint in the date range

  area:fetcharea:sourcesbugimpact:data-loss
  lanl/text-fetch#8 · Filter by author wshlavacek opened on Oct 2, 2026

• fetch --max-results default overrides the config and makes arXiv return nothing

  area:cliarea:sourcesbugimpact:data-loss
  lanl/text-fetch#7 · Filter by author wshlavacek opened on Oct 2, 2026

• Unified expansion fetches no expanded papers: citation records have no pmcid field

  area:expansionbugimpact:data-loss
  lanl/text-fetch#6 · Filter by author wshlavacek opened on Oct 2, 2026