Citation store: refresh Zotero metadata and URIs for six items - #14
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DougManuel wants to merge 2 commits into
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Citation store: refresh Zotero metadata and URIs for six items#14DougManuel wants to merge 2 commits into
DougManuel wants to merge 2 commits into
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In both field-codes.json files (protocol and manuscript), Manuel_HR_2020 carried the Health Canada item's Zotero URI, and Holford_AJPM_2014, Tam_AJPM_2023, Meza_J_2021 (and Rao_SM_1992 in the protocol store) had placeholder ids with no URI. Re-fetched all six from the Zotero library (Better BibTeX citekeys match); Tam_AJPM_2023 points at the Brazil paper (TZBN3JTZ), not the same-issue editorial that the citekey lookup returned. Holford_SM_2006, StatCan_CCHS_UserGuide_2022 and mitra2015 remain without URIs: they are not in the Zotero library.
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Pull request overview
Updates the docstyle citation stores used for Word rendering by refreshing Zotero-fetched metadata/URIs for a set of references, and adjusts the protocol docstyle section map to reflect updated paragraph positions/sections.
Changes:
- Refreshed Zotero item metadata and populated missing
urisfor several citation keys in both the protocol-specific and root docstyle stores. - Corrected/updated bibliographic fields (e.g., titles, ISSN, issued/accessed dates) for the affected items based on refetch.
- Updated
docs/protocol/_docstyle/section-map.jsonsection positions and added new section entries.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| docs/protocol/_docstyle/section-map.json | Updates section boundaries/paragraph positions for protocol Word rendering. |
| docs/protocol/_docstyle/field-codes.json | Refreshes protocol citation store metadata and Zotero URIs. |
| _docstyle/field-codes.json | Refreshes root citation store metadata and Zotero URIs. |
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| "ISSN": "0840-6529", | ||
| "issue": "11", | ||
| "page": "16-31", | ||
| "PMCID": "PMC3951759", |
| "ISSN": "0840-6529", | ||
| "issue": "11", | ||
| "page": "16-31", | ||
| "PMCID": "PMC3951759", |
… user guide The three items were added to the Zotero library (_inbox collection) with their citekeys pinned via Better BibTeX, so every entry in both field-codes.json files now carries a Zotero URI.
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Summary
Repairs the Zotero citation store used by the docstyle Word renders (
docs/protocol/_docstyle/field-codes.jsonand_docstyle/field-codes.json):Manuel_HR_2020carried the Health Canada item's Zotero URI.Holford_AJPM_2014,Tam_AJPM_2023,Meza_J_2021(andRao_SM_1992in the protocol store) had placeholder ids and no URI.All six re-fetched from the Zotero library via docstyle's fetcher (Better BibTeX citekeys match the project keys).
Tam_AJPM_2023is pinned to the Brazil paper (TZBN3JTZ); the citekey-based URI lookup had returned the same-issue editorial.Not in Zotero, so still without URIs:
Holford_SM_2006,StatCan_CCHS_UserGuide_2022,mitra2015.Verification
Protocol renders with 28 Zotero fields, valid XML. Note: harvest (
docx_to_qmd) still regenerates author-year citekeys —resolve_cite_keys()never readscitation-key— so this does not by itself make round-trips key-stable.🤖 Generated with Claude Code