Develop#611
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…Crossref
New public function completeMetadata() fills missing bibliographic
metadata for records that have a DOI, querying OpenAlex first (broader
coverage of AB/CR/C1/TC) and then Crossref for residual gaps. Existing
non-empty values are never overwritten - the per-cell vacancy predicate
matches the one used by missingData(). Provenance is recorded both as a
per-row M$ENRICH column (compact tags like "AB:OA; TC:OA; CR:CR") and as
a long-format attr(M, "enrichment") data frame (SR, field, source,
timestamp).
Coverage matrix is honest: ID (Keywords Plus) and WC (WoS categories) are
always skipped (WoS-proprietary), TC requires OpenAlex, DE is off by
default. OpenAlex is auto-skipped when M$DB[1] == "OPENALEX". TC = 0 is
treated as vacant for the TC field only, so Scopus exports with all-zero
citation counts can be refreshed via OpenAlex.
Biblioshiny integration:
- Complete and Undo buttons in the Missing Data audit modal
- Sub-modal pre-selects Poor/Critical/Completely-missing fields
- Polite email and OpenAlex API key are read from Settings (no per-modal
credential typing)
- New before/after comparison modal opened after each enrichment, with
per-tag Before %, After %, delta, and OpenAlex vs Crossref fill counts
Implementation:
- New R/completeMetadata.R (~530 lines): httr2-based Crossref client with
polite-pool UA + req_retry(); openalexR-based OpenAlex client with
referenced_works -> WoS-CR string resolution
- New R/resolveOAReferences.R: shared OpenAlex CR-string helpers
(abbreviate_source_name, format_cr_author, build_single_cr) extracted
from biblioshiny so they can be reused without a Shiny dependency
- httr2, jsonlite, xml2 moved to Imports (added in classic)
- 86 new offline unit tests covering DOI normaliser, vacancy predicate,
JATS abstract stripping, Crossref/OpenAlex extractors, fill-only merge
contract, two-pass aggregation, and M$ENRICH provenance
- TC vacancy predicate now matches missingData()'s collection-level rule:
TC = 0 is treated as vacant only when sum(M$TC) == 0, never per-cell.
Scopus exports with all-zero TC still get refreshed via OpenAlex while
collections with mixed legitimate zeros are no longer touched.
- M$ENRICH column projects the per-row provenance attribute into a
compact tag string (AB:OA; TC:OA; CR:CR) for at-a-glance inspection.
Biblioshiny - Metadata completion result modal:
- Fixed before/after percentages showing identical values: the "after"
snapshot is now read from completeMetadata()'s return value instead of
the reactive missingdf, which was stale because its host modal was
already closed when the result modal opened.
- Delta column rendered as coloured badges (blue down-arrow for gains,
red up-arrow for regressions). A leading icon prevents renderBibliobox
from auto-detecting the column as numeric and stripping the HTML.
Biblioshiny - Synonym / Stopword pop-ups:
- popUpGeneric() default size was "40%", which is not a valid
show_alert() enum and was silently dropped to a very narrow modal.
Changed to size = "l" and wrapped the term column values in
white-space: nowrap so single words like "bibliometrics" or
"entrepreneurship" no longer break mid-word.
Biblioshiny - Unified Text Editing layout:
- Stop Words / Synonyms boxes in Most Frequent Words, WordCloud, Treemap,
Word Dynamics and Trend Topics now use the same panel layout as the
Co-occurrence Network menu (orange Stop Words panel + green Synonyms
panel with icons). All existing input ids are preserved so no
server-side change was required.
NEWS / NEWS.md updated for both repos.
240/240 testthat assertions pass; biblioshiny ui.R parses cleanly.
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completeMetadata():
TC = 0 is treated as vacant only when sum(M$TC) == 0, never per-cell.
Scopus exports with all-zero TC still get refreshed via OpenAlex while
collections with mixed legitimate zeros are no longer touched.
compact tag string (AB:OA; TC:OA; CR:CR) for at-a-glance inspection.
Biblioshiny - Metadata completion result modal:
snapshot is now read from completeMetadata()'s return value instead of
the reactive missingdf, which was stale because its host modal was
already closed when the result modal opened.
red up-arrow for regressions). A leading icon prevents renderBibliobox
from auto-detecting the column as numeric and stripping the HTML.
Biblioshiny - Synonym / Stopword pop-ups:
show_alert() enum and was silently dropped to a very narrow modal.
Changed to size = "l" and wrapped the term column values in
white-space: nowrap so single words like "bibliometrics" or
"entrepreneurship" no longer break mid-word.
Biblioshiny - Unified Text Editing layout:
Word Dynamics and Trend Topics now use the same panel layout as the
Co-occurrence Network menu (orange Stop Words panel + green Synonyms
panel with icons). All existing input ids are preserved so no
server-side change was required.
NEWS / NEWS.md updated for both repos.
240/240 testthat assertions pass; biblioshiny ui.R parses cleanly.