update pubmed fetch code #292
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hdashnow
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Nov 6, 2025
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@laurelhiatt would you mind checking my edits here? Did I mess anything up?
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Besides the one closing parenthesis which is honestly probably unnecessary, it looks good to me! it seems to have worked and be in compatible formatting with downstream stuff from what I know, as soon as it's renamed
laurelhiatt
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Nov 6, 2025
| #joined_terms <- paste0('(', paste(or_terms, collapse = '[Title/Abstract] OR '), ')[Title/Abstract]') | ||
| # Construct the query with organized or_terms | ||
| query <- paste0('("repeat expansion"[Title/Abstract] OR "tandem repeat"[Title/Abstract]) AND ("discovered"[Title/Abstract] OR "identified"[Title/Abstract] OR "causative"[Title/Abstract] OR "underlie"[Title/Abstract] OR "basis"[Title/Abstract]) AND "English"[Language] AND ("disease"[Title/Abstract] OR "disorder"[Title/Abstract] OR "syndrome"[Title/Abstract] OR "condition*"[Title/Abstract]) AND ("journal article"[Publication Type] OR "letter"[Publication Type] OR "Case Reports"[Publication Type]) NOT "review"[Publication Type])') | ||
| query <- paste0('("repeat expansion"[Title/Abstract] OR "tandem repeat"[Title/Abstract]) AND ("discovered"[Title/Abstract] OR "identified"[Title/Abstract] OR "causative"[Title/Abstract] OR "underlie"[Title/Abstract] OR "basis"[Title/Abstract]) AND "English"[Language] AND ("disease"[Title/Abstract] OR "disorder"[Title/Abstract] OR "syndrome"[Title/Abstract] OR "condition*"[Title/Abstract]) AND ("journal article"[Publication Type] OR "letter"[Publication Type] OR "Case Reports"[Publication Type]) NOT "review"[Publication Type]') |
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do we need a closing parenthesis here?
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There was one extra ")" without a matching "(" at the start. So one was
extra. It was causing an error that didn't crash the program but was
confusing me so I decided to remove it.
Thanks for checking my work!
…On Thu, Nov 6, 2025 at 2:08 PM laurelhiatt ***@***.***> wrote:
***@***.**** commented on this pull request.
------------------------------
On scripts/get-literature.R
<#292 (comment)>:
Besides the one closing parenthesis which is honestly probably
unnecessary, it looks good to me! it seems to have worked and be in
compatible formatting with downstream stuff from what I know, as soon as
it's renamed
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Description
Changed the way pubmed queries are run using the new batch approach
Fixes: #290
To do before merge
Minor Changes
Checklist
CITATION.cff, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X.