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Created by Ryan Dix-Peek@ryandixpeekMaintainer0 of 2 tasks completed0/2 tasks

[NCRC] Update Kotahi database with all research object currently capture via shiny app DB (spreadsheet)

Description; the following spreadsheet contains articles that should not be imported into Kotahi when pulling content from bioRxiv/Pubmed API.

Articles should be in the system, but should not be displayed on UI.

Acceptance criteria;

  • Add all existing article data to Kotahi database in order to mitigate the inclusion of the previous articles entering the system for triage.
  • Delete all current articles from the Manuscripts view.

Notes from the client; this R code can read and combine to a single data frame of all considered papers. Note we froze using R version 3.6.3 since the googlesheets4 package changed a lot in R v4.0.

## latest paper
existing_papers = googlesheets4::sheets_speedread(
ss="1zQPXGIy2xsfQmri-_PLA-5YP3nPefJkpYaYY8rCGde8",
sheet="papers",
col_types = cols(
pubmed_id = col_integer(),
date = col_character(),
secondary_reviewer_initial = col_character(),
subtopic = col_character())
) %>%
dplyr::mutate(title_journal = paste0(title, " (", journal, ")"))

existing_papers$doi[is.na(existing_papers$doi)] = existing_papers$title_journal[is.na(existing_papers$doi)]

## hard-code previously considered papers
existing_papers_older = googlesheets4::sheets_speedread(
   ss="https://docs.google.com/spreadsheets/d/1Y0juNsPpMa_fddk82dPGYfjJbL_BFHoOHmI3HBLJYk8/edit#gid=0",
     sheet="papers",
   col_types = readr::cols(
     pubmed_id = col_integer(),
     date = col_character(),
     secondary_reviewer_initial = col_character(),
     subtopic = col_character())) %>%
 dplyr::mutate(title_journal = paste0(title, " (", journal, ")"))

existing_papers_old = googlesheets4::sheets_speedread(
 ss="https://docs.google.com/spreadsheets/d/1G8stDQUmDbI8qY0NK4vBru2A55j7wcPs956sBcfv3hY/edit#gid=0",
 sheet="papers", col_types = readr::cols(
   pubmed_id = col_integer(),
   date = col_character(),
   secondary_reviewer_initial = col_character(),
   subtopic = col_character())) %>%
 dplyr::mutate(title_journal = paste0(title, " (", journal, ")"))

## and join
existing_papers = rbind(existing_papers,
                         existing_papers_old,
                         existing_papers_older)
Edited by MihailGorceagEN