NEWS.md

In ropensci/fulltext: Full Text of 'Scholarly' Articles Across Many Data Sources

fulltext 2.0

MINOR IMPROVEMENTS

• ft_abstract(): change default from value from "plos" to "crossref" (#235)

BUG FIXES

• fix PLOS internals for ft_abstract() (#234)
• fix how Miscrosoft Academic query was structured before being sent off - affecting ft_search() (#236)

fulltext 1.7.0

NEW FEATURES

• The Cross Text and Data Mining program has ended. It ended officially at the end of 2020, but it took Wiley until early February to implement a TDM service. This impacts ft_get only, and impacts retrieval of only Wiley and Elsevier works (which is a lot since they're very large publishers). You now have to get a TDM key from both Wiley and Elsevier. See the "Authentication" section in ?fulltext for details. See also ?"ft_get-warnings": there's a new warning if we detect that you have a CROSSREF_TDM env var (#224)
• Added new ft_get plugin for Trans Tech Publications (#232)
• Import dependency crminer dropped. A few crminer functions brought over into this package and renamed. This is due to Crossref TDM program ending (#233)

MINOR IMPROVEMENTS

• new ft_search() docs section "Pagination" describing what parameter names to use for each data source to do pagination

BUG FIXES

• ft_search() fix: some data source specific options (e.g., plosopts) were being overridden by the global equivalent options (e.g., in ft_search(limit = 5, from = c("plos", "entrez"), plosopts = list(limit=10)) the limit sent to PLOS was 5 instead of 10). Fixed now so that data source specfiic options override the matching global option (#229)
• Internal API Fatcat changed its parameter name to limit what fields are returned. Fixed now (#231)

fulltext 1.6.0

NEW FEATURES

• HTTP requests previously made to the ftdoi.org API are now done locally with data/files cached locally; speeds up ft_get usage, especially if you're on a slow internet connection (#225) (#226)

MINOR IMPROVEMENTS

• all vignettes only available on docs site now: https://docs.ropensci.org/fulltext/ (#227)

BUG FIXES

• ft_links() opts parameters dropped (e.g., plosopts); no options can be passed down to each data source (#223)

fulltext 1.5.0

NEW FEATURES

• ft_abstract() gains new data source option: Semantic Scholar. Uses async http requests. Beware of rate limits. See 'Rate limits' in ?fulltext-package (#218)

MINOR IMPROVEMENTS

• using vcr for some tests (#212)
• improved documentation on proxy settings for Scopus data source added to the 'Authentication' section of the package level manual file, see ?fulltext-package (#220) thanks @behrica
• for ft_get() added new plugin helper for publisher Company of Biologists; and a fix in the Company of Biologists metadata returned from the ftdoi.org API (#216)
• cleaned out old code for brief data.frame printing, use tibble instead

BUG FIXES

• from parameter in ft_get() for specifying what data source to use should have been accepting more than 1 value, but was only accepting 1 value. Now from accepts 1 or more values (#222)

fulltext 1.4.0

NEW FEATURES

• ft_get() gains a new publisher plugin: Cambridge. its not available in the from parameter, but if you pass in a Cambridge DOI, a plugin now exists to attempt to get the pdf (xml not provided) (#195)

MINOR IMPROVEMENTS

• Wiley now provides xml (in addition to pdf) for at least some articles. So ft_get() for Wiley now supports type="xml" in addition to type="pdf" (#209)
• reduce duplicated code in ft_get plugins for checking type parameter (#210)
• changed Wiley plugin for ft_get(): using different URLs for attempting to fetch articles, those with base url api.wiley.com instead of onlinelibrary.wiley.com (#191)

BUG FIXES

• ft_get() wasn't allowing type="pdf" for PLOS data source; now allowed in addition to xml; also plos requests for articles now using http instead of http (#205) thanks @clbti for the report
• fix to internal fxn fat_cat_search_one() used inside of ft_get(): fixed data.frame subsetting error due to sometimes missing columns (#206)
• fix to ft_links(): was erroring when publisher not supported yet; now gives back no data (#207)
• ft_browse() was failing when what="macrodocs" selected; macrodocs.org is now dead; what parameter now defunct (#208)
• fix ft_table() - was failing on reading malformed files (e.g., an xml file with pdf content inside) (#211)

fulltext 1.3.0

NEW FEATURES

• ft_get() gains new data source: ScienceDirect (#196) thanks @knh11545
• performance improvement to ft_get(): when using internal fxn get_unknown(when publisher is not initially knowsn) we run another internal fxn get_publisher which is slow cause can only throw one DOI per request to Crossref API; We now use the FatCat (https://fatcat.wiki/) API to do more efficient publisher lookup (#192) (#201)

MINOR IMPROVEMENTS

• curl options can be passed into most functions now (#199)
• change to ft_get() when using Elsevier: we now by default detect if the downloaded file is abstact only and treat that as you dont have access - you can toggle this within elsevieropts - see ?ft_get for help (#200)
• fix link for fulltext manual, ropensci->ropenscilabs (#204)

BUG FIXES

• fix to ft_abstract(): when using plos, we were passing on identifiers to the wrong Solr parameter passed to PLOS Solr API (#202) thanks @mrweiler !
• fix to ft_links() with data from Entrez was failing when NULLs were encountered (#203)

fulltext 1.2.0

NEW FEATURES

• ft_get() gains a progress parameter, TRUE printing a progress bar and FALSE not. By default we do not print a progress bar to be consistent with the behavior of previous versions (#140) (#190)
• cache_options_set() gains new parameter full_path to set the entire path to the cache, use like cache_options_set(full_path = yourpath) (#185) thanks @bomeara for the feature request

DEFUNCT

• ft_chunks() and ft_tabularize() were deprecated in the previous version, and are now defunct. See the new package https://github.com/ropensci/pubchunks for the same (and improved) functionality (#146) (#181)
• ft_get_si() is defunct. It's been pulled out into a new package suppdata (#186) (#188)

BUG FIXES

• Fix to eupmc_search() internal function. At some piont Europe PMC changed the way they do paging, what parameters are used, etc. Fixed now. See examples for how to do paging; uses a cursor model instead of a rows/offset model (#184) thanks @jshleap for the report
• two hopefully fixes for Wiley URLs: a) try a 2nd url pattern if the first fails in general for Wiley links; and b) if highwire links found, replace with a url pattern that should work (#189) thanks @bomeara for the report

MINOR IMPROVEMENTS

• remaining httr code removed, now using crul for all HTTP requests (#187)
• filled out Scopus and Crossref TDM parts in the Authentication section of the package level manual file ?fulltext-package; and add more details on authentication in the ?ft_get manual file (#182) (#183)

fulltext 1.1.0

NEW FEATURES

• gains new function cache_file_info() to get information on possibly bad files in your cache - which you can use to remove files as you see fit (#142) (#174) thx @lucymerobinson for the push
• gains new function as.ft_data() to create the same output as ft_get() returns, but instead pulls all files from your cache (#142) (#172) thanks @lucymerobinson
• ft_get() gains new attribute of a data.frame in the errors slot with information on each article and what error we collected or NA_character_ if none; should help with sorting out problems across all requests (#176)
• scopus option in ft_search() gains support for facets; see ?scopus_search (#170) thanks @lucymerobinson

BUG FIXES

• fixed bug in ft_search() for microsoft academic plugin (#154)
• fixed bug in ft_search() for scopus plugin - we weren't looping over requests correctly (#161)
• fix bug in ft_links() - when result of ft_search() passed to ft_links with bad urls or with more than 1 then ft_links was failing; fix by filtering on intended-application field from Crossref via fix in dependency package crminer (#173)
• additional check added in ft_get() to check for an invalid file that gave a 200 status code (so passes the status code check) (#175)
• bring back support for start parameter in ft_search() for Scopus to offset what record a query starts at (#180)
• fix to ft_get() for entrez data source to loop internally when more than 50 ids requested to avoid 414 http error (URI too long) (#167) thanks @t088

MINOR IMPROVEMENTS

• change base url for EuropePMC to https
• use https for all doi.org requests (#155) thanks @katrinleinweber
• better explanation of the may opts parameters in ft_search() (#161)
• after many attempts, finally (I think) sorted out Microbiology Society for the ft_get() function (#163) thanks to @low-decarie
• mention suppdata package in the README (#164)
• clarify language in ft_collect() that we are saving files to disk locally only (#165)
• fix typos (#166) (#168) thanks @maelle @AugustT
• removed whisker package dependency (#156)
• scopus gains support for more parameters; see ?scopus_search (#152)
• updated docs with information on using NCBI Entrez API keys (#159)
• plugin for publisher Instituto de Investigaciones Filologicas to ft_get() added (#117) thanks @andreifoldes
• clarified in ft_search() docs that for some sources we loop internally to get whatever number of records the user wants, while others we can not (#162)

DEPRECATED

Continuing to focus the scope of this package the functions ft_chunks() and ft_tabularize() are now deprecated, and will be removed (defunct) in a future version of this package. See the new package pubchunks for the same and better functionality. (#181)

fulltext 1.0.1

BUG FIXES

• Fix bug in internal function get_ext() which parses either xml, pdf, or plain text from files on disk - it was failing on Linux maxchines due to a faulty regex (#151)

MINOR IMPROVEMENTS

• Updated formats vignette, three publishers that used to provide XML no longer do (#150)

fulltext 1.0

Check out the fulltext manual (https://books.ropensci.org/fulltext/) for detailed documentation.

fulltext has undergone a re-organization, which includes a bump in the major version to v1 to reinforce the large changes the package has undergone. Changes include:

• Function name standardization with the ft_ prefix. e,g, chunks is now ft_chunks
• ft_get has undergone major re-organization - biggest of which may be that all full text XML/plain text/PDF goes to disk to simplify the user interface.
• storr is now imported to manage mapping between real DOIs and file paths that include normalized DOIs - and aids in the function ft_table() for creating a data.frame of text results
• Note that with the ft_get() overhaul, the only option is to write to disk. Before we attempted to provide many different options for saving XML and PDF data, but it was too complicated. This has implications for using the output of ft_get() - the output is only the paths to the files - use ft_collect() to collect the text if you want to use ft_chunks() or other fulltext functions downstream.

NEW FEATURES

• chunks changed to ft_chunks (#139)
• collect changed to ft_collect (#139)
• tabularize changed to ft_tabularize (#139)
• get_text changed to ft_text (#139)
• ft_get() gains new parameter try_unknown that attempts to try to find full text for a given DOI/ID even if we don't have code plugins specifically for that publisher. This includes trying to get a full text link from Crossref and the ftdoi.org API (#137)
• Gains function ft_table that outputs a data.frame of all downloaded articles with DOIs, filenames, and the text of each article, similar to the readtext package (#134)
• Gains function ft_abstract for fetching abstracts, including support for getting abstracts from Scopus, Microsoft Academic, Crossref, and PLOS (#98) (#115)
• Microsoft Academic added as another data source both in ft_abstract and in ft_search via the microdemic package (#99) (#115)
• ft_get() gains an S3 method for ft_links - that is, you can pass the output of ft_links() to ft_get() (#103)
• ft_get() gains many new plugins, including for: Informa, Scientific Societies, Europe PMC, Elsevier, Wiley, xxx (#121) (#112) (#52) (#96) (#120) (#xxx)
• Gains new functions to list available plugins for each of ft_get()/ft_links()/ft_search(): ft_get_ls()/ft_links_ls()/ft_search_ls() (#122)
• ft_chunks() gains support for Elsevier XML (#116) (#118)
• Scopus added as a new datasource in both ft_search() and ft_abstract (#95)
• gains new object ftxt_cache for managing/listing details of cached files from ft_get()
• ft_search() gains Scopus and Microsoft Academic options
• ft_serialize() loses file, rcache, and redis options, retaining options for converting between list, JSON, and XML formats.
• The package level manual file at ?fulltext-package gains new sections on authentication and rate limiting
• gains new manual file for how to interpret warnings when using ft_get(); see ?ft_get-warnings

DEFUNCT

With the re-focusing of the package these functions seemed out of scope, so have been removed:

• pdfx, pdfx_html, and pdfx_targz are now defunct (#145)
• ft_extract_corpus is now defunct

The following functions have changed names. Usually I'd mark functions as deprecated in a version, then defunct in the next version, but since we're moving to v1 here, it made sense to rip the bandade off and make the old function names defunct.

• chunks is now defunct - function name changed to ft_chunks
• tabularize is now defunct - function name changed to ft_tabularize
• collect is now defunct - function name changed to ft_collect
• get_text is now defunct - function name changed to ft_text

Other defunct:

• cache_clear was never working anyway, and is now removed.

Along with the above changes and others the packages R.cache, rredis, digest, and tm have been removed from Imports

MINOR IMPROVEMENTS

• Replaced httr with crul mostly throughtout the package (#104)
• We are now using DOIs in file names written to disk from ft_get(). DOIs are normalized before using to create file paths (#138)
• Output of ft_get() should now be correctly named lists after the publisher and the DOI/ID (#126)
• Switched for eLife DOIs to attempt to get full text links from Crossref API instead of constructing by hand (#127)
• Now using hoardr package for managing cached files (#124)
• sending user agent string for this R pkg to the ftdoi.org API when calling it now (#141)
• Documented option to include your email address with Crossref API queries to get in their "fast lane" (#123)
• Documented how to get rate limit headers/information for Elsevier/Scopus requests (#109)
• For text extraction from PDFs - only using pdftools now - done away with other options (#82)
• biorxiv_search is now exported but the man file is hidden (using roxygen2 directive @internal), so you can still get to the manual file doing ?biorxiv_search

BUG FIXES

• New internal PLOS API method instead of a function from rplos because we need to write to disk instead of return parsed XML output (#148)
• ft_get() now appropriately using cached version of file if found (#130)
• The type parameter in ft_get() was ignored previously, now definitely used. (#128)
• Fix biorxiv_search (#97) (#113)

fulltext 0.1.8

MINOR IMPROVEMENTS

• require newest rcrossref and rplos versions that use dplyr::bind_rows() instead of dplyr::rbind_all() to avoid errors/warnings (#89) (#90)

fulltext 0.1.6

MINOR IMPROVEMENTS

• More documentation added for the from parameter for ft_get_si() to clarify its use, and fails better when used inappropriately (#68) (#77)
• ft_get_si() now gives file type information as attributes so that downstream uses can access that information instead of having to guess file types (#69)

BUG FIXES

• Fixes to ft_get_si() to work with changes in the publisher Wiley's URL changes (#71) (#73)

fulltext 0.1.4

NEW FEATURES

• New function ft_get_si() to grab supplementary files for any article (#61) (#62) - thanks @willpearse
• New function ft_links() to grab links for the full text version of an article from entire output of ft_search(), their individual components (i.e., data sources), or from character vector of DOIs (#36)

MINOR IMPROVEMENTS

• Lowercased all column headers from ft_search() (#63)
• DRYed out plugins for ft_get() to reduce code duplication (#48)

BUG FIXES

• Fixed bug in ft_search() where limit integer was too big (#57)
• Fix to ft_get() to create a directory if it doesn't exist already (#56)
• Fixed bug in ft_search() that caused problems in some scenarios (#55)
• Better error message when pdf passed to pdfx() function when pdf is not useable, that is, e.g., a scanned pdf (#53)

fulltext 0.1.0

• Released to CRAN.

ropensci/fulltext documentation built on Sept. 12, 2022, 7:57 a.m.