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Release 1.0.0#40

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jeanetteclark merged 150 commits intomainDataONEorg/scythe:mainfrom developDataONEorg/scythe:developCopy head branch name to clipboardSep 10, 2024

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Commits

Commits on May 5, 2021

• encode colons in plos search

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Commits on May 28, 2021

• Merge branch 'main' into develop

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• Fixed Jeanette's email address.

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Commits on Mar 15, 2022

• Add .jpg for logo. From Wikimedia Commons, 17th century pottery, man with a scythe.

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• Create R script to build logo

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Commits on Mar 16, 2022

• Added required packages to create hexsticker

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• Added basic hexSticker arguments. Succsessful creation of hex sticker

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• Tweaked hexsticker. Dark grey color theme, package title position, resolution, image position.

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• Changed package title font. Used google font

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• Tried different fonts - handwriting style

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• narrowed down font choices. Google fonts - 'Architects Daughter' and 'Nothing You Could Do'

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• 1st draft of logo complete - Architects Daugther font

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Commits on Mar 17, 2022

• Add 2 hex sticker logos .png files

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Commits on Mar 28, 2022

• Add package test to logo code

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• deleted runner up logo .png

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• created man/figures folder moved logo source .png to folder

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• changed logo location to man/figures

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• added code skeleton to build favicon

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• simplified logo file name

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• changed logo folder name to lower case

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• Added logo R code to .Rbuildignore

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• Add logo folder to .Rbuildignore not code script only

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• changed logo save location to man/figures

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• update code to read logo source image in from man/figures

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Commits on Mar 29, 2022

• updated logo code with image without a background. Darkened boarder gray.

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• logo file V2

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• cleaned up code for git conflict

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• removed unused google font

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• Created logo with backgroundless image. Cleaner cuts than previous version

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Commits on Mar 30, 2022

• Added image source url and information in script

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• Merge pull request #30 from theamarks/develop

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Commits on Apr 1, 2022

• create new citation_search_xDD function script. Copied from citation_search_scopus.R

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• remove get_key function. xDD does not require API key

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• temporarily removed API throttle message until known if xDD has a trottle.

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• Added xDD API 'snippets' URL to search 'term' parameter in documents full-text

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• create working example code outside of function

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• rename results dataframe

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• extract the number of citations (hits) for a single search result

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• pull number of citaitons (hits), article DOI, and title form results list

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• updated returned dataframe code. Not working in for loop. Check how other API results are returned compared to xDD

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Commits on Apr 2, 2022

• Next try using example of xDD results extraction found on github

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Commits on Apr 4, 2022

• successfully extracted doc info from xDD API results

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• not working for multiple identifers input. Need to deal with null results in building result dataframe

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• restructured adding results to data.frame. Function not working

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  8e10390

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• not working. error: 'list' object cannot be coerced to type 'double'. I think this is coming from the final rbind()

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Commits on Apr 5, 2022

• fixed else if () statement to run clean with example dois. error now in if(nrow(results[[i]]$success$data) == 0){}

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• Updated if() for 0 returned results. Full function running clean. Need to use length() on list not nrow(). Added annotations.

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• added to else printout statement if function fails

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• Add xDD to sources in citation_search() function

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• updated xDD funtion documentation

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• Added xDD to citation_search function

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• modified xDD API URL input to search beyond xDD full-text holdings default.

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Commits on Apr 7, 2022

• updated XDD function Roxygen2 citation

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• update package description and namespace with usethis::use_testthat() to add citation_search_xDD

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• Added xDD as source to test-sycthe.R

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Commits on Apr 11, 2022

• Added xDD documentation with devtools::document()

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Commits on Apr 12, 2022

• Add data citation only found by xDD to test-citations.csv. (dataset doi returns 2 papers, one is found by other sources, one only in xDD)

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Commits on Apr 13, 2022

• deleted sys.sleep() in xDD function. Not needed

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• remove unnecessary else() statement in citation_search_xDD()

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• Added dataset doi to test identifiers that produced 2 results in xDD

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• renamed xDD to xdd (lowercase) across functions and filenames. Congruent with package lowercase asthetic

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Commits on Apr 14, 2022

• Merge pull request #34 from theamarks/develop

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  jeanetteclark

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Commits on Apr 25, 2022

• add result column for journal title that the citation was found in. xdd function

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• added citation source column ("xdd") and corrected a couple upper case xDDs to lowercase

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• convert uppercase xDD to lowercase xdd withing function

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Commits on Apr 26, 2022

• add source column to citation_search_plos() output

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• added source column in output of citation_search_scopus()

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• add source output column to ciation_search_springer() function

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• removed NA results from citation_search_xdd()

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Commits on Apr 27, 2022

• Updated test-citation.csv to lowercase xdd. Was filtering out in tests.

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• Working on new test-sycthe.R test. Replacing pmap() test on all citations in test-citations.csv. Not working yet

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• changed output column name to source in plos search function

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• renamed source output in plos search function

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• added underscore to output source

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Commits on Apr 29, 2022

• Added test citation to test-citiatons.csv only found on springer, that cites a doi

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• clean up test file

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• reordered plos search output to align with other search functions

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• reordered xdd search output columns to align with other search functions

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Commits on Apr 30, 2022

• delete empty data.frame. Do not need to construct new data.frame for test.

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• reorganize scopus search function. Works with single citation search not with multiple

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• convert dplyr filter function to base r in testing script

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Commits on May 2, 2022

• corrected scopus search function when adding source column

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• fixed how source column is added to springer search function

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• Added missing ) to springer search function

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• removed uncessary result dataframe column rename for source in plos search function

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• Fixed error (column names not match) in plos search function rbind.

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• corrected typo in scopus search function

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Commits on May 6, 2022

• changed source column name in scopus search function to align with other functions

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• reordered xdd search function internal dataframe columns to match with other functions

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• change springer search function's column order to align with other sources searches

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• reordering xdd results to align with other functions

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• Created test for multiple dois in citation_search()

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• Wrote out expectations for each individual source search function. Only test single known doi through each source.

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• removed purr package and changed filter method to dplyr

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Commits on May 9, 2022

• Remove single citation tests from test-scythe.R Creating more test scripts for various functionalities

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• Create internal helper function for testing single DOIs across individual library search functions

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• break test helper functions into two separate functions

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Commits on May 10, 2022

• Fixed citation_test_doi() function to pull dataframe value not select part data.frame

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• Created springer specific test script to test if single known doi citation is found

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• commented out citation_test_doi() and removed unused line

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• Add api key to citation_test_doi() and change springer test to expect_equal

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• added clarification to citation_test_doi() api message if API key not needed

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• Created single doi test script for plos

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• Add test-xdd scipt and move test-plos to test folder

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• Added test-scopus and changed all library expect terms to expect_equal to account for multiple results

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• Added doi filter into scythe test script. Pass test()

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• updated xdd documentation .rd with lowercase name

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• Generated documentation for helper test functions. NOT exported (user-facing)

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• Created 3rd internal helper function to pull in API keys or to stop test during R-CMD-check. Still failing R-CMD-check.

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• updated helper function documentation

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• trying to account for NULL values in single doi test with API key not available. Not working

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• Trying to add NULL stop to test-scythe to stop test if API not available. Not working

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• Added logic to springer and scopus single doi tests to deal with NULLs from no API key during R-CMD-check

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• Move citation_test_doi helper function script to test folder

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• fixed null message in test-scythe

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• switched library parameter to source for clarify

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• updated roxygen2 documentation for helper functions

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Commits on May 11, 2022

• moved citation_test_doi.R back to /R, helper functions not accessable in /test folder for testing

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• replace get_test_doi() parameter back to library. source messes with filter that has citations$source column as an argurment.

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• function documentation updated

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• Renamed citation_test_doi.R to helper-test-functions.R and moved to /tests/testthat

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• update roxygen2 documentation

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Commits on May 19, 2022

• Merge pull request #36 from theamarks/develop

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  jeanetteclark

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• reformated all scripts within scythe package

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Commits on Jun 6, 2022

• Merge branch 'DataONEorg:develop' into develop

  theamarks

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• added @export to xdd search function

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• Merge branch 'develop' of https://github.com/theamarks/scythe into develop

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• Merge pull request #37 from theamarks/develop

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Commits on Jul 15, 2022

• fix a couple small bugs, one where the total number of results can be miscounted

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• housekeeping

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Commits on Aug 6, 2024

• remove rplos dependency

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• update setup r GHA

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• remove bash script

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Commits on Aug 15, 2024

• remove message, not needed and too loud

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• make the write citations function more robust

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• ignore data folder

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• depend on devel version of bib2df for now

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Commits on Aug 20, 2024

• cordon off the bib2df package into suggests

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Commits on Aug 26, 2024

• add optional arg to write_citation_pairs to pass to bib2df

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Commits on Sep 6, 2024

• skip scopus and springer tests if no key is set

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• update readme and description to prepare for release

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Commits on Sep 9, 2024

• make argument checking better, and refactor how the source functions are found

  jeanetteclark

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• fix indentation

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• styling and remove unnecessary lapply

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• formatting

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• add helper report estimated wait function

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• update docs

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• assign wait seconds early for easier time changing it if needed

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• remove unnecessary cleanup

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Commits on Sep 10, 2024

• add DOI and fix minor issue in springer search

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