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add tests for cr_abstract; tweak cr_Abstract egs
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‎R/cr_abstract.R

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#' @param ... Named parameters passed on to \code{\link[crul]{HttpClient}}
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#' @examples \dontrun{
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#' # abstract found
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#' cr_abstract(doi = '10.1109/TASC.2010.2088091')
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#' cr_abstract('10.1109/TASC.2010.2088091')
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#' cr_abstract("10.1175//2572.1")
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#' cr_abstract("10.1182/blood.v16.1.1039.1039")
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#'
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#' # doi not found
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#' # cr_abstract(doi = '10.5284/1011335')
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#'
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#' # abstract not found, throws warning
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#' # abstract not found, throws error
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#' # cr_abstract(doi = '10.1126/science.169.3946.635')
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#' # cr_abstract(doi = '10.1371/journal.pone.0033693')
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#' # cr_abstract(doi = '10.1007/12080.1874-1746')
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#'
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#' # a random DOI
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#' # cr_abstract(cr_r(1))
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#'
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#' # loop through many DOIs, allowing for failures
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#' dois <- cr_r(10, filter = c(has_abstract = TRUE))
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#' res <- lapply(dois, function(z) tryCatch(cr_abstract(z), error = function(e) e))
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#' }
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cr_abstract<-function(doi, ...) {
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url<- paste0('http://api.crossref.org/works/', doi, '.xml')
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url<- paste0('https://api.crossref.org/works/', doi, '.xml')
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cli<-crul::HttpClient$new(
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url=url,
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opts=list(followlocation=1),

‎tests/fixtures/cr_abstract.yml

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http_interactions:
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- request:
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method: get
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uri: https://api.crossref.org/works/10.1175//2572.1.xml
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body:
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encoding: ''
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string: ''
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headers:
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Accept-Encoding: gzip, deflate
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Accept: application/json, text/xml, application/xml, */*
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User-Agent: r-curl/4.3 crul/1.0.0 rOpenSci(rcrossref/1.1.0) (mailto:<crossref_email>)
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X-USER-AGENT: r-curl/4.3 crul/1.0.0 rOpenSci(rcrossref/1.1.0) (mailto:<crossref_email>)
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response:
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status:
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status_code: '200'
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message: OK
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explanation: Request fulfilled, document follows
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headers:
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status: HTTP/1.1 200 OK
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link: <http://dx.doi.org/10.1175//2572.1>; rel="canonical", <http://journals.ametsoc.org/mwr/article-pdf/131/8/1895/4208740/_2572_1.pdf>;
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version="vor"; type="application/pdf"; rel="item", <http://journals.ametsoc.org/mwr/article-pdf/131/8/1895/4208740/_2572_1.pdf>;
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version="vor"; rel="item"
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access-control-allow-origin: '*'
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access-control-allow-headers: X-Requested-With
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content-length: '7060'
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server: http-kit
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date: Fri, 02 Oct 2020 15:54:21 GMT
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x-rate-limit-limit: '50'
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x-rate-limit-interval: 1s
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connection: close
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body:
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encoding: UTF-8
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file: no
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string: "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<crossref_result xmlns=\"http://www.crossref.org/qrschema/3.0\"
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version=\"3.0\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.crossref.org/qrschema/3.0
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http://www.crossref.org/schemas/crossref_query_output3.0.xsd\">\r\n <query_result>\r\n
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\ <head>\r\n <doi_batch_id>none</doi_batch_id>\r\n </head>\r\n <body>\r\n
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\ <query status=\"resolved\">\r\n <doi type=\"journal_article\">10.1175//2572.1</doi>\r\n
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\ <crm-item name=\"publisher-name\" type=\"string\">American Meteorological
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Society</crm-item>\r\n <crm-item name=\"prefix-name\" type=\"string\">American
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Meteorological Society</crm-item>\r\n <crm-item name=\"member-id\"
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type=\"number\">12</crm-item>\r\n <crm-item name=\"citation-id\" type=\"number\">8407024</crm-item>\r\n
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\ <crm-item name=\"journal-id\" type=\"number\">5839</crm-item>\r\n
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\ <crm-item name=\"deposit-timestamp\" type=\"number\">2020061721302561500</crm-item>\r\n
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\ <crm-item name=\"owner-prefix\" type=\"string\">10.1175</crm-item>\r\n
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\ <crm-item name=\"last-update\" type=\"date\">2020-06-18T01:31:13Z</crm-item>\r\n
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\ <crm-item name=\"created\" type=\"date\">2003-07-25T16:26:33Z</crm-item>\r\n
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\ <crm-item name=\"citedby-count\" type=\"number\">19</crm-item>\r\n
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\ <doi_record>\r\n <crossref xmlns=\"http://www.crossref.org/xschema/1.1\"
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xsi:schemaLocation=\"http://www.crossref.org/xschema/1.1 http://doi.crossref.org/schemas/unixref1.1.xsd\">\r\n
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\ <journal>\r\n <journal_metadata language=\"en\">\r\n
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\ <full_title>Monthly Weather Review</full_title>\r\n <issn
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media_type=\"electronic\">1520-0493</issn>\r\n <issn media_type=\"print\">0027-0644</issn>\r\n
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\ </journal_metadata>\r\n <journal_issue>\r\n <publication_date
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media_type=\"print\">\r\n <month>08</month>\r\n <day>01</day>\r\n
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\ <year>2003</year>\r\n </publication_date>\r\n
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\ <journal_volume>\r\n <volume>131</volume>\r\n
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\ </journal_volume>\r\n <issue>8</issue>\r\n
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\ </journal_issue>\r\n <journal_article publication_type=\"full_text\">\r\n
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\ <titles>\r\n <title>A Numerical Study of
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Early Summer Regional Climate and Weather over LSA-East. Part I: Model Implementation
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and Verification</title>\r\n </titles>\r\n <contributors>\r\n
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\ <person_name sequence=\"first\" contributor_role=\"author\">\r\n
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\ <given_name>Da-Lin</given_name>\r\n <surname>Zhang</surname>\r\n
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\ <affiliation>Department of Meteorology, University of
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Maryland, College Park, College Park, Maryland</affiliation>\r\n </person_name>\r\n
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\ <person_name sequence=\"first\" contributor_role=\"author\">\r\n
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\ <given_name>Wei-Zhong</given_name>\r\n <surname>Zheng</surname>\r\n
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\ <affiliation>Department of Meteorology, University of
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Maryland, College Park, College Park, Maryland</affiliation>\r\n </person_name>\r\n
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\ <person_name sequence=\"additional\" contributor_role=\"author\">\r\n
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\ <given_name>Yong-Kang</given_name>\r\n <surname>Xue</surname>\r\n
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\ <affiliation>Department of Geography, University of California,
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Los Angeles, Los Angeles, California</affiliation>\r\n </person_name>\r\n
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\ </contributors>\r\n <jats:abstract xmlns:jats=\"http://www.ncbi.nlm.nih.gov/JATS1\">\r\n
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\ <jats:title>Abstract</jats:title>\r\n <jats:p>The
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Pennsylvania State University–NCAR Mesoscale Model (MM5) and a simplified
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simple biosphere (SSiB) scheme are modified and then coupled to study various
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regional climate and weather problems. These modifications include correcting
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the moisture and cloud hydrometeor fields to ensure the mass conservation;
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incorporating the effects of dissipative heating to ensure total energy conservation;
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decoupling soil and vegetation types in specifying various surface parameters;
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and eliminating the shortwave radiation reaching the surface at points where
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deep convection occurs.</jats:p>\r\n <jats:p>A 30-day integration
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of June 1998 over the Midwest states was used to examine the model's capability
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in capturing the observed wet regional climate and the passage of several
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mesoscale weather events. It is found that the coupled model reproduces the
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distribution and magnitude of monthly accumulated precipitation, the time
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series of area-integrated precipitation, surface pressures, and diurnal changes
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in surface temperatures, low-level winds and precipitation, as well as the
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evolution of precipitation systems across the central United States. In particular,
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the model reproduces well many daily weather events, including the distribution
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and intensity of low-level temperature and pressure perturbations and precipitation,
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even up to a month. The results suggest that the daily temperature, clouds,
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and precipitation events from the weekly to monthly scales, as well as their
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associated regional climate phenomena, could be reasonably simulated if the
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surface, boundary layer, radiation, and convective processes are realistically
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parameterized, and the large-scale forcing could be reasonably provided by
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general circulation models.</jats:p>\r\n </jats:abstract>\r\n
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\ <publication_date media_type=\"print\">\r\n <month>08</month>\r\n
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\ <day>01</day>\r\n <year>2003</year>\r\n
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\ </publication_date>\r\n <publication_date media_type=\"online\">\r\n
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\ <month>08</month>\r\n <day>01</day>\r\n
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\ <year>2003</year>\r\n </publication_date>\r\n
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\ <pages>\r\n <first_page>1895</first_page>\r\n
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\ <last_page>1909</last_page>\r\n </pages>\r\n
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\ <doi_data>\r\n <doi>10.1175//2572.1</doi>\r\n
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\ <resource>https://journals.ametsoc.org/mwr/article/131/8/1895/67449/A-Numerical-Study-of-Early-Summer-Regional-Climate</resource>\r\n
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\ <collection property=\"crawler-based\">\r\n <item
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crawler=\"iParadigms\">\r\n <resource>http://journals.ametsoc.org/mwr/article-pdf/131/8/1895/4208740/_2572_1.pdf</resource>\r\n
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\ </item>\r\n </collection>\r\n <collection
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property=\"syndication\">\r\n <item>\r\n <resource
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content_version=\"vor\" mime_type=\"application/pdf\">http://journals.ametsoc.org/mwr/article-pdf/131/8/1895/4208740/_2572_1.pdf</resource>\r\n
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\ </item>\r\n </collection>\r\n </doi_data>\r\n
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\ </journal_article>\r\n </journal>\r\n </crossref>\r\n
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\ </doi_record>\r\n </query>\r\n </body>\r\n </query_result>\r\n</crossref_result>"
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recorded_at: 2020-10-02 15:54:20 GMT
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recorded_with: vcr/0.5.4, webmockr/0.7.0

‎tests/fixtures/cr_abstract_not_found.yml

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http_interactions:
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- request:
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method: get
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uri: https://api.crossref.org/works/10.5284/1011335.xml
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body:
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encoding: ''
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string: ''
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headers:
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Accept-Encoding: gzip, deflate
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Accept: application/json, text/xml, application/xml, */*
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User-Agent: r-curl/4.3 crul/1.0.0 rOpenSci(rcrossref/1.1.0) (mailto:<crossref_email>)
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X-USER-AGENT: r-curl/4.3 crul/1.0.0 rOpenSci(rcrossref/1.1.0) (mailto:<crossref_email>)
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response:
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status:
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status_code: '404'
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message: Not Found
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explanation: Nothing matches the given URI
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headers:
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status: HTTP/1.1 404 Not Found
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content-type: text/plain
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access-control-allow-origin: '*'
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access-control-allow-headers: X-Requested-With
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content-length: '19'
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server: http-kit
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date: Fri, 02 Oct 2020 15:55:02 GMT
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x-rate-limit-limit: '50'
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x-rate-limit-interval: 1s
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connection: close
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body:
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encoding: UTF-8
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file: no
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string: Resource not found.
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recorded_at: 2020-10-02 15:55:01 GMT
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recorded_with: vcr/0.5.4, webmockr/0.7.0

‎tests/testthat/test-cr_abstract.R

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skip_on_cran()
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test_that("cr_abstract", {
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vcr::use_cassette("cr_abstract", {
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b<- cr_abstract("10.1175//2572.1")
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})
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expect_is(b, "character")
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expect_match(b, "University")
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expect_gt(nchar(b), 1000L)
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})
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test_that("cr_abstract not found", {
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vcr::use_cassette("cr_abstract_not_found", {
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expect_error(cr_abstract('10.5284/1011335'))
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})
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})

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