bolognese 1.8.9 → 1.8.10

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Files changed (7) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +13 -17
  3. data/lib/bolognese/readers/crossref_reader.rb +1 -1
  4. data/lib/bolognese/version.rb +1 -1
  5. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +449 -0
  6. data/spec/readers/crossref_reader_spec.rb +37 -2
  7. metadata +3 -2
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data/Gemfile.lock CHANGED
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+ bolognese (1.8.10)
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  activesupport (>= 4.2.5)
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  bibtex-ruby (>= 5.1.0)
@@ -30,7 +30,7 @@ PATH
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  namae (~> 1.0)
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  namae (~> 1.0)
@@ -75,7 +73,7 @@ GEM
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@@ -101,10 +99,10 @@ GEM
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@@ -155,7 +152,7 @@ GEM
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@@ -163,7 +160,7 @@ GEM
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@@ -175,12 +172,11 @@ GEM
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data/lib/bolognese/readers/crossref_reader.rb CHANGED
@@ -115,7 +115,7 @@ module Bolognese
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  end
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  end.compact
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  else
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- [{ "title" => ":{unav)" }]
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+ [{ "title" => ":(unav)" }]
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  end
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  date_published = crossref_date_published(bibliographic_metadata)
data/lib/bolognese/version.rb CHANGED
@@ -1,3 +1,3 @@
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  module Bolognese
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- VERSION = "1.8.9"
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+ VERSION = "1.8.10"
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data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml ADDED
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+ type=\"date\">2020-04-20T14:28:32Z</crm-item>\r\n <crm-item name=\"created\"
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+ publication_type=\"full_text\">\r\n <titles>\r\n <title>Finding
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+ function: evaluation methods for functional genomic data</title>\r\n </titles>\r\n
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+ sequence=\"first\">\r\n <given_name>Chad L</given_name>\r\n
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+ \ <surname>Myers</surname>\r\n </person_name>\r\n
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+ sequence=\"additional\">\r\n <given_name>Olga G</given_name>\r\n
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+ \ <surname>Troyanskaya</surname>\r\n </person_name>\r\n
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+ \ <month>7</month>\r\n <day>25</day>\r\n
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+ \ <publication_date media_type=\"print\">\r\n <month>12</month>\r\n
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+ mime_type=\"text/html\">http://link.springer.com/article/10.1186/1471-2164-7-187/fulltext.html</resource>\r\n
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+ \ <volume_title>Bioinformatics</volume_title>\r\n <unstructured_citation>Barutcuoglu
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+ Z, Schapire RE, Troyanskaya OG: Hierarchical multi-label prediction of gene
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+ GR, Deng M, Cristianini N, Jordan MI, Noble WS: Kernel-based data fusion and
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+ its application to protein function prediction in yeast. Pac Symp Biocomput.
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+ Comput Biol</journal_title>\r\n <author>P Pavlidis</author>\r\n
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+ \ <doi>10.1089/10665270252935539</doi>\r\n <unstructured_citation>Pavlidis
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+ P, Weston J, Cai J, Noble WS: Learning gene functional classifications from
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+ \ <journal_title>Bioinformatics</journal_title>\r\n <author>A
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+ 1</issue>\r\n <first_page>i38</first_page>\r\n <cYear>2005</cYear>\r\n
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+ A, Noble WS: Kernel methods for predicting protein-protein interactions. Bioinformatics.
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+ \ <journal_title>Science</journal_title>\r\n <author>R
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197
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200
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201
+ \ <journal_title>Science</journal_title>\r\n <author>I
202
+ Lee</author>\r\n <volume>306</volume>\r\n <issue>5701</issue>\r\n
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+ \ <first_page>1555</first_page>\r\n <cYear>2004</cYear>\r\n
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+ \ <journal_title>BMC Bioinformatics</journal_title>\r\n
209
+ \ <author>N Lin</author>\r\n <volume>5</volume>\r\n
210
+ \ <issue>1</issue>\r\n <first_page>154</first_page>\r\n
211
+ \ <cYear>2004</cYear>\r\n <doi>10.1186/1471-2105-5-154</doi>\r\n
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217
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218
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225
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+ Wong</author>\r\n <volume>21</volume>\r\n <issue>8</issue>\r\n
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232
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233
+ Kanehisa</author>\r\n <volume>28</volume>\r\n <issue>1</issue>\r\n
234
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235
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238
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239
+ \ <author>Y Yamanishi</author>\r\n <volume>20</volume>\r\n
240
+ \ <issue>Suppl 1</issue>\r\n <first_page>I363</first_page>\r\n
241
+ \ <cYear>2004</cYear>\r\n <doi>10.1093/bioinformatics/bth910</doi>\r\n
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244
+ Bioinformatics. 2004, 20 (Suppl 1): I363-I370. 10.1093/bioinformatics/bth910.</unstructured_citation>\r\n
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+ \ <unstructured_citation>GRIFn Home Page. [\r\n http://function.princeton.edu/GRIFn\r\n
247
+ \ \r\n ]</unstructured_citation>\r\n </citation>\r\n
248
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249
+ \ <author>AC Gavin</author>\r\n <volume>415</volume>\r\n
250
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251
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256
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258
+ Sprinzak</author>\r\n <volume>327</volume>\r\n <issue>5</issue>\r\n
259
+ \ <first_page>919</first_page>\r\n <cYear>2003</cYear>\r\n
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264
+ \ <journal_title>Nature</journal_title>\r\n <author>P
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+ Uetz</author>\r\n <volume>403</volume>\r\n <issue>6770</issue>\r\n
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267
+ \ <doi>10.1038/35001009</doi>\r\n <unstructured_citation>Uetz
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+ von Mering</author>\r\n <volume>417</volume>\r\n <issue>6887</issue>\r\n
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+ \ <doi>10.1038/nature750</doi>\r\n <unstructured_citation>von
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280
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+ Lee</author>\r\n <volume>20</volume>\r\n <issue>3</issue>\r\n
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+ Ashburner</author>\r\n <volume>25</volume>\r\n <issue>1</issue>\r\n
289
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+ \ <doi>10.1038/75556</doi>\r\n <unstructured_citation>Ashburner
291
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293
+ The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.</unstructured_citation>\r\n
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+ \ <journal_title>Nucleic Acids Res</journal_title>\r\n <author>CA
296
+ Ball</author>\r\n <volume>28</volume>\r\n <issue>1</issue>\r\n
297
+ \ <first_page>77</first_page>\r\n <cYear>2000</cYear>\r\n
298
+ \ <doi>10.1093/nar/28.1.77</doi>\r\n <unstructured_citation>Ball
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+ CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR,
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+ Sherlock G, Binkley G, Jin H: Integrating functional genomic information into
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+ the Saccharomyces genome database. Nucleic Acids Res. 2000, 28 (1): 77-80.
302
+ 10.1093/nar/28.1.77.</unstructured_citation>\r\n </citation>\r\n
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+ \ <citation key=\"570_CR21\">\r\n <journal_title>Nucleic
304
+ Acids Res</journal_title>\r\n <author>HW Mewes</author>\r\n
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+ \ <volume>30</volume>\r\n <issue>1</issue>\r\n
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+ \ <first_page>31</first_page>\r\n <cYear>2002</cYear>\r\n
307
+ \ <doi>10.1093/nar/30.1.31</doi>\r\n <unstructured_citation>Mewes
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+ HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B,
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+ Munsterkotter M, Rudd S, Weil B: MIPS: a database for genomes and protein
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+ sequences. Nucleic Acids Res. 2002, 30 (1): 31-34. 10.1093/nar/30.1.31.</unstructured_citation>\r\n
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+ \ <journal_title>Nucleic Acids Res</journal_title>\r\n <author>MC
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+ Costanzo</author>\r\n <volume>29</volume>\r\n <issue>1</issue>\r\n
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+ \ <first_page>75</first_page>\r\n <cYear>2001</cYear>\r\n
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+ \ <doi>10.1093/nar/29.1.75</doi>\r\n <unstructured_citation>Costanzo
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+ Bioinformatics</journal_title>\r\n <author>A Patil</author>\r\n
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+ \ <cYear>2003</cYear>\r\n <doi>10.1038/nature02026</doi>\r\n
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+ \ <author>CM Deane</author>\r\n <volume>1</volume>\r\n
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+ \ <cYear>2002</cYear>\r\n <doi>10.1074/mcp.M100037-MCP200</doi>\r\n
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+ \ <unstructured_citation>Deane CM, Salwinski L, Xenarios
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+ 10.1074/mcp.M100037-MCP200.</unstructured_citation>\r\n </citation>\r\n
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+ \ <citation key=\"570_CR27\">\r\n <author>Y
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+ Qi</author>\r\n <first_page>531</first_page>\r\n <cYear>2005</cYear>\r\n
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+ \ <volume_title>Pac Symp Biocomput</volume_title>\r\n <unstructured_citation>Qi
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+ \ <journal_title>Curr Opin Struct Biol</journal_title>\r\n
360
+ \ <author>P Bork</author>\r\n <volume>14</volume>\r\n
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+ \ <issue>3</issue>\r\n <first_page>292</first_page>\r\n
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+ \ <cYear>2004</cYear>\r\n <doi>10.1016/j.sbi.2004.05.003</doi>\r\n
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+ \ <unstructured_citation>Bork P, Jensen LJ, von Mering C,
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+ Ramani AK, Lee I, Marcotte EM: Protein interaction networks from yeast to
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+ human. Curr Opin Struct Biol. 2004, 14 (3): 292-299. 10.1016/j.sbi.2004.05.003.</unstructured_citation>\r\n
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+ \ </citation>\r\n <citation key=\"570_CR29\">\r\n
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+ \ <journal_title>Nucleic Acids Res</journal_title>\r\n <author>I
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+ Xenarios</author>\r\n <volume>28</volume>\r\n <issue>1</issue>\r\n
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+ \ <first_page>289</first_page>\r\n <cYear>2000</cYear>\r\n
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+ \ <doi>10.1093/nar/28.1.289</doi>\r\n <unstructured_citation>Xenarios
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+ of interacting proteins. Nucleic Acids Res. 2000, 28 (1): 289-291. 10.1093/nar/28.1.289.</unstructured_citation>\r\n
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+ \ </citation>\r\n <citation key=\"570_CR30\">\r\n
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+ \ <journal_title>Genome Biol</journal_title>\r\n <author>BJ
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+ Breitkreutz</author>\r\n <volume>4</volume>\r\n <issue>3</issue>\r\n
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+ \ <doi>10.1186/gb-2003-4-3-r23</doi>\r\n <unstructured_citation>Breitkreutz
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+ BJ, Stark C, Tyers M: The GRID: the General Repository for Interaction Datasets.
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+ Genome Biol. 2003, 4 (3): R23-10.1186/gb-2003-4-3-r23.</unstructured_citation>\r\n
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+ \ </citation>\r\n <citation key=\"570_CR31\">\r\n
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+ \ <doi provider=\"crossref\">10.1093/nar/gki051</doi>\r\n
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+ Lord</author>\r\n <volume>19</volume>\r\n <issue>10</issue>\r\n
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+ across the Gene Ontology: the relationship between sequence and annotation.
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+ \ <journal_title>BMC Bioinformatics</journal_title>\r\n
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+ \ <author>A Ben-Hur</author>\r\n <volume>7</volume>\r\n
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+ \ <issue>Suppl61</issue>\r\n <first_page>S2</first_page>\r\n
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+ \ <cYear>2005</cYear>\r\n <unstructured_citation>Ben-Hur
399
+ A, Noble WS: Choosing negative examples for the prediction of protein-protein
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+ interactions. BMC Bioinformatics. 2005, 7 (Suppl61): S2-</unstructured_citation>\r\n
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+ \ <journal_title>Proc Natl Acad Sci U S A</journal_title>\r\n
403
+ \ <author>T Ito</author>\r\n <volume>98</volume>\r\n
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+ \ <issue>8</issue>\r\n <first_page>4569</first_page>\r\n
405
+ \ <cYear>2001</cYear>\r\n <doi>10.1073/pnas.061034498</doi>\r\n
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+ \ <unstructured_citation>Ito T, Chiba T, Ozawa R, Yoshida
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+ yeast protein interactome. Proc Natl Acad Sci U S A. 2001, 98 (8): 4569-4574.
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+ 10.1073/pnas.061034498.</unstructured_citation>\r\n </citation>\r\n
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+ \ <citation key=\"570_CR35\">\r\n <journal_title>Science</journal_title>\r\n
411
+ \ <author>AH Tong</author>\r\n <volume>295</volume>\r\n
412
+ \ <issue>5553</issue>\r\n <first_page>321</first_page>\r\n
413
+ \ <cYear>2002</cYear>\r\n <doi>10.1126/science.1064987</doi>\r\n
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+ \ <unstructured_citation>Tong AH, Drees B, Nardelli G, Bader
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+ GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi
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+ S: A combined experimental and computational strategy to define protein interaction
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+ networks for peptide recognition modules. Science. 2002, 295 (5553): 321-324.
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+ 10.1126/science.1064987.</unstructured_citation>\r\n </citation>\r\n
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+ \ <citation key=\"570_CR36\">\r\n <journal_title>Nature</journal_title>\r\n
420
+ \ <author>Y Ho</author>\r\n <volume>415</volume>\r\n
421
+ \ <issue>6868</issue>\r\n <first_page>180</first_page>\r\n
422
+ \ <cYear>2002</cYear>\r\n <doi>10.1038/415180a</doi>\r\n
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+ \ <unstructured_citation>Ho Y, Gruhler A, Heilbut A, Bader
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+ GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K: Systematic
425
+ identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
426
+ Nature. 2002, 415 (6868): 180-183. 10.1038/415180a.</unstructured_citation>\r\n
427
+ \ </citation>\r\n <citation key=\"570_CR37\">\r\n
428
+ \ <journal_title>Mol Biol Cell</journal_title>\r\n <author>AP
429
+ Gasch</author>\r\n <volume>12</volume>\r\n <issue>10</issue>\r\n
430
+ \ <first_page>2987</first_page>\r\n <cYear>2001</cYear>\r\n
431
+ \ <doi>10.1091/mbc.12.10.2987</doi>\r\n <unstructured_citation>Gasch
432
+ AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO: Genomic expression
433
+ responses to DNA-damaging agents and the regulatory role of the yeast ATR
434
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435
+ \ </citation>\r\n <citation key=\"570_CR38\">\r\n
436
+ \ <journal_title>Mol Biol Cell</journal_title>\r\n <author>PT
437
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438
+ \ <first_page>3273</first_page>\r\n <cYear>1998</cYear>\r\n
439
+ \ <doi>10.1091/mbc.9.12.3273</doi>\r\n <unstructured_citation>Spellman
440
+ PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein
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+ D, Futcher B: Comprehensive identification of cell cycle-regulated genes of
442
+ the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell.
443
+ 1998, 9 (12): 3273-3297.</unstructured_citation>\r\n </citation>\r\n
444
+ \ </citation_list>\r\n </journal_article>\r\n </journal>\r\n
445
+ \ </crossref>\r\n </doi_record>\r\n </query>\r\n </body>\r\n
446
+ \ </query_result>\r\n</crossref_result>"
447
+ http_version:
448
+ recorded_at: Sun, 11 Oct 2020 05:26:32 GMT
449
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data/spec/readers/crossref_reader_spec.rb CHANGED
@@ -333,7 +333,7 @@ describe Bolognese::Metadata, vcr: true do
333
333
  expect(subject.url).to eq("https://dx.plos.org/10.1371/journal.pmed.0030277.g001")
334
334
  expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"article-journal", "resourceType"=>"SaComponent", "resourceTypeGeneral"=>"Text", "ris"=>"JOUR", "schemaOrg"=>"ScholarlyArticle")
335
335
  expect(subject.creators).to eq([{"name"=>":(unav)", "nameType"=>"Organizational"}])
336
- expect(subject.titles).to eq([{"title"=>":{unav)"}])
336
+ expect(subject.titles).to eq([{"title"=>":(unav)"}])
337
337
  expect(subject.descriptions).to be_empty
338
338
  expect(subject.dates).to eq([{"date"=>"2015-10-20", "dateType"=>"Issued"}, {"date"=>"2018-10-19T17:13:42Z", "dateType"=>"Updated"}])
339
339
  expect(subject.publication_year).to eq("2015")
@@ -555,6 +555,41 @@ describe Bolognese::Metadata, vcr: true do
555
555
  expect(subject.date_registered).to be_nil
556
556
  end
557
557
 
558
+ it "multiple titles with missing" do
559
+ input = "https://doi.org/10.1186/1471-2164-7-187"
560
+ subject = Bolognese::Metadata.new(input: input)
561
+ expect(subject.valid?).to be true
562
+ expect(subject.id).to eq("https://doi.org/10.1186/1471-2164-7-187")
563
+ expect(subject.url).to eq("https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-187")
564
+ expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"article-journal", "resourceType"=>"JournalArticle", "resourceTypeGeneral"=>"Text", "ris"=>"JOUR", "schemaOrg"=>"ScholarlyArticle")
565
+ expect(subject.creators).to eq([{"familyName"=>"Myers",
566
+ "givenName"=>"Chad L",
567
+ "name"=>"Myers, Chad L",
568
+ "nameType"=>"Personal"},
569
+ {"familyName"=>"Barrett",
570
+ "givenName"=>"Daniel R",
571
+ "name"=>"Barrett, Daniel R",
572
+ "nameType"=>"Personal"},
573
+ {"familyName"=>"Hibbs",
574
+ "givenName"=>"Matthew A",
575
+ "name"=>"Hibbs, Matthew A",
576
+ "nameType"=>"Personal"},
577
+ {"familyName"=>"Huttenhower",
578
+ "givenName"=>"Curtis",
579
+ "name"=>"Huttenhower, Curtis",
580
+ "nameType"=>"Personal"},
581
+ {"familyName"=>"Troyanskaya",
582
+ "givenName"=>"Olga G",
583
+ "name"=>"Troyanskaya, Olga G",
584
+ "nameType"=>"Personal"}])
585
+ expect(subject.titles).to eq([{"title"=>"Finding function: evaluation methods for functional genomic data"}])
586
+ expect(subject.dates).to include({"date"=>"2006-07-25", "dateType"=>"Issued"})
587
+ expect(subject.publication_year).to eq("2006")
588
+ expect(subject.publisher).to eq("Springer Science and Business Media LLC")
589
+ expect(subject.agency).to eq("crossref")
590
+ expect(subject.date_registered).to eq("2020-04-20T16:04:45Z")
591
+ end
592
+
558
593
  it "markup" do
559
594
  input = "https://doi.org/10.1098/rspb.2017.0132"
560
595
  subject = Bolognese::Metadata.new(input: input)
@@ -716,7 +751,7 @@ describe Bolognese::Metadata, vcr: true do
716
751
  expect(subject.url).to eq("http://ectrx.org/forms/ectrxcontentshow.php?doi_id=10.6002/ect.2015.0371")
717
752
  expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"article-journal", "resourceType"=>"JournalIssue", "resourceTypeGeneral"=>"Text", "ris"=>"JOUR", "schemaOrg"=>"PublicationIssue")
718
753
  expect(subject.creators).to eq([{"name"=>":(unav)", "nameType"=>"Organizational"}])
719
- expect(subject.titles).to eq([{"title"=>":{unav)"}])
754
+ expect(subject.titles).to eq([{"title"=>":(unav)"}])
720
755
  expect(subject.dates).to eq([{"date"=>"2018-10", "dateType"=>"Issued"}, {"date"=>"2018-10-03T12:09:12Z", "dateType"=>"Updated"}])
721
756
  expect(subject.publication_year).to eq("2018")
722
757
  expect(subject.publisher).to eq("Baskent University")
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bolognese
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.8.9
4
+ version: 1.8.10
5
5
  platform: ruby
6
6
  authors:
7
7
  - Martin Fenner
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2020-08-22 00:00:00.000000000 Z
11
+ date: 2020-10-11 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: maremma
@@ -920,6 +920,7 @@ files:
920
920
  - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/markup.yml
921
921
  - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/missing_creator.yml
922
922
  - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/multiple_titles.yml
923
+ - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml
923
924
  - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/not_found_error.yml
924
925
  - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/peer_review.yml
925
926
  - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/posted_content.yml