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Hyperlink DOIs to preferred resolver #6
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Hyperlink DOIs to preferred resolver #6
katrinleinweber
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petermr:master
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On Tue, Nov 19, 2019 at 7:01 PM Katrin Leinweber ***@***.***> wrote:
Follow-up to ContentMine/norma#75
<ContentMine/norma#75>. I search-and-replaced
automatically, so I might have caught DOI strings that might be more useful
to keep in the old form. In tests maybe?
What was the problem? a change of the DOI URL? Thanks for catching this.
Also, 33c1453
<33c1453>
& b2a04e4 update a DOI reg-ex to hopefully be more useful.
I ran mvn clean install and saw no DOI-related errors, but:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project ami3: Compilation failure
[ERROR] /Users/katrinleinweber/forks/ami3/src/main/java/org/contentmine/eucl/sternLibrary/data_structure/ThriftyList.java:[1043,30] reference to toArray is ambiguous
[ERROR] both method <T>toArray(java.util.function.IntFunction<T[]>) in java.util.Collection and method <U>toArray(U[]) in org.contentmine.eucl.sternLibrary.data_structure.ThriftyList match
------------------------------
I don't think the code is actually used. I'm guessing the problem is a
stricter version of the compiler.
… You can view, comment on, or merge this pull request online at:
#6
Commit Summary
- Hyperlink DOIs to preferred resolver
File Changes
- *M* src/main/java/org/contentmine/cproject/metadata/CMDOI.java
<https://github.com/petermr/ami3/pull/6/files#diff-0> (20)
- *M* src/main/java/org/contentmine/cproject/metadata/DOIResolver.java
<https://github.com/petermr/ami3/pull/6/files#diff-1> (4)
- *M*
src/main/java/org/contentmine/cproject/metadata/quickscrape/QSRecord.java
<https://github.com/petermr/ami3/pull/6/files#diff-2> (2)
- *M*
src/main/java/org/contentmine/cproject/metadata/quickscrape/QuickscrapeLog.java
<https://github.com/petermr/ami3/pull/6/files#diff-3> (2)
- *M* src/main/java/org/contentmine/cproject/util/CMineUtil.java
<https://github.com/petermr/ami3/pull/6/files#diff-4> (4)
- *M*
src/main/java/org/contentmine/norma/biblio/EPMCResultsJsonEntry.java
<https://github.com/petermr/ami3/pull/6/files#diff-5> (2)
- *M*
src/main/resources/org/contentmine/ami/plugins/dictionary/funders.xml
<https://github.com/petermr/ami3/pull/6/files#diff-6> (23122)
- *M*
src/main/resources/org/contentmine/ami/plugins/dictionary/organization.xml
<https://github.com/petermr/ami3/pull/6/files#diff-7> (23124)
- *M*
src/main/resources/org/contentmine/ami/tagger/hindawi/documentTagger.xml
<https://github.com/petermr/ami3/pull/6/files#diff-8> (2)
- *M* src/main/resources/org/contentmine/graphics/html/badhtml1.html
<https://github.com/petermr/ami3/pull/6/files#diff-9> (50)
- *M* src/main/resources/org/contentmine/graphics/html/badhtml1a.html
<https://github.com/petermr/ami3/pull/6/files#diff-10> (50)
- *M*
src/main/resources/org/contentmine/norma/pubstyle/hindawi/metadata.txt
<https://github.com/petermr/ami3/pull/6/files#diff-11> (2)
- *M* src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml
copy.xsl <https://github.com/petermr/ami3/pull/6/files#diff-12> (4)
- *M* src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl
<https://github.com/petermr/ami3/pull/6/files#diff-13> (4)
- *M*
src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl-old
<https://github.com/petermr/ami3/pull/6/files#diff-14> (4)
- *M* src/test/java/org/contentmine/cproject/CProjectCommandIT.java
<https://github.com/petermr/ami3/pull/6/files#diff-15> (2)
- *M* src/test/java/org/contentmine/cproject/CProjectCommandTest.java
<https://github.com/petermr/ami3/pull/6/files#diff-16> (56)
- *M*
src/test/java/org/contentmine/cproject/metadata/MetadataLongTest.java
<https://github.com/petermr/ami3/pull/6/files#diff-17> (20)
- *M*
src/test/java/org/contentmine/cproject/metadata/ProjectMetadataAnalyzerTest.java
<https://github.com/petermr/ami3/pull/6/files#diff-18> (40)
- *M*
src/test/java/org/contentmine/cproject/metadata/crossref/CrossrefTest.java
<https://github.com/petermr/ami3/pull/6/files#diff-19> (2)
- *M* src/test/java/org/contentmine/norma/json/ManifestTest.java
<https://github.com/petermr/ami3/pull/6/files#diff-20> (2)
- *M*
src/test/java/org/contentmine/norma/pubstyle/rs/RSDownloadTest.java
<https://github.com/petermr/ami3/pull/6/files#diff-21> (4)
- *M*
src/test/resources/org/contentmine/ami/oil5/PMC4391421/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-22> (2)
- *M*
src/test/resources/org/contentmine/ami/oil5/PMC5080681/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-23> (6)
- *M*
src/test/resources/org/contentmine/ami/oil5/PMC5132230/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-24> (12)
- *M*
src/test/resources/org/contentmine/ami/oil5/PMC5203915/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-25> (4)
- *M*
src/test/resources/org/contentmine/ami/oil5/PMC5237462/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-26> (4)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3113902/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-27> (154)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC320490/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-28> (26)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3289602/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-29> (12)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/fulltext.xml
<https://github.com/petermr/ami3/pull/6/files#diff-30> (28)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/scholarly.html
<https://github.com/petermr/ami3/pull/6/files#diff-31> (154)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/105_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-32> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/106_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-33> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/10_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-34> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/110_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-35> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/112_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-36> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/114_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-37> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/116_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-38> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/117_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-39> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/118_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-40> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/11_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-41> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/120_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-42> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/121_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-43> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/123_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-44> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/126_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-45> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/135_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-46> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/138_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-47> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/13_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-48> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/14_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-49> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/15_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-50> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/18_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-51> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/1_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-52> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/20_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-53> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/21_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-54> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/25_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-55> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/26_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-56> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/28_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-57> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/29_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-58> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/2_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-59> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/30_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-60> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/33_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-61> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/35_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-62> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/39_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-63> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/3_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-64> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/40_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-65> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/41_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-66> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/42_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-67> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/4_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-68> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/52_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-69> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/54_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-70> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/55_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-71> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/57_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-72> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/58_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-73> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/59_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-74> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/61_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-75> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/65_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-76> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/74_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-77> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/79_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-78> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/84_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-79> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/86_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-80> (2)
- *M*
src/test/resources/org/contentmine/ami/zika10/PMC3310194/sections/2_back/1_ref-list/88_ref.xml
<https://github.com/petermr/ami3/pull/6/files#diff-81> (2)
- *M*
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<https://github.com/petermr/ami3/pull/6/files#diff-82> (2)
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<https://github.com/petermr/ami3/pull/6/files#diff-83> (2)
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<https://github.com/petermr/ami3/pull/6/files#diff-84> (2)
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<https://github.com/petermr/ami3/pull/6/files#diff-85> (2)
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<https://github.com/petermr/ami3/pull/6/files#diff-87> (2)
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<https://github.com/petermr/ami3/pull/6/files#diff-91> (4)
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Patch Links:
- https://github.com/petermr/ami3/pull/6.patch
- https://github.com/petermr/ami3/pull/6.diff
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Peter Murray-Rust
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Reader Emeritus in Molecular Informatics
Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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Follow-up to ContentMine/norma#75. I search-and-replaced automatically, so I might have caught DOI strings that might be more useful to keep in the old form. In tests maybe?
Also, b2a04e4 & fbee50d update a DOI reg-ex to hopefully be more useful.
I ran
mvn clean install
and saw no DOI-related errors, but:which also occured before my commits.