Hyperlink DOIs to preferred resolver

[katrinleinweber]

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:

[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

which also occured before my commits.

[petermr]

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) - 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