├── .dockerignore ├── .gitattributes ├── .gitignore ├── Readme.md ├── config ├── elastic-settings.json └── glutton.yml ├── data └── .gitkeep ├── doc ├── API.md ├── Benchmarking.md ├── Build-Databases.md ├── Frequently-asked-questions.md ├── Install.md ├── Introduction.md ├── License.md ├── glutton-architecture.png ├── hal-doi-missing.tsv ├── hal-duplicated-records.tsv ├── index.md ├── references-doi-matching.json.gz └── requirements.txt ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── indexing ├── Readme.md ├── main.js ├── package.json └── resources │ ├── crossref_mapping.json │ ├── samples │ ├── entry1.beautified.json │ └── entry1.json │ └── settings.json ├── mkdocs.yml ├── notes.md ├── pubmed-glutton ├── Readme.md ├── build.gradle ├── doc │ ├── ISTEX.stats │ ├── commands.md │ └── core.md ├── gradle │ └── wrapper │ │ ├── gradle-wrapper.jar │ │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── script │ └── merge_records.py ├── settings.gradle └── src │ ├── main │ ├── java │ │ └── com │ │ │ └── scienceminer │ │ │ └── glutton │ │ │ ├── data │ │ │ ├── Affiliation.java │ │ │ ├── Biblio.java │ │ │ ├── BiblioAttribute.java │ │ │ ├── BiblioDefinitions.java │ │ │ ├── BiblioUtils.java │ │ │ ├── ClassificationClass.java │ │ │ ├── DateUtils.java │ │ │ ├── Grant.java │ │ │ ├── Identifier.java │ │ │ ├── Keyword.java │ │ │ ├── MeSHClass.java │ │ │ ├── Person.java │ │ │ └── Reference.java │ │ │ ├── export │ │ │ ├── PubMedExporter.java │ │ │ └── PubMedSerializer.java │ │ │ ├── ingestion │ │ │ ├── IstexPubMedMapper.java │ │ │ └── PubMedIndexer.java │ │ │ ├── main │ │ │ ├── Main.java │ │ │ └── MainArgs.java │ │ │ └── utilities │ │ │ ├── GluttonConfig.java │ │ │ ├── LangUtil.java │ │ │ ├── Utilities.java │ │ │ └── sax │ │ │ ├── DumbEntityResolver.java │ │ │ └── MedlineSaxHandler.java │ └── resources │ │ └── example-medline-31388315.xml │ └── test │ ├── java │ └── com │ │ └── scienceminer │ │ └── glutton │ │ ├── data │ │ └── TestDOILookup.java │ │ ├── export │ │ └── TestCrossrefExport.java │ │ └── ingestion │ │ └── TestIngestion.java │ └── resources │ ├── assistive_technologies_classes-mesh.csv │ ├── core-batch-coreID-sample.json │ ├── core-batch-repositoryID-sample.json │ └── org │ └── scienceminer │ └── glutton │ └── export │ └── example-medline-31388315.xml ├── readthedocs.yml ├── scripts ├── dump-istexid-and-other-ids.js ├── dump-istexid-metadata.js ├── oa_coverage.js └── package.json ├── settings.gradle ├── src ├── main │ ├── java │ │ └── com │ │ │ └── scienceminer │ │ │ └── glutton │ │ │ ├── command │ │ │ ├── GapUpdateCrossrefCommand.java │ │ │ ├── HALAuditCommand.java │ │ │ ├── IndexCommand.java │ │ │ ├── LoadCrossrefCommand.java │ │ │ ├── LoadHALCommand.java │ │ │ ├── LoadIstexIdsCommand.java │ │ │ ├── LoadPMIDCommand.java │ │ │ └── LoadUnpayWallCommand.java │ │ │ ├── configuration │ │ │ └── LookupConfiguration.java │ │ │ ├── data │ │ │ ├── Affiliation.java │ │ │ ├── Biblio.java │ │ │ ├── BiblioAttribute.java │ │ │ ├── BiblioDefinitions.java │ │ │ ├── BiblioUtils.java │ │ │ ├── ClassificationClass.java │ │ │ ├── DateUtils.java │ │ │ ├── Grant.java │ │ │ ├── Identifier.java │ │ │ ├── IstexData.java │ │ │ ├── Keyword.java │ │ │ ├── MatchingDocument.java │ │ │ ├── MeSHClass.java │ │ │ ├── OALocation.java │ │ │ ├── OAResource.java │ │ │ ├── OaIstexResource.java │ │ │ ├── Person.java │ │ │ ├── PmidData.java │ │ │ ├── Reference.java │ │ │ └── UnpayWallMetadata.java │ │ │ ├── exception │ │ │ ├── DataException.java │ │ │ ├── NotFoundException.java │ │ │ ├── ServiceException.java │ │ │ └── ServiceOverloadedException.java │ │ │ ├── harvester │ │ │ ├── HALAPIHarvester.java │ │ │ ├── HALAPIResponseParser.java │ │ │ ├── HALOAIPMHDomParser.java │ │ │ ├── HALOAIPMHHarvester.java │ │ │ ├── Harvester.java │ │ │ └── OAIPMHPathsItf.java │ │ │ ├── indexing │ │ │ ├── ElasticSearchAsyncIndexer.java │ │ │ ├── ElasticSearchIndexer.java │ │ │ ├── MetadataObj.java │ │ │ ├── MetadataObjBuilder.java │ │ │ └── SolrIndexer.java │ │ │ ├── reader │ │ │ ├── CrossrefJsonArrayReader.java │ │ │ ├── CrossrefJsonReader.java │ │ │ ├── CrossrefJsonlReader.java │ │ │ ├── IstexIdsReader.java │ │ │ ├── PmidReader.java │ │ │ └── UnpayWallReader.java │ │ │ ├── serialization │ │ │ └── BiblioSerializer.java │ │ │ ├── storage │ │ │ ├── DataEngine.java │ │ │ ├── LookupEngine.java │ │ │ ├── StorageEnvFactory.java │ │ │ └── lookup │ │ │ │ ├── CrossrefMetadataLookup.java │ │ │ │ ├── HALLookup.java │ │ │ │ ├── IstexIdsLookup.java │ │ │ │ ├── MetadataMatching.java │ │ │ │ ├── OALookup.java │ │ │ │ ├── PMIdsLookup.java │ │ │ │ ├── TransactionWrapper.java │ │ │ │ └── async │ │ │ │ ├── AsyncResponseWrapper.java │ │ │ │ └── ESClientWrapper.java │ │ │ ├── utils │ │ │ ├── BinarySerialiser.java │ │ │ ├── Compressors.java │ │ │ ├── LangUtil.java │ │ │ ├── Utilities.java │ │ │ ├── crossrefclient │ │ │ │ ├── CrossrefClient.java │ │ │ │ ├── CrossrefRequest.java │ │ │ │ ├── CrossrefResponse.java │ │ │ │ └── IncrementalLoaderTask.java │ │ │ ├── grobid │ │ │ │ ├── GrobidClient.java │ │ │ │ ├── GrobidClientAsync.java │ │ │ │ └── GrobidResponseStaxHandler.java │ │ │ └── xml │ │ │ │ ├── DumbEntityResolver.java │ │ │ │ ├── HALTEISaxHandler.java │ │ │ │ ├── MedlineSaxHandler.java │ │ │ │ ├── StaxParserContentHandler.java │ │ │ │ └── StaxUtils.java │ │ │ └── web │ │ │ ├── LookupServiceApplication.java │ │ │ ├── healthcheck │ │ │ └── LookupHealthCheck.java │ │ │ ├── module │ │ │ ├── LookupServiceModule.java │ │ │ ├── NotFoundExceptionMapper.java │ │ │ ├── ServiceExceptionMapper.java │ │ │ └── ServiceOverloadedExceptionMapper.java │ │ │ └── resource │ │ │ ├── DataController.java │ │ │ ├── LookupController.java │ │ │ ├── OAController.java │ │ │ └── OaIstexController.java │ └── resources │ │ ├── elasticSearch │ │ ├── crossref_mapping.json │ │ └── settings.json │ │ └── logback.xml └── test │ ├── java │ └── com │ │ └── scienceminer │ │ └── glutton │ │ ├── reader │ │ ├── IstexIdsReaderTest.java │ │ ├── PmidReaderTest.java │ │ └── UnpaidWallReaderTest.java │ │ ├── storage │ │ ├── LookupEngineTest.java │ │ └── lookup │ │ │ ├── DoiLookupTest.java │ │ │ └── IstexLookupTest.java │ │ ├── utils │ │ ├── BinarySerialiserTest.java │ │ ├── CompressorsTest.java │ │ └── grobid │ │ │ └── GrobidResponseStaxHandlerTest.java │ │ └── web │ │ └── resource │ │ └── LookupControllerTest.java.bak │ └── resources │ ├── com │ └── scienceminer │ │ └── glutton │ │ └── reader │ │ └── sample-istex-ids.json.gz │ ├── hal1.tei.xml │ ├── sample.grobid-2.xml │ ├── sample.grobid-3.xml │ ├── sample.grobid.xml │ └── unpaywall_sample.json.gz ├── test ├── Readme.md ├── biblio.data.article.test.csv ├── biblio.data.journals.test.csv ├── biblioList.shuf.csv └── biblioList.shuf.txt └── web-extension └── Readme.md /.dockerignore: -------------------------------------------------------------------------------- 1 | .git 2 | data 3 | logs/* 4 | 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