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Revision 39166

merging trunk changes with IIS-CDH-5.3.0 branch

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modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/ingest/pmc/citations/PmidMapping.avdl
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@namespace("eu.dnetlib.iis.ingest.pmc.citations.schemas")
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protocol IIS{
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    record PmidMapping {
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    	string entityType;
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        string pmId;
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        string oaId;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/ingest/pmc/citations/Citation.avdl
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@namespace("eu.dnetlib.iis.ingest.pmc.citations.schemas")
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protocol IIS{
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// At least one of rawText, destinationDocumentId, externalDestinationDocumentIds fields is not empty.
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    record Citation {
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//      citing document OA+ identifier
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        string sourceDocumentId;
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//      raw citation text
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        union { null , string } rawText = null;
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//      cited document OA+ identifier (if referenced document is present in OA+)
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        union { null , string }  destinationDocumentId = null;
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//      cited document identifiers (id type -> id)
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//      WARNING: Id types are extracted from PMC data without any processing thus are subject to change without notice.
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//               Currently (2014-05-12), the most popular types are "pmid" (PubMed ID) and "doi".
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//               These types are copied from "pub-id-type" attribute from PubMed XML. Some of the 
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//               values that appear as a value of this attribute are mentioned in JATS format specification here:
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//               http://jats.nlm.nih.gov/archiving/tag-library/1.0/n-j532.html.  
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        map<string> externalDestinationDocumentIds;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/metadataextraction/ReferenceBasicMetadata.avdl
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        union { null , string } series = null;
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        union { null , string } issue = null;
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        union { null , string } url = null;
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        union { null , map<string> } externalIds = null;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/metadataextraction/ExtractedDocumentMetadata.avdl
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        union { null , string } issue = null;
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//      page range in which the article is published
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        union { null , Range } pages = null;
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//      propagated from pmc ExtractedDocumentMetadata#entityType
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		union { null , string } publicationTypeName = null;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/citationmatching/Citation.avdl
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    record Citation {
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//      citing document identifier
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        string sourceDocumentId;
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//      raw citation text
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        union { null , string } rawText = null;
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//      position of citation in the bibliography of the source document
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        int position;
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//      cited document identifier
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        union { null , string } destinationDocumentId = null;
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        string destinationDocumentId;
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//      A number from [0, 1] range. The greater the value, the greater the
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//      confidence that the document->document citation link is correct.
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//      The `confidenceLevel` field is null if and only if the `destinationDocumentId` is null.
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//		Find more details on `confidenceLevel` constraints in eu/dnetlib/iis/README.markdown file.
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        union { null , float } confidenceLevel = null;
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        float confidenceLevel;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/citationmatching/direct/Citation.avdl
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@namespace("eu.dnetlib.iis.citationmatching.direct.schemas")
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protocol IIS{
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    record Citation {
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//      citing document OA+ identifier
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        string sourceDocumentId;
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//      position of citation in the bibliography of the source document
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        int position;
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//      cited document OA+ identifier
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        string destinationDocumentId;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/citationmatching/direct/DocumentMetadata.avdl
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@namespace("eu.dnetlib.iis.citationmatching.direct.schemas")
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protocol IIS{
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	record ReferenceMetadata {
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        // reference position in the bibliography
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        int position;
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        // external identifiers
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		union { null , map<string> } externalIds = null;
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    }
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    record DocumentMetadata {
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        string id;
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//      alternative identifier (e.g. internal publisher's identifiers)
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        union { null , map<string> } externalIdentifiers = null;
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//      detailed publication type name, originates from extracted metadata
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        union { null , string } publicationTypeName = null;
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        array<ReferenceMetadata> references;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/citationmatching/PartialCitation.avdl
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        string sourceDocumentId;
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//      position of citation in the bibliography of the source document
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        int position;
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//      raw citation text
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        union { null , string } rawText = null;
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//      cited document identifier
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        union { null , string } destinationDocumentId = null;
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        string destinationDocumentId;
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//      A number from [0, 1] range. The greater the value, the greater the
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//      confidence that the document->document citation link is correct.
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//      The `confidenceLevel` field is null if and only if the `destinationDocumentId` is null.
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//		Find more details on `confidenceLevel` constraints in eu/dnetlib/iis/README.markdown file.
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        union { null , float } confidenceLevel = null;
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        float confidenceLevel;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/transformers/metadatamerger/ExtractedDocumentMetadataMergedWithOriginal.avdl
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//      publisher name
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        union { null , string } publisher = null;
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//      end of: moved from DocumentBasicMetadata    
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//      publication type
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//      publication type, originates from metadata
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        PublicationType publicationType;
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//      references extracted from pfd document
......
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        union { null , string } issue = null;
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//      page range in which the article is published
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        union { null , eu.dnetlib.iis.metadataextraction.schemas.Range } pages = null;
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//      detailed publication type name, originates from extracted metadata
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        union { null , string } publicationTypeName = null;
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    }
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}
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/common/citations/CitationEntry.avdl
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// At least one of rawText, destinationDocumentId, externalDestinationDocumentIds fields is not empty.
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    record CitationEntry {
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//      position of citation in the bibliography of the source document
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        int position;
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//      raw citation text
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        union { null , string } rawText = null;
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//      cited document OA+ identifier (if referenced document is present in OA+)
modules/icm-iis-schemas/branches/IIS-CDH-5.3.0/src/main/resources/eu/dnetlib/iis/ingest/pmc/metadata/ExtractedDocumentMetadata.avdl
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    record ExtractedDocumentMetadata {
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//      OpenAIRE identifier of the document
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        string id;
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//      Pubmed identifier of the document
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        union { null , string } pmid = null;
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//      alternative identifier (e.g. pubmed identifier)
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        union { null , map<string> } externalIdentifiers = null;
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//      pubmed entity type        
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        string entityType;
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//      name of journal in which the article is published

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