/**
* This static method instanciates the fields with the appropriate paths in the different gold and
* extraction formats.
*/
public static void setUpFields(
List<FieldSpecification> headerFields,
List<FieldSpecification> fulltextFields,
List<FieldSpecification> citationsFields,
List<String> headerLabels,
List<String> fulltextLabels,
List<String> citationsLabels) {
// header
// title
FieldSpecification titleField = new FieldSpecification();
titleField.fieldName = "title";
titleField.isTextual = true;
titleField.grobidPath.add("//titleStmt/title/text()");
titleField.nlmPath.add("/article/front/article-meta/title-group/article-title//text()");
titleField.pdfxPath.add("/pdfx/article/front/title-group/article-title/text()");
headerFields.add(titleField);
headerLabels.add("title");
// authors
FieldSpecification authorField = new FieldSpecification();
authorField.fieldName = "authors";
authorField.isTextual = true;
// authorField.hasMultipleValue = true;
/*authorField.grobidPath.
add("//sourceDesc/biblStruct/analytic/author/persName/forename[@type=\"first\"]");
authorField.grobidPath.
add("//sourceDesc/biblStruct/analytic/author/persName/forename[@type=\"middle\"]");*/
authorField.grobidPath.add("//sourceDesc/biblStruct/analytic/author/persName/surname/text()");
// authorField.nlmPath.
// add("/article/front/article-meta/contrib-group/contrib[@contrib-type=\"author\"]/name/given-names");
authorField.nlmPath.add(
"/article/front/article-meta/contrib-group/contrib[@contrib-type=\"author\"]/name/surname/text()");
authorField.pdfxPath.add(
"/pdfx/article/front/contrib-group/contrib[@contrib-type=\"author\"]/name/text()");
headerFields.add(authorField);
headerLabels.add("authors");
// authors
FieldSpecification firstAuthorField = new FieldSpecification();
firstAuthorField.fieldName = "first_author";
firstAuthorField.isTextual = true;
/*firstAuthorField.grobidPath
.add("//sourceDesc/biblStruct/analytic/author/persName/forename[@type=\"first\"]");
firstAuthorField.grobidPath
.add("//sourceDesc/biblStruct/analytic/author/persName/forename[@type=\"middle\"]");*/
firstAuthorField.grobidPath.add(
"//sourceDesc/biblStruct/analytic/author[1]/persName/surname/text()");
// firstAuthorField.nlmPath
// .add("/article/front/article-meta/contrib-group/contrib[@contrib-type=\"author\"]/name/given-names");
firstAuthorField.nlmPath.add(
"/article/front/article-meta/contrib-group/contrib[@contrib-type=\"author\"][1]/name/surname/text()");
firstAuthorField.pdfxPath.add(
"/pdfx/article/front/contrib-group/contrib[@contrib-type=\"author\"][1]/name/text()");
headerFields.add(firstAuthorField);
headerLabels.add("first_author");
// affiliation
FieldSpecification affiliationField = new FieldSpecification();
affiliationField.fieldName = "affiliations";
affiliationField.isTextual = true;
// affiliationField.hasMultipleValue = true;
affiliationField.grobidPath.add(
"//sourceDesc/biblStruct/analytic/author/affiliation/orgName/text()");
affiliationField.nlmPath.add("/article/front/article-meta/contrib-group/aff/text()");
affiliationField.pdfxPath.add("/pdfx/article/front/contrib-group");
// headerFields.add(affiliationField);
// headerLabels.add("affiliations");
// date
FieldSpecification dateField = new FieldSpecification();
dateField.fieldName = "date";
dateField.grobidPath.add("//publicationStmt/date[1]/@when");
dateField.nlmPath.add(
"/article/front/article-meta/pub-date[@pub-type=\"pmc-release\"][1]//text()");
// headerFields.add(dateField);
// headerLabels.add("date");
// abstract
FieldSpecification abstractField = new FieldSpecification();
abstractField.fieldName = "abstract";
abstractField.isTextual = true;
abstractField.grobidPath.add("//profileDesc/abstract//text()");
abstractField.nlmPath.add("/article/front/article-meta/abstract//text()");
headerFields.add(abstractField);
headerLabels.add("abstract");
// keywords
FieldSpecification keywordsField = new FieldSpecification();
keywordsField.fieldName = "keywords";
keywordsField.isTextual = true;
keywordsField.grobidPath.add("//profileDesc/textClass/keywords//text()");
keywordsField.nlmPath.add("/article/front/article-meta/kwd-group/kwd/text()");
headerFields.add(keywordsField);
headerLabels.add("keywords");
// DOI
FieldSpecification doiField = new FieldSpecification();
doiField.fieldName = "doi";
doiField.grobidPath.add("//sourceDesc/biblStruct/idno[@type=\"DOI\"]/text()");
doiField.nlmPath.add("/article/front/article-meta/article-id[@pub-id-type=\"doi\"]/text()");
// headerFields.add(doiField);
// headerLabels.add("doi");
// citations
// the first field gives the base path for each citation structure
FieldSpecification baseCitation = new FieldSpecification();
baseCitation.fieldName = "base";
baseCitation.grobidPath.add("//back/div/listBibl/biblStruct");
baseCitation.nlmPath.add(
"//ref-list/ref"); // note: sometimes we just have the raw citation bellow this!
baseCitation.pdfxPath.add(
"//ref-list/ref"); // note: there is nothing beyond that in pdfx xml results!
citationsFields.add(baseCitation);
// the rest of the citation fields are relative to the base path
// title
FieldSpecification titleField2 = new FieldSpecification();
titleField2.fieldName = "title";
titleField2.isTextual = true;
titleField2.grobidPath.add("analytic/title/text()");
titleField2.nlmPath.add("*/article-title//text()");
citationsFields.add(titleField2);
citationsLabels.add("title");
// authors
FieldSpecification authorField2 = new FieldSpecification();
authorField2.fieldName = "authors";
authorField2.isTextual = true;
authorField2.grobidPath.add("analytic/author/persName/surname/text()");
authorField2.nlmPath.add("*//name/surname/text()");
citationsFields.add(authorField2);
citationsLabels.add("authors");
// authors
FieldSpecification firstAuthorField2 = new FieldSpecification();
firstAuthorField2.fieldName = "first_author";
firstAuthorField2.isTextual = true;
firstAuthorField2.grobidPath.add("analytic/author[1]/persName/surname/text()");
firstAuthorField2.nlmPath.add("*//name[1]/surname/text()");
citationsFields.add(firstAuthorField2);
citationsLabels.add("first_author");
// date
FieldSpecification dateField2 = new FieldSpecification();
dateField2.fieldName = "date";
dateField2.grobidPath.add("monogr/imprint/date/@when");
dateField2.nlmPath.add("*/year/text()");
citationsFields.add(dateField2);
citationsLabels.add("date");
// monograph title
FieldSpecification inTitleField2 = new FieldSpecification();
inTitleField2.fieldName = "inTitle";
inTitleField2.isTextual = true;
inTitleField2.grobidPath.add("monogr/title/text()");
inTitleField2.nlmPath.add("*/source/text()");
citationsFields.add(inTitleField2);
citationsLabels.add("inTitle");
// volume
FieldSpecification volumeField = new FieldSpecification();
volumeField.fieldName = "volume";
volumeField.grobidPath.add("monogr/imprint/biblScope[@unit=\"volume\"]/text()");
volumeField.nlmPath.add("*/volume/text()");
citationsFields.add(volumeField);
citationsLabels.add("volume");
// issue
FieldSpecification issueField = new FieldSpecification();
issueField.fieldName = "issue";
issueField.grobidPath.add("monogr/imprint/biblScope[@unit=\"issue\"]/text()");
issueField.nlmPath.add("*/issue/text()");
citationsFields.add(issueField);
citationsLabels.add("issue");
// first page
FieldSpecification pageField = new FieldSpecification();
pageField.fieldName = "page";
pageField.grobidPath.add("monogr/imprint/biblScope[@unit=\"page\"]/@from");
pageField.nlmPath.add("*/fpage/text()");
citationsFields.add(pageField);
citationsLabels.add("page");
// publisher
FieldSpecification publisherField = new FieldSpecification();
publisherField.fieldName = "publisher";
publisherField.isTextual = true;
publisherField.grobidPath.add("monogr/imprint/publisher/text()");
publisherField.nlmPath.add("*/publisher-name/text()");
// citationsFields.add(publisherField);
// citationsLabels.add("publisher");
// full text structures
/*FieldSpecification sectionReferenceField = new FieldSpecification();
sectionReferenceField.fieldName = "references";
sectionReferenceField.isTextual = true;
sectionReferenceField.grobidPath.
add("//back/div/listBibl/biblStruct//text()");
sectionReferenceField.nlmPath.
add("//ref-list/ref//text()");
fulltextFields.add(sectionReferenceField);
fulltextLabels.add("references");*/
FieldSpecification sectionTitleField = new FieldSpecification();
sectionTitleField.fieldName = "section_title";
sectionTitleField.isTextual = true;
sectionTitleField.grobidPath.add("//text/body/div/head/text()");
sectionTitleField.nlmPath.add("//body//sec/title/text()");
fulltextFields.add(sectionTitleField);
fulltextLabels.add("section_title");
FieldSpecification referenceMarkerField = new FieldSpecification();
referenceMarkerField.fieldName = "reference_citation";
referenceMarkerField.isTextual = true;
referenceMarkerField.grobidPath.add("//ref[@type=\"bibr\"]/text()");
referenceMarkerField.nlmPath.add("//xref[@ref-type=\"bibr\"]/text()");
fulltextFields.add(referenceMarkerField);
fulltextLabels.add("reference_citation");
FieldSpecification referenceFigureField = new FieldSpecification();
referenceFigureField.fieldName = "reference_figure";
referenceFigureField.isTextual = true;
referenceFigureField.grobidPath.add("//ref[@type=\"figure\"]/text()");
referenceFigureField.nlmPath.add("//xref[@ref-type=\"fig\"]/text()");
fulltextFields.add(referenceFigureField);
fulltextLabels.add("reference_figure");
FieldSpecification referenceTableField = new FieldSpecification();
referenceTableField.fieldName = "reference_table";
referenceTableField.isTextual = true;
referenceTableField.grobidPath.add("//ref[@type=\"table\"]/text()");
referenceTableField.nlmPath.add("//xref[@ref-type=\"table\"]/text()");
fulltextFields.add(referenceTableField);
fulltextLabels.add("reference_table");
FieldSpecification figureTitleField = new FieldSpecification();
figureTitleField.fieldName = "figure_title";
figureTitleField.isTextual = true;
figureTitleField.grobidPath.add("//figure[not(@type)]/head/text()");
figureTitleField.nlmPath.add("//fig/label/text()");
fulltextFields.add(figureTitleField);
fulltextLabels.add("figure_title");
FieldSpecification figureCaptionField = new FieldSpecification();
figureCaptionField.fieldName = "figure_caption";
figureCaptionField.isTextual = true;
figureCaptionField.grobidPath.add("//figure[not(@type)]/description/text()");
figureCaptionField.nlmPath.add("//fig/caption/p/text()");
fulltextFields.add(figureCaptionField);
fulltextLabels.add("figure_caption");
FieldSpecification tableTitleField = new FieldSpecification();
tableTitleField.fieldName = "table_title";
tableTitleField.isTextual = true;
tableTitleField.grobidPath.add("//figure[@type=\"table\"]/head/text()");
tableTitleField.nlmPath.add("//table-wrap/label/text()");
fulltextFields.add(tableTitleField);
fulltextLabels.add("table_title");
FieldSpecification tableCaptionField = new FieldSpecification();
tableCaptionField.fieldName = "table_caption";
tableCaptionField.isTextual = true;
tableCaptionField.grobidPath.add("//figure[@type=\"table\"]/description/text()");
tableCaptionField.nlmPath.add("//table-wrap/caption/p/text()");
fulltextFields.add(tableCaptionField);
fulltextLabels.add("figure_caption");
// labels.add("section_title");
// labels.add("paragraph");
// labels.add("citation_marker");
// labels.add("figure_marker");
// labels.add("table_marker");
}
