Examples with MedlineCitation org.jabref.logic.importer.fileformat.medline.MedlineCitation used on opensource projects

Example 1 with MedlineCitation

use of org.jabref.logic.importer.fileformat.medline.MedlineCitation in project jabref by JabRef.

the class MedlineImporter method parseArticle.

private void parseArticle(PubmedArticle article, List<BibEntry> bibItems) {
    Map<String, String> fields = new HashMap<>();
    if (article.getPubmedData() != null) {
        if (article.getMedlineCitation().getDateRevised() != null) {
            DateRevised dateRevised = article.getMedlineCitation().getDateRevised();
            addDateRevised(fields, dateRevised);
            putIfValueNotNull(fields, "pubstatus", article.getPubmedData().getPublicationStatus());
            if (article.getPubmedData().getArticleIdList() != null) {
                ArticleIdList articleIdList = article.getPubmedData().getArticleIdList();
                addArticleIdList(fields, articleIdList);
            }
        }
    }
    if (article.getMedlineCitation() != null) {
        MedlineCitation medlineCitation = article.getMedlineCitation();
        fields.put("status", medlineCitation.getStatus());
        DateCreated dateCreated = medlineCitation.getDateCreated();
        fields.put("created", convertToDateFormat(dateCreated.getYear(), dateCreated.getMonth(), dateCreated.getDay()));
        fields.put("pubmodel", medlineCitation.getArticle().getPubModel());
        if (medlineCitation.getDateCompleted() != null) {
            DateCompleted dateCompleted = medlineCitation.getDateCompleted();
            fields.put("completed", convertToDateFormat(dateCompleted.getYear(), dateCompleted.getMonth(), dateCompleted.getDay()));
        }
        fields.put(FieldName.PMID, medlineCitation.getPMID().getContent());
        fields.put(FieldName.OWNER, medlineCitation.getOwner());
        addArticleInformation(fields, medlineCitation.getArticle().getContent());
        MedlineJournalInfo medlineJournalInfo = medlineCitation.getMedlineJournalInfo();
        putIfValueNotNull(fields, "country", medlineJournalInfo.getCountry());
        putIfValueNotNull(fields, "journal-abbreviation", medlineJournalInfo.getMedlineTA());
        putIfValueNotNull(fields, "nlm-id", medlineJournalInfo.getNlmUniqueID());
        putIfValueNotNull(fields, "issn-linking", medlineJournalInfo.getISSNLinking());
        if (medlineCitation.getChemicalList() != null) {
            if (medlineCitation.getChemicalList().getChemical() != null) {
                addChemicals(fields, medlineCitation.getChemicalList().getChemical());
            }
        }
        if (medlineCitation.getCitationSubset() != null) {
            fields.put("citation-subset", join(medlineCitation.getCitationSubset(), ", "));
        }
        if (medlineCitation.getGeneSymbolList() != null) {
            addGeneSymbols(fields, medlineCitation.getGeneSymbolList());
        }
        if (medlineCitation.getMeshHeadingList() != null) {
            addMeashHeading(fields, medlineCitation.getMeshHeadingList());
        }
        putIfValueNotNull(fields, "references", medlineCitation.getNumberOfReferences());
        if (medlineCitation.getPersonalNameSubjectList() != null) {
            addPersonalNames(fields, medlineCitation.getPersonalNameSubjectList());
        }
        if (medlineCitation.getOtherID() != null) {
            addOtherId(fields, medlineCitation.getOtherID());
        }
        if (medlineCitation.getKeywordList() != null) {
            addKeyWords(fields, medlineCitation.getKeywordList());
        }
        if (medlineCitation.getSpaceFlightMission() != null) {
            fields.put("space-flight-mission", join(medlineCitation.getSpaceFlightMission(), ", "));
        }
        if (medlineCitation.getInvestigatorList() != null) {
            addInvestigators(fields, medlineCitation.getInvestigatorList());
        }
        if (medlineCitation.getGeneralNote() != null) {
            addNotes(fields, medlineCitation.getGeneralNote());
        }
    }
    BibEntry entry = new BibEntry("article");
    entry.setField(fields);
    bibItems.add(entry);
}