JabRef 5.15 · org.jabref.logic.importer.fileformat.MedlineImporter

Modifier and Type	Field and Description
private static final Locale	ENGLISH
private static final String	KEYWORD_SEPARATOR
private static final Logger	LOGGER Hides org.jabref.logic.importer.Importer.LOGGER.
private final XMLInputFactory	xmlInputFactory

Access	Constructor and Description
public	MedlineImporter()

Method Summary

Modifier and Type	Method and Description
private void	addAbstract(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	addArticleIdList(Map<Field, String> fields, List<ArticleId> articleIdList)
private void	addInvestigators(Map<Field, String> fields, List<Investigator> investigatorList)
private void	addKeywords(Map<Field, String> fields, List<String> keywordList)
private void	addMeshHeading(Map<Field, String> fields, List<MeshHeading> meshHeadingList)
private void	addNotes(Map<Field, String> fields, List<String> generalNoteList)
private void	addOtherId(Map<Field, String> fields, List<OtherId> otherIdList)
private void	addPagination(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	addPersonalNames(Map<Field, String> fields, List<PersonalNameSubject> personalNameSubjectList)
private void	addPubDate(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private String	extractYear(String medlineDate)
private String	fixPageRange(String pageRange) Convert medline page ranges from short form to full form.
public String	getDescription() Implements abstract org.jabref.logic.importer.Importer.getDescription. Returns the description of the import format.
public StandardFileType	getFileType() Implements abstract org.jabref.logic.importer.Importer.getFileType. Returns the type of files that this importer can read
public String	getId() Overrides org.jabref.logic.importer.Importer.getId. Returns a one-word ID which identifies this importer.
public String	getName() Implements abstract org.jabref.logic.importer.Importer.getName. Returns the name of this import format.
private void	handleAuthorList(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	handleElocationId(Map<Field, String> fields, XMLStreamReader reader, String eidType)
private void	handleTextElement(XMLStreamReader reader, List<String> textList, String startElement) Handles text entities that can have inner tags such as <i>, <b> etc. We ignore the tags and return only the characters present in the enclosing parent element.
public ParserResult	importDatabase(BufferedReader the input to read from input) Implements abstract org.jabref.logic.importer.Importer.importDatabase. Parse the database in the source.
private boolean	isCharacterXMLEvent(XMLStreamReader reader)
private boolean	isEndXMLEvent(XMLStreamReader reader)
public boolean	isRecognizedFormat(BufferedReader reader) Implements abstract org.jabref.logic.importer.Importer.isRecognizedFormat. Check whether the source is in the correct format for this importer.
private boolean	isStartXMLEvent(XMLStreamReader reader)
private void	parseArticle(XMLStreamReader reader, List<BibEntry> bibItems, String startElement)
private void	parseArticleInformation(XMLStreamReader reader, Map<Field, String> fields)
private void	parseAuthor(XMLStreamReader reader, List<String> authorNames)
private void	parseBookArticle(XMLStreamReader reader, List<BibEntry> bibItems, String startElement)
private void	parseBookDocument(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	parseBookInformation(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	parseChemicalList(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	parseDate(XMLStreamReader reader, Map<Field, String> fields, String startElement)
public List<BibEntry>	parseEntries(InputStream inputStream) Implements org.jabref.logic.importer.Parser.parseEntries.
private void	parseGeneSymbolList(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	parseInvestigator(XMLStreamReader reader, List<Investigator> investigatorList, String startElement)
private void	parseJournal(XMLStreamReader reader, Map<Field, String> fields)
private void	parseMedlineCitation(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	parseMedlineJournalInfo(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	parseMeshHeading(XMLStreamReader reader, List<MeshHeading> meshHeadingList, String startElement)
private void	parsePersonalNameSubject(XMLStreamReader reader, List<PersonalNameSubject> personalNameSubjectList, String startElement)
private void	parsePubmedData(XMLStreamReader reader, Map<Field, String> fields, String startElement)
private void	parseSections(XMLStreamReader reader, List<String> sectionTitleList)
private void	putIfValueNotNull(Map<Field, String> fields, Field field, String value)

Inherited from org.jabref.logic.importer.Importer:: compareTo equals getCharset getReader getReader hashCode importDatabase importDatabase isRecognizedFormat isRecognizedFormat toString

ENGLISH	back to summary
private static final Locale ENGLISH

KEYWORD_SEPARATOR	back to summary
private static final String KEYWORD_SEPARATOR

LOGGER	back to summary
private static final Logger LOGGER Hides org.jabref.logic.importer.Importer.LOGGER.

xmlInputFactory	back to summary
private final XMLInputFactory xmlInputFactory

MedlineImporter	back to summary
public MedlineImporter()

Method Detail

addAbstract	back to summary
private void addAbstract(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

addArticleIdList	back to summary
private void addArticleIdList(Map<Field, String> fields, List<ArticleId> articleIdList)

addInvestigators	back to summary
private void addInvestigators(Map<Field, String> fields, List<Investigator> investigatorList)

addKeywords	back to summary
private void addKeywords(Map<Field, String> fields, List<String> keywordList)

addMeshHeading	back to summary
private void addMeshHeading(Map<Field, String> fields, List<MeshHeading> meshHeadingList)

addNotes	back to summary
private void addNotes(Map<Field, String> fields, List<String> generalNoteList)

addOtherId	back to summary
private void addOtherId(Map<Field, String> fields, List<OtherId> otherIdList)

addPagination	back to summary
private void addPagination(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

addPersonalNames	back to summary
private void addPersonalNames(Map<Field, String> fields, List<PersonalNameSubject> personalNameSubjectList)

addPubDate	back to summary
private void addPubDate(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

extractYear	back to summary
private String extractYear(String medlineDate)

fixPageRange	back to summary
private String fixPageRange(String pageRange) Convert medline page ranges from short form to full form. Medline reports page ranges in a shorthand format. The last page is reported using only the digits which differ from the first page. i.e. 12345-51 refers to the actual range 12345-12351

getDescription back to summary

getDescription	back to summary
public String getDescription() Implements abstract org.jabref.logic.importer.Importer.getDescription. Doc from org.jabref.logic.importer.Importer.getDescription. Returns the description of the import format. The description should specify what kind of entries from what sources and based on what specification it is able to import by what criteria it `recognizes` an import format Returns:String description of the import format Annotations @Override

public String getDescription()

Implements abstract org.jabref.logic.importer.Importer.getDescription.

Doc from org.jabref.logic.importer.Importer.getDescription.

Returns the description of the import format.

The description should specify

what kind of entries from what sources and based on what specification it is able to import
by what criteria it recognizes an import format

Returns:String

description of the import format

Annotations

@Override

getFileType back to summary

getFileType	back to summary
public StandardFileType getFileType() Implements abstract org.jabref.logic.importer.Importer.getFileType. Doc from org.jabref.logic.importer.Importer.getFileType. Returns the type of files that this importer can read Returns:StandardFileType `FileType` corresponding to the importer Annotations @Override

public StandardFileType getFileType()

Implements abstract org.jabref.logic.importer.Importer.getFileType.

Doc from org.jabref.logic.importer.Importer.getFileType.

Returns the type of files that this importer can read

Returns:StandardFileType

FileType corresponding to the importer

Annotations

@Override

getId back to summary

getId	back to summary
public String getId() Overrides org.jabref.logic.importer.Importer.getId. Doc from org.jabref.logic.importer.Importer.getId. Returns a one-word ID which identifies this importer. Used for example, to identify the importer when used from the command line. Returns:String ID, must be unique and not `null` Annotations @Override

public String getId()

Overrides org.jabref.logic.importer.Importer.getId.

Doc from org.jabref.logic.importer.Importer.getId.

Returns a one-word ID which identifies this importer. Used for example, to identify the importer when used from the command line.

Returns:String

ID, must be unique and not null

Annotations

@Override

getName back to summary

getName	back to summary
public String getName() Implements abstract org.jabref.logic.importer.Importer.getName. Doc from org.jabref.logic.importer.Importer.getName. Returns the name of this import format. The name must be unique. Returns:String format name, must be unique and not `null` Annotations @Override

public String getName()

Implements abstract org.jabref.logic.importer.Importer.getName.

Doc from org.jabref.logic.importer.Importer.getName.

Returns the name of this import format.

The name must be unique.

Returns:String

format name, must be unique and not null

Annotations

@Override

handleAuthorList	back to summary
private void handleAuthorList(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

handleElocationId	back to summary
private void handleElocationId(Map<Field, String> fields, XMLStreamReader reader, String eidType)

handleTextElement	back to summary
private void handleTextElement(XMLStreamReader reader, List<String> textList, String startElement) throws XMLStreamException Handles text entities that can have inner tags such as <i>, <b> etc. We ignore the tags and return only the characters present in the enclosing parent element.

importDatabase	back to summary
public ParserResult importDatabase(BufferedReader input) throws IOException Implements abstract org.jabref.logic.importer.Importer.importDatabase. Doc from org.jabref.logic.importer.Importer.importDatabase. Parse the database in the source. This method can be called in two different contexts - either when importing in a specified format, or when importing in unknown format. In the latter case, JabRef cycles through all available import formats. No error messages or feedback is displayed from individual import formats in this case. If importing in a specified format and an empty library is returned, JabRef reports that no entries were found. This method should never return null. Parameters input:BufferedReader the input to read from Annotations @Override

importDatabase

back to summary

public ParserResult importDatabase(BufferedReader input) throws IOException

Implements abstract org.jabref.logic.importer.Importer.importDatabase.

Doc from org.jabref.logic.importer.Importer.importDatabase.

Parse the database in the source.

This method can be called in two different contexts - either when importing in a specified format, or when importing in unknown format. In the latter case, JabRef cycles through all available import formats. No error messages or feedback is displayed from individual import formats in this case.

If importing in a specified format and an empty library is returned, JabRef reports that no entries were found.

This method should never return null.

Parameters

input:BufferedReader: the input to read from

Annotations

@Override

isCharacterXMLEvent	back to summary
private boolean isCharacterXMLEvent(XMLStreamReader reader)

isEndXMLEvent	back to summary
private boolean isEndXMLEvent(XMLStreamReader reader)

isRecognizedFormat	back to summary
public boolean isRecognizedFormat(BufferedReader reader) throws IOException Implements abstract org.jabref.logic.importer.Importer.isRecognizedFormat. Doc from org.jabref.logic.importer.Importer.isRecognizedFormat. Check whether the source is in the correct format for this importer. The effect of this method is primarily to avoid unnecessary processing of files when searching for a suitable import format. If this method returns false, the import routine will move on to the next import format. Thus, the correct behaviour is to return false if it is certain that the file is not of the suitable type, and true otherwise. Returning true is the safe choice if not certain. Annotations @Override

isRecognizedFormat

back to summary

public boolean isRecognizedFormat(BufferedReader reader) throws IOException

Implements abstract org.jabref.logic.importer.Importer.isRecognizedFormat.

Doc from org.jabref.logic.importer.Importer.isRecognizedFormat.

Check whether the source is in the correct format for this importer.

The effect of this method is primarily to avoid unnecessary processing of files when searching for a suitable import format. If this method returns false, the import routine will move on to the next import format.

Thus, the correct behaviour is to return false if it is certain that the file is not of the suitable type, and true otherwise. Returning true is the safe choice if not certain.

Annotations

@Override

isStartXMLEvent	back to summary
private boolean isStartXMLEvent(XMLStreamReader reader)

parseArticle	back to summary
private void parseArticle(XMLStreamReader reader, List<BibEntry> bibItems, String startElement) throws XMLStreamException

parseArticleInformation	back to summary
private void parseArticleInformation(XMLStreamReader reader, Map<Field, String> fields) throws XMLStreamException

parseAuthor	back to summary
private void parseAuthor(XMLStreamReader reader, List<String> authorNames) throws XMLStreamException

parseBookArticle	back to summary
private void parseBookArticle(XMLStreamReader reader, List<BibEntry> bibItems, String startElement) throws XMLStreamException

parseBookDocument	back to summary
private void parseBookDocument(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

parseBookInformation	back to summary
private void parseBookInformation(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

parseChemicalList	back to summary
private void parseChemicalList(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

parseDate	back to summary
private void parseDate(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

parseEntries	back to summary
public List<BibEntry> parseEntries(InputStream inputStream) throws ParseException Implements org.jabref.logic.importer.Parser.parseEntries. Annotations @Override

parseEntries

back to summary

public List<BibEntry> parseEntries(InputStream inputStream) throws ParseException

Implements org.jabref.logic.importer.Parser.parseEntries.

Annotations

@Override

parseGeneSymbolList	back to summary
private void parseGeneSymbolList(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

parseInvestigator	back to summary
private void parseInvestigator(XMLStreamReader reader, List<Investigator> investigatorList, String startElement) throws XMLStreamException

parseJournal	back to summary
private void parseJournal(XMLStreamReader reader, Map<Field, String> fields) throws XMLStreamException

parseMedlineCitation	back to summary
private void parseMedlineCitation(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

parseMedlineJournalInfo	back to summary
private void parseMedlineJournalInfo(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

parseMeshHeading	back to summary
private void parseMeshHeading(XMLStreamReader reader, List<MeshHeading> meshHeadingList, String startElement) throws XMLStreamException

parsePersonalNameSubject	back to summary
private void parsePersonalNameSubject(XMLStreamReader reader, List<PersonalNameSubject> personalNameSubjectList, String startElement) throws XMLStreamException

parsePubmedData	back to summary
private void parsePubmedData(XMLStreamReader reader, Map<Field, String> fields, String startElement) throws XMLStreamException

parseSections	back to summary
private void parseSections(XMLStreamReader reader, List<String> sectionTitleList) throws XMLStreamException

putIfValueNotNull	back to summary
private void putIfValueNotNull(Map<Field, String> fields, Field field, String value)

public Class MedlineImporter

Field Summary

Constructor Summary

Method Summary

Field Detail

Constructor Detail

Method Detail