org.grobid.core.engines

Class Engine

java.lang.Object

org.grobid.core.engines.Engine

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class Engine
extends java.lang.Object
implements java.io.Closeable

Class for managing the extraction of bibliographical information from PDF documents or raw text.

Constructor Summary

Constructors

Constructor and Description
Engine(boolean loadModels) Constructor for the Grobid engine instance.

Method Summary

Modifier and Type	Method and Description
void	addAcceptedLanguages(java.lang.String lang) Add a language to the list of accepted languages.
java.lang.String	annotateAllCitationsInPDFPatent(java.lang.String pdfPath, int consolidateCitations, boolean includeRawCitations) Extract and parse both patent and non patent references within a patent in PDF format.
int	batchCreateTraining(java.lang.String directoryPath, java.lang.String resultPath, int ind) Process all the PDF in a given directory with a segmentation process and produce the corresponding training data format files for manual correction.
int	batchCreateTrainingBlank(java.lang.String directoryPath, java.lang.String resultPath, int ind) Process all the PDF in a given directory with a pdf extraction and produce blank training data, i.e.
int	batchCreateTrainingMonograph(java.lang.String directoryPath, java.lang.String resultPath, int ind) Process all the PDF in a given directory with a monograph process and produce the corresponding training data format files for manual correction.
int	batchCreateTrainingPatentcitations(java.lang.String directoryPath, java.lang.String resultPath) Process all the XML patent documents in a given directory with a patent citation extraction and produce the corresponding training data format files for manual correction.
void	close()
void	createTraining(java.io.File inputFile, java.lang.String pathRaw, java.lang.String pathTEI, int id) Create training data for all models based on the application of the current full text model on a new PDF
void	createTrainingBlank(java.io.File inputFile, java.lang.String pathRaw, java.lang.String pathTEI, int id) Generate blank training data from provided directory of PDF documents, i.e.
void	createTrainingMonograph(java.io.File inputFile, java.lang.String pathRaw, java.lang.String pathTEI, int id) Create training data for the monograph model based on the application of the current monograph text model on a new PDF
void	createTrainingPatentCitations(java.lang.String pathXML, java.lang.String resultPath) Process an XML patent document with a patent citation extraction and produce the corresponding training data format files for manual correction.
java.lang.String	downloadPDF(java.lang.String url, java.lang.String dirName, java.lang.String name) Download a PDF file.
java.util.List<ChemicalEntity>	extractChemicalEntities(java.lang.String text) Extract chemical names from text.
java.lang.String	fullTextToTEI(java.io.File inputFile, GrobidAnalysisConfig config) //TODO: remove invalid JavaDoc once refactoring is done and tested (left for easier reference) Parse and convert the current article into TEI, this method performs the whole parsing and conversion process.
Document	fullTextToTEIDoc(DocumentSource documentSource, GrobidAnalysisConfig config)
Document	fullTextToTEIDoc(java.io.File inputFile, GrobidAnalysisConfig config)
java.lang.String	getAbstract(Document doc) Print the abstract content.
java.util.List<java.lang.String>	getAcceptedLanguages() Give the list of languages for which an extraction is allowed.
static CntManager	getCntManager()
static Engine	getEngine(boolean preload)
EngineParsers	getParsers()
static java.lang.String	header2BibTeX(BiblioItem resHeader) Get the BibTeX string corresponding to the recognized header text
static java.lang.String	header2TEI(BiblioItem resHeader) Get the TEI XML string corresponding to the recognized header text
java.lang.String	printRefTitles(java.util.List<BibDataSet> resBib) Return all the reference titles.
java.util.List<Affiliation>	processAffiliation(java.lang.String addressBlock) Parse a text block corresponding to an affiliation+address.
java.util.List<java.util.List<Affiliation>>	processAffiliations(java.util.List<java.lang.String> addressBlocks) Parse a list of text blocks corresponding to an affiliation+address.
java.lang.String	processAllCitationsInPatent(java.lang.String text, java.util.List<BibDataSet> nplResults, java.util.List<PatentItem> patentResults, int consolidateCitations, boolean includeRawCitations) Extract and parse both patent and non patent references within a patent text.
java.lang.String	processAllCitationsInPDFPatent(java.lang.String pdfPath, java.util.List<BibDataSet> nplResults, java.util.List<PatentItem> patentResults, int consolidateCitations, boolean includeRawCitations) Extract and parse both patent and non patent references within a patent in PDF format.
java.lang.String	processAllCitationsInXMLPatent(java.lang.String xmlPath, java.util.List<BibDataSet> nplResults, java.util.List<PatentItem> patentResults, int consolidateCitations, boolean includeRawCitations) Extract and parse both patent and non patent references within a patent in ST.36 format.
java.util.List<Person>	processAuthorsCitation(java.lang.String authorSequence) Parse a sequence of authors from a citation, i.e.
java.util.List<java.util.List<Person>>	processAuthorsCitationLists(java.util.List<java.lang.String> authorSequences) Parse a list of independent sequences of authors from citations.
java.util.List<Person>	processAuthorsHeader(java.lang.String authorSequence) Parse a sequence of authors from a header, i.e.
java.util.List<Date>	processDate(java.lang.String dateBlock) Parse a raw string containing dates.
java.lang.String	processHeader(java.lang.String inputFile, GrobidAnalysisConfig config, BiblioItem result)
java.lang.String	processHeader(java.lang.String inputFile, int consolidate, BiblioItem result) Apply a parsing model for the header of a PDF file based on CRF, using dynamic range of pages as header
java.lang.String	processHeader(java.lang.String inputFile, int consolidate, boolean includeRawAffiliations, BiblioItem result) Apply a parsing model for the header of a PDF file based on CRF, using first three pages of the PDF
BiblioItem	processRawReference(java.lang.String reference, int consolidate) Apply a parsing model for a given single raw reference string based on CRF
java.util.List<BiblioItem>	processRawReferences(java.util.List<java.lang.String> references, int consolidate) Apply a parsing model for a set of raw reference text based on CRF
java.util.List<BibDataSet>	processReferences(java.io.File inputFile, int consolidate) Apply a parsing model to the reference block of a PDF file based on CRF
static java.lang.String	reference2BibTeX(java.lang.String path, java.util.List<BibDataSet> resBib, int i) Get the BibTeX string corresponding to the recognized citation section for a given citation
static java.lang.String	reference2TEI(java.lang.String path, java.util.List<BibDataSet> resBib, int i) Get the TEI XML string corresponding to the recognized citation section for a particular citation
java.lang.String	references2BibTeX(java.lang.String path, java.util.List<BibDataSet> resBib) Get the BibTeX string corresponding to the recognized citation section
static java.lang.String	references2TEI(java.lang.String path, java.util.List<BibDataSet> resBib) Get the TEI XML string corresponding to the recognized citation section, with pointers and advanced structuring
static java.lang.String	references2TEI2(java.lang.String path, java.util.List<BibDataSet> resBib) Get the TEI XML string corresponding to the recognized citation section
Language	runLanguageId(java.lang.String filePath) Basic run for language identification, default is on the body of the current document.
Language	runLanguageId(java.lang.String filePath, java.lang.String ext) Perform a language identification
java.lang.String	segmentAndProcessHeader(java.io.File inputFile, int consolidate, BiblioItem result) Use the segmentation model to identify the header section of a PDF file, then apply a parsing model for the header based on CRF
static void	setCntManager(CntManager cntManager)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Engine

public Engine(boolean loadModels)

Constructor for the Grobid engine instance.

Method Detail

processAuthorsHeader

public java.util.List<Person> processAuthorsHeader(java.lang.String authorSequence)
                                            throws java.lang.Exception

Parse a sequence of authors from a header, i.e. containing possibly reference markers.

Parameters:

authorSequence - - the string corresponding to a raw sequence of names

Returns:

the list of structured author object

Throws:

java.lang.Exception

processAuthorsCitation

public java.util.List<Person> processAuthorsCitation(java.lang.String authorSequence)
                                              throws java.lang.Exception

Parse a sequence of authors from a citation, i.e. containing no reference markers.

Parameters:

authorSequence - - the string corresponding to a raw sequence of names

Returns:

the list of structured author object

Throws:

java.lang.Exception

processAuthorsCitationLists

public java.util.List<java.util.List<Person>> processAuthorsCitationLists(java.util.List<java.lang.String> authorSequences)
                                                                   throws java.lang.Exception

Parse a list of independent sequences of authors from citations.

Parameters:

authorSequences - - the list of strings corresponding each to a raw sequence of names.

Returns:

the list of all recognized structured author objects for each sequence of authors.

Throws:

java.lang.Exception

processAffiliation

public java.util.List<Affiliation> processAffiliation(java.lang.String addressBlock)
                                               throws java.io.IOException

Parse a text block corresponding to an affiliation+address.

Parameters:

addressBlock - - the string corresponding to a raw affiliation+address

Returns:

the list of all recognized structured affiliation objects.

Throws:

java.io.IOException

processAffiliations

public java.util.List<java.util.List<Affiliation>> processAffiliations(java.util.List<java.lang.String> addressBlocks)
                                                                throws java.lang.Exception

Parse a list of text blocks corresponding to an affiliation+address.

Parameters:

addressBlocks - - the list of strings corresponding each to a raw affiliation+address.

Returns:

the list of all recognized structured affiliation objects for each sequence of affiliation + address block.

Throws:

java.lang.Exception

processDate

public java.util.List<Date> processDate(java.lang.String dateBlock)
                                 throws java.io.IOException

Parse a raw string containing dates.

Parameters:

dateBlock - - the string containing raw dates.

Returns:

the list of all structured date objects recognized in the string.

Throws:

java.io.IOException

processRawReference

public BiblioItem processRawReference(java.lang.String reference,
                                      int consolidate)

Apply a parsing model for a given single raw reference string based on CRF

Parameters:

reference - the reference string to be processed

consolidate - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

Returns:

the recognized bibliographical object

processRawReferences

public java.util.List<BiblioItem> processRawReferences(java.util.List<java.lang.String> references,
                                                       int consolidate)
                                                throws java.lang.Exception

Apply a parsing model for a set of raw reference text based on CRF

Parameters:

references - the list of raw reference strings to be processed

consolidate - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

Returns:

the list of recognized bibliographical objects

Throws:

java.lang.Exception

processReferences

public java.util.List<BibDataSet> processReferences(java.io.File inputFile,
                                                    int consolidate)

Apply a parsing model to the reference block of a PDF file based on CRF

Parameters:

inputFile - the path of the PDF file to be processed

consolidate - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

Returns:

the list of parsed references as bibliographical objects enriched with citation contexts

downloadPDF

public java.lang.String downloadPDF(java.lang.String url,
                                    java.lang.String dirName,
                                    java.lang.String name)

Download a PDF file.

Parameters:

url - URL of the PDF to download

dirName - directory where to store the downloaded PDF

name - file name

getAcceptedLanguages

public java.util.List<java.lang.String> getAcceptedLanguages()

Give the list of languages for which an extraction is allowed. If null, any languages will be processed

Returns:

the list of languages to be processed coded in ISO 3166.

addAcceptedLanguages

public void addAcceptedLanguages(java.lang.String lang)

Add a language to the list of accepted languages.

Parameters:

lang - the language in ISO 3166 to be added

runLanguageId

public Language runLanguageId(java.lang.String filePath,
                              java.lang.String ext)

Perform a language identification

Parameters:

ext - part

Returns:

language

runLanguageId

public Language runLanguageId(java.lang.String filePath)

Basic run for language identification, default is on the body of the current document.

Returns:

language id

processHeader

public java.lang.String processHeader(java.lang.String inputFile,
                                      int consolidate,
                                      boolean includeRawAffiliations,
                                      BiblioItem result)

Apply a parsing model for the header of a PDF file based on CRF, using first three pages of the PDF

Parameters:

inputFile - the path of the PDF file to be processed

consolidate - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

result - bib result

Returns:

the TEI representation of the extracted bibliographical information

processHeader

public java.lang.String processHeader(java.lang.String inputFile,
                                      int consolidate,
                                      BiblioItem result)

Apply a parsing model for the header of a PDF file based on CRF, using dynamic range of pages as header

Parameters:

inputFile - : the path of the PDF file to be processed

result - bib result

Returns:

the TEI representation of the extracted bibliographical information

processHeader

public java.lang.String processHeader(java.lang.String inputFile,
                                      GrobidAnalysisConfig config,
                                      BiblioItem result)

segmentAndProcessHeader

public java.lang.String segmentAndProcessHeader(java.io.File inputFile,
                                                int consolidate,
                                                BiblioItem result)

Use the segmentation model to identify the header section of a PDF file, then apply a parsing model for the header based on CRF

Parameters:

inputFile - the path of the PDF file to be processed

consolidate - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

result - bib result

Returns:

the TEI representation of the extracted bibliographical information

createTrainingMonograph

public void createTrainingMonograph(java.io.File inputFile,
                                    java.lang.String pathRaw,
                                    java.lang.String pathTEI,
                                    int id)

Create training data for the monograph model based on the application of the current monograph text model on a new PDF

Parameters:

inputFile - : the path of the PDF file to be processed

pathRaw - : the path where to put the CRF feature file

pathTEI - : the path where to put the annotated TEI representation (the file to be corrected for gold-level training data)

id - : an optional ID to be used in the TEI file and the full text file, -1 if not used

createTrainingBlank

public void createTrainingBlank(java.io.File inputFile,
                                java.lang.String pathRaw,
                                java.lang.String pathTEI,
                                int id)

Generate blank training data from provided directory of PDF documents, i.e. where TEI files are text only without tags. This can be used to start from scratch any new model.

Parameters:

inputFile - : the path of the PDF file to be processed

pathRaw - : the path where to put the CRF feature file

pathTEI - : the path where to put the annotated TEI representation (the file to be annotated for "from scratch" training data)

id - : an optional ID to be used in the TEI file and the full text file, -1 if not used

createTraining

public void createTraining(java.io.File inputFile,
                           java.lang.String pathRaw,
                           java.lang.String pathTEI,
                           int id)

Create training data for all models based on the application of the current full text model on a new PDF

Parameters:

inputFile - : the path of the PDF file to be processed

pathRaw - : the path where to put the CRF feature file

pathTEI - : the path where to put the annotated TEI representation (the file to be corrected for gold-level training data)

id - : an optional ID to be used in the TEI file, -1 if not used

fullTextToTEI

public java.lang.String fullTextToTEI(java.io.File inputFile,
                                      GrobidAnalysisConfig config)
                               throws java.lang.Exception

//TODO: remove invalid JavaDoc once refactoring is done and tested (left for easier reference) Parse and convert the current article into TEI, this method performs the whole parsing and conversion process. If onlyHeader is true, than only the tei header data will be created.

Parameters:

inputFile - - absolute path to the pdf to be processed

config - - Grobid config

Returns:

the resulting structured document as a TEI string.

Throws:

java.lang.Exception

fullTextToTEIDoc

public Document fullTextToTEIDoc(java.io.File inputFile,
                                 GrobidAnalysisConfig config)
                          throws java.lang.Exception

Throws:

java.lang.Exception

fullTextToTEIDoc

public Document fullTextToTEIDoc(DocumentSource documentSource,
                                 GrobidAnalysisConfig config)
                          throws java.lang.Exception

Throws:

java.lang.Exception

batchCreateTraining

public int batchCreateTraining(java.lang.String directoryPath,
                               java.lang.String resultPath,
                               int ind)

Process all the PDF in a given directory with a segmentation process and produce the corresponding training data format files for manual correction. The goal of this method is to help to produce additional traning data based on an existing model.

Parameters:

directoryPath - - the path to the directory containing PDF to be processed.

resultPath - - the path to the directory where the results as XML files shall be written.

ind - - identifier integer to be included in the resulting files to identify the training case. This is optional: no identifier will be included if ind = -1

Returns:

the number of processed files.

batchCreateTrainingMonograph

public int batchCreateTrainingMonograph(java.lang.String directoryPath,
                                        java.lang.String resultPath,
                                        int ind)

Process all the PDF in a given directory with a monograph process and produce the corresponding training data format files for manual correction. The goal of this method is to help to produce additional traning data based on an existing model.

Parameters:

directoryPath - - the path to the directory containing PDF to be processed.

resultPath - - the path to the directory where the results as XML files and CRF feature files shall be written.

ind - - identifier integer to be included in the resulting files to identify the training case. This is optional: no identifier will be included if ind = -1

Returns:

the number of processed files.

batchCreateTrainingBlank

public int batchCreateTrainingBlank(java.lang.String directoryPath,
                                    java.lang.String resultPath,
                                    int ind)

Process all the PDF in a given directory with a pdf extraction and produce blank training data, i.e. TEI files with text only without tags. This can be used to start from scratch any new model.

Parameters:

directoryPath - - the path to the directory containing PDF to be processed.

resultPath - - the path to the directory where the results as XML files and default CRF feature files shall be written.

ind - - identifier integer to be included in the resulting files to identify the training case. This is optional: no identifier will be included if ind = -1

Returns:

the number of processed files.

header2TEI

public static java.lang.String header2TEI(BiblioItem resHeader)

Get the TEI XML string corresponding to the recognized header text

header2BibTeX

public static java.lang.String header2BibTeX(BiblioItem resHeader)

Get the BibTeX string corresponding to the recognized header text

references2TEI2

public static java.lang.String references2TEI2(java.lang.String path,
                                               java.util.List<BibDataSet> resBib)

Get the TEI XML string corresponding to the recognized citation section

references2TEI

public static java.lang.String references2TEI(java.lang.String path,
                                              java.util.List<BibDataSet> resBib)

Get the TEI XML string corresponding to the recognized citation section, with pointers and advanced structuring

references2BibTeX

public java.lang.String references2BibTeX(java.lang.String path,
                                          java.util.List<BibDataSet> resBib)

Get the BibTeX string corresponding to the recognized citation section

reference2TEI

public static java.lang.String reference2TEI(java.lang.String path,
                                             java.util.List<BibDataSet> resBib,
                                             int i)

Get the TEI XML string corresponding to the recognized citation section for a particular citation

reference2BibTeX

public static java.lang.String reference2BibTeX(java.lang.String path,
                                                java.util.List<BibDataSet> resBib,
                                                int i)

Get the BibTeX string corresponding to the recognized citation section for a given citation

processAllCitationsInPatent

public java.lang.String processAllCitationsInPatent(java.lang.String text,
                                                    java.util.List<BibDataSet> nplResults,
                                                    java.util.List<PatentItem> patentResults,
                                                    int consolidateCitations,
                                                    boolean includeRawCitations)
                                             throws java.lang.Exception

Extract and parse both patent and non patent references within a patent text. Result are provided as a BibDataSet with offset position instanciated relative to input text and as PatentItem containing both "WISIWIG" results (the patent reference attributes as they appear in the text) and the attributes in DOCDB format (format according to WIPO and ISO standards). Patent references' offset positions are also given in the PatentItem object.

Parameters:

text - the string corresponding to the text body of the patent.

nplResults - the list of extracted and parsed non patent references as BiblioItem object. This list must be instantiated before calling the method for receiving the results.

patentResults - the list of extracted and parsed patent references as PatentItem object. This list must be instantiated before calling the method for receiving the results.

consolidateCitations - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

Returns:

the list of extracted and parserd patent and non-patent references encoded in TEI.

Throws:

java.lang.Exception

processAllCitationsInXMLPatent

public java.lang.String processAllCitationsInXMLPatent(java.lang.String xmlPath,
                                                       java.util.List<BibDataSet> nplResults,
                                                       java.util.List<PatentItem> patentResults,
                                                       int consolidateCitations,
                                                       boolean includeRawCitations)
                                                throws java.lang.Exception

Extract and parse both patent and non patent references within a patent in ST.36 format. Result are provided as a BibDataSet with offset position instantiated relative to input text and as PatentItem containing both "WISIWIG" results (the patent reference attributes as they appear in the text) and the attributes in DOCDB format (format according to WIPO and ISO standards). Patent references' offset positions are also given in the PatentItem object.

Parameters:

nplResults - the list of extracted and parsed non patent references as BiblioItem object. This list must be instanciated before calling the method for receiving the results.

patentResults - the list of extracted and parsed patent references as PatentItem object. This list must be instanciated before calling the method for receiving the results.

consolidateCitations - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

Returns:

the list of extracted and parserd patent and non-patent references encoded in TEI.

Throws:

java.lang.Exception - if sth. went wrong

processAllCitationsInPDFPatent

public java.lang.String processAllCitationsInPDFPatent(java.lang.String pdfPath,
                                                       java.util.List<BibDataSet> nplResults,
                                                       java.util.List<PatentItem> patentResults,
                                                       int consolidateCitations,
                                                       boolean includeRawCitations)
                                                throws java.lang.Exception

Extract and parse both patent and non patent references within a patent in PDF format. Result are provided as a BibDataSet with offset position instanciated relative to input text and as PatentItem containing both "WISIWIG" results (the patent reference attributes as they appear in the text) and the attributes in DOCDB format (format according to WIPO and ISO standards). Patent references' offset positions are also given in the PatentItem object.

Parameters:

pdfPath - pdf path

nplResults - the list of extracted and parsed non patent references as BiblioItem object. This list must be instanciated before calling the method for receiving the results.

patentResults - the list of extracted and parsed patent references as PatentItem object. This list must be instanciated before calling the method for receiving the results.

consolidateCitations - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

Returns:

the list of extracted and parserd patent and non-patent references encoded in TEI.

Throws:

java.lang.Exception - if sth. went wrong

annotateAllCitationsInPDFPatent

public java.lang.String annotateAllCitationsInPDFPatent(java.lang.String pdfPath,
                                                        int consolidateCitations,
                                                        boolean includeRawCitations)
                                                 throws java.lang.Exception

Extract and parse both patent and non patent references within a patent in PDF format. Results are provided as JSON annotations with coordinates of the annotations in the orignal PDF and reference informations in DOCDB format (format according to WIPO and ISO standards).

Parameters:

pdfPath - pdf path

consolidateCitations - the consolidation option allows GROBID to exploit Crossref web services for improving header information. 0 (no consolidation, default value), 1 (consolidate the citation and inject extra metadata) or 2 (consolidate the citation and inject DOI only)

Returns:

JSON annotations with extracted and parsed patent and non-patent references together with coordinates in the original PDF.

Throws:

java.lang.Exception

createTrainingPatentCitations

public void createTrainingPatentCitations(java.lang.String pathXML,
                                          java.lang.String resultPath)
                                   throws java.lang.Exception

Process an XML patent document with a patent citation extraction and produce the corresponding training data format files for manual correction. The goal of this method is to help to produce additional traning data based on an existing model.

Parameters:

pathXML - - the path to the XML patent document to be processed.

resultPath - - the path to the directory where the results as XML files shall be written.

Throws:

java.lang.Exception

batchCreateTrainingPatentcitations

public int batchCreateTrainingPatentcitations(java.lang.String directoryPath,
                                              java.lang.String resultPath)
                                       throws java.lang.Exception

Process all the XML patent documents in a given directory with a patent citation extraction and produce the corresponding training data format files for manual correction. The goal of this method is to help to produce additional traning data based on an existing model.

Parameters:

directoryPath - - the path to the directory containing XML files to be processed.

resultPath - - the path to the directory where the results as XML files shall be written.

Returns:

the number of processed files.

Throws:

java.lang.Exception

extractChemicalEntities

public java.util.List<ChemicalEntity> extractChemicalEntities(java.lang.String text)
                                                       throws java.lang.Exception

Extract chemical names from text.

Parameters:

text - - text to be processed.

Returns:

List of chemical entites as POJO.

Throws:

java.lang.Exception

getAbstract

public java.lang.String getAbstract(Document doc)
                             throws java.lang.Exception

Print the abstract content. Useful for term extraction.

Throws:

java.lang.Exception

printRefTitles

public java.lang.String printRefTitles(java.util.List<BibDataSet> resBib)
                                throws java.lang.Exception

Return all the reference titles. Maybe useful for term extraction.

Throws:

java.lang.Exception

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException

setCntManager

public static void setCntManager(CntManager cntManager)

getCntManager

public static CntManager getCntManager()

getParsers

public EngineParsers getParsers()

getEngine

public static Engine getEngine(boolean preload)

Returns:

a new engine from GrobidFactory if the execution is parallel, else return the instance of engine.