textractor.parsers
Class PubmedExtractor

java.lang.Object
  it.unimi.dsi.mg4j.util.parser.callback.DefaultCallback
      textractor.parsers.PubmedExtractor

All Implemented Interfaces:

Callback

Direct Known Subclasses:

ParsePubmedFast, PubmedLoadExtractor

public abstract class PubmedExtractor
extends DefaultCallback

Pumbed / medline XML parser.

Field Summary

static MutableString

EMPTY_MUTABLE_STRING An empty mutable string.

Fields inherited from interface it.unimi.dsi.mg4j.util.parser.callback.Callback

EMPTY_CALLBACK_ARRAY

Constructor Summary

protected

PubmedExtractor() Create the parser.

Method Summary

boolean	characters(char[] characters, int offset, int length, boolean flowBroken) Received XML characters.
void	configure(it.unimi.dsi.mg4j.util.parser.BulletParser parserVal) Configure the parser to parse text.
void	endDocument() End of document.
boolean	endElement(it.unimi.dsi.mg4j.util.parser.Element elementOrig) We have found an XML end-element tag.
abstract boolean	processAbstractText(MutableString pmidVal, MutableString titleVal, MutableString textVal, Map<String,Object> additionalFieldsMap) Process the text of this document.
abstract void	processNoticeOfRetraction(MutableString pmidVal, List<String> retractedPmidsVal, boolean createArticleVal) Process retraction notices.
void	setArticleElementName(String dummy) Deprecated.
void	startDocument() Start of document.
boolean	startElement(it.unimi.dsi.mg4j.util.parser.Element elementOrig, Map attrMap) We have found an XML end-element tag.
it.unimi.dsi.mg4j.util.parser.Element	translateElement(it.unimi.dsi.mg4j.util.parser.Element elementOrig) If the element is in elementIgnoreSet this will return null.

Methods inherited from class it.unimi.dsi.mg4j.util.parser.callback.DefaultCallback

cdata, getInstance

Methods inherited from class java.lang.Object

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

Field Detail

EMPTY_MUTABLE_STRING

public static final MutableString EMPTY_MUTABLE_STRING

An empty mutable string.

Constructor Detail

PubmedExtractor

protected PubmedExtractor()

Create the parser. Make sure we have an empty value for all known fields within singleArticleFieldsMap.

Method Detail

setArticleElementName

@Deprecated
public void setArticleElementName(String dummy)

Deprecated.

No longer supported. If you find a use for this, please modify the class to support it, but I couldn't tell that it was necessary any longer, so I modified this class to be more readable but that precludes the use of this property.

Parameters:

dummy - ignored value

configure

public final void configure(it.unimi.dsi.mg4j.util.parser.BulletParser parserVal)

Configure the parser to parse text.

Specified by:

configure in interface Callback

Overrides:

configure in class DefaultCallback

Parameters:

parserVal - parser to use

startDocument

public final void startDocument()

Start of document.

Specified by:

startDocument in interface Callback

Overrides:

startDocument in class DefaultCallback

endDocument

public void endDocument()

End of document.

Specified by:

endDocument in interface Callback

Overrides:

endDocument in class DefaultCallback

characters

public final boolean characters(char[] characters,
                                int offset,
                                int length,
                                boolean flowBroken)

Received XML characters. If they are for an element we are interested in, save them to the singleArticleFieldsMap for saving later.

Specified by:

characters in interface Callback

Overrides:

characters in class DefaultCallback

Parameters:

characters - the characters

offset - the offset of the characters we are interested in

length - the length of the characters we are interested in

flowBroken - true of flow is broken

Returns:

true

startElement

public final boolean startElement(it.unimi.dsi.mg4j.util.parser.Element elementOrig,
                                  Map attrMap)

We have found an XML end-element tag.

Specified by:

startElement in interface Callback

Overrides:

startElement in class DefaultCallback

Parameters:

elementOrig - the current element

attrMap - attributes map for this element

Returns:

true

endElement

public final boolean endElement(it.unimi.dsi.mg4j.util.parser.Element elementOrig)

We have found an XML end-element tag.

Specified by:

endElement in interface Callback

Overrides:

endElement in class DefaultCallback

Parameters:

elementOrig - the current element

Returns:

true

translateElement

public it.unimi.dsi.mg4j.util.parser.Element translateElement(it.unimi.dsi.mg4j.util.parser.Element elementOrig)

If the element is in elementIgnoreSet this will return null. If the element is in the elementTranslationsMap map, this will return the associated element. Otherwise this will return elementOrig.

Parameters:

elementOrig - the element to translate

Returns:

the translated element as described above

processAbstractText

public abstract boolean processAbstractText(MutableString pmidVal,
                                            MutableString titleVal,
                                            MutableString textVal,
                                            Map<String,Object> additionalFieldsMap)
                                     throws IOException,
                                            SentenceProcessingException

Process the text of this document.

Parameters:

pmidVal - the pmid of the document

titleVal - the title of the document

textVal - the text of the document

additionalFieldsMap - additional fields to index

Returns:

True if an article was created for this PMID.

Throws:

IOException - error processing sentence

SentenceProcessingException - error processing sentence

processNoticeOfRetraction

public abstract void processNoticeOfRetraction(MutableString pmidVal,
                                               List<String> retractedPmidsVal,
                                               boolean createArticleVal)

Process retraction notices.

Parameters:

pmidVal - the pmid of the retraction

retractedPmidsVal - the retracted pmids

createArticleVal - True if this method may create an article to represent the retraction notice