// $Id$ /* * Copyright 2010 Institute for Systems Biology * Seattle, Washington, USA. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package biotextEngine.xmlparsers.medline; import java.sql.PreparedStatement; import java.sql.SQLException; import java.sql.Types; import org.xml.sax.Attributes; import org.xml.sax.SAXException; import biotextEngine.xmlparsers.GenericXMLParser; import biotextEngine.xmlparsers.NodeHandler; /** * The main driving class of the MedlineCitation. Includes elements and * structures relevant to root element. * * @author Ariel Schwartz * @author Gaurav Bhalotia */ public class MedlineCitation extends NodeHandler { String pmid; private static PreparedStatement pstmt_delete = null; private static boolean isIncremental = true; /* * Default constructor * @param xmlFileName The name of the file that is being parsed, to be * stored in the record for medline_citation */ public MedlineCitation(String xmlFileName) throws Exception { ignoreDuplicateKeyError = true; /* * The table in which the parsed entries are to be entered from this * node */ tableName = "medline_citation"; /* The node name being handled by this class */ xmlNodeName = "MedlineCitation"; /* The various column names in the table */ String[] columnNameDef = { "pmid", "date_created", "date_completed", "date_revised", "pub_model", "issn", "issn_type", "cited_medium", "volume", "issue", "pub_date_year", "pub_date_month", "pub_date_day", "pub_date_season", "medline_date", "journal_title", "iso_abbreviation", "article_title", "medline_pgn", "abstract_text", "copyright_info", "article_affiliation", "article_author_list_comp_yn", "data_bank_list_comp_yn", "grantlist_complete_yn", "vernacular_title", "date_of_electronic_publication", "elec_pub_official_date_yn", "country", "medline_ta", "nlm_unique_id", "issn_linking", "xml_file_name", "number_of_references", "keyword_list_owner", "citation_owner", "citation_status" }; columnName = columnNameDef; /* * The corresponding XML tags, The tags names starts from the current * xmlnode */ String[] xmlElementNameDef = { "MedlineCitation.PMID", "MedlineCitation.DateCreated", "MedlineCitation.DateCompleted", "MedlineCitation.DateRevised", "MedlineCitation.Article.PubModel", "MedlineCitation.Article.Journal.ISSN", "MedlineCitation.Article.Journal.ISSN.IssnType", "MedlineCitation.Article.Journal.JournalIssue.CitedMedium", "MedlineCitation.Article.Journal.JournalIssue.Volume", "MedlineCitation.Article.Journal.JournalIssue.Issue", "MedlineCitation.Article.Journal.JournalIssue.PubDate.Year", "MedlineCitation.Article.Journal.JournalIssue.PubDate.Month", "MedlineCitation.Article.Journal.JournalIssue.PubDate.Day", "MedlineCitation.Article.Journal.JournalIssue.PubDate.Season", "MedlineCitation.Article.Journal.JournalIssue.PubDate.MedlineDate", "MedlineCitation.Article.Journal.Title", "MedlineCitation.Article.Journal.ISOAbbreviation", "MedlineCitation.Article.ArticleTitle", "MedlineCitation.Article.Pagination.MedlinePgn", "MedlineCitation.Article.Abstract.AbstractText", "MedlineCitation.Article.Abstract.CopyrightInformation", "MedlineCitation.Article.Affiliation", "MedlineCitation.Article.AuthorList.CompleteYN", "MedlineCitation.Article.DataBankList.CompleteYN", "MedlineCitation.Article.GrantList.CompleteYN", "MedlineCitation.Article.VernacularTitle", "MedlineCitation.Article.ElectronicPubDate", "MedlineCitation.Article.ElectronicPubDate.OfficialDateYN", "MedlineCitation.MedlineJournalInfo.Country", "MedlineCitation.MedlineJournalInfo.MedlineTA", "MedlineCitation.MedlineJournalInfo.NlmUniqueID", "MedlineCitation.MedlineJournalInfo.ISSNLinking", "XmlFileName", "MedlineCitation.NumberOfReferences", "MedlineCitation.KeywordList.Owner", "MedlineCitation.Owner", "MedlineCitation.Status" }; xmlElementName = xmlElementNameDef; /* The SQL types for the various columns above */ int columnTypeDef[] = { Types.INTEGER, // pmid Types.DATE, // date_created Types.DATE, // date_completed Types.DATE, // date_revised Types.VARCHAR, // pub_model Types.CHAR, // issn Types.VARCHAR, // issn_type Types.VARCHAR, // cited_medium Types.VARCHAR, // volume Types.VARCHAR, // issue Types.VARCHAR, // pub_date_year Types.VARCHAR, // pub_date_month Types.VARCHAR, // pub_date_day Types.VARCHAR, // pub_date_season Types.VARCHAR, // medline_date Types.VARCHAR, // journal_title Types.VARCHAR, // iso_abbreviation Types.VARCHAR, // article_title Types.VARCHAR, // medline_pgn Types.CLOB, // abstract_text Types.VARCHAR, // copyright_info Types.VARCHAR, // article_affiliation Types.CHAR, // article_author_list_comp_yn Types.CHAR, // data_bank_list_comp_yn Types.CHAR, // grantlist_complete_yn Types.VARCHAR, // vernacular_title Types.DATE, // date_of_electronic_publication Types.CHAR, // elec_pub_official_date_yn Types.VARCHAR, // country Types.VARCHAR, // medline_ta Types.VARCHAR, // nlm_unique_id Types.VARCHAR, // issn_linking Types.VARCHAR, // xml_file_name Types.INTEGER, // number_of_references Types.VARCHAR, // keyword_list_owner Types.VARCHAR, // citation_owner Types.VARCHAR // citation_status }; columnType = columnTypeDef; initialize(); /* Add any data that does not come through XML to the hashtable */ putColumnValue("XmlFileName", xmlFileName); } /** * The method to handle the event when a new element is found, this is * overwriting the method defined in the super class NodeHandler.java */ public void startElement(final String namespaceURI, final String localName, final String qName, final Attributes atts) throws SAXException { NodeHandler handler = null; /* * Take decisions based on the element found, if it needs to be handled * by a child handler then instantiate an object for the same and set * the handler else call the handler from the super class */ try { if (currentElement != null) { if (pmid == null) pmid = getColumnValue("MedlineCitation.PMID"); if (currentElement.equals("AuthorList") && qName.equals("Author")) { handler = new Author(pmid); } else if (currentElement.equals("AccessionNumberList") && qName.equals("AccessionNumber")) { String dataBankName = getColumnValue("MedlineCitation.Article.DataBankList.DataBank.DataBankName"); handler = new DataBank(pmid, dataBankName); } else if (currentElement.equals("ChemicalList") && qName.equals("Chemical")) { handler = new Chemical(pmid); } else if (currentElement.equals("GeneSymbolList") && qName.equals("GeneSymbol")) { handler = new GeneSymbol(pmid); } else if (currentElement.equals("KeywordList") && qName.equals("Keyword")) { handler = new Keyword(pmid); } else if (currentElement.equals("PublicationTypeList") && qName.equals("PublicationType")) { handler = new ArticlePublicationType(pmid); } else if (currentElement.equals("GrantList") && qName.equals("Grant")) { handler = new Grant(pmid); } else if (currentElement.equals("MeshHeadingList") && qName.equals("MeshHeading")) { handler = new MeshHeading(pmid); } else if (currentElement.equals("CommentsCorrectionsList") && qName.equals("CommentsCorrections")) { handler = new CommentsCorrections(pmid); } else if (qName.equals("CitationSubset")) { handler = new CitationSubset(pmid); } else if (qName.equals("Language")) { handler = new ArticleLanguage(pmid); } else if (qName.equals("ELocationID")) { handler = new ArticleELocationID(pmid); } else if (currentElement.equals("PersonalNameSubjectList") && qName.equals("PersonalNameSubject")) { handler = new PersonalNameSubject(pmid); } else if (qName.equals("OtherID")) { handler = new OtherID(pmid); } else if (qName.equals("OtherAbstract")) { handler = new OtherAbstract(pmid); } else if (qName.equals("SpaceFlightMission")) { handler = new SpaceFlightMission(pmid); } else if (currentElement.equals("InvestigatorList") && qName.equals("Investigator")) { handler = new Investigator(pmid); } else if (qName.equals("GeneralNote")) { handler = new GeneralNote(pmid); } else { super.startElement(namespaceURI, localName, qName, atts); } // if anybody in the previous if block initialized a handler, // set it if (null != handler) { setContentHandler( handler, namespaceURI, localName, qName, atts); } } else { super.startElement(namespaceURI, localName, qName, atts); } } catch (Exception e) { e.printStackTrace(); throw new SAXException("Problem creating Child. PMID: " + pmid + " for element " + qName); } } /* * Extends the endElement method from the super class NodeHandler checks if * a medline citation has ended, in which case flushes the values found * including all the childhandler to the database */ public void endElement(String namespaceURI, String localName, String qName) throws SAXException { super.endElement(namespaceURI, localName, qName); if (qName.equals(xmlNodeName)) { try { updateDB(); } catch (Exception e) { e.printStackTrace(); throw new SAXException("problem updating the database"); } } } /** * Handles SQLException. Should be overloaded by inheriting classes to * handle special cases * * @returns true if the exception has been handled, false otherwise */ protected boolean handleSQLException(SQLException e) { if (ignoreDuplicateKeyError && e.getErrorCode() == DB2_DUPLICATE_ERROR) { if (isIncremental) { try { if (pstmt_delete == null) { pstmt_delete = GenericXMLParser .getDbConnection() .prepareStatement( "DELETE FROM medline_citation where pmid = ?"); } pstmt_delete.setInt(1, Integer.parseInt(pmid)); pstmt_delete.executeUpdate(); /* * Execute the insert again. Note this could cause problems * in multithreaded implementation */ pstmt.executeUpdate(); return true; } catch (SQLException e1) { /* Doesn't work again so give up and report */ MedlineParser.eCount++; if (MedlineParser.eCount % 500 == 0) { System.out.println("Total " + MedlineParser.eCount + " Values not inserted"); } updateChildren = false; return true; } } else { MedlineParser.eCount++; if (MedlineParser.eCount % 500 == 0) { System.out.println("Total " + MedlineParser.eCount + " Values not inserted"); } updateChildren = false; return true; /* * Don't do anything, the tuple for this primary key has already * been inserted */ } } else { System.err.println("ERROR CODE == " + e.getErrorCode()); return false; } } }