Java tutorial
/* * EuroCarbDB, a framework for carbohydrate bioinformatics * * Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as * indicated by the @author tags or express copyright attribution * statements applied by the authors. * * This copyrighted material is made available to anyone wishing to use, modify, * copy, or redistribute it subject to the terms and conditions of the GNU * Lesser General Public License, as published by the Free Software Foundation. * A copy of this license accompanies this distribution in the file LICENSE.txt. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License * for more details. * * Last commit: $Rev: 1549 $ by $Author: glycoslave $ on $Date:: 2009-07-19 #$ */ package org.eurocarbdb.action.hplc; import java.util.*; import java.lang.*; import org.apache.log4j.Logger; import org.apache.commons.io.FileUtils; import org.eurocarbdb.action.*; import org.eurocarbdb.action.*; import org.eurocarbdb.dataaccess.*; import org.eurocarbdb.dataaccess.hplc.*; import org.eurocarbdb.dataaccess.core.*; import org.eurocarbdb.dataaccess.core.ref.*; import org.eurocarbdb.dataaccess.hibernate.*; import static org.eurocarbdb.dataaccess.Eurocarb.getEntityManager; import org.eurocarbdb.dataaccess.EntityManager; import org.hibernate.*; import org.hibernate.cfg.*; import com.opensymphony.xwork.Action; import com.opensymphony.xwork.Preparable; //script to add glycan structures references public class refUpload extends EurocarbAction implements RequiresLogin { EntityManager em = Eurocarb.getEntityManager(); private JournalReference journalReference = null; private List<Reference> references = null; private Reference reference = null; Reference tosave = null; protected static final Logger logger = Logger.getLogger(refUpload.class.getName()); public String execute() throws Exception { /*List<RefLink> refList; refList = em.getQuery("org.eurocarbdb.dataaccess.hplc.RefLink.SELECT_GROUP_ID").list(); //int value = em.getQuery("org.eurocarbdb.dataaccess.hplc.RefLink.SELECT_GROUP_ID").list(); //for (RefLink reference : refList) { for (Iterator iterRef = refList.iterator(); iterRef.hasNext();) { Object [] refObject = (Object []) iterRef.next(); Integer refGlycanId = (Integer) refObject[0]; //int glycanLookup = refs.getGlycanId(); logger.info("processing glycan:" + refGlycanId); */ int refGlycanIdtest = 1211; List<Ref> refInfo = em.getQuery("org.eurocarbdb.dataaccess.hplc.Ref.SELECT_REFERENCES_CORE").list(); for (Iterator iterRefDetails = refInfo.iterator(); iterRefDetails.hasNext();) { Object[] detailsObject = (Object[]) iterRefDetails.next(); String author = (String) detailsObject[0]; String title = (String) detailsObject[1]; String journal_name = (String) detailsObject[2]; //String volume = (String) detailsObject[3]; Integer vol = (Integer) detailsObject[3]; Short year = (Short) detailsObject[4]; Integer pubmed_id = (Integer) detailsObject[5]; Integer startPage = (Integer) detailsObject[6]; Integer endPage = (Integer) detailsObject[7]; logger.info("error check" + vol + "title" + title + "author" + author); //need to convert volume to int //int vol = Integer.parseInt(volume); //need to convert year int pubyear = year.intValue(); String pubmedId = pubmed_id.toString(); String type = "journal"; String comments = "Generated from GlycoBase entry"; String refName = "glycobase(dublin)"; JournalReference jr = new JournalReference(); /* Reference newr = new Reference(); newr.setReferenceType(type); newr.setExternalReferenceName(refName); newr.setExternalReferenceId(pubmedId); newr.storeOrLookup(); */ logger.info("Pubmed Id" + pubmed_id); jr.setJournal(Journal.createOrLookup(journal_name)); jr.setPubmedId(pubmed_id); jr.setAuthors(author); jr.setTitle(title); jr.setPublicationYear(pubyear); jr.setJournalVolume(vol); jr.setFirstPage(startPage); jr.setLastPage(endPage); jr.setContributor(Contributor.getCurrentContributor()); jr.setReferenceComments(comments); //jr.setReferenceType(type); jr.setExternalReferenceName(refName); //jr.setExternalReferenceId(pubmedId); //Eurocarb.getEntityManager().store(jr); jr.storeOrLookup(); } logger.info("successfully added all glycobase references. Now time for Seq-Ref associations"); //now need to associated each hplc strcture with a reference in the core schema /* List<Glycan> allGlycans = em.getQuery("org.eurocarbdb.dataaccess.hplc.Glycan.SELECT_ALL").list(); for (Iterator glycans = allGlycans.iterator(); glycans.hasNext();) { Object [] glycanStore = (Object []) glycans.next(); Integer glycanId = (Integer) glycanStore[0]; */ //test // logger.info("testingareahere"); logger.info("starting test from here"); int glycanId = 159; logger.info("looking up" + glycanId); List<RefLink> allReferences = em.getQuery("org.eurocarbdb.dataaccess.hplc.RefLink.IMPORT_REFERENCE_GWS") .setParameter("glycanId", glycanId).list(); for (Iterator glycanRef = allReferences.iterator(); glycanRef.hasNext();) { Object[] referenceStore = (Object[]) glycanRef.next(); Integer lookupPubmed = (Integer) referenceStore[0]; Integer lookupTranslationId = (Integer) referenceStore[1]; Integer lookupRefId = (Integer) referenceStore[3]; logger.info("ogbi translation id" + lookupTranslationId); GlycanSequence glycanSeq = em.lookup(GlycanSequence.class, lookupTranslationId); if (glycanSeq != null) { logger.info("finding gws with pubmed" + lookupPubmed); JournalReference lookupjr = JournalReference.createOrLookup(lookupPubmed); // test logger.info("check variables" + lookupPubmed + "trans" + lookupTranslationId + "ref" + lookupRefId); int storedCoreRefId = lookupjr.getReferenceId(); logger.info("the reference id dealing with is:" + storedCoreRefId); int numberUpdates = em.getQuery("org.eurocarbdb.dataaccess.hplc.RefLink.UPDATE_CORE_REFERENCE_ID") .setParameter("glycanId", glycanId).setParameter("storedCoreRefId", storedCoreRefId) .setParameter("lookupRefId", lookupRefId).executeUpdate(); // end test glycanSeq.addReference(lookupjr); /* getEntityManager().update(lookupjr); */ } } // } /* logger.info("am i testing"); //just try getting a reference for a glycan int glycanTest = 159; GlycanSequence glycanSeqTest = em.lookup (GlycanSequence.class, glycanTest); logger.info("get references for glycan"); glycanSeqTest.getReferences(); int sequence_id = glycanSeqTest.getGlycanSequenceId(); logger.info("i am indeed and the id is:" + sequence_id); List<GlycanSequence> glycanReferences = em.getQuery("org.eurocarbdb.dataaccess.core.GlycanSequence.HPLC_REFERENCE").setParameter("sequence_id", sequence_id).list(); //glycanSeqTest.getReferences(); */ return SUCCESS; } }