edu.scripps.fl.pubchem.app.assayxml.ProcessDocumentStage.java Source code

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Here is the source code for edu.scripps.fl.pubchem.app.assayxml.ProcessDocumentStage.java

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/*
 * Copyright 2010 The Scripps Research Institute
 *
 * 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 edu.scripps.fl.pubchem.app.assayxml;

import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.apache.commons.pipeline.StageException;
import org.apache.commons.pipeline.stage.BaseStage;
import org.dom4j.Document;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import edu.scripps.fl.pubchem.PubChemXMLParserFactory;
import edu.scripps.fl.pubchem.db.PCAssay;
import edu.scripps.fl.pubchem.web.entrez.EUtilsWebSession;
import edu.scripps.fl.util.ProgressWriter;

public class ProcessDocumentStage extends BaseStage {

    private static final Logger log = LoggerFactory.getLogger(ProcessDocumentStage.class);

    private Set<Long> onHoldAidSet;
    private Set<Long> rnaiAidSet;
    private Set<Long> smallMoleculeAidSet;
    ProgressWriter pw = new ProgressWriter("ProcessDocument");

    @Override
    public void preprocess() throws StageException {
        super.preprocess();
        try {
            //         onHoldAidSet = (Set<Long>) EUtilsWebSession.getInstance().getIds("\"hasonhold\"[filter]", "pcassay", new HashSet<Long>());
            rnaiAidSet = (Set<Long>) EUtilsWebSession.getInstance().getIds("\"rnai\"[filter]", "pcassay",
                    new HashSet<Long>());
            smallMoleculeAidSet = (Set<Long>) EUtilsWebSession.getInstance().getIds("\"small_molecule\"[filter]",
                    "pcassay", new HashSet<Long>());
        } catch (Exception ex) {
            throw new StageException(this, ex);
        }
    }

    @Override
    public void process(Object obj) throws StageException {
        pw.increment();
        try {
            Document document = (Document) obj;
            List<PCAssay> assays = PubChemXMLParserFactory.getInstance().populateAssaysFromXMLDocument(document,
                    false);
            PCAssay assay = assays.get(0);

            long aid = assay.getAID().longValue();
            if (rnaiAidSet.contains(aid))
                assay.setAssayType("RNAi");
            else if (smallMoleculeAidSet.contains(aid))
                assay.setAssayType("Small Molecule");
            else
                assay.setAssayType("");

            //         if (onHoldAidSet.contains(aid)) {
            //            assay.setOnHold(true);
            //         } else {
            //            assay.setOnHold(false);
            //         }

            emit(assay);
        } catch (Exception ex) {
            throw new StageException(this, ex);
        }
    }
}