ProjectDocHandler.java

package gov.nih.ncgc.bard.capextract.handler;

import gov.nih.ncgc.bard.capextract.CAPConstants;
import gov.nih.ncgc.bard.capextract.CAPUtil;
import gov.nih.ncgc.bard.capextract.CapResourceHandlerRegistry;
import gov.nih.ncgc.bard.capextract.ICapResourceHandler;
import gov.nih.ncgc.bard.capextract.jaxb.AbstractContextItemType;
import gov.nih.ncgc.bard.capextract.jaxb.ContextItemType;
import gov.nih.ncgc.bard.capextract.jaxb.ContextType;
import gov.nih.ncgc.bard.capextract.jaxb.Contexts;
import gov.nih.ncgc.bard.capextract.jaxb.Link;
import gov.nih.ncgc.bard.capextract.jaxb.Project;
import gov.nih.ncgc.bard.capextract.jaxb.ProjectExperiment;

import java.io.IOException;
import java.math.BigInteger;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.List;

/**
 * Process project related documents.
 *
 * @author Rajarshi Guha
 */
public class ProjectDocHandler extends CapResourceHandler implements ICapResourceHandler {

    public ProjectDocHandler() {
        super();
    }

    /**
     * Process a CAP entity that is located at some URL.
     *
     * @param url      The URL from which to retrieve the entity fron
     * @param resource The CAP resource that is meant to be processed. An implementing class
     *                 can choose to proceed or not based on this parameter.
     */
    public int process(String url, CAPConstants.CapResource resource) throws IOException {
        if (resource != CAPConstants.CapResource.PROJECTDOC) return CAPConstants.CAP_EXTRACT_LOAD_STATUS_FAILED;

        // get the Project object here
        Project project = getResponse(url, resource);

        String readyToXtract = project.getReadyForExtraction();
        String title = project.getProjectName();
        BigInteger pid = project.getProjectId();

        log.info("\taurl = [" + readyToXtract + "] for " + title + " pid " + pid);
        if (readyToXtract.equals("Ready")) {
            log.info("\tExtracting " + title);
            process(project);
        }
        
        return CAPConstants.CAP_EXTRACT_LOAD_STATUS_COMPLETE;
    }

    public void process(Project project) {
        String readyToXtract = project.getReadyForExtraction();
        if (!"Ready".equals(readyToXtract)) log.error("Proceeding even though project not ready: " + readyToXtract);

        String groupType = project.getGroupType();
        if (!"Project".equals(groupType)) log.error("Group type other than Project: " + groupType);

        // project steps should have already been loaded by hand !!!
        // do not create project if it has no experiments or steps
        if (project.getProjectSteps() == null) return;
        if (project.getProjectSteps().getProjectStep().size() == 0) return;

        try {
            Connection conn = CAPUtil.connectToBARD(CAPConstants.getBardDBJDBCUrl());
            Statement st = conn.createStatement();
            ResultSet result = st.executeQuery("select bard_proj_id, name, description from bard_project where cap_proj_id=" + project.getProjectId());
            if (result.next()) {
                int bardProjId = result.getInt(1);
                //String name = result.getString(2);
                //String description = result.getString(3);
                result.close();


//		if (name.equals("CAP")) { // hack to initially update project info from CAP
//	            PreparedStatement pst = conn.prepareStatement("update bard_project set name=?, description=? where cap_proj_id="+project.getBardProjectId());
//	            pst.setString(1, project.getProjectName());
//	            pst.setString(2, project.getDescription());
//	            pst.addBatch();
//	            pst.executeBatch();
//	            log.debug("Updated project name for bard project "+bardProjId+": "+project.getProjectName());
//		}

                // deal with project annotations
                PreparedStatement pst = conn.prepareStatement("insert into cap_project_annotation (bard_proj_id, cap_proj_id, source, entity, anno_id, anno_key, anno_value, anno_display, related, context_name, display_order) values (?,?,?,?,?,?,?,?,?,?,?)");
                Contexts contexts = project.getContexts();
                List<ContextType> contextTypes = contexts.getContext();
                for (ContextType contextType : contextTypes) {
                    int contextId = contextType.getId().intValue();
                    String contextName = contextType.getContextName();
                    log.info("Loading annotation " + contextId + " for " + project.getProjectId());

                    ContextType.ContextItems contextItems = contextType.getContextItems();
                    for (ContextItemType contextItemType : contextItems.getContextItem()) {

                        pst.setInt(1, bardProjId);
                        pst.setInt(2, project.getProjectId().intValue());
                        pst.setString(3, "cap");
                        pst.setString(4, "project");
                        pst.setInt(5, contextId);

                        // dict id for the annotation key
                        String key = null;
                        AbstractContextItemType.AttributeId attr = contextItemType.getAttributeId();
                        if (attr != null) {
                            String[] toks = attr.getLink().getHref().split("/");
                            key = toks[toks.length - 1];
                        }
                        pst.setString(6, key);

                        // dict id for the annotation value
                        String value = null;
                        AbstractContextItemType.ValueId vc = contextItemType.getValueId();
                        if (vc != null) {
                            String[] toks = vc.getLink().getHref().split("/");
                            value = toks[toks.length - 1];
                        }
                        pst.setString(7, value);

                        String valueDisplay = contextItemType.getValueDisplay();
                        pst.setString(8, valueDisplay);

                        String related = null;
                        if (contextItemType.getExtValueId() != null) related = contextItemType.getExtValueId();
                        pst.setString(9, related);
                        pst.setString(10, contextName);
                        pst.setInt(11, contextItemType.getDisplayOrder());

                        pst.addBatch();
                    }
                    pst.executeBatch();
                }

                // handle project steps

                // handle project documents
                for (Link link : project.getLink()) {
                    CAPConstants.CapResource res = CAPConstants.getResource(link.getType());
                    if (res != CAPConstants.CapResource.PROJECTDOC) continue;
                    ICapResourceHandler handler = CapResourceHandlerRegistry.getInstance().getHandler(res);
                    if (handler != null) handler.process(link.getHref(), res);
                }

                // handle the experiments associated with this project
                List<ProjectExperiment> experiments = project.getProjectExperiments().getProjectExperiment();
                for (ProjectExperiment experiment : experiments) {
                    Link exptLink = experiment.getExperimentRef().getLink();
                    CAPConstants.CapResource res = CAPConstants.getResource(exptLink.getType());
                    if (res != CAPConstants.CapResource.EXPERIMENT) continue;
                    ICapResourceHandler handler = CapResourceHandlerRegistry.getInstance().getHandler(res);
                    if (handler != null) handler.process(exptLink.getHref(), res);
                }
            } else {
                log.error("Database has no project with cap_proj_id=" + project.getProjectId());
            }
            conn.commit();
            st.close();
            conn.close();
        } catch (SQLException ex) {
            log.error("Failed to update database with cap_proj_id=" + project.getProjectId());
            ex.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }
    }

}