ValidationReportServiceImpl.java

package net.sourceforge.seqware.common.business.impl;

import static com.google.common.base.Preconditions.checkNotNull;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import java.util.List;
import java.util.Set;
import net.sourceforge.seqware.common.business.ValidationReportService;
import net.sourceforge.seqware.common.dao.FileDAO;
import net.sourceforge.seqware.common.model.Experiment;
import net.sourceforge.seqware.common.model.File;
import net.sourceforge.seqware.common.model.IUS;
import net.sourceforge.seqware.common.model.Lane;
import net.sourceforge.seqware.common.model.Processing;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.seqware.common.model.SequencerRun;
import net.sourceforge.seqware.common.model.Study;
import net.sourceforge.seqware.common.model.Workflow;
import net.sourceforge.seqware.common.model.WorkflowRun;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;

@Service
/**
 * <p>ValidationReportServiceImpl class.</p>
 *
 * @author boconnor
 * @version $Id: $Id
 */
public class ValidationReportServiceImpl implements ValidationReportService {

    @Autowired
    private FileDAO fileDao;

    /** {@inheritDoc} */
    @Override
    public List<ReportEntry> fileLinkReport() {
        List<File> files = fileDao.list();
        List<Integer> fileSwas = Lists.newArrayList();
        for (File file : files) {
            fileSwas.add(file.getSwAccession());
        }
        return fileLinkReport(fileSwas);
    }

    private void visitProcessing(Processing processing, int in, StringBuilder sb) {
        sb.append(indent(in)).append(processing.getAlgorithm()).append(" SWA: ").append(processing.getSwAccession());
        sb.append("\n");
        visitSequencerRun(processing, in, sb);
        visitLane(processing, in, sb);
        visitIus(processing, in, sb);
        visitSample(processing, in, sb);
        visitExperiment(processing, in, sb);
        visitStudy(processing, in, sb);
        if (visitWorkflowRun(processing, in, sb)) {
            in++;
        }
        for (Processing parent : processing.getParents()) {
            visitProcessing(parent, in, sb);
        }
    }

    private void visitSequencerRun(Processing processing, int in, StringBuilder sb) {
        for (SequencerRun link : processing.getSequencerRuns()) {
            sb.append(indent(in++)).append("LINK SequencerRun SWA: ").append(link.getSwAccession());
            sb.append('\n');
        }
    }

    private void visitLane(Processing processing, int in, StringBuilder sb) {
        for (Lane link : processing.getLanes()) {
            sb.append(indent(++in)).append("LINK Lane SWA: ").append(link.getSwAccession());
            sb.append('\n');
        }
    }

    private void visitIus(Processing processing, int in, StringBuilder sb) {
        for (IUS link : processing.getIUS()) {
            sb.append(indent(++in)).append("LINK IUS SWA: ").append(link.getSwAccession());
            sb.append('\n');
        }
    }

    private void visitSample(Processing processing, int in, StringBuilder sb) {
        for (Sample link : processing.getSamples()) {
            sb.append(indent(in++)).append("LINK Sample SWA: ").append(link.getSwAccession());
            sb.append('\n');
        }
    }

    private void visitExperiment(Processing processing, int in, StringBuilder sb) {
        for (Experiment link : processing.getExperiments()) {
            sb.append(indent(in++)).append("LINK Experiment SWA: ").append(link.getSwAccession());
            sb.append('\n');
        }
    }

    private void visitStudy(Processing processing, int in, StringBuilder sb) {
        for (Study link : processing.getStudies()) {
            sb.append(indent(in++)).append("LINK Study SWA: ").append(link.getSwAccession());
            sb.append('\n');
        }
    }

    private boolean visitWorkflowRun(Processing processing, int in, StringBuilder sb) {
        boolean result = false;
        WorkflowRun workflowRun = processing.getWorkflowRun();
        if (workflowRun != null) {
            Workflow workflow = workflowRun.getWorkflow();
            if (workflow != null) {
                sb.append(indent(in++)).append("WORKFLOW ").append(workflow.getFullName()).append(" SWA: ").append(workflow.getSwAccession());
                sb.append('\n');
                result = true;
            }
        }
        return result;
    }

    /**
     * {@inheritDoc}
     * 
     * @param swa
     */
    @Override
    public String fileReverseHierarchyDisplay(Integer swa) {
        checkNotNull(swa);
        StringBuilder sb = new StringBuilder();
        int in = 0;
        File file = fileDao.findBySWAccession(swa);
        sb.append(indent(in++)).append("FILE SWA: ").append(file.getSwAccession()).append(" FILE NAME: ").append(file.getFileName()).append(" Processing Children: ").append(file.getProcessings().size());
        sb.append("\n");
        for (Processing process : file.getProcessings()) {
            visitProcessing(process, in, sb);
        }
        return sb.toString();
    }

    private String indent(int indentSize) {
        StringBuilder sb = new StringBuilder();
        sb.append("");
        for (int i = 0; i < indentSize; i++) {
            sb.append("   ");
        }
        return sb.toString();
    }

    /** {@inheritDoc} */
    @Override
    public List<ReportEntry> fileLinkReport(List<Integer> fileSwas) {
        List<ReportEntry> result = Lists.newArrayList();
        for (Integer swa : fileSwas) {
            ReportEntry entry = new ReportEntry();
            result.add(entry);
            entry.setFileSwa(swa.toString());
            File file = fileDao.findBySWAccession(swa);
            entry.setFilename(file.getFileName());
            for (Processing process : file.getProcessings()) {
                walkProcessing(process, entry);
            }
        }
        return result;
    }

    private void walkProcessing(Processing processing, ReportEntry entry) {
        entry.setRootProcessingName(processing.getAlgorithm());
        entry.setRootProcessingSwa(processing.getSwAccession().toString());
        walkSequencerRun(processing, entry);
        walkLane(processing, entry);
        walkIus(processing, entry);
        walkSample(processing, entry);
        walkExperiment(processing, entry);
        walkStudy(processing, entry);
        for (Processing parent : processing.getParents()) {
            walkProcessing(parent, entry);
        }
    }

    private void walkSequencerRun(Processing processing, ReportEntry entry) {
        for (SequencerRun link : processing.getSequencerRuns()) {
            entry.getSequencerRunSwas().add(link.getSwAccession().toString());
        }
    }

    private void walkLane(Processing processing, ReportEntry entry) {
        for (Lane link : processing.getLanes()) {
            entry.getLaneSwas().add(link.getSwAccession().toString());
        }
    }

    private void walkIus(Processing processing, ReportEntry entry) {
        for (IUS link : processing.getIUS()) {
            entry.getIusSwas().add(link.getSwAccession().toString());
        }
    }

    private void walkSample(Processing processing, ReportEntry entry) {
        for (Sample link : processing.getSamples()) {
            entry.getSampleSwas().add(link.getSwAccession().toString());
        }
    }

    private void walkExperiment(Processing processing, ReportEntry entry) {
        for (Experiment link : processing.getExperiments()) {
            entry.getExperimentSwas().add(link.getSwAccession().toString());
        }
    }

    private void walkStudy(Processing processing, ReportEntry entry) {
        for (Study link : processing.getStudies()) {
            entry.getStudySwas().add(link.getSwAccession().toString());
        }
    }

    public class ReportEntry {
        private String filename;
        private String fileSwa;
        private String rootProcessingName;
        private String rootProcessingSwa;
        private Set<String> sequencerRunSwas = Sets.newHashSet();
        private Set<String> laneSwas = Sets.newHashSet();
        private Set<String> iusSwas = Sets.newHashSet();
        private Set<String> sampleSwas = Sets.newHashSet();
        private Set<String> experimentSwas = Sets.newHashSet();
        private Set<String> studySwas = Sets.newHashSet();

        public String getFilename() {
            return filename;
        }

        public void setFilename(String filename) {
            this.filename = filename;
        }

        public String getFileSwa() {
            return fileSwa;
        }

        public void setFileSwa(String fileSwa) {
            this.fileSwa = fileSwa;
        }

        public String getRootProcessingName() {
            return rootProcessingName;
        }

        public void setRootProcessingName(String rootProcessingName) {
            this.rootProcessingName = rootProcessingName;
        }

        public String getRootProcessingSwa() {
            return rootProcessingSwa;
        }

        public void setRootProcessingSwa(String rootProcessingSwa) {
            this.rootProcessingSwa = rootProcessingSwa;
        }

        public Set<String> getSequencerRunSwas() {
            return sequencerRunSwas;
        }

        public void setSequencerRunSwas(Set<String> sequencerRunSwas) {
            this.sequencerRunSwas = sequencerRunSwas;
        }

        public Set<String> getLaneSwas() {
            return laneSwas;
        }

        public void setLaneSwas(Set<String> laneSwas) {
            this.laneSwas = laneSwas;
        }

        public Set<String> getIusSwas() {
            return iusSwas;
        }

        public void setIusSwas(Set<String> iusSwas) {
            this.iusSwas = iusSwas;
        }

        public Set<String> getSampleSwas() {
            return sampleSwas;
        }

        public void setSampleSwas(Set<String> sampleSwas) {
            this.sampleSwas = sampleSwas;
        }

        public Set<String> getExperimentSwas() {
            return experimentSwas;
        }

        public void setExperimentSwas(Set<String> experimentSwas) {
            this.experimentSwas = experimentSwas;
        }

        public Set<String> getStudySwas() {
            return studySwas;
        }

        public void setStudySwas(Set<String> studySwas) {
            this.studySwas = studySwas;
        }

    }
}