MetaDataHelper.java | searchcode

/pride-inspector/branches/development/src/main/java/uk/ac/ebi/pride/gui/component/metadata/MetaDataHelper.java

http://pride-toolsuite.googlecode.com/
Java | 341 lines | 232 code | 48 blank | 61 comment | 69 complexity | 62debef1770b92776b8315627d71c1a1 MD5 | raw file

package uk.ac.ebi.pride.gui.component.metadata;



import uk.ac.ebi.pride.data.core.*;

import uk.ac.ebi.pride.gui.utils.Constants;

import uk.ac.ebi.pride.util.NumberUtilities;

import uk.ac.ebi.pride.util.RegExUtilities;



import java.util.ArrayList;

import java.util.Collection;

import java.util.List;



/**

 * Created by IntelliJ IDEA.

 * User: rwang

 * Date: 25-May-2010

 * Time: 10:52:22

 */

public class MetaDataHelper {

    /**

     * Get general metadata into a collection of paraemters

     *

     * @param metaData

     * @return

     */

    public static Collection<Parameter> getGeneralContent(MetaData metaData) {

        Collection<Parameter> params = new ArrayList<Parameter>();



        // id

        addUserParam(params, Constants.ID, metaData.getId());



        // accession

        addUserParam(params, Constants.ACCESSION, metaData.getAccession());



        // version

        addUserParam(params, Constants.VERSION, metaData.getVersion());



        // add experiment related meta data

        if (metaData instanceof Experiment) {

            addUserParam(params, Constants.TITLE, ((Experiment) metaData).getTitle());

            addUserParam(params, Constants.SHORT_LABEL, ((Experiment) metaData).getShortLabel());

            addUserParam(params, Constants.CREATION_DATE, ((Experiment) metaData).getCreationDate());

            addUserParam(params, Constants.PUBLIC_DATE, ((Experiment) metaData).getPublicDate());

        }



        // additional parameters

        addParamGroup(params, metaData, Constants.EMPTY);



        return params;

    }



    public static Collection<Parameter> getParamGroup(ParamGroup paramGroup) {

        Collection<Parameter> params = new ArrayList<Parameter>();

        addParamGroup(params, paramGroup, Constants.EMPTY);

        return params;

    }



    public static Collection<Parameter> getSourceFile(SourceFile sourceFile) {

        Collection<Parameter> params = new ArrayList<Parameter>();

        // id

        addUserParam(params, Constants.ID, sourceFile.getId());

        // name

        addUserParam(params, Constants.NAME, sourceFile.getName());

        // path

        addUserParam(params, Constants.PATH, sourceFile.getPath());



        // additional parameters

        addParamGroup(params, sourceFile, Constants.EMPTY);

        return params;

    }



    public static Collection<Parameter> getSample(Sample sample) {

        Collection<Parameter> params = new ArrayList<Parameter>();



        // id

        addUserParam(params, Constants.ID, sample.getId());

        // name

        addUserParam(params, Constants.NAME, sample.getName());

        // additional parameters

        addParamGroup(params, sample, Constants.EMPTY);



        return params;

    }



    public static Collection<Parameter> getContact(ParamGroup contact) {

        Collection<Parameter> params = getParamGroup(contact);



        // iterate over all params, check for email addresses.

        for (Parameter param : params) {

            if (RegExUtilities.isValidEmail(param.getValue())) {

                String email = param.getValue();

                param.setValue("<html><head></head><body><a href='mailto:" + email + "'>" + email + "</a></body></html>");

            }

        }



        return params;

    }



    public static Collection<Parameter> getSoftware(Software software) {

        Collection<Parameter> params = new ArrayList<Parameter>();

        // id

        addUserParam(params, Constants.ID, software.getId());

        // name

        addUserParam(params, Constants.VERSION, software.getVersion());

        // additional parameters

        addParamGroup(params, software, Constants.EMPTY);



        return params;

    }



    public static Collection<Parameter> getScanSetting(ScanSetting scanSetting) {

        Collection<Parameter> params = new ArrayList<Parameter>();

        // id

        addUserParam(params, Constants.ID, scanSetting.getId());

        // source file id

        List<SourceFile> sourceFiles = scanSetting.getSourceFile();

        if (sourceFiles != null) {

            for (SourceFile sourceFile : sourceFiles) {

                addUserParam(params, Constants.SOURCE_FILE_ID, sourceFile.getId());

            }

        }



        // targets

        List<ParamGroup> targets = scanSetting.getTargets();

        if (targets != null) {

            for (int i = 0; i < targets.size(); i++) {

                String prefix = Constants.TARGET + " " + (i + 1) + " - ";

                addParamGroup(params, targets.get(i), prefix);

            }

        }



        // additional parameters

        addParamGroup(params, scanSetting, Constants.EMPTY);



        return params;

    }



    public static Collection<Parameter> getInstrumentConfiguration(InstrumentConfiguration instrument) {

        Collection<Parameter> params = new ArrayList<Parameter>();

        // id

        addUserParam(params, Constants.ID, instrument.getId());

        // scan settings

        ScanSetting scanSetting = instrument.getScanSetting();

        if (scanSetting != null) {

            addUserParam(params, Constants.SCAN_SETTING_ID, scanSetting.getId());

        }

        // software

        Software software = instrument.getSoftware();

        if (software != null) {

            addUserParam(params, Constants.SOFTWARE_ID, software.getId());

        }

        // source

        // source order

        InstrumentComponent source = instrument.getSource();

        if (source != null) {

            String sourcePrefix = Constants.SOURCE + " - ";

            //addUserParam(params, sourcePrefix + SharedLabels.ORDER, source.getOrder());

            addParamGroup(params, source, sourcePrefix);

        }



        // analyzer

        InstrumentComponent analyzer = instrument.getAnalyzer();

        if (analyzer != null) {

            String analyzerPrefix = Constants.ANALYZER + " - ";

            //addUserParam(params, analyzerPrefix + SharedLabels.ORDER, analyzer.getOrder());

            addParamGroup(params, analyzer, analyzerPrefix);

        }



        // source

        InstrumentComponent detector = instrument.getDetector();

        if (detector != null) {

            String detectorPrefix = Constants.DETECTOR + " - ";

            //addUserParam(params, detectorPrefix + SharedLabels.ORDER, detector.getOrder());

            addParamGroup(params, detector, detectorPrefix);

        }



        // additional parameters

        addParamGroup(params, instrument, Constants.EMPTY);



        return params;

    }



    public static Collection<Parameter> getDataProcessing(DataProcessing dataProc) {

        Collection<Parameter> params = new ArrayList<Parameter>();

        // id

        addUserParam(params, Constants.ID, dataProc.getId());



        // processing methods

        List<ProcessingMethod> proMethods = dataProc.getProcessingMethods();

        if (proMethods != null) {

            for (int i = 0; i < proMethods.size(); i++) {

                String prefix = Constants.PROCESSING_METHOD + " " + (i + 1) + " - ";

                ProcessingMethod proMethod = proMethods.get(i);

                // order

                //addUserParam(params, prefix + SharedLabels.ORDER, proMethod.getOrder());

                // software

                Software software = proMethod.getSoftware();

                if (software != null) {

                    addUserParam(params, prefix + Constants.SOFTWARE_ID, software.getId());

                }

                // param group

                addParamGroup(params, proMethod, prefix);

            }

        }

        return params;

    }



    public static Collection<Parameter> getProtocol(Protocol protocol) {

        Collection<Parameter> params = new ArrayList<Parameter>();



        // id

        addUserParam(params, Constants.ID, protocol.getId());

        // name

        addUserParam(params, Constants.NAME, protocol.getName());

        // protocol steps

        List<ParamGroup> steps = protocol.getProtocolSteps();

        if (steps != null) {

            for (int i = 0; i < steps.size(); i++) {

                String prefix = Constants.PROTOCOL_STEP + " " + (i + 1) + " - ";

                ParamGroup step = steps.get(i);

                addParamGroup(params, step, prefix);

            }

        }

        // additaional param

        addParamGroup(params, protocol, Constants.EMPTY);



        return params;

    }



    public static Collection<Parameter> getReference(Reference reference) {

        Collection<Parameter> params = new ArrayList<Parameter>();



        // full reference

        addUserParam(params, Constants.FULL_REFERENCE, reference.getFullReference());

        // make a copy of the param group

        ParamGroup customParams = new ParamGroup();

        List<CvParam> originalCvParams = reference.getCvParams();

        if (originalCvParams != null) {

            customParams.addCvParams(originalCvParams);

        }



        List<UserParam> originalUserParams = reference.getUserParams();

        if (originalUserParams != null) {

            customParams.addUserParams(originalUserParams);

        }

        // find the pubmed cv param

        List<CvParam> cvParams = customParams.getCvParams();

        CvParam pubmedCvParam = null;

        CvParam doiCvParam = null;

        for (CvParam cvParam : cvParams) {

            if (cvParam.getCvLookupID().toLowerCase().equals("pubmed") || cvParam.getName().toLowerCase().equals("pubmed")) {

                pubmedCvParam = cvParam;

            } else if (cvParam.getCvLookupID().toLowerCase().equals("doi") || cvParam.getName().toLowerCase().equals("doi")) {

                doiCvParam = cvParam;

            }

        }



        // remove then set pubmed cv param

        if (pubmedCvParam != null) {

            customParams.removeCvParam(pubmedCvParam);

            // add pubmed cv param

            String acc = pubmedCvParam.getValue();

            if (acc == null || !NumberUtilities.isNumber(acc)) {

                acc = pubmedCvParam.getAccession();

            }



            if (acc != null || !NumberUtilities.isNumber(acc)) {

                String hyperLink = "<html><head></head><body><a href='http://www.ncbi.nlm.nih.gov/pubmed/" + acc + "'>" + acc + "</a></body></html>";

                CvParam newCvParam = new CvParam(acc, Constants.PUBMED, pubmedCvParam.getCvLookupID(),

                        hyperLink, pubmedCvParam.getUnitAcc(), pubmedCvParam.getUnitName(), pubmedCvParam.getUnitCVLookupID());

                params.add(newCvParam);

            }

        }



        // remove then set doi cv param

        if (doiCvParam != null) {

            customParams.removeCvParam(doiCvParam);

            // add doi cv param

            String doi = doiCvParam.getValue();

            if (doi == null) {

                doi = doiCvParam.getAccession();

            }



            if (doi != null) {

                String hyperLink = "<html><head></head><body><a href='http://dx.doi.org/" + doi + "'>" + doi + "</a></body></html>";

                CvParam newCvParam = new CvParam(doi, Constants.DOI, doiCvParam.getCvLookupID(),

                        hyperLink, doiCvParam.getUnitAcc(), doiCvParam.getUnitName(), doiCvParam.getUnitCVLookupID());

                params.add(newCvParam);

            }

        }



        // additional parameters

        addParamGroup(params, customParams, Constants.EMPTY);



        return params;

    }



    private static void addParamGroup(Collection<Parameter> params, ParamGroup paramGroup, String prefix) {

        if (paramGroup != null) {

            List<CvParam> cvParams = paramGroup.getCvParams();

            if (cvParams != null) {

                for (CvParam cvParam : cvParams) {

                    String name = cvParam.getName();

                    String value = cvParam.getValue();



                    if (value == null || "".equals(value.trim())) {

                        value = name;

                        name = prefix + Constants.PARAMETER;

                    } else {

                        name = prefix + name;

                    }

                    params.add(new CvParam(cvParam.getAccession(), name, cvParam.getCvLookupID(),

                            convertToHyperLink(value), cvParam.getUnitAcc(), cvParam.getUnitName(), cvParam.getUnitCVLookupID()));

                }

            }



            List<UserParam> userParams = paramGroup.getUserParams();

            if (userParams != null) {

                for (UserParam userParam : userParams) {

                    params.add(new UserParam(prefix + userParam.getName(), userParam.getType(), convertToHyperLink(userParam.getValue()),

                            userParam.getUnitAcc(), userParam.getUnitName(), userParam.getUnitCVLookupID()));

                }

            }

        }

    }



    private static String convertToHyperLink(String val) {

        if (val != null) {

            val = val.trim();

            if (val.startsWith("http") && !val.contains(" ")) {

                val = "<html><a href='" + val + "'> Link</a></html>";

            }

        }

        return val;

    }



    private static void addUserParam(Collection<Parameter> params, String name, Object value) {

        if (value != null) {

            params.add(new UserParam(name, null, value.toString(), null, null, null));

        }

    }

}