Examples with GetConfig massbank.GetConfig used on opensource projects

Example 6 with GetConfig

use of massbank.GetConfig in project MassBank-web by MassBank.

the class OpenDataUpdater method run.

/**
 * Starting the thread.
 */
public void run() {
    try {
        sleep(this.startDelay * TIME_SEC);
    } catch (Exception e) {
    }
    GetConfig conf = new GetConfig(MassBankEnv.get(MassBankEnv.KEY_BASE_URL));
    String myServerUrl = conf.getServerUrl();
    String[] urls = conf.getSiteUrl();
    String[] names = conf.getSiteName();
    String[] dbNames = conf.getDbName();
    String[] dbNames2 = conf.getSecondaryDBName();
    ArrayList<String> targetNameList = new ArrayList();
    ArrayList<String> targetDbNameList = new ArrayList();
    for (int i = 0; i < names.length; i++) {
        if (!urls[i].equals(myServerUrl) && !dbNames2[i].equals("")) {
            targetNameList.add(names[i]);
            targetDbNameList.add(dbNames2[i]);
        } else {
            targetNameList.add(names[i]);
            targetDbNameList.add(dbNames[i]);
        }
    }
    String[] targetNames = targetNameList.toArray(new String[] {});
    String[] targetDbNames = targetDbNameList.toArray(new String[] {});
    String dataRootPath = MassBankEnv.get(MassBankEnv.KEY_DATAROOT_PATH);
    if (targetNames.length == 0) {
        return;
    }
    do {
        for (int i = 0; i < targetNames.length; i++) {
            String repoDirName = targetNames[i];
            String dbName = targetDbNames[i];
            logger.info("[SVNService] OpenDataUpdater ** " + repoDirName + " **");
            String workCopyPath = SVNUtils.getWorkCopyPath(repoDirName, SVNOperation.WC_OPEN_DATA);
            this.srcRecordPath = dataRootPath + "annotation" + File.separator + dbName;
            this.destRecordPath = workCopyPath;
            File file = new File(srcRecordPath);
            if (file.exists()) {
                String[] fileNames = file.list();
                if (fileNames.length > 0) {
                    for (int j = 0; j < fileNames.length; j++) {
                        fileNames[j] = srcRecordPath + File.separator + fileNames[j];
                    }
                    String[] filePaths = SVNUtils.getLicenseOKFileList(fileNames);
                    if (filePaths.length > 0 && !isFileUpdating()) {
                        registerData(repoDirName);
                    }
                }
            }
            try {
                sleep(this.interval * TIME_SEC);
            } catch (Exception e) {
            }
            if (this.isTerminated) {
                return;
            }
        }
    } while (true);
}

Example 7 with GetConfig

use of massbank.GetConfig in project MassBank-web by MassBank.

the class RegistrationCommitter method run.

/**
 * Starting the thread.
 */
public void run() {
    try {
        sleep(this.startDelay * TIME_SEC);
    } catch (Exception e) {
    }
    this.isActive = true;
    GetConfig conf = new GetConfig(MassBankEnv.get(MassBankEnv.KEY_BASE_URL));
    String myServerUrl = conf.getServerUrl();
    String[] urls = conf.getSiteUrl();
    String[] names = conf.getSiteName();
    String[] dbNames = conf.getDbName();
    ArrayList<String> targetNameList = new ArrayList();
    ArrayList<String> targetDbNameList = new ArrayList();
    for (int i = 0; i < urls.length; i++) {
        if (i == 0 || urls[i].equals(myServerUrl)) {
            targetNameList.add(names[i]);
            targetDbNameList.add(dbNames[i]);
        }
    }
    String[] targetNames = targetNameList.toArray(new String[] {});
    String[] targetDbNames = targetDbNameList.toArray(new String[] {});
    String tempPath = System.getProperty("java.io.tmpdir");
    String dumpFilePath = tempPath + File.separator + "massbank_backup.sql";
    String[] tableNames = { "SPECTRUM", "RECORD", "PEAK", "CH_NAME", "CH_LINK", "INSTRUMENT", "TREE", "MOLFILE" };
    if (targetNames.length == 0) {
        return;
    }
    do {
        for (int i = 0; i < targetNames.length; i++) {
            String repoDirName = targetNames[i];
            String dbName = targetDbNames[i];
            logger.info("[SVNService] RegistrationCommitter ** " + repoDirName + " **");
            SVNOperation ope = null;
            try {
                ope = new SVNOperation(repoDirName, SVNOperation.WC_BACKUP_UPLOAD);
                if (ope.isWcModified()) {
                    boolean ret = FileUtil.execSqlDump("", dbName, tableNames, dumpFilePath);
                    if (ret) {
                        ope.addEntry(new String[] { dumpFilePath }, "other");
                        ope.commit();
                        FileUtils.deleteQuietly(new File(dumpFilePath));
                    }
                }
            } catch (Exception e) {
                e.printStackTrace();
            }
            ope.end();
            try {
                sleep(this.interval * TIME_SEC);
            } catch (Exception e) {
            }
            if (this.isTerminated) {
                return;
            }
        }
    } while (true);
}

Example 8 with GetConfig

use of massbank.GetConfig in project MassBank-web by MassBank.

the class SVNRegisterUtil method update.

/**
 * Update to the svn
 */
private static boolean update(String targetDbName, boolean isRecord) {
    String baseUrl = MassBankEnv.get(MassBankEnv.KEY_BASE_URL);
    GetConfig conf = new GetConfig(baseUrl);
    String[] confNames = conf.getSiteName();
    String[] confDbNames = conf.getDbName();
    boolean found = false;
    int i = 0;
    for (i = 0; i < confDbNames.length; i++) {
        if (targetDbName.equals(confDbNames[i])) {
            found = true;
            break;
        }
    }
    if (!found) {
        return false;
    }
    String basePath = "";
    String[] extensions = null;
    String subDirName = "";
    if (isRecord) {
        basePath = MassBankEnv.get(MassBankEnv.KEY_ANNOTATION_PATH);
        extensions = new String[] { "txt" };
        subDirName = "record";
    } else {
        basePath = MassBankEnv.get(MassBankEnv.KEY_MOLFILE_PATH);
        extensions = new String[] { "mol", "tsv" };
        subDirName = "molfile";
    }
    String repoDirName = confNames[i];
    String path1 = basePath + targetDbName;
    String path2 = SVNUtils.getWorkCopyPath(repoDirName, SVNOperation.WC_BACKUP_UPLOAD) + File.separator + subDirName;
    SVNOperation ope = null;
    try {
        ope = new SVNOperation(repoDirName, SVNOperation.WC_BACKUP_UPLOAD);
        File dir1 = new File(path1);
        File dir2 = new File(path2);
        if (!dir2.exists()) {
            dir2.mkdirs();
        }
        List<File> fileList1 = (List<File>) FileUtils.listFiles(dir1, extensions, false);
        List<File> fileList2 = (List<File>) FileUtils.listFiles(dir2, extensions, false);
        FileDifference diff = new FileDifference(fileList1, fileList2);
        String[] addFilePaths = diff.getAddFilePaths();
        String[] delFileNames = diff.getDeleteFileNames();
        if (addFilePaths.length > 0) {
            ope.addEntry(addFilePaths, subDirName);
        }
        if (delFileNames.length > 0) {
            ope.deleteEntry(delFileNames, subDirName);
        }
        ope.end();
        return true;
    } catch (Exception e) {
        e.printStackTrace();
        ope.end();
        return false;
    }
}

Example 9 with GetConfig

use of massbank.GetConfig in project MassBank-web by MassBank.

the class DisplayAll method init.

/**
 */
public void init() {
    setLayout(new BoxLayout(this.getContentPane(), BoxLayout.PAGE_AXIS));
    // �‹��ݒ�t�@�C������A�g�T�C�g��URL���擾
    String confPath = getCodeBase().toString();
    confPath = confPath.replaceAll("jsp/", "");
    GetConfig conf = new GetConfig(confPath);
    urlList = conf.getSiteUrl();
    serverUrl = conf.getServerUrl();
    baseUrl = serverUrl + "jsp/";
    // �s�[�N�����A�s�[�N���������̃p�����[�^�擾
    int paramMzNum = 0;
    if (getParameter("type") != null) {
        reqType = getParameter("type");
        if (reqType.equals("peak") || reqType.equals("diff")) {
            paramMzNum = Integer.parseInt(getParameter("pnum"));
            searchParam = "&num=" + paramMzNum;
            for (int i = 0; i < paramMzNum; i++) {
                String pnum = Integer.toString(i);
                String mz = getParameter("mz" + pnum);
                String tol = getParameter("tol" + pnum);
                String rInt = getParameter("int" + pnum);
                paramMz += mz + ",";
                paramTol += tol + ",";
                paramInt += rInt + ",";
                searchParam += "&mz" + pnum + "=" + mz;
                searchParam += "&tol" + pnum + "=" + tol;
                searchParam += "&int" + pnum + "=" + rInt;
            }
        }
    }
    numSpct = Integer.valueOf(getParameter("num"));
    plotPane = new PlotPane[numSpct];
    buttonPane = new ButtonPane[numSpct];
    clear();
    peaks1 = new Peak[numSpct];
    info = new RecordInfo[numSpct];
    cnt = new int[urlList.length];
    HashSet<String> compoundNameList = new HashSet();
    for (int i = 0; i < numSpct; i++) {
        // �p�����[�^�擾
        String pnum = Integer.toString(i + 1);
        int siteNo = Integer.parseInt(getParameter("site" + pnum));
        String id = getParameter("id" + pnum);
        String title = getParameter("name" + pnum);
        String formula = getParameter("formula" + pnum);
        String mass = getParameter("mass" + pnum);
        String ion = getParameter("ion" + pnum);
        int num = cnt[siteNo]++;
        info[i] = new RecordInfo(id, title, siteNo, num, formula, mass, ion);
        String[] items = title.split(";");
        compoundNameList.add(items[0]);
    }
    // �s�[�N�f�[�^�擾
    ArrayList resultList = getPeakData();
    // Molfile�f�[�^�擾
    Map<String, String> mapMolData = getMolData(compoundNameList);
    hitPeaks.mzInfoList = new ArrayList[numSpct];
    precursor = new String[numSpct];
    Vector<Vector<String>> mzAry = new Vector<Vector<String>>();
    for (int i = 0; i < numSpct; i++) {
        int siteNo = info[i].getSiteNo();
        int num = info[i].getNumber();
        ArrayList result = (ArrayList) resultList.get(siteNo);
        String line = (String) result.get(num);
        // �s�[�N�����A�s�[�N����������Ă΂ꂽ�ꍇ�A�q�b�g����m/z�l���Ԃ�̂Ŋi�[����
        String findStr = "hit=";
        int pos = line.indexOf(findStr);
        if (pos > 0) {
            String hit = line.substring(pos + 4);
            String[] hitMzInfo = hit.split("\t");
            boolean isDiff = false;
            // �s�[�N�����̏ꍇ
            if (reqType.equals("diff")) {
                isDiff = true;
            }
            // m/z�l���i�[
            ArrayList mzInfoList = hitPeaks.setMz(hitMzInfo, isDiff);
            hitPeaks.mzInfoList[i] = new ArrayList();
            hitPeaks.mzInfoList[i].addAll(mzInfoList);
            line = line.substring(0, pos);
        }
        // �v���J�[�T�[
        findStr = "precursor=";
        pos = line.indexOf(findStr);
        int posNext = 0;
        if (pos > 0) {
            posNext = line.indexOf("\t", pos);
            precursor[i] = line.substring(pos + findStr.length(), posNext);
            line = line.substring(0, pos);
        } else {
            precursor[i] = "";
        }
        String[] tmp = line.split("\t\t");
        Vector<String> mzs = new Vector<String>();
        // m/z�i�[
        for (int j = 0; j < tmp.length; j++) {
            mzs.add(tmp[j]);
        }
        mzAry.add(mzs);
    }
    for (int i = 0; i < numSpct; i++) {
        plotPane[i] = new PlotPane(i);
        plotPane[i].setPreferredSize(new Dimension(780, 200));
        plotPane[i].repaint();
        JPanel pane1 = new JPanel();
        String title = info[i].getTitle();
        String id = info[i].getID();
        String site = String.valueOf(info[i].getSiteNo());
        pane1.add(new NameButton(title, id, site));
        pane1.setLayout(new FlowLayout(FlowLayout.LEFT));
        pane1.setMaximumSize(new Dimension(pane1.getMaximumSize().width, 100));
        JPanel parentPane = new JPanel();
        JPanel childPane1 = new JPanel();
        JPanel childPane2 = new JPanel();
        childPane2.setBackground(Color.WHITE);
        childPane2.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
        childPane2.setMaximumSize(new Dimension(200, parentPane.getMaximumSize().height));
        childPane1.add(pane1);
        childPane1.add(plotPane[i]);
        buttonPane[i] = new ButtonPane(i);
        buttonPane[i].addDiffButton(plotPane[i].idPeak);
        buttonPane[i].setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
        buttonPane[i].setMaximumSize(new Dimension(buttonPane[i].getMaximumSize().width, 100));
        childPane1.add(buttonPane[i]);
        childPane1.setLayout(new BoxLayout(childPane1, BoxLayout.Y_AXIS));
        parentPane.add(childPane1);
        // ���p�l���E��: FORMULA��EXACT MASS��\��
        JLabel formuraLabel1 = new JLabel("    Formula: ");
        formuraLabel1.setOpaque(true);
        formuraLabel1.setBackground(Color.WHITE);
        formuraLabel1.setPreferredSize(new Dimension(84, 17));
        childPane2.add(formuraLabel1);
        JLabel formuraLabel2 = new JLabel(info[i].getFormula());
        formuraLabel2.setOpaque(true);
        formuraLabel2.setForeground(new Color(57, 127, 0));
        formuraLabel2.setBackground(Color.WHITE);
        formuraLabel2.setPreferredSize(new Dimension(116, 17));
        childPane2.add(formuraLabel2);
        JLabel emassLabel1 = new JLabel("    Exact Mass: ");
        emassLabel1.setOpaque(true);
        emassLabel1.setBackground(Color.WHITE);
        emassLabel1.setPreferredSize(new Dimension(84, 17));
        childPane2.add(emassLabel1);
        JLabel emassLabel2 = new JLabel();
        emassLabel2.setOpaque(true);
        emassLabel2.setForeground(new Color(57, 127, 0));
        emassLabel2.setBackground(Color.WHITE);
        emassLabel2.setPreferredSize(new Dimension(116, 17));
        String emass = info[i].getExactMass();
        if (!emass.equals("") && !emass.equals("0")) {
            emassLabel2.setText(emass);
        }
        childPane2.add(emassLabel2);
        // ���p�l���E��: Mol�\���\���p�l�����Z�b�g
        JPanel pane3 = null;
        String[] items = title.split(";");
        boolean isExist = false;
        String compoundName = items[0].toLowerCase();
        if (mapMolData.containsKey(compoundName)) {
            String moldata = mapMolData.get(compoundName);
            if (!moldata.equals("")) {
                pane3 = (MolViewPaneExt) new MolViewPaneExt(moldata, 200, this);
                isExist = true;
            }
        }
        if (!isExist) {
            // �f�[�^���擾�ł��Ȃ������ꍇ
            JLabel lbl = new JLabel("Not Available", JLabel.CENTER);
            lbl.setPreferredSize(new Dimension(180, 180));
            lbl.setBackground(new Color(0xF8, 0xF8, 0xFF));
            lbl.setBorder(new LineBorder(Color.BLACK, 1));
            lbl.setOpaque(true);
            GridBagLayout layout = new GridBagLayout();
            GridBagConstraints gbc = new GridBagConstraints();
            gbc.insets = new Insets(1, 1, 1, 1);
            layout.setConstraints(lbl, gbc);
            pane3 = new JPanel();
            pane3.setPreferredSize(new Dimension(200, 200));
            pane3.setBackground(Color.WHITE);
            pane3.add(lbl);
        }
        childPane2.add(pane3);
        // ���p�l���E��: �\�����\�������̗]��
        JLabel lbl3 = new JLabel("");
        lbl3.setPreferredSize(new Dimension(200, 30));
        childPane2.add(lbl3);
        childPane2.setPreferredSize(new Dimension(200, 260));
        parentPane.add(childPane2);
        parentPane.setLayout(new BoxLayout(parentPane, BoxLayout.X_AXIS));
        add(parentPane);
        // �㉺�X�y�N�g���̋�؂�
        JPanel spacePane = new JPanel();
        spacePane.setPreferredSize(new Dimension(800, 2));
        spacePane.setBackground(Color.white);
        JLabel lbl4 = new JLabel("");
        lbl4.setPreferredSize(new Dimension(800, 2));
        spacePane.add(lbl4);
        add(spacePane);
        String ion = info[i].getIon();
        peaks1[i] = new Peak((Vector<String>) mzAry.get(i), emass, ion);
    }
    initMass();
}

Example 10 with GetConfig

use of massbank.GetConfig in project MassBank-web by MassBank.

the class SearchPage method init.

/**
 * ���C���v���O����
 */
public void init() {
    // �A�v���b�g�R���e�L�X�g�擾
    context = getAppletContext();
    // �A�v���b�g������ʃT�C�Y�擾
    initAppletWidth = getWidth();
    initAppletHight = getHeight();
    // �‹��ݒ�t�@�C������A�g�T�C�g��URL���擾
    String confPath = getCodeBase().toString();
    confPath = confPath.replaceAll("/jsp", "");
    GetConfig conf = new GetConfig(confPath);
    siteNameList = conf.getSiteName();
    baseUrl = conf.getServerUrl();
    // Cookie��񃆁[�e�B���e�B������
    cm = new CookieManager(this, "SerchApplet", 30, conf.isCookie());
    // Precursor m/z��񏉊���
    initPreInfo();
    // Tolerance��񏉊���
    initTolInfo();
    // Cutoff Threshold��񏉊���
    initCutoffInfo();
    // ���u��ʏ�񏉊���
    instInfo = new GetInstInfo(confPath);
    initInstInfo();
    // MS��ʏ�񏉊���
    initMsInfo();
    // �C�I����ʏ�񏉊���
    initIonInfo();
    // �E�C���h�E����
    createWindow();
    // �������_�C�A���O
    this.dlg = new ProgressDialog(getFrame());
    // ���[�U�[�t�@�C���Ǎ���
    if (getParameter("file") != null) {
        loadFile(getParameter("file"));
    } else // ����ʂ���̃N�G���lj�
    if (getParameter("num") != null) {
        DefaultTableModel dm = (DefaultTableModel) querySorter.getTableModel();
        dm.setRowCount(0);
        int num = Integer.parseInt(getParameter("num"));
        for (int i = 0; i < num; i++) {
            String pnum = Integer.toString(i + 1);
            String id = getParameter("qid" + pnum);
            String name = getParameter("name" + pnum);
            String site = getParameter("site" + pnum);
            String[] idNameSite = new String[] { id, name, site };
            nameList.add(idNameSite);
            site = siteNameList[Integer.parseInt(site)];
            String[] idNameSite2 = new String[] { id, name, site, String.valueOf(i + 1) };
            dm.addRow(idNameSite2);
        }
    }
}