Package org.openbel.framework.core.df

Examples of org.openbel.framework.core.df.DatabaseServiceImpl

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    protected Kam testKam;

    protected void setupKamStore(final String kamName) {
        try {
            final SystemConfiguration syscfg = createSystemConfiguration();
            final DatabaseService dbs = new DatabaseServiceImpl();
            dbc = dbs.dbConnection(syscfg.getKamURL(),
                    syscfg.getKamUser(), syscfg.getKamPassword());
            ks = new KAMStoreImpl(dbc);
        } catch (IOException e) {
            e.printStackTrace();
            fail("Could not read system configuration.");
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                bail(ExitCode.DIRECTORY_CREATION_FAILED);
            }
            wrkdir.mkdir();
        }

        DatabaseService dbsvc = new DatabaseServiceImpl();

        // validate kamstore connection
        final String url = syscfg.getKamURL();
        final String user = syscfg.getKamUser();
        final String pass = syscfg.getKamPassword();
        try {
            if (!dbsvc.validConnection(url, user, pass)) {
                bail(ExitCode.KAM_CONNECTION_FAILURE);
            }
        } catch (DBConnectionFailure e) {
            reportable.error(e.getUserFacingMessage());
            bail(ExitCode.KAM_CONNECTION_FAILURE);
        }

        // If "--no-preserve" is not specified, query the database for an
        // existing KAM w/same name. If one exists, exit with proper ExitCode.
        if (!hasOption(LONG_OPT_NO_PRESERVE)){
            String kamName = getOptionValue("k");
            try{
                dbConnection = dbsvc.dbConnection(
                        syscfg.getKamURL(),
                        syscfg.getKamUser(),
                        syscfg.getKamPassword());
                kamStore = new KAMStoreImpl(dbConnection);
                kams = kamStore.getCatalog();
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        reportable.setOutputStream(System.out);
        setReportable(reportable);
    }

    private static boolean kamExists(String kam) {
        DatabaseService db = new DatabaseServiceImpl();
        SystemConfiguration sc = getSystemConfiguration();

        DBConnection c = null;
        try {
            c = db.dbConnection(sc.getKamURL(), sc.getKamUser(),
                    sc.getKamPassword());
            KAMStore store = new KAMStoreImpl(c);
            return store.getKamInfo(kam) != null;
        } catch (SQLException e) {
            return false;
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            }
        }
    }

    private static Kam kam(String kam) {
        DatabaseService db = new DatabaseServiceImpl();
        SystemConfiguration sc = getSystemConfiguration();

        DBConnection c = null;
        try {
            c = db.dbConnection(sc.getKamURL(), sc.getKamUser(),
                    sc.getKamPassword());
            KAMStore store = new KAMStoreImpl(c);
            return store.getKam(kam);
        } catch (SQLException e) {
            return null;
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            }
        }
    }

    private static KAMStore kamstore() {
        DatabaseService db = new DatabaseServiceImpl();
        SystemConfiguration sc = getSystemConfiguration();

        DBConnection c = null;
        try {
            c = db.dbConnection(sc.getKamURL(), sc.getKamUser(),
                    sc.getKamPassword());
            return new KAMStoreImpl(c);
        } catch (SQLException e) {
            return null;
        }
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        printApplicationInfo();

        initializeSystemConfiguration();
        sysconfig = getSystemConfiguration();
        dbservice = new DatabaseServiceImpl();
    }
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     */
    public PhaseFourApplication(String[] args) {
        super(args);

        sysconfig = getSystemConfiguration();
        DatabaseService dbservice = new DatabaseServiceImpl();
        KAMStoreSchemaService kamStoreSchemaService = new KAMStoreSchemaServiceImpl(
                dbservice);
        p4 = new PhaseFourImpl(dbservice, kamStoreSchemaService);
    }
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    }

    private void setUp() throws SQLException, IOException {

        // Setup a database connector to the KAM Store.
        dbservice = new DatabaseServiceImpl();

        if (verbose || debug) {
            reportable.output("Using KAM Store URL: " + sysconfig.getKamURL());
            reportable
                    .output("Using KAM Store User: " + sysconfig.getKamUser());
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Related Classes of org.openbel.framework.core.df.DatabaseServiceImpl

  • org.openbel.framework.common.DBConnectionFailure
  • org.openbel.framework.common.enums.DatabaseType
  • org.openbel.framework.test.KAMStoreTest
  • org.openbel.framework.tools.kamstore.KamComparator
  • org.openbel.framework.tools.kamstore.KamManager
  • org.openbel.framework.tools.OrthologizeTool
  • org.openbel.framework.tools.PhaseFourApplication
  • org.openbel.framework.tools.PhaseZeroApplication
  • java.sql.Statement
  • java.sql.Connection
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