Example usage for org.apache.commons.dbutils.handlers ScalarHandler ScalarHandler

List of usage examples for org.apache.commons.dbutils.handlers ScalarHandler ScalarHandler

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Introduction

In this page you can find the example usage for org.apache.commons.dbutils.handlers ScalarHandler ScalarHandler.

Prototype

public ScalarHandler()

Source Link

Document

Creates a new instance of ScalarHandler.

Usage

From source file:io.dockstore.client.cli.BasicET.java

/**
 * Tests the case where a manually registered quay container matching an automated build should be treated as a separate auto build (see issue 106)
 *//*from   w ww  .jav a2 s.  c om*/
@Test
public void testManualQuaySameAsAutoQuay() {
    Client.main(new String[] { "--config", ResourceHelpers.resourceFilePath("config_file.txt"), "tool",
            "manual_publish", "--registry", Registry.QUAY_IO.toString(), "--namespace", "dockstoretestuser",
            "--name", "quayandgithub", "--git-url", "git@github.com:DockstoreTestUser/dockstore-whalesay.git",
            "--git-reference", "master", "--toolname", "regular", "--script" });

    final CommonTestUtilities.TestingPostgres testingPostgres = getTestingPostgres();
    final long count = testingPostgres.runSelectStatement(
            "select count(*) from tool where mode != 'MANUAL_IMAGE_PATH' and path = 'quay.io/dockstoretestuser/quayandgithub' and toolname = 'regular'",
            new ScalarHandler<>());
    Assert.assertTrue("the container should be Auto", count == 1);
}

From source file:com.xeiam.yank.Yank.java

/**
 * Return just one scalar given a an SQL statement
 *
 * @param scalarType The Class of the desired return scalar matching the table
 * @param params The replacement parameters
 * @return The scalar Object/*from  w w w . j a v a 2  s  . c o m*/
 * @throws SQLStatementNotFoundException if an SQL statement could not be found for the given sqlKey String
 */
public static <T> T queryScalar(String sql, Class<T> scalarType, Object[] params) {

    T returnObject = null;

    try {

        ScalarHandler<T> resultSetHandler = new ScalarHandler<T>();

        returnObject = new QueryRunner(YANK_POOL_MANAGER.getDataSource()).query(sql, resultSetHandler, params);

    } catch (SQLException e) {
        handleSQLException(e);
    }

    return returnObject;
}

From source file:io.dockstore.client.cli.GeneralET.java

/**
 * Tests altering the cwl and dockerfile paths to invalid locations (quick registered)
 *///  w ww  . jav  a 2s.co  m
@Test
public void testVersionTagWDLCWLAndDockerfilePathsAlteration() {
    Client.main(new String[] { "--config", ResourceHelpers.resourceFilePath("config_file2.txt"), "tool",
            "version_tag", "update", "--entry", "quay.io/dockstoretestuser2/quayandgithub", "--name", "master",
            "--cwl-path", "/testDir/Dockstore.cwl", "--wdl-path", "/testDir/Dockstore.wdl", "--dockerfile-path",
            "/testDir/Dockerfile", "--script" });

    final CommonTestUtilities.TestingPostgres testingPostgres = getTestingPostgres();
    final long count = testingPostgres.runSelectStatement(
            "select count(*) from tag,tool_tag,tool where tool.path = 'quay.io/dockstoretestuser2/quayandgithub' and tool.toolname = '' and tool.id=tool_tag.toolid and tag.id=tool_tag.tagid and valid = 'f'",
            new ScalarHandler<>());
    Assert.assertTrue("there should now be an invalid tag, found " + count, count == 1);

    Client.main(new String[] { "--config", ResourceHelpers.resourceFilePath("config_file2.txt"), "tool",
            "version_tag", "update", "--entry", "quay.io/dockstoretestuser2/quayandgithub", "--name", "master",
            "--cwl-path", "/Dockstore.cwl", "--wdl-path", "/Dockstore.wdl", "--dockerfile-path", "/Dockerfile",
            "--script" });

    Client.main(new String[] { "--config", ResourceHelpers.resourceFilePath("config_file2.txt"), "tool",
            "refresh", "--entry", "quay.io/dockstoretestuser2/quayandgithub", "--script" });

    final long count2 = testingPostgres.runSelectStatement(
            "select count(*) from tag,tool_tag,tool where tool.path = 'quay.io/dockstoretestuser2/quayandgithub' and tool.toolname = '' and tool.id=tool_tag.toolid and tag.id=tool_tag.tagid and valid = 'f'",
            new ScalarHandler<>());
    Assert.assertTrue("the invalid tag should now be valid, found " + count2, count2 == 0);
}

From source file:io.dockstore.client.cli.ClientIT.java

@Test
public void manualRegisterABunchOfValidEntries() throws IOException {
    Client.main(new String[] { "--config", getConfigFileLocation(true), "manual_publish", "--registry",
            Registry.QUAY_IO.toString(), "--namespace", "pypi", "--name", "bd2k-python-lib", "--git-url",
            "git@github.com:funky-user/test2.git", "--git-reference", "refs/head/master" });
    Client.main(new String[] { "--config", getConfigFileLocation(true), "manual_publish", "--registry",
            Registry.QUAY_IO.toString(), "--namespace", "pypi", "--name", "bd2k-python-lib", "--git-url",
            "git@github.com:funky-user/test2.git", "--git-reference", "refs/head/master", "--toolname",
            "test1" });
    Client.main(new String[] { "--config", getConfigFileLocation(true), "manual_publish", "--registry",
            Registry.QUAY_IO.toString(), "--namespace", "pypi", "--name", "bd2k-python-lib", "--git-url",
            "git@github.com:funky-user/test2.git", "--git-reference", "refs/head/master", "--toolname",
            "test2" });
    Client.main(new String[] { "--config", getConfigFileLocation(true), "manual_publish", "--registry",
            Registry.DOCKER_HUB.toString(), "--namespace", "pypi", "--name", "bd2k-python-lib", "--git-url",
            "git@github.com:funky-user/test2.git", "--git-reference", "refs/head/master" });
    Client.main(new String[] { "--config", getConfigFileLocation(true), "manual_publish", "--registry",
            Registry.DOCKER_HUB.toString(), "--namespace", "pypi", "--name", "bd2k-python-lib", "--git-url",
            "git@github.com:funky-user/test2.git", "--git-reference", "refs/head/master", "--toolname",
            "test1" });

    // verify DB/* w  w w  .  j ava  2 s. co m*/
    final TestingPostgres testingPostgres = getTestingPostgres();
    final long count = testingPostgres.runSelectStatement(
            "select count(*) from container where name = 'bd2k-python-lib'", new ScalarHandler<>());
    Assert.assertTrue("should see three entries", count == 5);
}

From source file:io.dockstore.client.cli.BasicET.java

/**
 * Tests the case where a manually registered quay container has the same path as an auto build but different git repo
 *///from  w ww . j a v a  2 s.  c  om
@Test
public void testManualQuayToAutoSamePathDifferentGitRepo() {
    Client.main(new String[] { "--config", ResourceHelpers.resourceFilePath("config_file.txt"), "tool",
            "manual_publish", "--registry", Registry.QUAY_IO.toString(), "--namespace", "dockstoretestuser",
            "--name", "quayandgithub", "--git-url",
            "git@github.com:DockstoreTestUser/dockstore-whalesay-alternate.git", "--git-reference", "master",
            "--toolname", "alternate", "--cwl-path", "/testDir/Dockstore.cwl", "--dockerfile-path",
            "/testDir/Dockerfile", "--script" });

    final CommonTestUtilities.TestingPostgres testingPostgres = getTestingPostgres();
    final long count = testingPostgres.runSelectStatement(
            "select count(*) from tool where mode = 'MANUAL_IMAGE_PATH' and path = 'quay.io/dockstoretestuser/quayandgithub' and toolname = 'alternate'",
            new ScalarHandler<>());
    Assert.assertTrue("the container should be Manual still", count == 1);
}

From source file:io.dockstore.client.cli.GeneralWorkflowET.java

/**
 * This tests attempting to publish a workflow with no valid versions
 */// www  .  ja  v  a  2  s.  c om
@Test
public void testRefreshAndPublishInvalid() {
    // Set up DB
    final CommonTestUtilities.TestingPostgres testingPostgres = getTestingPostgres();

    // refresh all
    Client.main(new String[] { "--config", ResourceHelpers.resourceFilePath("config_file2.txt"), "workflow",
            "refresh", "--script" });

    // refresh individual
    Client.main(new String[] { "--config", ResourceHelpers.resourceFilePath("config_file2.txt"), "workflow",
            "refresh", "--entry", "DockstoreTestUser2/dockstore_empty_repo", "--script" });

    // check that no valid versions
    final long count = testingPostgres
            .runSelectStatement("select count(*) from workflowversion where valid='t'", new ScalarHandler<>());
    Assert.assertTrue("there should be 0 valid versions, there are " + count, count == 0);

    // try and publish
    systemExit.expectSystemExitWithStatus(Client.API_ERROR);
    Client.main(new String[] { "--config", ResourceHelpers.resourceFilePath("config_file2.txt"), "workflow",
            "publish", "--entry", "DockstoreTestUser2/dockstore_empty_repo", "--script" });
}

From source file:com.aw.core.dao.DAOSql.java

/**
 * Helper method used to retrieve a COLUMN using standard SQL sintaxis
 * The query must return a single column
 *
 * @param sql        SQL query//from   w  w w .  j  av a  2 s  . c o m
 * @param filterKeys key used to restrict the search
 * @return First Row First column , NULL if no row
 */
public Object findObjectGetColumn(String sql, Object[] filterKeys) {
    try {
        return new QueryRunner().query(getHibernateConnection(), sql, filterKeys, new ScalarHandler());
    } catch (SQLException e) {
        throw AWBusinessException.wrapUnhandledException(logger, e);
    }
}

From source file:info.pancancer.arch3.persistence.PostgreSQL.java

public long getProvisionCount(ProvisionState status) {
    return this.runSelectStatement("select count(*) from provision where status = ?", new ScalarHandler<Long>(),
            status.toString());// w  ww  .  ja  v a 2 s .  c  om
}

From source file:io.dockstore.client.cli.WorkflowET.java

/**
 * This test checks that a user can successfully refresh their workflows (only stubs)
 * @throws IOException//from www.  j  av a  2 s. com
 * @throws TimeoutException
 * @throws ApiException
 */
@Test
public void testRefreshAllForAUser() throws IOException, TimeoutException, ApiException {
    final CommonTestUtilities.TestingPostgres testingPostgres = getTestingPostgres();
    testingPostgres
            .runUpdateStatement("update enduser set isadmin = 't' where username = 'DockstoreTestUser2';");
    long userId = 1;

    final ApiClient webClient = getWebClient();
    UsersApi usersApi = new UsersApi(webClient);
    final List<Workflow> workflow = usersApi.refreshWorkflows(userId);

    // Check that there are multiple workflows
    final long count = testingPostgres.runSelectStatement("select count(*) from workflow",
            new ScalarHandler<>());
    assertTrue("Workflow entries should exist", count > 0);

    // Check that there are only stubs (no workflow version)
    final long count2 = testingPostgres.runSelectStatement("select count(*) from workflowversion",
            new ScalarHandler<>());
    assertTrue("No entries in workflowversion", count2 == 0);
    final long count3 = testingPostgres.runSelectStatement(
            "select count(*) from workflow where mode = '" + Workflow.ModeEnum.FULL + "'",
            new ScalarHandler<>());
    assertTrue("No workflows are in full mode", count3 == 0);

}

From source file:com.aw.core.dao.DAOSql.java

/**
 * Helper method used to retrieve the select count(*)
 *
 * @param sqlFromWhereClause SQL query without the SELECT section: "FROM x where X=y"
 * @param filterKeys         key used to restrict the search
 * @return number of rows that return the query
 *///ww w.j  ava  2 s.c  o m
public int findCountRows(String sqlFromWhereClause, Object[] filterKeys) {
    String sql = "SELECT count(*) " + sqlFromWhereClause;
    try {
        if (logger.isDebugEnabled()) {
            logger.debug("Executing:" + AWQueryRunner.buildSQLLog(sql, filterKeys));
        }
        Number num = (Number) new QueryRunner().query(getHibernateConnection(), sql, filterKeys,
                new ScalarHandler());
        return num.intValue();
    } catch (SQLException e) {
        throw AWBusinessException.wrapUnhandledException(logger, e);
    }
}