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

Introduction

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

Prototype

public ArrayListHandler() 

Source Link

Document

Creates a new instance of ArrayListHandler using a BasicRowProcessor for conversions.

Usage

From source file:ch.admin.suis.msghandler.log.DbLogService.java

/**
 * Creates the CSV-file in the directory in which the database files are located. If the service was not initialized,
 * this method silently returns./*from ww w.j  a va  2s. c  o  m*/
 */
@SuppressWarnings("unchecked")
public void dump() {
    if (null == connection) {
        // this service was not initialized
        LOG.error("cannot create the DB dump file: the log service was not initialized");
        return;
    }

    File dumpFile = new File(base, "dump.csv"); // TODO make this configurable

    try (BufferedWriter writer = new BufferedWriter(
            new OutputStreamWriter(new FileOutputStream(dumpFile), "ISO-8859-1"))) {

        // read all the available records from the DB
        ArrayList<Object[]> rowSet = (ArrayList<Object[]>) runner.query(connection, "select * from status",
                new ArrayListHandler());

        for (Object[] row : rowSet) {
            for (int i = 0; i < row.length; i++) {
                // replace the null values with empty strings
                row[i] = null == row[i] ? "" : row[i];
            }
            writer.write(MessageFormat.format(DUMP_LINE, row));
        }
    } catch (UnsupportedEncodingException e) {
        LOG.fatal(e);
    } catch (FileNotFoundException e) {
        LOG.fatal("cannot create the DB dump file " + dumpFile.getAbsolutePath() + ". Error : " + e);
    } catch (SQLException e) {
        LOG.fatal("cannot read from the status table: " + e);
    } catch (IOException e) {
        LOG.fatal("cannot write to the dump file: " + e);
    }
}

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From source file:io.seqware.pipeline.plugins.WorkflowSchedulerTest.java

@Test
public void testMetadataOff() {
    launchPlugin("--workflow-accession", "2860", "--host", FileTools.getLocalhost(null).hostname,
            "--no-metadata");

    String s = getOut();//from   w  ww  .  ja  v  a 2  s . c o m
    String firstWorkflowRun = getAndCheckSwid(s);

    BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator();
    List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(),
            "select r.status, r.workflow_id, r.workflow_engine from workflow_run r\n" + "WHERE \n"
                    + "r.sw_accession = ?\n" + "; ",
            Integer.valueOf(firstWorkflowRun));
    Assert.assertTrue(
            "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " "
                    + runQuery.get(0)[1].toString(),
            runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(15));
    WorkflowRun workflowRun = metadata.getWorkflowRun(Integer.valueOf(firstWorkflowRun));
    // check that default keys are present
    Map<String, String> baseMap = MapTools.iniString2Map(workflowRun.getIniFile());
    Assert.assertTrue("base map is metadata", baseMap.containsKey("metadata"));
    Assert.assertTrue("base map has incorrect values", baseMap.get("metadata").equals("no-metadata"));
}

---

From source file:ch.admin.suis.msghandler.log.DbLogService.java

@Override
public List<String> getFiles(String messageId) throws LogServiceException {
    try {//from ww  w .  j av  a 2 s .  co  m
        ArrayList<Object[]> rowSet = (ArrayList<Object[]>) runner.query(connection, SELECT_FILENAME_STATEMENT,
                new Object[] { messageId }, new ArrayListHandler());

        List<String> result = new ArrayList<>(rowSet.size());
        for (Object[] row : rowSet) {
            // we have only one element in the array - the filename and it is a
            // string
            result.add((String) row[0]);
        }

        return result;
    } catch (SQLException e) {
        throw new LogServiceException(e);
    }
}

---

From source file:ch.admin.suis.msghandler.log.DbLogService.java

/**
 * {@inheritDoc }/*from   www .j a va  2s.  c o  m*/
 */
@Override
public List<DBLogEntry> getAllEntries() throws LogServiceException {
    try {
        ArrayList<Object[]> rowSet = (ArrayList<Object[]>) runner.query(connection, SELECT_ALL_STATEMENT,
                new Object[] {}, new ArrayListHandler());

        List<DBLogEntry> results = new ArrayList<>(rowSet.size());
        for (Object[] row : rowSet) {
            DBLogEntry logEntry = parseDBLogEntry(row);
            results.add(logEntry);
        }

        return results;
    } catch (SQLException e) {
        throw new LogServiceException(e);
    }
}

---

From source file:ch.admin.suis.msghandler.log.DbLogService.java

@Override
public List<String> getMessages(LogStatus status) throws LogServiceException {
    try {//from  www  . ja v  a  2 s .  c o  m
        ArrayList<Object[]> rowSet = (ArrayList<Object[]>) runner.query(connection,
                SELECT_MESSAGE_ID_ALL_STATEMENT, new Object[] { status.getCode() }, new ArrayListHandler());

        List<String> result = new ArrayList<>(rowSet.size());
        for (Object[] row : rowSet) {
            // we have only one element in the array - the message ID and it is a
            // string
            result.add((String) row[0]);
        }

        return result;
    } catch (SQLException e) {
        throw new LogServiceException(e);
    }
}

---

From source file:ch.admin.suis.msghandler.log.DbLogService.java

@Override
public boolean isTransparent(String messageId) throws LogServiceException {
    try {//  w  w w  .ja v a 2  s. c o  m
        ArrayList<Object[]> rowSet = (ArrayList<Object[]>) runner.query(connection, SELECT_SOURCE_STATEMENT,
                new Object[] { messageId }, new ArrayListHandler());

        List<Integer> result = new ArrayList<>(rowSet.size());
        for (Object[] row : rowSet) {
            // we have only one element in the array - the message ID and it is a
            // string
            result.add((Integer) row[0]);
        }

        // nothing found, otherwise return the first encountered value
        return result.isEmpty() || Mode.TRANSP.getCode() == result.get(0);
    } catch (SQLException e) {
        throw new LogServiceException(e);
    }
}

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From source file:net.sourceforge.seqware.pipeline.plugins.AttributeAnnotatorET.java

/**
 * Annotate skip with an implicit key of "skip"
 *
 * @param type/*from w  w w.j  a  va 2  s.  c  o m*/
 * @param accession
 * @throws IOException
 */
public void annotateSkipImplicitly(AttributeType type, int accession) throws IOException {
    String query = "SELECT t2." + type.table_name + "_attribute_id, t2.tag, t2.value FROM " + type.table_name
            + "_attribute t2, " + type.table_name + " t1 WHERE " + "t1." + type.table_name + "_id=t2."
            + type.attribute_id_prefix + "_id AND t1.sw_accession=? ORDER BY " + type.table_name
            + "_attribute_id";
    Log.info(query);
    String value = "\"Improperly entered into the LIMS\"";

    String listCommand = "-p net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator " + "-- --"
            + type.parameter_prefix + "-accession " + accession + " --skip true --value " + value;
    int expectedReturnValue = type.skippable ? ReturnValue.SUCCESS : ReturnValue.INVALIDPARAMETERS;
    ITUtility.runSeqWareJar(listCommand, expectedReturnValue, null);
    if (type.skippable) {
        Object[] runQuery = dbCreator.runQuery(new ArrayHandler(),
                "SELECT skip FROM " + type.table_name + " WHERE sw_accession=?", accession);
        Assert.assertTrue("skip value incorrect", runQuery.length == 1 && runQuery[0].equals(true));
        List<Object[]> runQuery1 = dbCreator.runQuery(new ArrayListHandler(), query, accession);
        Assert.assertTrue("first annotation incorrect", runQuery1.size() == 1);
        Assert.assertTrue("first tag incorrect", runQuery1.get(0)[1].equals("skip"));
        Assert.assertTrue("first value incorrect", runQuery1.get(0)[2].equals(value));
    }
}

---

From source file:net.sourceforge.seqware.pipeline.plugins.AttributeAnnotatorET.java

/**
 * Annotate an attribute with both a key and value. Re-annotate and ensure
 * that no duplicates are formed.//  ww w.j av a2 s .com
 *
 * @param type
 * @param accession
 * @throws IOException
 */
public void annotateAndReannotate(AttributeType type, int accession) throws IOException {
    final String funky_key = "funky_key";
    final String funky_second_value = "funky_second_value";
    final String funky_initial_value = "funky_initial_value";
    final String groovy_key = "groovy_key";
    final String groovy_value = "groovy_value";

    String listCommand = "-p net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator " + "-- --"
            + type.parameter_prefix + "-accession " + accession + " --key " + funky_key + " --value "
            + funky_initial_value;
    ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS, null);
    String query = "SELECT t2." + type.table_name + "_attribute_id, t2.tag, t2.value FROM " + type.table_name
            + "_attribute t2, " + type.table_name + " t1 WHERE " + "t1." + type.table_name + "_id=t2."
            + type.attribute_id_prefix + "_id AND t1.sw_accession=? ORDER BY " + type.table_name
            + "_attribute_id";
    Log.info(query);
    List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), query, accession);
    Assert.assertTrue("first annotation incorrect", runQuery.size() == 1);
    Assert.assertTrue("first tag incorrect", runQuery.get(0)[1].equals(funky_key));
    Assert.assertTrue("first value incorrect", runQuery.get(0)[2].equals(funky_initial_value));
    // count records in the database to check for cascading deletes
    List<Object[]> count1 = dbCreator.runQuery(new ArrayListHandler(), COUNT_DB_SIZE);
    // reannotate with same key, different value
    listCommand = "-p net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator " + "-- --"
            + type.parameter_prefix + "-accession " + accession + " --key " + funky_key + " --value "
            + funky_second_value;
    ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS, null);
    // ensure that duplicates are not formed in the database
    runQuery = dbCreator.runQuery(new ArrayListHandler(), query, accession);
    Assert.assertTrue("incorrect resulting number of duplicate annotations, found " + runQuery.size(),
            runQuery.size() == 1);
    Assert.assertTrue("second tag incorrect", runQuery.get(0)[1].equals(funky_key));
    Assert.assertTrue("second value incorrect", runQuery.get(0)[2].equals(funky_second_value));
    // check against cascading deletes
    List<Object[]> count2 = dbCreator.runQuery(new ArrayListHandler(), COUNT_DB_SIZE);
    compareTwoCounts(count1.get(0), count2.get(0));
    // try unrelated annotation
    listCommand = "-p net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator " + "-- --"
            + type.parameter_prefix + "-accession " + accession + " --key " + groovy_key + " --value "
            + groovy_value;
    ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS, null);
    // check results of unrelated annotation
    runQuery = dbCreator.runQuery(new ArrayListHandler(), query, accession);
    Assert.assertTrue("incorrect resulting number of unrelated annotations, found: " + runQuery.size(),
            runQuery.size() == 2);
    Assert.assertTrue("second tag incorrect", runQuery.get(0)[1].equals(funky_key));
    Assert.assertTrue("second value incorrect", runQuery.get(0)[2].equals(funky_second_value));
    Assert.assertTrue("third tag incorrect", runQuery.get(1)[1].equals(groovy_key));
    Assert.assertTrue("third value incorrect", runQuery.get(1)[2].equals(groovy_value));
    List<Object[]> count3 = dbCreator.runQuery(new ArrayListHandler(), COUNT_DB_SIZE);
    compareTwoCounts(count2.get(0), count3.get(0));
}

---

From source file:net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.WorkflowRunConventionsPlugin.java

@Override
public void check(SelectQueryRunner qRunner, SortedMap<Level, Set<String>> result) throws SQLException {
    try {//from   w ww.  j  a va 2 s  .c om
        /**
         * May not be true for downsteam workflow runs
        * List<Integer> executeQuery = qRunner.executeQuery("select sw_accession from workflow_run WHERE workflow_run_id NOT IN (select workflow_run_id FROM ius_workflow_runs);", new ColumnListHandler<Integer>());
        * CheckDB.processOutput(result, Level.TRIVIAL,  "Workflow runs not connected to an IUS via ius_workflow_runs: " , executeQuery);
        **/
        // workflow runs not connected to a study
        String query = IOUtils.toString(
                AttributePlugin.class.getResourceAsStream("workflow_runs_not_connected_to_study.sql"));
        List<Object[]> workflow_run_study_pairs = qRunner.executeQuery(query, new ArrayListHandler());

        List<Integer> unreachableByStudy = new ArrayList<>();
        // number studies -> workflow runs
        SortedMap<Integer, SortedSet<Integer>> reachableByMultipleStudies = new TreeMap<>();

        for (Object[] pair : workflow_run_study_pairs) {
            int studyCount = Integer.valueOf(pair[1].toString());
            if (pair[0] == null) {
                continue;
            }
            int sw_accession = Integer.valueOf(pair[0].toString());
            if (studyCount == 0) {
                unreachableByStudy.add(sw_accession);
            } else if (studyCount > 1) {
                if (!reachableByMultipleStudies.containsKey(studyCount)) {
                    reachableByMultipleStudies.put(studyCount, new TreeSet<Integer>());
                }
                reachableByMultipleStudies.get(studyCount).add(sw_accession);
            }
        }
        CheckDB.processOutput(result, Level.SEVERE, "'Completed' Workflow runs not reachable by studies: ",
                unreachableByStudy);
        // workflow runs connected to more than one study
        if (reachableByMultipleStudies.size() > 0) {
            for (Entry<Integer, SortedSet<Integer>> e : reachableByMultipleStudies.entrySet()) {
                CheckDB.processOutput(result, Level.WARNING,
                        "'Completed' Workflow runs reachable by " + e.getKey() + " studies: ",
                        new ArrayList<>(e.getValue()));
            }
        }
        query = IOUtils.toString(
                AttributePlugin.class.getResourceAsStream("workflow_runs_not_connected_in_hierarchy.sql"));
        List<Integer> executeQuery = qRunner.executeQuery(query, new ColumnListHandler<Integer>());
        CheckDB.processOutput(result, Level.SEVERE,
                "'Completed' Workflow runs reachable by ius_workflow_runs but not via the processing_hierarchy: ",
                executeQuery);

        query = IOUtils.toString(AttributePlugin.class.getResourceAsStream("new_input_files_versus_old.sql"));
        executeQuery = qRunner.executeQuery(query, new ColumnListHandler<Integer>());
        CheckDB.processOutput(result, Level.TRIVIAL,
                "Workflow runs with input files via workflow_run_input_files but not via the processing hierarchy: ",
                executeQuery);

        query = IOUtils.toString(AttributePlugin.class.getResourceAsStream("old_input_files_versus_new.sql"));
        executeQuery = qRunner.executeQuery(query, new ColumnListHandler<Integer>());
        CheckDB.processOutput(result, Level.TRIVIAL,
                "Workflow runs with input files via the processing hierarchy but not via workflow_run_input_files: ",
                executeQuery);

    } catch (IOException ex) {
        throw new RuntimeException(ex);
    }

}

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From source file:net.sourceforge.seqware.pipeline.plugins.FileLinkerTest.java

@Test
public void testFileLinkerNormal() {
    String path = FileLinkerTest.class.getResource("file_linker_test.txt").getPath();

    launchPlugin("--workflow-accession", "4", "--file-list-file", path);

    String s = getOut();//from  ww w . j av a2  s .c  o  m
    String firstWorkflowRun = getAndCheckSwid(s);

    BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator();
    List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(),
            "select f.file_path, f.meta_type, i.sw_accession from workflow_run r, processing p, processing_files pf, file f, processing_ius pi, ius i\n"
                    + "WHERE \n" + "r.sw_accession = ?\n" + "AND p.workflow_run_id = r.workflow_run_id\n"
                    + "AND p.processing_id = pf.processing_id\n" + "AND pf.file_id = f.file_id\n"
                    + "AND p.processing_id = pi.processing_id \n" + "AND pi.ius_id = i.ius_id\n"
                    + "ORDER BY f.sw_accession\n" + "; ",
            Integer.valueOf(firstWorkflowRun));
    Assert.assertTrue("first file values were incorrect",
            runQuery.get(0)[0].equals("funky_file1.gz") && runQuery.get(0)[1].equals("txt"));
    Assert.assertTrue("second file values were incorrect",
            runQuery.get(1)[0].equals("funky_file2.gz") && runQuery.get(1)[1].equals("txt"));
    Assert.assertTrue("ius links  were correct",
            runQuery.get(0)[2].equals(4765) && runQuery.get(1)[2].equals(4765));
    // check that we can get them back via metadata methods as well
    WorkflowRun workflowRun = metadata.getWorkflowRunWithWorkflow(firstWorkflowRun);
    Assert.assertTrue("could not retrieve optional fields via metadata",
            workflowRun.getSwAccession().equals(Integer.valueOf(firstWorkflowRun)));
    Assert.assertTrue("parent workflow incorrect", workflowRun.getWorkflow().getSwAccession() == 4);
    String workflowRunReport = metadata.getWorkflowRunReport(Integer.valueOf(firstWorkflowRun));
    // look for files using the gross metadata way
    Assert.assertTrue("files could not be found using the metadata workflow run report",
            workflowRunReport.contains("funky_file1.gz") && workflowRunReport.contains("funky_file2.gz"));
    s = s.split("\n")[1];
    int secondWorkflowRun = Integer.valueOf(getAndCheckSwid(s));
    workflowRunReport = metadata.getWorkflowRunReport(secondWorkflowRun);
    Assert.assertTrue("second set of files could not be found using the metadata workflow run report",
            workflowRunReport.contains("abc1.gz") && workflowRunReport.contains("abc2.gz"));
}

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