Example usage for org.apache.commons.lang ArrayUtils addAll

List of usage examples for org.apache.commons.lang ArrayUtils addAll

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Introduction

In this page you can find the example usage for org.apache.commons.lang ArrayUtils addAll.

Prototype

public static double[] addAll(double[] array1, double[] array2)

Source Link

Document

Adds all the elements of the given arrays into a new array.

Usage

From source file:edu.harvard.iq.dvn.ingest.dsb.impl.DvnRJobRequest.java

public List<String> getUpdatedVariableTypesAsString() {
    int[] vt;/*from   w  w w .j a  va  2  s .co m*/

    if (hasRecodedVariables()) {
        vt = ArrayUtils.addAll(getVariableTypes(), getRecodedVarTypeSet());
    } else {
        vt = getVariableTypes();
    }

    List<String> vts = new ArrayList<String>();

    for (int i = 0; i < vt.length; i++) {
        vts.add(Integer.toString(vt[i]));
    }
    return vts;
}

From source file:de.tudarmstadt.ukp.dkpro.core.corenlp.CoreNlpDependencyParserTest.java

private JCas runTest(String aLanguage, String aVariant, String aText, Object... aExtraParams) throws Exception {
    AssumeResource.assumeResource(CoreNlpDependencyParser.class, "depparser", aLanguage, aVariant);

    AggregateBuilder aggregate = new AggregateBuilder();

    aggregate.add(createEngineDescription(CoreNlpPosTagger.class));
    Object[] params = new Object[] { CoreNlpDependencyParser.PARAM_VARIANT, aVariant,
            CoreNlpDependencyParser.PARAM_PRINT_TAGSET, true };
    params = ArrayUtils.addAll(params, aExtraParams);
    aggregate.add(createEngineDescription(CoreNlpDependencyParser.class, params));

    return TestRunner.runTest(aggregate.createAggregateDescription(), aLanguage, aText);
}

From source file:edu.harvard.iq.dvn.ingest.dsb.impl.DvnRJobRequest.java

public List<String> getUpdatedVariableTypesWithBooleanAsString() {
    int[] vt;//  w  w  w . j  av  a2s  .c o  m

    if (hasRecodedVariables()) {
        vt = ArrayUtils.addAll(getVariableTypesWithBoolean(), getRecodedVarTypeSet());
    } else {
        vt = getVariableTypesWithBoolean();
    }

    List<String> vts = new ArrayList<String>();

    for (int i = 0; i < vt.length; i++) {
        vts.add(Integer.toString(vt[i]));
    }
    return vts;
}

From source file:canreg.client.gui.analysis.FrequenciesByYearInternalFrame.java

public void createPivot(String fileName) {
    String[] columnNames = new String[resultTable.getColumnCount()];

    // We need 3 columns to work with        
    if (columnNames.length != 3) {
        return;//  w  w w.  ja v a 2 s .  c  o m
    }
    // TODO Extend this to at least 4
    String[] nextLine = new String[resultTable.getColumnCount()];

    // Find the column names
    for (int j = 0; j < columnNames.length; j++) {
        columnNames[j] = resultTable.getColumnName(j);
    }

    // variable we lock
    String lockVariable = columnNames[1];

    HashMap<String, HashMap> data = new HashMap<String, HashMap>();
    HashMap<String, String> years;
    Set<String> allYears = new TreeSet<String>();

    // load up the data
    for (int i = 0; i < resultTable.getRowCount(); i++) {
        String year, cases, code;

        for (int j = 0; j < nextLine.length; j++) {
            nextLine[j] = resultTable.getValueAt(i, j).toString();
        }
        year = nextLine[0];
        if (year.trim().length() == 0) {
            year = "MISSING";
        }

        allYears.add(year);

        code = nextLine[1];

        if (code.trim().length() == 0) {
            code = "MISSING";
        }

        cases = nextLine[2];

        years = data.get(code);
        if (years == null) {
            years = new HashMap<String, String>();
            data.put(code, years);
        }
        years.put(year, cases);
    }

    // find variables element for the lockedvariable
    DatabaseVariablesListElement lockedDatabaseVariablesListElement = null;
    for (DatabaseVariablesListElement vle : chosenVariables) {
        if (vle.getShortName().compareToIgnoreCase(lockVariable) == 0) {
            lockedDatabaseVariablesListElement = vle;
        }
    }

    if (lockedDatabaseVariablesListElement == null) {
        return;
    } // this happens if user has updated the selection of variables

    int dictionaryID = lockedDatabaseVariablesListElement.getDictionaryID();
    Dictionary dict = null;
    if (dictionaryID >= 0) {
        dict = dictionary.get(dictionaryID);
    }

    String[] allYearsArray = allYears.toArray(new String[0]);
    Writer writer = null;
    try {
        writer = new FileWriter(fileName);

        // Write the column names
        String[] codeArray = { lockedDatabaseVariablesListElement.getFullName(), lockVariable };

        String[] headers = (String[]) ArrayUtils.addAll(codeArray, allYearsArray);

        String[] codes = data.keySet().toArray(new String[0]);
        Arrays.sort(codes);

        CSVFormat format = CSVFormat.DEFAULT.withDelimiter(',').withHeader(headers);

        CSVPrinter csvPrinter = new CSVPrinter(writer, format);

        // write the rows    
        for (String code : codes) {
            LinkedList<String> row = new LinkedList<String>();
            if (dict != null) {
                DictionaryEntry dictionaryEntry = dict.getDictionaryEntry(code);
                if (dictionaryEntry != null) {
                    row.add(dictionaryEntry.getDescription());
                } else {
                    row.add("");
                }
            } else {
                row.add("");
            }
            row.add(code);

            years = data.get(code);
            for (String year : allYears) {
                String cell = years.get(year);
                if (cell == null) {
                    row.add("0");
                } else {
                    row.add(cell);
                }
            }
            csvPrinter.printRecord(row);
        }
        csvPrinter.flush();

    } catch (IOException ex) {
        // JOptionPane.showMessageDialog(this, "File NOT written.\n" + ex.getLocalizedMessage(), "ERROR", JOptionPane.ERROR_MESSAGE);
        Logger.getLogger(FrequenciesByYearInternalFrame.class.getName()).log(Level.SEVERE, null, ex);
    } finally {
        try {
            if (writer != null) {
                writer.close();
            }
        } catch (IOException ex) {
            Logger.getLogger(FrequenciesByYearInternalFrame.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
}

From source file:com.oneops.inductor.WorkOrderExecutor.java

private Set<String> syncServiceCookbooks(CmsWorkOrderSimple wo, String woBomCircuit, String user,
        String[] rsyncCmdLineWithKey, String host, String port, String logKey, String keyFile) {
    logger.info("checking for any service cookbook to be rsynched ..");
    //rsync cloud services cookbooks
    String cloudName = wo.getCloud().getCiName();
    Set<String> serviceCookbookPaths = new HashSet<>();
    Map<String, Map<String, CmsCISimple>> services = wo.getServices();
    if (services != null) {
        for (String serviceName : services.keySet()) { // for each service
            CmsCISimple serviceCi = services.get(serviceName).get(cloudName);
            if (serviceCi != null) {
                String serviceClassName = serviceCi.getCiClassName();
                String serviceCookbookCircuit = getCookbookPath(serviceClassName);
                if (!serviceCookbookCircuit.equals(woBomCircuit)) {
                    //this service class is not in the same circuit as that of the bom ci getting deployed.
                    //Go ahead and include the cookbook of this service to rsync to remote
                    String serviceCookbookBaseDir = config.getCircuitDir().replace("packer",
                            serviceCookbookCircuit);
                    String serviceClassNameShort = serviceClassName
                            .substring(serviceClassName.lastIndexOf(".") + 1);
                    String serviceCookbookPath = serviceCookbookBaseDir + "/components/cookbooks/"
                            + serviceClassNameShort.toLowerCase() + "/";
                    logger.info("service-serviceCookbookPath: " + serviceCookbookPath);
                    if (new File(serviceCookbookPath).exists()) {
                        String serviceCookbookCircuitPath = "/home/" + user + "/" + serviceCookbookCircuit
                                + "/components/cookbooks";
                        serviceCookbookPaths.add(serviceCookbookCircuitPath);
                        String destination = serviceCookbookCircuitPath + "/"
                                + serviceClassNameShort.toLowerCase() + "/";

                        String remoteCmd = "mkdir -p " + destination;
                        String[] cmd = (String[]) ArrayUtils.addAll(sshCmdLine,
                                new String[] { keyFile, "-p " + port, user + "@" + host, remoteCmd });
                        logger.info(logKey + " ### EXEC: " + user + "@" + host + " " + remoteCmd);
                        ProcessResult result = processRunner.executeProcessRetry(
                                new ExecutionContext(wo, cmd, getLogKey(wo), getRetryCountForWorkOrder(wo)));
                        if (result.getResultCode() != 0) {
                            logger.error(logKey + " Error while creating service cookbook directory on remote");
                        }// w  ww . ja  v  a2 s. com

                        String[] cmdLine = (String[]) ArrayUtils.addAll(rsyncCmdLineWithKey,
                                new String[] { serviceCookbookPath, user + "@" + host + ":" + destination });

                        logger.info(logKey + " ### SYNC Service cookbook: " + serviceCookbookPath);

                        if (!host.equals(TEST_HOST)) {
                            result = processRunner
                                    .executeProcessRetry(new ExecutionContext(wo, cmdLine, logKey, retryCount));
                            if (result.getResultCode() > 0) {
                                wo.setComments("FATAL: "
                                        + generateRsyncErrorMessage(result.getResultCode(), host + ":" + port));
                                return null;
                            }
                        }
                    } else {
                        logger.warn("Cookbook " + serviceCookbookPath + " does not exist on this inductor");
                    }
                }
            }
        }
    }
    return serviceCookbookPaths;
}

From source file:au.org.ala.biocache.web.WMSController.java

/**
 * Get bounding box for a query.//from  ww w. j  av  a  2  s . c o m
 *
 * @param requestParams
 * @return
 * @throws Exception
 */
double[] getBBox(SpatialSearchRequestParams requestParams) throws Exception {
    double[] bbox = new double[4];
    String[] sort = { "longitude", "latitude", "longitude", "latitude" };
    String[] dir = { "asc", "asc", "desc", "desc" };

    //remove instances of null longitude or latitude
    String[] fq = (String[]) ArrayUtils.addAll(getFq(requestParams),
            new String[] { "longitude:[* TO *]", "latitude:[* TO *]" });
    requestParams.setFq(fq);
    requestParams.setPageSize(10);

    for (int i = 0; i < sort.length; i++) {
        requestParams.setSort(sort[i]);
        requestParams.setDir(dir[i]);
        requestParams.setFl(sort[i]);

        SolrDocumentList sdl = searchDAO.findByFulltext(requestParams);
        if (sdl != null && sdl.size() > 0) {
            if (sdl.get(0) != null) {
                bbox[i] = (Double) sdl.get(0).getFieldValue(sort[i]);
            } else {
                logger.error("searchDAO.findByFulltext returning SolrDocumentList with null records");
            }
        }
    }
    return bbox;
}

From source file:gda.hrpd.pmac.EpicsCVScanController.java

private double[] get2Theta() {
    double[] x1 = ArrayUtils.EMPTY_DOUBLE_ARRAY;
    try {//from ww w .j  a v  a  2s  .  c o m
        // logger.info("gets MAC1X");
        x1 = getMAC1X();
        // logger.info("gets MAC1X DONE");
    } catch (TimeoutException e) {
        logger.error("Timeout while gets MAC1X", e);
        e.printStackTrace();
    } catch (CAException e) {
        logger.error("CAException while gets MAC1X", e);
        e.printStackTrace();
    } catch (InterruptedException e) {
        logger.error("InterruptedException while gets MAC1X", e);
    }
    double[] x2 = ArrayUtils.EMPTY_DOUBLE_ARRAY;
    try {
        // logger.info("gets MAC2X");
        x2 = getMAC2X();
        // logger.info("gets MAC2X DONE");
    } catch (TimeoutException e) {
        logger.error("Timeout while gets MAC2X", e);
        e.printStackTrace();
    } catch (CAException e) {
        logger.error("CAException while gets MAC2X", e);
        e.printStackTrace();
    } catch (InterruptedException e) {
        logger.error("InterruptedException while gets MAC2X", e);
    }
    double[] x3 = ArrayUtils.EMPTY_DOUBLE_ARRAY;
    try {
        // logger.info("gets MAC3X");
        x3 = getMAC3X();
        // logger.info("gets MAC3X DONE");
    } catch (TimeoutException e) {
        logger.error("Timeout while gets MAC3X", e);
        e.printStackTrace();
    } catch (CAException e) {
        logger.error("CAException while gets MAC3X", e);
        e.printStackTrace();
    } catch (InterruptedException e) {
        logger.error("InterruptedException while gets MAC3X", e);
    }
    double[] x4 = ArrayUtils.EMPTY_DOUBLE_ARRAY;
    try {
        // logger.info("gets MAC4X");
        x4 = getMAC4X();
        // logger.info("gets MAC4X DONE");
    } catch (TimeoutException e) {
        logger.error("Timeout while gets MAC4X", e);
        e.printStackTrace();
    } catch (CAException e) {
        logger.error("CAException while gets MAC4X", e);
        e.printStackTrace();
    } catch (InterruptedException e) {
        logger.error("InterruptedException while gets MAC4X", e);
    }
    double[] x5 = ArrayUtils.EMPTY_DOUBLE_ARRAY;
    try {
        // logger.info("gets MAC5X");
        x5 = getMAC5X();
        // logger.info("gets MAC5X DONE");
    } catch (TimeoutException e) {
        logger.error("Timeout while gets MAC5X", e);
        e.printStackTrace();
    } catch (CAException e) {
        logger.error("CAException while gets MAC5X", e);
        e.printStackTrace();
    } catch (InterruptedException e) {
        logger.error("InterruptedException while gets MAC5X", e);
    }
    return ArrayUtils.subarray(
            ArrayUtils.addAll(ArrayUtils.addAll(ArrayUtils.addAll(ArrayUtils.addAll(x1, x2), x3), x4), x5),
            16500, 305000);
}

From source file:au.org.ala.biocache.dao.SearchDAOImpl.java

/**
 * Writes the index fields to the supplied output stream in CSV format.
 *
 * DM: refactored to split the query by month to improve performance.
 * Further enhancements possible:/*from w  ww.jav  a  2s  .c o  m*/
 * 1) Multi threaded
 * 2) More filtering, by year or decade..
 *
 * @param downloadParams
 * @param out
 * @param includeSensitive
 * @throws Exception
 */
public Map<String, Integer> writeResultsFromIndexToStream(final DownloadRequestParams downloadParams,
        OutputStream out, boolean includeSensitive, final DownloadDetailsDTO dd, boolean checkLimit)
        throws Exception {
    long start = System.currentTimeMillis();
    final Map<String, Integer> uidStats = new HashMap<String, Integer>();
    if (server == null) {
        initServer();
    }
    try {
        SolrQuery solrQuery = new SolrQuery();
        formatSearchQuery(downloadParams);

        String dFields = downloadParams.getFields();

        if (includeSensitive) {
            //include raw latitude and longitudes
            dFields = dFields
                    .replaceFirst("decimalLatitude.p",
                            "sensitive_latitude,sensitive_longitude,decimalLatitude.p")
                    .replaceFirst(",locality,", ",locality,sensitive_locality,");
        }

        StringBuilder sb = new StringBuilder(dFields);
        if (!downloadParams.getExtra().isEmpty()) {
            sb.append(",").append(downloadParams.getExtra());
        }

        String[] requestedFields = sb.toString().split(",");
        List<String>[] indexedFields = downloadFields.getIndexFields(requestedFields);
        logger.debug("Fields included in download: " + indexedFields[0]);
        logger.debug("Fields excluded from download: " + indexedFields[1]);
        logger.debug("The headers in downloads: " + indexedFields[2]);

        //set the fields to the ones that are available in the index
        final String[] fields = indexedFields[0].toArray(new String[] {});
        solrQuery.setFields(fields);
        StringBuilder qasb = new StringBuilder();
        if (!"none".equals(downloadParams.getQa())) {
            solrQuery.addField("assertions");
            if (!"all".equals(downloadParams.getQa())) {
                //add all the qa fields
                qasb.append(downloadParams.getQa());
            }
        }
        solrQuery.addField("institution_uid").addField("collection_uid").addField("data_resource_uid")
                .addField("data_provider_uid");

        //add context information
        updateQueryContext(downloadParams);
        solrQuery.setQuery(buildSpatialQueryString(downloadParams));
        solrQuery.setFacetMinCount(1);
        solrQuery.setFacetLimit(-1);

        //get the assertion facets to add them to the download fields
        boolean getAssertionsFromFacets = "all".equals(downloadParams.getQa());
        SolrQuery monthAssertionsQuery = getAssertionsFromFacets
                ? solrQuery.getCopy().addFacetField("month", "assertions")
                : solrQuery.getCopy().addFacetField("month");
        if (getAssertionsFromFacets) {
            //set the order for the facet to be based on the index - this will force the assertions to be returned in the same order each time
            //based on alphabetical sort.  The number of QA's may change between searches so we can't guarantee that the order won't change
            monthAssertionsQuery.add("f.assertions.facet.sort", "index");
        }
        QueryResponse facetQuery = runSolrQuery(monthAssertionsQuery, downloadParams.getFq(), 0, 0, "score",
                "asc");

        //set the totalrecords for the download details
        dd.setTotalRecords(facetQuery.getResults().getNumFound());
        if (checkLimit && dd.getTotalRecords() < MAX_DOWNLOAD_SIZE) {
            checkLimit = false;
        }

        //get the month facets to add them to the download fields get the assertion facets.
        List<Count> splitByFacet = null;

        for (FacetField facet : facetQuery.getFacetFields()) {
            if (facet.getName().equals("assertions") && facet.getValueCount() > 0) {
                for (FacetField.Count facetEntry : facet.getValues()) {
                    if (qasb.length() > 0)
                        qasb.append(",");
                    qasb.append(facetEntry.getName());
                }
            }
            if (facet.getName().equals("month") && facet.getValueCount() > 0) {
                splitByFacet = facet.getValues();
            }
        }

        String qas = qasb.toString();
        final String[] qaFields = qas.equals("") ? new String[] {} : qas.split(",");
        String[] qaTitles = downloadFields.getHeader(qaFields, false);

        String[] header = org.apache.commons.lang3.ArrayUtils.addAll(indexedFields[2].toArray(new String[] {}),
                qaTitles);

        //construct correct RecordWriter based on the supplied fileType
        final au.org.ala.biocache.RecordWriter rw = downloadParams.getFileType().equals("csv")
                ? new CSVRecordWriter(out, header, downloadParams.getSep(), downloadParams.getEsc())
                : new ShapeFileRecordWriter(downloadParams.getFile(), out,
                        (String[]) ArrayUtils.addAll(fields, qaFields));

        if (rw instanceof ShapeFileRecordWriter) {
            dd.setHeaderMap(((ShapeFileRecordWriter) rw).getHeaderMappings());
        }

        //order the query by _docid_ for faster paging
        solrQuery.addSortField("_docid_", ORDER.asc);

        //for each month create a separate query that pages through 500 records per page
        List<SolrQuery> queries = new ArrayList<SolrQuery>();
        if (splitByFacet != null) {
            for (Count facet : splitByFacet) {
                if (facet.getCount() > 0) {
                    SolrQuery splitByFacetQuery = solrQuery.getCopy()
                            .addFilterQuery(facet.getFacetField().getName() + ":" + facet.getName());
                    splitByFacetQuery.setFacet(false);
                    queries.add(splitByFacetQuery);
                }
            }
            SolrQuery remainderQuery = solrQuery.getCopy()
                    .addFilterQuery("-" + splitByFacet.get(0).getFacetField().getName() + ":[* TO *]");
            queries.add(0, remainderQuery);
        } else {
            queries.add(0, solrQuery);
        }

        //multi-thread the requests...
        ExecutorService pool = Executors.newFixedThreadPool(6);
        Set<Future<Integer>> futures = new HashSet<Future<Integer>>();
        final AtomicInteger resultsCount = new AtomicInteger(0);
        final boolean threadCheckLimit = checkLimit;

        //execute each query, writing the results to stream
        for (final SolrQuery splitByFacetQuery : queries) {
            //define a thread
            Callable<Integer> solrCallable = new Callable<Integer>() {

                int startIndex = 0;

                @Override
                public Integer call() throws Exception {
                    QueryResponse qr = runSolrQuery(splitByFacetQuery, downloadParams.getFq(),
                            downloadBatchSize, startIndex, "_docid_", "asc");
                    int recordsForThread = 0;
                    logger.debug(splitByFacetQuery.getQuery() + " - results: " + qr.getResults().size());

                    while (qr != null && !qr.getResults().isEmpty()) {
                        logger.debug("Start index: " + startIndex + ", " + splitByFacetQuery.getQuery());
                        int count = 0;
                        synchronized (rw) {
                            count = processQueryResults(uidStats, fields, qaFields, rw, qr, dd,
                                    threadCheckLimit, resultsCount);
                            recordsForThread += count;
                        }
                        startIndex += downloadBatchSize;
                        //we have already set the Filter query the first time the query was constructed rerun with he same params but different startIndex
                        if (!threadCheckLimit || resultsCount.intValue() < MAX_DOWNLOAD_SIZE) {
                            if (!threadCheckLimit) {
                                //throttle the download by sleeping
                                try {
                                    Thread.currentThread().sleep(throttle);
                                } catch (InterruptedException e) {
                                    //don't care if the sleep was interrupted
                                }
                            }
                            qr = runSolrQuery(splitByFacetQuery, null, downloadBatchSize, startIndex, "_docid_",
                                    "asc");
                        } else {
                            qr = null;
                        }
                    }
                    return recordsForThread;
                }
            };
            futures.add(pool.submit(solrCallable));
        }

        //check the futures until all have finished
        int totalDownload = 0;
        Set<Future<Integer>> completeFutures = new HashSet<Future<Integer>>();
        boolean allComplete = false;
        while (!allComplete) {
            for (Future future : futures) {
                if (!completeFutures.contains(future)) {
                    if (future.isDone()) {
                        totalDownload += (Integer) future.get();
                        completeFutures.add(future);
                    }
                }
            }
            allComplete = completeFutures.size() == futures.size();
            if (!allComplete) {
                Thread.sleep(1000);
            }
        }
        pool.shutdown();
        rw.finalise();
        out.flush();

        long finish = System.currentTimeMillis();
        long timeTakenInSecs = (finish - start) / 1000;
        if (timeTakenInSecs == 0)
            timeTakenInSecs = 1;
        logger.info("Download of " + resultsCount + " records in " + timeTakenInSecs + " seconds. Record/sec: "
                + resultsCount.intValue() / timeTakenInSecs);

    } catch (SolrServerException ex) {
        logger.error("Problem communicating with SOLR server while processing download. " + ex.getMessage(),
                ex);
    }
    return uidStats;
}

From source file:com.rapidminer.operator.preprocessing.transformation.aggregation.AggregationOperator.java

@Override
public OperatorVersion[] getIncompatibleVersionChanges() {
    return (OperatorVersion[]) ArrayUtils.addAll(super.getIncompatibleVersionChanges(),
            new OperatorVersion[] { VERSION_5_1_6, VERSION_5_2_8, VERSION_6_0_6 });
}

From source file:com.oneops.inductor.WorkOrderExecutor.java

/**
 * Installs base software needed for chef / oneops
 *
 * @param pr      ProcessRunner/*from   w w w. j  a  v  a2  s .c om*/
 * @param wo      CmsWorkOrderSimple
 * @param host    remote host
 * @param port    remote port
 * @param logKey
 * @param keyFile
 */
public void runBaseInstall(ProcessRunner pr, CmsWorkOrderSimple wo, String host, String port, String logKey,
        String keyFile) {

    long t1 = System.currentTimeMillis();
    // amazon public images use ubuntu user for ubuntu os
    String cloudName = wo.getCloud().getCiName();
    String osType = "";
    if (wo.getPayLoad().containsKey("DependsOn")
            && wo.getPayLoad().get("DependsOn").get(0).getCiClassName().contains("Compute"))
        osType = wo.getPayLoad().get("DependsOn").get(0).getCiAttributes().get("ostype");
    else
        osType = wo.getRfcCi().getCiAttributes().get("ostype");

    if (osType.equals("default-cloud")) {

        if (!wo.getServices().containsKey("compute")) {
            wo.setComments("missing compute service");
            return;
        }

        osType = wo.getServices().get("compute").get(cloudName).getCiAttributes().get("ostype");
        logger.info("using default-cloud ostype: " + osType);
    }
    String user = getUserForOsAndCloud(osType, wo);

    String sudo = "";
    if (!user.equals("root"))
        sudo = "sudo ";

    String setup = "";

    // rackspace images don't have rsync installed
    if (wo.getCloud().getCiName().indexOf("rackspace") > -1) {
        setup = "yum -d0 -e0 -y install rsync; apt-get -y install rsync; true; ";
        // fedora in aws needs it too
    } else if (osType.indexOf("edora") > -1) {
        setup = "sudo yum -d0 -e0 -y install rsync; ";
    }

    // make prerequisite dirs for /opt/oneops and cookbooks
    String prepCmdline = setup + sudo + "mkdir -p /opt/oneops/workorder /home/" + user + "/components" + ";"
            + sudo + "chown -R " + user + ":" + user + " /opt/oneops;" + sudo + "chown -R " + user + ":" + user
            + " /home/" + user + "/components";

    // double -t args are needed
    String[] cmd = (String[]) ArrayUtils.addAll(sshInteractiveCmdLine,
            new String[] { keyFile, "-p " + port, user + "@" + host, prepCmdline });

    // retry initial ssh 10x slow hypervisors hosts
    if (!host.equals(TEST_HOST)) {
        ProcessResult result = pr.executeProcessRetry(cmd, logKey, 10);
        if (result.getResultCode() > 0) {
            wo.setComments("failed : can't:" + prepCmdline);
            return;
        }
    }

    // install os package repos - repo_map keyed by os
    ArrayList<String> repoCmdList = new ArrayList<String>();
    if (wo.getServices().containsKey("compute")
            && wo.getServices().get("compute").get(cloudName).getCiAttributes().containsKey("repo_map")
            && wo.getServices().get("compute").get(cloudName).getCiAttributes().get("repo_map")
                    .indexOf(osType) > 0) {

        String repoMap = wo.getServices().get("compute").get(cloudName).getCiAttributes().get("repo_map");
        repoCmdList = getRepoListFromMap(repoMap, osType);
    } else {
        logger.warn("no key in repo_map for os: " + osType);
    }

    // add repo_list from compute
    if (wo.getRfcCi().getCiAttributes().containsKey("repo_list")) {
        repoCmdList.addAll(getRepoList(wo.getRfcCi().getCiAttributes().get("repo_list")));
    }

    if (repoCmdList.size() > 0) {

        String[] cmdTmp = (String[]) ArrayUtils.addAll(sshInteractiveCmdLine,
                new String[] { keyFile, "-p " + port, user + "@" + host });

        // add ";" to each cmd
        for (int i = 0; i < repoCmdList.size(); i++) {
            repoCmdList.set(i, repoCmdList.get(i) + "; ");
        }

        // add infront so env can be set before repo cmds
        repoCmdList.add(0, getProxyEnvVars(wo));

        cmd = (String[]) ArrayUtils.addAll(cmdTmp, repoCmdList.toArray());
        if (!host.equals(TEST_HOST)) {
            ProcessResult result = pr.executeProcessRetry(cmd, logKey, retryCount);
            if (result.getResultCode() > 0) {
                wo.setComments("failed : Replace the compute and retry the deployment");
                wo.putSearchTag(BASE_INSTALL_TIME, Long.toString(System.currentTimeMillis() - t1));
                return;
            }
        }
    }

    // put ci cookbooks. "/" needed to get around symlinks
    String cookbookPath = getCookbookPath(wo.getRfcCi().getCiClassName());
    String cookbook = config.getCircuitDir().replace("packer", cookbookPath) + "/";
    String[] rsyncCmdLineWithKey = rsyncCmdLine.clone();
    rsyncCmdLineWithKey[4] += "-p " + port + " -qi " + keyFile;
    String[] deploy = (String[]) ArrayUtils.addAll(rsyncCmdLineWithKey,
            new String[] { cookbook, user + "@" + host + ":/home/" + user + "/" + cookbookPath });
    if (!host.equals(TEST_HOST)) {
        ProcessResult result = pr.executeProcessRetry(deploy, logKey, retryCount);
        if (result.getResultCode() > 0) {
            wo.setComments("FATAL: " + generateRsyncErrorMessage(result.getResultCode(), host + ":" + port));
            wo.putSearchTag(BASE_INSTALL_TIME, Long.toString(System.currentTimeMillis() - t1));
            return;
        }
    }

    // put shared cookbooks
    cookbook = config.getCircuitDir().replace("packer", "shared") + "/";
    rsyncCmdLineWithKey = rsyncCmdLine.clone();
    rsyncCmdLineWithKey[4] += "-p " + port + " -qi " + keyFile;
    deploy = (String[]) ArrayUtils.addAll(rsyncCmdLineWithKey,
            new String[] { cookbook, user + "@" + host + ":/home/" + user + "/shared" });
    if (!host.equals(TEST_HOST)) {
        ProcessResult result = pr.executeProcessRetry(deploy, logKey, retryCount);
        if (result.getResultCode() > 0) {
            wo.setComments("FATAL: " + generateRsyncErrorMessage(result.getResultCode(), host + ":" + port));
            wo.putSearchTag(BASE_INSTALL_TIME, Long.toString(System.currentTimeMillis() - t1));
            return;
        }
    }

    // install base: oneops user, ruby, chef
    // double -t args are needed
    String[] classParts = wo.getRfcCi().getCiClassName().split("\\.");
    String baseComponent = classParts[classParts.length - 1].toLowerCase();
    String[] cmdTmp = (String[]) ArrayUtils.addAll(sshInteractiveCmdLine,
            new String[] { keyFile, "-p " + port, user + "@" + host, sudo + "/home/" + user + "/" + cookbookPath
                    + "/components/cookbooks/" + baseComponent + "/files/default/install_base.sh" });

    String[] proxyList = new String[] { getProxyBashVars(wo) };
    cmd = (String[]) ArrayUtils.addAll(cmdTmp, proxyList);

    if (!host.equals(TEST_HOST)) {
        ProcessResult result = pr.executeProcessRetry(cmd, logKey, retryCount);
        if (result.getResultCode() > 0) {
            wo.setComments("failed : can't run install_base.sh");
            wo.putSearchTag(BASE_INSTALL_TIME, Long.toString(System.currentTimeMillis() - t1));
            return;
        }
    }
    wo.putSearchTag(BASE_INSTALL_TIME, Long.toString(System.currentTimeMillis() - t1));
}