Examples with ExtractPropertyBean org.akaza.openclinica.bean.extract.ExtractPropertyBean used on opensource projects

Example 1 with ExtractPropertyBean

use of org.akaza.openclinica.bean.extract.ExtractPropertyBean in project OpenClinica by OpenClinica.

the class CoreResources method findExtractProperties.

private ArrayList<ExtractPropertyBean> findExtractProperties() throws OpenClinicaSystemException {
    ArrayList<ExtractPropertyBean> ret = new ArrayList<ExtractPropertyBean>();
    // ExtractPropertyBean epbean = new ExtractPropertyBean();
    int i = 1;
    int maxExtractOption = getMaxExtractCounterValue();
    while (i <= maxExtractOption) {
        if (!getExtractField("extract." + i + ".file").equals("")) {
            ExtractPropertyBean epbean = new ExtractPropertyBean();
            epbean.setId(i);
            // we will implement a find by id function in the front end
            // check to make sure the file exists, if not throw an exception and system will abort to start.
            checkForFile(getExtractFields("extract." + i + ".file"));
            epbean.setFileName(getExtractFields("extract." + i + ".file"));
            // file name of the xslt stylesheet
            epbean.setFiledescription(getExtractField("extract." + i + ".fileDescription"));
            // description of the choice of format
            epbean.setHelpText(getExtractField("extract." + i + ".helpText"));
            // help text, currently in the alt-text of the link
            epbean.setLinkText(getExtractField("extract." + i + ".linkText"));
            // link text of the choice of format
            // epbean.setRolesAllowed(getExtractField("xsl.allowed." + i).split(","));
            // which roles are allowed to see the choice?
            epbean.setFileLocation(getExtractField("extract." + i + ".location"));
            // destination of the copied files
            // epbean.setFormat(getExtractField("xsl.format." + i));
            // if (("").equals(epbean.getFormat())) {
            // }
            // formatting choice. currently permenantly set at oc1.3
            /*
                 * String clinica = getExtractField("extract."+i+".odmType"); if(clinica!=null) {
                 * if(clinica.equalsIgnoreCase("clinical_data")) epbean.setFormat("occlinical_data"); else
                 * epbean.setFormat("oc1.3"); } else
                 */
            epbean.setOdmType(getExtractField("extract." + i + ".odmType"));
            epbean.setFormat("oc1.3");
            // destination file name of the copied files
            epbean.setExportFileName(getExtractFields("extract." + i + ".exportname"));
            // post-processing event after the creation
            String whichFunction = getExtractField("extract." + i + ".post").toLowerCase();
            // added by JN: Zipformat comes from extract properties returns true by default
            epbean.setZipFormat(getExtractFieldBoolean("extract." + i + ".zip"));
            epbean.setDeleteOld(getExtractFieldBoolean("extract." + i + ".deleteOld"));
            epbean.setSuccessMessage(getExtractField("extract." + i + ".success"));
            epbean.setFailureMessage(getExtractField("extract." + i + ".failure"));
            epbean.setZipName(getExtractField("extract." + i + ".zipName"));
            if (epbean.getFileName().length != epbean.getExportFileName().length)
                throw new OpenClinicaSystemException("The comma seperated values of file names and export file names should correspond 1 on 1 for the property number" + i);
            if ("sql".equals(whichFunction)) {
                // set the bean within, so that we can access the file locations etc
                SqlProcessingFunction function = new SqlProcessingFunction(epbean);
                String whichSettings = getExtractField("xsl.post." + i + ".sql");
                if (!"".equals(whichSettings)) {
                    function.setDatabaseType(getExtractFieldNoRep(whichSettings + ".dataBase").toLowerCase());
                    function.setDatabaseUrl(getExtractFieldNoRep(whichSettings + ".url"));
                    function.setDatabaseUsername(getExtractFieldNoRep(whichSettings + ".username"));
                    function.setDatabasePassword(getExtractFieldNoRep(whichSettings + ".password"));
                } else {
                    // set default db settings here
                    function.setDatabaseType(getField("dataBase"));
                    function.setDatabaseUrl(getField("url"));
                    function.setDatabaseUsername(getField("username"));
                    function.setDatabasePassword(getField("password"));
                }
                // also pre-set the database connection stuff
                epbean.setPostProcessing(function);
            // System.out.println("found db password: " + function.getDatabasePassword());
            } else if ("pdf".equals(whichFunction)) {
                // TODO add other functions here
                epbean.setPostProcessing(new PdfProcessingFunction());
            } else if ("sas".equals(whichFunction)) {
                epbean.setPostProcessing(new SasProcessingFunction());
            } else if (!whichFunction.isEmpty()) {
                String postProcessorName = getExtractField(whichFunction + ".postProcessor");
                if (postProcessorName.equals("pdf")) {
                    epbean.setPostProcessing(new PdfProcessingFunction());
                    epbean.setPostProcDeleteOld(getExtractFieldBoolean(whichFunction + ".deleteOld"));
                    epbean.setPostProcZip(getExtractFieldBoolean(whichFunction + ".zip"));
                    epbean.setPostProcLocation(getExtractField(whichFunction + ".location"));
                    epbean.setPostProcExportName(getExtractField(whichFunction + ".exportname"));
                } else // since the database is the last option TODO: think about custom post processing options
                {
                    SqlProcessingFunction function = new SqlProcessingFunction(epbean);
                    function.setDatabaseType(getExtractFieldNoRep(whichFunction + ".dataBase").toLowerCase());
                    function.setDatabaseUrl(getExtractFieldNoRep(whichFunction + ".url"));
                    function.setDatabaseUsername(getExtractFieldNoRep(whichFunction + ".username"));
                    function.setDatabasePassword(getExtractFieldNoRep(whichFunction + ".password"));
                    epbean.setPostProcessing(function);
                }
            } else {
                // add a null here
                epbean.setPostProcessing(null);
            }
            ret.add(epbean);
        }
        i++;
    }
    // System.out.println("found " + ret.size() + " records in extract.properties");
    return ret;
}

Example 2 with ExtractPropertyBean

use of org.akaza.openclinica.bean.extract.ExtractPropertyBean in project OpenClinica by OpenClinica.

the class CoreResources method findExtractPropertyBeanById.

// JN: by using static when u click same export link from 2 different datasets the first one stays in tact and is
// saved in
// there.
/**
 */
public ExtractPropertyBean findExtractPropertyBeanById(int id, String datasetId) {
    boolean notDone = true;
    ArrayList<ExtractPropertyBean> epBeans = findExtractProperties();
    ExtractPropertyBean returnBean = null;
    for (ExtractPropertyBean epbean : epBeans) {
        if (epbean.getId() == id) {
            epbean.setDatasetId(datasetId);
            notDone = false;
            // returnBean = epbean;
            return epbean;
        }
    }
    return returnBean;
}

Example 3 with ExtractPropertyBean

use of org.akaza.openclinica.bean.extract.ExtractPropertyBean in project OpenClinica by OpenClinica.

the class XsltTransformJob method executeInternal.

@Override
protected void executeInternal(JobExecutionContext context) {
    logger.info("Job " + context.getJobDetail().getFullName() + " started.");
    initDependencies(context.getScheduler());
    // need to generate a Locale for emailing users with i18n
    // TODO make dynamic?
    Locale locale = new Locale("en-US");
    ResourceBundleProvider.updateLocale(locale);
    ResourceBundle pageMessages = ResourceBundleProvider.getPageMessagesBundle();
    List<File> markForDelete = new LinkedList<File>();
    Boolean zipped = true;
    Boolean deleteOld = true;
    Boolean exceptions = false;
    JobDataMap dataMap = context.getMergedJobDataMap();
    String localeStr = dataMap.getString(LOCALE);
    String[] doNotDeleteUntilExtract = new String[4];
    int cnt = dataMap.getInt("count");
    DatasetBean datasetBean = null;
    if (localeStr != null) {
        locale = new Locale(localeStr);
        ResourceBundleProvider.updateLocale(locale);
        pageMessages = ResourceBundleProvider.getPageMessagesBundle();
    }
    // get the file information from the job
    String alertEmail = dataMap.getString(EMAIL);
    java.io.InputStream in = null;
    FileOutputStream endFileStream = null;
    UserAccountBean userBean = null;
    try {
        // init all fields from the data map
        int userAccountId = dataMap.getInt(USER_ID);
        int studyId = dataMap.getInt(STUDY_ID);
        String outputPath = dataMap.getString(POST_FILE_PATH);
        // get all user info, generate xml
        logger.debug("found output path: " + outputPath);
        String generalFileDir = dataMap.getString(XML_FILE_PATH);
        int dsId = dataMap.getInt(DATASET_ID);
        // JN: Change from earlier versions, cannot get static reference as
        // static references don't work. Reason being for example there could be
        // datasetId as a variable which is different for each dataset and
        // that needs to be loaded dynamically
        ExtractPropertyBean epBean = (ExtractPropertyBean) dataMap.get(EP_BEAN);
        File doNotDelDir = new File(generalFileDir);
        if (doNotDelDir.isDirectory()) {
            doNotDeleteUntilExtract = doNotDelDir.list();
        }
        zipped = epBean.getZipFormat();
        deleteOld = epBean.getDeleteOld();
        long sysTimeBegin = System.currentTimeMillis();
        userBean = (UserAccountBean) userAccountDao.findByPK(userAccountId);
        StudyBean currentStudy = (StudyBean) studyDao.findByPK(studyId);
        StudyBean parentStudy = (StudyBean) studyDao.findByPK(currentStudy.getParentStudyId());
        String successMsg = epBean.getSuccessMessage();
        String failureMsg = epBean.getFailureMessage();
        final long start = System.currentTimeMillis();
        datasetBean = (DatasetBean) datasetDao.findByPK(dsId);
        ExtractBean eb = generateFileService.generateExtractBean(datasetBean, currentStudy, parentStudy);
        // generate file directory for file service
        datasetBean.setName(datasetBean.getName().replaceAll(" ", "_"));
        logger.debug("--> job starting: ");
        HashMap<String, Integer> answerMap = odmFileCreation.createODMFile(epBean.getFormat(), sysTimeBegin, generalFileDir, datasetBean, currentStudy, "", eb, currentStudy.getId(), currentStudy.getParentStudyId(), "99", (Boolean) dataMap.get(ZIPPED), false, (Boolean) dataMap.get(DELETE_OLD), epBean.getOdmType(), userBean);
        // won't save a record of the XML to db
        // won't be a zipped file, so that we can submit it for
        // transformation
        // this will have to be toggled by the export data format? no, the
        // export file will have to be zipped/not zipped
        String ODMXMLFileName = "";
        int fId = 0;
        Iterator<Entry<String, Integer>> it = answerMap.entrySet().iterator();
        while (it.hasNext()) {
            JobTerminationMonitor.check();
            Entry<String, Integer> entry = it.next();
            String key = entry.getKey();
            Integer value = entry.getValue();
            // JN: Since there is a logic to
            ODMXMLFileName = key;
            // delete all the intermittent
            // files, this file could be a zip
            // file.
            Integer fileID = value;
            fId = fileID.intValue();
            logger.debug("found " + fId + " and " + ODMXMLFileName);
        }
        logger.info("Finished ODM generation of job " + context.getJobDetail().getFullName());
        // create dirs
        File output = new File(outputPath);
        if (!output.isDirectory()) {
            output.mkdirs();
        }
        int numXLS = epBean.getFileName().length;
        int fileCntr = 0;
        String xmlFilePath = new File(generalFileDir + ODMXMLFileName).toURI().toURL().toExternalForm();
        String endFile = null;
        File oldFilesPath = new File(generalFileDir);
        while (fileCntr < numXLS) {
            JobTerminationMonitor.check();
            String xsltPath = dataMap.getString(XSLT_PATH) + File.separator + epBean.getFileName()[fileCntr];
            in = new java.io.FileInputStream(xsltPath);
            Transformer transformer = transformerFactory.newTransformer(new StreamSource(in));
            endFile = outputPath + File.separator + epBean.getExportFileName()[fileCntr];
            endFileStream = new FileOutputStream(endFile);
            transformer.transform(new StreamSource(xmlFilePath), new StreamResult(endFileStream));
            // JN...CLOSE THE STREAM...HMMMM
            in.close();
            endFileStream.close();
            fileCntr++;
            JobTerminationMonitor.check();
        }
        if (oldFilesPath.isDirectory()) {
            markForDelete = Arrays.asList(oldFilesPath.listFiles());
        // logic to prevent deleting the file being created.
        }
        final double done = setFormat(new Double(System.currentTimeMillis() - start) / 1000);
        logger.info("--> job completed in " + done + " ms");
        // run post processing
        ProcessingFunction function = epBean.getPostProcessing();
        String subject = "";
        String jobName = dataMap.getString(XsltTriggerService.JOB_NAME);
        StringBuffer emailBuffer = new StringBuffer("");
        emailBuffer.append("<p>" + pageMessages.getString("email_header_1") + " " + EmailEngine.getAdminEmail() + " " + pageMessages.getString("email_header_2") + " Job Execution " + pageMessages.getString("email_header_3") + "</p>");
        emailBuffer.append("<P>Dataset: " + datasetBean.getName() + "</P>");
        emailBuffer.append("<P>Study: " + currentStudy.getName() + "</P>");
        if (function != null && function.getClass().equals(org.akaza.openclinica.bean.service.SqlProcessingFunction.class)) {
            String dbUrl = ((org.akaza.openclinica.bean.service.SqlProcessingFunction) function).getDatabaseUrl();
            int lastIndex = dbUrl.lastIndexOf('/');
            String schemaName = dbUrl.substring(lastIndex);
            int HostIndex = dbUrl.substring(0, lastIndex).indexOf("//");
            String Host = dbUrl.substring(HostIndex, lastIndex);
            emailBuffer.append("<P>Database: " + ((org.akaza.openclinica.bean.service.SqlProcessingFunction) function).getDatabaseType() + "</P>");
            emailBuffer.append("<P>Schema: " + schemaName.replace("/", "") + "</P>");
            emailBuffer.append("<P>Host: " + Host.replace("//", "") + "</P>");
        }
        emailBuffer.append("<p>" + pageMessages.getString("html_email_body_1") + datasetBean.getName() + pageMessages.getString("html_email_body_2_2") + "</p>");
        if (function != null) {
            function.setTransformFileName(outputPath + File.separator + dataMap.getString(POST_FILE_NAME));
            function.setODMXMLFileName(endFile);
            function.setXslFileName(dataMap.getString(XSL_FILE_PATH));
            function.setDeleteOld((Boolean) dataMap.get(POST_PROC_DELETE_OLD));
            function.setZip((Boolean) dataMap.get(POST_PROC_ZIP));
            function.setLocation(dataMap.getString(POST_PROC_LOCATION));
            function.setExportFileName(dataMap.getString(POST_PROC_EXPORT_NAME));
            File[] oldFiles = getOldFiles(outputPath, dataMap.getString(POST_PROC_LOCATION));
            function.setOldFiles(oldFiles);
            File[] intermediateFiles = getInterFiles(dataMap.getString(POST_FILE_PATH));
            ProcessingResultType message = function.run();
            // Delete these files only in case when there is no failure
            if (message.getCode().intValue() != 2) {
                deleteOldFiles(intermediateFiles);
            }
            final long done2 = System.currentTimeMillis() - start;
            logger.info("--> postprocessing completed in " + done2 + " ms, found result type " + message.getCode());
            logger.info("--> postprocessing completed in " + done2 + " ms, found result type " + message.getCode());
            if (!function.getClass().equals(org.akaza.openclinica.bean.service.SqlProcessingFunction.class)) {
                String archivedFile = dataMap.getString(POST_FILE_NAME) + "." + function.getFileType();
                // download the zip file
                if (function.isZip()) {
                    archivedFile = archivedFile + ".zip";
                }
                // post processing as well.
                if (function.getClass().equals(org.akaza.openclinica.bean.service.PdfProcessingFunction.class)) {
                    archivedFile = function.getArchivedFileName();
                }
                ArchivedDatasetFileBean fbFinal = generateFileRecord(archivedFile, outputPath, datasetBean, done, new File(outputPath + File.separator + archivedFile).length(), ExportFormatBean.PDFFILE, userAccountId);
                if (successMsg.contains("$linkURL")) {
                    successMsg = successMsg.replace("$linkURL", "<a href=\"" + CoreResources.getField("sysURL.base") + "AccessFile?fileId=" + fbFinal.getId() + "\">" + CoreResources.getField("sysURL.base") + "AccessFile?fileId=" + fbFinal.getId() + " </a>");
                }
                emailBuffer.append("<p>" + successMsg + "</p>");
                logger.debug("System time begining.." + sysTimeBegin);
                logger.debug("System time end.." + System.currentTimeMillis());
                double sysTimeEnd = setFormat((System.currentTimeMillis() - sysTimeBegin) / 1000);
                logger.debug("difference" + sysTimeEnd);
                if (fbFinal != null) {
                    fbFinal.setFileSize((int) bytesToKilo(new File(archivedFile).length()));
                    fbFinal.setRunTime(sysTimeEnd);
                }
            }
            // otherwise don't do it
            if (message.getCode().intValue() == 1) {
                if (jobName != null) {
                    subject = "Success: " + jobName;
                } else {
                    subject = "Success: " + datasetBean.getName();
                }
            } else if (message.getCode().intValue() == 2) {
                if (jobName != null) {
                    subject = "Failure: " + jobName;
                } else {
                    subject = "Failure: " + datasetBean.getName();
                }
                if (failureMsg != null && !failureMsg.isEmpty()) {
                    emailBuffer.append(failureMsg);
                }
                emailBuffer.append("<P>").append(message.getDescription());
                postErrorMessage(message.getDescription(), context);
            } else if (message.getCode().intValue() == 3) {
                if (jobName != null) {
                    subject = "Update: " + jobName;
                } else {
                    subject = "Update: " + datasetBean.getName();
                }
            }
        } else {
            // extract ran but no post-processing - we send an email with
            // success and url to link to
            // generate archived dataset file bean here, and use the id to
            // build the URL
            String archivedFilename = dataMap.getString(POST_FILE_NAME);
            // the zip file
            if (zipped) {
                archivedFilename = dataMap.getString(POST_FILE_NAME) + ".zip";
            }
            // delete old files now
            List<File> intermediateFiles = generateFileService.getOldFiles();
            String[] dontDelFiles = epBean.getDoNotDelFiles();
            // JN: The following is the code for zipping up the files, in case of more than one xsl being provided.
            if (dontDelFiles.length > 1 && zipped) {
                logger.debug("count =====" + cnt + "dontDelFiles length==---" + dontDelFiles.length);
                logger.debug("Entering this?" + cnt + "dontDelFiles" + dontDelFiles);
                String path = outputPath + File.separator;
                logger.debug("path = " + path);
                logger.debug("zipName?? = " + epBean.getZipName());
                String zipName = epBean.getZipName() == null || epBean.getZipName().isEmpty() ? endFile + ".zip" : path + epBean.getZipName() + ".zip";
                archivedFilename = new File(zipName).getName();
                zipAll(path, epBean.getDoNotDelFiles(), zipName);
                String[] tempArray = { archivedFilename };
                dontDelFiles = tempArray;
                endFile = archivedFilename;
            } else if (zipped) {
                markForDelete = zipxmls(markForDelete, endFile);
                endFile = endFile + ".zip";
                String[] temp = new String[dontDelFiles.length];
                int i = 0;
                while (i < dontDelFiles.length) {
                    temp[i] = dontDelFiles[i] + ".zip";
                    i++;
                }
                dontDelFiles = temp;
                // Actually deleting all the xml files which are produced
                // since its zipped
                FilenameFilter xmlFilter = new XMLFileFilter();
                File tempFile = new File(generalFileDir);
                deleteOldFiles(tempFile.listFiles(xmlFilter));
            }
            ArchivedDatasetFileBean fbFinal = generateFileRecord(archivedFilename, outputPath, datasetBean, done, new File(outputPath + File.separator + archivedFilename).length(), ExportFormatBean.TXTFILE, userAccountId);
            if (jobName != null) {
                subject = "Job Ran: " + jobName;
            } else {
                subject = "Job Ran: " + datasetBean.getName();
            }
            if (successMsg == null || successMsg.isEmpty()) {
                logger.info("email buffer??" + emailBuffer);
            } else {
                if (successMsg.contains("$linkURL")) {
                    successMsg = successMsg.replace("$linkURL", "<a href=\"" + CoreResources.getField("sysURL.base") + "AccessFile?fileId=" + fbFinal.getId() + "\">" + CoreResources.getField("sysURL.base") + "AccessFile?fileId=" + fbFinal.getId() + " </a>");
                }
                emailBuffer.append("<p>" + successMsg + "</p>");
            }
            if (deleteOld) {
                deleteIntermFiles(intermediateFiles, endFile, dontDelFiles);
                deleteIntermFiles(markForDelete, endFile, dontDelFiles);
            }
        }
        // email the message to the user
        emailBuffer.append("<p>" + pageMessages.getString("html_email_body_5") + "</p>");
        try {
            // @pgawade 19-April-2011 Log the event into audit_event table
            if (null != dataMap.get("job_type") && ((String) dataMap.get("job_type")).equalsIgnoreCase("exportJob")) {
                String extractName = (String) dataMap.get(XsltTriggerService.JOB_NAME);
                TriggerBean triggerBean = new TriggerBean();
                triggerBean.setDataset(datasetBean);
                triggerBean.setUserAccount(userBean);
                triggerBean.setFullName(extractName);
                String actionMsg = "You may access the " + (String) dataMap.get(XsltTriggerService.EXPORT_FORMAT) + " file by changing your study/site to " + currentStudy.getName() + " and selecting the Export Data icon for " + datasetBean.getName() + " dataset on the View Datasets page.";
                auditEventDAO.createRowForExtractDataJobSuccess(triggerBean, actionMsg);
            }
            mailSender.sendEmail(alertEmail, EmailEngine.getAdminEmail(), subject, emailBuffer.toString(), true);
        } catch (OpenClinicaSystemException ose) {
            // Do Nothing, In the future we might want to have an email
            // status added to system.
            logger.info("exception sending mail: " + ose.getMessage());
            logger.error("exception sending mail: " + ose.getMessage());
        }
        logger.info("just sent email to " + alertEmail + ", from " + EmailEngine.getAdminEmail());
        if (successMsg == null) {
            successMsg = " ";
        }
        postSuccessMessage(successMsg, context);
    } catch (JobInterruptedException e) {
        logger.info("Job was cancelled by the user");
        exceptions = true;
    } catch (TransformerConfigurationException e) {
        sendErrorEmail(e.getMessage(), context, alertEmail);
        postErrorMessage(e.getMessage(), context);
        logger.error("Error executing extract", e);
        exceptions = true;
    } catch (FileNotFoundException e) {
        sendErrorEmail(e.getMessage(), context, alertEmail);
        postErrorMessage(e.getMessage(), context);
        logger.error("Error executing extract", e);
        exceptions = true;
    } catch (TransformerFactoryConfigurationError e) {
        sendErrorEmail(e.getMessage(), context, alertEmail);
        postErrorMessage(e.getMessage(), context);
        logger.error("Error executing extract", e);
        exceptions = true;
    } catch (TransformerException e) {
        sendErrorEmail(e.getMessage(), context, alertEmail);
        postErrorMessage(e.getMessage(), context);
        logger.error("Error executing extract", e);
        exceptions = true;
    } catch (Exception ee) {
        sendErrorEmail(ee.getMessage(), context, alertEmail);
        postErrorMessage(ee.getMessage(), context);
        logger.error("Error executing extract", ee);
        exceptions = true;
        if (null != dataMap.get("job_type") && ((String) dataMap.get("job_type")).equalsIgnoreCase("exportJob")) {
            TriggerBean triggerBean = new TriggerBean();
            triggerBean.setUserAccount(userBean);
            triggerBean.setFullName((String) dataMap.get(XsltTriggerService.JOB_NAME));
            auditEventDAO.createRowForExtractDataJobFailure(triggerBean);
        }
    } finally {
        if (in != null)
            try {
                in.close();
            } catch (IOException e) {
                logger.error("Error executing extract", e);
            }
        if (endFileStream != null)
            try {
                endFileStream.close();
            } catch (IOException e) {
                logger.error("Error executing extract", e);
            }
        if (exceptions) {
            logger.debug("EXCEPTIONS... EVEN TEHN DELETING OFF OLD FILES");
            String generalFileDir = dataMap.getString(XML_FILE_PATH);
            File oldFilesPath = new File(generalFileDir);
            if (oldFilesPath.isDirectory()) {
                markForDelete = Arrays.asList(oldFilesPath.listFiles());
            }
            logger.debug("deleting the old files reference from archive dataset");
            if (deleteOld) {
                deleteIntermFiles(markForDelete, "", doNotDeleteUntilExtract);
            }
        }
        if (datasetBean != null)
            resetArchiveDataset(datasetBean.getId());
        logger.info("Job " + context.getJobDetail().getFullName() + " finished.");
    }
}

Example 4 with ExtractPropertyBean

use of org.akaza.openclinica.bean.extract.ExtractPropertyBean in project OpenClinica by OpenClinica.

the class SystemController method getExtractModule.

/**
 * @api {get} /pages/auth/api/v1/system/extract Retrieve Extract Properties
 * @apiName getExtractProperties
 * @apiPermission Authenticate using api-key. admin
 * @apiVersion 3.8.0
 * @apiGroup System
 * @apiDescription Retrieves Extract Properties
 * @apiSuccessExample {json} Success-Response: HTTP/1.1 200 OK
 *                    {
 *                    "extract.properties": {
 *                    "extract.number": {
 *                    "extract.number": "99"
 *                    },
 *                    "extract.1": {
 *                    "zip": "true",
 *                    "failure": "",
 *                    "fileDescription": "CDISC ODM XML 1.3 Full with OpenClinica extensions",
 *                    "linkText": "Run Now",
 *                    "deleteOld": "true",
 *                    "location": "$exportFilePath/$datasetName/ODM_1.3_Full",
 *                    "file": "[copyXML.xsl]",
 *                    "helpText": "CDISC ODM XML 1.3 Full with OpenClinica extensions. Includes discrepancy notes
 *                    and audit trails.",
 *                    "exportname": "[odm1.3_full$datasetName_$dateTime.xml]",
 *                    "success": "The extract completed successfully. The file is available for download $linkURL.",
 *                    "odmType": "full"
 *                    },
 *                    "extract.2": {
 *                    "zip": "true",
 *                    "failure": "",
 *                    "fileDescription": "CDISC ODM XML 1.3 Clinical Data with OpenClinica extensions",
 *                    "linkText": "Run Now",
 *                    "deleteOld": "true",
 *                    "location": "$exportFilePath/$datasetName/ODM_1.3_Extensions",
 *                    "file": "[copyXML.xsl]",
 *                    "helpText": "CDISC ODM XML 1.3 Clinical Data with OpenClinica extensions. Does not include
 *                    discrepancy notes or audit trails.",
 *                    "exportname": "[odm1.3_clinical_ext_$datasetName_$dateTime.xml]",
 *                    "success": "Your extract job completed successfully. The file is available for download
 *                    $linkURL.",
 *                    "odmType": "clinical_data"
 *                    }
 *                    ...
 *                    }
 *                    }
 */
@RequestMapping(value = "/extract", method = RequestMethod.GET)
public ResponseEntity<HashMap> getExtractModule() throws Exception {
    ResourceBundleProvider.updateLocale(new Locale("en_US"));
    HashMap<String, Object> map = new HashMap<>();
    ResourceBundle resLicense = ResourceBundleProvider.getLicensingBundle();
    HashMap<String, Object> extractMap = new HashMap<>();
    ArrayList<ExtractPropertyBean> extracts = CoreResources.getExtractProperties();
    int n = 0;
    for (ExtractPropertyBean extract : extracts) {
        n++;
        HashMap<String, String> extractmap = new HashMap<>();
        extractmap.put("odmType", extract.getOdmType());
        extractmap.put("file", Arrays.toString(extract.getFileName()));
        extractmap.put("fileDescription", extract.getFiledescription());
        extractmap.put("linkText", extract.getLinkText());
        extractmap.put("helpText", extract.getHelpText());
        extractmap.put("location", extract.getFileLocation());
        extractmap.put("exportname", Arrays.toString(extract.getExportFileName()));
        extractmap.put("zip", String.valueOf(extract.getZipFormat()));
        extractmap.put("deleteOld", String.valueOf(extract.getDeleteOld()));
        extractmap.put("success", extract.getSuccessMessage());
        extractmap.put("failure", extract.getFailureMessage());
        extractMap.put("extract." + n, extractmap);
    }
    HashMap<String, String> extractDatamart = new HashMap<>();
    HashMap<String, String> datamartRole = new HashMap<>();
    String username = CoreResources.getExtractField("db1.username");
    String password = CoreResources.getExtractField("db1.password");
    String url = CoreResources.getExtractField("db1.url");
    extractDatamart.put("db1.username", username);
    extractDatamart.put("db1.url", url);
    extractDatamart.put("db1.dataBase", CoreResources.getExtractField("db1.dataBase"));
    HashMap<String, String> extractNumber = new HashMap<>();
    extractNumber.put("extract.number", CoreResources.getExtractField("extract.number"));
    extractMap.put("extract.number", extractNumber);
    // extractMap.put("DataMart", extractDatamart);
    HashMap<String, String> datamartMap = new HashMap();
    try (Connection conn = DriverManager.getConnection(url, username, password)) {
        datamartRole = getDbRoleProperties(conn, datamartRole, username);
        datamartMap.put("connection", "Open");
    } catch (Exception e) {
        datamartMap.put("connection", "Close");
    }
    // map.put("Datamart Facts", datamartMap);
    map.put("extract.properties", extractMap);
    return new ResponseEntity<HashMap>(map, org.springframework.http.HttpStatus.OK);
}

Example 5 with ExtractPropertyBean

use of org.akaza.openclinica.bean.extract.ExtractPropertyBean in project OpenClinica by OpenClinica.

the class SystemController method getDatamartModule.

public HashMap<String, Object> getDatamartModule(StudyBean studyBean) {
    HashMap<String, String> datamartRole = new HashMap<>();
    String username = CoreResources.getExtractField("db1.username");
    String password = CoreResources.getExtractField("db1.password");
    String url = CoreResources.getExtractField("db1.url");
    ArrayList<ExtractPropertyBean> extracts = CoreResources.getExtractProperties();
    String enabled = "False";
    for (ExtractPropertyBean extract : extracts) {
        if (extract.getFiledescription().equalsIgnoreCase("Datamart")) {
            enabled = "True";
            break;
        }
    }
    String result = "";
    try (Connection conn = DriverManager.getConnection(url, username, password)) {
        datamartRole = getDbRoleProperties(conn, datamartRole, username);
        result = "ACTIVE";
    } catch (Exception e) {
        result = "INACTIVE";
    }
    HashMap<String, Object> mapMetadata = new HashMap<>();
    mapMetadata.put("db1.username", username);
    mapMetadata.put("db1.url", url);
    mapMetadata.put("db1.dataBase", CoreResources.getExtractField("db1.dataBase"));
    mapMetadata.put("Role Properties", datamartRole);
    HashMap<String, Object> mapDatamart = new HashMap<>();
    mapDatamart.put("enabled", enabled);
    mapDatamart.put("status", result);
    mapDatamart.put("metadata", mapMetadata);
    HashMap<String, Object> mapModule = new HashMap<>();
    mapModule.put("Datamart", mapDatamart);
    return mapModule;
}