Examples with NcbiXmlParseException ca.corefacility.bioinformatics.irida.exceptions.NcbiXmlParseException used on opensource projects

Example 1 with NcbiXmlParseException

use of ca.corefacility.bioinformatics.irida.exceptions.NcbiXmlParseException in project irida by phac-nml.

the class ExportUploadService method updateRunningUploads.

/**
 * Check local database for submissions which may have updates on the NCBI
 * server and update them as necessary.
 */
public synchronized void updateRunningUploads() {
    logger.trace("Getting running exports");
    List<NcbiExportSubmission> submissionsWithState = exportSubmissionService.getSubmissionsWithState(updateableStates);
    FTPClient client = null;
    try {
        for (NcbiExportSubmission submission : submissionsWithState) {
            // connect to FTP site
            client = getFtpClient();
            try {
                logger.trace("Getting report for submission " + submission.getId());
                InputStream xmlStream = getLatestXMLStream(client, submission);
                if (xmlStream != null) {
                    NcbiExportSubmission updateSubmissionForXml = updateSubmissionForXml(submission, xmlStream);
                    exportSubmissionService.update(updateSubmissionForXml);
                    xmlStream.close();
                }
            } catch (NcbiXmlParseException e) {
                logger.error("Error getting response", e);
                submission.setUploadState(ExportUploadState.UPLOAD_ERROR);
                submission = exportSubmissionService.update(submission);
                emailController.sendNCBIUploadExceptionEmail(notificationAdminEmail, e, submission.getId());
            } catch (IOException e) {
                logger.error("Error closing XML stream", e);
            }
        }
        disconnectFtpCient(client);
    } catch (Exception e) {
        logger.error("Couldn't connect to FTP site", e);
    } finally {
        disconnectFtpCient(client);
    }
}

Example 2 with NcbiXmlParseException

use of ca.corefacility.bioinformatics.irida.exceptions.NcbiXmlParseException in project irida by phac-nml.

the class ExportUploadService method updateSubmissionForXml.

/**
 * Get the updates from the result.#.xml file for the given submission and
 * update the object. XML will look like the following:
 *
 * <pre>
 * <?xml version='1.0' encoding='utf-8'?>
 * <SubmissionStatus submission_id="SUB1234" status="processed-ok">
 *   <Action action_id="SUB1234-submission12345" target_db="SRA" status="processed-ok" notify_submitter="true">
 *     <Response status="processed-ok">
 *       <Object target_db="SRA" object_id="RUN:4567" spuid_namespace="NML" spuid="submission12345" accession="SRR6789" status="updated">
 *         <Meta>
 *           <SRAStudy>SRP012345</SRAStudy>
 *         </Meta>
 *       </Object>
 *     </Response>
 *   </Action>
 * </SubmissionStatus>
 * </pre>
 *
 * @param submission
 *            {@link NcbiExportSubmission} to update
 * @param xml
 *            {@link InputStream} of xml
 * @return Updated {@link NcbiExportSubmission}
 * @throws NcbiXmlParseException
 *             if the xml couldn't be parsed
 */
private NcbiExportSubmission updateSubmissionForXml(NcbiExportSubmission submission, InputStream xml) throws NcbiXmlParseException {
    try {
        // read the incoming xml file
        DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
        DocumentBuilder docBuilder = docBuilderFactory.newDocumentBuilder();
        Document doc = docBuilder.parse(xml);
        XPath xPath = XPathFactory.newInstance().newXPath();
        // get the submission status and set it in the submission
        String submissionStatusString = xPath.compile("SubmissionStatus/@status").evaluate(doc);
        if (submissionStatusString == null) {
            throw new NcbiXmlParseException("result file should have 1 SubmissionStatus element with a status");
        }
        ExportUploadState submissionStatus = ExportUploadState.fromString(submissionStatusString);
        submission.setUploadState(submissionStatus);
        logger.trace("Root export state is " + submissionStatus);
        // get all the sample files objects by name
        Map<String, NcbiBioSampleFiles> sampleMap = getSampleNameMap(submission);
        // get the actions
        NodeList actions = (NodeList) xPath.compile("SubmissionStatus/Action").evaluate(doc, XPathConstants.NODESET);
        for (int i = 0; i < actions.getLength(); i++) {
            if (actions.item(i).getNodeType() == Node.ELEMENT_NODE) {
                Element action = (Element) actions.item(i);
                // get the status and action id
                String status = action.getAttribute("status");
                String actionId = action.getAttribute("action_id");
                // action id is of the form SUBMISSIONID-sampleid
                String sampleId = actionId.substring(actionId.indexOf("-") + 1);
                // get the sample for this action
                NcbiBioSampleFiles ncbiBioSampleFiles = sampleMap.get(sampleId);
                ExportUploadState sampleStatus = ExportUploadState.fromString(status);
                ncbiBioSampleFiles.setSubmissionStatus(sampleStatus);
                logger.trace("Sample export state for sample " + ncbiBioSampleFiles.getId() + " is " + sampleStatus);
                String accession = xPath.compile("Response/Object/@accession").evaluate(action);
                if (accession != null && !accession.isEmpty()) {
                    logger.trace("Found accession " + accession);
                    ncbiBioSampleFiles.setAccession(accession);
                }
            }
        }
    } catch (XPathExpressionException | ParserConfigurationException | SAXException | IOException e) {
        logger.error("Couldn't parse response XML", e);
        throw new NcbiXmlParseException("Error parsing NCBI response", e);
    }
    return submission;
}

Example 3 with NcbiXmlParseException

use of ca.corefacility.bioinformatics.irida.exceptions.NcbiXmlParseException in project irida by phac-nml.

the class ExportUploadService method getLatestXMLStream.

/**
 * Get the latest result.#.xml file for the given submission
 *
 * @param client
 *            {@link FTPClient} to use for the connection
 * @param submission
 *            {@link NcbiExportSubmission} to get results for
 * @return {@link InputStream} for the newest file if found. null if no file
 *         was found
 * @throws NcbiXmlParseException
 *             if the file couldn't be found
 */
private InputStream getLatestXMLStream(FTPClient client, NcbiExportSubmission submission) throws NcbiXmlParseException {
    InputStream retrieveFileStream = null;
    try {
        String directoryPath = submission.getDirectoryPath();
        // cd to submission base directory
        if (!client.changeWorkingDirectory(directoryPath)) {
            throw new NcbiXmlParseException("Couldn't change to base directory " + baseDirectory + " : " + client.getReplyString());
        }
        Pattern regex = Pattern.compile("report.(\\d+).xml");
        String latestFile = null;
        int highestNumber = 0;
        // search for the highest number in the report.#.xml files
        FTPFile[] listFiles = client.listFiles();
        for (FTPFile file : listFiles) {
            String fileName = file.getName();
            Matcher matcher = regex.matcher(fileName);
            if (matcher.matches()) {
                int reportNumber = Integer.parseInt(matcher.group(1));
                if (reportNumber > highestNumber) {
                    highestNumber = reportNumber;
                    latestFile = fileName;
                }
            }
        }
        if (latestFile != null) {
            logger.trace("newest file is " + latestFile);
            retrieveFileStream = client.retrieveFileStream(latestFile);
        }
    } catch (IOException e) {
        throw new NcbiXmlParseException("Couldn't get response xml", e);
    }
    return retrieveFileStream;
}