Examples with AnalysisOutputFile ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile used on opensource projects

Example 16 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class FileUtilities method createAnalysisOutputFileZippedResponse.

/**
 * Utility method for download a zip file containing all output files from
 * an analysis.
 *
 * @param response
 *            {@link HttpServletResponse}
 * @param fileName
 *            Name fo the file to create
 * @param files
 *            Set of {@link AnalysisOutputFile}
 */
public static void createAnalysisOutputFileZippedResponse(HttpServletResponse response, String fileName, Set<AnalysisOutputFile> files) {
    /*
		 * Replacing spaces and commas as they cause issues with
		 * Content-disposition response header.
		 */
    fileName = fileName.replaceAll(" ", "_");
    fileName = fileName.replaceAll(",", "");
    logger.debug("Creating zipped file response. [" + fileName + "]");
    // set the response headers before we do *ANYTHING* so that the filename
    // actually appears in the download dialog
    response.setHeader(CONTENT_DISPOSITION, ATTACHMENT_FILENAME + fileName + EXTENSION_ZIP);
    // for zip file
    response.setContentType(CONTENT_TYPE_APPLICATION_ZIP);
    try (ServletOutputStream responseStream = response.getOutputStream();
        ZipOutputStream outputStream = new ZipOutputStream(responseStream)) {
        for (AnalysisOutputFile file : files) {
            if (!Files.exists(file.getFile())) {
                response.setStatus(404);
                throw new FileNotFoundException();
            }
            // 1) Build a folder/file name
            fileName = formatName(fileName);
            StringBuilder zipEntryName = new StringBuilder(fileName);
            zipEntryName.append("/").append(file.getLabel());
            // 2) Tell the zip stream that we are starting a new entry in
            // the archive.
            outputStream.putNextEntry(new ZipEntry(zipEntryName.toString()));
            // 3) COPY all of thy bytes from the file to the output stream.
            Files.copy(file.getFile(), outputStream);
            // 4) Close the current entry in the archive in preparation for
            // the next entry.
            outputStream.closeEntry();
            ObjectMapper objectMapper = new ObjectMapper();
            byte[] bytes = objectMapper.writeValueAsBytes(file);
            outputStream.putNextEntry(new ZipEntry(zipEntryName.toString() + "-prov.json"));
            outputStream.write(bytes);
            outputStream.closeEntry();
        }
        // Tell the output stream that you are finished downloading.
        outputStream.finish();
        outputStream.close();
    } catch (IOException e) {
        // this generally means that the user has cancelled the download
        // from their web browser; we can safely ignore this
        logger.debug("This *probably* means that the user cancelled the download, " + "but it might be something else, see the stack trace below for more information.", e);
    } catch (Exception e) {
        logger.error("Download failed...", e);
    }
}

Example 17 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class SISTRSampleUpdater method update.

/**
 * Add SISTR results to the metadata of the given {@link Sample}s
 *
 * @param samples  The samples to update.
 * @param analysis the {@link AnalysisSubmission} to apply to the samples
 * @throws PostProcessingException if the method cannot read the "sistr-predictions" output file
 */
@Override
public void update(Collection<Sample> samples, AnalysisSubmission analysis) throws PostProcessingException {
    AnalysisOutputFile sistrFile = analysis.getAnalysis().getAnalysisOutputFile(SISTR_FILE);
    Path filePath = sistrFile.getFile();
    Map<String, MetadataEntry> stringEntries = new HashMap<>();
    try {
        // Read the JSON file from SISTR output
        @SuppressWarnings("resource") String jsonFile = new Scanner(new BufferedReader(new FileReader(filePath.toFile()))).useDelimiter("\\Z").next();
        // map the results into a Map
        ObjectMapper mapper = new ObjectMapper();
        List<Map<String, Object>> sistrResults = mapper.readValue(jsonFile, new TypeReference<List<Map<String, Object>>>() {
        });
        if (sistrResults.size() > 0) {
            Map<String, Object> result = sistrResults.get(0);
            // loop through each of the requested fields and save the entries
            SISTR_FIELDS.entrySet().forEach(e -> {
                if (result.containsKey(e.getKey()) && result.get(e.getKey()) != null) {
                    String value = result.get(e.getKey()).toString();
                    PipelineProvidedMetadataEntry metadataEntry = new PipelineProvidedMetadataEntry(value, "text", analysis);
                    stringEntries.put(e.getValue(), metadataEntry);
                }
            });
            // convert string map into metadata fields
            Map<MetadataTemplateField, MetadataEntry> metadataMap = metadataTemplateService.getMetadataMap(stringEntries);
            // save metadata back to sample
            samples.forEach(s -> {
                s.mergeMetadata(metadataMap);
                sampleService.updateFields(s.getId(), ImmutableMap.of("metadata", s.getMetadata()));
            });
        } else {
            throw new PostProcessingException("SISTR results for file are not correctly formatted");
        }
    } catch (IOException e) {
        throw new PostProcessingException("Error parsing JSON from SISTR results", e);
    }
}

Example 18 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class CSVView method renderMergedOutputModel.

/**
 * {@inheritDoc}
 */
@Override
protected void renderMergedOutputModel(Map<String, Object> model, HttpServletRequest request, HttpServletResponse response) throws Exception {
    AnalysisOutputFile sfr = (AnalysisOutputFile) model.get(RESTGenericController.RESOURCE_NAME);
    Path fileContent = sfr.getFile();
    String filename = fileContent.getFileName().toString();
    logger.trace("Sending file to client [" + filename + "]");
    response.setHeader(HttpHeaders.CONTENT_DISPOSITION, "attachment; filename=\"" + filename + "\"");
    response.setHeader(HttpHeaders.CONTENT_TYPE, DEFAULT_CONTENT_TYPE);
    response.setHeader(HttpHeaders.CONTENT_LENGTH, String.valueOf(Files.size(fileContent)));
    OutputStream os = response.getOutputStream();
    Files.copy(fileContent, os);
    os.flush();
    os.close();
}

Example 19 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class NewickFileView method renderMergedOutputModel.

/**
 * {@inheritDoc}
 */
@Override
protected void renderMergedOutputModel(Map<String, Object> model, HttpServletRequest request, HttpServletResponse response) throws Exception {
    AnalysisOutputFile sfr = (AnalysisOutputFile) model.get(RESTGenericController.RESOURCE_NAME);
    Path fileContent = sfr.getFile();
    String filename = fileContent.getFileName().toString();
    logger.trace("Sending file to client [" + filename + "]");
    response.setHeader(HttpHeaders.CONTENT_DISPOSITION, "attachment; filename=\"" + filename + "\"");
    response.setHeader(HttpHeaders.CONTENT_TYPE, DEFAULT_CONTENT_TYPE);
    response.setHeader(HttpHeaders.CONTENT_LENGTH, String.valueOf(Files.size(fileContent)));
    OutputStream os = response.getOutputStream();
    Files.copy(fileContent, os);
    os.flush();
    os.close();
}

Example 20 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class RESTAnalysisSubmissionController method getAnalysisOutputFileContents.

/**
 * Get the actual file contents for an analysis output file.
 *
 * @param submissionId
 *            The {@link AnalysisSubmission} id
 * @param fileType
 *            The {@link AnalysisOutputFile} type as defined in the
 *            {@link Analysis} subclass
 * @return a {@link FileSystemResource} containing the contents of the
 *         {@link AnalysisOutputFile}.
 */
@RequestMapping(value = "/{submissionId}/analysis/file/{fileType}", produces = MediaType.TEXT_PLAIN_VALUE)
@ResponseBody
public FileSystemResource getAnalysisOutputFileContents(@PathVariable Long submissionId, @PathVariable String fileType) {
    AnalysisSubmission read = analysisSubmissionService.read(submissionId);
    if (read.getAnalysisState() != AnalysisState.COMPLETED) {
        throw new EntityNotFoundException("Analysis is not completed");
    }
    AnalysisOutputFile analysisOutputFile = read.getAnalysis().getAnalysisOutputFile(fileType);
    return new FileSystemResource(analysisOutputFile.getFile().toFile());
}