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

Example 1 with AnalysisOutputFile

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

the class AnalysisController method getOutputFile.

/**
 * Read some lines or text from an {@link AnalysisOutputFile}.
 *
 * @param id       {@link AnalysisSubmission} id
 * @param fileId   {@link AnalysisOutputFile} id
 * @param limit    Optional limit to number of lines to read from file
 * @param start    Optional line to start reading from
 * @param end      Optional line to stop reading at
 * @param seek     Optional file byte position to seek to and begin reading
 * @param chunk    Optional number of bytes to read from file
 * @param response HTTP response object
 * @return JSON with file text or lines as well as information about the file.
 */
@RequestMapping(value = "/ajax/{id}/outputs/{fileId}", method = RequestMethod.GET)
@ResponseBody
public AnalysisOutputFileInfo getOutputFile(@PathVariable Long id, @PathVariable Long fileId, @RequestParam(defaultValue = "100", required = false) Long limit, @RequestParam(required = false) Long start, @RequestParam(required = false) Long end, @RequestParam(defaultValue = "0", required = false) Long seek, @RequestParam(required = false) Long chunk, HttpServletResponse response) {
    AnalysisSubmission submission = analysisSubmissionService.read(id);
    Analysis analysis = submission.getAnalysis();
    final Optional<AnalysisOutputFile> analysisOutputFile = analysis.getAnalysisOutputFiles().stream().filter(x -> Objects.equals(x.getId(), fileId)).findFirst();
    if (analysisOutputFile.isPresent()) {
        final AnalysisOutputFile aof = analysisOutputFile.get();
        final Path aofFile = aof.getFile();
        final ToolExecution tool = aof.getCreatedByTool();
        final AnalysisOutputFileInfo contents = new AnalysisOutputFileInfo();
        contents.setId(aof.getId());
        contents.setAnalysisSubmissionId(submission.getId());
        contents.setAnalysisId(analysis.getId());
        contents.setFilename(aofFile.getFileName().toString());
        contents.setFileExt(FileUtilities.getFileExt(aofFile.getFileName().toString()));
        contents.setFileSizeBytes(aof.getFile().toFile().length());
        contents.setToolName(tool.getToolName());
        contents.setToolVersion(tool.getToolVersion());
        try {
            final File file = aofFile.toFile();
            final RandomAccessFile randomAccessFile = new RandomAccessFile(file, "r");
            randomAccessFile.seek(seek);
            if (seek == 0) {
                if (chunk != null && chunk > 0) {
                    contents.setText(FileUtilities.readChunk(randomAccessFile, seek, chunk));
                    contents.setChunk(chunk);
                    contents.setStartSeek(seek);
                } else {
                    final BufferedReader reader = new BufferedReader(new FileReader(randomAccessFile.getFD()));
                    final List<String> lines = FileUtilities.readLinesLimit(reader, limit, start, end);
                    contents.setLines(lines);
                    contents.setLimit((long) lines.size());
                    contents.setStart(start);
                    contents.setEnd(start + lines.size());
                }
            } else {
                if (chunk != null && chunk > 0) {
                    contents.setText(FileUtilities.readChunk(randomAccessFile, seek, chunk));
                    contents.setChunk(chunk);
                    contents.setStartSeek(seek);
                } else {
                    final List<String> lines = FileUtilities.readLinesFromFilePointer(randomAccessFile, limit);
                    contents.setLines(lines);
                    contents.setStartSeek(seek);
                    contents.setStart(start);
                    contents.setLimit((long) lines.size());
                }
            }
            contents.setFilePointer(randomAccessFile.getFilePointer());
        } catch (IOException e) {
            logger.error("Could not read output file '" + aof.getId() + "' " + e);
            response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
            contents.setError("Could not read output file");
        }
        return contents;
    } else {
        response.setStatus(HttpServletResponse.SC_NOT_FOUND);
        return null;
    }
}

Example 2 with AnalysisOutputFile

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

the class AnalysisController method getAjaxDownloadAnalysisSubmissionIndividualFile.

/**
 * Download single output files from an {@link AnalysisSubmission}
 *
 * @param analysisSubmissionId Id for a {@link AnalysisSubmission}
 * @param fileId               the id of the file to download
 * @param response             {@link HttpServletResponse}
 */
@RequestMapping(value = "/ajax/download/{analysisSubmissionId}/file/{fileId}")
public void getAjaxDownloadAnalysisSubmissionIndividualFile(@PathVariable Long analysisSubmissionId, @PathVariable Long fileId, HttpServletResponse response) {
    AnalysisSubmission analysisSubmission = analysisSubmissionService.read(analysisSubmissionId);
    Analysis analysis = analysisSubmission.getAnalysis();
    Set<AnalysisOutputFile> files = analysis.getAnalysisOutputFiles();
    Optional<AnalysisOutputFile> optFile = files.stream().filter(f -> f.getId().equals(fileId)).findAny();
    if (!optFile.isPresent()) {
        throw new EntityNotFoundException("Could not find file with id " + fileId);
    }
    FileUtilities.createSingleFileResponse(response, optFile.get());
}

Example 3 with AnalysisOutputFile

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

the class AnalysisController method getAjaxDownloadAnalysisSubmission.

/**
 * Download all output files from an {@link AnalysisSubmission}
 *
 * @param analysisSubmissionId Id for a {@link AnalysisSubmission}
 * @param response             {@link HttpServletResponse}
 */
@RequestMapping(value = "/ajax/download/{analysisSubmissionId}", produces = MediaType.APPLICATION_JSON_VALUE)
public void getAjaxDownloadAnalysisSubmission(@PathVariable Long analysisSubmissionId, HttpServletResponse response) {
    AnalysisSubmission analysisSubmission = analysisSubmissionService.read(analysisSubmissionId);
    Analysis analysis = analysisSubmission.getAnalysis();
    Set<AnalysisOutputFile> files = analysis.getAnalysisOutputFiles();
    FileUtilities.createAnalysisOutputFileZippedResponse(response, analysisSubmission.getName(), files);
}

Example 4 with AnalysisOutputFile

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

the class AnalysisController method tree.

// ************************************************************************************************
// Analysis view setup
// ************************************************************************************************
/**
 * Construct the model parameters for an {@link AnalysisType#PHYLOGENOMICS}
 * {@link Analysis}
 *
 * @param submission The analysis submission
 * @param model      The model to add parameters
 * @throws IOException If the tree file couldn't be read
 */
private void tree(AnalysisSubmission submission, Model model) throws IOException {
    final String treeFileKey = "tree";
    Analysis analysis = submission.getAnalysis();
    AnalysisOutputFile file = analysis.getAnalysisOutputFile(treeFileKey);
    List<String> lines = Files.readAllLines(file.getFile());
    model.addAttribute("analysis", analysis);
    model.addAttribute("newick", lines.get(0));
    // inform the view to display the tree preview
    model.addAttribute("preview", "tree");
}

Example 5 with AnalysisOutputFile

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

the class AnalysisController method getAnalysisOutputFileInfo.

/**
 * Get {@link AnalysisOutputFileInfo}.
 *
 * @param submission {@link AnalysisSubmission} of {@code analysis}
 * @param analysis   {@link Analysis} to get {@link AnalysisOutputFile}s from
 * @param outputName Workflow output name
 * @return {@link AnalysisOutputFile} info
 */
private AnalysisOutputFileInfo getAnalysisOutputFileInfo(AnalysisSubmission submission, Analysis analysis, String outputName) {
    final ImmutableSet<String> BLACKLIST_FILE_EXT = ImmutableSet.of("zip");
    // set of file extensions for indicating whether the first line of the file should be read
    final ImmutableSet<String> FILE_EXT_READ_FIRST_LINE = ImmutableSet.of("tsv", "txt", "tabular", "csv", "tab");
    final AnalysisOutputFile aof = analysis.getAnalysisOutputFile(outputName);
    final Long aofId = aof.getId();
    final String aofFilename = aof.getFile().getFileName().toString();
    final String fileExt = FileUtilities.getFileExt(aofFilename);
    if (BLACKLIST_FILE_EXT.contains(fileExt)) {
        return null;
    }
    final ToolExecution tool = aof.getCreatedByTool();
    final String toolName = tool.getToolName();
    final String toolVersion = tool.getToolVersion();
    final AnalysisOutputFileInfo info = new AnalysisOutputFileInfo();
    info.setId(aofId);
    info.setAnalysisSubmissionId(submission.getId());
    info.setAnalysisId(analysis.getId());
    info.setOutputName(outputName);
    info.setFilename(aofFilename);
    info.setFileSizeBytes(aof.getFile().toFile().length());
    info.setToolName(toolName);
    info.setToolVersion(toolVersion);
    info.setFileExt(fileExt);
    if (FILE_EXT_READ_FIRST_LINE.contains(fileExt)) {
        addFirstLine(info, aof);
    }
    return info;
}