Examples with ArachneSystemRuntimeException com.odysseusinc.arachne.portal.exception.ArachneSystemRuntimeException used on opensource projects

Example 1 with ArachneSystemRuntimeException

use of com.odysseusinc.arachne.portal.exception.ArachneSystemRuntimeException in project ArachneCentralAPI by OHDSI.

the class AnalysisFilesSavingServiceImpl method saveFile.

@Override
@PreAuthorize("hasPermission(#analysis, " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).UPLOAD_ANALYSIS_FILES)")
public AnalysisFile saveFile(MultipartFile multipartFile, IUser user, A analysis, String label, Boolean isExecutable, DataReference dataReference) throws AlreadyExistException {
    ensureLabelIsUnique(analysis.getId(), label);
    String originalFilename = multipartFile.getOriginalFilename();
    String fileNameLowerCase = UUID.randomUUID().toString();
    try {
        Path analysisPath = analysisHelper.getAnalysisPath(analysis);
        Path targetPath = Paths.get(analysisPath.toString(), fileNameLowerCase);
        Files.copy(multipartFile.getInputStream(), targetPath, REPLACE_EXISTING);
        final String contentType = CommonFileUtils.getContentType(originalFilename, targetPath.toString());
        AnalysisFile analysisFile = buildNewAnalysisFileEntry(user, analysis, label, isExecutable, originalFilename, fileNameLowerCase, contentType);
        analysisFile.setDataReference(dataReference);
        AnalysisFile saved = analysisFileRepository.save(analysisFile);
        analysis.getFiles().add(saved);
        preprocessorService.preprocessFile(analysis, analysisFile);
        eventPublisher.publishEvent(new AntivirusJobEvent(this, new AntivirusJob(saved.getId(), saved.getName(), new FileInputStream(targetPath.toString()), AntivirusJobFileType.ANALYSIS_FILE)));
        return saved;
    } catch (IOException | RuntimeException ex) {
        String message = "error save file to disk, filename=" + fileNameLowerCase + " ex=" + ex.toString();
        log.error(message, ex);
        throw new ArachneSystemRuntimeException(message);
    }
}

Example 2 with ArachneSystemRuntimeException

use of com.odysseusinc.arachne.portal.exception.ArachneSystemRuntimeException in project ArachneCentralAPI by OHDSI.

the class ToPdfConverter method recreateJodConverterWorkingFolderIfNoLongerExists.

private void recreateJodConverterWorkingFolderIfNoLongerExists() {
    if (officeManager != null) {
        final File tempFile = officeManager.makeTemporaryFile();
        final Path currentTempDir = tempFile.toPath().getParent();
        if (!currentTempDir.toFile().exists()) {
            log.info("Recreating JodConverter temp folder: {}", currentTempDir);
            try {
                Files.createDirectories(currentTempDir);
            } catch (IOException ex) {
                throw new ArachneSystemRuntimeException("Cannot restore officeManager temp folder: " + currentTempDir, ex);
            }
        }
    }
}

Example 3 with ArachneSystemRuntimeException

use of com.odysseusinc.arachne.portal.exception.ArachneSystemRuntimeException in project ArachneCentralAPI by OHDSI.

the class SearchIndexesRefresher method rebuildAllIndexes.

private void rebuildAllIndexes() {
    try {
        dataSourceService.indexAllBySolr();
        userService.indexAllBySolr();
        studyService.indexAllBySolr();
        analysisService.indexAllBySolr();
        paperService.indexAllBySolr();
    } catch (Exception ex) {
        throw new ArachneSystemRuntimeException(ex);
    }
}

Example 4 with ArachneSystemRuntimeException

use of com.odysseusinc.arachne.portal.exception.ArachneSystemRuntimeException in project ArachneCentralAPI by OHDSI.

the class AnalysisFilesSavingServiceImpl method saveCohortAnalysisArchive.

@PreAuthorize("hasPermission(#analysis, " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).UPLOAD_ANALYSIS_FILES)")
public void saveCohortAnalysisArchive(A analysis, DataReference dataReference, IUser user, List<MultipartFile> files) {
    MultipartFile genericSqlFile = files.stream().filter(file -> file.getName().endsWith(OHDSI_SQL_EXT)).findAny().orElseThrow(() -> new ArachneSystemRuntimeException(String.format("There is no sql file for %s analysis.", analysis.getId())));
    Collection<MultipartFile> filesForArchive = files.stream().filter(file -> ObjectUtils.notEqual(file, genericSqlFile)).filter(file -> !StringUtils.equals(ANALYSIS_INFO_FILE_DESCRIPTION, file.getName())).collect(Collectors.toList());
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    try (ZipOutputStream zos = new ZipOutputStream(out)) {
        generateFilesForEachDialectAndAddToZip(zos, genericSqlFile);
        ZipUtil.addZipEntries(zos, filesForArchive);
    } catch (IOException e) {
        log.error("Failed to create zip file for {} analysis", analysis.getId(), e);
        throw new ArachneSystemRuntimeException(e);
    }
    String fileName = AnalysisArchiveUtils.getArchiveFileName(CommonAnalysisType.COHORT, getAnalysisName(genericSqlFile));
    MultipartFile sqlArchive = new MockMultipartFile(fileName, fileName, "application/zip", out.toByteArray());
    try {
        saveFile(sqlArchive, user, analysis, fileName, false, dataReference);
    } catch (Exception e) {
        log.error("Failed to save zip file for {} analysis", analysis.getId(), e);
        throw new ArachneSystemRuntimeException(e);
    }
}