Examples with ANALYSIS_INFO_FILE_DESCRIPTION com.odysseusinc.arachne.commons.utils.CommonFileUtils.ANALYSIS_INFO_FILE_DESCRIPTION used on opensource projects

Example 1 with ANALYSIS_INFO_FILE_DESCRIPTION

use of com.odysseusinc.arachne.commons.utils.CommonFileUtils.ANALYSIS_INFO_FILE_DESCRIPTION in project ArachneCentralAPI by OHDSI.

the class AnalysisFilesSavingServiceImpl method saveFiles.

@PreAuthorize("hasPermission(#analysis, " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).UPLOAD_ANALYSIS_FILES)")
protected List<AnalysisFile> saveFiles(List<MultipartFile> multipartFiles, IUser user, A analysis, DataReference dataReference, BiPredicate<String, CommonAnalysisType> checkFileExecutabilityPredicate) {
    List<MultipartFile> filteredFiles = multipartFiles.stream().filter(file -> !(CommonAnalysisType.COHORT.equals(analysis.getType()) && file.getName().endsWith(OHDSI_JSON_EXT))).filter(file -> !file.getName().startsWith(ANALYSIS_INFO_FILE_DESCRIPTION)).collect(Collectors.toList());
    List<AnalysisFile> savedFiles = new ArrayList<>();
    List<String> errorFileMessages = new ArrayList<>();
    for (MultipartFile file : filteredFiles) {
        try {
            final boolean isExecutable = checkFileExecutabilityPredicate.test(file.getOriginalFilename(), analysis.getType());
            savedFiles.add(saveFile(file, user, analysis, file.getName(), isExecutable, dataReference));
        } catch (AlreadyExistException e) {
            errorFileMessages.add(e.getMessage());
        }
    }
    if (!errorFileMessages.isEmpty()) {
        throw new ValidationRuntimeException("Failed to save files", ImmutableMap.of(dataReference.getGuid(), errorFileMessages));
    }
    return savedFiles;
}

Example 2 with ANALYSIS_INFO_FILE_DESCRIPTION

use of com.odysseusinc.arachne.commons.utils.CommonFileUtils.ANALYSIS_INFO_FILE_DESCRIPTION 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);
    }
}