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Example 1 with RuntimeIOException

use of org.assertj.core.api.exception.RuntimeIOException in project ArachneCentralAPI by OHDSI.

the class BaseAnalysisController method doAddCommonEntityToAnalysis.

protected void doAddCommonEntityToAnalysis(T analysis, DataReference dataReference, IUser user, CommonAnalysisType analysisType, List<MultipartFile> files) throws IOException {
    files.stream().filter(f -> !CommonAnalysisType.COHORT.equals(analysisType) || !f.getName().endsWith(CommonFileUtils.OHDSI_JSON_EXT)).forEach(f -> {
        try {
            analysisService.saveFile(f, user, analysis, f.getName(), detectExecutable(analysisType, f), dataReference);
        } catch (IOException e) {
            LOGGER.error("Failed to save file", e);
        }
    });
    if (analysisType.equals(CommonAnalysisType.COHORT)) {
        final ByteArrayOutputStream out = new ByteArrayOutputStream();
        class StringContainer {

            String value = CommonAnalysisType.COHORT.getTitle();
        }
        final StringContainer generatedFileName = new StringContainer();
        try (final ZipOutputStream zos = new ZipOutputStream(out)) {
            files.forEach(file -> {
                try {
                    if (file.getName().endsWith(CommonFileUtils.OHDSI_SQL_EXT)) {
                        String statement = org.apache.commons.io.IOUtils.toString(file.getInputStream(), "UTF-8");
                        String renderedSql = SqlRender.renderSql(statement, null, null);
                        DBMSType[] dbTypes = new DBMSType[] { DBMSType.POSTGRESQL, DBMSType.ORACLE, DBMSType.MS_SQL_SERVER, DBMSType.REDSHIFT, DBMSType.PDW };
                        String baseName = FilenameUtils.getBaseName(file.getOriginalFilename());
                        String extension = FilenameUtils.getExtension(file.getOriginalFilename());
                        for (final DBMSType dialect : dbTypes) {
                            final String sql = SqlTranslate.translateSql(renderedSql, DBMSType.MS_SQL_SERVER.getOhdsiDB(), dialect.getOhdsiDB());
                            final String fileName = baseName + "." + dialect.getLabel().replaceAll(" ", "-") + "." + extension;
                            ZipUtil.addZipEntry(zos, fileName, new ByteArrayInputStream(sql.getBytes("UTF-8")));
                        }
                        final String shortBaseName = baseName.replaceAll("\\.ohdsi", "");
                        if (!generatedFileName.value.contains(shortBaseName)) {
                            generatedFileName.value += "_" + shortBaseName;
                        }
                    } else {
                        String fileName = file.getName();
                        ZipUtil.addZipEntry(zos, fileName, file.getInputStream());
                    }
                } catch (IOException e) {
                    LOGGER.error("Failed to add file to archive", e);
                    throw new RuntimeIOException(e.getMessage(), e);
                }
            });
        }
        String fileName = generatedFileName.value + ".zip";
        final MultipartFile sqlArchive = new MockMultipartFile(fileName, fileName, "application/zip", out.toByteArray());
        analysisService.saveFile(sqlArchive, user, analysis, fileName, false, dataReference);
    }
}
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Aggregations

CommonAnalysisType (com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType)1 CommonEntityRequestDTO (com.odysseusinc.arachne.commons.api.v1.dto.CommonEntityRequestDTO)1 OptionDTO (com.odysseusinc.arachne.commons.api.v1.dto.OptionDTO)1 JsonResult (com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult)1 NO_ERROR (com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.NO_ERROR)1 PERMISSION_DENIED (com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.PERMISSION_DENIED)1 VALIDATION_ERROR (com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.VALIDATION_ERROR)1 ProducerConsumerTemplate (com.odysseusinc.arachne.commons.service.messaging.ProducerConsumerTemplate)1 DBMSType (com.odysseusinc.arachne.commons.types.DBMSType)1 CommonFileUtils (com.odysseusinc.arachne.commons.utils.CommonFileUtils)1 AnalysisCreateDTO (com.odysseusinc.arachne.portal.api.v1.dto.AnalysisCreateDTO)1 AnalysisDTO (com.odysseusinc.arachne.portal.api.v1.dto.AnalysisDTO)1 AnalysisFileDTO (com.odysseusinc.arachne.portal.api.v1.dto.AnalysisFileDTO)1 AnalysisLockDTO (com.odysseusinc.arachne.portal.api.v1.dto.AnalysisLockDTO)1 AnalysisUnlockRequestDTO (com.odysseusinc.arachne.portal.api.v1.dto.AnalysisUnlockRequestDTO)1 AnalysisUpdateDTO (com.odysseusinc.arachne.portal.api.v1.dto.AnalysisUpdateDTO)1 Commentable (com.odysseusinc.arachne.portal.api.v1.dto.Commentable)1 DataReferenceDTO (com.odysseusinc.arachne.portal.api.v1.dto.DataReferenceDTO)1 FileDTO (com.odysseusinc.arachne.portal.api.v1.dto.FileDTO)1 ShortBaseAnalysisDTO (com.odysseusinc.arachne.portal.api.v1.dto.ShortBaseAnalysisDTO)1