/**
* Test method for {@link cpath.converter.internal.UniprotCleanerImpl#cleane(java.lang.String)}.
*
* @throws IOException
*/
@Test
public void testCleaner() throws IOException {
// read data from file and look for accessions before being cleaned
ByteArrayOutputStream os = new ByteArrayOutputStream();
CPathUtils.unzip(
new ZipInputStream(
CPathUtils.LOADER.getResource("/test_uniprot_data.dat.zip").getInputStream()),
os);
byte[] bytes = os.toByteArray();
String data = new String(bytes);
assertTrue(data.indexOf(CALR3_HUMAN_BEFORE) != -1);
assertTrue(data.indexOf(CALRL_HUMAN_BEFORE) != -1);
Cleaner cleaner = new UniProtCleanerImpl();
os.reset();
cleaner.clean(new ByteArrayInputStream(bytes), os);
bytes = os.toByteArray();
data = new String(bytes);
assertTrue(data.indexOf(CALR3_HUMAN_AFTER) != -1);
assertTrue(data.indexOf(CALRL_HUMAN_AFTER) != -1);
// dump owl for review
String outFilename =
getClass().getClassLoader().getResource("").getPath()
+ File.separator
+ "testCleanUniProt.out.dat";
Writer out = new OutputStreamWriter(new FileOutputStream(outFilename));
out.write(data);
out.close();
}
// Upload (and replace if exists) a data archive for the existing data source
@RequestMapping(value = "/admin/datasources/{identifier}/file", method = RequestMethod.POST)
public void uploadDataArchive(
@PathVariable String identifier,
MultipartHttpServletRequest multiRequest,
HttpServletResponse response)
throws IOException {
Metadata m = service.metadata().findByIdentifier(identifier);
if (m == null) {
response.sendError(
Status.NO_RESULTS_FOUND.getErrorCode(),
Status.NO_RESULTS_FOUND.getErrorMsg()
+ "; Metadata object with identifier: "
+ identifier
+ " not found.");
}
Map<String, MultipartFile> files = multiRequest.getFileMap();
Assert.state(!files.isEmpty(), "No files to validate");
String filename = files.keySet().iterator().next();
MultipartFile file = files.get(filename);
String origFilename = file.getOriginalFilename();
if (file.getBytes().length == 0
|| filename == null
|| "".equals(filename)
|| !origFilename.endsWith(".zip")) {
log.error("uploadDataArchive(), empty data file or null: " + origFilename);
response.sendError(
Status.BAD_REQUEST.getErrorCode(),
"File (" + origFilename + ") UPLOAD failed; id:" + identifier);
} else {
// create or update the input source data file (must be ZIP archive!)
CPathUtils.write(file.getBytes(), m.getDataArchiveName());
log.info(
"uploadDataArchive(), saved uploaded file:"
+ origFilename
+ " as "
+ m.getDataArchiveName());
}
}
