diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
index 5b2123c18abba4161fdb550f1d251723a0f50e0a..c72cebeccb5ee56222b7f9e0096c996e9388ba2d 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
@@ -21,14 +21,13 @@ import jarray
from ch.systemsx.cisd.openbis.dss.generic.server import DataStoreServer
from ch.systemsx.cisd.openbis.generic.client.web.client.exception import UserFailureException
# Zip Format
-from java.io import File
+from java.io import File, BufferedInputStream
from java.io import FileInputStream
from java.io import FileOutputStream
from java.lang import String
from java.lang import StringBuilder
from java.util import ArrayList
-from java.util.zip import ZipEntry, Deflater
-from java.util.zip import ZipOutputStream
+from java.util.zip import ZipEntry, Deflater, ZipOutputStream, CRC32
from org.apache.commons.io import FileUtils
# Java Core
from org.apache.commons.io import IOUtils
@@ -263,7 +262,7 @@ def cleanUp(tempDirPath, tempZipFilePath):
FileUtils.forceDelete(File(tempZipFilePath));
-def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath):
+def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, deflated=True):
# Services used during the export process
v3 = ServiceProvider.getV3ApplicationService();
v3d = ServiceProvider.getApplicationContext().getBean(V3_DSS_BEAN);
@@ -364,7 +363,7 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath):
rawFile = File(tempDirPath + filePath + ".json");
rawFile.getParentFile().mkdirs();
IOUtils.copyLarge(rawFileInputStream, FileOutputStream(rawFile));
- addToZipFile(filePath, rawFile, zos);
+ addToZipFile(filePath, rawFile, zos, deflated=deflated);
emptyZip = False
# To avoid empty directories on the zip file, it makes the first found entity the base directory
@@ -382,20 +381,20 @@ def generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath):
if entityObj is not None and entityFilePath is not None:
# JSON
entityJson = String(objectMapper.writeValueAsString(entityObj));
- fileMetadatum = addFile(tempDirPath, entityFilePath, "json", entityJson.getBytes(), zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "json", entityJson.getBytes(), zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
emptyZip = False
# TEXT
entityTXT = String(getTXT(entityObj, v3, sessionToken, False));
- fileMetadatum = addFile(tempDirPath, entityFilePath, "txt", entityTXT.getBytes(), zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "txt", entityTXT.getBytes(), zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
# DOCX
entityDOCX = getDOCX(entityObj, v3, sessionToken, False);
- fileMetadatum = addFile(tempDirPath, entityFilePath, "docx", entityDOCX, zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "docx", entityDOCX, zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
# HTML
entityHTML = getDOCX(entityObj, v3, sessionToken, True);
- fileMetadatum = addFile(tempDirPath, entityFilePath, "html", entityHTML, zos);
+ fileMetadatum = addFile(tempDirPath, entityFilePath, "html", entityHTML, zos, deflated=deflated);
fileMetadata.append(fileMetadatum)
operationLog.info("--> Entity type: " + type + " permId: " + permId + " post html.");
if emptyZip:
@@ -651,12 +650,12 @@ def objToStrArray(objArray):
return result
-def addFile(tempDirPath, entityFilePath, extension, fileContent, zos):
+def addFile(tempDirPath, entityFilePath, extension, fileContent, zos, deflated=True):
entityFileNameWithExtension = entityFilePath + "." + extension
entityFile = File(tempDirPath + entityFileNameWithExtension);
entityFile.getParentFile().mkdirs();
IOUtils.write(fileContent, FileOutputStream(entityFile));
- addToZipFile(entityFileNameWithExtension, entityFile, zos);
+ addToZipFile(entityFileNameWithExtension, entityFile, zos, deflated=deflated);
FileUtils.forceDelete(entityFile);
extensionToMimeType = {
@@ -685,9 +684,17 @@ def getFilePath(spaceCode, projCode, expCode, sampCode, dataCode):
fileName += "/" + dataCode;
return fileName;
-def addToZipFile(path, file, zos):
+def addToZipFile(path, file, zos, deflated=True):
fis = FileInputStream(file);
zipEntry = ZipEntry(path[1:]); # Making paths relative to make them compatible with Windows zip implementation
+ if not deflated:
+ zipEntry.setMethod(ZipOutputStream.STORED)
+ zipEntry.setSize(file.length())
+ zipEntry.setCompressedSize(-1)
+ crc = getFileCRC(file)
+ zipEntry.setCrc(crc)
+ else:
+ zipEntry.setMethod(ZipOutputStream.DEFLATED)
zos.putNextEntry(zipEntry);
bytes = jarray.zeros(1024, "b");
@@ -699,6 +706,21 @@ def addToZipFile(path, file, zos):
zos.closeEntry();
fis.close();
+def getFileCRC(file):
+ bis = None
+ crc = CRC32()
+ try:
+ bis = BufferedInputStream(FileInputStream(file), 1024)
+ b = jarray.zeros(1024, "b")
+ i = bis.read(b)
+ while i != -1:
+ crc.update(b, 0, i)
+ i = bis.read(b)
+ finally:
+ if bis is not None:
+ bis.close()
+ return crc.getValue()
+
def getConfigurationProperty(transaction, propertyName):
threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties();
try:
@@ -719,9 +741,10 @@ def generateZipFile(entities, params, tempDirPath, tempZipFilePath, deflated=Tru
fos = FileOutputStream(tempZipFilePath)
zos = ZipOutputStream(fos)
if not deflated:
+ zos.setMethod(ZipOutputStream.STORED)
zos.setLevel(Deflater.NO_COMPRESSION)
- fileMetadata = generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath)
+ fileMetadata = generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath, deflated=deflated)
finally:
if zos is not None:
zos.close()
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
index e7ec266b7609e990e4a8992e5563e7457dc9d623..2c48c58426a2dd243546ee575f825c3ae7296423 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
@@ -228,9 +228,10 @@ def generateExternalZipFile(params, exportDirPath, contentZipFilePath, contentZi
fos = FileOutputStream(exportZipFileName)
zos = ZipOutputStream(fos)
if not deflated:
+ zos.setMethod(ZipOutputStream.STORED)
zos.setLevel(Deflater.NO_COMPRESSION)
- addToZipFile(' ' + contentZipFileName, File(contentZipFilePath), zos)
+ addToZipFile(' ' + contentZipFileName, File(contentZipFilePath), zos, deflated)
generateXML(zipOutputStream=zos, fileMetadata=fileMetadata, exportDirPath=exportDirPath,
userInformation=userInformation, entities=entities, params=params)