def storeToken(self, tokenObject):
self.resetErrors()
index = "resumptionTokens-STORE"
table = "resumptionTokens"
fields = {
"token": tokenObject.getToken(),
"metadataPrefix": tokenObject.getMetadataPrefix(),
"expiry": Timestamp(tokenObject.getExpiry()),
"nextToken": tokenObject.getNextToken(),
"resultJson": ""
}
FileUtils.writeStringToFile(
File(
FascinatorHome.getPath("oaipmh-results") + "/" +
tokenObject.getToken()), tokenObject.getResultJson())
#self.log.debug("=== storeToken()")
#self.log.debug("=== TOKEN: '{}'", tokenObject.getToken())
#self.log.debug("=== METADATAPREFIX: '{}'", tokenObject.getMetadataPrefix())
#self.log.debug("=== EXPIRY: '{}'", tokenObject.getExpiry())
#self.log.debug("=== TOTALFOUND: '{}'", tokenObject.getTotalFound())
#self.log.debug("=== START: '{}'", tokenObject.getStart())
try:
self.db.insert(self.dbName, index, table, fields)
except Exception, e:
msg = self.parseError(e)
if msg == "Duplicate record!":
# Expected failure
self.log.error("Duplicate record already exists in table!")
else:
# Something is wrong
self.log.error("ERROR: ", e)
self.error = True
self.errorMsg = msg
def storeToken(self, tokenObject):
self.resetErrors()
index = "resumptionTokens-STORE"
table = "resumptionTokens"
fields = {
"token": tokenObject.getToken(),
"metadataPrefix": tokenObject.getMetadataPrefix(),
"expiry": Timestamp(tokenObject.getExpiry()),
"nextToken": tokenObject.getNextToken(),
"resultJson": ""
}
FileUtils.writeStringToFile(File(FascinatorHome.getPath("oaipmh-results")+ "/"+tokenObject.getToken()),tokenObject.getResultJson())
#self.log.debug("=== storeToken()")
#self.log.debug("=== TOKEN: '{}'", tokenObject.getToken())
#self.log.debug("=== METADATAPREFIX: '{}'", tokenObject.getMetadataPrefix())
#self.log.debug("=== EXPIRY: '{}'", tokenObject.getExpiry())
#self.log.debug("=== TOTALFOUND: '{}'", tokenObject.getTotalFound())
#self.log.debug("=== START: '{}'", tokenObject.getStart())
try:
self.db.insert(self.dbName, index, table, fields)
except Exception, e:
msg = self.parseError(e)
if msg == "Duplicate record!":
# Expected failure
self.log.error("Duplicate record already exists in table!")
else:
# Something is wrong
self.log.error("ERROR: ", e)
self.error = True
self.errorMsg = msg
def getKeysArray(self):
keysFile = FileUtils.getFile(self.systemConfig.getString("", "api", "apiKeyFile"))
keysFile.createNewFile()
try:
keysJsonSimple = JsonSimple(keysFile)
except IOException, ParseException:
self.log.warn("File may be blank. Creating empty json api keys file...")
FileUtils.writeStringToFile(keysFile, '{"api": {"clients": []}}')
keysJsonSimple = JsonSimple(keysFile)
def validate_package(self, zipped_package):
working_dir, working_dir_path, unzipped_package_path = self._setup_working_dir()
try:
self._extract_package(zipped_package, str(unzipped_package_path.toAbsolutePath()))
for output in self._execute_validation(working_dir):
print output
finally:
FileUtils.deleteDirectory(working_dir.toFile())
def empty_user(self):
strRootDir = request.getServletContext().getRealPath("/")
strUserHtmlDir = strRootDir + "html" + File.separator + "user" + File.separator
dirFile = File(strUserHtmlDir)
if dirFile.exists() == False or dirFile.isDirectory() == False:
request.setAttribute("errorMessage", u"用户缓存文件夹不存在！")
return
FileUtils.deleteQuietly(dirFile)
request.setAttribute("errorMessage", u"删除所有用户缓存完毕！")
def writeResponseToStatusResponseCache(self, jobId, jobStatus):
curationStatusRespones = File(FascinatorHome.getPath() +
"/curation-status-responses")
if curationStatusRespones.exists():
FileUtils.forceMkdir(curationStatusRespones)
FileUtils.writeStringToFile(
File(curationStatusRespones.getPath() +
"/" + Integer(jobId).toString() + ".json"),
jobStatus.toString(True))
def decode_archive():
try:
print 'decoding archive...'
encoded_archive_bytes = FileUtils.readFileToByteArray(
File(node_archive_path))
decoded_archive_bytes = Base64.getMimeDecoder().decode(
encoded_archive_bytes)
FileUtils.writeByteArrayToFile(File(archive_name),
decoded_archive_bytes)
print 'successfully decoded archive'
except:
print 'Decoding application archive failed'
print dumpStack()
apply(traceback.print_exception, sys.exc_info())
exit(exitcode=1)
def onCall(self, value, fileStream, fileStream2):
if not sponge.getVariable("demo.readOnly", False):
uploaded = "Uploaded"
uploadDir = "{}/upload/".format(sponge.home)
# Single file.
if fileStream.hasNext():
FileUtils.copyInputStreamToFile(fileStream.inputStream, File(uploadDir + fileStream.filename))
uploaded += " " + fileStream.filename
print "Writing " + fileStream.filename
# Multiple files.
while fileStream2.hasNext():
fs2 = fileStream2.next()
FileUtils.copyInputStreamToFile(fs2.inputStream, File(uploadDir + fs2.filename))
print "Writing " + fs2.filename
uploaded += " " + fs2.filename
return uploaded
def __createFromSelected(self):
self.vc("log").debug("Creating package from selected...")
packageType, jsonConfigFile = self.__getPackageTypeAndJsonConfigFile()
#self.vc("log").debug("packageType = '{}'", packageType)
#self.vc("log").debug("jsonConfigFile = '{}'", jsonConfigFile)
# if modifying existing manifest, we already have an identifier,
# otherwise create a new one
manifestId = self.__getActiveManifestId()
if manifestId is None:
manifestHash = "%s.tfpackage" % uuid.uuid4()
else:
manifestHash = self.__getActiveManifestPid()
# store the manifest file for harvesting
packageDir = FascinatorHome.getPathFile("packages")
packageDir.mkdirs()
manifestFile = File(packageDir, manifestHash)
outStream = FileOutputStream(manifestFile)
outWriter = OutputStreamWriter(outStream, "UTF-8")
manifest = self.__getActiveManifest()
oldType = manifest.getType()
if oldType is None:
manifest.setType(packageType)
else:
manifest.setType(oldType)
#self.vc("log").debug("Manifest: {}", manifest)
outWriter.write(manifest.toString(True))
outWriter.close()
try:
if manifestId is None:
# harvest the package as an object
username = self.vc("sessionState").get("username")
if username is None:
username = "******" # necessary?
harvester = None
# set up config files, and make sure they are both deployed
workflowsDir = FascinatorHome.getPathFile("harvest/workflows")
configFile = self.__getFile(workflowsDir, jsonConfigFile)
rulesFile = self.__getFile(workflowsDir, "packaging-rules.py")
# run the harvest client with our packaging workflow config
harvester = HarvestClient(configFile, manifestFile, username)
harvester.start()
manifestId = harvester.getUploadOid()
harvester.shutdown()
else:
# update existing object
object = StorageUtils.getDigitalObject(Services.getStorage(), manifestId)
manifestStream = FileUtils.openInputStream(manifestFile)
StorageUtils.createOrUpdatePayload(object, manifestHash, manifestStream)
manifestStream.close()
object.close()
except Exception, ex:
error = "Packager workflow failed: %s" % str(ex)
log.error(error, ex)
if harvester is not None:
harvester.shutdown()
return '{ "status": "failed" }'
def undeploy_package(self, zipped_package):
working_dir, working_dir_path, undeploy_package_path = self._setup_working_dir()
try:
unzipped_package_path = Files.createDirectory(working_dir.resolve("undeploy_root"))
self._extract_package(zipped_package, str(unzipped_package_path.toAbsolutePath()))
package_xml_file = unzipped_package_path.resolve("package.xml")
root = ET.parse(str(package_xml_file.toAbsolutePath())).getroot()
ns = {'sf': 'http://soap.sforce.com/2006/04/metadata'}
version = root.find('sf:version', ns).text
Files.copy(package_xml_file, undeploy_package_path.resolve('destructiveChanges.xml'))
Files.write(undeploy_package_path.resolve("package.xml"), bytearray(self.empty_package_template(version)))
for output in self._execute(working_dir):
print output
finally:
FileUtils.deleteDirectory(working_dir.toFile())
def getToken(self, tokenId):
self.resetErrors()
index = "resumptionTokens-GET"
sql = """
SELECT *
FROM resumptionTokens
WHERE token = ?
"""
fields = [tokenId]
try:
result = self.db.select(self.dbName, index, sql, fields)
# Make sure we got a response
if result is None or result.isEmpty():
return None
# Create the new token to return
metadataPrefix = result.get(0).get("METADATAPREFIX")
expiryStr = result.get(0).get("EXPIRY")
# Jython does not support %f microseconds in time parsing, makes
# this more awkward then it should be in 2.6+ Python
# 1: split into basic time + micro seconds
(basicTime, mSecs) = expiryStr.strip().split(".")
# 2: Parse the basic time
expiryDt = datetime.strptime(basicTime, "%Y-%m-%d %H:%M:%S")
# 3: Convert into a 'epoch' long and then to a string (has an extra ".0" on the end)
epoch = "%s" % time.mktime(expiryDt.timetuple())
# 4: Remove the extraneous trailing zero and re-attach microseconds
expiry = "%s%s" % (epoch.replace(".0", ""), mSecs)
nextToken = result.get(0).get("NEXTTOKEN")
file = File(
FascinatorHome.getPath("oaipmh-results") + "/" + tokenId)
resultJson = FileUtils.readFileToString(file)
FileUtils.deleteQuietly(file)
token = ResumptionToken(tokenId, metadataPrefix, nextToken,
resultJson)
token.setExpiry(expiry)
return token
except Exception, e:
# Something is wrong
self.log.error("ERROR: ", e)
self.error = True
self.errorMsg = self.parseError(e)
return None
def getYaraTargetFromGhidra():
yaraTargetPath = askFile('Choose a file where Ghidra Program bytes will be saved.', 'Choose file:')
if yaraTargetPath is None:
sys.exit(1)
if os.path.exists(yaraTargetPath.getPath()):
os.remove(yaraTargetPath.getPath())
CHUNK_SIZE = 4096
buf = jarray.zeros(CHUNK_SIZE,"b")
fBytes = currentProgram.getMemory().getAllFileBytes().get(0)
sizeFBytes = fBytes.getSize()
for k in range(0, sizeFBytes+1, CHUNK_SIZE):
count = fBytes.getOriginalBytes(k,buf,0,CHUNK_SIZE)
if count == 0:
break
buf2 = buf[0:count]
FileUtils.writeByteArrayToFile(yaraTargetPath, buf2, True)
return yaraTargetPath.getPath()
def getToken(self, tokenId):
self.resetErrors()
index = "resumptionTokens-GET"
sql = """
SELECT *
FROM resumptionTokens
WHERE token = ?
"""
fields = [tokenId]
try:
result = self.db.select(self.dbName, index, sql, fields)
# Make sure we got a response
if result is None or result.isEmpty():
return None
# Create the new token to return
metadataPrefix = result.get(0).get("METADATAPREFIX")
expiryStr = result.get(0).get("EXPIRY")
# Jython does not support %f microseconds in time parsing, makes
# this more awkward then it should be in 2.6+ Python
# 1: split into basic time + micro seconds
(basicTime, mSecs) = expiryStr.strip().split(".")
# 2: Parse the basic time
expiryDt = datetime.strptime(basicTime, "%Y-%m-%d %H:%M:%S")
# 3: Convert into a 'epoch' long and then to a string (has an extra ".0" on the end)
epoch = "%s" % time.mktime(expiryDt.timetuple())
# 4: Remove the extraneous trailing zero and re-attach microseconds
expiry = "%s%s" % (epoch.replace(".0", ""), mSecs)
nextToken = result.get(0).get("NEXTTOKEN")
file = File(FascinatorHome.getPath("oaipmh-results")+ "/"+tokenId)
resultJson = FileUtils.readFileToString(file)
FileUtils.deleteQuietly(file)
token = ResumptionToken(tokenId, metadataPrefix,nextToken,resultJson)
token.setExpiry(expiry)
return token
except Exception, e:
# Something is wrong
self.log.error("ERROR: ", e)
self.error = True
self.errorMsg = self.parseError(e)
return None
def removeToken(self, tokenObject):
self.resetErrors()
index = "resumptionTokens-DELETE"
table = "resumptionTokens"
fields = {
"token": tokenObject.getToken()
}
try:
self.db.delete(self.dbName, index, table, fields)
file = File(FascinatorHome.getPath("oaipmh-results")+ "/"+tokenObject.getToken())
FileUtils.deleteQuietly(file)
self.log.info("Delete successful! TOKEN='{}'", tokenObject.getToken())
return True
except Exception, e:
# Something is wrong
self.log.error("Delete failed! TOKEN='{}'", tokenObject.getToken())
self.log.error("ERROR: ", e)
self.error = True
self.errorMsg = self.parseError(e)
return False
def getSavedGitUrl():
RELOAD_LOCK.lock()
try:
gitUrlFile = File(getGitUrlFile())
if gitUrlFile.isFile():
url = FileUtils.readFileToString(gitUrlFile).strip()
return url if len(url) > 0 else None
else:
return None
finally:
RELOAD_LOCK.unlock()
def getSavedGitBranch():
RELOAD_LOCK.lock()
try:
gitBranchFile = File(getGitBranchFile())
if gitBranchFile.isFile():
branch = FileUtils.readFileToString(gitBranchFile).strip()
return branch if len(branch) > 0 else None
else:
return None
finally:
RELOAD_LOCK.unlock()
def removeToken(self, tokenObject):
self.resetErrors()
index = "resumptionTokens-DELETE"
table = "resumptionTokens"
fields = {"token": tokenObject.getToken()}
try:
self.db.delete(self.dbName, index, table, fields)
file = File(
FascinatorHome.getPath("oaipmh-results") + "/" +
tokenObject.getToken())
FileUtils.deleteQuietly(file)
self.log.info("Delete successful! TOKEN='{}'",
tokenObject.getToken())
return True
except Exception, e:
# Something is wrong
self.log.error("Delete failed! TOKEN='{}'", tokenObject.getToken())
self.log.error("ERROR: ", e)
self.error = True
self.errorMsg = self.parseError(e)
return False
def execute(self):
unitService = __jitar__.unitService
siteNavService = __spring__.getBean("siteNavService")
unit_list = unitService.getAllUnitOrChildUnitList(None)
print unit_list
for u in unit_list:
self.siteNavArray = []
unitId = u.unitId
site_list = siteNavService.getAllSiteNav(True, 1, unitId)
for sn in site_list:
if self.checkExists(sn) == True:
siteNavService.deleteSiteNav(sn)
else:
self.siteNavArray.append(sn)
strFile = request.getServletContext().getRealPath("/")
strFile = strFile + "html" + File.separator + "unit" + File.separator
file = File(strFile)
if file.exists():
FileUtils.deleteDirectory(file)
response.writer.write(u"代码已经执行完毕。")
def onCall(self, filename):
if not sponge.getVariable("demo.readOnly", False):
uploaded = "Uploaded"
uploadDir = "{}/upload/".format(sponge.home)
file = File(uploadDir + filename)
streamValue = OutputStreamValue(lambda output: FileUtils.copyFile(file, output)).withHeader(
u"Content-Disposition", 'attachment; filename="{}"'.format(filename))
mimeType = Files.probeContentType(file.toPath())
if mimeType:
streamValue.withContentType(mimeType)
return streamValue
def deleteDirectory(self, sPath):
# 如果sPath不以文件分隔符结尾，自动添加文件分隔符
dirFile = File(sPath)
# 如果dir对应的文件不存在，或者不是一个目录，则退出
if dirFile.exists() == False or dirFile.isDirectory() == False:
return
FileUtils.deleteQuietly(dirFile)
return
"""
换一种新的方法，以下代码不用了
"""
# 删除文件夹下的所有文件(包括子目录)
files = dirFile.listFiles()
if files == None or len(files) == 0: return
for f in files:
# 删除子文件
if f.isFile():
f.delete()
else:
self.deleteDirectory(f.getAbsolutePath())
#/删除当前目录
dirFile.delete()
dirFile = None
def __activate__(self, context):
self.auth = context["page"].authentication
self.errorMsg = ""
self.request = context["request"]
self.response = context["response"]
self.formData = context["formData"]
self.log = context["log"]
self.reportManager = context["Services"].getService("reportManager")
self.reportName = None
if (self.auth.is_logged_in()):
if (self.auth.is_admin()==True):
pass
else:
self.errorMsg = "Requires Admin / Librarian / Reviewer access."
else:
self.errorMsg = "Please login."
if self.errorMsg == "":
self.reportName = self.formData.get("reportName")
if (self.reportName):
self.report = self.reportManager.getReport(self.reportName)
self.func = self.formData.get("func", "")
if self.func == "" and self.request.getParameter("func"):
self.func = self.request.getParameter("func")
if self.func == "action":
self.action = self.request.getParameter("action")
if self.action == "create":
self.createReport()
out = self.response.getPrintWriter("text/plain; charset=UTF-8")
out.println("{\"id\":\""+self.report.getReportName()+"\"}")
out.close()
return
if self.action == "edit":
self.editReport()
out = self.response.getPrintWriter("text/plain; charset=UTF-8")
out.println("{\"id\":\""+self.report.getReportName()+"\"}")
out.close()
return
if self.action == "options":
out = self.response.getPrintWriter("text/plain; charset=UTF-8")
out.println(FileUtils.readFileToString(File(FascinatorHome.getPath("reports")+"/reportCriteriaOptions.json")))
out.close()
return
if self.action == "get-json":
out = self.response.getPrintWriter("text/plain; charset=UTF-8")
report = self.reportManager.getReports().get(self.request.getParameter("reportName"))
queryFilters = report.config.getObject("query", "filter")
jsonMap = HashMap()
elementIds = ArrayList()
for elementId in queryFilters:
elementIds.add(elementId)
Collections.sort(elementIds)
for elementId in elementIds:
jsonMap.put(elementId,queryFilters.get(elementId).get("value"))
jsonMap.put("reportName",report.getLabel())
JsonObject.writeJSONString(jsonMap,out)
out.close()
return
def __handleAlert(self, file):
'''Sends the alert off to the relevant handler and then pushes the metadata to ReDBox
Parameters:
file -- the file (path, not object) to be processed
'''
successCount = 0
failedCount = 0
handler = None
self.logInfo(file, "Processing file " + file)
self.__log.info("Alert system is processing file %s" % file)
ext = file.rpartition('.')[2]
if not ext in self.handlers:
self.logInfo(
file, "Did not process file as extension is not configured")
return (0, 0)
#Add the timestamp to a copy of baseline
baseline = dict(self.baseline)
timestamp = time.gmtime(os.path.getmtime(self.pBase(file)))
for field in self.timestampFields:
val = time.strftime("%Y-%m-%d %H:%M:%S", timestamp)
baseline[field] = val
if self.handlers[ext] == "CSVAlertHandler":
config = self.config['CSVAlertHandlerParams']['configMap'][ext]
handler = CSVAlertHandler(self.pBase(file), config, baseline)
self.logInfo(
file,
"Using the CSVAlertHandler for file with extension %s" % ext)
elif self.handlers[ext] == "XMLAlertHandler":
config = self.config['XMLAlertHandlerParams']['configMap'][ext]
handler = XMLAlertHandler(self.pBase(file), config, baseline)
self.logInfo(
file,
"Using the XMLAlertHandler for file with extension %s" % ext)
else:
raise AlertException("Unknown file handler: '%s'" %
self.handlers[ext])
jsonList = handler.process()
if jsonList is None:
self.logInfo(file, "No records were returned.")
return (0, 0)
## Now all of the JSON Objects need to be ingested into the tool chain
id = 0
for json in jsonList:
id += 1
#use an incremental filename in case the data file contains more than 1 record
meta_file_name = "%s.%s" % (file, id)
meta_file = self.pTemp(meta_file_name)
self.logInfo(file, "Using metadata file: %s" % meta_file)
try:
oid = self.__ingestJson(file, meta_file, json)
successCount += 1
except Exception, e:
failedCount += 1
self.logInfo(
file, "Moving failed metadata file [%s] to %s." %
(meta_file, self.__DIR_FAILED))
filepath = os.path.join(self.__DIR_FAILED, meta_file_name)
FileUtils.moveFile(File(meta_file), File(filepath))
continue
self.logInfo(
file, "Moving successful metadata file [%s] to %s." %
(meta_file, self.__DIR_SUCCESS))
filepath = os.path.join(self.__DIR_SUCCESS, meta_file_name)
#python library seems to dislike mixed \ and / in path
FileUtils.moveFile(File(meta_file), File(filepath))
def execute(self):
if self.loginUser == None:
request.setAttribute("error", u"请重新登录。")
return "/WEB-INF/ftl/show_resource_swf.ftl"
param = ParamUtil(request)
resourceId = self.params.safeGetIntParam("resource")
resourceService = __jitar__.getResourceService()
if resourceId == 0:
request.setAttribute("error", u"缺少文件信息。")
return "/WEB-INF/ftl/show_resource_swf.ftl"
resource = resourceService.getResource(resourceId)
if resource == None:
request.setAttribute("error", u"无法加载资源。")
return "/WEB-INF/ftl/show_resource_swf.ftl"
#=======================================================================
# enc = EncryptDecrypt("zhongjiaoqixing")
# try:
# resfile = enc.decrypt(resfile)
# except:
# request.setAttribute("error", u"解压缩过程中出现错误。")
# return "/WEB-INF/ftl/show_resource.ftl"
# finally:
# encc = None
#=======================================================================
try:
resfile = resource.href
filename = resfile.lower()
fileUserConfigPath = request.getSession().getServletContext(
).getInitParameter("userPath")
if fileUserConfigPath == None or fileUserConfigPath == "":
resfileapth = request.getSession().getServletContext(
).getRealPath("/" + resfile)
else:
if fileUserConfigPath.endswith("\\") == False:
fileUserConfigPath = fileUserConfigPath + "\\"
resfileapth = fileUserConfigPath + resfile.replace("/", "\\")
ff = File(resfileapth)
if ff.isFile() == False or ff.exists() == False:
request.setAttribute("error", u"资源文件不存在，无法进行预览。")
return "/WEB-INF/ftl/show_resource_swf.ftl"
#这些文件直接显示
if filename.endswith(".jpg") or filename.endswith(
".gif") or filename.endswith(".png"):
response.sendRedirect(CommonUtil.getSiteUrl(request) + resfile)
return
if filename.endswith(".txt"):
content = FileUtils.readFileToString(
ff, CommonUtil.getFileEncoding(resfileapth))
request.setAttribute("content", content)
return "/WEB-INF/ftl/show_resource_txt.ftl"
#PDF2SWFPath = request.getSession().getServletContext().getInitParameter("pdf2swfPath")
#if PDF2SWFPath == None or PDF2SWFPath == "":
#request.setAttribute("error", u"没有配置文件转换服务。")
#return "/WEB-INF/ftl/show_resource_swf.ftl"
if filename.endswith(".doc") or filename.endswith(
".docx"
): # or filename.endswith(".ppt") or filename.endswith(".pptx") or filename.endswith(".xls") or filename.endswith(".xlsx"):
swf = resfileapth[0:resfileapth.find(".")] + ".swf"
file = File(swf)
if file.isFile() == False or file.exists() == False:
#converter = DocConverter(JacobPDFConverter(), SWFToolsSWFConverter(PDF2SWFPath))
#converter.convert(resfileapth)
#converter = None
#转换服务
server_ip = request.getSession().getServletContext(
).getInitParameter("server_ip")
server_port = request.getSession().getServletContext(
).getInitParameter("server_port")
timeout = request.getSession().getServletContext(
).getInitParameter("timeout")
fcs = FCSConverter()
fcs.fcs(
server_ip, server_port, timeout, resource.title,
resfileapth[0:resfileapth.find(".")] + "." +
filename.split(".")[-1], file.toString(), "0")
request.setAttribute("resourceId", resourceId)
request.setAttribute(
"showWaiting",
self.params.safeGetStringParam("showWaiting"))
swf = CommonUtil.getSiteUrl(
request) + resfile[0:resfile.find(".")] + ".swf"
request.setAttribute("swf", swf)
return "/WEB-INF/ftl/show_resource_swf.ftl"
#if filename.endswith(".pdf"):
#swf = resfileapth[0:resfileapth.find(".")] + ".swf"
#file = File(swf)
#if file.isFile() == False or file.exists() == False:
#converter = SWFToolsSWFConverter(PDF2SWFPath)
#converter.convert2SWF(resfileapth)
#converter = None
#request.setAttribute("resourceId", resourceId)
#request.setAttribute("showWaiting", self.params.safeGetStringParam("showWaiting"))
#swf = CommonUtil.getSiteUrl(request) + resfile[0:resfile.find(".")] + ".swf"
#request.setAttribute("swf", swf)
#return "/WEB-INF/ftl/show_resource_swf.ftl"
if filename.endswith(".swf"):
file = File(resfileapth)
if file.isFile() == False or file.exists() == False:
request.setAttribute("error", u"swf 文件不存在，无法进行预览。")
return "/WEB-INF/ftl/show_resource_swf.ftl"
swf = CommonUtil.getSiteUrl(request) + resfile
request.setAttribute("orginIsSwf", "")
request.setAttribute("swf", swf)
return "/WEB-INF/ftl/show_resource_swf.ftl"
request.setAttribute("error", u"此文件不支持预览。")
return "/WEB-INF/ftl/show_resource_swf.ftl"
except BaseException, varExption:
if varExption != None:
request.setAttribute(
"error", u"预览此文件时出错，并且已经被捕获。<br/><br/>" + str(varExption))
else:
request.setAttribute("error", u"预览此文件时出错，并且并且没有捕获到错误信息。")
return "/WEB-INF/ftl/show_resource_swf.ftl"
def __activate__(self, context):
self.auth = context["page"].authentication
self.errorMsg = ""
self.request = context["request"]
self.response = context["response"]
self.formData = context["formData"]
self.log = context["log"]
self.reportManager = context["Services"].getService("reportManager")
self.reportName = None
if (self.auth.is_logged_in()):
if (self.auth.is_admin() == True):
pass
else:
self.errorMsg = "Requires Admin / Librarian / Reviewer access."
else:
self.errorMsg = "Please login."
if self.errorMsg == "":
self.reportName = self.formData.get("reportName")
if (self.reportName):
self.report = self.reportManager.getReport(self.reportName)
self.func = self.formData.get("func", "")
if self.func == "" and self.request.getParameter("func"):
self.func = self.request.getParameter("func")
if self.func == "action":
self.action = self.request.getParameter("action")
if self.action == "create":
self.createReport()
out = self.response.getPrintWriter(
"text/plain; charset=UTF-8")
out.println("{\"id\":\"" + self.report.getReportName() +
"\"}")
out.close()
return
if self.action == "edit":
self.editReport()
out = self.response.getPrintWriter(
"text/plain; charset=UTF-8")
out.println("{\"id\":\"" + self.report.getReportName() +
"\"}")
out.close()
return
if self.action == "options":
out = self.response.getPrintWriter(
"text/plain; charset=UTF-8")
out.println(
FileUtils.readFileToString(
File(
FascinatorHome.getPath("reports") +
"/reportCriteriaOptions.json")))
out.close()
return
if self.action == "get-json":
out = self.response.getPrintWriter(
"text/plain; charset=UTF-8")
report = self.reportManager.getReports().get(
self.request.getParameter("reportName"))
queryFilters = report.config.getObject("query", "filter")
jsonMap = HashMap()
elementIds = ArrayList()
for elementId in queryFilters:
elementIds.add(elementId)
Collections.sort(elementIds)
for elementId in elementIds:
jsonMap.put(elementId,
queryFilters.get(elementId).get("value"))
jsonMap.put("reportName", report.getLabel())
JsonObject.writeJSONString(jsonMap, out)
out.close()
return
def onCall(self):
file = "{}/resources/index.html".format(sponge.home)
return OutputStreamValue(lambda output: FileUtils.copyFile(File(file), output)).withContentType("text/html; charset=\"UTF-8\"")
def processExperiment(self, experimentNode):
"""Register an IExperimentUpdatable based on the Experiment XML node.
@param experimentNode An XML node corresponding to an Experiment
@return IExperimentUpdatable experiment
"""
# Get the experiment version
expVersion = experimentNode.attrib.get("version")
if expVersion is None:
expVersion = "0"
# Get the openBIS identifier
openBISIdentifier = experimentNode.attrib.get("openBISIdentifier")
# Get the experiment name
expName = experimentNode.attrib.get("name")
# Get the experiment date and reformat it to be compatible
# with postgreSQL
expDate = self.formatExpDateForPostgreSQL(experimentNode.attrib.get("date"))
# Get the description
description = experimentNode.attrib.get("description")
# Get the acquisition hardware
acqHardware = experimentNode.attrib.get("acq_hardware")
# Get the acquisition software
acqSoftware = experimentNode.attrib.get("acq_software")
# Get the owner name
owner = experimentNode.attrib.get("owner_name")
# Get attachments
attachments = experimentNode.attrib.get("attachments")
# Create the experiment (with corrected ID if needed: see above)
openBISExperiment = self.createExperiment(openBISIdentifier, expName)
if not openBISExperiment:
msg = "Could not create experiment " + openBISIdentifier
self._logger.error(msg)
raise Exception(msg)
# Get comma-separated tag list
tagList = experimentNode.attrib.get("tags")
if tagList != None and tagList != "":
# Retrieve or create the tags
openBISTags = self.retrieveOrCreateTags(tagList)
# Set the metaprojects (tags)
for openBISTag in openBISTags:
openBISTag.addEntity(openBISExperiment)
# Set the experiment version
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_VERSION",
expVersion)
# Set the date
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_DATE",
expDate)
# Set the description
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_DESCRIPTION",
description)
# Set the acquisition hardware
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_ACQ_HARDWARE",
acqHardware)
# Set the acquisition hardware friendly name
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_ACQ_HARDWARE_FRIENDLY_NAME",
self._machinename)
# Set the acquisition software
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_ACQ_SOFTWARE",
acqSoftware)
# Set the experiment owner
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_OWNER",
owner)
# Add the attachments
if attachments is not None:
# Extract all relative file names
attachmentFiles = attachments.split(";")
for f in attachmentFiles:
# This is an additional security step
if f == '':
continue
# Inform
msg = "Adding file attachment " + f
self._logger.info(msg)
# Build the full path
attachmentFilePath = os.path.join(self._incoming.getAbsolutePath(),
f)
# Extract the file name
attachmentFileName = os.path.basename(attachmentFilePath)
# Read the attachment into a byte array
javaFile = java.io.File(attachmentFilePath)
byteArray = FileUtils.readFileToByteArray(javaFile)
# Add attachment
openBISExperiment.addAttachment(attachmentFilePath,
attachmentFileName,
"", byteArray)
# Return the openBIS Experiment object
return openBISExperiment
def getUrls(self):
return FileUtils.readLines(self.__getHistoryFile())
def saveGitUrl(url):
RELOAD_LOCK.lock()
try:
FileUtils.writeStringToFile(File(getGitUrlFile()), url)
finally:
RELOAD_LOCK.unlock()
def saveGitBranch(branch):
RELOAD_LOCK.lock()
try:
FileUtils.writeStringToFile(File(getGitBranchFile()), branch)
finally:
RELOAD_LOCK.unlock()
def get_file_contents(self, path):
return FileUtils.readFileToString(File(path))
def writeResponseToStatusResponseCache(self, jobId, jobStatus):
curationStatusRespones = File(FascinatorHome.getPath()+ "/curation-status-responses")
if curationStatusRespones.exists():
FileUtils.forceMkdir(curationStatusRespones)
FileUtils.writeStringToFile(File(curationStatusRespones.getPath()+ "/" + Integer(jobId).toString() + ".json"), jobStatus.toString(True))
def processExperiment(self, experimentNode,
openBISExpType="MICROSCOPY_EXPERIMENT"):
"""Register an IExperiment based on the Experiment XML node.
@param experimentNode An XML node corresponding to an Experiment
@param openBISExpType The experiment type
@return IExperiment experiment
"""
# Get the experiment version
expVersion = experimentNode.attrib.get("version")
if expVersion is None:
expVersion = "0"
# Get the openBIS identifier
openBISIdentifier = experimentNode.attrib.get("openBISIdentifier")
# Get the experiment name
expName = experimentNode.attrib.get("name")
# Get the experiment date and reformat it to be compatible
# with postgreSQL
# TODO: Add this
# expDate = self.formatExpDateForPostgreSQL(experimentNode.attrib.get("date"))
# Get the description
description = experimentNode.attrib.get("description")
# Get the acquisition hardware
# TODO: Add this
# acqHardware = experimentNode.attrib.get("acq_hardware")
# Get the acquisition software
# TODO: Add this
# acqSoftware = experimentNode.attrib.get("acq_software")
# Get the owner name
# TODO: Add this
# owner = experimentNode.attrib.get("owner_name")
# Get attachments
attachments = experimentNode.attrib.get("attachments")
# Make sure to keep the code length within the limits imposed by
# openBIS for codes
if len(openBISIdentifier) > 41:
openBISIdentifier = openBISIdentifier[0:41]
# Create univocal ID
openBISIdentifier = openBISIdentifier + "_" + self.getCustomTimeStamp()
# Make sure to create a new Experiment
openBISExperiment = self._transaction.createNewExperiment(openBISIdentifier, openBISExpType)
print(type(openBISExperiment))
if not openBISExperiment:
msg = "PROCESSOR::processExperiment(): " + \
"Could not create experiment " + openBISIdentifier
self._logger.error(msg)
raise Exception(msg)
# Get comma-separated tag list
tagList = experimentNode.attrib.get("tags")
if tagList != None and tagList != "":
# Retrieve or create the tags
openBISTags = self.retrieveOrCreateTags(tagList)
# Set the metaprojects (tags)
for openBISTag in openBISTags:
openBISTag.addEntity(openBISExperiment)
# Set the date
# TODO: Add this
# openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_DATE",
# expDate)
# Store the name
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_NAME", expName)
# Set the experiment version
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_VERSION",
expVersion)
# Set the description -- but only if is not empty.
# This makes sure that the description of an already existing experiment
# is not overridden by an empty string.
if description != "":
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_DESCRIPTION",
description)
else:
currentDescription = openBISExperiment.getPropertyValue("MICROSCOPY_EXPERIMENT_DESCRIPTION")
if (currentDescription is None or currentDescription == ""):
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_DESCRIPTION", "")
# TODO: Add this
# openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_ACQ_HARDWARE",
# acqHardware)
# Set the acquisition hardware friendly name
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_ACQ_HARDWARE_FRIENDLY_NAME",
self._machinename)
# Set the acquisition software
# TODO: Add this
# openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_ACQ_SOFTWARE",
# acqSoftware)
# Set the experiment owner
# TODO: Add this
# openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_OWNER",
# owner)
# Add the attachments
if attachments is not None:
# Extract all relative file names
attachmentFiles = attachments.split(";")
for f in attachmentFiles:
# This is an additional security step
if f == '':
continue
# Inform
msg = "Adding file attachment " + f
self._logger.info(msg)
# Build the full path
attachmentFilePath = os.path.join(self._incoming.getAbsolutePath(),
f)
# Extract the file name
attachmentFileName = os.path.basename(attachmentFilePath)
# Read the attachment into a byte array
javaFile = java.io.File(attachmentFilePath)
byteArray = FileUtils.readFileToByteArray(javaFile)
# Add attachment
openBISExperiment.addAttachment(attachmentFilePath,
attachmentFileName,
"", byteArray)
# Return the openBIS Experiment object
return openBISExperiment
#
# THIS CODE AND INFORMATION ARE PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND/OR FITNESS
# FOR A PARTICULAR PURPOSE. THIS CODE AND INFORMATION ARE NOT SUPPORTED BY XEBIALABS.
#
from java.io import File
from java.net import URL
from org.apache.commons.io import FileUtils
from com.perfectomobile.selenium import MobileDriver
driver = MobileDriver(perfectomobileServer['url'], perfectomobileServer['username'], perfectomobileServer['password'])
try:
file = File.createTempFile("application","maf")
FileUtils.copyURLToFile(URL(applicationUrl), file, 300000, 300000)
driver.uploadMedia(repositoryKey, file)
for key in deviceIds:
device = driver.getDevice(key)
device.open()
device.installApplication(repositoryKey)
finally:
driver.quit()
def processExperiment(self, experimentNode):
"""Register an IExperimentUpdatable based on the Experiment XML node.
@param experimentNode An XML node corresponding to an Experiment
@return IExperimentUpdatable experiment
"""
# Get the experiment version
expVersion = experimentNode.attrib.get("version")
if expVersion is None:
expVersion = "0"
# Get the openBIS identifier
openBISIdentifier = experimentNode.attrib.get("openBISIdentifier")
# Get the experiment name
expName = experimentNode.attrib.get("name")
# Get the experiment date and reformat it to be compatible
# with postgreSQL
expDate = self.formatExpDateForPostgreSQL(
experimentNode.attrib.get("date"))
# Get the description
description = experimentNode.attrib.get("description")
# Get the acquisition hardware
acqHardware = experimentNode.attrib.get("acq_hardware")
# Get the acquisition software
acqSoftware = experimentNode.attrib.get("acq_software")
# Get the owner name
owner = experimentNode.attrib.get("owner_name")
# Get attachments
attachments = experimentNode.attrib.get("attachments")
# Create the experiment (with corrected ID if needed: see above)
openBISExperiment = self.createExperiment(openBISIdentifier, expName)
if not openBISExperiment:
msg = "Could not create experiment " + openBISIdentifier
self._logger.error(msg)
raise Exception(msg)
# Get comma-separated tag list
tagList = experimentNode.attrib.get("tags")
if tagList != None and tagList != "":
# Retrieve or create the tags
openBISTags = self.retrieveOrCreateTags(tagList)
# Set the metaprojects (tags)
for openBISTag in openBISTags:
openBISTag.addEntity(openBISExperiment)
# Set the experiment version
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_VERSION",
expVersion)
# Set the date
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_DATE",
expDate)
# Set the description
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_DESCRIPTION",
description)
# Set the acquisition hardware
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_ACQ_HARDWARE",
acqHardware)
# Set the acquisition hardware friendly name
openBISExperiment.setPropertyValue(
"FACS_ARIA_EXPERIMENT_ACQ_HARDWARE_FRIENDLY_NAME",
self._machinename)
# Set the acquisition software
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_ACQ_SOFTWARE",
acqSoftware)
# Set the experiment owner
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_OWNER", owner)
# Add the attachments
if attachments is not None:
# Extract all relative file names
attachmentFiles = attachments.split(";")
for f in attachmentFiles:
# This is an additional security step
if f == '':
continue
# Inform
msg = "Adding file attachment " + f
self._logger.info(msg)
# Build the full path
attachmentFilePath = os.path.join(
self._incoming.getAbsolutePath(), f)
# Extract the file name
attachmentFileName = os.path.basename(attachmentFilePath)
# Read the attachment into a byte array
javaFile = java.io.File(attachmentFilePath)
byteArray = FileUtils.readFileToByteArray(javaFile)
# Add attachment
openBISExperiment.addAttachment(attachmentFilePath,
attachmentFileName, "",
byteArray)
# Return the openBIS Experiment object
return openBISExperiment
def saveUrl(self, url):
historyFile = self.__getHistoryFile()
if historyFile.exists():
urls = FileUtils.readLines(historyFile)
urls.add(url)
FileUtils.writeLines(historyFile, [url])
def __createFromSelected(self):
self.vc("log").debug("Creating package from selected...")
packageType, jsonConfigFile = self.__getPackageTypeAndJsonConfigFile()
#self.vc("log").debug("packageType = '{}'", packageType)
#self.vc("log").debug("jsonConfigFile = '{}'", jsonConfigFile)
# if modifying existing manifest, we already have an identifier,
# otherwise create a new one
manifestId = self.__getActiveManifestId()
if manifestId is None:
manifestHash = "%s.tfpackage" % uuid.uuid4()
else:
manifestHash = self.__getActiveManifestPid()
# store the manifest file for harvesting
packageDir = FascinatorHome.getPathFile("packages")
packageDir.mkdirs()
manifestFile = File(packageDir, manifestHash)
outStream = FileOutputStream(manifestFile)
outWriter = OutputStreamWriter(outStream, "UTF-8")
manifest = self.__getActiveManifest()
oldType = manifest.getType()
if oldType is None:
manifest.setType(packageType)
else:
manifest.setType(oldType)
self.vc("log").debug("Manifest: %s" % manifest)
outWriter.write(manifest.toString(True))
outWriter.close()
try:
if manifestId is None:
# harvest the package as an object
username = self.vc("sessionState").get("username")
if username is None:
username = "******" # necessary?
harvester = None
# set up config files, and make sure they are both deployed
workflowsDir = FascinatorHome.getPathFile("harvest/workflows")
configFile = self.__getFile(workflowsDir, jsonConfigFile)
rulesFile = self.__getFile(workflowsDir, "packaging-rules.py")
# run the harvest client with our packaging workflow config
harvester = HarvestClient(configFile, manifestFile, username)
harvester.start()
manifestId = harvester.getUploadOid()
harvester.shutdown()
else:
# update existing object
object = StorageUtils.getDigitalObject(Services.getStorage(),
manifestId)
manifestStream = FileUtils.openInputStream(manifestFile)
StorageUtils.createOrUpdatePayload(object, manifestHash,
manifestStream)
manifestStream.close()
object.close()
except Exception, ex:
error = "Packager workflow failed: %s" % str(ex)
self.vc("log").error(error, ex)
if harvester is not None:
harvester.shutdown()
return '{ "status": "failed" }'
def save_screenshot(self, filepath):
tempfile = self.__firefoxDriver.getScreenshotAs(OutputType.FILE)
FileUtils.copyFile(tempfile, File(filepath))
def __handleAlert(self, file):
'''Sends the alert off to the relevant handler and then pushes the metadata to ReDBox
Parameters:
file -- the file (path, not object) to be processed
'''
successCount = 0
failedCount = 0
handler = None
self.logInfo(file, "Processing file " + file)
self.__log.info("Alert system is processing file %s" % file)
ext = file.rpartition('.')[2]
if not ext in self.handlers:
self.logInfo(file, "Did not process file as extension is not configured")
return (0,0)
#Add the timestamp to a copy of baseline
baseline = dict(self.baseline)
timestamp = time.gmtime(os.path.getmtime(self.pBase(file)))
for field in self.timestampFields:
val = time.strftime("%Y-%m-%d %H:%M:%S", timestamp)
baseline[field] = val
if self.handlers[ext] == "CSVAlertHandler":
config = self.config['CSVAlertHandlerParams']['configMap'][ext]
handler = CSVAlertHandler(self.pBase(file), config, baseline)
self.logInfo(file, "Using the CSVAlertHandler for file with extension %s" % ext)
elif self.handlers[ext] == "XMLAlertHandler":
config = self.config['XMLAlertHandlerParams']['configMap'][ext]
handler = XMLAlertHandler(self.pBase(file), config, baseline)
self.logInfo(file, "Using the XMLAlertHandler for file with extension %s" % ext)
else:
raise AlertException("Unknown file handler: '%s'" % self.handlers[ext])
jsonList = handler.process()
if jsonList is None:
self.logInfo(file, "No records were returned.")
return(0,0)
## Now all of the JSON Objects need to be ingested into the tool chain
id = 0
for json in jsonList:
id += 1
#use an incremental filename in case the data file contains more than 1 record
meta_file_name = "%s.%s" % (file,id)
meta_file = self.pTemp(meta_file_name)
self.logInfo(file, "Using metadata file: %s" % meta_file)
try:
oid = self.__ingestJson(file, meta_file, json)
successCount += 1
except Exception, e:
failedCount += 1
self.logInfo(file, "Moving failed metadata file [%s] to %s." % (meta_file, self.__DIR_FAILED))
filepath = os.path.join(self.__DIR_FAILED,meta_file_name)
FileUtils.moveFile(File(meta_file),File(filepath));
continue
self.logInfo(file, "Moving successful metadata file [%s] to %s." % (meta_file, self.__DIR_SUCCESS))
filepath = os.path.join(self.__DIR_SUCCESS,meta_file_name)
#python library seems to dislike mixed \ and / in path
FileUtils.moveFile(File(meta_file),File(filepath));
def get_file_contents(self, path):
return FileUtils.readFileToString(File(path))
