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Commit 92add8cc authored by vkovtun's avatar vkovtun
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SSDM-13794: Improved error messages in default ELN dropbox.

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ui-eln-lims/src/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py
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import re
import uuid
from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions import ExperimentFetchOptions
from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id import ExperimentIdentifier
from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleFetchOptions
from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id import SampleIdentifier
from ch.systemsx.cisd.common.mail import EMailAddress
from ch.systemsx.cisd.openbis.generic.client.web.client.exception import UserFailureException
from ch.systemsx.cisd.openbis.dss.generic.shared import ServiceProvider
from ch.systemsx.cisd.openbis.generic.client.web.client.exception import UserFailureException
from java.io import File
from java.nio.file import Files, Paths, StandardCopyOption
from java.util import List
from org.json import JSONObject
from org.apache.commons.io import FileUtils
from org.json import JSONObject
INVALID_FORMAT_ERROR_MESSAGE = "Invalid format for the folder name, should follow the pattern <ENTITY_KIND>+<SPACE_CODE>+<PROJECT_CODE>+[<EXPERIMENT_CODE>|<SAMPLE_CODE>]+<OPTIONAL_DATASET_TYPE>+<OPTIONAL_NAME>";
ILLEGAL_CHARACTERS_IN_FILE_NAMES_ERROR_MESSAGE = "Directory or its content contain illegal characters: \"', ~, $, %\"";
......@@ -25,174 +23,184 @@ EXPERIMENT_MISSING_ERROR_MESSAGE = "Experiment not found";
NAME_PROPERTY_SET_IN_TWO_PLACES_ERROR_MESSAGE = "$NAME property specified twice, it should just be in either folder name or metadata.json"
EMAIL_SUBJECT = "ELN LIMS Dropbox Error";
ILLEGAL_FILES = ["desktop.ini", "IconCache.db", "thumbs.db"];
ILLEGAL_FILES_ERROR_MESSAGE = "Directory or contains illegal files: " + str(ILLEGAL_FILES);
HIDDEN_FILES_ERROR_MESSAGE = "Directory or contains hidden files: files starting with '.'";
ILLEGAL_FILES_ERROR_MESSAGE = "Directory contains illegal files: " + str(ILLEGAL_FILES);
HIDDEN_FILES_ERROR_MESSAGE = "Directory contains hidden files: files starting with '.'";
errorMessages = []
def process(transaction):
incoming = transaction.getIncoming();
folderName = incoming.getName();
if not folderName.startswith('.'):
datasetInfo = folderName.split("+");
entityKind = None;
sample = None;
experiment = None;
datasetType = None;
name = None;
# Parse entity Kind
if len(datasetInfo) >= 1:
entityKind = datasetInfo[0];
else:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_ERROR_MESSAGE);
v3 = ServiceProvider.getV3ApplicationService();
sessionToken = transaction.getOpenBisServiceSessionToken();
projectSamplesEnabled = v3.getServerInformation(sessionToken)['project-samples-enabled'] == 'true'
# Parse entity Kind Format
if entityKind == "O":
if len(datasetInfo) >= 4 and projectSamplesEnabled:
sampleSpace = datasetInfo[1];
projectCode = datasetInfo[2];
sampleCode = datasetInfo[3];
emailAddress = getSampleRegistratorsEmail(transaction, sampleSpace, projectCode, sampleCode)
sample = transaction.getSample("/" + sampleSpace + "/" + projectCode + "/" + sampleCode);
if sample is None:
reportIssue(transaction,
INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE,
None);
if len(datasetInfo) >= 5:
datasetType = datasetInfo[4];
if len(datasetInfo) >= 6:
name = datasetInfo[5];
if len(datasetInfo) > 6:
reportIssue(transaction,
INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE,
emailAddress)
elif len(datasetInfo) >= 3 and not projectSamplesEnabled:
sampleSpace = datasetInfo[1];
sampleCode = datasetInfo[2];
emailAddress = getSampleRegistratorsEmail(transaction, sampleSpace, None, sampleCode)
sample = transaction.getSample("/" + sampleSpace + "/" + sampleCode);
if sample is None:
reportIssue(transaction,
INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE,
None);
emailAddress = None
try:
if not folderName.startswith('.'):
datasetInfo = folderName.split("+");
entityKind = None;
sample = None;
experiment = None;
datasetType = None;
name = None;
# Parse entity Kind
if len(datasetInfo) >= 1:
entityKind = datasetInfo[0];
else:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_ERROR_MESSAGE);
v3 = ServiceProvider.getV3ApplicationService();
sessionToken = transaction.getOpenBisServiceSessionToken();
projectSamplesEnabled = v3.getServerInformation(sessionToken)['project-samples-enabled'] == 'true'
# Parse entity Kind Format
if entityKind == "O":
if len(datasetInfo) >= 4 and projectSamplesEnabled:
sampleSpace = datasetInfo[1];
projectCode = datasetInfo[2];
sampleCode = datasetInfo[3];
emailAddress = getSampleRegistratorsEmail(transaction, sampleSpace, projectCode, sampleCode)
sample = transaction.getSample("/" + sampleSpace + "/" + projectCode + "/" + sampleCode);
if sample is None:
reportIssue(INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE)
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE)
if len(datasetInfo) >= 5:
datasetType = datasetInfo[4];
if len(datasetInfo) >= 6:
name = datasetInfo[5];
if len(datasetInfo) > 6:
reportIssue(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE)
elif len(datasetInfo) >= 3 and not projectSamplesEnabled:
sampleSpace = datasetInfo[1];
sampleCode = datasetInfo[2];
emailAddress = getSampleRegistratorsEmail(transaction, sampleSpace, None, sampleCode)
sample = transaction.getSample("/" + sampleSpace + "/" + sampleCode);
if sample is None:
reportIssue(INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE)
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE)
if len(datasetInfo) >= 4:
datasetType = datasetInfo[3];
if len(datasetInfo) >= 5:
name = datasetInfo[4];
if len(datasetInfo) > 5:
reportIssue(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE)
else:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE);
hiddenFiles = getHiddenFiles(incoming)
if hiddenFiles:
reportIssue(HIDDEN_FILES_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE + ":\n" + pathListToStr(hiddenFiles))
illegalFiles = getIllegalFiles(incoming)
if illegalFiles:
reportIssue(ILLEGAL_FILES_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE + ":\n" + pathListToStr(illegalFiles))
filesWithIllegalCharacters = getFilesWithIllegalCharacters(incoming)
if filesWithIllegalCharacters:
reportIssue(ILLEGAL_CHARACTERS_IN_FILE_NAMES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE + ":\n" + pathListToStr(filesWithIllegalCharacters))
readOnlyFiles = getReadOnlyFiles(incoming)
if readOnlyFiles:
reportIssue(FOLDER_CONTAINS_NON_DELETABLE_FILES_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE + ":\n" + pathListToStr(readOnlyFiles));
if entityKind == "E":
if len(datasetInfo) >= 4:
datasetType = datasetInfo[3];
if len(datasetInfo) >= 5:
name = datasetInfo[4];
if len(datasetInfo) > 5:
reportIssue(transaction,
INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE,
emailAddress)
experimentSpace = datasetInfo[1];
projectCode = datasetInfo[2];
experimentCode = datasetInfo[3];
emailAddress = getExperimentRegistratorsEmail(transaction, experimentSpace, projectCode,
experimentCode);
experiment = transaction.getExperiment("/" + experimentSpace + "/" + projectCode + "/" + experimentCode);
if experiment is None:
reportIssue(INVALID_FORMAT_ERROR_MESSAGE + ":" + EXPERIMENT_MISSING_ERROR_MESSAGE)
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + EXPERIMENT_MISSING_ERROR_MESSAGE)
if len(datasetInfo) >= 5:
datasetType = datasetInfo[4];
if len(datasetInfo) >= 6:
name = datasetInfo[5];
if len(datasetInfo) > 6:
reportIssue(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE);
else:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE);
hiddenFiles = getHiddenFiles(incoming)
if hiddenFiles:
reportIssue(HIDDEN_FILES_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE + ":\n" + pathListToStr(hiddenFiles))
illegalFiles = getIllegalFiles(incoming)
if illegalFiles:
reportIssue(ILLEGAL_FILES_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE + ":\n" + pathListToStr(illegalFiles))
filedWithIllegalCharacters = getFilesWithIllegalCharacters(incoming)
if filedWithIllegalCharacters:
reportIssue(ILLEGAL_CHARACTERS_IN_FILE_NAMES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE + ":\n" + pathListToStr(filedWithIllegalCharacters))
readOnlyFiles = getReadOnlyFiles(incoming)
if readOnlyFiles:
reportIssue(FOLDER_CONTAINS_NON_DELETABLE_FILES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE + ":\n" + pathListToStr(readOnlyFiles))
# Create dataset
dataSet = None;
if datasetType is not None: # Set type if found
dataSet = transaction.createNewDataSet(datasetType);
else:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE);
if hasFolderHiddenFiles(incoming):
reportIssue(transaction, HIDDEN_FILES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE, emailAddress);
if hasFolderIllegalFiles(incoming):
reportIssue(transaction, ILLEGAL_FILES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE, emailAddress);
if hasFolderIllegalCharacters(incoming):
reportIssue(transaction, ILLEGAL_CHARACTERS_IN_FILE_NAMES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE, emailAddress);
if hasFolderReadOnlyFiles(incoming):
reportIssue(transaction, FOLDER_CONTAINS_NON_DELETABLE_FILES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE, emailAddress);
if entityKind == "E":
if len(datasetInfo) >= 4:
experimentSpace = datasetInfo[1];
projectCode = datasetInfo[2];
experimentCode = datasetInfo[3];
emailAddress = getExperimentRegistratorsEmail(transaction, experimentSpace, projectCode,
experimentCode);
experiment = transaction.getExperiment("/" + experimentSpace + "/" + projectCode + "/" + experimentCode);
if experiment is None:
reportIssue(transaction,
INVALID_FORMAT_ERROR_MESSAGE + ":" + EXPERIMENT_MISSING_ERROR_MESSAGE,
None);
if len(datasetInfo) >= 5:
datasetType = datasetInfo[4];
if len(datasetInfo) >= 6:
name = datasetInfo[5];
if len(datasetInfo) > 6:
reportIssue(transaction,
INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE,
emailAddress);
dataSet = transaction.createNewDataSet();
if name is not None:
dataSet.setPropertyValue("$NAME", name); # Set name if found
# Set sample or experiment
if sample is not None:
dataSet.setSample(sample);
else:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE);
if hasFolderHiddenFiles(incoming):
reportIssue(transaction, HIDDEN_FILES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE, emailAddress);
if hasFolderIllegalFiles(incoming):
reportIssue(transaction, ILLEGAL_FILES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE, emailAddress);
if hasFolderIllegalCharacters(incoming):
reportIssue(transaction, ILLEGAL_CHARACTERS_IN_FILE_NAMES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE, emailAddress);
if hasFolderReadOnlyFiles(incoming):
reportIssue(transaction, FOLDER_CONTAINS_NON_DELETABLE_FILES_ERROR_MESSAGE + ":"
+ FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE, emailAddress);
# Create dataset
dataSet = None;
if datasetType is not None: # Set type if found
dataSet = transaction.createNewDataSet(datasetType);
else:
dataSet = transaction.createNewDataSet();
if name is not None:
dataSet.setPropertyValue("$NAME", name); # Set name if found
# Set sample or experiment
if sample is not None:
dataSet.setSample(sample);
else:
dataSet.setExperiment(experiment);
# Move folder to dataset
filesInFolder = incoming.listFiles();
itemsInFolder = 0;
datasetItem = None;
for item in filesInFolder:
fileName = item.getName()
if fileName == "metadata.json":
root = JSONObject(FileUtils.readFileToString(item, "UTF-8"))
properties = root.get("properties")
for propertyKey in properties.keys():
if propertyKey == "$NAME" and name is not None:
raise UserFailureException(NAME_PROPERTY_SET_IN_TWO_PLACES_ERROR_MESSAGE)
propertyValue = properties.get(propertyKey)
if propertyValue is not None:
propertyValueString = str(propertyValue)
dataSet.setPropertyValue(propertyKey, propertyValueString)
dataSet.setExperiment(experiment);
# Move folder to dataset
filesInFolder = incoming.listFiles();
itemsInFolder = 0;
datasetItem = None;
for item in filesInFolder:
fileName = item.getName()
if fileName == "metadata.json":
root = JSONObject(FileUtils.readFileToString(item, "UTF-8"))
properties = root.get("properties")
for propertyKey in properties.keys():
if propertyKey == "$NAME" and name is not None:
raise UserFailureException(NAME_PROPERTY_SET_IN_TWO_PLACES_ERROR_MESSAGE)
propertyValue = properties.get(propertyKey)
if propertyValue is not None:
propertyValueString = str(propertyValue)
dataSet.setPropertyValue(propertyKey, propertyValueString)
else:
itemsInFolder = itemsInFolder + 1;
datasetItem = item;
if itemsInFolder > 1:
tmpPath = incoming.getAbsolutePath() + "/default";
tmpDir = File(tmpPath);
tmpDir.mkdir();
try:
for inputFile in filesInFolder:
Files.move(inputFile.toPath(), Paths.get(tmpPath, inputFile.getName()),
StandardCopyOption.ATOMIC_MOVE);
transaction.moveFile(tmpDir.getAbsolutePath(), dataSet);
finally:
if tmpDir is not None:
tmpDir.delete();
else:
itemsInFolder = itemsInFolder + 1;
datasetItem = item;
if itemsInFolder > 1:
tmpPath = incoming.getAbsolutePath() + "/default";
tmpDir = File(tmpPath);
tmpDir.mkdir();
try:
for inputFile in filesInFolder:
Files.move(inputFile.toPath(), Paths.get(tmpPath, inputFile.getName()),
StandardCopyOption.ATOMIC_MOVE);
transaction.moveFile(tmpDir.getAbsolutePath(), dataSet);
finally:
if tmpDir is not None:
tmpDir.delete();
else:
transaction.moveFile(datasetItem.getAbsolutePath(), dataSet);
transaction.moveFile(datasetItem.getAbsolutePath(), dataSet);
finally:
reportAllIssues(transaction, emailAddress)
def pathListToStr(list):
return "\n".join(list)
def getContactsEmailAddresses(transaction):
......@@ -200,62 +208,69 @@ def getContactsEmailAddresses(transaction):
return re.split("[,;]", emailString) if emailString is not None else []
def reportIssue(transaction, errorMessage, emailAddress):
contacts = getContactsEmailAddresses(transaction);
allAddresses = [emailAddress] + contacts if emailAddress is not None else contacts;
sendMail(transaction, map(lambda address: EMailAddress(address), allAddresses), EMAIL_SUBJECT, errorMessage);
raise UserFailureException(errorMessage);
def reportIssue(errorMessage):
errorMessages.append(errorMessage)
def reportAllIssues(transaction, emailAddress):
if len(errorMessages) > 0:
contacts = getContactsEmailAddresses(transaction)
allAddresses = [emailAddress] + contacts if emailAddress is not None else contacts
joinedErrorMessages = "\n".join(errorMessages)
sendMail(transaction, map(lambda address: EMailAddress(address), allAddresses), EMAIL_SUBJECT, joinedErrorMessages);
raise UserFailureException(joinedErrorMessages)
def hasFolderIllegalCharacters(incoming):
if bool(re.search(r"['~$%]", incoming.getName())):
return True;
def getFilesWithIllegalCharacters(folder):
result = []
if bool(re.search(r"['~$%]", folder.getPath())):
result.append(folder.getName())
files = incoming.listFiles()
files = folder.listFiles()
if files is not None:
for f in files:
if hasFolderIllegalCharacters(f):
return True;
result.extend(getFilesWithIllegalCharacters(f))
return False;
def hasFolderHiddenFiles(incoming):
if incoming.getName().startswith("."):
return True;
def getHiddenFiles(folder):
result = []
if folder.getName().startswith("."):
result.append(folder.getPath())
files = incoming.listFiles()
files = folder.listFiles()
if files is not None:
for f in files:
if hasFolderHiddenFiles(f):
return True;
result.extend(getHiddenFiles(f))
return result
return False;
def hasFolderIllegalFiles(incoming):
if incoming.getName() in ILLEGAL_FILES:
return True;
def getIllegalFiles(folder):
result = []
if folder.getName() in ILLEGAL_FILES:
result.append(folder.getPath())
files = incoming.listFiles()
files = folder.listFiles()
if files is not None:
for f in files:
if hasFolderIllegalFiles(f):
return True;
result.extend(getIllegalFiles(f))
return False;
return result
def hasFolderReadOnlyFiles(incoming):
if not incoming.renameTo(incoming):
return True;
def getReadOnlyFiles(folder):
result = []
if not folder.renameTo(folder):
result.append(folder.getPath())
files = incoming.listFiles()
files = folder.listFiles()
if files is not None:
for f in files:
if hasFolderReadOnlyFiles(f):
return True;
result.extend(getReadOnlyFiles(f))
return False;
return result
def sendMail(transaction, emailAddresses, subject, body):
......
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