diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py b/ui-eln-lims/src/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py
index 95f3762335386ab4446357123d92637bf0c111b6..129057a1740f1375b96666b234de8c991b7bf399 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py
@@ -1,18 +1,16 @@
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):