diff --git a/CHANGELOG.md b/CHANGELOG.md index 5190ed1a..32e81588 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog + +## 1.5.0 2020-11-03 + +* New maintenance task: update missing checksum once, after dss starts. +* Fix for nanopore registration: rename folders for pooling case +* Fix for experiment update: force identifier into a string to support v3 API objects + ## 1.4.1 2020-11-03 * Imgag dropbox: raise an exception, if files of unknown type are part of the transaction diff --git a/drop-boxes/register-nanopore-dropbox/register-nanopore.py b/drop-boxes/register-nanopore-dropbox/register-nanopore.py index bc6b2a0c..7ae690ac 100644 --- a/drop-boxes/register-nanopore-dropbox/register-nanopore.py +++ b/drop-boxes/register-nanopore-dropbox/register-nanopore.py @@ -226,12 +226,15 @@ def registerUnclassifiedData(transaction, unclassifiedDataMap, runExperiment, cu # moves a subset of nanopore data to a new target path, needed to add fastq and fast5 subfolders to the same dataset def prepareDataFolder(incomingPath, currentPath, destinationPath, dataObject, suffix): name = dataObject.getName() + # if pooled data, folder is named using barcode and needs to be adapted + if not "_" in name: + name = name + "_" + suffix relativePath = dataObject.getRelativePath() # the source path of the currently handled data object (e.g. fast5_fail folder) sourcePath = os.path.join(os.path.dirname(currentPath), relativePath) checksumFile = createChecksumFileForFolder(incomingPath, sourcePath) # destination path containing data type (fastq or fast5), as well as the parent sample code, so pooled samples can be handled - destination = os.path.join(destinationPath, name + "_" + suffix) + destination = os.path.join(destinationPath, name) os.rename(sourcePath, destination) def createSampleWithData(transaction, space, parentSampleCode, mapWithDataForSample, openbisExperiment, currentPath, absLogPath): diff --git a/maintenance-tasks/checksum-maintenance/plugin.properties b/maintenance-tasks/checksum-maintenance/plugin.properties new file mode 100644 index 00000000..25de8e99 --- /dev/null +++ b/maintenance-tasks/checksum-maintenance/plugin.properties @@ -0,0 +1,3 @@ +# Updates missing checksums +class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseChecksumCalculationTask +execute-only-once = true diff --git a/reporting-plugins/update-experiment-metadata/update.py b/reporting-plugins/update-experiment-metadata/update.py index 5c826561..d39ba2a3 100644 --- a/reporting-plugins/update-experiment-metadata/update.py +++ b/reporting-plugins/update-experiment-metadata/update.py @@ -1,5 +1,3 @@ -import smtplib -from email.mime.text import MIMEText def process(tr, parameters, tableBuilder): """Change properties of experiment @@ -9,30 +7,9 @@ def process(tr, parameters, tableBuilder): if not user == None: tr.setUserId(user) expId = parameters.get("identifier") - exp = tr.getExperimentForUpdate(expId) + exp = tr.getExperimentForUpdate(str(expId)) properties = parameters.get("properties") for prop in properties.keySet(): exp.setPropertyValue(prop, properties.get(prop)) - - #server = "smtpserv.uni-tuebingen.de" - #fromA = "notification_service@qbis.qbic.uni-tuebingen.de" - - # TODO get emails of space users - # Get it via liferay and pass it to this service ? - #toA = "mohr@informatik.uni-tuebingen.de" - #subject = "Update information for Experiment %s" % expId - #text = "Status of Experiment %s has been updated" % expId #, properties.get("Q_CURRENT_STATUS")) - - #msg = MIMEText(text) - #msg['From'] = fromA - #msg['To'] = toA - #msg['Subject'] = subject - # check for info@qbic.uni-tuebingen.de - #msg['reply-to'] = "mohr@informatik.uni-tuebingen.de" - - #smtpServer = smtplib.SMTP(server) - #smtpServer.sendmail(fromA, toA, msg.as_string()) - #smtpServer.close() -