Release/1.5.0 (#53)

* Feature/checksum maintenance (#50)

This PR introduces a maintenance task that will refresh the path info db and update missing checksums

* Feature/checksum maintenance (#52)

This PR favors the ChecksumCalculationTask over the path info db refresh task and has been confirmed to work in a openbis 18.06.2 test instance.

* Update CL

* Add new line at end of file
Add new line at end of file

* convert experiment id to string for v3 objects

* Convert experiment id to string for v3 objects (#55)

* Rename data folder for pooled data (#54)

* adapt changelog

Co-authored-by: wow-such-code <[email protected]>

Author: sven1103

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

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):

maintenance-tasks/checksum-maintenance/plugin.properties

@@ -0,0 +1,3 @@
+# Updates missing checksums
+class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseChecksumCalculationTask
+execute-only-once = true

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 = "[email protected]"
-
-  # TODO get emails of space users
-  # Get it via liferay and pass it to this service ?
-  #toA = "[email protected]"
-  #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 [email protected]
-  #msg['reply-to'] = "[email protected]"
-
-  #smtpServer = smtplib.SMTP(server)
-  #smtpServer.sendmail(fromA, toA, msg.as_string())
-  #smtpServer.close()
-