Prepare release 1.11.0 (#96)

* change ms conversion server

* remove some log files dependent on origin lab (#95)

Co-authored-by: Tobias Koch <[email protected]>

* handle data without unclassified reads

* Update CL (#92)

Co-authored-by: Tobias Koch <[email protected]>
Co-authored-by: Sven F <[email protected]>

Author: 3 people

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+# 1.11.0 2022-05-09
+
+* Nanopore data: allows new result structure with barcode alignment file and 'other reports' folder (requires core-utils-lib 1.11.0 or later)
+* Nanopore data: introduces map to remove log files that should not be saved dependent on different datamover origins
+* Fix for nanopore: data without unclassified reads does not lead to error upon registration
+* Ptx mass spec data: change msconvert server
+
 # 1.10.0 2021-07-26
 
 * Provides new ETL for MTB project data that are not supposed to be stored in QUK17 [(#89)](https://github.com/qbicsoftware/etl-scripts/pull/89)

drop-boxes/register-convert-ms-vendor-format/etl_msconvert.py

@@ -67,7 +67,7 @@
 DROPBOX_PATH = "/mnt/DSS1/openbis_dss/QBiC-convert-register-ms-vendor-format/"
 VENDOR_FORMAT_EXTENSIONS = {'.raw':'RAW_THERMO', '.d':'D_BRUKER'}#,'.wiff':'WIFF_SCIEX'}
 WATERS_FORMAT = "RAW_WATERS"
-MSCONVERT_HOST = "qmsconvert.am10.uni-tuebingen.de"
+MSCONVERT_HOST = "qmsconvert2.am10.uni-tuebingen.de"
 MSCONVERT_USER = "qbic"
 REMOTE_BASE = "/cygdrive/d/etl-convert"
 CONVERSION_TIMEOUT = 7200
@@ -971,4 +971,4 @@ def process(transaction):
 
         for f in os.listdir(incomingPath):
             if ".testorig" in f:
-                os.remove(os.path.realpath(os.path.join(incomingPath, f)))
+                os.remove(os.path.realpath(os.path.join(incomingPath, f)))

drop-boxes/register-nanopore-dropbox/register-nanopore.py

@@ -58,6 +58,9 @@
 usedExperimentIdentifiers = set()
 checksumMap = {}
 
+# facilities that want us to remove certain log files
+blacklistedByFacility = {"qeana03-imgagdna": ["DutyTimeLog", "FinalSummaryLog", "ReportMdLog", "ReportPDFLog", "ThroughputLog", "DriftCorrectionLog", "MuxScanDataLog"]}
+
 def createNewSample(transaction, space, parentSampleCode):
     run = 0
     sampleExists = True
@@ -100,15 +103,26 @@ def getTimeStamp():
     ts = str(now.minute)+str(now.second)+str(now.microsecond)
     return ts
 
+def copyFileTo(file, filePath, targetFolderPath):
+    sourcePath = os.path.join(filePath, file.getName())
+    shutil.copy2(sourcePath, targetFolderPath)
+    src = os.path.join(filePath, file.getName())
+    shutil.copy2(src, targetFolderPath)
+
 # copies log files from a folder that may contain other files to another path
-def copyLogFilesTo(logFiles, filePath, targetFolderPath):
+# log files that are blacklisted are not copied and thus not registered (after metadata extraction)
+def copyLogFilesTo(logFiles, filePath, targetFolderPath, facilityName):
+    # return list of files to remove for this facility or empty list
+    blacklist = blacklistedByFacility.get(facilityName, [])
+    numIgnoredFiles = 0
     for logFile in logFiles:
-        sourcePath = os.path.join(filePath, logFile.getName())
-        shutil.copy2(sourcePath, targetFolderPath)
-        src = os.path.join(filePath, logFile.getName())
-        shutil.copy2(src, targetFolderPath)
+        fileType = logFile.__class__.__name__
+        if fileType in blacklist:
+            numIgnoredFiles += 1
+        else :
+            copyFileTo(logFile, filePath, targetFolderPath)
     copiedContent = os.listdir(targetFolderPath)
-    if len(copiedContent) != len(logFiles):
+    if len(copiedContent) + numIgnoredFiles != len(logFiles):
         raise AssertionError("Not all log files have been copied successfully to target log folder.")
 
 def createLogFolder(targetPath):
@@ -117,6 +131,9 @@ def createLogFolder(targetPath):
     os.makedirs(newLogFolder)
     return newLogFolder
 
+def containsUnclassifiedData(unclassifiedMap):
+    return not all(v is None for v in unclassifiedMap.values())
+
 def createExperimentFromMeasurement(transaction, currentPath, space, project, measurement, origin, rawDataPerSample):
     """ Register the experiment with samples in openBIS.
     In order to register the Nanopore experiment with its measurements in openBIS, 
@@ -162,10 +179,10 @@ def createExperimentFromMeasurement(transaction, currentPath, space, project, me
         datamap = rawDataPerSample.get(barcode)
         newLogFolder = createLogFolder(currentPath)
         # 3.) Aggregate all log files into an own log folder per measurement
-        copyLogFilesTo(measurement.getLogFiles(), currentPath, newLogFolder)
+        copyLogFilesTo(measurement.getLogFiles(), currentPath, newLogFolder, origin)
         createSampleWithData(transaction, space, barcode, datamap, runExperiment, currentPath, newLogFolder)
     unclassifiedMap = measurement.getUnclassifiedData()
-    if len(unclassifiedMap) > 0:
+    if containsUnclassifiedData(unclassifiedMap):
         registerUnclassifiedData(transaction, unclassifiedMap, runExperiment, currentPath, measurement.getFlowcellId())
 
 # fills the global dictionary containing all checksums for paths from the global checksum file