LMS-2323 Fixes to handlers for BaSynthec.

SVN: 21679

eu_basynthec/dist/etc/data-set-handler.py

-from datetime import datetime
-
-def retrieve_or_create_experiment(tr):
-	# Create an experiment
-	now_str = datetime.today().strftime('%Y%m%d-%H%M%S')
-	expid = "/SHARED/SHARED/" + now_str
-	exp = tr.getExperiment(expid)
-
-	if None == exp:
-		exp = tr.createNewExperiment(expid, 'BASYNTHEC')
-		exp.setPropertyValue("DESCRIPTION", "An experiment created on " + now_str)
-		
-	return exp
-
+"""Just import the data into openbis"""
 tr = service.transaction(incoming)
-exp = retrieve_or_create_experiment(tr)
 dataSet = tr.createNewDataSet()
-dataSet.setExperiment(exp)
 tr.moveFile(incoming.getAbsolutePath(), dataSet)
 

eu_basynthec/dist/etc/data-set-validator.py

@@ -2,8 +2,5 @@ import os
 import re
  
 def validate_data_set_file(file):
-    errors = []
-    if False:
-        errors.append(createFileValidationError(file.getName() + " is not a valid data set. The file name cannot contain 'invalid'."))
- 
-    return errors
+	errors = []
+	return errors

eu_basynthec/dist/etc/service.properties

@@ -104,7 +104,7 @@ inputs = main-thread, metabolomics, growth-profiles, transcriptomics, proteomics
 # ---------------------------------------------------------------------------
 # main thread configuration
 # ---------------------------------------------------------------------------
-main-thread.incoming-dir = ${data-folder}/incoming
+main-thread.incoming-dir = ${root}/incoming
 
 # Determines when the incoming data should be considered complete and ready to be processed.
 # Allowed values: 
@@ -116,52 +116,52 @@ main-thread.delete-unidentified = true
 
 main-thread.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
 main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-main-thread.script-path = etc/data-set-handler.py
-main-thread.validation-script-path = etc/data-set-validator.py
+main-thread.script-path = /local0/openbis/jython_scripts/data-set-handler.py
+main-thread.validation-script-path = /local0/openbis/jython_scripts/data-set-validator.py
 
 # ---------------------------------------------------------------------------
 # metabolomics thread configuration
 # ---------------------------------------------------------------------------
-metabolomics.incoming-dir = ${data-folder}/incoming-metabolomics
+metabolomics.incoming-dir = ${root}/incoming-metabolomics
 metabolomics.incoming-data-completeness-condition = auto-detection
 metabolomics.delete-unidentified = true
 metabolomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
 metabolomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-metabolomics.script-path = etc/metabolomics/data-set-handler.py
-metabolomics.validation-script-path = etc/metabolomics/data-set-validator.py
+metabolomics.script-path = /local0/openbis/jython_scripts/metabolomics/data-set-handler.py
+metabolomics.validation-script-path = /local0/openbis/jython_scripts/metabolomics/data-set-validator.py
 
 # ---------------------------------------------------------------------------
 # growth-profiles thread configuration
 # ---------------------------------------------------------------------------
-growth-profiles.incoming-dir = ${data-folder}/incoming-od600
+growth-profiles.incoming-dir = ${root}/incoming-od600
 growth-profiles.incoming-data-completeness-condition = auto-detection
 growth-profiles.delete-unidentified = true
 growth-profiles.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
 growth-profiles.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-growth-profiles.script-path = etc/growth-profiles/data-set-handler.py
-growth-profiles.validation-script-path = etc/growth-profiles/data-set-validator.py
+growth-profiles.script-path = /local0/openbis/jython_scripts/growth-profiles/data-set-handler.py
+growth-profiles.validation-script-path = /local0/openbis/jython_scripts/growth-profiles/data-set-validator.py
 
 # ---------------------------------------------------------------------------
 # transcriptomics thread configuration
 # ---------------------------------------------------------------------------
-transcriptomics.incoming-dir = ${data-folder}/incoming-transcriptomics
+transcriptomics.incoming-dir = ${root}/incoming-transcriptomics
 transcriptomics.incoming-data-completeness-condition = auto-detection
 transcriptomics.delete-unidentified = true
 transcriptomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
 transcriptomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-transcriptomics.script-path = etc/transcriptomics/data-set-handler.py
-transcriptomics.validation-script-path = etc/transcriptomics/data-set-validator.py
+transcriptomics.script-path = /local0/openbis/jython_scripts/transcriptomics/data-set-handler.py
+transcriptomics.validation-script-path = /local0/openbis/jython_scripts/transcriptomics/data-set-validator.py
 
 # ---------------------------------------------------------------------------
 # proteomics thread configuration
 # ---------------------------------------------------------------------------
-proteomics.incoming-dir = ${data-folder}/incoming-proteomics
+proteomics.incoming-dir = ${root}/incoming-proteomics
 proteomics.incoming-data-completeness-condition = auto-detection
 proteomics.delete-unidentified = true
 proteomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
 proteomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-proteomics.script-path = etc/proteomics/data-set-handler.py
-proteomics.validation-script-path = etc/proteomics/data-set-validator.py
+proteomics.script-path = /local0/openbis/jython_scripts/proteomics/data-set-handler.py
+proteomics.validation-script-path = /local0/openbis/jython_scripts/proteomics/data-set-validator.py
 
 
 #