Resolve conflicts for master (#81)

Related to merging master into dev

Author: wow-such-code

drop-boxes/register-omero-metadata/backendinterface.py

@@ -407,7 +407,6 @@ def get_args():
             key_value = pair.split("::")
             key_value_data.append(key_value)
 
-
         add_annotations_to_image(conn, str(args.image_id), key_value_data)
 
         print "0"

drop-boxes/register-omero-metadata/image_registration_process.py

@@ -24,6 +24,7 @@ def __init__(self, transaction, env_name="omero_env_0", project_code="", sample_
         self._sample_code = sample_code
 
         ### set exec. env
+
         self._conda_path = conda_home_path
         if not conda_path is None:
             self._conda_path = conda_path
@@ -47,6 +48,7 @@ def __init__(self, transaction, env_name="omero_env_0", project_code="", sample_
         self._init_cmd_list.append('export PATH=$PATH:' + self._conda_path + 'envs/' + env_name + '/bin')
 
         # move to the dir where backendinterface.py lives for exec.
+
         self._init_cmd_list.append('cd ' + self._etl_path)
 
     def fetchOpenBisSampleCode(self):
@@ -63,6 +65,7 @@ def fetchOpenBisSampleCode(self):
 
     def searchOpenBisSample(self, sample_code):
         # find specific sample
+
         sc = SearchCriteria()
         sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample_code))
         foundSamples = self._search_service.searchForSamples(sc)
@@ -100,7 +103,7 @@ def requestOmeroDatasetId(self, project_code=None, sample_code=None):
         return ds_id
 
     def registerImageFileInOmero(self, file_path, dataset_id):
-        
+
         cmd_list = list(self._init_cmd_list)
         cmd_list.append( "python backendinterface.py -f " + file_path + " -d " + str(dataset_id) )
 
@@ -123,6 +126,7 @@ def triggerOMETiffConversion(self):
         pass
 
     #ToDo Check if Metadata file is provided as defined
+
     def extractMetadataFromTSV(self, tsv_file_path):
         tsvFileMap = {}
         try:
@@ -147,6 +151,7 @@ def registerOmeroKeyValuePairs(self, image_id, property_map):
         cmd_list = list(self._init_cmd_list)
 
         # string format: key1::value1//key2::value2//key3::value3//...
+
         key_value_str = ""
         for key in property_map.keys(): 
             key_value_str = key_value_str + str(key) + "::" + str(property_map[key]) + "//"
@@ -161,7 +166,6 @@ def registerOmeroKeyValuePairs(self, image_id, property_map):
         process = Popen( "/bin/bash", shell=False, universal_newlines=True, stdin=PIPE, stdout=PIPE, stderr=PIPE )
         out, err = process.communicate( commands )
 
-
         return 0
 
 

drop-boxes/register-omero-metadata/register-omero.py

@@ -55,13 +55,11 @@
 # and delete the data!
 #####
 
-
 INCOMING_DATE_FORMAT = '%d.%m.%Y'
 OPENBIS_DATE_FORMAT = '%Y-%m-%d'
 
 PROPPERTY_FILTER_LIST = ["IMAGE_FILE_NAME", "INSTRUMENT_USER", "IMAGING_DATE"]
 
-
 def mapDateString(date_string):
 	return datetime.datetime.strptime(date_string, INCOMING_DATE_FORMAT).strftime(OPENBIS_DATE_FORMAT)
 
@@ -245,6 +243,8 @@ def process(transaction):
 
 	# 1. Initialize the image registration process
 	registrationProcess = irp.ImageRegistrationProcess(transaction)
+
+	print "started reg. process"
 
 	# 2. We want to get the openBIS sample code from the incoming data
 	# This tells us to which biological sample the image data was aquired from.
@@ -253,13 +253,14 @@ def process(transaction):
 	#find specific sample
 	tissueSample = registrationProcess.searchOpenBisSample(sample_code)
 	space = tissueSample.getSpace()
-	
+
 	# 3. We now request the associated omero dataset id for the openBIS sample code.
 	# Each dataset in OMERO contains the associated openBIS biological sample id, which
 	# happened during the experimental design registration with the projectwizard.
 
 	# Starts omero registration
 	# returns -1 if fetching dataset-id operation failed
+
 	omero_dataset_id = registrationProcess.requestOmeroDatasetId(project_code=project_code, sample_code=sample_code)
 
 	print "omero dataset id:"
@@ -342,3 +343,4 @@ def process(transaction):
 
 		# 7. Last but not least we create the open science file format for images which is
 		# OMERO-Tiff and store it in OMERO next to the proprierary vendor format.
+