Release/1.8.0

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## 1.8.0 2021-05-11
+
+* Add example Java dropbox
+
 ## 1.7.0 2021-03-19
 
 * Provides fully tested functionality to register generic imaging data, with OMERO server support (v5.4.10). [Link to PR](https://github.com/qbicsoftware/etl-scripts/pull/78)

README.md

@@ -30,6 +30,11 @@ OpenBIS loads Java libararies on startup, if they are provided in a `lib` folder
 
 We decoupled some shared functionality in the [data-model-lib](https://github.com/qbicsoftware/data-model-lib) and the [core-utils-lib](https://github.com/qbicsoftware/core-utils-lib). Please make sure to deploy them as well in of the lib folders, such that the classes are loaded by the etlserver class loader and available during runtime.
 
+##4. Dependencies for the example dropbox written in pure Java/Groovy
+
+Just deploy the compiled JAR of the [Java openBIS dropbox](https://github
+.com/qbicsoftware/java-openbis-dropboxes) in the `lib` folder of the dropbox (`
+./register-example-java-dropbox/lib`).
 
 ## Data format guidelines
 

drop-boxes/register-example-java-dropbox/README.md

@@ -0,0 +1,16 @@
+# Example openBIS dropbox written in Java
+
+Please find the source code of the ETL routine that this article is referring to in the
+[Java openBIS dropboxes](https://github.com/qbicsoftware/java-openbis-dropboxes) Github repository.
+
+## Installation
+
+Please provide the Java binaries as JAR from the [Java openBIS dropbox](https://github.com/qbicsoftware/java-openbis-dropboxes) in this directories
+folder `./lib`.
+
+The DSS needs to be restarted in order to activate this dropbox.
+
+## ETL routine
+
+This dropbox expects a file of any type and creates a new openBIS dataset from it. This dataset
+is then attached to a fixed sample with id `/TEST28/QXEGD018AW` for demonstration purposes.

drop-boxes/register-example-java-dropbox/lib/README.md

@@ -0,0 +1,2 @@
+Put the compiled Java binaries as JARs in this directory in order
+to be loaded by the openBIS DSS class loader on DSS startup.

drop-boxes/register-example-java-dropbox/plugin.properties

@@ -0,0 +1,11 @@
+#
+# Drop box for registering a fastq file as a data set
+#
+# Variables:
+#   incoming-root-dir
+#     Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/QBiC-register-example-java-data
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2
+program-class = life.qbic.registration.MainETL
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor

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.
+