Apply suggestions from code review

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

Author: sven1103

CHANGELOG.md

@@ -2,9 +2,9 @@
 
 # 1.9.0 2021-06-28
 
-* Provides new ETL routine written in Java, that will replace all Jython scripts at some point [PR](https://github.com/qbicsoftware/etl-scripts/pull/85)
-* Support for nf-core pipeline result registration [PR](https://github.com/qbicsoftware/etl-scripts/pull/85)
-* Provides metadata validation for imaging data (OMERO etl). [PR](https://github.com/qbicsoftware/etl-scripts/pull/83)
+* Provides new ETL routine written in Java, that will replace all Jython scripts at some point [(#85)](https://github.com/qbicsoftware/etl-scripts/pull/85)
+* Support for nf-core pipeline result registration [(#85)](https://github.com/qbicsoftware/etl-scripts/pull/85)
+* Provides metadata validation for imaging data (OMERO etl). [(#85)](https://github.com/qbicsoftware/etl-scripts/pull/83)
 
 ## 1.8.0 2021-05-11
 

drop-boxes/register-all-dropbox/README.md

@@ -5,12 +5,12 @@ Please find the source code of the ETL routine that this article is referring to
 
 ## Installation
 
-Please provide the Java binaries as JAR from the [Java openBIS dropbox](https://github.com/qbicsoftware/java-openbis-dropboxes) in this directories
+Please provide the Java binaries as JAR from the [Java openBIS dropbox](https://github.com/qbicsoftware/java-openbis-dropboxes) in this repositories
 folder `./lib`.
 
 The DSS needs to be restarted in order to activate this dropbox.
 
 ## ETL routine
 
 This dropbox expects a folder containing data and creates new openBIS dataset from it. For more information
-please visit [Java openBIS dropbox](https://github.com/qbicsoftware/java-openbis-dropboxes).
+please visit [Java openBIS dropbox](https://github.com/qbicsoftware/java-openbis-dropboxes).

drop-boxes/register-all-dropbox/plugin.properties

@@ -1,11 +1,12 @@
 #
 # 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-all-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
+# Variables:
+#   incoming-root-dir
+#     Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/QBiC-register-all-data

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

@@ -61,7 +61,6 @@
 
 PROPPERTY_FILTER_LIST = ["IMAGE_FILENAME", "INSTRUMENT_USER", "IMAGING_DATE"]
 
-
 def mapDateString(date_string):
 	return datetime.datetime.strptime(date_string, INCOMING_DATE_FORMAT).strftime(OPENBIS_DATE_FORMAT)
 
@@ -380,4 +379,3 @@ 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.
-