diff --git a/CHANGELOG.md b/CHANGELOG.md index 0917be5..d7b4f9c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,13 +1,10 @@ # Changelog -# 1.10.0 2021-06-25 +# 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) - -## 1.9.0 2021-05-18 - -* 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 diff --git a/drop-boxes/register-all-dropbox/README.md b/drop-boxes/register-all-dropbox/README.md index 22ba0ed..20dbdf3 100644 --- a/drop-boxes/register-all-dropbox/README.md +++ b/drop-boxes/register-all-dropbox/README.md @@ -5,7 +5,7 @@ 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. @@ -13,4 +13,4 @@ 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). \ No newline at end of file +please visit [Java openBIS dropbox](https://github.com/qbicsoftware/java-openbis-dropboxes). diff --git a/drop-boxes/register-all-dropbox/plugin.properties b/drop-boxes/register-all-dropbox/plugin.properties index 3b9572c..f49d390 100644 --- a/drop-boxes/register-all-dropbox/plugin.properties +++ b/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 diff --git a/drop-boxes/register-omero-metadata/register-omero.py b/drop-boxes/register-omero-metadata/register-omero.py index 7a72134..ea51a45 100755 --- a/drop-boxes/register-omero-metadata/register-omero.py +++ b/drop-boxes/register-omero-metadata/register-omero.py @@ -379,4 +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. -