From b86b358abbebed68505602093b136b9919d58a6a Mon Sep 17 00:00:00 2001 From: wow-such-code Date: Tue, 11 May 2021 14:31:06 +0200 Subject: [PATCH] Release/1.8.0 (#82) * Sync development with master (#61) * Provide java example dropbox Co-authored-by: Sven F Co-authored-by: luiskuhn <38211686+luiskuhn@users.noreply.github.com> --- CHANGELOG.md | 4 ++++ README.md | 5 +++++ .../register-example-java-dropbox/README.md | 16 ++++++++++++++++ .../register-example-java-dropbox/lib/README.md | 2 ++ .../plugin.properties | 11 +++++++++++ 5 files changed, 38 insertions(+) create mode 100644 drop-boxes/register-example-java-dropbox/README.md create mode 100644 drop-boxes/register-example-java-dropbox/lib/README.md create mode 100644 drop-boxes/register-example-java-dropbox/plugin.properties diff --git a/CHANGELOG.md b/CHANGELOG.md index 7039bf9..9c57935 100644 --- a/CHANGELOG.md +++ b/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) diff --git a/README.md b/README.md index 860ad62..e3395ed 100644 --- a/README.md +++ b/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 diff --git a/drop-boxes/register-example-java-dropbox/README.md b/drop-boxes/register-example-java-dropbox/README.md new file mode 100644 index 0000000..6b59fc1 --- /dev/null +++ b/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. \ No newline at end of file diff --git a/drop-boxes/register-example-java-dropbox/lib/README.md b/drop-boxes/register-example-java-dropbox/lib/README.md new file mode 100644 index 0000000..8b06845 --- /dev/null +++ b/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. \ No newline at end of file diff --git a/drop-boxes/register-example-java-dropbox/plugin.properties b/drop-boxes/register-example-java-dropbox/plugin.properties new file mode 100644 index 0000000..0a31c61 --- /dev/null +++ b/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