Test our PubFlow JIRA-plugin demo

Mar 15, 2017

Visit [not longer available] to test the latest version of our PubFlow JIRA-plugin!

The workflow in our example is the transformation of raw data to a correctly formatted file which can be uploaded to PANGAEA, a world data centre for earth and environmental science.

Currently we are testing our plugin together with the KDMI at the GEOMAR Helmholtz Centre for Ocean Research Kiel.

There are three different roles/groups:

  • The scientists, creating a new issues in JIRA, appending the experiment results and committing it to the data managers
  • The data managers, receiving the data from the scientists and working off a predefined workflow in JIRA
  • The librarians, responsible for aquiring needed author identifications like ORCID


There are two workflows for to publish scientific data.  Both have to be executed.

The first workflow is not provided in this demo. It would contain the following steps:

  • The scientist creates a new issue, appends the raw data, adds some meta data as a comment and commits it to the data manager
  • The data manager checks if the data is complete and has not been uploaded to Pangaea yet.
  • The DM starts the import of the data into the local institutional database (OCN [Ocean])


The second workflow creates 4D-files for PANGAEA from files in the local institutional database. Thereby, the following steps have to be executed:

  • The datamanager creates a new issue of this workflow and provides information which data should be published.
  • The DM provides the names of the authors for whom identification is needed.
  • The librarian manually searches for for the corresponding identifications and submits the results.
  • The DM prepares the data processing through PubFlow by adding meta information to the issue in predefined fields. for example about the cruise, crew, etc. Afterwards the data manager commits the issue to PubFlow.
  • (sub workflow): PubFlow collects the required data from the database (OCN), checks if the data is valid and consistent (e.g. negative measuring values) and generates log comments in case of abnormal data. It scans the quality flags, automatically maps OCN parameter ids to Pangaea parameter ids and generates a file that is correctly formatted for an import do Pangaea.
  • The DM checks the result file and uploads it to PANGAEA



To test our setup you will need the following logins:

login: SampleDataManager , password: datamanager

login: SampleScientist , password: scientist

login: SampleLibrarian , password: librarian


Note: the SampleDataManager is also in group 'scientists' so basically there is no need to log in as user SampleScientist but feel free to try it!

In the 'PREPARE FOR PUBFLOW'-step it is absolutely nessecary to enter 12013 as 'leg id', otherwise you won't get an result.

The final imported result of leg no. 12013 can be found here: