/gdc_submitter_translation_ui

Primary LanguageHTMLApache License 2.0Apache-2.0

GDC submitter translation UI

This application is to help submitter create YAML and CONF input files for the GDC submitter.

Installation

We suggest to work in the python virtual environment.

  • Download source code: git clone git@github.com:NCI-GDC/gdc_submitter_translation_ui.git
  • Install dependencies: python setup.py install
  • Run the app: python submitter_ui/app.py
  • Open a web browser, and go to localhost:5000/

More about the UI

The YAML and CONF files created here are for the GDC submitter only. If you desired to submit through API, please refer to GDC doc site.

The YAML tells the GDC submitter which properties it should be looking for and where it could be found in your uploaded TSV file.

  • For required properties, there is no way to deselect. However, they do not have to be in the TSV, since many of them could be just selected from enum.
  • For optional properties, not including links, submitter is able to deselect the node by delete button. Unfortunately, the current UI does not have a undo or restore function. If submitter accidentally deletes a desired node, one has to refresh the page. :(
  • s3_loc is not a property in the API, but in the GDC submitter. It exists in all the node in this UI, please feel free to delete it if you do not need.
  • For properties that are also links, they would not be presented in the YAML output, but in CONF. Please see more details below.

The CONF tells the GDC submitter what is the link/anchor node and where it is in the TSV.

  • The current design of the GDC submitter only supports ONE link/anchor node in the CONF. However, the current UI is able to present all the links that submitter selects in the CONF which will unfortunately crash the GDC submitter. A better designed UI would then have to create multiple YAMLs based on selected links in order to cooperate, which will be happening soon.
  • Because of the above issue, submitter now has to be responsible to select only one link/anchor node, and delete others.
  • The link_id_type is basically telling the GDC submitter which id you are using in your TSV. It's either id or submitter_id.
  • If submitter is going to perform a replacement upon the submission, one has to create a to_be_deleted.yaml by selecting the checkbox. It will then popup 2 new fields which will be in the final output, and provides the info that the GDC submitter needs.