Skip to content

README-upload-download.md

Latest commit

 

History

History
89 lines (63 loc) · 3.77 KB

README-upload-download.md

File metadata and controls

89 lines (63 loc) · 3.77 KB

Adding an upload/download script (draft)

Creating a full upload and download for a new datatype or data source is one of the more complex activities to attempt in KBase. This guide will is not a comphrensive guide, but will walk though the high-level steps and explain how development is done in the deplooy_dev docker environment.

Overview

An upload/download requires creating several configurations (both for the UI pieces and the conversion pieces), creating scripts to do validation and conversion, and modifying some Javascript files in the narrative. In the future we hope to combine this pieces so that everything can be specified in a single repository.

Preparing the environment

Start by cloning the deploy_dev environment and following the instructions to starting a isolated development version of KBase. See the top-level README for instructions.

Fork and clone:

Clone the transform fork directly in the deploy_dev directory.
The others can be forked in a different area. For example:

cd deploy_dev
GITUSER=<username>
git clone git@github.com:$GITUSER/transform.git
cd ..
git clone git@github.com:$GITUSER/narrative.git -b docker
git clone git@github.com:$GITUSER/narrative_method_specs_ci.git

Modify the Dockerfile to your modifications to the above directories into your image build. Add the lines below to the Dockerfile in the base of your deploy_dev directory.


ADD ./transform /kb/dev_container/modules/transform
RUN cd /kb/dev_container/modules/transform && . ../../user-env.sh && make && make deploy

Modify the method-spec-git-repo parameter in your cluster.ini file to point to your fork of narrative_method_specs_ci. Also modify the method-spec-git-repo-branch to match the branch you will push changes to. For example:

[NarrativeMethodStore]
method-spec-git-repo-branch=master
method-spec-git-repo=https://github.com/<username>/narrative_method_specs_ci

Make the changes

Creating the scripts

Follow the guide at https://github.com/kbase/project_guides/blob/master/How_to_add_a_new_data_type.md. Create the scripts in your clone of the transform repo.

Create the UI specs

Create configuration in your fork and clone of the narrative_method_specs. Conculst the README in that repo for details.

Add the type to the sidebar

The narrative data pane has a pop out window to perform upload/download operations. Currently you need to modify a javascript file to recongnize the new type. Edit the file at:

src/notebook/ipython_profiles/profile_narrative/kbase_templates/static/kbase/js/widgets/narrative_core/kbaseNarrativeSideImportTab.js

Build and Test

To test your modifications you will need to rebuild thhe narrative image and redeploy.

cd ../narrative
docker build -t kbase/narrative:1.0.3 .
cd ../deploy_dev
./deploy.sh

The deploy will rebuild the primary image which will include your modifications to transform and use your method specs file. If services were already runing you will need to restart them. You can do this by using the DELETE/kill URL to kill the running service. You can then poke the normal service url to restart the service. You will need to do this anytime you make changes to a service.

. ./site.cfg
curl -X DELETE http://${PUBLIC_ADDRESS}:8080/kill/transform
curl http://${PUBLIC_ADDRESS}:8080/services/transform
curl -X DELETE http://${PUBLIC_ADDRESS}:8080/kill/narrativemethodstore
curl http://${PUBLIC_ADDRESS}:8080/services/narrativemethodstore

At this point you should be able to navigate to the narrative site and try opening the data tab and test your changes.