Skip to content

[docs] Add diagrams to docs #443

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Sep 10, 2022
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
30 changes: 30 additions & 0 deletions docs/diagrams/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
# Diagrams

This folder contains diagrams about functionalities of CWL Viewer.
The source file for the diagrams is stored in a SVG file. We suggest
contributors to use Inkscape to edit the SVG file.
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@mr-c ☝️

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The source is included as docs/diagrams/cwlviewer.svg

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Did you make this by hand using inkscape? Or is this SVG an export from some other tool?

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

By hand.


## Flowcharts

When a user submits a workflow to the CWL Viewer, the Spring controller
will handle the request delegating most of the work to Spring services.

![flow part 1](cwlviewer_flowchat_01.png)

The first part of the flow is responsible for validating the request and
checking if the workflow exists in the Postgres database, and if not
creating a `QueuedWorkflow` in the database.

![flow part 2](cwlviewer_flowchat_02.png)

An asynchronous task is then scheduled to parse the CWL workflow with
`cwltool`, use Apache Jena to create the workflow graph, and to store the
`Workflow` object (not queued anymore) in the Postgres database.

![flow part 3](cwlviewer_flowchat_03.png)

This final part of the flow is also an asynchronous task, responsible for
creating the Research Objects bundle file. It uses Apache Taverna API
to create a `Bundle`, and stores parts of the Git repository, graph
images generated by the `cwltool` and Jena graph data, and extra data
for provenance. The result is updated in the `Workflow` object in Postgres.
Loading