rabix / cottontail

[Historical] Ancestor to Rabix Composer

Rabix has grown up!

Reproducible Analyses for Bioinformatics is now a reality!

Please see

• Common Workflow Language (github) for the specfication that the language part of Rabix merged into.
• Rabix Composer for a visual editor for CWL workflows
• This list of executors/runners that can run workflows in CWL on anything from your laptop to your HPC to your cloud.

If you want to see the old documentation for the project please see here

cottontail's Issues

Implement the file content caching system with state reducers

Add update button for WF steps

Should use same update logic as original editors, but simply use local file as source.

Remove search bar from WF editor toolbox

Create a Travis build procedure

It would be nice to have a continuous integration with Travis.

Detect a difference between a working copy of a file and the file system version

If the working copy of a file (what users see in the editor) differs from its original state in the system, it should be visually indicated; probably with an asterisk sign in the tab title.

Implement a "save" functionality

When editing files, we need to be able to persist the current state of the file.

add sandstorm.io support for free live demo hosting

https://sandstorm.io/developer

Free public demo service for all Sandstorm apps: https://sandstorm.io/news/2015-02-06-app-demo

Write a README.md for the new cottontail

README should include:

• Installation and setup
• Architecture description
• Code style (#70 by @ivanbatic)
• Contribution guidelines

User should be able to delete a selected file.

Insufficient deletion permissions and errors should be shown to the user.

Merge fixes from internal branch

Upgrade to sass-loader-4.0.0

https://github.com/jtangelder/sass-loader/blob/master/CHANGELOG.md

Replace the DynamicallyCompiledComponentDirective with ComponentCompilerDirective in the modal component

Create files through context menu actions

At the moment, new files are created by clicking on the "New File" button, then specifying the file name.
File system is a tree, and it would be very impractical to make users type in the full path to nested directory they want to put the new file into.

I suggest we create a context menu for the file tree; right clicking on folders would bring up the list of actions, amongst which would be the "New File..." action.

Show validation errors and hints in Ace editor

Depends on #43

Switch to Apache 2 license

Add refresh button to app toolbox

Create a CWL validator

The validator should be relatively optimal in terms of feedback speed.
The errors are to be reported to the user in the Ace editor.

Implement initial JSON/GUI tool editor views

Create install package

Files from root directory not shown in tree view

Button to switch between GUI/Text modes

Replace store with a central observable hub

State based architecture isn't proving very beneficial, it should be replaced with a more reactive, subscriber/observer pattern.

When a new file is created, the directory tree needs to be updated accordingly

Fix tests configuration

The test can't be debugged because every file without a '.spec' extension gets minified.

Detect if the loaded file is a CWL tool and its specification

Map API responses to data models

We should have a stable domain models to work with, and see API responses as one way to hydrate them.

• Create interfaces for all API response types
• Create data models for all data service endpoints
• Make the backend service always return domain models

Test coverage to be >50%

Newly created JSON file is not syntax highlighted in code editor

Cottontail crashes when loading large files (e.g. 100GB)

We should limit the size of files we load and notify if exceeded.

Replace Typings with @types

As of [email protected], the typings repository is provided as a language service without the need for external tools.
More info: https://blogs.msdn.microsoft.com/typescript/2016/06/15/the-future-of-declaration-files/

Import/include directives not resolved

As quick fix, files with these directives should be opened in text mode. Later, prompt the user to choose text or gui mode since inclusions will be embedded on save.

Implement resolving for import and include for files (cache URLs)/ Ref resolver

[Discussion] The CWL file should be mapped to an abstract CWL model used by the editor, so that operations done on the text translate to the same basic principles, regardless of the draft of the specification.

Prompt upon trying to close the tab with an unsaved content

When user changes the content of the file, does not save it, and tries to close the tab, we should prompt them and make them confirm the loss of data.

Create preview panes for workflow GUI and CLI

Review the complete application state and its slices

Upgrade to angular-2.0.0-rc.3

Make the directory tree accept the tree state from a reducer

The tree should be able to manage it's visual representation by applying a state that comes in from a reducer.

• Make a reducer for the state slice
• Make the tree work with the complete state
• Make subcomponents dumb

Prompt when loading YAML files

Prompt user to either open in GUI or text editor, since saving changes would result in loss of formatting.

Add error log reporting

A file created with a "save as..." is not shown in the directory tree

Switching between file tabs depends on getting file form registry

If a component is instantiated for a file inside that file's tab, but doesn't pull the file from the registry, switching tabs doesn't work.

move ref-resolver to HapiJs

User needs to be able to create a file in a nested directory

Open the newly created file in the code editor

When a new file is created, it should be automatically opened in a new code editor tab.

Create smart autocompletion for CWL

Implement the directory content caching with file reducers

Clean up compilation errors

We should have no Typescript compilation errors.
@matesk8 @mayacoda Let's clean these, everybody in their own code.

Implement a "save as..." functionality

Use gulp for builds