repronim/brainverse

BrainVerse is an electronic laboratory notebook built as an open-source, cross-platform desktop application to help researchers manage, track and share information in a comprehensive format.

brainverse's Issues

Add logger to BrainverseApp

Explored different logging packages exist, e.g winstorn, bunyan, npmlog, log4js.
In expressjs, it is recommended to use winston or bunyan.

[EP] 'Add Participant' to an experiment plan

Add participant to a project plan.
Customize the plan for the participant
Add a button ‘execute’ on a participant plan board
Click on checkbox when the task/instrument is done

Save all the forms created or data generated using Brainverse App outside the App

Specific Module/Internal API Design

@satra Need some examples to start working on this.

Unable to delete primary packaged folder

• On mac, authentication required to delete created package folder, and even then, does not delete folder
• ADVISORY WARNING: Only way to delete so far is in console: rm -rf

[EP] 'Edit Column header' in the Kanban board display

Create ' Add a Participant' form.

(Refer: Slide 5 of the design doc)

Score calculation data element

Currently, while previewing the form, the fields that needs to be calculated based on the previous fields values are also shown without any indication that they needs to be calculated and the dependency structure.
We need some attributes to indicate the dependency structure. As per Hauke's presentation, we could store score calculations or any transform in separately and then can use a graphical workflow interface to specify the score calculation on a group of fields.
We need more discussion to come up with the model.

Create a single .ttl file for saving experiment plans

Currently, for each new experiment plan submitted, a new turtle file is created. Each plan is represented as a RDF graph. We decided to serialize all plans to a single file and loads/query the qraph as required.

Acquisition Form save button

Acquisition Form on clicking 'save' button allows saving the form even mandatory input fields not entered.
Save button needs to be disabled until form validation is passed.

Update README

• App configuration information
• App Packaging info
• Node installation
• Accessing as Webapp

Create a form based on the fields selected in the 'Add a New Project form'.

(Refer Slide 3 of the design doc)

Add ' Create a New Project' form.

Refer: Slide 2 of the design doc.

Populate the drop down menu with the fields name specified in a sample json file.

NDA Updated Form Versioning

Each NDA data dictionary has 'shortName' field which is unique and has some version information on it. With NDA Editor allowing to edit a form, the challenge is how to version the updated form and preserve the provenance information.
As a first step, we added a new term, 'derivedFrom' denoting the original form shortname from which it is derived from. The new shortName for the updated form is oldShortName followed by randomNumber. However, we need a more concrete scheme to solve this problem as we start updating the original NDA form more collaboratively, versioning plays a crucial role.

Checking the draft changes of data structure using NDA API

Even though every time we pull the data dictionary from NDA using NDA REST API before editing or resuse, as per David's feedback, there is a chance that by the time the pull request is submitted and accepted, there might be draft changes to the form. We should check the hash of the form before creating a pull request to make sure we are making changes to the origin form. Again this is related to the issue #75

[EP] Implement 'Add Item' in the Kanban board display

Files Needs to be back up other than user's local disk

probably, drop box

Add different icons for major features in Brainverse App

Look into http://fontawesome.io/examples/

Add parser for an OWL/turtle

Given a nidm experiment in OWL/turtle/jsonld file format, the parser needs to parse the file to obtain field names for the forms

[EP] 'Delete Item' in the kanban board display

Remove the corresponding node from the graph.

Implement 'Moving Items around' to update the Plans in the Kaban board display

Buttons Alignment in nda import

In the NDAImport form, buttons - select all, clear, PreviewForm, save, go to main page, fill up form needs to be rearranged. Right now, buttons stack up.

[Beg] If number of values is 2, convert dropdown to radio button

Add Brainverse Introduction Tutorial

Look into Intro.js

Add a sample OWL/turtle file

Add NIDM experiment turtle/OWL file

Add 'link' to instrument form and allow data collection

Export ReproNim curated form to NDA csv format

[EP] Implement 'Edit Items' in Kanban Board Display

Add 'Create an Experiment' form.

(Refer: Slide 4 from the design doc)

Add Field validation

Use field 'type', eg., string, number, or any variety to validate the field's input entered by the user

Add new endpoints to serve request for history of a plan

Add a sample json file with all fields names for the project

[EP] 'Delete Column' in the Kanban board display

Improving the UI of the Editor interface

There is lots of scrolling in the editor Interface. We could improve on it.

• Once the file is saved it should pop up and show message that it has saved the file.

Options parsing for select/radio buttons

Radio button style and options not showing as desired.
For example, in grit01, Grit Total Score not displaying all the 5 options. If we look at the term (shown below for reference), in the 'valueRange' field, it has 5 values while in the 'notes', it has 2 values. Though for a human, it is easy to understand, for machine we need to provide rules for such case for parsing.
One solution might be to check of number of options specified in valueRange field matches with the 'notes' field. If it does not, which ever filed provides more options should be considered and the other fields information can go into the tooltip.

{
"id": 2081184,
"required": "Required",
"condition": null,
"aliases": [],
"filterElement": "1",
"position": 18,
"dataElementId": 1289666,
"name": "grit_total",
"type": "Float",
"size": null,
"description": "Grit Total score",
"valueRange": "1::5",
"notes": "1=not at all gritty; 5=extremely gritty",
"translations": []
}

[EP] Implement 'Add Column' to the Kanban Board Display

Add spinning wheel while waiting for data in an async operation

Finding alias for a new data element

While creating a new data element, the new data element could be similar to an existing one. A list of alias suggestion could be provided. If the new data element is created, then the list will be added to the alias field.

Validation of data elements

Currently, we have minimal validation based on the required field and field type. We need to enhance the validation based on other fields such as size.
Also, we could use validation API (from David's demo) or if standalone package provided (similar to Hauke's RedCap importer) to improve this.

Parsing NDA Data Element fields

We have been so far parsing two fields - ValueRange and Notes. We need to parse/add other field details while allowing editing of a data element, e.g. Translation, size. In addition to that, there are several forms, ValueRange and Notes are not properly being parsed.

[EP] Add Participant nodes to the graph

Create a Project Page listing all fields, experiments, files, processes.

(Refer: Slide 6 of design doc)

Select all and Select none options for NDARimport

Once authenticated, the user does not need to provide credentials for subsequent logins within few hours

Preview form display

Preview form could be shown as modal that pops out and display. With current implementation, it should align with the fields selection div container.

[NDA] Preview form stays even after NDARImport save button is clicked

When NDAR save button is clicked, the preview form stays and does not disappear.

[Beg] Instead of<Source, type, category>, just fetch all datastructures

Files needs to be saved outside the app storage

Currently, all the files created are saved within the App resource. We need it outside the directory of the app to save it permanently

Create doumentation for NDA Editor module

Beck Depression Inventory preview form failing

When one selects all fields of Beck Depression Inventory and click on preview form, it fails to show the preview. However, if one select few fields, preview works fine.
@derry0822 any idea on this?