bobbylight / random-acts-of-kinase Goto Github PK

All of the tables in the "Missing Data" admin tab should be filterable by compound name.

See tpki-102 fix file.csv in dropbox for a simple test case.

At soe point, the 0 value is turned into null.

CSV columns must match those in the database. Duplicates result in a warning that they will be discarded, except in the case where a SMILES string (or some other empty field) is specified, in which it will be added (assuming all other fields match their current values).

A summary of what changes will be made should be showed and must be confirmed before taking effect.

When creating a development environment on a new machine, we need a script to create and populate a schema with our real kinase data. Working with it is much nicer than working with the dummy data in the dev Spring profile.

• Any compounds without 468 activity profiles?
• List compounds without SMILES strings
• Any other anomalies we can point out?

Add the ability for folks to import and search for nanoBRET data.

Primary sort should be on KD value, from smallest to largest. null values come last.

Provide a more specific error message if the uploaded file has too many or too few columns. Right now it just says "file has an invalid format", which is not obvious if e.g. Excel has added a column of all blank values.

Like it says on the tin.

Like it says on the tin

When logged in as an admin, a user should be able to edit the fields of a compound when viewing it. This provides a quick-and-dirty way to update individual compounds so folks don't have to upload a 1-line CSV file.

The currently displayed build date is just a stub; it's always new Date(). It should be the actual build date.

Export includes solubility column, import expects that column to not be there. Need to make import expect it, and in the same order as columns are exported.

Despite the dropzones saying "Drag data here, or click to browse...", dragging files into the dropzones doesn't work.

Only Chrome. Not sure about IE. Oops.

Seems a child <i> on a <button> isn't such a good idea, not sure what I was thinking.

Excel converts true/false columns to TRUE/FALSE, which jackson-csv cannot convert to a Java Boolean. Hopefully we can figure out a way around this.

Semantic UI is nice, but you have to jump through several hoops to do a custom build, and I can't get it working at all in travis-ci.

When opening a specific compound's details and returning, search info is lost. It should be preserved. Should we use vuex?

The Audit tab in the admin section should be filterable on all admin fields.

A new tab in the app labeled "News". This should fetch blog entries from an api/blogPosts REST endpoint. User should be able to page through say 10 at a time.

Blog post properties:

• Title
• Body
• Author
• Post date
• View count
• Card image

The blog post body should be stored and rendered as markdown.

Clicking to open a full blog post will be a future ticket and not handled here.

Store partners in database, and show them somehow in the UI.

Simple login capability to allow certain folks to upload new data and perform other administrative tasks.

Stuff you can do after logging in will be handled in other tickets; this is just for the login feature itself.

I'm told we can allow the user to switch between searching kinase/% control and kinase/kd. This will require new queries as well as a tweak to the UI to allow the toggle.

To reproduce:

• Open a compound
• Click on the "x" in its tab
• Note the tab doesn't close

This is becuase we are adding a child <i> element to <v-btn>, which is taboo because it ends up as DOM content inside a <button> which isn't allowed. We'll have to fix this by making navbar-pills a little more complex.

• Search section better separated and styled
• What style/layout to use for kinase list?

Simple mechanism for feedback

Right now, you can only search by compound name. Updating the kinase/activity fields in the UI does nothing. It sould instead search on those criteria.

Add a network diagram, in which users can add compounds and how reactive they were to various kinases. Can be used to find other compounds that can be used to target the first compound's primary kinases.

Somehow, importing one clears values imported from the other.

Test compound files to flip-flop values:

• sgc010-01-s-00001_Kd-report.csv
• sgc015-01-p-00001_Data-report.csv

MarvinJS?

The app needs a home screen that describes its purpose. Needs trendy stock images, mission statement, etc.

Admins should be able to log in via username & password. An "Admin" tab can be available, but what exact content is in it can come later. This ticket is just to add logon and security bits.

To reproduce:

1. Open tabs for two compounds
2. Click bewteen them a couple of times
3. Close one
4. Close the other

Expected: You'll end up back on the "search" tab
Actual: The prior tab is magically reopened and focused.

When a compound tab is closed, all references to it should be removed from the history, not just the "top" one.

Once a kinase is selected, you cannot clear it.

All tables in the application should support sorting on more than one column. The service already supports this.

Add fields to the compound resource to record the primary literature reference.

Admins should see hidden compounds in search results. Further, the search result should have some sort of icon or indication that it is hidden.

Admin UI should allow the import of CSV files with structure matching our compound table. Compounds will be created, or edited if they already exist.

The UI should provide some idea of what is being changed, though it doesn't have to be too detailed.

The REST endpoint(s) for this should be protected and accessible by admins only.

SVG is nice for the webapp, but users should be able to save images as PNG files to facilitate using them in other apps such as PowerPoint (SVG is only supported in Office 365).

This should be doable in the lightbox for the images. Perhaps a dropdown allowing download options:

• SVG
• PNG (100 x 100)
• PNG (200 x 200)
• PNG (300 x 300)
• PNG (400 x 400)
• PNG (500 x 500)
• PNG (600 x 600)

The grid component displays a "warning" in a browser alert dialog when receiving null values. Oddly, datatables requires you to tell you that null values are OK, and just to render empty string for them.