intermine / intermine-registry

Registry to store and browse all known instances of InterMine. Developed during GSoC 2017 by Leonardo Kuffo

InterMine Registry

InterMine Registry is a place where all the up-to-date instances information is stored and can be consumed by applications like Blue Genes, iOS, InterMine R, the friendly mine tool or available to everyone who needs it. The core of InterMine Registry is its RESTful API. Running over Node.js integrated with MongoDB, it contains methods (endpoints) to administer the instances on the registry (add, update & delete) and search among them. Furthermore, InterMine Registry also includes a nice fully responsive front-end web application, from which everyone can see all the InterMine instances and search among them.

GSoC 2017

InterMine registry was entirely implemented and developed as a GSoC 2017 program project by the student Leonardo Kuffo. Click here to find all of Leonardo's contributions for the project as evidence of his work.

Registry API

The core of the InterMine Registry App is the restFUL API. It contains endpoints to search and administer instances. These endpoints can be reached through the following base path: http://intermine.org/registry/service/

• POST /instances Add an instance to the registry.
• GET /instances Get all the instances from the registry.
• GET /instances/{instanceIdOrName} Get an instance by its ID or Name.
• PUT /instances/{instanceId} Update an instance.
• DELETE /instances/{instanceId} Deletes an instance.
• PUT /synchronize Update the branding & version information of every instance.
• PUT /synchronize/{instanceIdOrName} Update the branding & version information of the specified instance.

You can check the detailed API documentation for more information and testing.

Installation

Please visit getting started

Troubleshooting tips - The installation might fail because of the bcrypt dependency if you're not running on a stable version of node. Bcrypt doesn't support unstable version of node, so switch to the current stable version of the node , you can use nvm to manage your node version.

Configure the API Docs

The API-DOCS are generated based on the swagger.json file in the repository. In order for the API-DOCS to work correctly, on this file you have to specify the "HOST" and the "SCHEME" of the app (http or https).

Detailed Documentation

For more in-deep information about the code, and detailed guidelines on the project, please, visit the following link.

intermine-registry's Issues

Versions should not being expected as input during the instance creation

These 3 endpoints should be used instead
service/version (the oldest implemented endpoint)
service/version/intermine
service/version/release
TO NOTE
Some instances might use an old version of intermine. In that case, the most recent endpoints (service/version/intermine and service/version/release) return wrong info, in particular, they return the same value of service/version.
If service/version=service/version/intermine we shouldn’t set the intermine_version field. Same for release_version.

Clear .idea files

This repo contains a .idea folder which does not look good. Removing it would be better.

Check instance with the same name already exist

Grid View: focus on the top

When you click on the box, the focus moves on the top of the page, instead to stay on the preview box

World view map only shows one instance if there are 2 with the same locations

See FlyMine and HumanMine: they have same locations but instances world only shows one

Add sync to FE

Add sync functionality on the webapp. Sync all (maybe next to Add instance) and Sync instance (maybe next to Update)

Ambiguous entries in the service instance of registry API

In the service instance of registry API (https://registry.intermine.org/service/instances), we have certain ambiguous entries. For example,

1. We can find that in the entries for mines namely ThaleMine, WormMine, YeastMine and ZebrafishMine, we have twitter key field values start with '@' while in all other mines, the twitter key field start without '@'.
2. We can also find the ambiguities in the neighborhood lists. In MaizeMine, the neighborhood list contains Plants but starts with space, while all other entries start without space.
   There could possibly be other ambiguities, but till now I found just these two.

Add all the instances in the registry

You can build a script calling the POST /instances in order to add name and url.
Here https://github.com/intermine/mineversions/blob/master/index.html#L89 you can find all the instances.

Add print stylesheet with aim to fit everything on one A4 page

The InterMine Registry is pretty awesome. When we go to conferences it would be nice to print out a few sheets containing a list of all the InterMines, straight from the registry.

We'd need to show the following fields:

• top of page:
  • header (e.g. "InterMine Registry")
  • registry URL (Note: URLs can be extracted from the href value using css pseudo-elements and attr(), like this: http://jsbin.com/fekanow/edit?html,css,output )
• Once per intermine:
  • mine name (e.g. "BovineMine")
  • organisms found in each mine
  • ideally URL of each mine if it fits?

The end goal of this exercise is to make this a nice, compact sheet that people interested in InterMine can visually scan to see if their favourite organism is present, and if so, where to go to find it.

More info on print stylesheets: https://www.smashingmagazine.com/2015/01/designing-for-print-with-css/

Grid View: reduce preview box

reduce the size of the preview box. Title + description + buttons on the left side, fields on the right side.
Logo close to title

Add confiramtion message before delete instance from the preview box

Instances World View doesn't dispalys some instances

For instance, beanmine has "location":{"latitude":"35.636600","longitude":"-105.959222"} but doesn't appear on the world view

Buttons order

Always same order for the buttons: Update, Synchronize, Delete, Close

List view: use the field image:logo.

HumanMine already returns the correct logo, not yet displayed

Registry URL

Problem when missing the last / in the url webapp

Instance URL validation

POST /instances service should validate the url field to avoid typo

Delete button doesn't work in the preview box (Instances Grid View)

Description field in update mode

If you update an instance with the description empty, the field shows : Enter your Username

Updating isProduction via API doesn't work

I can't update isProduction field from true to false

Add a link to github repo

I would like the registry to include a github (or wherever) link to the repository linked to the mine.

Optional of course! but useful for me.

Dev Mine checkbox doesn't work

When you add an instance and check the flag "Dev Mine", the instance is created with the attribute isProduction set to true

List view: add ordering by name

Error with installation

On following the instructions as given in the README.md of the repo, I faced the following MongoDB error when I did npm start

Can someone help me?
Did I get something wrong?

Synchronize All button takes ages

the rest endpoint via curl
time curl -X PUT "http://intermine-registry.herokuapp.com/service/synchronize" -H "accept: application/json" -H "authorization: Basic....."
takes about 15sec

If no results are found no Fallback Message is given

Issue: If no result for a pirticular mine is found no error message or fallback message is given

Screenshot:

I would like to work on this.

UI improvements

Listed here https://docs.google.com/document/d/14Gn29NjLa2QtR6duBhsuhvR-kACYW2yU7BjkXoNjRig/edit?usp=sharing

Investigate if we can use the header fields (main and text) in the grid view

Now the registry uses images

Image and logo should not being expected as input during the instance creation

use /branding instead.
Old endpoint, every instance should have it

Rename the label on the button Submit Query -> Save

Error returned when number of instances returned by the query is zero

While searching for mines in the registry, if query returns an empty set, the status code is set to 404 which gives an error in chrome console.

For example if you click on the following link, it returns a status code of 404.
http://registry.intermine.org/service/instances/?q=abc

Returning an empty query is not an error and it should be returned with a 200 status code.

Here, the if condition, checking for empty set should be removed.

if (instances.length === 0){
            api_response.statusCode = 404;
}

Add authentication on BE

Using passport.js. Only one user, for not set as environment variable

Request: automatically synchronise new instances

I've added instances to the registry via the UI a couple of times. Both times they don't show up until I manually synchronise them.

It might be better to automatically sync new instances?

Add authentication on FE

Automatic upload mechanism for images ang logos

every 24 h

Grid view: more details on the preview

The preview panel should contain the same fields we display when the user clicks on the instance, in the list view

Icon Missing http://registry.intermine.org/

Update api-docs to query instances using mines parameter

At the moment, you can't query the dev instances using the swagger

Mandatory fields

Not all the filed are mandatory when a new instance is created via POST /instances

List view: remove the dot in the organism field

Nicer user messages

automatic upload mechanism for the versions

All data related to the versions should be updated every 24 h using the existing endpoints

Add custom fields to registry - maintainer name and url

We'd like to add the option to include the maintainer organisation of any given intermine and a link to their site, eg. the json properties for flymine or humanmine might look like this:

maintainerOrgName : "InterMine core team, Micklem Lab",
maintainerUrl : "http://intermine.org/"

(from intermine/intermine#1751)

See also the registry docs here: https://docs.google.com/document/d/1ODWOBPA0XePfXmpKN75GQoBPjvFH9Rnp5yIooD1szXw/edit#

cc @danielabutano @amand1996

Organism values displayed in alphabetical order

It would be nice to have the values, in the organism field, displayed in alphabetical order

Text suggestion

Do you agree that when the registry says

    All InterMine instances up-to-date information in one place.

it should probably say something like

    Information on all registered InterMine instances in one place.

There are other mines out there that are private or haven't been registered. Also the grammar of the exiting phrase might not be quite right ;-)

Request: add a new parameter to mine to indicate if it's a dev or production intermine

We have apps using the registry now. Yay! Great job!

We've just realised something though, we need to differentiate between live InterMines and dev InterMines.

1. New apps are using the live mines and knocking them over. Need to use dev mines ONLY until the app is thoroughly tested!
2. End users (of the iOS app for example) do not want to see the dev mines.

So the registry needs to differentiate between live InterMines, meant for public consumption and development mines, meant for testing only.

Can you do this:

• Add new parameter to a mine, a boolean named isProduction
• Mark as true except for beta humanmine and beta flymine and yeastmine dev
• /instances Only return production mines by default
• /instances Add optional parameter to specify which InterMines to retrieve.

Request	Action
`/instances`	Returns production mines ONLY, isProduction=TRUE
`/instances?mines=all`	Returns all mines
`/instances?mines=dev`	Returns only non-production mines, isProduction=FALSE
`/instances?mines=prod`	Returns all production mines, isProduction=TRUE

Overlapping buttons in mobile

Description

The "Visit website" button is overlapping with the "Organisms" in mobile at a few places.

Screenshot

@yochannah, shall I work on this if it is an appropriate issue?

Location values not shown on the update form

Try to update the instance Flymine, via webapp. The Location fields (lat + long) are not set with the values: "location":{"latitude":"52.199236","longitude":"0.122280"}

Rename web_version to release_version

Search case sensitive

GET /instances/{instanceIdOrName} should not be case sensitive
/instances/flymine should return the FlyMine instance

Can’t set the organism field as empty

If you update an instance with an organism already setted, you can’t set the organism field as empty