tilde-lab / optimade.science Goto Github PK

A "sky-scanner" Optimade browser-only GUI

License: MIT License

HTML 0.92% JavaScript 17.73% Svelte 44.83% TypeScript 20.77% SCSS 15.75%

computational-materials computational-materials-engineering materials-data materials-genome materials-informatics materials-platform materials-science optimade

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optimade.science's Issues

Equals sign from the query filter is dropped

How to reproduce:

Try rather complex query e.g. elements HAS ANY "C","Si","Ge","Sn","Pb" AND nelements=2: https://optimade.science/?filter=elements%20HAS%20ANY%20"C","Si","Ge","Sn","Pb"%20AND%20nelements=2&providers=threedd while only one provider is enabled.

Then enable arbitrary other new one, clicking by its avatar. The query in the input box changes on its own.

The problem is in the = sign in this part of the query: nelements=2

Version check and update push

See e.g. Telegram web-app or Hetzner cloud GUI, relevant for a long-living cached instance

Compilation warning

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â”‚                Please update to version 7 of PostCSS Preset Env.                â”‚
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Husky formatting

I hope, the changes in the codebase won't be huge, otherwise may be it's not so good idea...

Popup-stopper for IE<=11 and all the smartphones

Unfortunately, a current one doesn’t work for IE.

Add favicon

@Valexr are you aware if favicons are in either way supported on GitHub?

Use project logos for the avatars

To increase the loading speed, I'd propose generating a single sprite for all the logos, similar to https://mpds.io/aets.jpg vs. https://mpds.io/#polyhedra

@Valexr what do you think?

Heisenbug in click avatars logic

Click MPDS so that it should be selected alone (exclusively). By some reason, another provider is also always selected.

make link to optimade standard more visible

Just copying this from an earlier email to evgeny:

I was going to suggest to add a link to the optimade standard (so that people can understand what to put in the search fied) - then I realized that there was already a link at the bottom of the page.
It might make sense to move the footer (or at least the link to the standard) up to where the content of the page ends - I guess many people will be like me and overlook it at the very bottom of the page. I attach a screenshot just to illustrate the dimensions on my screen.
Or one could add a link to either directly to the "filter=" or on a Questionmark icon close to there that directly links to the optimade filter language specification

clarify pagination / results limits

With the query nelements > 0 (which should return all structures in the databases), I currently get 20 structures for the materials project and odbx and less for the cod.

I guess the limit is currently 20, which would be nice to indicate with something like "..."
(even nicer would be to actually be able to paginate).

Furthermore, I notice that the client currently doesn't return any results for the "nested" materials cloud databases - is this an issue with the client or on the materials cloud side?
On https://optimadeclient.materialscloud.io/ I am able to query the materials cloud endpoints...

Individual entry preview generates incorrect URLs

I tried accessing data in the COD from the search results (https://optimade.science/#filter=elements%20HAS%20%22Ca%22), but the following URL of an individual entry is not supported in the COD:

https://www.crystallography.net/cod/optimade/structures/?filter=id=1000007

Note the / before ?, should be structures?filter=id=1000007 (without / before ?). I believe the following line is responsible:

optimade.science/index.html

Line 502 in be60495

 url = window.optimade_gui.active_providers[ids[0]].url + '/?filter=id=' + ids.slice(1).join('/'); 

Wrong version for most providers

It looks like this is primarily pinging the v0 endpoint, whereas most implementations have settled on the first implementation being v1. That's causing the app to not find any sources other than pcod or tcod.

Bottleneck in showing the search results

It seems there's a bottleneck in showing the search results, by the slowest provider. Until it returns the results, no other much faster providers' results are shown. This is strange, since the Optimade client per se is asynchronous.

Click on a pagination is subject to throttling

We have to wait a throttling delay while using pagination, which worsens UX

Algo for avatar abbreviations should be improved

See Avatar component https://github.com/tilde-lab/optimade.science/tree/master/src/components/Avatar

No progress-bar is shown

Clearly visible if off-line...

Impossible to copy parts of JSON

At the result view, where JSON is displayed, certain fields can be nicely expanded, but CANNOT be copied...

Pagination requests `page_number=0` which is unsupported

When trying to query e.g. odbx, all filters return an error about page_number=0 being requested. OPTIMADE standardizes 3 different pagination types, number-based, offset-based an cursor-based. page_number=0 is invalid as number-based pagination starts at 1. Most databases actually use offset-based pagination, perhaps this should be used here instead?

IMO we should standardize an error code/message in the specification for unsupported pagination types, as it is not clear how to negotiate with a provider to figure this out...

A question regarding how to query underlying data sources

Hi,

May I just ask you a question regarding how you get the data from Materials Project for instance?
Do you use any python library? I'm not familiar with Svelte and TypeScript so that it's a bit difficult for me to find out in the code.

I'm trying to query chemical formula anonymous is "A" by using OPTIMADE API for Materials Project, with following request. But I did not get correct result.
https://optimade.materialsproject.org/v1/structures?chemical_formula_anonymous=%22A%22

Best,
Huanyu

Differentiate no results from invalid/unsupported filters

When searching for spacegroup="P1" on https://optimade.science, all providers but MPDS result in "No results". However, filter spacegroup="P1" is not defined in the OPTIMADE standard, thus it is nonstandard. Therefore, replies "No results" from other providers give false impressions that these databases do not contain P1 structures, which some of them do. Therefore I propose catching HTTP 4xx and 5xx from providers and reporting them as such.