martenson/public-galaxy-servers

Machine readable list of public Galaxy servers & utilities, visualized:

Hi there 👋

public-galaxy-servers's Issues

uptime checks - how often?

Programmatically Generate this list from the Public Galaxy Server List page

@martin, @erasche, @bebatut,

Since we migrated the public Galaxy server list on the hub from a monolithic web page to directory based approach, I think it would be easy to programmatically generate this CSV from that directory structure. Here's how:

Current columns

name

This is title in the server page metadata

url

This is url in the server page metadata. Would require checking that everyone of these actually point to the server. (I think they do - I'll be visiting every page anyway.)

support

As far as I can tell, these are all email addresses. These do not exist in the current metadata, although sometimes they are in the User Support section of the page content.

Are these all supposed to be a single email address? Are there other options we could do here, like a semicolon separated list of emails, or a URL?

See email_contacts below.

location

This is a standard two letter country code.
See home_country_code below

tags

I was thinking about adding tags to the server pages and I asked @dannon to look into metalsmith support for tags, but I also told him it was an unimaginably low priority. We can support tags in the page metadata before we do anything with them in the hub. Some of the tags are already on the pages, but with a different name:

server_group: "general"

There are three groups: general, domain, and tool-publishing. general maps to genomics, and tool-publishing maps to tools. Those two are easy.

Domain-specific tags like phage aren't currently supported in the hub.

See tags below.

Proposed new columns and metadata

info_page, in CSV

URL of the server's information page on the hub.

email_contacts, in Hub

Copied from support in CSV.

home_country_code, in Hub

Copied from location in CSV.

But ...

Country codes are not as informative as country names

Displaying "DK" in the hub is not informative. But, country names are ambiguous and 5 names can map to one country.

What say ye?

More location?

@bebatut and I have discussed having Event locations be free form text, but be specific enough that we could pass the string to a mapping service, and it would return some geolocation.

Should we do that with location, or is country all we'll ever care about (or all we care about now :-)?

I'm OK with country code for now.

I just don't want to display it, and it's easy to change this programmatically later if we want to go there.

tags, in Hub

Initially populated from tags in CSV. Combined with server_group when updating tags in CSV.

Mixed Model

We don't have to go fully one way or the other. We could use a mixed model where the file can be both programmatically and manually updated. The program would read in the CSV first, and then update information in place. It would report on any updates it did, and on anything that's in the CSV, but not in the Hub.

Differences would be reconciled before the new CSV is pushed.

license

I'm good with pretty much anything (though always fond of gpl.)

Requirements to be listed / Target Audience

cc @tnabtaf @martenson

I noticed the following the other day:

$ grep -c http: servers.csv
72
$ grep -c https: servers.csv
19

In my personal opinion we shouldn't be telling our potential users to use insecure servers. But I guess this raises the question of who we are pushing to these domain-specific servers and if there should be some bar to entry for the free advertising we give them. It's surely also partially advertising for galaxy project, and I understand that, but

• SSL certificates are so insanely easy to get these days with letsencrypt. This should be a bare-minimum, there's absolutely no excuse for not having them.
• I'd love to enforce that they're on a release of galaxy supported for security but I guess this is more for the server owner and a less user-focused concern.

Enable travis testing

I've already configured the .travis.yml @martenson! :)

Merge in data from bgruening/galaxy-maps and hub?