MichelaNGLo-api

A python module to interact with the Michelaɴɢʟo server (https://michelanglo.sgc.ox.ac.uk) programmatically.

Installation

Python 3.6 or higher.

pip3 install michelanglo-api

Documentation for VenusAPI

venus = VenusAPI()
# venus = VenusAPI(url='http://0.0.0.0:8088/') for local
data = venus.analyse(gene='LZTR1', mutation='S244C') # dictionary with data.
venus.match_species('pink')  # ['Clove pink', 'Pink fawn lily', 'Pink hibiscus mealybug', 'Pink tip anemone',...]
venus.get_taxid('cat')  # 9685
venus.get_uniprot('LTR1', 9606)  # Q8N653
venus.from_transcript(enst, gene_mutation)  # uniprot and protein mutation
venus.random() # uniprot, protein mutation and species

Documentation for MikeAPI

Notes

The details of the requests accepted by Michelaɴɢʟo are described in its documentation.
You may interact with the server however you please. This code is just to make life easier.

There are three tiers of users. Basic, priviledged, admin. Basic users cannot add JS to the site as this is a security threat (cookie theft)... And it prevents users from making pages that behave maliciously or similar.

Authenticate

To start, authenticate.

mike = MikeAPI('username','password')

The argument url sets other address outside of the SGC one, such as http://0.0.0.0:8088. The password and username can be ommitted, in which case they are either read from the environment variables MICHELANGLO_PASSWORD and MICHELANGLO_USERNAME or the user is prompted.

To check all worked mike.verify_user(). This will show your rank (see user priviledges in the site).

Instance attributes:

• .url is 'https://michelanglo.sgc.ox.ac.uk/' unless altered (e.g. local version of Michelanglo)
• .username is the username
• .password is the raw password, so do not share pickles!
• .visited_pages, .owned_pages and .public_pages are lists filled by .refresh_pages()
• .request is the requests session object.

Instance methods:

• .post(route, data=None, headers=None) does the requests for other methods...
• .post_json(route, data=None, headers=None) as above but decodes the json reply...
• .login(). called automatically during initialisation.
• .verify_user(). check whether you are still logged in.
• .refresh_pages(). gets the lists .visited_pages, .owned_pages and .public_pages (and .all if admin)
• .get_page(uuid) returns the MikePage instance for a given page. See below.
• .set_page(uuid, data) sets the MikePage instance for a given page. See below.
• .delete_page(uuid) delete. See below.

Page editing

To see what pages you own, you can use:

• mike.owned_pages Pages you created/edited
• mike.visited_pages Pages you visited
• mike.public_pages All pages in gallery
• mike.all_pages (admin only)

These are lists of MikePage instances that are not retrieved. Retrieval would reset the expiration date and would be heavy.

page = mike.owned_pages[0].retrieve()

A specific page can be explicitly retrieved.

page = mike.get_page('abcdedf-uuid-string-of-page')

Pages can be edited:

page.title = 'Hello World'
page.commit()

But not all attribute changes are allowed. To understand what does an attribute do (apart from using help) you can query it with:

page.what_is('location_viewport')

Note that two properties are Enums, .public handled by Privacy and .location_viewport handled by Location. This is to avoid arbitrary values:

p.public = Privacy['public']
p.public = p.public.__class__['public'] # if you forgot/don't want to import `Privacy`.

In addition two methods alter the page with new keys (commit still required). page.clear_revisions() and page.refresh_image().

To display in a Jupyter notebook a link and a thumbnail use page.show_link(), however will not work in terminal.

Some methods are duplicated between MikeAPI and MikePage.

• page.retrieve() = mike.set_page(uuid)
• page.commit() = mike.set_page(uuid, page)
• page.delete() = mike.del_page(uuid)
• page.shorten(short) = mike.shorten_page(uuid, short)

There is no difference.

Altering 'loadfun' (the JS) and 'pdb' is restricted to admin and approved users.

As changing the variable name in 'proteins' for the PDB code requires it to be changed in 'pdb'.

page.proteins[2]['value'] = 'altered_variable_name'
page.pdb['altered_variable_name']

The method .rename_protein_variable() does this for you.

Proteins stored in GitHub can be added via page.append_github_entry(self, username, repo, path) where the name will be a sluggified filename.

Page creation

New pages can be added using either a pdb code or a filename with additional arguments as used by prolinks, but with underscores instead of spaces.

new_page = mike.convert_pdb(code='1UBQ', data_focus='residue', data_selection='20:A')
new_page = mike.convert_pdb(filename='/home/my_protein.pdb')

Admin commands

Some commands are for admins only. Please do not try them out or you will get automatically blocked.

Tables

See table.md

"Merging"

The object MikePage does not have a merge uuids like the website has. The reason for this is because this would be rather redundant and convoluted. To add structures to a page use the following methods:

• append_github_entry
• append_pdbfile
• append_pdbblock
• remove_protein

Or operate upon the manually. PDBBlocks are stored in .pdbs (Dict[str: str]), while .proteins (List[dict]) stores the protein information.

More

For more, see Sphinx generated documentation.

To Do

• Get Uniprot chain definitions
• read/write MD from/to cell

Plotly

With JS priviledges it is possible to add a Plotly plot, by exporting via fig.write_html("file.html", include_plotlyjs='cdn') and getting the content of <body> and adding to the description (with corrected indentation). Unfortunately, whereas the path-element of class .point contains the data values to determine what residue it is, I am not sure how to detect a specific click as this detects a click for the whole series...

document.getElementById('xxxx').on('plotly_hover', data =>
    data.points.forEach(d => NGL.getStage().compList[0].addRepresentation("hyperball", { sele: ''+d.data.x[0]}))
)