Add list manipulation features

[yochannah]

Unless I've missed it, there doesn't appear to be any inbuilt way to handles lists, e.g.

• fetch a list by name
• save a list
• Perform list ops like difference, subtract, intersect, etc.
• delete lists
• get a list of lists

Referring to http://intermine.org/intermine-ws-python/intermine.lists.html#module-intermine.lists.listmanager might help to selec useful methods and gain parity for our packages

[yochannah]

Fetching list contents can be worked around with a query like this:

# Fetch a public Gene list from HumanMine
# Create a new query
Pax6List = newQuery(
  #here we're choosing which columns of data we'd like to see
  view = c("Gene.primaryIdentifier",
           "Gene.symbol"))

# constrain genes to be in our (pre-existing) list
listConstraint = setConstraints(
  paths = c("Gene"),
  operators = c("IN"),
  values = list("PL_Pax6_Targets")
)

# add constraint to the query
Pax6List$where <- listConstraint

# Now we have the query set up the way we want, let's actually *run* the query! 
pax <-  runQuery(im = im, qry = Pax6List)

#preview the data
head(pax)

[yochannah]

I've added the Hacktoberfest label to this issue - in order to implement methods that manipulate lists you'll probably want to look at the python package mentioned above, as well as these python tutorials: https://github.com/intermine/intermine-ws-python-docs/ (especially tutorial 8)

Other resources that are likely to be useful:

• In order to save / manipulate lists, you'll need to be authenticated - make sure to accept a token as an argument. You'll need to create an account on a live InterMine to test this - perhaps try flymine.org.
• User docs for working with InterMine lists are here: https://flymine.readthedocs.io/en/latest/lists/index.html
• InterMine has interactive API docs: http://iodocs.apps.intermine.org/
• Further InterMine docs are here: https://intermine.readthedocs.io/en/latest/web-services/ and here: http://intermine.org/developers/

if you want to pick up this task

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2. When you're ready, add your work to the repo and create a pull request.

What to do if you need help

Mention @yochannah, tweet @yoyehudi, pop by to say hi on chat or if needed email [email protected]. Don't forget we're usually only available during uk office hours and will not be able to respond at other times :)

[yochannah]

@celions is currently working on this task 🚀