noctua-repl
v0.1.5
Published
Interactive programming interface for Noctua (Barista->Minerva).
Downloads
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Readme
Overview
This is a REPL environment for the Noctua annotation tool. This gets you some nice things:
- You don't have to wait until UI functionality makes it into the graph (or some other) editor--if the low-level API is capable of expressing it, you can easily do it in the REPL.
- For some operations, it is easier to express them succinctly with commands rather than work with a UI.
- An extremely easy way of prototyping new functionality.
- Spooky action at a distance.
Usage
Given that you have logged in to a Noctua instance, look at the URL and copy your token (the variable is "barista_token").
Know your target installation well enough to know where your Barista is hiding. Copy that URL down.
You might also need to know your Barista definition--is defaults to "minerva_local".
Should then be as simple as:
npm install
node ./bin/noctua-repl.js --token=xyz321abc987 --server http://127.0.0.1:3400
See the examples section for more information.
Examples
CLI examples
Connect to a local server with:
~/local/src/git/noctua-repl$:) reset && node ./bin/noctua-repl.js --token=123 --server http://localhost:3400
Connection to labs with:
~/local/src/git/noctua-repl$:) reset && node ./bin/noctua-repl.js --token=123 --server http://toaster.lbl.gov:3399 --definition minerva_public_dev
Connect to a local server and dump meta-information to a file using CLI:
~/local/src/git/noctua-repl$:) reset && node ./bin/noctua-repl.js --token=123 --server http://localhost:3400 --definition minerva_local --command "get_meta(); show(response)" > /tmp/foo.txt
Connect to a local server local and dump meta-information to a file using a script:
~/local/src/git/noctua-repl$:) reset && node ./bin/noctua-repl.js --token=123 --server http://localhost:3400 --definition minerva_local --file ./scripts/run-script-test.repl.js > /tmp/bar.txt
REPL examples
Get all of the meta-information for the current instance.
get_meta()
Assign environment to a known model, then add a couple of new individuals to it.
model_id = 'gomodel:taxon_9606-5539842e0000002'
add_individual('GO:0022008')
add_individual(intersection(['GO:0022008', 'GO:0008150']))
Add a new model, which gets the default assignment when done. Then add two new individuals as arguments to a new fact.
add_model()
var r = new_request_set()
r.add_fact([r.add_individual('GO:0022008'), r.add_individual('GO:0008150'), 'part_of'] )
request_with(r)
API/Objects
This is a list of symbols that are defined or used in the REPL/scripting environment beyond what comes with node. Remember that you can do any of the normal things that you might want in this environment--it's just node!
Helpers.
- 'bbop' the bbop-core package
- 'us' underscore
- 'manager' the bbop-rest-manager with bbop-reponse-minerva
- 'show' function to display objects more intelligently
Auto-variables--these are attempted to be sent after every call.
- 'token'
- 'model'
- 'model_id'
- 'request_set'
- 'response'
- 'query_url'
Class expressions--package class-expression.
- 'union'
- 'intersection'
- 'svf'
- 'cls'
Manager actions--these are manager functions mapped up to the top-level.
- 'get_meta'
- 'get_model'
- 'add_model'
- 'save_model'
- 'add_individual'
- 'new_request_set'
- 'request_with'
Bigger fun function macros.
- 'show_models' show summary information for all current models; can take a single string argument of "id", "title", "deprecated", "modified-p", "contributor", "model-state", or "date" for sorting
- 'show_response'
- 'silent' supress/re-enable the display of action results
Limitations/TODOs
We're actually feeling pretty good about this right now. Let us know.