Repo used for testing: https://github.com/yochannah/cytoscape-intermine/tree/cors-investigations - cors investigation branch.
To test:
cors-investigations branchnpm install dependencies.npm install ../some/path/to/locally/compiled/imjscytoscape-intermine/node_moduled/imjs directory change main : build/service to main : dist/im.js if needed.
| #load InterMineR | |
| library(InterMineR) | |
| # Select WormMine | |
| wormMine <- listMines()["WormMine"] | |
| im <- initInterMine(mine=wormMine) # IMPORTANT: ADD YOUR TOKEN HERE IF THIS IS A LIST YOU SAVE TO YOUR OWN ACCOUNT | |
| # EXAMPLE: im <- initInterMine(mine=wormMine, "YOUR TOKEN") | |
| # fetch the list of widgets available from WormMine | |
| widgets <- getWidgets(im) |
This will produce a 400 error in the current (June 2019) InterMineR version.
library(InterMineR)
# Begin by initialising against an InterMine - in this case HumanMine
im <- initInterMine(mine=listMines()["HumanMine"], "SOME TOP SECRET TOKEN")
# initialise a variable to hold a new query
expressedPancreas = newQuery()| ```json | |
| //json in here | |
| ``` |
Export JSON from the GSoC dashbaord. When signed in as an org admin, for 2019, it's this URL: https://summerofcode.withgoogle.com/api/om/program/2019/proposal/?ignored=false&is_complete=true&order=title_lower&page=1&page_size=50&shared_with_org_members=true
Paste it into the script.js file.
To run the script, navigate to the directory where the script is stored, e.g.
| project | interest level |
|---|---|
| imjs | 🔥🔥🔥 |
| data viz | 🔥🔥 |
| spring migration | 🔥🔥🔥 |
| data modeller | 🔥🔥🔥🔥 |
| cloud | 🔥🔥 |
| InterMineR | 🔥🔥🔥 |
| link validation | 🔥 |
| similarity | 🔥 |
| <!doctype html> | |
| <html> | |
| <head> | |
| <meta name="description" content="Sample imjs query"> | |
| <script src="https://cdn.jsdelivr.net/npm/imjs@3.16.0/dist/im.js"></script> | |
| </head> | |
| <body> | |
| <script> | |
| var intermine = new imjs.Service({root: 'http://www.flymine.org/flymine/service/'}); |
Ones I know a little less about:
| var templates = { | |
| "templates": { | |
| "ChromRegion_Genes": { | |
| "model": { | |
| "name": "genomic" | |
| }, | |
| "title": "Region --> Genes", | |
| "description": "Show the genes located between two points on a chromosome. [Keywords: span, region, co-ordinates]", | |
| "select": ["Chromosome.primaryIdentifier", "Chromosome.locatedFeatures.feature.primaryIdentifier", "Chromosome.locatedFeatures.feature.symbol", "Chromosome.locatedFeatures.feature.chromosomeLocation.start", "Chromosome.locatedFeatures.feature.chromosomeLocation.end", "Chromosome.locatedFeatures.feature.chromosomeLocation.strand"], | |
| "constraintLogic": "A and B and C and E", |
Testing.
rgba(255,255,255,0.4) /* 40% opaque white */
rgba(255,255,0,0.7) /* 70% opaque yellow */