Yo Yehudi yochannah

## cors-investigation-notes.md

      
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                yochannah
                / cors-investigation-notes.md
            
            
              Created
              August 6, 2019 12:17
            
          
    CORS investigation notes

Repo used for testing: https://github.com/yochannah/cytoscape-intermine/tree/cors-investigations - cors investigation branch.
To test:

Clone the repo and checkout cors-investigations branch
npm install dependencies.
npm install ../some/path/to/locally/compiled/imjs
In the cytoscape-intermine/node_moduled/imjs directory change main : build/service to main : dist/im.js if needed.


## wormMineEnrichmentPublicList.r
#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)

## whoopsiedaisy.md

      
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                yochannah
                / whoopsiedaisy.md
            
            
              Created
              June 12, 2019 15:45
            
              
                more InterMineR error logging
              
          
    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()

  
## md.txt
```json
//json in here
```

## README.md

      
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                yochannah
                / README.md
            
            
              Last active
              April 9, 2019 16:36
            
              
                GSoC proposal export for our student grading sheet
              
          
    Instructions

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.


## techdoctools.md

      
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                yochannah
                / techdoctools.md
            
            
              Created
              April 25, 2017 12:50
            
              
                Writing technical documentation for open source projects
              
          
    Documentation for software often requires programmers to write in specific formats, like MarkDown (which this Gist is written in) or reStructuredText, which InterMine uses for Sphinx, hosted on readthedocs.org.
Personally, I prefer to use MarkDown - it seems more ubiquitous to me, given that StackOverflow and GitHub both use markdown by default. Here are a few of my favourite tools to handle this:

StackEdit - a fabulous melding of Google Docs with a realtime markdown preview and collaborative editing. A great way to work on a doc with others before uploading it to your official documentation section.
Pandoc - and especially their online converter - write in most common formats, convert to other common formats. For me, that means I can write InterMine document


## student-interest.md

      
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                yochannah
                / student-interest.md
            
            
              Created
              March 22, 2019 12:33
            
              
                March 22 student einterest level GSoC InterMine
              
          
project
interest level


imjs
🔥🔥🔥


data viz
🔥🔥


spring migration
🔥🔥🔥


data modeller
🔥🔥🔥🔥


cloud
🔥🔥


InterMineR
🔥🔥🔥


link validation
🔥


similarity
🔥


## example html page.html
<!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/'});

## opensource.md

      
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                yochannah
                / opensource.md
            
            
              Created
              February 24, 2019 11:53
            
              
                Interesting open source conferences
              
          
FOSDEM - next conf in 2020 - Brussels
Mozilla Festival - Late October 2019 - London, UK
Various PyCons - all around the world at various dates
Opencons around the world check again in a month or two for dates
Git Merge europe - next one will be 2020

Ones I know a little less about:

Linux Foundation Events


## templates.js
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",
	#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)
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/'});
	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",