caMicroscope API Guide (Draft)

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/ImageLoader

The /ImageLoader resource is a Node application that extracts image metadata (such as width and height of the image) from the existing whole slide image and stores it in a Mongo database.

HTTP Verb	QueryEndpoint	Query Parameters(Input)	Output(Description)
POST	/submitImage	case_id, File_location, subject_id	{“status”: “Success”} on success

Example of /ImageLoader

curl -v -F case_id=TCGA-02-0001 -F file_location=@TCGA-02-0001-01Z-00-DX1.83fce43e-42ac-4dcd-b156-2908e75f2e47.svs http://localhost:32799/submitData

Optional study_id Return type: json On success returns: {"status":"success"}

case_id: The unique identifier for the image

file_location: Location of the image on file system

/uAIMDataLoader

Node application that converts masks (aperio and binary masks) to GeoJSON objects and stores them in a Mongo database. Need input, output, and command for each.

HTTP Verb

QueryEndpoint

Query Parameters(Input)

Output(Description)

POST

/submitMaskOrder

Case_id,

Execution_id,

Height,

Width,

X,

Y,

Type(optional)

{“jobId”: 12}

GET

/job/:id

None

{“status”:”incomplete”}

Example of /uAIMDataLoader

Example curl command(aperio):

$ curl localhost:6000/submitMaskOrder -F mask=@1.png -F case_id=cbtc_test_11 -F execution_id=ganesh:test2 -F width=1743 -F height=2017 -F x=0 -F y=0

Example curl command(binary mask):

$ curl localhost:6000/submitMaskOrder -F mask=@1.xml -F case_id=cbtc_test_11 -F execution_id=ganesh:test2 -F width=1743 -F height=2017 -F x=0 -F y=0 -F type= maskfile

Variable	Definition
case_id	The unique identifier for the image
execution_id	The name(label) of the algorithm/run
width	width of the image/roi
height	height of the image/roi
x	top left x coordinate of the image/roi (Default: 0)
y	top left y coordinate of the image/roi (Default: 0)

/ImageData

Bindaas APIs for handling Image Metadata. (Internal APIs, not meant to be exposed)

HTTP Verb	QueryEndpoint	Query Parameters(Input)	Output(Description)	Questions
GET	/fileLocation	case_id	Get file location of image	Need explanation
	/mpp	case_id	Get mpp-x, mpp-y of the image	Need explanation
	/metadata	case_id	Get all metadata of the image(width, height, mpp etc.)	Need explanation
	/md5	case_id	Get MD5 of the image file	Need explanation
POST	/json	metdata	metadata of the image in JSON format	What are you posting? What is in the mongo database about this image?

Example of /ImageData

Need explanation of reason to use each item above.

POST http://www.example.com/customers
POST http://www.example.com/customers/12345/orders

/MarkupData

Bindaas

HTTP Verb

QueryEndpoint

Query Parameters(Input)

Output(Description)

Questions

GET

/multipleMarkups

Case_id,

x1,y1,x2,y2,footprint,algorithms

GeoJSON

Need explanation

x1,y1,x2,y2 are different than what is in caMicroscope demo (had x, y, width, height)

N/A

/executionIds

case_id

List of execution IDs available for case

Need explanation. How would one get these execution IDs for a specific slide? Need to explain the difference between a caseID and an executionID–also any of the query modifiers.

Examples of /MarkupData

/uAIMTemplates

Schema: https://github.com/joshfire/jsonform

HTTP Verb	QueryEndpoint	Query Parameters(Input)	Output(Description)
GET	/template	id?	Jsonform template
POST	/json	N/A	N/A

Examples of /uAIMTemplates

Examples here

/Tasks

Firebase/Kue???

HTTP Verb	QueryEndpoint	Query Parameters(Input)	Output(Description)
POST	/task	N/A	N/A
GET	/task	task_id	N/A

Examples of /Tasks