caMicroscope API Guide (Draft)

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Naming

case_id: Used to uniquely identify an image.
execution_id: Used to uniquely identify an algorithm. A case_id can have multiple execution_ids associated with it.
subject_id: Used to uniquely idenify a patient. A subject_id can have multiple case_ids associated with it.

/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 Aperio and binary masks to GeoJSON objects and stores them in a Mongo database

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	Used by caMicroscope viewer to give the image location to its backend server
	/mpp	case_id	Get mpp-x, mpp-y of the image	Used by the viewer to adjust the scales
	/metadata	case_id	Get all metadata of the image(width, height, mpp etc.)	Used by dynamic services to get width, height and file location of image
	/md5	case_id	Get MD5 of the image file	Used to check the MD5 to make sure that the image was loaded successfully
POST	/json	metdata	metadata of the image in JSON format	Stored in Mongo(db: Camicroscope, collection: ImageData)

Example of /ImageData

POST

$ curl -H "Content-Type: application/json" -X POST -d '{"case_id": "TCGA-01-0001", "width": 30000, "height": 31000}' http://localhost:9099/Camicroscope/ImageData/json

GET

$ curl http://localhost:9099/Camicroscope/ImageData/fileLocation

/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	N/A	Jsonform template
POST	/json	Form in JSON format(see this)	200 OK

Examples of /uAIMTemplates

Examples of authoring a JSON form can be seen here

Jobs

APIs for posting and retrieving tasks for caMicroscope. It uses Kue(https://github.com/Automattic/kue) to mantain all the tasks. It is well documented.

HTTP Verb	QueryEndpoint	Query Parameters(Input)	Output(Description)
POST	/job	Job data in JSON format	N/A
GET	/job	task_id	N/A

Examples of /Tasks

Example of POSTing a task

$ curl -H "Content-Type: application/json" -X POST -d \
    '{
       "type": "order",
       "data": {
      
       },
       "options" : {
         "attempts": 5,
         "priority": "high"
       }
     }' http://localhost:3000/job

will output:

  {"message": "job created", "id": 3}

This ID can be used to query the status of the job

GET /job/:id

curl http://localhost/job/3

Example of GETting status of a task

{"id":"3","type":"queue","data":{},"priority":-10,"progress":"100","state":"complete","attempts":null,"created_at":"1309973155248","updated_at":"1309973155248","duration":"15002"}

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