lastlegion/cami-docker.md

## cami-docker.md

      
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              cami-docker.md
            
          
    Camicroscope Docker Distribution

Architecture


Application => Viewer
Data => Data
Backend => Loader

Installation

Build images


docker build -t camicroscope_data data/
docker build -t camicroscope_loaders loaders/
docker build -t camicroscope_viewer viewer/

Might wanna grab a coffee and then some because the builds take about an hour.
Running the containers

Data

Set environment variables on host machine for Images and Data directories
export $CAMIC_IMAGES_DIR=<path to images directory>
export $CAMIC_DATA_DIR=<path to data directory>
Set Bindaas port
$CAMIC_BINDAAS_PORT=9099
docker run -itd -p $CAMIC_BINDAAS_PORT:9099 -v $CAMIC_IMAGES_DIR:/data/images -v $CAMIC_DATA_DIR:/data/db camicroscope_data
Run docker inspect to find the IP address for Data container.
we'll use <CAMIC_DATA_IP> as a placeholder
Loaders

Setup environment variables:
$CAMIC_KUE_PORT=5000
$CAMIC_MARKUPLOADER_PORT=6000
$CAMIC_DATALOADER_PORT=6002
Run the container:
docker run -itd  -p $CAMIC_KUE_PORT:3000 -p $CAMIC_MARKUPLOADER_PORT:3001 -p $CAMIC_DATALOADER_PORT:3002 -v $CAMIC_IMAGES_DIR:/data/images -e "dataloader_host=http://<CAMIC_DATA_IP>:9099" -e "annotations_host=http://<CAMIC_DATA_IP>:9099" camicroscope_loaders
Note that -p $CAMIC_KUE_PORT:3000 -p $CAMIC_MARKUPLOADER_PORT:3001 -p $CAMIC_DATALOADER_PORT:3002 is optional
Viewer

Setup environment variables:
$CAMIC_VIEWER_PORT=1337
<HTML_DIRECTORY> is /viewer/html. Provide the absolute path
Run:
docker run -itd -p $CAMIC_VIEWER_PORT:80 -v <HTML_DIRECTORY>/html:/var/www/html -v $CAMIC_IMAGES_DIR:/data/images camicroscope_viewer
You should now be able to load the images and see them
http://localhost:$CAMIC_VIEWER_PORT/camicroscope2/osdCamicroscope.php?tissueId=<Case_ID>


Documentation for Loaders

Data Loader

Dataloader API

Following examples assume $CAMIC_DATALOADER_PORT==32799 and is accessible from the host machine.
POST /submitData

curl -v -F case_id=TCGA-02-0001 -F upload=@TCGA-02-0001-01Z-00-DX1.83fce43e-42ac-4dcd-b156-2908e75f2e47.svs http://localhost:32799/submitData
Return type: json
On success returns: {"status":"success"}
GET /subjectIdExists

curl localhost:32799/subjectIdExists?SubjectUID=TCGA-02-0001
Returns an array with subjectID and file path.
Empty array if subject Id doesnt exist
GET /getMD5ForImage

curl localhost:32799/getMD5ForImage?imageFileName=TCGA-02-0001-01Z-00-DX1.83fce43e-42ac-4dcd-b156-2908e75f2e47.svs
Returns an array with MD5 of the image
[{"md5sum":"418a0724b0a2113bcd2956bacae105b7"}]
Annotation Loader

Examples assume that $CAMIC_MARKUPLOADER_PORT=6000
POST /submitMaskOrder

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
You can track you jobs through Kue.
In the browser you can go to http://localhost:5000 and see the status of the jobID.
Here

mask accepts a mask file
case_id is the image id (the same as dataloader)
execution_id name of the run
width width of the image(extract from dataloader)
height height of the image(extract from dataloader)

Viewer


Open viewer/html/camicroscope/api/Configuration/config.php
Change $baseURL="<DATA_CONTAINER_IP>:9099"