ChRIS reduces the barrier to cloud and distributed computing for researchers and developers. Re-use your existing code with minimal hassle and fuss or quickly create new apps.
Code. Deploy. Replicate. Always.
Run consistent analyses anywhere.
Born of biomedical image science and tempered by scientific workflows, ChRIS is ideal for running any complex analyses on any data almost anywhere. You can run your pipelines of analysis where you want: your local workstation, a local compute cluster, a cloud as well as anywhere and everywhere in between.
Built for researchers - no need to be a cloud computing expert.
Developed with scientific researchers in mind, ChRIS greatly reduces the barrier-to-entry for cloud-based containerized compute. In most cases, a cookie-cutter generated half-page "box" of python code is all that is needed to integrate your existing research analytics within the ChRIS platform.
Focus on your analytics, not on building computing infrastructure.
You focus on your code/analytics. The ChRIS platform takes care of getting the right data to your code where ever it runs. And where is simply anywhere it makes most sense to run your analysis: in a secure hospital environments with direct access to patient data, on a high performance cluster, even out on some cloud with access to huge repositories of public accessible data.
As more and more of our lives become ever intimately impacted by computing,
now more than ever, open source, open standards, and open platforms are
fundamentally important for our research community.
You can make an app for that.
ChRIS makes running your analysis as simple as running a container.
ChRIS guides you through the steps to containerize your complex analytics. Then, behind the scenes, ChRIS launches your app, taking care of connecting your container seamlessly to whatever data it needs and crunching it where it makes most sense. Apps for AI and Deep Learning, apps for reporting and image processing... even plain old workhorse apps that convert data from one format to another. It's all here.
Learn more >
The many faces of ChRIS: from web-GUIs to shell scripts. We've got you covered.
With your new app in hand, you can now link it to other apps in the ecosystem using an intuitive React-based web front end.
Don't worry though -- you can also script up complex workflows in shell and python... even javascript! Fire them up from the comfort and power of your terminal and then hop onto the GUI to see them self-construct visually; or just draw the whole workflow from the beginning to the end in the GUI. Do things your way.
ChRIS is an open, scalable, shareable platform with a beautiful front-end that enables researchers to create, share, and run analytic workflows in the cloud from a growing library of graphical interfaces.
#!/bin/bash
#
source ./ffe.sh
# \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
# start feedflow specification section
# |||||||||||||||||||||||||||||||||||||
#
# The following array declares the specific containers in the workflow
# as well as the arguments to be passed to each. This is a WIP attempt
# to templatize/describe feedflow structure.
#
declare -a a_WORKFLOWSPEC=(
"0:0|
fnndsc/pl-mri10yr06mo01da_normal: ARGS;
--title=BrainMRI_MPC"
"0:1|
fnndsc/pl-freesurfer_pp: ARGS;
--ageSpec=10-06-01;
--copySpec=sag,cor,tra,stats,3D,mri,surf;
--title=FreeSurfer;
--previous_id=@prev_id"
"1:2*_n:l1|
fnndsc/pl-mpcs: ARGS;
--random;
--seed=1;
--posRange=3.0;
--negRange=-3.0;
--title=MultiPartyCompute;
--previous_id=@prev_id"
"2*_n:3*_n:l1|
fnndsc/pl-z2labelmap: ARGS;
--imageSet=../data/set1;
--negColor=B;
--posColor=R;
--title=RegionalHeatMap;
--previous_id=@prev_id"
)
declare -a a_PLUGINS=()
declare -a a_ARGS=()
pluginArray_filterFromWorkflow "a_WORKFLOWSPEC[@]" "a_PLUGINS"
argArray_filterFromWorkflow "a_WORKFLOWSPEC[@]" "a_ARGS"
# ||||||||||||||||||||||||||||||||||
# end feedflow specification section
# //////////////////////////////////
SYNOPSIS="
NAME
RedHatSummit2018.sh
SYNPOSIS
RedHatSummit2018.sh [-l ] \\
[-C ] \\
[-r ] \\
[-p ] \\
[-a ] \\
[-u ] \\
[-w ] \\
[-G ] \\
[-i ] \\
[-s ]
DESC
'RedHatSummit2018.sh' posts a workflow to a CUBE instance that
implements the following:
⬤:0 pl-mri10yr06mo01da_normal
│
│
↓
⬤:1 pl-freesurfer_pp
╱│╲
╱ │ ╲
╱ │ ╲
╱ │ ╲
╱ │ ╲
↓ ↓ ↓
⬤:2 ⬤:4 ⬤:6 pl-mpcs
│ │ │
↓ ↓ ↓
⬤:3 ⬤:5 ⬤:7 pl-z2labelmap
ARGS
[-l ]
Create branches. Default is 3.
[-s ]
Default is '0'. Adds an explicit system ``sleep`` after executing
a plugin. This can be useful in not overloading the ancillary
services when large amount of plugins are being dispatched
concurrently.
[-S]
If specified, save each plugin POST command on the filesystem. Useful
for debugging.
[-G ]
If specified, write two graphviz .dot files called
-nodes.dot
-nodes-args.dot
that describes the workflow in graphviz format. The first dot file
contains only the nodes in the tree, while the second contains the nodes
with graph edges labeled with the CLI args denoting the tranition from
one node to another.
These dot files are suitable for rendering by graphviz parsers, e.g.
http://dreampuf.github.io/GraphvizOnline
http://viz-js.com
[-r ] (http)
[-p ] (8000)
[-a ] (%HOSTIP)
[-u ] (chris)
[-w ] (chris1234)
A set of values to specify the details of the CUBE instance to use
for running the workflow. Each of the above has (defaults) as shown.
This information can also be specified by passing a JSON string with
the [-C ].
Using one of these specific args, however, is generally simpler. Most
often, the [-a ] will be used.
[-C ]
If specified, interpret passed JSON string as the CUBE instance
on which to schedule the run. The default is of the form:
'{
\"protocol\": \"http\",
\"port\": \"8000\",
\"address\": \"%HOSTIP\",
\"user\": \"chris\",
\"password\": \"chris1234\"
}'
Note the single quotes about the structure. The '%HOSTIP' is a special
construct that will be dynamically replaced by the fully qualified IP
of the current host. This is useful in some proxied networks where the
string 'localhost' can be problematic.
EXAMPLES
Typical execution:
$ ./RedHatSummit2018.sh -C '{
\"protocol\": \"http\",
\"port\": \"8000\",
\"address\": \"megalodon.local\",
\"user\": \"chris\",
\"password\": \"chris1234\"
}'
or equivalently:
$ ./RedHatSummit2018.sh -a megalodon.local
"
PROTOCOL="http"
PORT="8000"
ADDRESS="%%HOSTIP"
USER="chris"
PASSWD="chris1234"
CUBE_FMT='{
"protocol": "%s",
"port": "%s",
"address": "%s",
"user": "%s",
"password": "%s"
}'
GRAPHVIZHEADER='digraph G {
rankdir="LR";
subgraph cluster_0 {
style=filled;
color=lightgrey;
label = "ChRIS COVID-NET Graph";
node [style=filled,fillcolor=white,fontname="mono",fontsize=8];
edge [fontname="mono", fontsize=8];
'
GRAPHVIZBODY=""
GRAPHVIZBODYARGS=""
declare -i b_respSuccess=0
declare -i b_respFail=0
declare -i STEP=0
declare -i b_CUBEjson=0
declare -i b_graphviz=0
declare -i sleepAfterPluginRun=0
declare -i b_saveCalls=0
IMAGESTOPROCESS=""
GRAPHVIZFILE=""
declare -i branches=3
while getopts "C:G:l:xr:p:a:u:w:s:S" opt; do
case $opt in
C) b_CUBEjson=1
CUBEJSON=$OPTARG ;;
l) branches=$OPTARG ;;
G) b_graphviz=1
GRAPHVIZFILE=$OPTARG ;;
S) b_saveCalls=1 ;;
s) sleepAfterPluginRun=$OPTARG ;;
r) PROTOCOL=$OPTARG ;;
p) PORT=$OPTARG ;;
a) ADDRESS=$OPTARG ;;
u) USER=$OPTARG ;;
w) PASSWD=$OPTARG ;;
x) echo "$SYNOPSIS"; exit 0 ;;
*) exit 1 ;;
esac
done
CUBE=$(printf "$CUBE_FMT" "$PROTOCOL" "$PORT" "$ADDRESS" "$USER" "$PASSWD")
if (( b_CUBEjson )) ; then
CUBE="$CUBEJSON"
fi
ADDRESS=$(echo $CUBE | jq -r .address)
# Global variable that contains the "current" ID returned
# from a call to CUBE
ID="-1"
title -d 1 "Checking on required dependencies..."
boxcenter "Verify that various command line tools needed to construct this "
boxcenter "workflow exist on the UNIX path. If any of the below files are "
boxcenter "not found, please install them according to the requirements of "
boxcenter "your OS. "
boxcenter ""
dep_check "jq,chrispl-search,chrispl-run,http"
windowBottom
if (( b_respFail > 0 )) ; then exit 4 ; fi
title -d 1 "Checking for plugin IDs on CUBE...." \
"(ids below denote plugin ids)"
#
# This section queries CUBE for IDs of all plugins in the plugin
# array structure.
#
# If any failures were flagged, the script will exit.
#
b_respSuccess=0
b_respFail=0
boxcenter "Verify that all the plugins that constitute this workflow are "
boxcenter "registered to the CUBE instance with which we are communicating."
boxcenter ""
for plugin in "${a_PLUGINS[@]}" ; do
cparse $plugin "REPO" "CONTAINER" "MMN" "ENV"
opBlink_feedback "$ADDRESS:$PORT" "::CUBE->$plugin" \
"op-->" "search"
windowBottom
RESP=$(
chrispl-search --for id \
--using name="$CONTAINER" \
--onCUBE "$CUBE"
)
opRet_feedback "$?" \
"$ADDRESS:$PORT" "::CUBE->$plugin" \
"result-->" "pid = $(echo $RESP | awk '{print $3}')"
done
postQuery_report
windowBottom
if (( b_respFail > 0 )) ; then exit 2 ; fi
title -d 1 "Start constructing the Feed by POSTing the root FS and next nodes..."
ROOTID=-1
retState=""
filesInNode=""
dcmFiles=""
# Post the root node, wait for it to finish, and
# collect a list of output files
boxcenter "Run the root and first nodes in series. "
boxcenter ""
windowBottom
#\\\\\\\\\\\\\\\\\\
# Core logic here ||
plugin_run "0:0" "a_WORKFLOWSPEC[@]" "$CUBE" ROOTID \
$sleepAfterPluginRun && id_check $ROOTID
# waitForNodeState "$CUBE" "finishedSuccessfully" $ROOTID retState
# dataInNode_get fname "$CUBE" $ROOTID filesInNode
plugin_run "0:1" "a_WORKFLOWSPEC[@]" "$CUBE" ID1 \
$sleepAfterPluginRun "@prev_id=$ROOTID" && id_check $ID1
digraph_add "GRAPHVIZBODY" "GRAPHVIZBODYARGS" ":0;$ROOTID" ":1;$ID1" \
"a_WORKFLOWSPEC[@]"
# Core logic here ||
#///////////////////
windowBottom
title -d 1 "Build the branching structure workflow..."
boxcenter "Construct and run each branch, one per MPC comparison. "
boxcenter ""
# Now the branch(es)
b_respSuccess=1
b_respFail=0
boxcenter ""
boxcenter ""
for LOOP in $(seq 1 $branches); do
echo -en "\033[2A\033[2K"
boxcenter ""
boxcenter "Building prediction branch $LOOP..." ${LightGray}
boxcenter ""
boxcenter ""
plugin_run ":2" "a_WORKFLOWSPEC[@]" "$CUBE" ID2 $sleepAfterPluginRun \
"@prev_id=$ID1" && id_check $ID2
digraph_add "GRAPHVIZBODY" "GRAPHVIZBODYARGS" ":1;$ID1" ":2;$ID2" \
"a_WORKFLOWSPEC[@]"
plugin_run ":3" "a_WORKFLOWSPEC[@]" "$CUBE" ID3 $sleepAfterPluginRun \
"@prev_id=$ID2" && id_check $ID3
digraph_add "GRAPHVIZBODY" "GRAPHVIZBODYARGS" ":2;$ID2" ":3;$ID3" \
"a_WORKFLOWSPEC[@]"
done
echo -en "\033[2A\033[2K"
postRun_report
windowBottom
if (( b_respFail > 0 )) ; then exit 3 ; fi
if (( b_graphviz )) ; then
graphVis_printFile "$GRAPHVIZHEADER" \
"$GRAPHVIZBODY" \
"$GRAPHVIZBODYARGS" \
"$GRAPHVIZFILE"
fi
Through our strong partnership with Red Hat and the Mass Open Cloud (MOC), you can deploy workflows to the MOC — while still maintaining ownership of your own data.