PR for everything I've done so far on my fork

demo.m

@@ -0,0 +1,13 @@
+
+addpath(getenv('SCA_SERVICE_DIR'))
+addpath(genpath('/N/u/hayashis/Karst/life/vistasoft-master'))
+addpath(genpath('./data'))
+
+life_demo()
+
+saveas(ans(0), 'figure0.png')
+saveas(ans(1), 'figure1.png')
+saveas(ans(2), 'figure2.png')
+saveas(ans(3), 'figure3.png')
+saveas(ans(4), 'figure4.png')
+saveas(ans(5), 'figure5.png')

package.json

@@ -0,0 +1,25 @@
+{
+  "name": "sca-service-life",
+  "version": "1.0.0",
+  "description": "run life demo application",
+  "main": "index.js",
+  "directories": {
+    "test": "test"
+  },
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1",
+    "start": "start.sh",
+    "stop": "stop.sh",
+    "status": "status.sh"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/soichih/sca-service-life.git"
+  },
+  "author": "Soichi Hayashi <[email protected]>",
+  "license": "ISC",
+  "bugs": {
+    "url": "https://github.com/soichih/sca-service-life/issues"
+  },
+  "homepage": "https://github.com/soichih/sca-service-life#readme"
+}

scripts/life_demo.m

@@ -61,6 +61,7 @@
 % This helps speeding up computations espacially for large conenctomes.
 feOpenLocalCluster;
 
+
 %% Build the file names for the diffusion data, the anatomical MRI.
 dwiFile       = fullfile(lifeDemoDataPath('diffusion'),'life_demo_scan1_subject1_b2000_150dirs_stanford.nii.gz');
 dwiFileRepeat = fullfile(lifeDemoDataPath('diffusion'),'life_demo_scan2_subject1_b2000_150dirs_stanford.nii.gz');
@@ -76,13 +77,17 @@
 % The final connectome and data astructure will be saved with this name:
 feFileName    = 'life_build_model_demo_CSD_PROB';
 
+webwrite(getenv('SCA_PROGRESS_URL'), struct('msg','Initializing the LiFE model structure','progress', 0), weboptions('MediaType','application/json'));
+
 %% (1.1) Initialize the LiFE model structure, 'fe' in the code below. 
 % This structure contains the forward model of diffusion based on the
 % tractography solution. It also contains all the information necessary to
 % compute model accuracry, and perform statistical tests. You can type
 % help('feBuildModel') in the MatLab prompt for more information.
 fe = feConnectomeInit(dwiFile,fgFileName,feFileName,[],dwiFileRepeat,t1File);
 
+webwrite(getenv('SCA_PROGRESS_URL'), struct('msg','Fitting the model','progress', 0.25), weboptions('MediaType','application/json'));
+
 %% (1.2) Fit the model. 
 % Hereafter we fit the forward model of tracrography using a least-squared
 % method. The information generated by fitting the model (fiber weights
@@ -110,6 +115,8 @@
 % fascicle in the connectome.
 prob.w      = feGet(fe,'fiber weights');
 
+webwrite(getenv('SCA_PROGRESS_URL'), struct('msg','Plotting graphs','progress', 0.4), weboptions('MediaType','application/json'));
+
 %% (1.7) Plot a histogram of the RMSE. 
 % We plot the histogram of  RMSE across white-mater voxels.
 [fh(1), ~, ~] = plotHistRMSE(prob);
@@ -121,6 +128,9 @@
 
 %% (1.9) Plot a histogram of the fitted fascicle weights. 
 [fh(3), ~] = plotHistWeights(prob);
+
+webwrite(getenv('SCA_PROGRESS_URL'), struct('msg','Initializing the LiFE model structure (2)','progress', 0.5), weboptions('MediaType','application/json'));
+
 fe = feConnectomeInit(dwiFile,fgFileName,feFileName,[],dwiFileRepeat,t1File);
 
 %% Extract the coordinates of the white-matter voxels
@@ -143,6 +153,7 @@
 % tractography solution. It also contains all the information necessary to
 % compute model accuracry, and perform statistical tests. You can type
 % help('feBuildModel') in the MatLab prompt for more information.
+webwrite(getenv('SCA_PROGRESS_URL'), struct('msg','Initializing the LiFE model structure (3)','progress', 0.7), weboptions('MediaType','application/json'));
 fe = feConnectomeInit(dwiFile,fgFileName,feFileName,[],dwiFileRepeat,t1File);
 
 %% (2.2) Fit the model. 
@@ -172,6 +183,8 @@
 % fascicle in the connectome.
 det.w      = feGet(fe,'fiber weights');
 
+webwrite(getenv('SCA_PROGRESS_URL'), struct('msg','Plotting graphs (2)','progress', 0.8), weboptions('MediaType','application/json'));
+
 %% (2.7) Plot a histogram of the RMSE. 
 % We plot the histogram of  RMSE across white-mater voxels.
 [fh(1), ~, ~] = plotHistRMSE(det);
@@ -219,6 +232,8 @@
 det.rmse       = det.rmse( det.coordsIdx);
 clear p d
 
+webwrite(getenv('SCA_PROGRESS_URL'), struct('msg','Plotting graphs (3)','progress', 0.95), weboptions('MediaType','application/json'));
+
 %% (3.2) Make a scatter plot of the RMSE of the two tractography models
 fh(4) = scatterPlotRMSE(det,prob);
 
@@ -238,6 +253,8 @@
 % Movers Distance between the distributions.
 fh(6) = distributionPlotEarthMoversDistance(se);
 
+webwrite(getenv('SCA_PROGRESS_URL'), struct('msg','Completed','progress', 1), weboptions('MediaType','application/json'));
+
 end
 
 % ---------- Local Plot Functions ----------- %

start.sh

@@ -0,0 +1,142 @@
+#!/bin/bash
+
+#make sure jq is installed on $SCA_SERVICE_DIR
+if [ ! -f $SCA_SERVICE_DIR/jq ];
+then
+        echo "installing jq"
+        wget https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64 -O $SCA_SERVICE_DIR/jq
+        chmod +x $SCA_SERVICE_DIR/jq
+fi
+
+#patch libssl issue caused by some module overriding libpath
+unset LD_LIBRARY_PATH
+
+#TODO - clean.sh?
+echo "clean up from previous run"
+rm products.json
+rm finished 
+
+#find out which environment we are in
+hostname | grep karst > /dev/null
+if [ $? -eq 0 ]; then
+    execenv=karst 
+fi
+echo $HOME | grep -i bigred > /dev/null
+if [ $? -eq 0 ]; then
+    execenv=bigred
+fi
+
+#create pbs script
+if [ $execenv == "karst" ]; then
+    cat <<EOT > task.pbs
+#!/bin/bash
+#PBS -l nodes=1:ppn=16:dc2
+#PBS -l walltime=1:00:00
+#PBS -N sca-service-life
+#PBS -V
+#Karst
+EOT
+fi
+
+if [ $execenv == "bigred" ]; then
+    cat <<EOT > task.pbs
+#!/bin/bash
+#PBS -l nodes=1:ppn=32:dc2
+#PBS -l walltime=1:00:00
+#PBS -l gres=ccm
+#PBS -N lifedemo
+#PBS -V
+#BigRed2
+EOT
+fi
+
+cat <<EOT >> task.pbs
+
+#fixing .module sometimes causes curl / git to fail
+unset LD_LIBRARY_PATH
+
+curl -X POST -H "Content-Type: application/json" -d "{\"progress\": 0, \"status\": \"running\"}" $SCA_PROGRESS_URL
+
+cd \$PBS_O_WORKDIR
+
+#data might be already staged if user is rerunning this
+#but.. sometime data could get corrupted.. so let's remove it for now.
+rm -rf data
+
+#if [ ! -d data ]
+#then
+    echo "untarring input data"
+    input_task_id=`$SCA_SERVICE_DIR/jq -r '.input_task_id' config.json`
+    filename=`$SCA_SERVICE_DIR/jq -r '.files[0] .filename' config.json`
+
+    curl -X POST -H "Content-Type: application/json" -d "{\"msg\":\"Untarring \$filename\"}" $SCA_PROGRESS_URL
+    tar -xzf ../\$input_task_id/\$filename
+#fi
+EOT
+
+#create pbs script
+if [ $execenv == "karst" ]; then
+    cat <<EOT >> task.pbs
+curl -X POST -H "Content-Type: application/json" -d "{\"msg\":\"running matlab\"}" $SCA_PROGRESS_URL
+
+module load matlab
+matlab -nodisplay -nosplash < $SCA_SERVICE_DIR/demo.m
+ret=\$?
+#fix LD_LIBRARY_PATH so that curl works
+unset LD_LIBRARY_PATH
+EOT
+fi
+
+if [ $execenv == "bigred" ]; then
+    cat <<EOT >> task.pbs
+curl -X POST -H "Content-Type: application/json" -d "{\"msg\":\"running matlab with ccmrun\"}" $SCA_PROGRESS_URL
+
+module load matlab
+module load ccm
+ccmrun matlab -nodisplay -nosplash < $SCA_SERVICE_DIR/demo.m
+ret=\$?
+#fix broken curl due to matlab
+#export LD_LIBRARY_PATH=/usr/lib64/:\$LD_LIBRARY_PATH
+unset LD_LIBRARY_PATH
+EOT
+fi
+
+#rest is about the same for everyone
+cat <<EOT >> task.pbs
+
+if [ \$ret -eq 0 ]
+then
+    status="finished"
+    msg="Successfully ran lifedemo"
+
+    #output products.json (should be part of the life_demo)
+    cat <<EOTP > products.json
+[
+    {
+        "type": "soichih/life/out",
+        "graphs": {
+             "error_distribution": {"filename": "figure1.png", "type": "image/png"},
+             "error_ratio": {"filename": "figure2.png", "type": "image/png"},
+             "fascicles": {"filename": "figure3.png", "type": "image/png"},
+             "heat": {"filename": "figure4.png", "type": "image/png"},
+             "evidence":  {"filename": "figure5.png", "type": "image/png"}
+         }
+    }
+]
+EOTP
+
+else
+    status="failed"
+    msg="lifedemo returned code:\$ret"
+fi
+
+curl -X POST -H "Content-Type: application/json" -d "{\"status\": \"\$status\", \"msg\":\"\$msg\"}" $SCA_PROGRESS_URL
+
+echo \$ret > finished
+exit \$ret #tell pbs the return code?
+EOT
+
+jobid=`qsub task.pbs`
+echo $jobid > jobid
+curl -X POST -H "Content-Type: application/json" -d "{\"status\": \"waiting\", \"progress\": 0, \"msg\":\"Job: $jobid Waiting in PBS queue on $execenv\"}" $SCA_PROGRESS_URL
+

status.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+
+#return code 0 = running
+#return code 1 = finished successfully
+#return code 2 = failed
+
+##now wait for running to go away
+#progress_url={$SCA_PROGRESS_URL}/{$SCA_PROGRESS_KEY}
+
+if [ -f finished ]; then
+    code=`cat finished`
+    if [ $code -eq 0 ]; then
+        echo "finished successfully"
+        exit 1 #success!
+    else
+        echo "finished with code:$code"
+        exit 2 #failed
+    fi
+fi
+
+#if [ -f started ]; then
+#    echo "running"
+#    exit 0 #running!
+#fi
+
+if [ -f jobid ]; then
+    jobid=`cat jobid`
+    jobstate=`qstat -f $jobid | grep job_state | cut -b17`
+    if [ $jobstate == "Q" ]; then
+        echo "Waiting in the queue"
+        eststart=`showstart $jobid | grep start`
+        curl -X POST -H "Content-Type: application/json" -d "{\"msg\":\"Waiting in the PBS queue : $eststart\"}" $SCA_PROGRESS_URL
+        exit 0 #running!
+    fi
+    if [ $jobstate == "R" ]; then
+        echo "Running"
+        exit 0 #running!
+    fi
+
+    #assume failed for all other state
+    echo "Jobs failed - PBS job state: $jobstate"
+    exit 2
+fi
+
+echo "can't determine the status!"
+exit 3
+
+#echo "running.job.id is gone.. job must have finished"
+#code=`cat exit.code`
+#curl -X POST -H "Content-Type: application/json" -d "{\"status\": \"finished\", \"msg\":\"lifedemo ended with code:$code\"}" $progress_url
+#echo "job finished with code $code"
+#exit $code

stop.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+#if [ -f finished ]; then
+#    echo "can't stop job that's already finished"
+#    exit 1
+#fi
+
+jobid=`cat jobid`
+echo "running qdel $jobid"
+qdel $jobid