updated to use docker-compose for fully local development environment

.dockerignore

@@ -0,0 +1,5 @@
+ui
+handler
+workdir
+test
+bids-specification

Dockerfile

@@ -0,0 +1,9 @@
+FROM node:16
+
+COPY . /app
+
+WORKDIR /app
+RUN npm install -g pm2 typescript
+
+RUN npm install
+

README.md

@@ -99,5 +99,11 @@ We ask that you the following articles when publishing papers that used data, co
 
 1. Avesani, P., McPherson, B., Hayashi, S. et al. The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Sci Data 6, 69 (2019). [https://doi.org/10.1038/s41597-019-0073-y](https://doi.org/10.1038/s41597-019-0073-y)
 
+### This repo was bootstrapped by
+
+```
+npm init vite@latest ui2 -- --template vue-ts
+```
+
 Copyright © 2020 brainlife.io at University of Texas at Austin and Indiana University
 

api/controllers.ts

@@ -29,7 +29,7 @@ router.get('/health', (req, res, next) => {
         status = "failed";
         message = err;
     }
-    res.json({status, message});
+    res.json({status, message, date: new Date()});
 });
 
 router.post('/session', (req, res, next)=>{

api/dev.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+tsc --watch &
+pm2 start ezbids.js --attach --watch --ignore-watch="*.log test *.sh ui bin example .git **/*.ts"

dev.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+set -ex
+
+git submodule update --init --recursive
+
+(cd api && npm install)
+(cd ui && npm install)
+
+mkdir -p /tmp/upload
+mkdir -p /tmp/workdir
+
+#docker-compose up --build
+docker-compose up
+
+

docker-compose.yml

@@ -0,0 +1,67 @@
+version: "3"
+
+services:
+
+  mongodb:
+    image: mongo:4.4.15
+    volumes: 
+      - /data/db
+    healthcheck:
+      test: echo 'db.runCommand("ping").ok' | mongo localhost:27017/test --quiet
+      interval: 10s
+      timeout: 10s
+      retries: 5
+    ports:
+      - 27417:27017 #for local debuggin
+
+  api:
+    build: .
+    volumes:
+      - ./api:/app/api
+      - /tmp:/tmp
+    depends_on:
+      mongodb:
+        condition: service_healthy
+    healthcheck:
+        test: ["CMD", "curl", "-f", "http://localhost:8080/health"]
+    working_dir: /app/api
+    command: ./dev.sh
+    ports:
+      - 8082:8080
+
+  handler:
+    build: ./handler
+    volumes:
+      - .:/app
+      - /tmp:/tmp
+    depends_on:
+      mongodb:
+        condition: service_healthy
+    tty:
+        true #turn on color for bids-validator output
+    command: pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules"
+
+  ui:
+    build: ./ui
+    volumes:
+      - ./ui/src:/ui/src #don't copy node_modules which might be compiled for mac (vite won't work)
+    environment:
+      VITE_APIHOST: http://localhost:8082
+    healthcheck:
+        test: ["CMD", "curl", "-f", "http://localhost:3000"]
+    ports:
+      - 3000:3000
+
+#  nginx:
+#    image: nginx:1.18
+#    depends_on:
+#      api:
+#        condition: service_healthy
+#      ui:
+#        condition: service_healthy
+#    volumes:
+#      - ./config/nginx/nginx.conf:/etc/nginx/nginx.conf
+#    ports:
+#      - 8082:80
+
+

handler/container/Dockerfile → handler/Dockerfile

@@ -1,5 +1,3 @@
-#FROM ubuntu:20.04
-#FROM brainlife/fsl-mini:6.0.3
 FROM neurodebian:nd20.04-non-free
 
 ENV DEBIAN_FRONTEND noninteractive
@@ -28,18 +26,22 @@ RUN . $FSLDIR/etc/fslconf/fsl.sh
 ENV FSLOUTPUTTYPE=NIFTI_GZ
 
 #make sure fslpython is properly installed
-RUN which imcp
+#RUN which imcp
 
 RUN apt install -y curl
 RUN curl -fsSL https://deb.nodesource.com/setup_14.x | bash -
 RUN apt install -y nodejs
 
 # Get dcm2niix from github and compile
-RUN cd /tmp && \
-    git clone https://github.com/rordenlab/dcm2niix.git -b v1.0.20211006 && \
-    cd dcm2niix && mkdir build && cd build && \
-    cmake -DBATCH_VERSION=ON -DUSE_OPENJPEG=ON .. && \
-    make && make install
+#RUN cd /tmp && \
+#    git clone https://github.com/rordenlab/dcm2niix.git -b v1.0.20211006 && \
+#    cd dcm2niix && mkdir build && cd build && \
+#    cmake -DBATCH_VERSION=ON -DUSE_OPENJPEG=ON .. && \
+#    make && make install
+
+RUN wget https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20220720/dcm2niix_lnx.zip -O /tmp/dcm2niix_lnx.zip
+RUN unzip /tmp/dcm2niix_lnx.zip
+RUN mv dcm2niix /usr/local/bin
 
 # Get bids-specification from github
 RUN cd && git clone https://github.com/bids-standard/bids-specification
@@ -51,7 +53,9 @@ RUN pip3 install numpy nibabel pandas==1.0.1 matplotlib pyyaml==5.4.1 natsort #n
 RUN pip3 install quickshear
 
 #install ROBEX
-COPY ROBEXv12.linux64.tar.gz /
+#COPY ROBEXv12.linux64.tar.gz /
+ADD https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1 /
+RUN ls -la
 RUN tar -xzf /ROBEXv12.linux64.tar.gz
 ENV PATH=$PATH:/ROBEX
 
@@ -61,8 +65,11 @@ RUN pip3 install pydeface
 RUN rm /bin/sh && ln -s /bin/bash /bin/sh
 
 #install bids-validator
-RUN npm install -g [email protected].3
+RUN npm install -g [email protected].6
 
 RUN apt-get install -y rename zstd
 
 WORKDIR /app/handler
+RUN npm install -g pm2 #for dev
+
+

ui/Dockerfile

@@ -0,0 +1,8 @@
+FROM node:16
+
+COPY . /ui
+WORKDIR /ui
+
+RUN npm install
+
+CMD [ "npm", "run", "dev" ]