Merge pull request #274 from SynBioDex/synbio-suite-repair

Merge synbio-suite branch into final

.gitignore

@@ -0,0 +1,3 @@
+desktop.ini
+*.war
+*.class

Dockerfile

@@ -1,49 +1,46 @@
-FROM node:12-alpine
-
-RUN apk add openjdk8 bash
-
-ENV JAVA_HOME=/usr/lib/jvm/java-1.8-openjdk
-ENV PATH="$JAVA_HOME/bin:${PATH}"
-
-WORKDIR /opt/backend
-
-COPY . .
-
-# This should be in the Dockerfile, but for now it's a script
-RUN resources/build_automation/build_backend.sh
-
-## Build angular stuff and copy into WEB-INF
-RUN apk add --update nodejs npm
-RUN npm install -g @angular/cli
-RUN apk add git
-
-WORKDIR ./SBOLCanvasFrontend
-RUN npm install
-RUN npm rebuild node-sass
-RUN node --max-old-space-size=8192
-RUN npm run prebuild.prod
-RUN ng build --prod --build-optimizer --vendor-chunk --progress --output-hashing=all --stats-json --source-map=true --base-href=/canvas/
-
-#RUN resources/build_automation/build_frontend.sh
-
-# New container
-FROM tomcat:9.0-jdk8-openjdk
-
-# Copy backend
-COPY --from=0 /opt/backend/SBOLCanvasBackend/WebContent/api.war webapps
-
-# Copy frontend
-COPY --from=0 /opt/backend/SBOLCanvasFrontend/dist/SBOLCanvasFrontend webapps/canvas
-
-# Copying configs for tomcat
-ARG TOMCAT_AUTOMATION_DIR=/opt/backend/resources/server_automation/tomcat
-#COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/tomcat-users.xml ${TOMCAT_AUTOMATION_DIR}/base_config_files/web.xml conf/
-#COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/server.xml conf/
-#COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/manager-context.xml webapps/manager/META-INF/context.xml 
-#COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/host-manager-context.xml webapps/host-manager/META-INF/context.xml 
-COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/ROOT_config/index.jsp webapps/ROOT/index.jsp 
-
-COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_context.html webapps/canvas/META-INF/context.html 
-COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_rewrite.config webapps/canvas/WEB-INF/rewrite.config 
-COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_web.xml webapps/canvas/WEB-INF/web.xml 
-
+FROM node:12-alpine as frontend-build
+
+RUN apk add git
+
+# copy files -- need to copy whole repo for gitversion
+COPY . /opt/canvas
+
+# build frontend
+WORKDIR /opt/canvas/SBOLCanvasFrontend
+RUN npm install
+RUN npm run gitversion
+RUN npm run build
+
+
+FROM tomcat:9.0-jdk8-openjdk as server
+
+# copy backend files
+WORKDIR /opt/backend
+COPY SBOLCanvasBackend .
+
+# make directories
+RUN mkdir -p WebContent/WEB-INF/classes
+
+# compile java files
+RUN javac -source 1.8 -target 1.8 -sourcepath src -d WebContent/WEB-INF/classes -cp ".:WebContent/WEB-INF/lib/*:/usr/local/tomcat/lib/*" src/**/*.java
+
+# build WAR file -- directly into tomcat webapps directory
+RUN jar -cf /usr/local/tomcat/webapps/api.war WebContent/*
+
+
+WORKDIR /usr/local/tomcat
+
+# copy built frontend files
+COPY --from=frontend-build /opt/canvas/SBOLCanvasFrontend/dist webapps/canvas
+
+# copy configs for tomcat
+ARG TOMCAT_AUTOMATION_DIR=resources/server_automation/tomcat
+# COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/tomcat-users.xml ${TOMCAT_AUTOMATION_DIR}/base_config_files/web.xml conf/
+# COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/server.xml conf/
+# COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/manager-context.xml webapps/manager/META-INF/context.xml 
+# COPY --from=0 ${TOMCAT_AUTOMATION_DIR}/base_config_files/host-manager-context.xml webapps/host-manager/META-INF/context.xml 
+COPY ${TOMCAT_AUTOMATION_DIR}/ROOT_config/index.jsp webapps/ROOT/index.jsp 
+
+COPY ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_context.html webapps/canvas/META-INF/context.html 
+COPY ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_rewrite.config webapps/canvas/WEB-INF/rewrite.config 
+COPY ${TOMCAT_AUTOMATION_DIR}/frontend_config_files/frontend_web.xml webapps/canvas/WEB-INF/web.xml 

README.md

@@ -1,16 +1,83 @@
-SBOLCavas is a web application for creation and editing of genetic constructs using the SBOL data and visual standard. SBOLCanvas allows a user to create a genetic design from start to finish, with the option to incorporate existing SBOL data from a SynBioHub repository. SBOLCanvas is created as part of [SynBioKS](https://synbioks.github.io/).
 
-### DOCKER:
+# SBOLCanvas
 
--SBOLCanvas is a dockerized application and can be found at the repository synbiohub/sbolcanvas. A github action is configured so that upon a commit into the main branch 'final' a new image will be built and pushed to Docker Hub. A running instance of the application can be found at http://canvas.synbioks.org/canvas/
+SBOLCanvas is a web application for creation and editing of genetic constructs using the SBOL data and visual standard. SBOLCanvas allows a user to create a genetic design from start to finish, with the option to incorporate existing SBOL data from a SynBioHub repository. SBOLCanvas is created as part of SynBioKS.
 
-#### To build & run the docker image locally:<br/>
-(from the top level directory of this repository)<br/>
--$docker build -t sbolcanvas/sbolcanvas .<br/>
--$docker run -p 8080:8080 sbolcanvas/sbolcanvas:latest
+## SynBioSuite Branch
 
-#### To run the latest version on the dockerhub repository locally:<br/>
--$docker run --rm -p 8080:8080 synbiohub/sbolcanvas
+This branch is specifically for SBOLCanvas as embedded in the [SynBioSuite app](https://github.com/MyersResearchGroup/SynBioSuite);
+however, it can still function as a standalone application. 
+## Repository Structure
 
-#### To run the current release on the dockerhub repository locally:<br/>
--$docker run --rm -p 8080:8080 synbiohub/sbolcanvas:1.2.0 
+This is a monorepo containing an Angular app as a frontend (in the frontend directory)
+and a Dockerized Java API (in the backend directory) that handles things like 
+conversion, communication with SynBioHub, etc.
+
+This differs from the *final* branch, which Dockerizes the frontend and backend
+together, and serves the Angular app from the backend.
+
+The changes made were an optimization to allow the API to be deployed serverlessly
+and the frontend to be deployed as a static web app served from CDNs. 
+## Run Locally
+
+Clone the project
+
+```bash
+git clone -b synbio-suite https://github.com/SynBioDex/SBOLCanvas
+```
+
+Go to the backend directory
+
+```bash
+cd SBOLCanvas/backend
+```
+
+Ensure you have nodemon installed
+
+```bash
+npm install -g nodemon
+```
+
+Run nodemon to build and run the backend in a container
+
+```bash
+npx nodemon
+```
+
+Go to the frontend directory
+
+```bash
+cd ../SBOLCanvas/frontend
+```
+
+Install dependencies
+
+```bash
+npm install
+```
+
+Start the Angular development server
+
+```bash
+npm run dev
+```
+## Deployment
+
+To build the frontend, from the frontend directory, run
+
+```bash
+npm run build
+```
+
+The built output will be available in frontend/dist and can be deployed anywhere
+a static web app can be deployed. Genetic Logic Lab's weapon of choice is 
+[Azure Static Web Apps](https://azure.microsoft.com/en-us/products/app-service/static/).
+
+To build the backend, from the backend directory, run
+
+```bash
+docker build -t sbolcanvas .
+```
+
+The resulting Docker image can be deployed anywhere you can run Docker containers.
+Genetic Logic Lab uses [Azure Container Apps](https://azure.microsoft.com/en-us/products/container-apps/).

SBOLCanvasBackend/WebContent/META-INF/MANIFEST.MF

@@ -1,3 +1,2 @@
 Manifest-Version: 1.0
-Class-Path: 
-
+Class-Path: 

SBOLCanvasBackend/src/data/InteractionInfo.java

@@ -65,7 +65,7 @@ public Hashtable<String, String> getTargetRefinement() {
 	}
 
 	public void setTargetRefinement(Hashtable<String, String> targetRefinement) {
-		this.targetRefinement = targetRefinement;
+		this.targetRefinement = targetRefinement; 
 	}
 
 	public Hashtable<String, String> getFromURI() {