Devex

.dockerignore

@@ -0,0 +1,2 @@
+logs/
+wildbook-data/

Dockerfile

@@ -0,0 +1,78 @@
+# Stage 1: Build Wildbook WAR
+FROM maven:3.9.6-eclipse-temurin-21 AS build
+
+# Install build-essential, Node.js and npm
+# build-essential is needed for some native npm modules
+RUN apt-get update && \
+  apt-get install -y build-essential curl gnupg && \
+  curl -fsSL https://deb.nodesource.com/setup_18.x | bash - && \
+  apt-get install -y nodejs rsync && \
+  apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Set working directory to the application root
+WORKDIR /app
+
+COPY local-repo /app/local-repo
+
+# Copy pom.xml and download Maven dependencies
+COPY pom.xml ./
+RUN mvn verify clean --fail-never
+
+COPY ./frontend /app/frontend
+COPY ./src/main/webapp/javascript /app/src/main/webapp/javascript
+
+WORKDIR /app/frontend
+ENV PUBLIC_URL=/react/
+ENV SITE_NAME="Wildbook"
+RUN npm install react-app-rewired
+RUN npm ci
+RUN npm run build
+RUN mkdir -p /app/src/main/webapp/react && rsync -a ./build/ /app/src/main/webapp/react/
+
+WORKDIR /app
+COPY . .
+# Build the WAR file, skipping tests and front end build for faster build
+ENV SKIP_FRONTEND_BUILD=true
+RUN mvn -T 4 clean install -DskipTests -Dmaven.antrun.skip=true
+
+
+# Stage 2: Deploy to Tomcat
+FROM tomcat:9.0.113-jre17-temurin-jammy
+
+# Install envsubst for environment variable substitution
+RUN apt-get update && apt-get install -y gettext-base imagemagick && rm -rf /var/lib/apt/lists/*
+
+
+# Create staging location for config files (seeded into mounted volume at runtime)
+RUN mkdir -p /opt/wildbook_seed/WEB-INF/classes/bundles
+
+# Create empty AnnotationLiteCache.json file with valid JSON to prevent startup warning
+# RUN echo '{}' > /usr/local/tomcat/webapps/wildbook_data_dir/WEB-INF/AnnotationLiteCache.json
+
+# Set environment variables for runtime configuration
+ENV JAVA_OPTS="-Djava.awt.headless=true -Xms4096m -Xmx4096m"
+
+# Copy config and bundle files to staging location (seeded into mounted volume at runtime)
+COPY --from=build /app/src/main/resources/bundles/ /opt/wildbook_seed/WEB-INF/classes/bundles/
+
+# Copy Docker-specific configuration files to staging
+COPY ./devops/development/.dockerfiles/tomcat/server.xml /usr/local/tomcat/conf/server.xml
+COPY ./devops/development/.dockerfiles/tomcat/watermark.png /usr/local/tomcat/watermark.png
+COPY ./devops/development/.dockerfiles/tomcat/IA-wbia.json /opt/wildbook_seed/WEB-INF/classes/bundles/IA.json
+COPY ./devops/development/.dockerfiles/tomcat/IA-wbia.properties /opt/wildbook_seed/WEB-INF/classes/bundles/IA.properties
+COPY ./devops/development/.dockerfiles/tomcat/commonConfiguration.properties /opt/wildbook_seed/WEB-INF/classes/bundles/commonConfiguration.properties
+COPY ./devops/development/.dockerfiles/tomcat/jdoconfig.properties.template /opt/wildbook_seed/WEB-INF/classes/bundles/jdoconfig.properties.template
+
+
+# Copy the built WAR file from the build stage to Tomcat's webapps directory as ROOT.war
+COPY --from=build /app/target/wildbook-*.war /usr/local/tomcat/webapps/ROOT.war
+
+# Copy startup script
+COPY ./devops/development/.dockerfiles/tomcat/wildbook-start.sh /usr/local/bin/wildbook-start.sh
+RUN chmod +x /usr/local/bin/wildbook-start.sh
+
+# Expose the port on which Tomcat will run
+EXPOSE 8080
+
+# Use custom startup script
+CMD ["/usr/local/bin/wildbook-start.sh"]

README.md

@@ -9,75 +9,54 @@ Wildbook is an open source software framework to support mark-recapture, molecul
 - provides a platform for animal biometrics that supports easy data access and facilitates matching application deployment for multiple species
 
 ## Getting Started with Wildbook
-Wildbook is a long-standing tool that support a wide variety of researchers and species. The Wild Me team is working on revamping the tool as a true open source project, so if you have ideas and are excited to help, reach out to us on the [Wild Me Development Discord](https://discord.gg/zw4tr3RE4R)!
 
-## Pull Request Workflow
-All contributions should be made from a fork off of the Wildbook repo. While there are a number of repositories for specific Wildbook communities, large scale development is driven from the main repository. 
+Wildbook is a long-standing tool that support a wide variety of researchers and species. 
+The Wild Me team is working on revamping the tool as a true open source project, so if you have ideas and are excited to help, reach out to us on the [Wild Me Development Discord](https://discord.gg/zw4tr3RE4R)!
 
-### Fork Wildbook
-To start, you will need to be signed in to your GitHub account, have admin access to your OS's terminal, and have Git installed.
-1. From your browser, in the top right corner of the [Wildbook repo](https://github.com/WildMeOrg/Wildbook), click the **Fork** button. Confirm to be redirected to your own fork (check the url for your USERNAME in the namespace).
-1. In your terminal, enter the command `git clone https://github.com/USERNAME/Wildbook`
-1. Once the Wildbook directory becomes available in your working directory, move to it with the command `cd Wildbook`
-1. Add a reference to the original repo, denoting it as the upstream repo.
+### Quick Start with Docker
+
+The easiest way to run Wildbook locally is with Docker Compose. This builds the full application (including the frontend) and starts all required services.
+
+**Prerequisites:** Docker and Docker Compose installed on your system.
+
+```bash
+# 1. Create your .env file from the repo root's .env defaults
+#    (defaults already provided no changes needed for local dev)
+
+cp devops/development/_env.template .env
+
+# 2. Start all services
+
+docker compose up -d
 ```
-git remote add upstream https://github.com/WildMeOrg/Wildbook
-git fetch upstream
+
+The first build will take a few minutes as it compiles the Java project and builds the React frontend. Subsequent starts are faster.
+
+**What's running:**
+
+| Service      | Description                      | Port                   |
+| ------------ | -------------------------------- | ---------------------- |
+| `wildbook`   | Tomcat with Wildbook application | `8080`                 |
+| `db`         | PostgreSQL database              | `5433`                 |
+| `opensearch` | Search index                     | `9200`                 |
+| `mailhog`    | Email capture for dev            | SMTP `1025`, UI `8025` |
+| `wbia`       | Image analysis (Wildbook IA)     | `82`                   |
+
+Once started, open **http://localhost:8080** in your browser. Default login: `tomcat` / `tomcat123`.
+
+Outbound emails are captured by MailHog. View them at **http://localhost:8025**.
+
+**Note:** OpenSearch requires a higher `vm.max_map_count` on Linux. Run once:
+
+```bash
+sudo sysctl -w vm.max_map_count=262144
 ```
+### Legacy development
+For legacy docker build and instructions on locally building the .war file see [`devops/README.md`](devops/README.md) for detailed instructions.
 
-### Create Local Branch
-You will want to work in a branch when doing any feature development you want to provide to the original project.
-1. Verify you are on the main branch. The branch you have checked out will be used as the base for your new branch, so you typically want to start from main.
-`git checkout main`
-1. Create your feature branch. It can be helpful to include the issue number (ISSUENUMBER) you are working to address.
-`git branch ISSUENUMBER-FEATUREBRANCHNAME`
-1. Change to your feature branch so your changes are grouped together.
-`git checkout ISSUENUMBER-FEATUREBRANCHNAME`
-1. Update your branch (this is not needed if you just created new branch, but is a good habit to get into).
-` git pull upstream main`
-
-### Set Up Development Environment with Docker
-For easiest development, you will need to set up your development environment to work with Docker. See [`devops/README.md`](devops/README.md) for detailed instructions.
-
-### Making Local Changes
-Make the code changes necessary for the issue you're working on. You will need to either redeploy your war file (see [`devops/README.md`](devops/README.md)) or redeploy your front end directly (see [`frontend.README.md`](frontend/README.md)) for testing locally. 
-
-The following git commands may prove useful.
-* `git log`: lastest commits of current branch
-* `git status`: current staged and unstaged modifications
-* `git diff --staged`:  the differences between the staging area and the last commit
-* `git add <filename>: add files that have changes to staging in preparation for commit
-* `git commit`: commits the stagged files, opens a text editor for you to write a commit log
-
-### Unit Tests
-We are working on building up test coverage. Current requirements are:
-* Do not drop the percentage of test coverage (exceptions will be made for large scale changes on case-by-case basis)
-* Do not break existing tests
-
-See [test coverage guidelines](src/test/README.md) for how to develop your tests.
-
-### Submit PR
-Up to this point, all changes have been done to your local copy of Wildbook. You need to push the new commits to a remote branch to start the PR process.
-
-1. Now's the time clean up your PR if you choose to squash commits, but this is not required. If you're looking for more information on these practices, see this [pull request tutorial](https://yangsu.github.io/pull-request-tutorial/).
-1. Push to the remote version of your branch ` git push <remote> <local branch>`
-`git push origin ISSUENUMBER-FEATUREBRANCHNAME`
-1. When prompted, provide your username and GitHub Personal Access Token. If you do not have a GitHub Personal Access Token, or do not have one with the correct permissions for your newly forked repository, you will need to [create a Personal Access Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token).
-1. Check the fork's page on GitHub to verify that you see a new branch with your added commits. You should see a line saying "This branch is X commits ahead" and a **Pull request** link. 
-1. Click the **Pull request** link to open a form that says "Able to merge". (If it says there are merge conflicts, go the  for help).
-1. Use an explicit title for the PR and provide details in the comment area. Details can include text, or images, and should provide details as to what was done and why design decisions were made.
-1. Click **Create a pull request**. 
-
-### Respond to feedback
-At this point, it's on us to get you feedback on your submission! Someone from the Wild Me team will review the project and provide any feedback that may be necessary. If changes are recommended, you'll need to checkout the branch you were working from, update the branch, and make these changes locally.
-
-1. `git checkout ISSUENUMBER-FEATUREBRANCHNAME`
-1. `git pull upstream main`
-1. Make required changes
-1. `git add <filename>` for all files impacted by changes
-1. Determine which method would be most appropriate for updating your PR  
-  * `git commit --ammend` if the changes are small stylistic changes
-  * `git commit` if the changes involved significant rework and require additional details
+### Frontend-Only Development
+
+If you are only making changes to the React frontend, see [`frontend/README.md`](frontend/README.md) for a faster rebuild cycle.
 
 ## Machine Learning in Wildbook
 
@@ -90,14 +69,15 @@ Wild Me (wildme.org) engineering staff provide support for Wildbook. You can con
 We provide support during regular office hours on Mondays and Tuesdays.
 
 ## Support resources
-* User documentation is available at [Wild Me Documentation](http://wildbook.docs.wildme.org)
-* For user support, visit the [Wild Me Community Forum](https://community.wildme.org)
-* For contribution guidelines, visit [Wildbook Code Contribution Guidelines](https://wildbook.docs.wildme.org/contribute/code-guide.html)
-* For developer support, visit the [Wild Me Development Discord](https://discord.gg/zw4tr3RE4R)
-* Email the team at opensource@wildme.org
+
+- User documentation is available at [Wild Me Documentation](http://wildbook.docs.wildme.org)
+- For user support, visit the [Wild Me Community Forum](https://community.wildme.org)
+- For contribution guidelines, visit [Wildbook Code Contribution Guidelines](https://wildbook.docs.wildme.org/contribute/code-guide.html)
+- For developer support, visit the [Wild Me Development Discord](https://discord.gg/zw4tr3RE4R)
+- Email the team at opensource@wildme.org
 
 ## History
-Wildbook started as a collaborative software platform for globally-coordinated whale shark (Rhincodon typus ) research as deployed in the Wildbook for Whale Sharks (now part of http://www.sharkbook.ai). After many requests to use our software outside of whale shark research, it is now an open source, community-maintained standard for mark-recapture studies.
 
+Wildbook started as a collaborative software platform for globally-coordinated whale shark (Rhincodon typus ) research as deployed in the Wildbook for Whale Sharks (now part of http://www.sharkbook.ai). After many requests to use our software outside of whale shark research, it is now an open source, community-maintained standard for mark-recapture studies.
 
 Wildbook is a trademark of [Conservation X Labs](https://conservationxlabs.com/), a 501(c)(3) non-profit organization, and is supported by the [Wild Me](https://wildme.org) team.

devops/development/.dockerfiles/tomcat/jdoconfig.properties.template

@@ -0,0 +1,27 @@
+#DataNucleus parameters for object persistence - Docker Configuration with Environment Variables
+
+# PostgreSQL connection for Docker environment
+datanucleus.ConnectionDriverName=org.postgresql.Driver
+datanucleus.ConnectionURL=${WILDBOOK_DB_CONNECTION_URL}
+
+javax.jdo.PersistenceManagerFactoryClass = org.datanucleus.api.jdo.JDOPersistenceManagerFactory
+datanucleus.ConnectionUserName = ${WILDBOOK_DB_USER}              
+datanucleus.ConnectionPassword = ${WILDBOOK_DB_PASSWORD}
+datanucleus.schema.autoCreateAll = true
+datanucleus.NontransactionalRead = true
+datanucleus.Multithreaded = true
+datanucleus.RestoreValues = true
+datanucleus.storeManagerType = rdbms
+datanucleus.maxFetchDepth = -1
+datanucleus.cache.collections.lazy = false
+
+#connection pooling
+datanucleus.connectionPoolingType = dbcp2
+
+# DBCP2 Pooling of Connections
+datanucleus.connectionPool.maxIdle=10
+datanucleus.connectionPool.minIdle=5
+datanucleus.connectionPool.maxActive=30
+datanucleus.connectionPool.maxWait=-1
+datanucleus.connectionPool.testSQL=SELECT 1
+datanucleus.connectionPool.timeBetweenEvictionRunsMillis=240000

devops/development/.dockerfiles/tomcat/server.xml

@@ -161,7 +161,7 @@
       <Host name="localhost"  appBase="webapps"
             unpackWARs="true" deployOnStartup="false" autoDeploy="false">
 
-	      <Context path="" docBase="wildbook"></Context>
+        <Context path="" docBase="ROOT"></Context>
 
 	      <Context docBase="/usr/local/tomcat/webapps/wildbook_data_dir" path="/wildbook_data_dir" />
 

devops/development/.dockerfiles/tomcat/wildbook-start.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+# Set defaults for database configuration
+export WILDBOOK_DB_CONNECTION_URL=${WILDBOOK_DB_CONNECTION_URL:-"jdbc:postgresql://db:5432/wildbook"}
+export WILDBOOK_DB_USER=${WILDBOOK_DB_USER:-"wildbook"}
+export WILDBOOK_DB_PASSWORD=${WILDBOOK_DB_PASSWORD:-"development"}
+
+# Seed config files from staging into mounted wildbook_data_dir on first boot
+DATA_DIR=/usr/local/tomcat/webapps/wildbook_data_dir
+SEED_DIR=/opt/wildbook_seed
+
+if [ ! -f "$DATA_DIR/WEB-INF/classes/bundles/commonConfiguration.properties" ]; then
+  echo "Seeding configuration into $DATA_DIR..."
+  mkdir -p "$DATA_DIR/WEB-INF/classes/bundles"
+  cp -a "$SEED_DIR/." "$DATA_DIR/"
+fi
+
+# Create symlink for legacy path compatibility
+mkdir -p /data
+ln -sf "$DATA_DIR" /data/wildbook_data_dir
+mkdir -p "$DATA_DIR/WEB-IN"
+
+# Create required runtime directories on persisted volume
+mkdir -p "$DATA_DIR/encounters"
+mkdir -p "$DATA_DIR/users"
+mkdir -p "$DATA_DIR/upload"
+
+# Substitute environment variables in jdoconfig.properties
+envsubst < "$DATA_DIR/WEB-INF/classes/bundles/jdoconfig.properties.template" > "$DATA_DIR/WEB-INF/classes/bundles/jdoconfig.properties"
+
+# Fix containerName for WBIA communication
+sed -i 's/^containerName=.*/containerName=wildbook/' "$DATA_DIR/WEB-INF/classes/bundles/commonConfiguration.properties"
+
+# Override SMTP host for MailHog
+sed -i 's/^mailHost=.*/mailHost=mailhog/' "$DATA_DIR/WEB-INF/classes/bundles/commonConfiguration.properties"
+
+# Start Tomcat
+exec catalina.sh run

devops/development/_env.template

@@ -4,6 +4,7 @@
 #   - $WILDBOOK_BASE_DIR/logs/      (logs will go here)
 
 WILDBOOK_BASE_DIR=~/wildbook-dev
+SERVER_URL=http://localhost:80
 
 
 # for smtp (postfix) usage: