Migrate UI to Bootstrap 5, remove legacy JS/CSS #375

Workflow file for this run

.github/workflows/tomcat-deploy.yml at 3421990

	name: Tomcat Deployment Test

	on:
	push:
	branches: [ main, master, develop ]
	pull_request:
	branches: [ main, master, develop ]
	workflow_dispatch:

	jobs:
	build-and-deploy-tomcat:
	name: Build WARs and Deploy to Tomcat
	runs-on: ubuntu-latest

	permissions:
	contents: read

	services:
	postgres:
	image: postgres:12
	env:
	POSTGRES_DB: treebasedb
	POSTGRES_USER: treebase_user
	POSTGRES_PASSWORD: treebase_pass
	options: >-
	--health-cmd pg_isready
	--health-interval 10s
	--health-timeout 5s
	--health-retries 5
	ports:
	- 5432:5432

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up JDK 17
	uses: actions/setup-java@v4
	with:
	java-version: '17'
	distribution: 'temurin'
	cache: 'maven'

	- name: Configure Maven settings for better reliability
	run: \|
	mkdir -p ~/.m2
	cat > ~/.m2/settings.xml << 'EOF'
	<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
	https://maven.apache.org/xsd/settings-1.0.0.xsd">
	<profiles>
	<profile>
	<id>default</id>
	<properties>
	<downloadSources>false</downloadSources>
	<downloadJavadocs>false</downloadJavadocs>
	</properties>
	<repositories>
	<repository>
	<id>central</id>
	<url>https://repo1.maven.org/maven2</url>
	<releases>
	<enabled>true</enabled>
	<updatePolicy>never</updatePolicy>
	</releases>
	<snapshots>
	<enabled>false</enabled>
	</snapshots>
	</repository>
	</repositories>
	<pluginRepositories>
	<pluginRepository>
	<id>central</id>
	<url>https://repo1.maven.org/maven2</url>
	<releases>
	<enabled>true</enabled>
	<updatePolicy>never</updatePolicy>
	</releases>
	<snapshots>
	<enabled>false</enabled>
	</snapshots>
	</pluginRepository>
	</pluginRepositories>
	</profile>
	</profiles>
	<activeProfiles>
	<activeProfile>default</activeProfile>
	</activeProfiles>
	</settings>
	EOF

	- name: Configure database properties for building
	run: \|
	mkdir -p /tmp/mesquite

	# Create jdbc.properties for treebase-core
	cat > treebase-core/src/main/resources/jdbc.properties << EOF
	jdbc.driverClassName=org.postgresql.Driver
	jdbc.url=jdbc:postgresql://localhost:5432/treebasedb
	jdbc.username=treebase_user
	jdbc.password=treebase_pass
	mesquite.folder_dir=/tmp/mesquite
	EOF

	# Create context.xml for treebase-web
	cat > treebase-web/src/main/webapp/META-INF/context.xml << EOF
	<?xml version="1.0" encoding="UTF-8"?>
	<Context reloadable="true">
	<Resource name="jdbc/TreebaseDB" auth="Container"
	type="javax.sql.DataSource"
	description="The JNDI DataSource for the Treebase postgres instance."
	driverClassName="org.postgresql.Driver"
	url="jdbc:postgresql://localhost:5432/treebasedb"
	username="treebase_user"
	password="treebase_pass"
	maxActive="20" maxIdle="10" maxWait="-1" />
	<Environment name="tb2/MesquiteFolder" value="/tmp/mesquite"
	type="java.lang.String" override="false"
	description="Absolute path to the directory where headless Mesquite is unpacked on the host system."/>
	<Environment name="tb2/SiteUrl" value="http://localhost:8080/treebase-web/"
	type="java.lang.String" override="false"
	description="The base URL from which this Treebase instance is served."/>
	<Environment name="tb2/PurlBase" value="http://purl.org/phylo/treebase/phylows/"
	type="java.lang.String" override="false"
	description="The base URL of a PURL service that redirects to this Treebase instance."/>
	<Environment name="tb2/SmtpHost" value="localhost"
	type="java.lang.String" override="false"
	description="Host name of an SMTP server that your instance can use without authentication."/>
	</Context>
	EOF

	# Create jdbc.properties for OAI-PMH data provider
	mkdir -p oai-pmh_data_provider/data_provider_web/src/main/resources
	cat > oai-pmh_data_provider/data_provider_web/src/main/resources/jdbc.properties << EOF
	jdbc.driverClassName=org.postgresql.Driver
	jdbc.url=jdbc:postgresql://localhost:5432/treebasedb
	jdbc.username=treebase_user
	jdbc.password=treebase_pass
	mesquite.folder_dir=/tmp/mesquite
	EOF

	# Create context.xml for OAI-PMH data provider
	mkdir -p oai-pmh_data_provider/data_provider_web/src/main/webapp/META-INF
	cat > oai-pmh_data_provider/data_provider_web/src/main/webapp/META-INF/context.xml << EOF
	<?xml version="1.0" encoding="UTF-8"?>
	<Context reloadable="true">
	<Resource name="jdbc/TreebaseDB" auth="Container"
	type="javax.sql.DataSource"
	description="The JNDI DataSource for the Treebase postgres instance."
	driverClassName="org.postgresql.Driver"
	url="jdbc:postgresql://localhost:5432/treebasedb"
	username="treebase_user"
	password="treebase_pass"
	maxActive="20" maxIdle="10" maxWait="-1" />
	<Environment name="tb2/MesquiteFolder" value="/tmp/mesquite"
	type="java.lang.String" override="false"
	description="Absolute path to the directory where headless Mesquite is unpacked on the host system."/>
	<Environment name="tb2/SiteUrl" value="http://localhost:8080/data_provider_web/"
	type="java.lang.String" override="false"
	description="The base URL from which this Treebase instance is served."/>
	<Environment name="tb2/PurlBase" value="http://purl.org/phylo/treebase/phylows/"
	type="java.lang.String" override="false"
	description="The base URL of a PURL service that redirects to this Treebase instance."/>
	<Environment name="tb2/SmtpHost" value="localhost"
	type="java.lang.String" override="false"
	description="Host name of an SMTP server that your instance can use without authentication."/>
	</Context>
	EOF

	- name: Initialize database schema
	run: \|
	sudo apt-get update
	sudo apt-get install -y postgresql-client
	cd treebase-core/db/schema
	PGPASSWORD=treebase_pass psql -h localhost -U treebase_user -d treebasedb -f init_db_uptodate.pg

	- name: Build treebase-core and install to local repository
	run: \|
	# Retry Maven build up to 3 times to handle transient Maven Central issues
	for i in 1 2 3; do
	echo "Build attempt $i..."
	if mvn -B clean install -DskipTests -f treebase-core/pom.xml; then
	echo "Build succeeded on attempt $i"
	break
	else
	if [ $i -lt 3 ]; then
	echo "Build failed on attempt $i, retrying in 10 seconds..."
	sleep 10
	else
	echo "Build failed after 3 attempts"
	exit 1
	fi
	fi
	done

	- name: Build treebase-web WAR
	run: \|
	# Retry Maven build up to 3 times to handle transient Maven Central issues
	for i in 1 2 3; do
	echo "Build attempt $i..."
	if mvn -B clean package -DskipTests -f treebase-web/pom.xml; then
	echo "Build succeeded on attempt $i"
	break
	else
	if [ $i -lt 3 ]; then
	echo "Build failed on attempt $i, retrying in 10 seconds..."
	sleep 10
	else
	echo "Build failed after 3 attempts"
	exit 1
	fi
	fi
	done

	- name: Build OAI-PMH data provider WAR
	run: \|
	# Retry Maven build up to 3 times to handle transient Maven Central issues
	for i in 1 2 3; do
	echo "Build attempt $i..."
	if mvn -B clean package -DskipTests -f oai-pmh_data_provider/pom.xml; then
	echo "Build succeeded on attempt $i"
	break
	else
	if [ $i -lt 3 ]; then
	echo "Build failed on attempt $i, retrying in 10 seconds..."
	sleep 10
	else
	echo "Build failed after 3 attempts"
	exit 1
	fi
	fi
	done

	- name: Verify WAR files were created
	run: \|
	echo "Checking for treebase-web.war..."
	ls -lh treebase-web/target/treebase-web.war
	echo "Checking for data_provider_web.war..."
	ls -lh oai-pmh_data_provider/data_provider_web/target/data_provider_web.war

	- name: Install Tomcat 9
	run: \|
	# Download and install Tomcat 9
	cd /tmp
	wget -q https://archive.apache.org/dist/tomcat/tomcat-9/v9.0.85/bin/apache-tomcat-9.0.85.tar.gz
	tar xzf apache-tomcat-9.0.85.tar.gz
	export CATALINA_HOME=/tmp/apache-tomcat-9.0.85
	echo "CATALINA_HOME=/tmp/apache-tomcat-9.0.85" >> $GITHUB_ENV

	# Download PostgreSQL JDBC driver
	wget -q -O $CATALINA_HOME/lib/postgresql-42.7.1.jar https://jdbc.postgresql.org/download/postgresql-42.7.1.jar

	# Make scripts executable
	chmod +x $CATALINA_HOME/bin/*.sh

	- name: Deploy WAR files to Tomcat
	run: \|
	# Copy WAR files to Tomcat webapps directory
	cp treebase-web/target/treebase-web.war $CATALINA_HOME/webapps/
	cp oai-pmh_data_provider/data_provider_web/target/data_provider_web.war $CATALINA_HOME/webapps/

	echo "WAR files deployed to Tomcat webapps directory:"
	ls -lh $CATALINA_HOME/webapps/*.war

	# Copy DTD files to workspace root to fix validator configuration
	# The validator XML files reference ./dtd/validator_1_3_0.dtd which gets resolved
	# relative to the working directory during Spring initialization
	echo "Copying DTD files to workspace root for validator..."
	cp -r $GITHUB_WORKSPACE/treebase-web/src/main/webapp/WEB-INF/dtd $GITHUB_WORKSPACE/dtd
	ls -la $GITHUB_WORKSPACE/dtd/

	- name: Start Tomcat and deploy applications
	run: \|
	# Set Java options for Tomcat
	export JAVA_OPTS="-Djava.awt.headless=true -Xmx512m -XX:+UseG1GC"
	export CATALINA_OPTS="--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"

	# Start Tomcat
	JAVA_OPTS="$JAVA_OPTS" CATALINA_OPTS="$CATALINA_OPTS" $CATALINA_HOME/bin/catalina.sh start

	echo "Tomcat started. Waiting for applications to deploy and initialize..."

	# Wait for applications to fully deploy (60 seconds should be sufficient)
	sleep 60

	# Verify Tomcat is still running
	if ! pgrep -f "catalina" > /dev/null; then
	echo "ERROR: Tomcat process died during startup!"
	echo "Showing last 100 lines of catalina.out:"
	tail -100 $CATALINA_HOME/logs/catalina.out \|\| true
	exit 1
	fi

	echo "Tomcat is running. Applications should be deployed."

	- name: Check Tomcat logs for severe errors
	run: \|
	echo "=========================================="
	echo "Checking Tomcat logs for SEVERE errors..."
	echo "=========================================="

	# Display summary of all log files first
	echo ""
	echo "All Tomcat log files:"
	ls -lh $CATALINA_HOME/logs/
	echo ""

	# Initialize counters
	TOTAL_SEVERE=0
	TOTAL_ERROR=0
	HAS_FAILURES=0

	# Check all .log files and catalina.out
	echo "Scanning all log files for errors..."
	for logfile in $CATALINA_HOME/logs/*.log $CATALINA_HOME/logs/catalina.out; do
	if [ -f "$logfile" ]; then
	BASENAME=$(basename "$logfile")
	echo ""
	echo "----------------------------------------"
	echo "Checking: $BASENAME"
	echo "----------------------------------------"

	SEVERE_COUNT=$(grep -c "SEVERE" "$logfile" 2>/dev/null \|\| true)
	ERROR_COUNT=$(grep -c " ERROR " "$logfile" 2>/dev/null \|\| true)

	# Also check for common error patterns
	EXCEPTION_COUNT=$(grep -c "Exception" "$logfile" 2>/dev/null \|\| true)

	TOTAL_SEVERE=$((TOTAL_SEVERE + SEVERE_COUNT))
	TOTAL_ERROR=$((TOTAL_ERROR + ERROR_COUNT))

	echo " SEVERE: $SEVERE_COUNT"
	echo " ERROR: $ERROR_COUNT"
	echo " Exceptions: $EXCEPTION_COUNT"

	# Show SEVERE errors with context
	if [ $SEVERE_COUNT -gt 0 ]; then
	echo ""
	echo " SEVERE errors in $BASENAME:"
	grep -B 3 -A 10 "SEVERE" "$logfile" 2>/dev/null \| head -100 \|\| true
	HAS_FAILURES=1
	fi
	fi
	done

	# Show last 100 lines of catalina.out for full context
	echo ""
	echo "=========================================="
	echo "Last 100 lines of catalina.out:"
	echo "=========================================="
	if [ -f "$CATALINA_HOME/logs/catalina.out" ]; then
	tail -100 "$CATALINA_HOME/logs/catalina.out"
	fi

	# Final summary and exit decision
	echo ""
	echo "=========================================="
	echo "LOG CHECK SUMMARY"
	echo "=========================================="
	echo "Total SEVERE errors across all logs: $TOTAL_SEVERE"
	echo "Total ERROR messages across all logs: $TOTAL_ERROR"
	echo ""

	if [ $HAS_FAILURES -eq 1 ]; then
	echo "❌ FAILED: SEVERE errors detected in Tomcat logs"
	echo "Please review the errors above and the uploaded log artifacts"
	echo "=========================================="
	exit 1
	else
	echo "✓ SUCCESS: No SEVERE errors found in Tomcat logs"
	echo "=========================================="
	fi

	- name: Test application endpoints
	run: \|
	echo "=========================================="
	echo "Testing application endpoints..."
	echo "=========================================="

	FAILED=0

	# Test treebase-web
	echo "Testing treebase-web..."
	HTTP_CODE=$(curl -s -o /dev/null -w "%{http_code}" http://localhost:8080/treebase-web/ \|\| echo "000")
	echo "treebase-web HTTP status: $HTTP_CODE"

	if [ "$HTTP_CODE" = "200" ] \|\| [ "$HTTP_CODE" = "302" ]; then
	echo "✓ treebase-web is responding"
	else
	echo "✗ treebase-web returned unexpected status: $HTTP_CODE"
	# Show error response body for debugging
	echo "Response body:"
	curl -s http://localhost:8080/treebase-web/ \| head -100
	FAILED=1
	fi

	# Test data_provider_web
	echo "Testing data_provider_web..."
	HTTP_CODE=$(curl -s -o /dev/null -w "%{http_code}" http://localhost:8080/data_provider_web/ \|\| echo "000")
	echo "data_provider_web HTTP status: $HTTP_CODE"

	if [ "$HTTP_CODE" = "200" ] \|\| [ "$HTTP_CODE" = "302" ] \|\| [ "$HTTP_CODE" = "404" ]; then
	echo "✓ data_provider_web is deployed (status: $HTTP_CODE)"
	else
	echo "✗ data_provider_web returned unexpected status: $HTTP_CODE"
	# Show error response body for debugging
	echo "Response body:"
	curl -s http://localhost:8080/data_provider_web/ \| head -100
	FAILED=1
	fi

	if [ "$FAILED" = "1" ]; then
	echo "=========================================="
	echo "FAILURE: One or more endpoints returned errors"
	echo "=========================================="
	exit 1
	fi

	- name: Upload Tomcat logs as artifact
	if: always()
	uses: actions/upload-artifact@v4
	with:
	name: tomcat-logs
	path: /tmp/apache-tomcat-9.0.85/logs/
	retention-days: 7

	- name: Shutdown Tomcat
	if: always()
	run: \|
	if [ -f "$CATALINA_HOME/bin/catalina.sh" ]; then
	$CATALINA_HOME/bin/catalina.sh stop \|\| true
	sleep 5
	# Force kill if still running
	pkill -9 -f catalina \|\| true
	fi

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Migrate UI to Bootstrap 5, remove legacy JS/CSS #375

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Migrate UI to Bootstrap 5, remove legacy JS/CSS #375

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