Merge pull request #30 from BioPAX/using-paxtools6

Validator v6 using paxtools v6

Author: IgorRodchenkov

.github/workflows/maven.yml

@@ -20,8 +20,8 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 20
           distribution: 'temurin'
           cache: maven
-      - name: Build with Maven and JDK-17
+      - name: Build with Maven (JDK-20)
         run: mvn --batch-mode --update-snapshots package

README.md

@@ -12,7 +12,7 @@
 The BioPAX Validator is a command line tool, Java library, and online
 web service for BioPAX formatted pathway data validation. The validator
 checks for more than a hundred BioPAX Level3 rules and best practices, 
-provides human readable reports and can automatically fix some common 
+provides human-readable reports and can automatically fix some common 
 mistakes in data (can also process Level1 and Level2 data, which are 
 first auto-converted to the Level3, and then Level3 rules apply). 
 The validator is in use by the BioPAX community and is continuously being
@@ -27,7 +27,17 @@ pathway databases and tools that support BioPAX.
 
 ## Usage
 
-Download and expand the latest ZIP distribution from <http://www.biopax.org/downloads/validator/>.
+Download and expand the latest ZIP distribution from <http://www.biopax.org/downloads/validator/> 
+
+Or build it from the sources:
+
+```
+mvn clean install
+cd dist
+mvn assembly:assembly
+```
+
+then use the resulting `biopax-validator-${version}-all.zip` (move somewhere, expand)
 
 ### Console (batch)
 
@@ -71,14 +81,11 @@ Use --help parameter to see all the server options (e.g., httpPort, ajpPort)
 
 ## Developer notes
 
-It's built with Java ${java.version} (requires 8 or above), Paxtools ${paxtools.version} (BioPAX Model API, Java library), 
-Spring Framework ${spring.version}, OXM, @AspectJ, AOP, LTW, etc. Validation _Rules_ are java 
-objects that implement _Rule<E>_ interface, extend _AbstractRule<E>_, where _E_
-is usually either a BioPAX class or _Model_. Controlled vocabulary rules 
-extend _AbstractCvRule_ and use _CvRestriction_ and OBO Ontology Manager 
-(based on PSIDEV EBI sources) to lookup for valid ontology terms and synonyms.
-Rules may call other rules, but usually it is not recommended, for they are 
-better keep simple and independent. 
+Validation _Rules_ are java objects that implement _Rule<E>_ interface and 
+extend _AbstractRule<E>_, where _<E>_ is usually either a BioPAX class or _Model_. 
+Controlled vocabulary rules extend _AbstractCvRule_ and use _CvRestriction_ and 
+OBO Ontology Manager (derived from PSIDEV EBI code) to lookup for valid ontology terms and synonyms.
+Validation Rules can call other Rules, but this is not recommended (better keep it simple, independent). 
 
 _Post-model_ validation mode is to check 
 all the rules/objects after the BioPAX model is built (created in memory or 
@@ -92,8 +99,8 @@ BioPAX error types, levels, categories, messages, cases are reported.
 Spring AOP, MessageSource, resource bundles, and OXM help collect the errors, 
 translate to human-readable messages and write the validation report (xml or html).
 Settings such as _behavior_ (level), error code, category and message templates
-are configured via the resource bundles: rules.properties, codes.properties and 
-profiles.properties (e.g., /rules_fr_CA.properties can be added to see messages 
+are configured via the resource bundles: `rules.properties`, `codes.properties` and 
+`profiles.properties` (e.g., `/rules_fr_CA.properties` can be added to see messages 
 in French). 
 
 To disable LTW AOP, set ```<context:load-time-weaver aspectj-weaving="off"/>```
@@ -116,3 +123,36 @@ or revert to the default configuration)
 
 The validator-core module is not specific to BioPAX; 
 it could be used for another domain with alternative validation rules module.
+
+You can also start the web app with maven (plugin)
+
+```
+mvn clean install
+cd biopax-validator-web
+mvn spring-boot:run
+```
+
+and also access it at localhost:8080 (live reload is enabled - can edit js/css/html/jsp and immediately see the effect 
+without restarting the app)
+
+This is convenient for development but the problem is that LTW does not properly/fully wok for some reason, -
+the validator will not catch syntax errors or unknown property errors, unlike when it's run via `sh server.sh` or 
+when docker container (i.e. when the app was run using e.g. `java -javaagent:agent.jar ... -jar app.war` command)
+
+## Docker
+
+### build the project and image(s) from sources
+```
+mvn clean install
+cd biopax-validator-web
+mvn dockerfile:build
+#mvn dockerfile:tag
+#mvn dockerfile:push
+```
+
+### run
+Run with docker (can also do with compose or terraform)
+```
+docker run --name validator -it pathwaycommons/biopax-validator -p 8080:8080
+```
+

biopax-validator-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>org.biopax.validator</groupId>
 		<artifactId>parent</artifactId>
-		<version>5.1.1-SNAPSHOT</version>
+		<version>6.0.0-SNAPSHOT</version>
 	</parent>
 
     <artifactId>biopax-validator-client</artifactId>
@@ -26,6 +26,17 @@
 			<artifactId>httpmime</artifactId>
 			<version>4.5.14</version>
 		</dependency>
+		<dependency>
+			<groupId>jakarta.xml.bind</groupId>
+			<artifactId>jakarta.xml.bind-api</artifactId>
+			<version>4.0.0</version>
+		</dependency>
+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-impl</artifactId>
+			<version>4.0.3</version>
+			<scope>runtime</scope>
+		</dependency>
 	</dependencies>
 
 	<build>
@@ -49,19 +60,6 @@
 						</configuration>
 					</execution>
 				</executions>
-				<dependencies>
-					<dependency>
-						<groupId>org.glassfish.jaxb</groupId>
-						<artifactId>jaxb-runtime</artifactId>
-						<version>2.4.0-b180830.0438</version>
-						<scope>runtime</scope>
-					</dependency>
-					<dependency>
-						<groupId>com.sun.activation</groupId>
-						<artifactId>javax.activation</artifactId>
-						<version>1.2.0</version>
-					</dependency>
-				</dependencies>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>

biopax-validator-client/src/main/java/org/biopax/validator/BiopaxValidatorClient.java

@@ -1,14 +1,10 @@
 package org.biopax.validator;
 
-/*
- *
- */
-
 import java.io.*;
 import java.nio.charset.Charset;
 import java.util.*;
 
-import javax.xml.bind.*;
+import jakarta.xml.bind.*;
 import javax.xml.transform.Source;
 import javax.xml.transform.stream.StreamSource;
 
@@ -40,7 +36,7 @@ public class BiopaxValidatorClient {
 	 * Default BioPAX Validator's URL
 	 */
 	public static final String 
-		DEFAULT_VALIDATOR_URL = "http://www.biopax.org/validator/check.html";
+		DEFAULT_VALIDATOR_URL = "https://www.biopax.org/validator/check.html";
 
 	/**
 	 * The Java Option to set a BioPAX Validator URL 

biopax-validator-client/src/test/java/BiopaxValidatorClientTest.java

@@ -3,15 +3,17 @@
  */
 import java.io.*;
 
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBException;
 
 import org.biopax.validator.BiopaxValidatorClient;
 import org.biopax.validator.BiopaxValidatorClient.RetFormat;
 import org.biopax.validator.jaxb.ValidatorResponse;
-import org.junit.*;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
 
 // remove @Ignore when biopax.org/biopax-validator/  is available
-@Ignore
+@Disabled
 public class BiopaxValidatorClientTest {
 
 	@Test
@@ -43,12 +45,12 @@ public void testClientXml() throws IOException, JAXBException {
 
 		//System.out.println(baos.toString());
 
-		Assert.assertTrue(baos.size()>0);
+		Assertions.assertTrue(baos.size()>0);
 
 		ValidatorResponse resp = client.unmarshal(baos.toString());
 
-		Assert.assertNotNull(resp);
-		Assert.assertFalse(resp.getValidation().isEmpty());
+		Assertions.assertNotNull(resp);
+		Assertions.assertFalse(resp.getValidation().isEmpty());
 
 		System.out.println(resp.getValidation().get(0).getSummary()
 				+ "; cases: " + resp.getValidation().get(0).getTotalProblemsFound());

biopax-validator-web/Dockerfile

@@ -1,6 +1,10 @@
-FROM openjdk:8-jdk-alpine
+FROM eclipse-temurin:latest
 VOLUME /tmp
-ARG JAR_FILE
-COPY ${JAR_FILE} app.jar
-ENTRYPOINT ["java","-Djava.security.egd=file:/dev/./urandom", "-Xmx1g", "-jar","/app.jar"]
+ARG APP_JAR
+ARG AGENT_JAR
+COPY ${APP_JAR} app.war
+COPY ${AGENT_JAR} agent.jar
+ENV JDK_JAVA_OPTIONS="--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"
+ENTRYPOINT ["java", "-server", "-javaagent:agent.jar", \
+"-Djava.security.egd=file:/dev/./urandom", "-Xmx4g", "-Dfile.encoding=UTF-8", "-jar", "app.war", "--server.port=8080"]
 EXPOSE 8080