diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1119f4eb90a39da2d0e1580e1377fc39f11ad0b4..5fea75d9258a6063a2e3677a793e2085a3541b62 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -15,7 +15,7 @@ variables:
MAVEN_OPTS: "-Dmaven.repo.local=.m2/repository -Dmaven.artifact.threads=10"
MAIN_BRANCH: "main"
RELEASE_BRANCH: "release"
- CLI_PATH: "/disks/data01/wildfly/wildfly-26.1.3.Final/bin"
+ CLI_PATH: "/disks/data01/wildfly/wildfly-34.0.1.Final/bin"
TMP_PATH: "/home/deployer/gitlab_tmp"
DEPLOYMENT_PATH: "/home/wildfly/deployments"
ARCHIVE_PATH: "/home/wildfly/archive"
diff --git a/README.md b/README.md
index 1e3fbebcf2b57e208efaff4ca8b8ea78226ba005..65c1c0b5cae4bd4cce64bc38976df6e7a9739e4c 100644
--- a/README.md
+++ b/README.md
@@ -34,7 +34,7 @@ $ mvnw.cmd clean install
**PLEASE NOTE that this builds the package without any models. See "Adding models" below for more information**
-Download and install [WildFly](https://www.wildfly.org/) == 26.1.3
+Download and install [WildFly](https://www.wildfly.org/) == 34.0.1
Deploy the build from this project in Wildfly.
diff --git a/models.xml b/models.xml
index 60f57c35dcbe9d157b34cfdad4c7a2449eba3b1b..45ec129b0884d1efe81915e8bbcbb80534cbb78a 100644
--- a/models.xml
+++ b/models.xml
@@ -2,112 +2,112 @@
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>RoughageNutritionModel</artifactId>
- <version>1.1.12</version>
+ <version>1.1.13</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>AlternariaModel</artifactId>
- <version>1.1.14</version>
- </dependency>
- <dependency>
- <groupId>no.nibio.vips.model</groupId>
- <artifactId>BarleyNetBlotchModel</artifactId>
- <version>1.1.9</version>
+ <version>1.1.15</version>
</dependency>
<dependency>
<groupId>fi.luke.vips.model</groupId>
<artifactId>FinnCerealModels</artifactId>
- <version>1.1.9</version>
+ <version>1.1.10</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>Model_LEAFBLOTCH</artifactId>
- <version>1.1.9</version>
+ <version>1.1.10</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>NaerstadModel</artifactId>
- <version>1.1.9</version>
+ <version>1.1.10</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>SeptoriaHumidityModel</artifactId>
- <version>1.1.9</version>
+ <version>1.1.10</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>AppleScabModel</artifactId>
- <version>1.1.8</version>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
- <artifactId>BremiaLactucaeModel</artifactId>
- <version>1.1.8</version>
+ <artifactId>DeliaRadicumModel</artifactId>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
- <artifactId>DeliaRadicumModel</artifactId>
- <version>1.1.8</version>
+ <artifactId>DeliaRadicumFloralisObservationModel</artifactId>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
- <artifactId>DeliaRadicumFloralisObservationModel</artifactId>
- <version>1.1.8</version>
+ <artifactId>BremiaLactucaeModel</artifactId>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>DOWNCASTModel</artifactId>
- <version>1.1.8</version>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>GrassDryingModel</artifactId>
- <version>1.1.8</version>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>LygusRugulipennisModel</artifactId>
- <version>1.1.8</version>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>Model_MAIZEPHENO</artifactId>
- <version>1.1.8</version>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>MamestraBrassicaeModel</artifactId>
- <version>1.1.8</version>
+ <version>1.1.9</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>OatFloweringModel</artifactId>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>NegativePrognosisModel</artifactId>
- <version>1.1.8</version>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>PsilaRosaeObservationModel</artifactId>
- <version>1.1.8</version>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
- <artifactId>OatFloweringModel</artifactId>
- <version>1.1.8</version>
+ <artifactId>PsilaRosaeTempModel</artifactId>
+ <version>1.1.9</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
- <artifactId>PsilaRosaeTempModel</artifactId>
- <version>1.1.8</version>
+ <artifactId>BarleyNetBlotchModel</artifactId>
+ <version>1.1.10</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>SeptoriaApiicolaModel</artifactId>
- <version>1.1.7</version>
+ <version>1.1.8</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
<artifactId>SeptoriaReferenceHumidityModel</artifactId>
- <version>1.1.7</version>
+ <version>1.1.8</version>
</dependency>
<dependency>
<groupId>no.nibio.vips.model</groupId>
diff --git a/pom.xml b/pom.xml
index 427812b073711a6df2e9d3344cda4d63e1d9e0c0..0a7ad709eb2d403a95b00ab7c6991b6534f9b296 100755
--- a/pom.xml
+++ b/pom.xml
@@ -9,7 +9,7 @@
<groupId>no.nibio</groupId>
<artifactId>VIPSCore</artifactId>
<packaging>war</packaging>
- <version>2.0.15-SNAPSHOT</version>
+ <version>3.0.0-SNAPSHOT</version>
<name>VIPSCore</name>
<url>http://maven.apache.org</url>
@@ -32,12 +32,12 @@
<dependency>
<groupId>io.github.classgraph</groupId>
<artifactId>classgraph</artifactId>
- <version>4.8.165</version>
+ <version>4.8.179</version>
</dependency>
<dependency>
<groupId>com.thetransactioncompany</groupId>
<artifactId>cors-filter</artifactId>
- <version>2.10</version>
+ <version>3.0</version>
</dependency>
<dependency>
@@ -66,13 +66,7 @@
<dependency>
<groupId>no.nibio.vips</groupId>
<artifactId>VIPSCommon</artifactId>
- <version>2.1.1</version>
- </dependency>
- <dependency>
- <groupId>javax</groupId>
- <artifactId>javaee-web-api</artifactId>
- <version>8.0.1</version>
- <type>jar</type>
+ <version>3.0.0</version>
</dependency>
<dependency>
<groupId>junit</groupId>
@@ -80,11 +74,6 @@
<version>4.13.2</version>
<scope>test</scope>
</dependency>
- <dependency>
- <groupId>axis</groupId>
- <artifactId>axis</artifactId>
- <version>1.4</version>
- </dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
@@ -92,16 +81,10 @@
<scope>provided</scope>
</dependency>
<dependency>
- <groupId>javax.servlet</groupId>
- <artifactId>servlet-api</artifactId>
- <version>2.5</version>
- <scope>provided</scope>
- </dependency>
- <dependency>
- <groupId>javax.servlet.jsp</groupId>
- <artifactId>jsp-api</artifactId>
- <version>2.2</version>
- <scope>provided</scope>
+ <groupId>jakarta.servlet</groupId>
+ <artifactId>jakarta.servlet-api</artifactId>
+ <version>6.1.0</version>
+ <scope>test</scope>
</dependency>
<dependency>
<groupId>commons-validator</groupId>
@@ -110,9 +93,9 @@
<type>jar</type>
</dependency>
<dependency>
- <groupId>javax</groupId>
- <artifactId>javaee-api</artifactId>
- <version>8.0.1</version>
+ <groupId>jakarta.platform</groupId>
+ <artifactId>jakarta.jakartaee-api</artifactId>
+ <version>10.0.0</version>
<scope>provided</scope>
</dependency>
<dependency>
@@ -145,8 +128,8 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.12.1</version>
<configuration>
- <source>11</source>
- <target>11</target>
+ <source>17</source>
+ <target>17</target>
</configuration>
</plugin>
<plugin>
diff --git a/src/main/java/no/nibio/vips/core/VIPSCoreApplication.java b/src/main/java/no/nibio/vips/core/VIPSCoreApplication.java
index 52f93d819f72e2923c3eadb005b727137d57d0b6..7e141f8c64d0495715090ec1299d14fdc7eaa2ab 100755
--- a/src/main/java/no/nibio/vips/core/VIPSCoreApplication.java
+++ b/src/main/java/no/nibio/vips/core/VIPSCoreApplication.java
@@ -20,8 +20,8 @@
package no.nibio.vips.core;
import java.util.Set;
-import javax.ws.rs.ApplicationPath;
-import javax.ws.rs.core.Application;
+import jakarta.ws.rs.ApplicationPath;
+import jakarta.ws.rs.core.Application;
/**
diff --git a/src/main/java/no/nibio/vips/core/config/JacksonConfig.java b/src/main/java/no/nibio/vips/core/config/JacksonConfig.java
index ce4eb98517711dcaaa3ed71a5220627f76d3a38d..9e136d4ad282c847e985e75b6b932318149d8569 100755
--- a/src/main/java/no/nibio/vips/core/config/JacksonConfig.java
+++ b/src/main/java/no/nibio/vips/core/config/JacksonConfig.java
@@ -20,14 +20,14 @@ package no.nibio.vips.core.config;
import com.bedatadriven.jackson.datatype.jts.JtsModule;
import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.ext.ContextResolver;
-import javax.ws.rs.ext.Provider;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import com.fasterxml.jackson.databind.module.SimpleModule;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.ext.ContextResolver;
+import jakarta.ws.rs.ext.Provider;
import net.ipmdecisions.weather.entity.LocationWeatherData;
import no.nibio.vips.ipmdecisions.LocationWeatherDataDeserializer;
diff --git a/src/main/java/no/nibio/vips/core/service/ModelResourceImpl.java b/src/main/java/no/nibio/vips/core/service/ModelResourceImpl.java
index 257b3b8bd13d9c36b86482c3225e16d4ef0f0124..969307326fd47ba826d1a050967606d28a8179dc 100755
--- a/src/main/java/no/nibio/vips/core/service/ModelResourceImpl.java
+++ b/src/main/java/no/nibio/vips/core/service/ModelResourceImpl.java
@@ -18,19 +18,20 @@
package no.nibio.vips.core.service;
+import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.WebApplicationException;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
import no.nibio.vips.entity.ModelConfiguration;
import no.nibio.vips.entity.Result;
import no.nibio.vips.ipmdecisions.DataTransformer;
@@ -115,7 +116,7 @@ public class ModelResourceImpl implements ModelResource{
{
retVal.append(mF.getModelInstance(key).getModelName(language));
}
- catch(DuplicateModelIdException ex)
+ catch(DuplicateModelIdException | SecurityException | NoSuchMethodException | InvocationTargetException ex)
{
retVal.append(ex.getMessage());
}
@@ -149,7 +150,7 @@ public class ModelResourceImpl implements ModelResource{
{
try {
retVal.append(key).append(" ").append(mF.getModelInstance(key).getModelName(language)).append("\n");
- } catch (InstantiationException | IllegalAccessException | NoSuchModelException | DuplicateModelIdException ex) {
+ } catch (InstantiationException | IllegalAccessException | NoSuchModelException | DuplicateModelIdException | SecurityException | NoSuchMethodException | InvocationTargetException ex) {
retVal.append(key).append(" ").append(ex.getMessage()).append("\n");
Logger.getLogger(ModelResourceImpl.class.getName()).log(Level.SEVERE, null, ex);
}
@@ -231,7 +232,7 @@ public class ModelResourceImpl implements ModelResource{
{
sampleConfig = ModelFactory.getInstance().getModelInstance(modelId).getSampleConfig();
}
- catch(NoSuchModelException | DuplicateModelIdException ex)
+ catch(NoSuchModelException | DuplicateModelIdException | SecurityException | NoSuchMethodException | InvocationTargetException ex)
{
sampleConfig = ex.getMessage();
}
@@ -261,7 +262,7 @@ public class ModelResourceImpl implements ModelResource{
}
else throw new ModelExcecutionException("Model returned NULL Result");
}
- catch(InstantiationException | IllegalAccessException | ConfigValidationException | ModelExcecutionException | NoSuchModelException | DuplicateModelIdException ex)
+ catch(InstantiationException | IllegalAccessException | ConfigValidationException | ModelExcecutionException | NoSuchModelException | DuplicateModelIdException | SecurityException | NoSuchMethodException | InvocationTargetException ex)
{
Logger.getLogger(ModelResourceImpl.class.getName()).log(Level.SEVERE, null, ex);
return Response.serverError().entity(ex.getMessage()).build();
diff --git a/src/main/java/no/nibio/vips/core/startup/StartupListener.java b/src/main/java/no/nibio/vips/core/startup/StartupListener.java
index a4dcfd1fde4a4ff171d1cd806587e99b739867b5..badb23779c430f94bc4fe8e648a6eec666e7208d 100755
--- a/src/main/java/no/nibio/vips/core/startup/StartupListener.java
+++ b/src/main/java/no/nibio/vips/core/startup/StartupListener.java
@@ -18,8 +18,7 @@
package no.nibio.vips.core.startup;
-import javax.servlet.ServletContextEvent;
-
+import jakarta.servlet.ServletContextEvent;
import no.nibio.vips.model.factory.ModelFactory;
/**
* This class is created and method contextInitialized called when the application
@@ -28,7 +27,7 @@ import no.nibio.vips.model.factory.ModelFactory;
* @copyright 2013 {@link http://www.nibio.no NIBIO}
* @author Tor-Einar Skog <tor-einar.skog@nibio.no>
*/
-public class StartupListener implements javax.servlet.ServletContextListener{
+public class StartupListener implements jakarta.servlet.ServletContextListener{
/**
* Called when the application
diff --git a/src/main/java/no/nibio/vips/model/factory/ModelFactory.java b/src/main/java/no/nibio/vips/model/factory/ModelFactory.java
index c49e78217d44b1ef6a0b1df2ece4fd5d65674170..635339f6797026a497f6ffb61fd48046e23c220f 100755
--- a/src/main/java/no/nibio/vips/model/factory/ModelFactory.java
+++ b/src/main/java/no/nibio/vips/model/factory/ModelFactory.java
@@ -18,9 +18,6 @@
package no.nibio.vips.model.factory;
-import io.github.classgraph.ClassGraph;
-import io.github.classgraph.ClassInfo;
-import io.github.classgraph.ScanResult;
import java.lang.reflect.InvocationTargetException;
import java.util.HashMap;
import java.util.HashSet;
@@ -28,6 +25,9 @@ import java.util.Map;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ClassInfo;
+import io.github.classgraph.ScanResult;
import no.nibio.vips.model.Model;
/**
@@ -96,34 +96,6 @@ public class ModelFactory {
* Builds an inventory.
*/
private void init(){
- /*
- * Reflections API insists on using at least one package prefix. So we scan
- * through all TLDs. List is compiled from
- * http://en.wikipedia.org/wiki/List_of_Internet_top-level_domains
- */
- String[] defaultTopDomains = {
- "aero","asia","biz","cat","com","coop","info","int","jobs","mobi",
- "museum","name","net","org","post","pro","tel","travel","edu","gov",
- "ac","ad","ae","af","ag","ai","al","am","an","ao","aq","ar","as","at",
- "au","aw","ax","az","ba","bb","bd","be","bf","bg","bh","bi","bj","bm",
- "bn","bo","br","bs","bt","bv","bw","by","bz","ca","cc","cd","cf","cg",
- "ch","ci","ck","cl","cm","cn","co","cr","cs","cu","cv","cx","cy","cz",
- "dd","de","dj","dk","dm","do","dz","ec","ee","eg","eh","er","es","et",
- "eu","fi","fj","fk","fm","fo","fr","ga","gb","gd","ge","gf","gg","gh",
- "gi","gl","gm","gn","gp","gq","gr","gs","gt","gu","gw","gy","hk","hm",
- "hn","hr","ht","hu","id","ie","il","im","in","io","iq","ir","is","it",
- "je","jm","jo","jp","ke","kg","kh","ki","km","kn","kp","kr","kw","ky",
- "kz","la","lb","lc","li","lk","lr","ls","lt","lu","lv","ly","ma","mc",
- "md","me","mg","mh","mk","ml","mm","mn","mo","mp","mq","mr","ms","mt",
- "mu","mv","mw","mx","my","mz","na","nc","ne","nf","ng","ni","nl","no",
- "np","nr","nu","nz","om","pa","pe","pf","pg","ph","pk","pl","pm","pn",
- "pr","ps","pt","pw","py","qa","re","ro","rs","ru","rw","sa","sb","sc",
- "sd","se","sg","sh","si","sj","sk","sl","sm","sn","so","sr","ss","st",
- "su","sv","sx","sy","sz","tc","td","tf","tg","th","tj","tk","tl","tm",
- "tn","to","tp","tr","tt","tv","tw","tz","ua","ug","uk","us","uy","uz",
- "va","vc","ve","vg","vi","vn","vu","wf","ws","ye","yt","yu","za","zm",
- "zw",
- };
/**
* Warning: This generates a WARNING from a filesystem/JARfile scan error
@@ -131,19 +103,14 @@ public class ModelFactory {
* this in log files.
*/
- Set<Class<? extends Model>> subTypes = new HashSet();
+ Set<Class<? extends Model>> subTypes = new HashSet<>();
- /*for(String topDomain: defaultTopDomains)
- {
- reflections = new Reflections(topDomain);
- subTypes.addAll(reflections.getSubTypesOf(Model.class));
- }*/
boolean verboseClassGraph = System.getProperty("no.nibio.vips.core.VERBOSE_CLASSGRAPH") != null && System.getProperty("no.nibio.vips.core.VERBOSE_CLASSGRAPH").equals("true");
- try (ScanResult scanResult = // Assign scanResult in try-with-resources
+ try (ScanResult scanResult = // Assign scanResult in try-with-resources
new ClassGraph() // Create a new ClassGraph instance
- .verbose(verboseClassGraph) // If you want to enable logging to stderr
- .enableClassInfo() // Scan classes, methods, fields, annotations
- //.acceptPackages("com.xyz") // Scan com.xyz and subpackages
+ .verbose(verboseClassGraph) // If you want to enable logging to stderr
+ .enableClassInfo() // Scan classes, methods, fields, annotations
+ //.acceptPackages("no.nibio") // Scan no.nibio and subpackages
.scan()) { // Perform the scan and return a ScanResult
//ClassInfoList classInfoList =
@@ -156,7 +123,7 @@ public class ModelFactory {
/**
* Iterates and instantiates one object for each class
*/
- this.models = new HashMap();
+ this.models = new HashMap<>();
for(Class<? extends Model> subType : subTypes)
{
try {
@@ -303,7 +270,10 @@ public class ModelFactory {
InstantiationException,
IllegalAccessException,
DuplicateModelIdException,
- NoSuchModelException
+ NoSuchModelException,
+ SecurityException,
+ NoSuchMethodException,
+ InvocationTargetException
{
if(this.isDuplicateModelId(modelId))
{
@@ -313,7 +283,7 @@ public class ModelFactory {
{
throw new NoSuchModelException("ERROR: No model found with id = " + modelId);
}
- return this.models.get(modelId).getClass().newInstance();
+ return this.models.get(modelId).getClass().getDeclaredConstructor().newInstance();
}
private void addDuplicateModelId(String modelId) {