diff --git a/.gitignore b/.gitignore
index ad51c41df864275930ecb96fa6433bba3823c5e1..0efe793b666a005b665be120a32db0150a920249 100755
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ jboss/
/.idea/
.vscode/settings.json
.settings/org.eclipse.core.resources.prefs
+pom_with_models.xml
diff --git a/README.md b/README.md
index 9a6fa8a66e9630572a507933084d17cb7dd7c138..80c1300b5dba8f25bc5dc5ba955c280b259cc34b 100644
--- a/README.md
+++ b/README.md
@@ -26,6 +26,8 @@ or on Windows
$ 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/) >= 25.0.1
Deploy the build from this project in Wildfly.
@@ -33,36 +35,22 @@ Deploy the build from this project in Wildfly.
Wildfly should run on Java >= 11
### Adding models
-To add models, create this folder in WildFly:
-`[WILDFLY_ROOT]/modules/no/nibio/vips/modelcontainer/main/`
-Add the model jar file, and edit module.xml accordingly.
-
-``` xml
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!--
- © 2019 NIBIO
- Author: Tor-Einar Skog <tor-einar.skog@nibio.no>
- -->
-
-<module xmlns="urn:jboss:module:1.1" name="no.nibio.vips.modelcontainer">
- <resources>
- <resource-root path="PsilaRosaeTempModel-1.0-SNAPSHOT.jar"/>
- </resources>
- <dependencies>
- <module name="no.nibio.vips.VIPSCommon" export="false"/>
- <module name="com.fasterxml.jackson.core.jackson-core" export="false"/>
- <module name="com.fasterxml.jackson.core.jackson-databind" export="false"/>
- <module name="com.vividsolutions.jts" export="false"/>
- <module name="org.renjin" export="false"/>
- <module name="org.slf4j" export="false"/>
- </dependencies>
-
-</module>
+Models are listed as dependencies in the POM and built into the WARfile. In order to make it possible
+to configure your own set of models to include, we have separated the model dependencies out in a
+separate file. The default is `models.xml`, and contains the models that VIPS in Norway are using
+currently.
+
+To build the package with the default set of models, run
+```bash
+$ build_with_models.py
```
-You also need to make sure you have the dependency modules available.
+To build with your preferred set of models, create a new file called e.g. `my_models.xml` and run
+
+```bash
+$ build_with_models.py my_models.xml
+```
## Implement a model
See [implement_model.md](./docs/implement_model.md)
diff --git a/build_with_models.py b/build_with_models.py
index 240d19cddd28500c45acd2c3710cc50515d661df..c6b0a8560680582c6a9d25149ae469a084567ada 100755
--- a/build_with_models.py
+++ b/build_with_models.py
@@ -1,26 +1,57 @@
#!/usr/bin/python3
+'''
+Merges pom.xml and models.xml (default) into pom_with_models.xml and
+runs mvn clean install -f pom_with_models.xml
+
+Copyright (C) 2023 NIBIO
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+@author Tor-Einar Skog <tor-einar.skog@nibio.no>
+'''
import sys
-from xml.dom.minidom import parse, parseString
+import subprocess
+from xml.dom.minidom import parse
+# Default
models_xml_path = "models.xml"
+merged_pom_filename = "pom_with_models.xml"
+# Accept alternative models.xml file
if len(sys.argv) > 1:
models_xml_path = sys.argv[1]
-pom_file = open("pom.xml")
-models_file = open(models_xml_path)
-
-pom_dom = parse(pom_file)
-models_dom = parse(models_file)
+# Read contents
+pom_dom = parse("pom.xml")
+try:
+ models_dom = parse(models_xml_path)
+except FileNotFoundError:
+ print("ERROR: File %s not found." % models_xml_path)
+ exit(1)
-pom_deps_element = pom_dom.getElementsByTagName("dependencies")
+# Merge the dependency elements from models.xml into pom.xml
+pom_deps_element = pom_dom.getElementsByTagName("dependencies")[0]
model_dep_elements = models_dom.getElementsByTagName("dependency")
for dep in model_dep_elements:
- pom_deps_element.append(dep)
+ pom_deps_element.appendChild(dep)
-print(pom_dom.toprettyxml())
+# Write the modified pom dom to file
+pom_with_models_file = open(merged_pom_filename,"w")
+pom_dom.writexml(pom_with_models_file)
+pom_with_models_file.close()
-models_file.close()
-pom_file.close()
+# Build VIPSCore with Maven, using the merged pom
+subprocess.run("./mvnw clean install -f %s" % merged_pom_filename, shell=True)
diff --git a/models.xml b/models.xml
index 4f4b6b5f646aa551bff493a363ab2c74d2a91a15..c5c0bf5ad90624af838febcea3290bee9523fbd9 100644
--- a/models.xml
+++ b/models.xml
@@ -1,12 +1,112 @@
<dependencies>
- <dependency>
- <groupId>no.nibio.vips.model</groupId>
- <artifactId>BremiaLactucaeModel</artifactId>
- <version>2.0.0</version>
- </dependency>
- <dependency>
- <groupId>no.nibio.vips.model</groupId>
- <artifactId>PsilaRosaeTempModel</artifactId>
- <version>1.0.0</version>
- </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>AlternariaModel</artifactId>
+ <version>1.0.2</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>AppleScabModel</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>BarleyNetBlotchModel</artifactId>
+ <version>1.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>BremiaLactucaeModel</artifactId>
+ <version>2.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips</groupId>
+ <artifactId>DeliaRadicumModel</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>DeliaRadicumFloralisObservationModel</artifactId>
+ <version>1.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>DOWNCASTModel</artifactId>
+ <version>2.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>fi.luke.vips.model</groupId>
+ <artifactId>FinnCerealModels</artifactId>
+ <version>1.0.0</version>
+</dependency>
+ <dependency>
+ <groupId>no.nibio.vips</groupId>
+ <artifactId>GrassDryingModel</artifactId>
+ <version>2.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>LygusRugulipennisModel</artifactId>
+ <version>1.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>MamestraBrassicaeModel</artifactId>
+ <version>1.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.model</groupId>
+ <artifactId>Model_LEAFBLOTCH</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.model</groupId>
+ <artifactId>Model_MAIZEPHENO</artifactId>
+ <version>2.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>NaerstadModel</artifactId>
+ <version>2.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>NegativePrognosisModel</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>OatFloweringModel</artifactId>
+ <version>1.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>PsilaRosaeObservationModel</artifactId>
+ <version>2.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>PsilaRosaeTempModel</artifactId>
+ <version>1.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>RoughageNutritionModel</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+ <dependency>
+ <groupId>no.bioforsk.vips.model</groupId>
+ <artifactId>SeptoriaApiicolaModel</artifactId>
+ <version>1.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>SeptoriaHumidityModel</artifactId>
+ <version>2.0.0</version>
+ </dependency>
+ <dependency>
+ <groupId>no.nibio.vips.model</groupId>
+ <artifactId>SeptoriaReferenceHumidityModel</artifactId>
+ <version>1.0.1</version>
+ </dependency>
</dependencies>
\ No newline at end of file
diff --git a/models_sample.xml b/models_sample.xml
index 22171b4b0859b4f216a56b728bcf9b9d501a2f26..6355573e291df29da5546da51371ef2489578976 100644
--- a/models_sample.xml
+++ b/models_sample.xml
@@ -1,3 +1,4 @@
+<!-- Example alternative list of model dependencies. Copy and use according to README.md -->
<dependencies>
<dependency>
<groupId>no.nibio.vips.model</groupId>
diff --git a/pom.xml b/pom.xml
index 76e717425cfff25a091f16452534674c1db93154..84920f92d8abf18c542c513ded97e256b207f0a3 100755
--- a/pom.xml
+++ b/pom.xml
@@ -161,7 +161,7 @@
<name>copyright</name>
<!-- copyright tag for classes and interfaces -->
<placement>t</placement>
- <head>© Copyright</head>
+ <head>Copyright</head>
</tag>
</tags>
</configuration>
diff --git a/src/main/webapp/WEB-INF/jboss-deployment-structure.xml b/src/main/webapp/WEB-INF/jboss-deployment-structure.xml
index 0d8a4e7d4cfd034496218dcac00a9110bf1c63cf..acc7ff4f0051b77a911bd6bfadfda38af5e42bfe 100755
--- a/src/main/webapp/WEB-INF/jboss-deployment-structure.xml
+++ b/src/main/webapp/WEB-INF/jboss-deployment-structure.xml
@@ -22,6 +22,8 @@ along with VIPSCore. If not, see <http://www.nibio.no/licenses/>.
<dependencies>
</dependencies>
-
+ <exclusions>
+ <module name="org.jboss.resteasy.resteasy-json-binding-provider"/>
+ </exclusions>
</deployment>
</jboss-deployment-structure>