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Commit 71479aa6 authored by Tor-Einar Skog's avatar Tor-Einar Skog
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Include all current models, add to README

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1 merge request!7Gnuaffero
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Stage: test
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.gitignore
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...@@ -8,3 +8,4 @@ jboss/ ...@@ -8,3 +8,4 @@ jboss/
/.idea/ /.idea/
.vscode/settings.json .vscode/settings.json
.settings/org.eclipse.core.resources.prefs .settings/org.eclipse.core.resources.prefs
pom_with_models.xml
README.md
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...@@ -26,6 +26,8 @@ or on Windows ...@@ -26,6 +26,8 @@ or on Windows
$ mvnw.cmd clean install $ 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 Download and install [WildFly](https://www.wildfly.org/) >= 25.0.1
Deploy the build from this project in Wildfly. Deploy the build from this project in Wildfly.
...@@ -33,36 +35,22 @@ 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 Wildfly should run on Java >= 11
### Adding models ### Adding models
To add models, create this folder in WildFly: Models are listed as dependencies in the POM and built into the WARfile. In order to make it possible
`[WILDFLY_ROOT]/modules/no/nibio/vips/modelcontainer/main/` to configure your own set of models to include, we have separated the model dependencies out in a
Add the model jar file, and edit module.xml accordingly. separate file. The default is `models.xml`, and contains the models that VIPS in Norway are using
currently.
``` xml
<?xml version="1.0" encoding="UTF-8"?> To build the package with the default set of models, run
<!--
&copy; 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>
```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 ## Implement a model
See [implement_model.md](./docs/implement_model.md) See [implement_model.md](./docs/implement_model.md)
......
build_with_models.py
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#!/usr/bin/python3 #!/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 import sys
from xml.dom.minidom import parse, parseString import subprocess
from xml.dom.minidom import parse
# Default
models_xml_path = "models.xml" models_xml_path = "models.xml"
merged_pom_filename = "pom_with_models.xml"
# Accept alternative models.xml file
if len(sys.argv) > 1: if len(sys.argv) > 1:
models_xml_path = sys.argv[1] models_xml_path = sys.argv[1]
pom_file = open("pom.xml") # Read contents
models_file = open(models_xml_path) pom_dom = parse("pom.xml")
try:
pom_dom = parse(pom_file) models_dom = parse(models_xml_path)
models_dom = parse(models_file) 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") model_dep_elements = models_dom.getElementsByTagName("dependency")
for dep in model_dep_elements: 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() # Build VIPSCore with Maven, using the merged pom
pom_file.close() subprocess.run("./mvnw clean install -f %s" % merged_pom_filename, shell=True)
models.xml
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<dependencies> <dependencies>
<dependency> <dependency>
<groupId>no.nibio.vips.model</groupId> <groupId>no.nibio.vips.model</groupId>
<artifactId>BremiaLactucaeModel</artifactId> <artifactId>AlternariaModel</artifactId>
<version>2.0.0</version> <version>1.0.2</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>no.nibio.vips.model</groupId> <groupId>no.nibio.vips.model</groupId>
<artifactId>PsilaRosaeTempModel</artifactId> <artifactId>AppleScabModel</artifactId>
<version>1.0.0</version> <version>1.0.1</version>
</dependency> </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> </dependencies>
\ No newline at end of file
models_sample.xml
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<!-- Example alternative list of model dependencies. Copy and use according to README.md -->
<dependencies> <dependencies>
<dependency> <dependency>
<groupId>no.nibio.vips.model</groupId> <groupId>no.nibio.vips.model</groupId>
......
pom.xml
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...@@ -161,7 +161,7 @@ ...@@ -161,7 +161,7 @@
<name>copyright</name> <name>copyright</name>
<!-- copyright tag for classes and interfaces --> <!-- copyright tag for classes and interfaces -->
<placement>t</placement> <placement>t</placement>
<head>&copy; Copyright</head> <head>Copyright</head>
</tag> </tag>
</tags> </tags>
</configuration> </configuration>
......
src/main/webapp/WEB-INF/jboss-deployment-structure.xml
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...@@ -22,6 +22,8 @@ along with VIPSCore. If not, see <http://www.nibio.no/licenses/>. ...@@ -22,6 +22,8 @@ along with VIPSCore. If not, see <http://www.nibio.no/licenses/>.
<dependencies> <dependencies>
</dependencies> </dependencies>
<exclusions>
<module name="org.jboss.resteasy.resteasy-json-binding-provider"/>
</exclusions>
</deployment> </deployment>
</jboss-deployment-structure> </jboss-deployment-structure>
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