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Merge pull request #1 from junqi108/AoMedium_plugin-functionality
Update from upstream
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,3 +1,3 @@ | ||
| [submodule "templates"] | ||
| path = templates | ||
| url = https://github.com/junqi108/functional-structural-model-templates.git | ||
| url = https://github.com/junqi108/functional-structural-model-templates |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,19 @@ | ||
| import java.io.File; | ||
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| import com.fasterxml.jackson.databind.ObjectMapper; | ||
| import com.fasterxml.jackson.dataformat.yaml.YAMLFactory; | ||
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| import models.config.ConfigFile; | ||
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| public class FileReader { | ||
| // public FileReader() { | ||
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| // } | ||
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| // public ConfigFile readConfig(String path) { | ||
| // File file = new File("src/simulationModels/test.json"); | ||
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| // ObjectMapper mapper = new ObjectMapper(); | ||
| // ConfigFile config = mapper.readValue(file, ConfigFile.class); | ||
| // } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,31 @@ | ||
| package functions; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| public class FunctionCollector { | ||
| // XCompiler unable to compile <> with type <IFunction>, so left generic | ||
| private List functions; | ||
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| public FunctionCollector() { | ||
| init(); | ||
| } | ||
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| public void init() { | ||
| functions = new ArrayList(); | ||
| } | ||
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| public void run() { | ||
| for (IFunction function : functions) { | ||
| function.run(); | ||
| } | ||
| } | ||
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| public void add(IFunction function) { | ||
| functions.add(function); | ||
| } | ||
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| public List getFunctions() { | ||
| return functions; | ||
| } | ||
| } |
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| @@ -0,0 +1,11 @@ | ||
| package functions; | ||
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| public class Growth implements IFunction { | ||
| public void init() { | ||
| println("init Growth"); | ||
| } | ||
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| public void run() { | ||
| println("run Growth"); | ||
| } | ||
| } |
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| @@ -0,0 +1,6 @@ | ||
| package functions; | ||
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| public interface IFunction { | ||
| void init(); | ||
| void run(); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| package functions; | ||
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| public class LightInterception implements IFunction { | ||
| public void init() { | ||
| println("init LightInterception"); | ||
| } | ||
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| public void run() { | ||
| println("run LightInterception"); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,49 +1,43 @@ | ||
| /** | ||
| * The base module for all organs. | ||
| * | ||
| * @author James Bristow | ||
| * @version 1.0 | ||
| * @since 04-08-2022 | ||
| */ | ||
| abstract module Organ(float len) extends Sphere(0.1) | ||
| { | ||
| {setShader(GREEN);} | ||
| } | ||
| import java.util.List; | ||
| import java.util.ArrayList; | ||
| import java.io.File; | ||
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| /** | ||
| * The bud organ. | ||
| * | ||
| * @author James Bristow | ||
| * @version 1.0 | ||
| * @since 04-08-2022 | ||
| */ | ||
| module Bud extends Organ(0.1) { | ||
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| protected int ID; | ||
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| /** | ||
| * Gets a plant ID value. | ||
| * | ||
| * @return The organ ID. | ||
| */ | ||
| public int getID() { | ||
| return ID; | ||
| } | ||
| } | ||
| import com.fasterxml.jackson.databind.ObjectMapper; | ||
| import com.fasterxml.jackson.databind.JsonNode; | ||
| import com.fasterxml.jackson.dataformat.yaml.YAMLFactory; | ||
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| import models.*; | ||
| import functions.*; | ||
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| static List organs = new ArrayList(); | ||
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| protected void init() { | ||
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| Leaf leaf = new Leaf(); | ||
| File organConfig = new File("/var/model/src/organConfig.yml"); | ||
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| /** | ||
| * Initialise the model. | ||
| * | ||
| */ | ||
| protected void init () | ||
| [ | ||
| Axiom ==> Bud; | ||
| ] | ||
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| /** | ||
| * Runs each time step of the simulation. | ||
| */ | ||
| public void run () | ||
| [ | ||
| Bud ==> F(0.5) [RU(30) RH(90) Bud] [RU(-30) RH(90) Bud]; | ||
| ] | ||
| ObjectMapper mapper = new ObjectMapper(new YAMLFactory()); | ||
| JsonNode organTree = mapper.readTree(organConfig); | ||
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| for (JsonNode organNode : organTree) { | ||
| // Create organ instances | ||
| String organName = organNode.get("name"); | ||
| Class organClass = Class.forName(organName); | ||
| GenericOrgan organ = (GenericOrgan) organClass.getDeclaredConstructor().newInstance(); | ||
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| JsonNode functions = organNode.get("functions"); | ||
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| for (JsonNode functionName : functions) { | ||
| String className = functionName.asText(); | ||
| Class functionClass = Class.forName(className); | ||
| IFunction function = (IFunction) functionClass.getDeclaredConstructor().newInstance(); | ||
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| organ.getCollector().add(function); | ||
| } | ||
| } | ||
| } | ||
| public void run() { | ||
| for (GenericOrgan organ : organs) { | ||
| organ.run(); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| import models.GenericOrgan; | ||
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| public class Fruit extends GenericOrgan { | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| package models; | ||
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| import functions.FunctionCollector; | ||
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| public abstract class GenericOrgan { | ||
| private FunctionCollector collector; | ||
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| public FunctionCollector getCollector() { | ||
| return collector; | ||
| } | ||
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| public void run() { | ||
| collector.run(); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| import models.GenericOrgan; | ||
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| public class Leaf extends GenericOrgan { | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| package models.config; | ||
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| public class BooleanField extends Field { | ||
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| private boolean value; | ||
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| public BooleanField(String name, boolean value) { | ||
| super(name); | ||
| this.value = value; | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| package models.config; | ||
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| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.Map; | ||
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| import com.fasterxml.jackson.annotation.*; | ||
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| public class ConfigFile { | ||
| private Map fields; | ||
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| public ConfigFile() { | ||
| fields = new HashMap(); | ||
| } | ||
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| @JsonAnySetter | ||
| public void addField(String name, String value) { | ||
| fields.put(name, value); | ||
| } | ||
|
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| public Map getFields() { | ||
| return fields; | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| package models.config; | ||
|
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| abstract class Field { | ||
| private String name; | ||
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| public Field(String name) { | ||
| this.name = name; | ||
| } | ||
|
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| public String getName() { | ||
| return name; | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| leaf: | ||
| name: models.Leaf | ||
| functions: | ||
| - functions.Growth | ||
| - functions.LightInterception | ||
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| fruit: | ||
| name: models.Fruit | ||
| functions: | ||
| - functions.Growth |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| name: Simple Model | ||
| configs: | ||
| - environmentConfig.yml | ||
| - organConfig.yml |