initial commit

Author: olinux

.github/workflows/build.yml

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+# MIT licensed
+name: openMINDS_java_build_pipeline
+
+on:
+  push:
+      branches:
+        - pipeline
+  workflow_dispatch: # This triggers the workflow when a webhook is received
+
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout Repository
+      uses: actions/checkout@v3
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.11
+
+    - name: Run build
+      run: |
+        pip install -r requirements.txt
+        python build.py
+
+    - name: Checkout main branch
+      uses: actions/checkout@v3
+      with:
+        ref: main
+        path: main
+        token: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Push to main
+      run: |
+        cp -R target/* main
+        cd main
+        rm -rf build openMINDS.egg-info
+        git config --global user.email "openminds@ebrains.eu"
+        git config --global user.name "openMINDS pipeline"
+        if [[ $(git add . --dry-run | wc -l) -gt 0 ]]; then
+            git add .
+            git commit -m "build triggered by submodule ${{ inputs.repository }} version ${{ inputs.branch }}"
+            git push -f
+        else
+            echo "Nothing to commit"
+        fi

.gitignore

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+sources/**
+target/**
+.idea/**
+src/**

build.py

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+import os.path
+import shutil
+
+from jinja2 import Environment, PackageLoader, select_autoescape
+
+from pipeline.translator import JavaBuilder
+from pipeline.utils import clone_sources, SchemaLoader
+
+print("***************************************")
+print(f"Triggering the generation of Java classes for openMINDS")
+print("***************************************")
+
+# Step 1 - clone central repository in main branch to get the latest sources
+clone_sources()
+schema_loader = SchemaLoader()
+if os.path.exists("target"):
+    shutil.rmtree("target")
+
+ignored_versions = ["v1.0", "v2.0"]
+relevant_versions = [v for v in schema_loader.get_schema_versions() if v not in ignored_versions]
+
+
+def build_central():
+    env = Environment(
+        loader=PackageLoader("generator"),
+        autoescape=select_autoescape()
+    )
+    template = env.get_template("OpenMINDS.java.j2")
+    result = template.render(
+        relevant_versions = built_versions,
+        packages_by_version = packages_by_version
+    )
+    target_file = "target/src/main/java/org/openmetadatainitiative/openminds/OpenMINDS.java"
+    os.makedirs(os.path.dirname(target_file), exist_ok=True)
+    with open(target_file, "w") as target_file:
+        target_file.write(result)
+
+built_versions = []
+packages_by_version = {}
+
+
+for schema_version in relevant_versions:
+    # Step 2 - find all involved schemas for the current version
+    schemas_file_paths = schema_loader.find_schemas(schema_version)
+    type_to_class_name = {}
+    implemented_interfaces = {}
+    builders = []
+    for schema_file_path in schemas_file_paths:
+        builder = JavaBuilder(schema_file_path, schema_loader.schemas_sources)
+        if builder.version not in packages_by_version:
+            packages_by_version[builder.version] = {}
+        if builder.relative_path_without_extension[0] not in packages_by_version[builder.version]:
+            packages_by_version[builder.version][builder.relative_path_without_extension[0]] = []
+        packages_by_version[builder.version][builder.relative_path_without_extension[0]].append((builder.class_name, builder.canonical_class_name()))
+        if builder.version not in built_versions:
+            built_versions.append(builder.version)
+        for property, types in builder.additional_interfaces.items():
+            for t in types:
+                if t not in implemented_interfaces:
+                    implemented_interfaces[t] = []
+                implemented_interfaces[t].append(f"{builder.interface_path(property).replace('/', '.')}")
+        type_to_class_name[builder.type]=builder.canonical_class_name()
+        builders.append(builder)
+
+
+    for builder in builders:
+        # Step 3 - translate and build each openMINDS schema as JSON-Schema
+        builder.build(type_to_class_name, implemented_interfaces)
+
+build_central()

generator/__init__.py

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+package org.openmetadatainitiative.openminds;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.openmetadatainitiative.openminds.utils.Instance;
+import org.openmetadatainitiative.openminds.utils.OpenMINDSContext;
+import org.openmetadatainitiative.openminds.utils.ParsingUtils;
+import org.openmetadatainitiative.openminds.utils.LocalId;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Stream;
+
+/**
+ * ATTENTION! This is an autogenerated file based on the openMINDS schema - do not apply manual changes since they are going to be overwritten.
+ */
+public class OpenMINDS {
+
+    private final OpenMINDSContext context;
+
+    private OpenMINDS(OpenMINDSContext context){
+        this.context = context;
+    }
+
+    private static void persist(String targetDirectory, Stream<Instance> instances){
+        File dir = new File(targetDirectory);
+        if(!dir.exists()){
+            dir.mkdirs();
+        }
+        instances.forEach(i -> {
+            File f = new File(targetDirectory+File.separator+i.getLocalId().id()+".jsonld");
+            try {
+                ParsingUtils.OBJECT_MAPPER.writerWithDefaultPrettyPrinter().writeValue(f, i);
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        });
+    }
+
+    {% for version in relevant_versions %}
+    public static OpenMINDS.{{version[0]|upper}}{{version[1:]}} {{version}}(){
+        return {{version}}(OpenMINDSContext.defaultContext());
+    }
+
+    public static OpenMINDS.{{version[0]|upper}}{{version[1:]}} {{version}}(String idPrefix){
+        return {{version}}(new OpenMINDSContext(idPrefix, true));
+    }
+
+    private static OpenMINDS.{{version[0]|upper}}{{version[1:]}} {{version}}(OpenMINDSContext context) {
+        return new OpenMINDS(context).new {{version[0]|upper}}{{version[1:]}}();
+    }
+
+
+
+    public class {{version[0]|upper}}{{version[1:]}} {
+
+        private final List<org.openmetadatainitiative.openminds.utils.Builder<?>> builders = new ArrayList<>();
+
+        {% for package in packages_by_version[version].keys() %}
+        public final OpenMINDS.{{version[0]|upper}}{{version[1:]}}.{{package[0]|upper}}{{package[1:]}} {{package}} = new {{package[0]|upper}}{{package[1:]}}();
+
+
+        public class {{package[0]|upper}}{{package[1:]}}{
+
+            {% for class in packages_by_version[version][package] %}
+            public final OpenMINDS.{{version[0]|upper}}{{version[1:]}}.{{package[0]|upper}}{{package[1:]}}.{{class[0]}} {{class[0][0]|lower}}{{class[0][1:]}} = new {{class[0]}}();
+
+            public class {{class[0]}} {
+
+                public {{class[1]}}.Builder create(String localId){
+                    final {{class[1]}}.Builder builder = {{class[1]}}.create(new LocalId(localId));
+                    builders.add(builder);
+                    return builder;
+                }
+            }
+            {% endfor %}
+        }
+        {% endfor %}
+
+       public void persist(String targetDirectory) {
+            OpenMINDS.persist(targetDirectory, builders.stream().map(Builder::build));
+        }
+    }
+
+    {% endfor %}
+
+}

generator/templates/OpenMINDS.java.j2

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+package {{package_name}};
+
+import org.openmetadatainitiative.openminds.utils.ByTypeDeserializer;
+import org.openmetadatainitiative.openminds.utils.Entity;
+import org.openmetadatainitiative.openminds.utils.Reference;
+
+/**
+ * ATTENTION! This is an autogenerated file based on the openMINDS schema - do not apply manual changes since they are going to be overwritten.
+ */
+public interface {{additional_interface}} extends Entity {
+   Reference<? extends {{additional_interface}}> getReference();
+
+   class Deserializer extends ByTypeDeserializer<{{additional_interface}}> {
+        public Deserializer() {
+            super({{types|join(', ')}});
+        }
+    }
+}

generator/templates/interface.java.j2

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+package {{package_name}};
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import org.openmetadatainitiative.openminds.utils.*;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+
+{% for import in imports %}import {{import}};
+{% endfor %}
+
+import static {{package_name}}.{{ class_name }}.*;
+/**
+ {{java_doc}}
+ *
+ * ATTENTION! This is an autogenerated file based on the openMINDS schema - do not apply manual changes since they are going to be overwritten.
+ */
+@InstanceType(SEMANTIC_NAME)
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class {{ class_name }} extends Instance {% if implemented_interfaces %}implements {{ implemented_interfaces|join(', ') }}{% endif %}{
+    static final String SEMANTIC_NAME = "{{ type }}";
+
+    @JsonIgnore
+    public Reference<{{ class_name }}> getReference() {
+        return doGetReference();
+    }
+
+    public static Reference<{{ class_name }}> createReference(InstanceId instanceId) {
+        return new Reference<>(instanceId);
+    }
+
+    private {{ class_name }}(LocalId localId ) {
+        super(localId);
+    }
+
+
+    public class Builder implements org.openmetadatainitiative.openminds.utils.Builder<{{ class_name }}>{
+        {% for property in properties %}{% for line in builder_for_properties[property] %}
+        {{ line }}
+        {% endfor %}{% endfor %}
+
+        public {{ class_name }} build() {
+            if ({{ class_name }}.this.id == null) {
+                {{ class_name }}.this.id = new InstanceId(UUID.randomUUID().toString());
+            }
+            if({{ class_name }}.this.types == null || {{ class_name }}.this.types.isEmpty() || !{{ class_name }}.this.types.contains(SEMANTIC_NAME)){
+                final List<String> oldValues = {{ class_name }}.this.types;
+                {{ class_name }}.this.types = new ArrayList<>();
+                {{ class_name }}.this.types.add(SEMANTIC_NAME);
+                if(oldValues != null){
+                    {{ class_name }}.this.types.addAll(oldValues);
+                }
+            }
+            return {{ class_name }}.this;
+        }
+    }
+
+{% for property in properties %}   @JsonProperty(value = "{%if property in absolute_property_translations%}{{absolute_property_translations[property]}}{%else%}{{property}}{%endif%}")
+    {{member_for_properties[property]}}
+    {%if property in property_descriptions and property_descriptions[property] %}
+    /**
+    * {{property_descriptions[property]}}
+    */{% endif %}
+    {{getter_for_properties[property]}}
+
+ {% endfor %}
+    public static {{ class_name }}.Builder create(LocalId localId){
+        return new {{ class_name }}(localId).new Builder();
+    }
+
+    public {{ class_name }}.Builder copy(){
+        return ParsingUtils.OBJECT_MAPPER.convertValue(this, {{ class_name }}.class).new Builder();
+    }
+}