Merge pull request #37 from NeuroML/development

Updates for v2.3
NeuroML · Sep 20, 2023 · fe071d7 · fe071d7
2 parents 981e8b6 + 3639254
commit fe071d7
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Showing 9 changed files with 130 additions and 38 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -15,69 +15,71 @@ jobs:
     runs-on: ${{ matrix.runs-on }}
     strategy:
       fail-fast: false
-      matrix:        
-        java: [ '8', '11', '16', '17' ]
-        runs-on: [ubuntu-latest, macos-11, windows-latest]
+      matrix:
+        java: [ '8', '11', '16', '17', '19' ]
+        runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up JDK ${{ matrix.Java }}
-      uses: actions/setup-java@v2
+      uses: actions/setup-java@v3
       with:
         java-version: ${{ matrix.Java }}
         distribution: 'temurin'
-        
+
     - name: Install and test (non Win)
+      env:
+        main_repo_branch: ${GITHUB_REF_NAME}
       if: ${{ matrix.runs-on != 'windows-latest' }}
       run: |
         # Install org.neuroml.model.injectingplugin
-        
+
         export main_repo_branch=${{env.main_repo_branch}}
         if [[ ${main_repo_branch} != "master" && ${main_repo_branch} != "development" && ${main_repo_branch} != "experimental" && ${main_repo_branch} != *"osb"* ]]; then main_repo_branch=development ; fi
         echo Using branch $main_repo_branch
-        
+
         git clone https://github.com/NeuroML/org.neuroml.model.injectingplugin.git
         cd org.neuroml.model.injectingplugin
         git checkout $main_repo_branch
         mvn install
         cd ..
-        
+
         # Install NeuroML2
         git clone https://github.com/NeuroML/NeuroML2.git
         cd NeuroML2
         git checkout $main_repo_branch
         mvn install
         cd ..
-        
+
         # Install this package and test with Maven
         pwd
         mvn install
         mvn dependency:tree
-        
+
     - name: Install and test (Win)
       if: ${{ matrix.runs-on == 'windows-latest' }}
       run: |
         # Install org.neuroml.model.injectingplugin
-        
+
         $env:main_repo_branch=$env:GITHUB_REF_NAME
         if ( $env:main_repo_branch -ne "master" -and $env:main_repo_branch -ne "development" -and $env:main_repo_branch -ne "experimental" -and $env:main_repo_branch -notlike '*osb*' ) { $env:main_repo_branch="development" }
         echo "Using branch $env:main_repo_branch..."
-        
+
         git clone https://github.com/NeuroML/org.neuroml.model.injectingplugin.git
         cd org.neuroml.model.injectingplugin
         git checkout $env:main_repo_branch
         mvn install
         cd ..
-        
+
         # Install NeuroML2
         echo Using branch $env:GITHUB_REF_NAME
         git clone https://github.com/NeuroML/NeuroML2.git
         cd NeuroML2
         git checkout $env:main_repo_branch
         mvn install
         cd ..
-        
+
         # Install this package and test with Maven
         pwd
         mvn install

diff --git a/.github/workflows/javadocs.yml b/.github/workflows/javadocs.yml
@@ -2,7 +2,7 @@ name: Publish javadocs
 
 on:
   push:
-    branches: [ development ]
+    branches: [ development, experimental ]
 
 jobs:
   build:
@@ -11,10 +11,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v1
       with:
-        java-version: 11
+        java-version: 17
         java-package: jdk
 
     - name: Set up Python 3.9

diff --git a/README.md b/README.md
@@ -2,6 +2,9 @@ NeuroML v2 Model Java API
 =========================
 
 [![Java CI with Maven](https://github.com/NeuroML/org.neuroml.model/actions/workflows/ci.yml/badge.svg)](https://github.com/NeuroML/org.neuroml.model/actions/workflows/ci.yml)
+[![pages-build-deployment](https://github.com/NeuroML/org.neuroml.model/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/NeuroML/org.neuroml.model/actions/workflows/pages/pages-build-deployment)
+[![Publish javadocs](https://github.com/NeuroML/org.neuroml.model/actions/workflows/javadocs.yml/badge.svg)](https://github.com/NeuroML/org.neuroml.model/actions/workflows/javadocs.yml)
+
 [![GitHub](https://img.shields.io/github/license/NeuroML/org.neuroml.model)](https://github.com/NeuroML/org.neuroml.model/blob/master/LICENSE.lesser)
 [![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuroML/org.neuroml.model)](https://github.com/NeuroML/org.neuroml.model/pulls)
 [![GitHub issues](https://img.shields.io/github/issues/NeuroML/org.neuroml.model)](https://github.com/NeuroML/org.neuroml.model/issues)
@@ -23,4 +26,6 @@ A collection of models in NeuroML can be found on the [Open Source Brain](http:/
 
 This code is distributed under the terms of the GNU Lesser General Public License.
 
-API documentation can be found [here](http://neuroml.github.io/org.neuroml.model/index.html).
+API documentation can be found [here](http://neuroml.github.io/org.neuroml.model/index.html).  
+
+
diff --git a/pom.xml b/pom.xml
@@ -3,10 +3,10 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.neuroml.model</groupId>
     <artifactId>org.neuroml.model</artifactId>
-    <version>1.8.1</version>
+    <version>1.9.1</version>
     <packaging>bundle</packaging>
     <properties>
-        <build.version2>2.1</build.version2>
+        <build.version2>2.3</build.version2>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     </properties>
     <dependencies>
@@ -19,12 +19,12 @@
         <dependency>
             <groupId>org.neuroml.model.injectingplugin</groupId>
             <artifactId>org.neuroml.model.injectingplugin</artifactId>
-            <version>1.8.1</version>
+            <version>1.9.1</version>
         </dependency>
         <dependency>
             <groupId>org.neuroml.core</groupId>
             <artifactId>neuroml2-base-definitions</artifactId>
-            <version>1.8.1</version>
+            <version>1.9.1</version>
         </dependency>
 
         <dependency>
@@ -64,7 +64,7 @@
                             &lt;br /&gt;
                             &lt;br /&gt;
                     </top>
-                    <bottom>Copyright NeuroML Contributors 2021</bottom>
+                    <bottom>Copyright NeuroML Contributors 2022</bottom>
                 </configuration>
             </plugin>
             <plugin>
@@ -105,7 +105,7 @@
                         </goals>
                         <configuration>
                             <resourceBundles>
-                                <resourcebundle>org.neuroml.core:neuroml2-base-definitions:1.8.1</resourcebundle>
+                                <resourcebundle>org.neuroml.core:neuroml2-base-definitions:1.9.1</resourcebundle>
                             </resourceBundles>
                         </configuration>
                     </execution>
@@ -198,7 +198,7 @@
                                 <plugin>
                                     <groupId>org.neuroml.model.injectingplugin</groupId>
                                     <artifactId>org.neuroml.model.injectingplugin</artifactId>
-                                    <version>1.8.1</version>
+                                    <version>1.9.1</version>
                                 </plugin>
                             </plugins>
                         </configuration>

diff --git a/src/main/java/org/neuroml/model/util/NeuroML2Validator.java b/src/main/java/org/neuroml/model/util/NeuroML2Validator.java
@@ -44,8 +44,6 @@
 import org.xml.sax.SAXException;
 
 /*
- *        
- *        WORK IN PROGRESS!!!
  *        
  * TODO: Needs to be moved to a separate package for validation!
  */
@@ -488,7 +486,33 @@ public void testValidityAgainstNeuroML2Schema(File xmlFile) throws SAXException,
 			testValidity(xmlFile, new StreamSource(in));
 			validity.append(VALID_AGAINST_SCHEMA);
 		} catch (Exception e) {
-			validity.append("File: "+ xmlFile.getAbsolutePath()+" is not valid against the schema: "+NeuroMLElements.LATEST_SCHEMA+"!!\n"+e.getMessage());
+            String error = e.getMessage();
+
+            StringBuilder formatted = new StringBuilder("  Error when parsing against Schema ("+e.getClass()+"): \n\n    ");
+
+            String indent = new String("    ");
+            for (int i=0; i<error.length(); i++) {
+                char c = error.charAt(i);
+                formatted.append(c);
+                if (c==';') {formatted.append("\n"+indent);}
+                if (c=='.' && i<error.length()-1 && error.charAt(i+1)==' ') {formatted.append("\n"+indent); i+=1;}
+            }
+
+			validity.append("File: "+ xmlFile.getAbsolutePath()+" is not valid against the schema: "+NeuroMLElements.LATEST_SCHEMA+"!!\n"+formatted);
+
+            if (error.indexOf("is not allowed to appear in element")>0) {
+			    validity.append("\n\n  Please check which attributes are allowed in that NeuroML element");
+            }
+            if (error.indexOf("end-tag")>0) {
+			    validity.append("\n\n  Please make sure the XML is formatted correctly");
+            }
+            if (error.indexOf("cvc-complex-type.2.4")>=0) {
+			    validity.append("\n\n  Note 1: if the above mentioned element is not a part of the core NeuroML elements, then the document can't be validated against the Schema. This may not matter if a definition in LEMS is available for that element (e.g. a new ComponentType has been defined and included) and the model should be able to run in simulators that support new LEMS elements." 
+                + "\n\n  Note 2: If the element giving trouble is a core NeuroML element, remember that when validating with the NeuroML Schema, the order of the elements is important. Try switching the order of the above mentioned elements in line with how they are defined in the Schema, keeping elements of the same type together.");
+            }
+
+
+
 		}
 	}
 
@@ -515,11 +539,12 @@ public static void testValidity(File xmlFile, StreamSource schemaFileSource) thr
 
 
 	public static void main(String[] args) throws Exception {
+        File f = new File("../neuroConstruct/osb/showcase/BlueBrainProjectShowcase/NMC/NeuroML2/CaDynamics_E2_NML2.nml");
         //File f = new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/pyr_4_sym.cell.nml");
         //File f = new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/MediumNet.net.nml");
         //File f = new File("../OpenCortex/examples/Deterministic.net.nml");
         //File f = new File("../neuroConstruct/osb/cerebellum/cerebellar_granule_cell/GranuleCell/neuroConstruct/generatedNeuroML2/GranuleCell.net.nml");
-        File f = new File("../git/Documentation/source/Userdocs/NML2_examples/olm.cell.nml");
+        //File f = new File("../git/Documentation/source/Userdocs/NML2_examples/olm.cell.nml");
 
 
         NeuroML2Validator nv = new NeuroML2Validator();

diff --git a/src/main/java/org/neuroml/model/util/NeuroMLElements.java b/src/main/java/org/neuroml/model/util/NeuroMLElements.java
@@ -2,7 +2,7 @@
 
 public class NeuroMLElements {
 
-    public static final String ORG_NEUROML_MODEL_VERSION = "1.8.1";
+    public static final String ORG_NEUROML_MODEL_VERSION = "1.9.1";
 
     public static final String NAMESPACE_URI_VERSION_2 = "http://www.neuroml.org/schema/neuroml2";
 
@@ -16,10 +16,12 @@ public class NeuroMLElements {
     public static final String DEFAULT_SCHEMA_LOCATION_VERSION_2_0 = "https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.0.xsd";
     public static final String DEFAULT_SCHEMA_LOCATION_VERSION_2_1 = "https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.1.xsd";
     public static final String DEFAULT_SCHEMA_LOCATION_VERSION_2_2 = "https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.2.xsd";
+    public static final String DEFAULT_SCHEMA_LOCATION_VERSION_2_3 = "https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd";
 
 
-    public static final String LATEST_SCHEMA = "/Schemas/NeuroML2/NeuroML_v2.2.xsd";
-    public static final String LATEST_SCHEMA_LOCATION = DEFAULT_SCHEMA_LOCATION_VERSION_2_2;
+    public static final String LATEST_SCHEMA_VERSION = "2.3";
+    public static final String LATEST_SCHEMA = "/Schemas/NeuroML2/NeuroML_v"+LATEST_SCHEMA_VERSION+".xsd";
+    public static final String LATEST_SCHEMA_LOCATION = DEFAULT_SCHEMA_LOCATION_VERSION_2_3;
 
     // Top level...
     public static final String NEUROML_ROOT = "neuroml";

diff --git a/src/main/resources/bindings/NeuroML_v2.2.xjb b/src/main/resources/bindings/NeuroML_v2.2.xjb
@@ -0,0 +1,23 @@
+
+<jxb:bindings version="2.0"
+               xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
+               xmlns:xs="http://www.w3.org/2001/XMLSchema">
+
+    <jxb:bindings schemaLocation="../NeuroML_v2.2.xsd" node="/xs:schema">
+
+        <jxb:schemaBindings>
+            <jxb:package name="org.neuroml.model"/>
+        </jxb:schemaBindings>
+
+        <jxb:bindings node=".//xs:attribute[@name='morphology']">
+            <jxb:property name="morphologyAttr"/>
+        </jxb:bindings>
+
+        <jxb:bindings node=".//xs:attribute[@name='biophysicalProperties']">
+            <jxb:property name="biophysicalPropertiesAttr"/>
+        </jxb:bindings>
+
+
+    </jxb:bindings>
+
+</jxb:bindings>
diff --git a/src/main/resources/bindings/NeuroML_v2.3.xjb b/src/main/resources/bindings/NeuroML_v2.3.xjb
@@ -0,0 +1,23 @@
+
+<jxb:bindings version="2.0"
+               xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
+               xmlns:xs="http://www.w3.org/2001/XMLSchema">
+
+    <jxb:bindings schemaLocation="../NeuroML_v2.3.xsd" node="/xs:schema">
+
+        <jxb:schemaBindings>
+            <jxb:package name="org.neuroml.model"/>
+        </jxb:schemaBindings>
+
+        <jxb:bindings node=".//xs:attribute[@name='morphology']">
+            <jxb:property name="morphologyAttr"/>
+        </jxb:bindings>
+
+        <jxb:bindings node=".//xs:attribute[@name='biophysicalProperties']">
+            <jxb:property name="biophysicalPropertiesAttr"/>
+        </jxb:bindings>
+
+
+    </jxb:bindings>
+
+</jxb:bindings>
diff --git a/src/test/java/org/neuroml/model/test/AppTest.java b/src/test/java/org/neuroml/model/test/AppTest.java
@@ -16,11 +16,8 @@
  */
 public class AppTest extends TestCase {
 
-    public void testVersions() throws IOException {
-        System.out.println("Running a test on version usage, making all references to versions are: v" + NeuroMLElements.ORG_NEUROML_MODEL_VERSION + "...");
-
+    private boolean isInPom(String s) throws IOException{
         File pom = new File("pom.xml");
-        String toFind = "<artifactId>org.neuroml.model</artifactId><version>"+NeuroMLElements.ORG_NEUROML_MODEL_VERSION+"</version>";
         InputStream ins = new FileInputStream(pom);
         InputStreamReader insr = new InputStreamReader(ins);
         BufferedReader fr = new BufferedReader(insr);
@@ -32,7 +29,22 @@ public void testVersions() throws IOException {
         fr.close();
         String sdat = sb.toString();
 
-        assert(sdat.indexOf(toFind)>0);
+        return sdat.indexOf(s)>0;
+    }
+
+    public void testVersions() throws IOException {
+        System.out.println("Running a test on version usage, making all references to versions are: v" + NeuroMLElements.ORG_NEUROML_MODEL_VERSION + "...");
+
+
+        String toFind = "<artifactId>org.neuroml.model</artifactId><version>"+NeuroMLElements.ORG_NEUROML_MODEL_VERSION+"</version>";
+
+        assert(isInPom(toFind));
+
+        toFind = "<build.version2>"+NeuroMLElements.LATEST_SCHEMA_VERSION+"</build.version2>";
+
+        assert(isInPom(toFind));
+
+        assert(NeuroMLElements.LATEST_SCHEMA_LOCATION.indexOf(NeuroMLElements.LATEST_SCHEMA_VERSION)>0);
 
     }