Added documentation for JavaScript.

README.md

@@ -126,4 +126,7 @@ With the default configuration the initial setup user interface can be accessed
 ### API for Administration and Mapping
 The adapter provides REST interfaces for administration and mapping. The documentation is currently generated automatically when building the adapter. Unit test execution must not be skipped in this case when building the adapter. The documentation can be 
  found at docs/api-guide.html. If the Adapter has been started by command line without changing the port, then the guide is available at http://localhost:8081/docs/api-guide.html.
+
+The JavaScript API that is used to create rules and transformations is generated automatically when running the adapter. The script can be 
+ found at scripts/to-dhis2-all-mapping.js. If the Adapter has been started by command line without changing the port, then the guide is available at http://localhost:8081/scripts/to-dhis2-all-mapping.js.
 

app/src/main/java/org/dhis2/fhir/adapter/WebSecurityConfig.java

@@ -83,6 +83,7 @@ protected void configure( @Nonnull HttpSecurity http ) throws Exception
             .antMatchers( HttpMethod.GET, "/actuator/info" ).permitAll()
             .antMatchers( HttpMethod.GET, "/docs/**" ).permitAll()
             .antMatchers( HttpMethod.GET, "/dhis/metadata/**" ).permitAll()
+            .antMatchers( HttpMethod.GET, "/script/**" ).permitAll()
             .antMatchers( HttpMethod.OPTIONS, "/api/**" ).permitAll()
             .antMatchers( "/actuator/**" ).hasRole( AdapterAuthorities.ADMINISTRATION_AUTHORITY )
             .anyRequest().authenticated()

app/src/main/java/org/dhis2/fhir/adapter/setup/ReferenceSetup.java

@@ -28,6 +28,7 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+import org.apache.commons.lang3.StringUtils;
 import org.dhis2.fhir.adapter.dhis.model.Reference;
 import org.dhis2.fhir.adapter.dhis.model.ReferenceType;
 
@@ -101,7 +102,7 @@ public void setReferenceValue( String referenceValue )
     @Nonnull
     public Reference getReference()
     {
-        return new Reference( getReferenceValue(), getReferenceType() );
+        return new Reference( StringUtils.trimToNull( getReferenceValue() ), getReferenceType() );
     }
 
     @Nonnull

common/pom.xml

@@ -54,5 +54,10 @@
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-data-redis</artifactId>
     </dependency>
+
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-text</artifactId>
+    </dependency>
   </dependencies>
 </project>

common/src/main/java/org/dhis2/fhir/adapter/geo/GeoBasePackage.java

@@ -0,0 +1,38 @@
+package org.dhis2.fhir.adapter.geo;
+
+/*
+ * Copyright (c) 2004-2018, University of Oslo
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * Neither the name of the HISP project nor the names of its contributors may
+ * be used to endorse or promote products derived from this software without
+ * specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/**
+ * Marker interface that is used to reference package as base package.
+ *
+ * @author volsch
+ */
+public interface GeoBasePackage
+{
+}

common/src/main/java/org/dhis2/fhir/adapter/geo/Geometry.java

@@ -28,7 +28,7 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import org.dhis2.fhir.adapter.Scriptable;
+import org.dhis2.fhir.adapter.scriptable.Scriptable;
 
 /**
  * Base interface for geometry objects.

common/src/main/java/org/dhis2/fhir/adapter/geo/Location.java

@@ -28,7 +28,9 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-import org.dhis2.fhir.adapter.Scriptable;
+import org.dhis2.fhir.adapter.scriptable.ScriptMethod;
+import org.dhis2.fhir.adapter.scriptable.ScriptType;
+import org.dhis2.fhir.adapter.scriptable.Scriptable;
 
 import java.io.Serializable;
 import java.util.Objects;
@@ -39,6 +41,7 @@
  * @author volsch
  */
 @Scriptable
+@ScriptType( value = "Location", description = "Point geometry with a longitude and latitude." )
 public class Location implements Geometry, Serializable
 {
     private static final long serialVersionUID = 7916805545140123930L;
@@ -58,17 +61,20 @@ public Location( double longitude, double latitude )
         this.latitude = latitude;
     }
 
+    @ScriptMethod( description = "Returns the longitude of the point geometry." )
     public double getLongitude()
     {
         return longitude;
     }
 
+    @ScriptMethod( description = "Returns the latitude of the point geometry." )
     public double getLatitude()
     {
         return latitude;
     }
 
     @Override
+    @ScriptMethod
     public boolean equals( Object o )
     {
         if ( this == o ) return true;

common/src/main/java/org/dhis2/fhir/adapter/scriptable/ScriptMethod.java

@@ -0,0 +1,63 @@
+package org.dhis2.fhir.adapter.scriptable;
+
+/*
+ * Copyright (c) 2004-2018, University of Oslo
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * Neither the name of the HISP project nor the names of its contributors may
+ * be used to endorse or promote products derived from this software without
+ * specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+import java.lang.annotation.Documented;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Methods that are annotated by this annotation are either included in
+ * script type as properties with optional getters and setters or as functions
+ * (depending on their signature.
+ *
+ * @author volsch
+ */
+@Target( { ElementType.METHOD } )
+@Retention( RetentionPolicy.RUNTIME )
+@Documented
+public @interface ScriptMethod
+{
+    /**
+     * @return the description of the script method.
+     */
+    String description() default "";
+
+    /**
+     * @return the definition of the script method arguments.
+     */
+    ScriptMethodArg[] args() default {};
+
+    /**
+     * @return the description of the return value (if any).
+     */
+    String returnDescription() default "";
+}

common/src/main/java/org/dhis2/fhir/adapter/scriptable/ScriptMethodArg.java

@@ -0,0 +1,57 @@
+package org.dhis2.fhir.adapter.scriptable;
+
+/*
+ * Copyright (c) 2004-2018, University of Oslo
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * Neither the name of the HISP project nor the names of its contributors may
+ * be used to endorse or promote products derived from this software without
+ * specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+import java.lang.annotation.Documented;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Method arguments that are annotated by this annotation are documented in the
+ * script with the specified documentation.
+ *
+ * @author volsch
+ */
+@Target( { ElementType.PARAMETER } )
+@Retention( RetentionPolicy.RUNTIME )
+@Documented
+public @interface ScriptMethodArg
+{
+    /**
+     * @return the name of the script method argument.
+     */
+    String value();
+
+    /**
+     * @return the description of the script method argument.
+     */
+    String description() default "";
+}

common/src/main/java/org/dhis2/fhir/adapter/scriptable/ScriptType.java

@@ -0,0 +1,71 @@
+package org.dhis2.fhir.adapter.scriptable;
+
+/*
+ * Copyright (c) 2004-2018, University of Oslo
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * Neither the name of the HISP project nor the names of its contributors may
+ * be used to endorse or promote products derived from this software without
+ * specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+import java.lang.annotation.Documented;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Inherited;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Classes or interfaces that are annotated by this annotation will be includes
+ * as a class in a scripting language. An instance of this class will be available
+ * as variable.
+ *
+ * @author volsch
+ */
+@Target( { ElementType.TYPE } )
+@Retention( RetentionPolicy.RUNTIME )
+@Documented
+@Inherited
+public @interface ScriptType
+{
+    /**
+     * @return the name of the type (can be instantiated with new in script).
+     */
+    String value();
+
+    /**
+     * @return the name of the variable to which the instance of this type is assigned.
+     */
+    String var() default "";
+
+    /**
+     * @return the description of the script type.
+     */
+    String description() default "";
+
+    /**
+     * @return the name of the transformation data type that is associated with this type
+     * or an empty string if no transformation data type is associated with this type.
+     */
+    String transformDataType() default "";
+}

common/src/main/java/org/dhis2/fhir/adapter/Scriptable.java → common/src/main/java/org/dhis2/fhir/adapter/scriptable/Scriptable.java

@@ -1,4 +1,4 @@
-package org.dhis2.fhir.adapter;
+package org.dhis2.fhir.adapter.scriptable;
 
 /*
  * Copyright (c) 2004-2018, University of Oslo

common/src/main/java/org/dhis2/fhir/adapter/scriptable/generator/JavaScriptGeneratorConfig.java

@@ -0,0 +1,51 @@
+package org.dhis2.fhir.adapter.scriptable.generator;
+
+/*
+ * Copyright (c) 2004-2018, University of Oslo
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * Neither the name of the HISP project nor the names of its contributors may
+ * be used to endorse or promote products derived from this software without
+ * specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/**
+ * The configuration of the JavaScript generator. If this configuration is
+ * present as bean the controller will also be available.
+ *
+ * @author volsch
+ */
+public class JavaScriptGeneratorConfig
+{
+    private Class[] basePackageClasses;
+
+    public Class[] getBasePackageClasses()
+    {
+        return basePackageClasses;
+    }
+
+    public JavaScriptGeneratorConfig setBasePackageClasses( Class... basePackageClasses )
+    {
+        this.basePackageClasses = basePackageClasses;
+        return this;
+    }
+}