Integrated the possibility to import limited metadata by Excel workbo…

…ok. (#1)

* Adds support for importing from Excel sheet.

app/pom.xml

@@ -69,6 +69,11 @@
       <artifactId>dhis2-fhir-adapter-fhir</artifactId>
       <version>${project.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.dhis2.fhir.adapter</groupId>
+      <artifactId>dhis2-fhir-adapter-metadata-sheet</artifactId>
+      <version>${project.version}</version>
+    </dependency>
     <dependency>
       <groupId>org.dhis2.fhir.adapter</groupId>
       <artifactId>dhis2-fhir-adapter-fhir-dstu3</artifactId>

app/src/main/resources/default-application.yml

@@ -32,6 +32,12 @@ server:
   port: 8081
 
 spring:
+  servlet:
+    # Configuration of multipart requests. These are used for metadata sheet
+    # upload only.
+    multipart:
+      max-file-size: 50MB
+      max-request-size: 50MB
   # Settings for the database connection.
   datasource:
     # The JDBC URL of the database in which the Adapter tables are located.

common/src/main/java/org/dhis2/fhir/adapter/model/ValueType.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter.model;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -68,7 +68,7 @@ public enum ValueType
     USERNAME( String.class ),
     FILE_RESOURCE( String.class ),
     COORDINATE( Location.class ),
-    ORGANIZATION_UNIT( Id.class ),
+    ORGANISATION_UNIT( Id.class ),
     AGE( ZonedDateTime.class ),
     URL( String.class ),
     IMAGE( String.class );

common/src/main/java/org/dhis2/fhir/adapter/util/NameUtils.java

@@ -39,6 +39,8 @@
 
 /**
  * Name utilities for converting to enum constants and class names.
+ *
+ * @author volsch
  */
 public abstract class NameUtils
 {
@@ -90,7 +92,7 @@ public static String toEnumName( @Nullable Object value )
         {
             return stringValue;
         }
-        if ( StringUtils.isAllUpperCase( stringValue ) )
+        if ( containsNoLowerCase( stringValue ) )
         {
             return stringValue.replace( '-', '_' );
         }
@@ -99,6 +101,21 @@ public static String toEnumName( @Nullable Object value )
             .filter( v -> !v.equals( "_" ) ).collect( Collectors.joining( "_" ) ).toUpperCase();
     }
 
+    private static boolean containsNoLowerCase( @Nonnull String value )
+    {
+        final int length = value.length();
+
+        for ( int i = 0; i < length; i++ )
+        {
+            if ( Character.isLowerCase( value.charAt( i ) ) )
+            {
+                return false;
+            }
+        }
+
+        return true;
+    }
+
     private NameUtils()
     {
         super();

common/src/test/java/org/dhis2/fhir/adapter/util/NameUtilsTest.java

@@ -89,6 +89,12 @@ public void toEnumNameCamelCaseLower()
         Assert.assertEquals( "TEST_VALUE_1", NameUtils.toEnumName( "testValue1" ) );
     }
 
+    @Test
+    public void toEnumNameUnchanged2()
+    {
+        Assert.assertEquals( "DSTU3", NameUtils.toEnumName( "DSTU3" ) );
+    }
+
     @Test
     public void toClassNameNull()
     {

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/converter/StringToReferenceConverter.java

@@ -58,10 +58,22 @@ public StringToReferenceConverter()
     public Reference doConvert( @Nonnull String source ) throws ConversionException
     {
         final int index = source.indexOf( SEPARATOR );
+        final ReferenceType referenceType;
+
         if ( (index <= 0) || (index + 1 == source.length()) )
         {
             throw new ConversionException( "Reference does not include required separator: " + source );
         }
-        return new Reference( source.substring( index + 1 ), NameUtils.toEnumValue( ReferenceType.class, source.substring( 0, index ) ) );
+
+        try
+        {
+            referenceType = NameUtils.toEnumValue( ReferenceType.class, source.substring( 0, index ) );
+        }
+        catch ( IllegalArgumentException e )
+        {
+            throw new ConversionException( "Reference type is invalid: " + source );
+        }
+
+        return new Reference( source.substring( index + 1 ), referenceType );
     }
 }

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/DataElement.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter.dhis.model;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -39,7 +39,7 @@
  * @author volsch
  */
 @Scriptable
-public interface DataElement
+public interface DataElement extends DhisType
 {
     String getId();
 

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/ImmutableDataElement.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter.dhis.model;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -36,6 +36,7 @@
 
 import javax.annotation.Nonnull;
 import java.io.Serializable;
+import java.util.Set;
 
 /**
  * Immutable implementation of {@link DataElement} that may delegate to a mutable
@@ -106,4 +107,19 @@ public OptionSet getOptionSet()
     {
         return (delegate.getOptionSet() == null) ? null : new ImmutableOptionSet( delegate.getOptionSet() );
     }
+
+    @JsonIgnore
+    @Nonnull
+    @Override
+    public Set<Reference> getAllReferences()
+    {
+        return delegate.getAllReferences();
+    }
+
+    @JsonIgnore
+    @Override
+    public boolean isReference( @Nonnull Reference reference )
+    {
+        return delegate.isReference( reference );
+    }
 }

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/ReferenceAttributeConverter.java

@@ -59,10 +59,12 @@ public Reference convertToEntityAttribute( String dbData )
             return null;
         }
         final int index = dbData.indexOf( SEPARATOR );
+
         if ( (index <= 0) || (index + 1 == dbData.length()) )
         {
             throw new IllegalArgumentException( "Reference does not include required separator: " + dbData );
         }
+
         return new Reference( dbData.substring( index + 1 ), NameUtils.toEnumValue( ReferenceType.class, dbData.substring( 0, index ) ) );
     }
 }

dhis/src/main/java/org/dhis2/fhir/adapter/dhis/model/WritableDataElement.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter.dhis.model;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -38,7 +38,7 @@
  *
  * @author volsch
  */
-public class WritableDataElement implements DataElement, Serializable
+public class WritableDataElement extends AbstractDhisType implements DataElement, Serializable
 {
     private static final long serialVersionUID = -3933887626350878763L;
 

dhis/src/test/java/org/dhis2/fhir/adapter/dhis/converter/StringToReferenceConverterTest.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter.dhis.converter;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -55,7 +55,7 @@ public void convert()
         Assert.assertEquals( new Reference( "678", ReferenceType.CODE ), converter.convert( "CODE:678" ) );
     }
 
-    @Test( expected = IllegalArgumentException.class )
+    @Test( expected = ConversionException.class )
     public void convertInvalidCode()
     {
         converter.convert( "COD:678" );

fhir/pom.xml

@@ -111,8 +111,6 @@
   </dependencies>
 
   <build>
-    <finalName>dhis2-fhir-adapter</finalName>
-
     <plugins>
       <plugin>
         <groupId>com.mysema.maven</groupId>

fhir/src/main/java/org/dhis2/fhir/adapter/fhir/metadata/model/Code.java

@@ -64,7 +64,7 @@
 @Entity
 @Table( name = "fhir_code" )
 @JsonFilter( value = AdapterBeanPropertyFilter.FILTER_NAME )
-public class Code extends VersionedBaseMetadata implements Serializable
+public class Code extends VersionedBaseMetadata implements CodeCategoryAware, Serializable
 {
     private static final long serialVersionUID = 6376382638316116368L;
 

fhir/src/main/java/org/dhis2/fhir/adapter/fhir/metadata/model/CodeCategory.java

@@ -39,6 +39,7 @@
 import javax.validation.constraints.NotBlank;
 import javax.validation.constraints.Size;
 import java.io.Serializable;
+import java.util.UUID;
 
 /**
  * Contains the category of a {@linkplain Code code}. E.g. there may be multiple codes for the category "vaccine".
@@ -56,6 +57,8 @@ public class CodeCategory extends VersionedBaseMetadata implements Serializable
 
     public static final int MAX_CODE_LENGTH = 50;
 
+    public static final UUID UNSPECIFIED_CATEGORY_ID = UUID.fromString( "8f0363dc-632d-4ccf-ba07-0da5eff6be97" );
+
     @NotBlank
     @Size( max = MAX_NAME_LENGTH )
     private String name;

fhir/src/main/java/org/dhis2/fhir/adapter/fhir/metadata/model/CodeCategoryAware.java

@@ -0,0 +1,47 @@
+package org.dhis2.fhir.adapter.fhir.metadata.model;
+
+/*
+ * Copyright (c) 2004-2019, 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.
+ */
+
+/**
+ * Implemented by metadata classes that contain a code category.
+ *
+ * @author volsch
+ */
+public interface CodeCategoryAware
+{
+    /**
+     * @return the assigned code category.
+     */
+    CodeCategory getCodeCategory();
+
+    /**
+     * @param codeCategory the code category to assign.
+     */
+    void setCodeCategory( CodeCategory codeCategory );
+}

fhir/src/main/java/org/dhis2/fhir/adapter/fhir/metadata/model/CodeSet.java

@@ -62,7 +62,7 @@
 @Entity
 @Table( name = "fhir_code_set" )
 @JsonFilter( AdapterBeanPropertyFilter.FILTER_NAME )
-public class CodeSet extends VersionedBaseMetadata implements Serializable
+public class CodeSet extends VersionedBaseMetadata implements CodeCategoryAware, Serializable
 {
     private static final long serialVersionUID = 1177970691904984600L;
 
@@ -136,7 +136,7 @@ public void setCodeCategory( CodeCategory codeCategory )
     }
 
     @JsonCacheIgnore
-    @Access( AccessType.PROPERTY )
+    @Access( AccessType.FIELD )
     @OneToMany( orphanRemoval = true, mappedBy = "codeSet", cascade = CascadeType.ALL )
     @OrderBy( "id" )
     @BatchSize( size = 100 )

fhir/src/main/java/org/dhis2/fhir/adapter/fhir/metadata/repository/CodeSetRepository.java

@@ -40,6 +40,7 @@
 
 import javax.annotation.Nonnull;
 import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 
 /**
@@ -61,6 +62,10 @@ default Class<CodeSet> getEntityType()
         return CodeSet.class;
     }
 
+    @Nonnull
+    @RestResource( exported = false )
+    Optional<CodeSet> findOneByCode( @Nonnull String code );
+
     @Override
     @Nonnull
     @CacheEvict( allEntries = true )

fhir/src/main/java/org/dhis2/fhir/adapter/fhir/metadata/repository/CustomProgramStageRuleRepository.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter.fhir.metadata.repository;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -29,6 +29,7 @@
  */
 
 import org.dhis2.fhir.adapter.dhis.model.Reference;
+import org.dhis2.fhir.adapter.fhir.metadata.model.MappedTrackerProgram;
 import org.dhis2.fhir.adapter.fhir.metadata.model.ProgramStageRule;
 import org.dhis2.fhir.adapter.fhir.metadata.model.RuleInfo;
 import org.springframework.data.rest.core.annotation.RestResource;
@@ -47,4 +48,7 @@ public interface CustomProgramStageRuleRepository
     @RestResource( exported = false )
     @Nonnull
     Collection<RuleInfo<ProgramStageRule>> findAllExp( @Nonnull Collection<Reference> programReferences, @Nonnull Collection<Reference> programStageReferences, @Nullable Collection<Reference> dataReferences );
+
+    @RestResource( exported = false )
+    void deleteAllByProgram( @Nonnull MappedTrackerProgram program );
 }

fhir/src/main/java/org/dhis2/fhir/adapter/fhir/metadata/repository/ExecutableScriptRepository.java

@@ -40,6 +40,7 @@
 
 import javax.annotation.Nonnull;
 import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 
 /**
@@ -61,6 +62,10 @@ default Class<ExecutableScript> getEntityType()
         return ExecutableScript.class;
     }
 
+    @Nonnull
+    @RestResource( exported = false )
+    Optional<ExecutableScript> findOneByCode( @Nonnull String code );
+
     @Override
     @Nonnull
     @CacheEvict( allEntries = true )