Develop

.gitignore

@@ -125,3 +125,4 @@ nb-configuration.xml
 .nb-gradle/
 
 # Created by .ignore support plugin (hsz.mobi)
+/phenopacket-validation.tsv

README.md

@@ -9,3 +9,8 @@ Library and tools to help validate phenopackets
 This app uses version 2.0.0 (branch v2) of [phenopacket-schema](https://github.com/phenopackets/phenopacket-schema).
 To build this app, clone phenopacket-schema and ``mvn install`` the ``v2`` branch locally. The you should be
 able to build and run this app with standard maven/java. Note the app requires Java 11 or higher.
+
+It also uses version 0.0.1-SNAPSHOT of [phenopacket-tools](https://github.com/phenopackets/phenopacket-tools)
+to create the test cases. It also needs to be install locally using maven.
+
+We plan to put all requirements into maven central shortly to simplify the build.

pom.xml

@@ -4,15 +4,19 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
-    <groupId>org.phenopackets.phenopacket-schema</groupId>
+    <groupId>org.phenopackets.validator</groupId>
     <artifactId>validator</artifactId>
     <version>0.1.1-SNAPSHOT</version>
 
     <packaging>pom</packaging>
+    <name>Phenopacket validator</name>
+    <description>Library and tools to help validate phenopackets</description>
 
     <modules>
         <module>validator-core</module>
         <module>validator-cli</module>
+        <module>validator-jsonschema</module>
+        <module>validator-ontology</module>
     </modules>
 
     <parent>
@@ -60,7 +64,12 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <java.version>11</java.version>
+        <java.version>16</java.version>
+
+        <phenol.version>1.6.3</phenol.version>
+        <protobuf.version>3.14.0</protobuf.version>
+        <phenopacket-schema.version>2.0.0</phenopacket-schema.version>
+
         <junit.jupiter.version>5.7.1</junit.jupiter.version>
     </properties>
 
@@ -83,39 +92,76 @@
         </plugins>
     </build>
 
+    <dependencyManagement>
+        <dependencies>
+            <dependency>
+                <groupId>org.monarchinitiative.phenol</groupId>
+                <artifactId>phenol-core</artifactId>
+                <version>${phenol.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.monarchinitiative.phenol</groupId>
+                <artifactId>phenol-io</artifactId>
+                <version>${phenol.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.phenopackets</groupId>
+                <artifactId>phenopacket-schema</artifactId>
+                <version>${phenopacket-schema.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>com.google.protobuf</groupId>
+                <artifactId>protobuf-java-util</artifactId>
+                <version>${protobuf.version}</version>
+                <exclusions>
+                    <exclusion>
+                        <groupId>com.google.guava</groupId>
+                        <artifactId>guava</artifactId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+
+            <dependency>
+                <groupId>com.networknt</groupId>
+                <artifactId>json-schema-validator</artifactId>
+                <version>1.0.42</version>
+            </dependency>
+
+            <!--     TEST DEPENDENCIES       -->
+            <dependency>
+                <groupId>org.mockito</groupId>
+                <artifactId>mockito-core</artifactId>
+                <version>3.12.4</version>
+            </dependency>
+        </dependencies>
+    </dependencyManagement>
+
     <dependencies>
         <!-- logging -->
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
         </dependency>
+        <!-- TEST DEPENDENCIES -->
         <dependency>
-            <groupId>ch.qos.logback</groupId>
-            <artifactId>logback-classic</artifactId>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
             <scope>test</scope>
         </dependency>
-        <!-- TEST DEPENDENCIES -->
-        <!--<dependency>-->
-        <!--<groupId>org.springframework.boot</groupId>-->
-        <!--<artifactId>spring-boot-starter-test</artifactId>-->
-        <!--<scope>test</scope>-->
-        <!--</dependency>-->
         <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-api</artifactId>
-            <version>${junit.jupiter.version}</version>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest-core</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
-              <groupId>org.junit.jupiter</groupId>
-              <artifactId>junit-jupiter-engine</artifactId>
-              <version>${junit.jupiter.version}</version>
-              <scope>test</scope>
-          </dependency>
-          <dependency>
-              <groupId>org.hamcrest</groupId>
-              <artifactId>hamcrest-core</artifactId>
-              <scope>test</scope>
-          </dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-simple</artifactId>
+            <scope>test</scope>
+        </dependency>
       </dependencies>
   </project>

validator-cli/pom.xml

@@ -5,58 +5,36 @@
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
-        <groupId>org.phenopackets.phenopacket-schema</groupId>
+        <groupId>org.phenopackets.validator</groupId>
         <artifactId>validator</artifactId>
         <version>0.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>validator-cli</artifactId>
-    <version>0.1.1-SNAPSHOT</version>
-    <packaging>jar</packaging>
 
     <name>validator-cli</name>
     <description>Command-line utility for validating phenopackets</description>
 
-    <properties>
-        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <java.version>1.8</java.version>
-    </properties>
-
     <dependencies>
         <dependency>
-            <groupId>org.phenopackets.phenopacket-schema</groupId>
-            <artifactId>validator-core</artifactId>
+            <groupId>org.phenopackets.validator</groupId>
+            <artifactId>validator-jsonschema</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
         <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-autoconfigure</artifactId>
+            <groupId>org.phenopackets.validator</groupId>
+            <artifactId>validator-ontology</artifactId>
+            <version>${project.parent.version}</version>
         </dependency>
         <dependency>
-            <groupId>ch.qos.logback</groupId>
-            <artifactId>logback-classic</artifactId>
+            <groupId>org.monarchinitiative.phenol</groupId>
+            <artifactId>phenol-io</artifactId>
         </dependency>
         <dependency>
             <groupId>info.picocli</groupId>
-            <artifactId>picocli-spring-boot-starter</artifactId>
+            <artifactId>picocli</artifactId>
             <version>4.6.1</version>
         </dependency>
     </dependencies>
 
-    <build>
-        <resources>
-            <resource>
-                <directory>src/main/resources</directory>
-                <filtering>true</filtering>
-            </resource>
-        </resources>
-        <plugins>
-            <plugin>
-                <groupId>org.springframework.boot</groupId>
-                <artifactId>spring-boot-maven-plugin</artifactId>
-            </plugin>
-        </plugins>
-    </build>
-
 </project>