Update dependencies

.github/workflows/maven.yml

@@ -12,23 +12,20 @@ on:
 jobs:
   build:
     runs-on: ${{ matrix.os }}
-    env:
-      JDK_VERSION: ${{ matrix.jdk }}
 
     strategy:
       fail-fast: false
       matrix:
         os: [ windows-latest, macOS-latest, ubuntu-latest ]
-        jdk: [ 11 ]
 
     steps:
       - uses: actions/checkout@v2
 
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: '11'
+          java-version: '17'
           distribution: 'adopt'
 
       - name: Build with Maven
-        run: ./mvnw -B verify --file pom.xml
+        run: ./mvnw --batch-mode verify

pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.6.10</version>
+        <version>3.0.5</version>
     </parent>
 
     <properties>
@@ -32,8 +32,9 @@
         <maven.compiler.source>${java.version}</maven.compiler.source>
         <maven.compiler.target>${java.version}</maven.compiler.target>
 
-        <phenol.version>2.0.0-RC2</phenol.version>
-        <silent.genes.version>0.2.0</silent.genes.version>
+        <phenol.version>2.0.0</phenol.version>
+        <phenopacket-tools.version>1.0.0-RC2</phenopacket-tools.version>
+        <silent.genes.version>0.2.5</silent.genes.version>
         <h2.version>1.4.200</h2.version>
     </properties>
 
@@ -101,6 +102,11 @@
                 <artifactId>silent-genes-io</artifactId>
                 <version>${silent.genes.version}</version>
             </dependency>
+            <dependency>
+                <groupId>org.phenopackets.phenopackettools</groupId>
+                <artifactId>phenopacket-tools-io</artifactId>
+                <version>${phenopacket-tools.version}</version>
+            </dependency>
 
             <dependency>
                 <groupId>org.phenopackets</groupId>
@@ -125,7 +131,7 @@
             <dependency>
                 <groupId>com.github.samtools</groupId>
                 <artifactId>htsjdk</artifactId>
-                <version>2.23.0</version>
+                <version>3.0.5</version>
                 <exclusions>
                     <exclusion>
                         <groupId>org.tukaani</groupId>

svanna-cli/pom.xml

@@ -19,6 +19,10 @@
             <artifactId>svanna-configuration</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.phenopackets.phenopackettools</groupId>
+            <artifactId>phenopacket-tools-io</artifactId>
+        </dependency>
         <dependency>
             <groupId>info.picocli</groupId>
             <artifactId>picocli</artifactId>
@@ -27,21 +31,11 @@
             <groupId>org.freemarker</groupId>
             <artifactId>freemarker</artifactId>
         </dependency>
-
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-csv</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>org.phenopackets</groupId>
-            <artifactId>phenopacket-schema</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.google.protobuf</groupId>
-            <artifactId>protobuf-java-util</artifactId>
-        </dependency>
-
         <!--    TESTS    -->
         <dependency>
             <groupId>org.monarchinitiative.svanna</groupId>
@@ -63,33 +57,7 @@
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-maven-plugin</artifactId>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-resources-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <id>copy-resources</id>
-                        <phase>validate</phase>
-                        <goals>
-                            <goal>copy-resources</goal>
-                        </goals>
-                        <configuration>
-                            <outputDirectory>${project.build.directory}/assembly-resources</outputDirectory>
-                            <resources>
-                                <resource>
-                                    <directory>src/examples</directory>
-                                    <filtering>true</filtering>
-                                    <includes>
-                                        <include>example.csv</include>
-                                        <include>example.vcf</include>
-                                        <include>run_examples.sh</include>
-                                    </includes>
-                                </resource>
-                            </resources>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-assembly-plugin</artifactId>

svanna-cli/src/assemble/distribution.xml

@@ -24,12 +24,12 @@
                 <include>svanna-cli-${version}.jar</include>
             </includes>
         </fileSet>
+        <!-- Include example data -->
         <fileSet>
-            <directory>${project.build.directory}/assembly-resources</directory>
+            <directory>${project.basedir}/src/examples</directory>
             <outputDirectory>./examples</outputDirectory>
             <includes>
-                <include>example.vcf</include>
-                <include>run_examples.sh</include>
+                <include>**/**</include>
             </includes>
         </fileSet>
     </fileSets>

svanna-cli/src/examples/example-phenopacket.json → svanna-cli/src/examples/example-phenopacket.v1.json

@@ -1,7 +1,7 @@
 {
-  "id": "example",
+  "id": "example-phenopacket",
   "subject": {
-    "id": "example",
+    "id": "Sample",
     "ageAtCollection": {
       "age": "P2Y"
     }
@@ -12,11 +12,6 @@
       "label": "Reduced von Willebrand factor activity"
     }
   }],
-  "htsFiles": [{
-    "uri": "file:///***/***/example.vcf",
-    "htsFormat": "VCF",
-    "genomeAssembly": "hg38"
-  }],
   "metaData": {
     "created": "2021-07-13T15:08:53.846Z",
     "createdBy": "ExampleOrg:ExampleCurator",

svanna-cli/src/examples/example-phenopacket.v2.json

@@ -0,0 +1,30 @@
+{
+  "id": "example-phenopacket",
+  "subject": {
+    "id": "Sample",
+    "timeAtLastEncounter": {
+      "age": {
+        "iso8601duration": "P2Y"
+      }
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0008330",
+      "label": "Reduced von Willebrand factor activity"
+    }
+  }],
+  "metaData": {
+    "created": "2021-07-13T15:08:53.846Z",
+    "createdBy": "ExampleOrg:ExampleCurator",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "unknown HPO version",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }],
+    "phenopacketSchemaVersion": "2.0.0"
+  }
+}

svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/cmd/AnalysisData.java

@@ -0,0 +1,50 @@
+package org.monarchinitiative.svanna.cli.cmd;
+
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import java.nio.file.Path;
+import java.util.List;
+import java.util.Objects;
+
+/**
+ * SvAnna requires these inputs for the analysis.
+ */
+class AnalysisData {
+
+    private final List<TermId> phenotypeTerms;
+    private final Path vcf;
+
+    AnalysisData(List<TermId> phenotypeTerms, Path vcf) {
+        this.phenotypeTerms = phenotypeTerms;
+        this.vcf = vcf;
+    }
+
+    List<TermId> phenotypeTerms() {
+        return phenotypeTerms;
+    }
+
+    Path vcf() {
+        return vcf;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        AnalysisData that = (AnalysisData) o;
+        return Objects.equals(phenotypeTerms, that.phenotypeTerms) && Objects.equals(vcf, that.vcf);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(phenotypeTerms, vcf);
+    }
+
+    @Override
+    public String toString() {
+        return "AnalysisData{" +
+                "phenotypeTerms=" + phenotypeTerms +
+                ", vcf=" + vcf +
+                '}';
+    }
+}

svanna-cli/src/main/java/org/monarchinitiative/svanna/cli/cmd/AnalysisInputException.java

@@ -0,0 +1,28 @@
+package org.monarchinitiative.svanna.cli.cmd;
+
+import org.monarchinitiative.svanna.core.SvAnnaRuntimeException;
+
+/**
+ * An exception thrown if inputs for the analysis are incomplete or otherwise invalid.
+ */
+class AnalysisInputException extends SvAnnaRuntimeException {
+    AnalysisInputException() {
+        super();
+    }
+
+    AnalysisInputException(String message) {
+        super(message);
+    }
+
+    AnalysisInputException(String message, Throwable cause) {
+        super(message, cause);
+    }
+
+    AnalysisInputException(Throwable cause) {
+        super(cause);
+    }
+
+    AnalysisInputException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace) {
+        super(message, cause, enableSuppression, writableStackTrace);
+    }
+}