Merge pull request #81 from julesjacobsen/master

Add obographs-cli
geneontology · Apr 29, 2022 · f10fa43 · f10fa43
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diff --git a/README.md b/README.md
@@ -1,7 +1,6 @@
-[![Build Status](https://travis-ci.org/geneontology/obographs.svg?branch=master)](https://travis-ci.org/geneontology/obographs)
-[![Maven Central](https://maven-badges.herokuapp.com/maven-central/org.geneontology/obographs/badge.svg)](https://maven-badges.herokuapp.com/maven-central/org.geneontology/obographs)
-[![Javadoc](https://javadoc-emblem.rhcloud.com/doc/org.geneontology/obographs/badge.svg)](http://www.javadoc.io/doc/org.geneontology/obographs)
-
+[![Build Status](https://travis-ci.com/geneontology/obographs.svg?branch=master)](https://app.travis-ci.com/github/geneontology/obographs)
+[![Maven Central](https://maven-badges.herokuapp.com/maven-central/org.geneontology.obographs/obographs/badge.svg)](https://maven-badges.herokuapp.com/maven-central/org.geneontology.obographs/obographs)
+[![javadoc](https://javadoc.io/badge2/org.geneontology.obographs/obographs-core/javadoc.svg)](https://javadoc.io/doc/org.geneontology.obographs/obographs-core)
 # OBO Graphs : Developer-friendly graph-oriented ontology JSON/YAML
 
 This repo contains both a specification for a JSON/YAML format for

diff --git a/obographs-cli/pom.xml b/obographs-cli/pom.xml
@@ -0,0 +1,133 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <artifactId>obographs</artifactId>
+        <groupId>org.geneontology.obographs</groupId>
+        <version>0.3.0</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>obographs-cli</artifactId>
+
+    <properties>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.geneontology.obographs</groupId>
+            <artifactId>obographs-core</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.geneontology.obographs</groupId>
+            <artifactId>obographs-owlapi</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>info.picocli</groupId>
+            <artifactId>picocli</artifactId>
+            <version>4.6.3</version>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+            <version>1.2.11</version>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <resources>
+            <resource>
+                <directory>${basedir}/src/main/resources</directory>
+                <filtering>true</filtering>
+                <includes>
+                    <include>**/application*.yml</include>
+                    <include>**/application*.yaml</include>
+                    <include>**/application*.properties</include>
+                </includes>
+            </resource>
+            <resource>
+                <directory>${basedir}/src/main/resources</directory>
+                <excludes>
+                    <exclude>**/application*.yml</exclude>
+                    <exclude>**/application*.yaml</exclude>
+                    <exclude>**/application*.properties</exclude>
+                </excludes>
+            </resource>
+        </resources>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>3.2.0</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <mainClass>org.geneontology.obographs.cli.OboGraphs</mainClass>
+                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+                <version>3.2.0</version>
+                <configuration>
+                    <propertiesEncoding>${project.build.sourceEncoding}</propertiesEncoding>
+                    <delimiters>
+                        <delimiter>${resource.delimiter}</delimiter>
+                    </delimiters>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.2.4</version>
+                <configuration>
+                    <keepDependenciesWithProvidedScope>true</keepDependenciesWithProvidedScope>
+                    <createDependencyReducedPom>true</createDependencyReducedPom>
+                    <filters>
+                        <filter>
+                            <artifact>*:*</artifact>
+                            <excludes>
+                                <exclude>module-info.class</exclude>
+                                <exclude>META-INF/*.SF</exclude>
+                                <exclude>META-INF/*.DSA</exclude>
+                                <exclude>META-INF/*.RSA</exclude>
+                            </excludes>
+                        </filter>
+                    </filters>
+                </configuration>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <annotationProcessorPaths>
+                        <path>
+                            <groupId>info.picocli</groupId>
+                            <artifactId>picocli-codegen</artifactId>
+                            <version>4.6.3</version>
+                        </path>
+                    </annotationProcessorPaths>
+                    <compilerArgs>
+                        <arg>-Aproject=${project.groupId}/${project.artifactId}</arg>
+                    </compilerArgs>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>
diff --git a/obographs-cli/src/main/java/org/geneontology/obographs/cli/OboGraphs.java b/obographs-cli/src/main/java/org/geneontology/obographs/cli/OboGraphs.java
@@ -0,0 +1,35 @@
+package org.geneontology.obographs.cli;
+
+import org.geneontology.obographs.cli.commands.Convert;
+import org.geneontology.obographs.cli.commands.ManifestVersionProvider;
+import org.geneontology.obographs.cli.commands.Validate;
+import picocli.CommandLine;
+import picocli.CommandLine.Model.CommandSpec;
+
+import static picocli.CommandLine.Command;
+import static picocli.CommandLine.Spec;
+
+@Command(name = "obographs",
+        versionProvider = ManifestVersionProvider.class,
+        mixinStandardHelpOptions = true,
+        description = "OBO Graphs: Developer-friendly graph-oriented ontology in JSON/YAML",
+        subcommands = {
+                Convert.class,
+                Validate.class,
+        }
+)
+public class OboGraphs implements Runnable {
+
+    @Spec
+    CommandSpec spec;
+
+    @Override
+    public void run() {
+        // if the command was invoked without subcommand, show the usage help
+        spec.commandLine().usage(System.err);
+    }
+
+    public static void main(String[] args) {
+        System.exit(new CommandLine(new OboGraphs()).execute(args));
+    }
+}
diff --git a/obographs-cli/src/main/java/org/geneontology/obographs/cli/commands/Convert.java b/obographs-cli/src/main/java/org/geneontology/obographs/cli/commands/Convert.java
@@ -0,0 +1,118 @@
+package org.geneontology.obographs.cli.commands;
+
+import org.geneontology.obographs.core.io.OgJsonGenerator;
+import org.geneontology.obographs.core.io.OgYamlGenerator;
+import org.geneontology.obographs.core.model.GraphDocument;
+import org.geneontology.obographs.owlapi.FromOwl;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import picocli.CommandLine.Command;
+
+import java.io.IOException;
+import java.nio.file.*;
+import java.util.List;
+import java.util.concurrent.Callable;
+
+import static picocli.CommandLine.Option;
+import static picocli.CommandLine.Parameters;
+
+@Command(name = "convert", description = "converts OWL to obographs JSON")
+public class Convert implements Callable<Integer> {
+
+    // obographs convert *.owl -o .
+    // obographs convert owl/*.owl -o obographs/. -f all
+    // obographs convert *.owl -o . -f json
+    @Parameters(arity = "1..*", paramLabel = "FILE", description = "OWL/OBO file(s) to process.")
+    private List<Path> inputPaths;
+
+    @Option(names = {"-o", "--out-dir"}, description = "Output directory for converted files (defaults to input directory).")
+    Path outDir;
+
+    @Option(names = {"-f", "--format"}, paramLabel = "<format>", description = {
+            "Output format for obograph files.",
+            "The format parameter is optional (defaults to `all`), and is used to specify the output format(s) of converted files.",
+            "The possible options are:",
+            " * @|yellow json|@ - Write to JSON.",
+            " * @|yellow yaml|@ - Write to YAML.",
+            " * @|yellow all|@ - Write both JSON and YAML."
+    })
+    Format outFormat = Format.all;
+
+    enum Format {json, yaml, all}
+
+    @Override
+    public Integer call() {
+        if (outDir != null) {
+            try {
+                createDirectoryIfNotPresent(outDir);
+            } catch (IOException ex) {
+                System.err.println("Output " + outDir + " must be a writeable directory!");
+                return 1;
+            }
+        }
+        List<Format> formats = parseFormats(outFormat);
+        OWLOntologyManager owlOntologyManager = OWLManager.createOWLOntologyManager();
+        FromOwl fromOwl = new FromOwl();
+        int exitCode = 0;
+        for (Path inputFile : inputPaths) {
+            try {
+                System.err.println("Reading " + inputFile);
+                OWLOntology owlOntology = owlOntologyManager.loadOntologyFromOntologyDocument(inputFile.toFile());
+                GraphDocument graphDocument = fromOwl.generateGraphDocument(owlOntology);
+                for (Format format : formats) {
+                    Path outFile = outFile(inputFile, format);
+                    if (format == Format.json) {
+                        OgJsonGenerator.write(outFile.toFile(), graphDocument);
+                    }
+                    if (format == Format.yaml) {
+                        OgYamlGenerator.write(outFile.toFile(), graphDocument);
+                    }
+                    System.err.println("Written " + outFile.toAbsolutePath());
+                }
+            } catch (Exception e) {
+                System.err.println(e.getMessage());
+                exitCode = 1;
+            }
+        }
+        return exitCode;
+    }
+
+    private List<Format> parseFormats(Format format) {
+        if (format == Format.json) {
+            return List.of(Format.json);
+        } else if (format == Format.yaml) {
+            return List.of(Format.yaml);
+        }
+        return List.of(Format.json, Format.yaml);
+    }
+
+    private Path outFile(Path inputFile, Format format) {
+        String outFileName = outFileName(inputFile, format);
+        if (outDir == null) {
+            return inputFile.toAbsolutePath().getParent().resolve(outFileName);
+        }
+        return outDir.resolve(outFileName);
+    }
+
+    private String outFileName(Path inputFile, Format format) {
+        String fileName = inputFile.getFileName().toString();
+        if (fileName.endsWith(".obo")) {
+            return fileName.replace(".obo", "." + format);
+        } else if (fileName.endsWith(".owl")) {
+            return fileName.replace(".owl", "." + format);
+        }
+        throw new IllegalArgumentException("Input file " + inputFile + " must be in OWL or OBO format");
+    }
+
+    private Path createDirectoryIfNotPresent(Path dir) throws IOException {
+        try {
+            return Files.createDirectory(dir);
+        } catch (FileAlreadyExistsException x) {
+            if (!Files.isDirectory(dir, LinkOption.NOFOLLOW_LINKS)) {
+                throw new NotDirectoryException("Not a directory: " + dir);
+            }
+        }
+        return dir;
+    }
+}
diff --git a/...hs-cli/src/main/java/org/geneontology/obographs/cli/commands/ManifestVersionProvider.java b/...hs-cli/src/main/java/org/geneontology/obographs/cli/commands/ManifestVersionProvider.java
@@ -0,0 +1,49 @@
+package org.geneontology.obographs.cli.commands;
+
+import picocli.CommandLine;
+import picocli.CommandLine.IVersionProvider;
+
+import java.io.IOException;
+import java.net.URL;
+import java.util.Enumeration;
+import java.util.jar.Attributes;
+import java.util.jar.Manifest;
+
+/**
+ * {@link IVersionProvider} implementation that returns version information from the obographs-cli-x.x.jar file's {@code /META-INF/MANIFEST.MF} file.
+ * Requires building with maven-jar-plugin using the manifest.addDefaultImplementationEntries=true option.
+ *
+ * Adapted from https://github.com/remkop/picocli/blob/main/picocli-examples/src/main/java/picocli/examples/VersionProviderDemo2.java.
+ */
+public class ManifestVersionProvider implements IVersionProvider {
+
+    private static final String MAVEN_ARTIFACT_ID = "obographs-cli";
+
+    public String[] getVersion() throws Exception {
+        Enumeration<URL> resources = CommandLine.class.getClassLoader().getResources("META-INF/MANIFEST.MF");
+        while (resources.hasMoreElements()) {
+            URL url = resources.nextElement();
+            try {
+                Manifest manifest = new Manifest(url.openStream());
+                // This is the Maven ${project.name} generated from the artifactId in the project pom.xml
+                if (isApplicableManifest(manifest, MAVEN_ARTIFACT_ID)) {
+                    Attributes attr = manifest.getMainAttributes();
+                    var version = (String) get(attr, "Implementation-Version");
+                    return new String[]{MAVEN_ARTIFACT_ID + " version \"" + version + "\""};
+                }
+            } catch (IOException ex) {
+                return new String[]{"Unable to read from " + url + ": " + ex};
+            }
+        }
+        return new String[0];
+    }
+
+    private boolean isApplicableManifest(Manifest manifest, String mavenArtifactId) {
+        Attributes attributes = manifest.getMainAttributes();
+        return mavenArtifactId.equals(get(attributes, "Implementation-Title"));
+    }
+
+    private static Object get(Attributes attributes, String key) {
+        return attributes.get(new Attributes.Name(key));
+    }
+}