Add --config-file to import config json file (#13)

Signed-off-by: Paolo Di Tommaso <[email protected]>
Co-authored-by: Paolo Di Tommaso <[email protected]>

app/build.gradle

@@ -37,6 +37,7 @@ dependencies {
     testImplementation ("org.objenesis:objenesis:3.2")
     testImplementation ("org.spockframework:spock-core:2.3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
     testImplementation ('org.spockframework:spock-junit4:2.3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
+    testImplementation 'com.github.tomakehurst:wiremock:2.27.2'
 }
 
 test {

app/src/main/java/io/seqera/wavelit/App.java

@@ -16,8 +16,10 @@
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.InputStream;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
@@ -47,12 +49,11 @@
 import picocli.CommandLine;
 import static io.seqera.wave.util.DockerHelper.addPackagesToSpackFile;
 import static io.seqera.wave.util.DockerHelper.spackPackagesToSpackFile;
+import static io.seqera.wavelit.util.Checkers.isEnvVar;
 import static org.apache.commons.lang3.StringUtils.isEmpty;
 import static picocli.CommandLine.Command;
 import static picocli.CommandLine.Option;
 
-import static io.seqera.wavelit.util.Checkers.isEnvVar;
-
 /**
  * Wavelit main class
  */
@@ -111,6 +112,9 @@ public class App implements Runnable {
     @Option(names = {"--config-entrypoint"}, paramLabel = "''", description = "Overwrite the default ENTRYPOINT of the image.")
     private String entrypoint;
 
+    @Option(names = {"--config-file"}, paramLabel = "''", description = "Configuration file in JSON format to overwrite the default configuration of the image.")
+    private String configFile;
+
     @Option(names = {"--config-working-dir"}, paramLabel = "''", description = "Overwrite the default WORKDIR of the image e.g. /some/work/dir.")
     private String workingDir;
 
@@ -340,7 +344,9 @@ private String encodePathBase64(String value) {
                 return null;
             // read the text from a URI resource and encode to base64
             if( value.startsWith("file:/") || value.startsWith("http://") || value.startsWith("https://")) {
-                return Base64.getEncoder().encodeToString(Files.readAllBytes(Path.of(new URI(value))));
+                try(InputStream stream=new URI(value).toURL().openStream()) {
+                    return Base64.getEncoder().encodeToString(stream.readAllBytes());
+                }
             }
             // read the text from a local file and encode to base64
             return Base64.getEncoder().encodeToString(Files.readAllBytes(Path.of(value)));
@@ -380,7 +386,13 @@ protected BuildContext prepareContext()  {
     }
 
     protected ContainerConfig prepareConfig() {
-        final ContainerConfig result = new ContainerConfig();
+        ContainerConfig result = new ContainerConfig();
+
+        // add configuration from config file if specified
+        if( configFile != null ){
+            if( "".equals(configFile.trim()) ) throw new IllegalCliArgumentException("The specified config file is an empty string");
+            result = readConfig(configFile);
+        }
 
         // add the entrypoint if specified
         if( entrypoint!=null )
@@ -490,4 +502,25 @@ protected String dumpOutput(SubmitContainerTokenResponse resp) {
                 ? resp.containerImage
                 : resp.targetImage;
     }
+
+    protected ContainerConfig readConfig(String path) {
+        try {
+            if( path.startsWith("http://") || path.startsWith("https://") || path.startsWith("file:/")) {
+                try (InputStream stream=new URL(path).openStream()) {
+                    return JsonHelper.fromJson(new String(stream.readAllBytes()), ContainerConfig.class);
+                }
+            }
+            else {
+                return JsonHelper.fromJson(Files.readString(Path.of(path)), ContainerConfig.class);
+            }
+        }
+        catch (FileNotFoundException | NoSuchFileException e) {
+            throw new IllegalCliArgumentException("Invalid container config file - File not found: " + path);
+        }
+        catch (IOException e) {
+            String msg = String.format("Unable to read container config file: %s - Cause: %s", path, e.getMessage());
+            throw new IllegalCliArgumentException(msg, e);
+        }
+    }
+
 }

app/src/test/groovy/io/seqera/wavelit/AppCondaOptsTest.groovy

@@ -17,6 +17,7 @@ import io.seqera.wavelit.exception.IllegalCliArgumentException
 import picocli.CommandLine
 import spock.lang.Specification
 /**
+ * Test App Conda prefixed options
  *
  * @author Paolo Di Tommaso <[email protected]>
  */

app/src/test/groovy/io/seqera/wavelit/AppConfigOptsTest.groovy

@@ -0,0 +1,233 @@
+/*
+ *  Copyright (c) 2023, Seqera Labs.
+ *
+ *  This Source Code Form is subject to the terms of the Mozilla Public
+ *  License, v. 2.0. If a copy of the MPL was not distributed with this
+ *  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ *  This Source Code Form is "Incompatible With Secondary Licenses", as
+ *  defined by the Mozilla Public License, v. 2.0.
+ */
+
+package io.seqera.wavelit
+
+import java.nio.file.Files
+
+import com.github.tomakehurst.wiremock.WireMockServer
+import com.github.tomakehurst.wiremock.client.WireMock
+import com.github.tomakehurst.wiremock.core.WireMockConfiguration
+import io.seqera.wave.api.ContainerConfig
+import io.seqera.wavelit.exception.IllegalCliArgumentException
+import picocli.CommandLine
+import spock.lang.Specification
+
+/**
+ * Test App config prefixed options
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+class AppConfigOptsTest extends Specification {
+
+    def CONFIG_JSON = '''\
+            {
+              "entrypoint": [ "/some", "--entrypoint" ],
+              "layers": [
+                {
+                  "location": "https://location",
+                  "gzipDigest": "sha256:gzipDigest",
+                  "gzipSize": 100,
+                  "tarDigest": "sha256:tarDigest",
+                  "skipHashing": true
+                }
+              ]
+            }
+            '''
+
+    WireMockServer wireMockServer
+    def setup() {
+        wireMockServer = new WireMockServer(WireMockConfiguration.wireMockConfig().port(8080))
+        wireMockServer.start()
+
+        WireMock.stubFor(
+                WireMock.get(WireMock.urlEqualTo("/api/data"))
+                        .willReturn(
+                                WireMock.aResponse()
+                                        .withStatus(200)
+                                        .withHeader("Content-Type", "application/json")
+                                        .withBody(CONFIG_JSON)
+                        )
+        )
+    }
+
+    def cleanup() {
+        wireMockServer.stop()
+    }
+
+
+    def "test valid entrypoint"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-entrypoint", "entryPoint"]
+        def cli = new CommandLine(app)
+
+        when:
+        cli.parseArgs(args)
+        then:
+        app.@entrypoint == "entryPoint"
+
+        when:
+        def config = app.prepareConfig()
+        then:
+        config == new ContainerConfig(entrypoint: ['entryPoint'])
+    }
+
+    def "test invalid entrypoint"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-entrypoint"]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+
+        then:
+        thrown(CommandLine.MissingParameterException)
+    }
+
+    def "test valid command"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-cmd", "/some/command"]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        then:
+        app.@command == "/some/command"
+
+        when:
+        def config = app.prepareConfig()
+        then:
+        config == new ContainerConfig(cmd: ['/some/command'])
+    }
+
+    def "test invalid command"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-cmd", ""]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        app.prepareConfig()
+        then:
+        thrown(IllegalCliArgumentException)
+
+    }
+
+    def "test valid environment"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-env", "var1=value1","--config-env", "var2=value2"]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        then:
+        app.@environment[0] == "var1=value1"
+        app.@environment[1] == "var2=value2"
+
+        when:
+        def config = app.prepareConfig()
+        then:
+        config == new ContainerConfig(env: ['var1=value1', 'var2=value2'])
+    }
+
+    def "test invalid environment"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-env", "VAR"]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        app.prepareConfig()
+        then:
+        def e = thrown(IllegalCliArgumentException)
+        e.message == 'Invalid environment variable syntax - offending value: VAR'
+
+    }
+
+    def "test valid working directory"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-working-dir", "/work/dir"]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        then:
+        app.@workingDir == "/work/dir"
+
+        when:
+        def config = app.prepareConfig()
+        then:
+        config == new ContainerConfig(workingDir: '/work/dir')
+    }
+
+    def "test invalid working directory"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-working-dir", "  "]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        app.prepareConfig()
+        then:
+        thrown(IllegalCliArgumentException)
+
+    }
+
+    def "test valid config file from a path"() {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def configFile = folder.resolve('config.json')
+        configFile.text = CONFIG_JSON
+        and:
+        def app = new App()
+        String[] args = ["--config-file", configFile.toString()]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        then:
+        app.@configFile == configFile.toString()
+
+        when:
+        def config = app.prepareConfig()
+        then:
+        config.entrypoint == [ "/some", "--entrypoint" ]
+        def layer = config.layers[0]
+        layer.location == "https://location"
+        layer.gzipDigest == "sha256:gzipDigest"
+        layer.tarDigest == "sha256:tarDigest"
+        layer.gzipSize == 100
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
+    def "test valid config file from a URL"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-file", "http://localhost:8080/api/data"]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        then:
+        app.@configFile == "http://localhost:8080/api/data"
+
+        when:
+        def config = app.prepareConfig()
+        then:
+        config.entrypoint == [ "/some", "--entrypoint" ]
+        def layer = config.layers[0]
+        layer.location == "https://location"
+        layer.gzipDigest == "sha256:gzipDigest"
+        layer.tarDigest == "sha256:tarDigest"
+        layer.gzipSize == 100
+    }
+}

app/src/test/groovy/io/seqera/wavelit/AppSpackOptsTest.groovy

@@ -17,6 +17,7 @@ import io.seqera.wavelit.exception.IllegalCliArgumentException
 import picocli.CommandLine
 import spock.lang.Specification
 /**
+ * Test App Spack prefixed options
  *
  * @author Paolo Di Tommaso <[email protected]>
  */