[WIP] alignment export command

src/main/groovy/to/wetransform/halecli/project/alignment/ExportAlignmentCommand.groovy

@@ -0,0 +1,55 @@
+/*
+ * Copyright (c) 2018 wetransform GmbH
+ *
+ * All rights reserved. This program and the accompanying materials are made
+ * available under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the License,
+ * or (at your option) any later version.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this distribution. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     wetransform GmbH <http://www.wetransform.to>
+ */
+
+package to.wetransform.halecli.project.alignment
+
+import java.net.URI
+
+import eu.esdihumboldt.hale.common.cli.project.AbstractProjectEnvironmentCommand
+import eu.esdihumboldt.hale.common.core.report.ReportHandler
+import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
+import eu.esdihumboldt.util.cli.CommandContext
+import groovy.util.OptionAccessor
+import to.wetransform.halecli.util.AlignmentCLI
+
+/**
+ * Command to export an alignment.
+ *
+ * @author Simon Templer
+ */
+class ExportAlignmentCommand extends AbstractProjectEnvironmentCommand {
+
+  void setupOptions(CliBuilder cli) {
+    super.setupOptions(cli)
+
+    // options for saving alignment
+    AlignmentCLI.saveAlignmentOptions(cli)
+  }
+
+  @Override
+  public boolean runForProject(ProjectTransformationEnvironment project, URI projectLocation, OptionAccessor options,
+      CommandContext context, ReportHandler reports) {
+    //FIXME restrict to use with single project?! Or support multi-project execution?
+
+    AlignmentCLI.saveAlignment(project.alignment, project.sourceSchema, project.targetSchema, options)
+
+    return true
+  }
+
+  final String shortDescription = 'Export a project alignment with specific settings'
+
+  final boolean experimental = true
+
+}

src/main/groovy/to/wetransform/halecli/util/AlignmentCLI.groovy

@@ -0,0 +1,107 @@
+/*
+ * Copyright (c) 2018 wetransform GmbH
+ *
+ * All rights reserved. This program and the accompanying materials are made
+ * available under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the License,
+ * or (at your option) any later version.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this distribution. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     wetransform GmbH <http://www.wetransform.to>
+ */
+
+package to.wetransform.halecli.util
+
+import static eu.esdihumboldt.hale.app.transform.ExecUtil.fail;
+import static to.wetransform.halecli.util.HaleIOHelper.*
+
+import java.io.InputStream
+import java.net.URI;
+import java.util.Map
+
+import eu.esdihumboldt.hale.common.align.io.AlignmentWriter
+import eu.esdihumboldt.hale.common.align.model.Alignment
+import eu.esdihumboldt.hale.common.cli.HaleCLIUtil;
+import eu.esdihumboldt.hale.common.core.io.HaleIO
+import eu.esdihumboldt.hale.common.core.io.Value
+import eu.esdihumboldt.hale.common.core.io.impl.LogProgressIndicator;
+import eu.esdihumboldt.hale.common.core.io.project.model.IOConfiguration;
+import eu.esdihumboldt.hale.common.core.io.report.IOReport;
+import eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier;
+import eu.esdihumboldt.hale.common.core.io.supplier.LocatableInputSupplier;
+import eu.esdihumboldt.hale.common.core.report.ReportHandler
+import eu.esdihumboldt.hale.common.instance.io.InstanceReader
+import eu.esdihumboldt.hale.common.instance.io.InstanceWriter;
+import eu.esdihumboldt.hale.common.instance.model.InstanceCollection;
+import eu.esdihumboldt.hale.common.schema.io.SchemaIO;
+import eu.esdihumboldt.hale.common.schema.io.SchemaReader
+import eu.esdihumboldt.hale.common.schema.io.SchemaWriter;
+import eu.esdihumboldt.hale.common.schema.model.Schema
+import eu.esdihumboldt.hale.common.schema.model.SchemaSpace;
+import eu.esdihumboldt.hale.common.schema.model.impl.DefaultSchemaSpace
+import eu.esdihumboldt.util.Pair;
+import eu.esdihumboldt.util.cli.CLIUtil
+import groovy.transform.CompileStatic
+import groovy.util.CliBuilder
+import groovy.util.OptionAccessor;;;;
+
+/**
+ * Common utility functions for setting up a CliBuilder for processing alignments.
+ *
+ * @author Simon Templer
+ */
+class AlignmentCLI {
+
+  // save alignment
+
+  static void saveAlignmentOptions(CliBuilder cli, String argName = 'target', String descr = 'Target location') {
+    cli._(longOpt: argName, args:1, argName: 'file-or-URI', descr)
+    cli._(longOpt: argName + '-setting', args:2, valueSeparator:'=', argName:'setting=value',
+      'Setting for target writer (optional, repeatable)')
+    cli._(longOpt: argName + '-writer', args:1, argName: 'provider-id',
+      'Identifier of alignment writer to use')
+  }
+
+  private static AlignmentWriter getWriter(OptionAccessor options, String argName = 'target') {
+    def location = options."$argName"
+    if (location) {
+      URI loc = CLIUtil.fileOrUri(location)
+
+      def settings = options."${argName}-settings"
+      settings = settings ? settings.toSpreadMap() : [:]
+
+      String providerId = options."${argName}-writer" ?: null
+
+      return getWriter(loc, settings, providerId)
+    }
+    else {
+      return null
+    }
+  }
+
+  @CompileStatic
+  private static AlignmentWriter getWriter(URI loc, Map<String, String> settings, String providerId) {
+    return prepareWriter(providerId, AlignmentWriter, settings, loc);
+  }
+
+  @CompileStatic
+  static IOReport saveAlignment(Alignment alignment, SchemaSpace sourceSchema, SchemaSpace targetSchema,
+      OptionAccessor options, String argName = 'target') {
+    AlignmentWriter writer = getWriter(options, argName)
+    def loc = writer.getTarget()?.location
+    println "Writing alignment to ${loc}..."
+
+    writer.setAlignment(alignment)
+    writer.setSourceSchema(sourceSchema)
+    writer.setTargetSchema(targetSchema)
+
+    IOReport report = writer.execute(new LogProgressIndicator())
+    HaleCLIUtil.createReportHandler(options).publishReport(report)
+
+    return report
+  }
+
+}

src/main/resources/plugin.xml

@@ -72,5 +72,11 @@
             id="hale-cli.schema.rewrite"
             name="rewrite">
       </command>
+      <command
+            class="to.wetransform.halecli.project.alignment.ExportAlignmentCommand"
+            group="project.alignment"
+            id="hale-cli.project.alignment.export"
+            name="export">
+      </command>
    </extension>
 </plugin>