From b3b7c4dc2e2740b2dbacd59edff1412e7e0095e7 Mon Sep 17 00:00:00 2001
From: Simon Templer <simon@wetransform.to>
Date: Thu, 22 Mar 2018 11:53:13 +0100
Subject: [PATCH] WIP alignment export command
---
.../alignment/ExportAlignmentCommand.groovy | 55 +++++++++
.../halecli/util/AlignmentCLI.groovy | 107 ++++++++++++++++++
src/main/resources/plugin.xml | 6 +
3 files changed, 168 insertions(+)
create mode 100644 src/main/groovy/to/wetransform/halecli/project/alignment/ExportAlignmentCommand.groovy
create mode 100644 src/main/groovy/to/wetransform/halecli/util/AlignmentCLI.groovy
diff --git a/src/main/groovy/to/wetransform/halecli/project/alignment/ExportAlignmentCommand.groovy b/src/main/groovy/to/wetransform/halecli/project/alignment/ExportAlignmentCommand.groovy
new file mode 100644
index 0000000..6a74c54
--- /dev/null
+++ b/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
+
+}
diff --git a/src/main/groovy/to/wetransform/halecli/util/AlignmentCLI.groovy b/src/main/groovy/to/wetransform/halecli/util/AlignmentCLI.groovy
new file mode 100644
index 0000000..76524ad
--- /dev/null
+++ b/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
+ }
+
+}
diff --git a/src/main/resources/plugin.xml b/src/main/resources/plugin.xml
index 110c8e1..fddf737 100644
--- a/src/main/resources/plugin.xml
+++ b/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>