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Merge pull request #14 from scijava/tableioservice-options
2 parents 5c5925f + fcbd5ab commit a305794

9 files changed

Lines changed: 550 additions & 23 deletions

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‎pom.xml‎

Lines changed: 6 additions & 1 deletion
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@@ -5,7 +5,7 @@
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<parent>
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<groupId>org.scijava</groupId>
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<artifactId>pom-scijava</artifactId>
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<version>28.0.0</version>
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<version>29.0.0-beta-3</version>
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<relativePath />
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</parent>
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@@ -109,6 +109,11 @@ Wisconsin-Madison, and Friedrich Miescher Institute for Biomedical Research.</li
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<groupId>org.scijava</groupId>
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<artifactId>scijava-common</artifactId>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-optional</artifactId>
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<version>1.0.0</version>
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</dependency>
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<!-- Test scope dependencies -->
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<dependency>

‎src/main/java/org/scijava/table/io/ColumnTableIOOptions.java‎

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@@ -0,0 +1,65 @@
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/*
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* #%L
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* Table structures for SciJava.
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* %%
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* Copyright (C) 2012 - 2020 Board of Regents of the University of
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* Wisconsin-Madison, and Friedrich Miescher Institute for Biomedical Research.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.table.io;
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import org.scijava.optional.AbstractOptions;
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import java.util.function.Function;
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/**
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* @author Deborah Schmidt
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*/
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public class ColumnTableIOOptions extends AbstractOptions<ColumnTableIOOptions> {
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public final ColumnTableIOOptions.Values values = new ColumnTableIOOptions.Values();
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private static final String parserKey = "parser";
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private static final String formatterKey = "formatter";
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ColumnTableIOOptions formatter(Function<Object, String> formatter) {
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return setValue(formatterKey, formatter);
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}
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ColumnTableIOOptions parser(Function<String, Object> parser) {
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return setValue(parserKey, parser);
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}
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public class Values extends AbstractValues {
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public Function<Object, String> formatter() {
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return getValueOrDefault(formatterKey, String::valueOf);
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}
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public Function<String, Object> parser() {
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return getValueOrDefault(parserKey, String::valueOf);
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}
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}
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}

‎src/main/java/org/scijava/table/io/DefaultTableIOService.java‎

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@@ -71,6 +71,16 @@ public boolean canSave(Table<?, ?> table, String destination) {
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throw new UnsupportedOperationException("No compatible opener found.");
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}
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@Override
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public Table<?, ?> open(String source, TableIOOptions options) throws IOException {
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IOPlugin<?> opener = ioService.getOpener(source);
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if (opener != null && Table.class.isAssignableFrom(opener.getDataType())
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&& TableIOPlugin.class.isAssignableFrom(opener.getClass())) {
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return ((TableIOPlugin)opener).open(source, options);
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}
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throw new UnsupportedOperationException("No compatible opener found.");
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}
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@Override
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public void save(Table<?, ?> table, String destination) throws IOException {
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IOPlugin<Table<?, ?>> saver = ioService.getSaver(table, destination);
@@ -81,4 +91,15 @@ public void save(Table<?, ?> table, String destination) throws IOException {
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throw new UnsupportedOperationException("No compatible saver found.");
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}
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}
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@Override
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public void save(Table<?, ?> table, String destination, TableIOOptions options) throws IOException {
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IOPlugin<Table> saver = ioService.getSaver(table, destination);
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if (saver != null && TableIOPlugin.class.isAssignableFrom(saver.getClass())) {
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((TableIOPlugin)saver).save(table, destination, options);
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}
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else {
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throw new UnsupportedOperationException("No compatible saver found.");
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}
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}
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}

‎src/main/java/org/scijava/table/io/ExportTableCommand.java‎

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@@ -49,6 +49,15 @@
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@Menu(label = "Export"), @Menu(label = "Table...") })
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public class ExportTableCommand extends ContextCommand {
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@Parameter(required = false, label = "Write column headers")
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private boolean writeColHeaders = true;
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@Parameter(required = false, label = "Write row headers")
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private boolean writeRowHeaders = true;
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@Parameter(required = false, label = "Column delimiter")
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private char columnDelimiter = ',';
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@Parameter
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private LogService log;
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@@ -68,7 +77,11 @@ public class ExportTableCommand extends ContextCommand {
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@Override
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public void run() {
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try {
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tableIO.save(tableDisplay.get(0), outputFile.getAbsolutePath());
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TableIOOptions options = new TableIOOptions()
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.writeColumnHeaders(writeColHeaders)
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.writeRowHeaders(writeRowHeaders)
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.columnDelimiter(columnDelimiter);
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tableIO.save(tableDisplay.get(0), outputFile.getAbsolutePath(), options);
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}
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catch (IOException exc) {
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log.error(exc);

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