+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.bin.argparser;
import java.io.File;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import jalview.bin.Cache;
+import jalview.gui.Desktop;
@Test(singleThreaded = true)
public class ArgParserTest
Cache.loadProperties("test/jalview/testProps.jvprops");
}
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
@Test(groups = "Functional", dataProvider = "argLines")
public void parseArgsTest(String commandLineArgs, Arg a, String other)
{
{
String[] args = commandLineArgs.split("\\s+");
ArgParser argparser = new ArgParser(args);
- ArgValuesMap avm = argparser.linkedArgs(linkedId);
+ ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
ArgValue av = avm.getArgValue(a);
SubVals sv = av.getSubVals();
String testString = null;
public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
String linkedId, Arg a, String filename)
{
- // { "--open=filename0 --increment --open=filename1", "JALVIEW:1", Arg.OPEN,
- // "filename1" },
+ // { "--append=filename0 --new --append=filename1", "JALVIEW:1",
+ // Arg.OPEN, "filename1" },
String[] args = commandLineArgs.split("\\s+");
ArgParser argparser = new ArgParser(args);
- ArgValuesMap avm = argparser.linkedArgs(linkedId);
+ ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
ArgValue av = avm.getArgValue(a);
Assert.assertEquals(av.getValue(), filename);
}
Assert.assertTrue(b.contains(a));
if (a == Arg.PROPS)
{
- Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
+ Properties bP = Cache.bootstrapProperties(b.getValue(Arg.PROPS));
+ Assert.assertNotNull(bP);
Assert.assertTrue(other.equals(bP.get(Cache.BOOTSTRAP_TEST)));
Assert.assertFalse(bP.contains("NOT" + Cache.BOOTSTRAP_TEST));
}
else if (a == Arg.ARGFILE)
{
- List<String> filenames = b.getList(a);
+ List<String> filenames = b.getValueList(a);
boolean found = false;
for (String s : filenames)
{
BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
Assert.assertTrue(b.contains(a));
- Assert.assertFalse(b.contains(Arg.OPEN));
+ Assert.assertFalse(b.contains(Arg.APPEND));
if (a == Arg.PROPS)
{
- Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
+ Properties bP = Cache.bootstrapProperties(b.getValue(Arg.PROPS));
Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
}
}
@DataProvider(name = "argLines")
public Object[][] argLines()
{
- return new Object[][] {
- { "--debug --open=test/jalview/bin/argparser/testfiles/test1.fa",
+ return new Object[][] { {
+ "--append=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
+ Arg.PROPS, "true" },
+ { "--debug --append=test/jalview/bin/argparser/testfiles/test1.fa",
Arg.DEBUG, null },
- { "--open=test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ { "--append=test/jalview/bin/argparser/testfiles/test1.fa --headless",
Arg.HEADLESS, null },
- { "--open=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
- Arg.PROPS, "true" },
+
{ "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
Arg.ARGFILE,
"test/jalview/bin/argparser/testfiles/argfile0.txt" },
@DataProvider(name = "argSubValsAndLinkedIds")
public Object[][] argSubValsAndLinkedIds()
{
- return new Object[][] { {
- "--debug --open=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
- "JALVIEW:0", Arg.OPEN, "hi", "true", true },
- { "--open[linkedId1]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
- "linkedId1", Arg.OPEN, "new", "true", true },
- { "--open[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
- "linkedId2", Arg.OPEN, "hello", "world", true },
- { "--open[linkedId3]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
- "linkedId3", Arg.OPEN, "GETINDEX", "1", true },
- { "--open[linkedId4]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId5]=[notnew;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
- "linkedId5", Arg.OPEN, "new", "true", false },
- { "--open[linkedId5]=[new;hello=worlddomination;1]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
- "linkedId5", Arg.OPEN, "hello", "world", false },
- { "--open[linkedId6]=[new;hello=world;0]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId7]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
- "linkedId7", Arg.OPEN, "GETINDEX", "0", false }, };
+ return new Object[][] {
+ //
+ /*
+ */
+ { "--debug --append=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
+ "JALVIEW:0", Arg.APPEND, "hi", "true", true },
+ { "--append[linkedId1]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId1", Arg.APPEND, "new", "true", true },
+ { "--append[linkedId2]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId2", Arg.APPEND, "hello", "world", true },
+ { "--append[linkedId3]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId3", Arg.APPEND, "GETINDEX", "1", true },
+ { "--append[linkedId4]=[new,hello=world,1]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId5]=[notnew;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId5", Arg.APPEND, "new", "true", false },
+ { "--append[linkedId5]=[new,hello=worlddomination,1]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId5", Arg.APPEND, "hello", "world", false },
+ { "--append[linkedId6]=[new,hello=world,0]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId7]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ "linkedId7", Arg.APPEND, "GETINDEX", "0", false },
+ /*
+ */
+ //
+ };
}
@DataProvider(name = "argAutoIndexAndSubstitutions")
public Object[][] argAutoIndexAndSubstitutions()
{
- return new Object[][] { { "--open=filename0 --open=filename1",
- "JALVIEW:0", Arg.OPEN, "filename0" },
- { "--open=filename0 --increment --open=filename1", "JALVIEW:1",
- Arg.OPEN, "filename1" },
- { "--open=filename0 --increment --increment --open=filename2",
- "JALVIEW:0", Arg.OPEN, "filename0" },
- { "--open=filename0 --increment --increment --open=filename2",
- "JALVIEW:2", Arg.OPEN, "filename2" },
- { "--open[linkA-{n}]=filenameA0 --open[linkA-{++n}]=filenameA1",
+ return new Object[][] {
+ //
+ /*
+ */
+ { "--append=filename0 --append=filename1", "JALVIEW:0", Arg.APPEND,
+ "filename0" },
+ { "--append=filename0 --new --append=filename1", "JALVIEW:1",
+ Arg.APPEND, "filename1" },
+ { "--append=filename0 --new --new --append=filename2", "JALVIEW:0",
+ Arg.APPEND, "filename0" },
+ { "--append=filename0 --new --new --append=filename2", "JALVIEW:2",
+ Arg.APPEND, "filename2" },
+ { "--append[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
+ "linkA-0", Arg.APPEND, "filenameA0" },
+ { "--append[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
+ "linkB-1", Arg.APPEND, "filenameB1" },
+ { "--append[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
+ "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
+ { "--append[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
+ "linkD-0", Arg.IMAGE, "outputD0.txt" },
+ { "--append[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
+ "linkE-0", Arg.IMAGE, "output-E0.txt" },
+ { "--append[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
+ "linkF-1", Arg.IMAGE, "outputF1.txt" },
+ { "--append[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
+ "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
+ { "--append[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
+ "linkH-0", Arg.IMAGE, "output-H0.txt" },
+ { "--open=filename0 --append=filename1", "JALVIEW:0", Arg.OPEN,
+ "filename0" },
+ { "--open=filename0 --new --append=filename1", "JALVIEW:1",
+ Arg.APPEND, "filename1" },
+ { "--open=filename0 --new --new --append=filename2", "JALVIEW:0",
+ Arg.OPEN, "filename0" },
+ { "--open=filename0 --new --new --append=filename2", "JALVIEW:2",
+ Arg.APPEND, "filename2" },
+ { "--open[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
"linkA-0", Arg.OPEN, "filenameA0" },
- { "--open[linkB-{n}]=filenameB0 --open[linkB-{++n}]=filenameB1",
- "linkB-1", Arg.OPEN, "filenameB1" },
+ { "--open[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
+ "linkB-1", Arg.APPEND, "filenameB1" },
{ "--open[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
"linkC-0", Arg.IMAGE, "outputC{n}.txt" },
{ "--open[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
{ "--open[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
"linkG-1", Arg.IMAGE, "outputG{n}.txt" },
{ "--open[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
- "linkH-0", Arg.IMAGE, "output-H0.txt" }, };
+ "linkH-0", Arg.IMAGE, "output-H0.txt" },
+ /*
+ */
+
+ //
+ };
}
@DataProvider(name = "argFiles")
"--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
}
-}
+
+ @Test(groups = "Functional", dataProvider = "allLinkedIdsData")
+ public void allLinkedIdsTest(String pwd, String commandLineArgs, Arg a,
+ String[] values, String[] nonvalues)
+ {
+ String userDir = System.getProperty("user.dir");
+ if (pwd != null)
+ {
+ File pwdFile = new File(pwd);
+ System.setProperty("user.dir", pwdFile.getAbsolutePath());
+ }
+ String[] args = commandLineArgs.split("\\s+");
+ ArgParser argparser = new ArgParser(args);
+
+ int num = values.length;
+ List<String> linkedIds = argparser.getLinkedIds();
+ Assert.assertEquals(linkedIds.size(), num,
+ "Wrong number of linkedIds: " + linkedIds.toString());
+ for (int i = 0; i < num; i++)
+ {
+ String value = values[i];
+ String linkedId = linkedIds.get(i);
+ ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
+ if (value == null)
+ {
+ Assert.assertTrue(avm.containsArg(a),
+ "Arg value for " + a.argString()
+ + " not applied correctly to linkedId '" + linkedId
+ + "'");
+ }
+ else
+ {
+ ArgValues avs = avm.getArgValues(a);
+ ArgValue av = avs.getArgValue();
+ String v = av.getValue();
+ value = new File(value).getPath();
+ Assert.assertEquals(v, value, "Arg value for " + a.argString()
+ + " not applied correctly to linkedId '" + linkedId + "'");
+ }
+ }
+
+ System.setProperty("user.dir", userDir);
+ }
+
+ @DataProvider(name = "allLinkedIdsData")
+ public Object[][] allLinkedIdsData()
+ {
+ return new Object[][] {
+ //
+ /*
+ */
+ { null,
+ "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+ Arg.CLOSE, new String[]
+ { null, null, null },
+ null },
+ { null,
+ "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+ Arg.OUTPUT, new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk", },
+ null },
+ { null,
+ "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+ Arg.IMAGE, new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.png",
+ "test/jalview/bin/argparser/testfiles/test2.png",
+ "test/jalview/bin/argparser/testfiles/test3.png", },
+ null },
+ /*
+ * Find a way to change pwd reliably -- need to match "*.fa" against some files!
+ { "test/jalview/bin/argparser/testfiles",
+
+ "--open=*.fa --image={dirname}/{basename}.png --close",
+ Arg.IMAGE, new String[]
+ { "./test1.png", "./test2.png", "./test3.png", }, null },
+ */
+ //
+ };
+ }
+
+ @Test(groups = "Functional", dataProvider = "bootstrapArgsData")
+ public void bootstrapArgsValuesAndHeadlessModeTest(String commandLineArgs,
+ Arg a, String valS, boolean valB, boolean headlessValue)
+ {
+ String[] args = commandLineArgs.split("\\s+");
+ BootstrapArgs bsa = BootstrapArgs.getBootstrapArgs(args);
+ if (a != null)
+ {
+ if (valS != null)
+ {
+ Assert.assertEquals(bsa.getValue(a), valS,
+ "BootstrapArg " + a.argString()
+ + " value does not match expected '" + valS + "'");
+ }
+ else
+ {
+ Assert.assertEquals(bsa.getBoolean(a), valB,
+ "Boolean/Unary value of BootstrapArg " + a.argString()
+ + "' is not the expected '" + valB + "'");
+ }
+ }
+
+ boolean isHeadless = bsa.isHeadless();
+ Assert.assertEquals(isHeadless, headlessValue,
+ "Assumed headless setting '" + isHeadless + "' is wrong.");
+ }
+
+ @DataProvider(name = "bootstrapArgsData")
+ public Object[][] bootstrapArgsData()
+ {
+ return new Object[][] {
+ /*
+ * cmdline args
+ * Arg (null if only testing headless)
+ * String value if there is one (null otherwise)
+ * boolean value if String value is null
+ * expected value of isHeadless()
+ */
+ /*
+ */
+ { "--open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
+ Arg.JABAWS, "https://forwardsandbackwards.com/", false, true },
+ { "--help-all --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
+ Arg.HELP, null, true, true },
+ { "--help-all --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
+ Arg.NEWS, null, false, true },
+ { "--help --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
+ Arg.NEWS, null, false, true },
+ { "--help-opening --nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
+ Arg.NEWS, null, false, true },
+ { "--nonews --open thisway.fa --output thatway.fa --jabaws https://forwardsandbackwards.com/",
+ Arg.NEWS, null, false, true },
+ { "--open thisway.fa --image thatway.png", null, null, false,
+ true },
+ { "--open thisway.fa --output thatway.png", null, null, false,
+ true },
+ { "--open thisway.fa --image thatway.png --noheadless", null, null,
+ false, false },
+ { "--open thisway.fa --output thatway.png --noheadless", null, null,
+ false, false },
+ { "--open thisway.fa --image thatway.png --gui", null, null, false,
+ false },
+ { "--open thisway.fa --output thatway.png --gui", null, null, false,
+ false },
+ // --gui takes precedence
+ { "--open thisway.fa --image thatway.png --gui --headless", null,
+ null, false, false },
+ { "--open thisway.fa --output thatway.png --gui --headless", null,
+ null, false, false },
+ //
+ };
+ }
+
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff