--- /dev/null
+package jalview.bin.argparser;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Properties;
+
+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
+{
+ @AfterClass(alwaysRun = true)
+ public static void resetProps()
+ {
+ 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);
+ }
+
+ @Test(groups = "Functional", dataProvider = "argSubValsAndLinkedIds")
+ public void parseSubValsAndLinkedIdsTest(String commandLineArgs,
+ String linkedId, Arg a, String subvalKey, String value,
+ boolean trueOrFalse)
+ {
+ String[] args = commandLineArgs.split("\\s+");
+ ArgParser argparser = new ArgParser(args);
+ ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
+ ArgValue av = avm.getArgValue(a);
+ SubVals sv = av.getSubVals();
+ String testString = null;
+ if (subvalKey.equals("GETINDEX"))
+ {
+ testString = String.valueOf(sv.getIndex());
+ }
+ else
+ {
+ testString = sv.get(subvalKey);
+ }
+ if (trueOrFalse)
+ {
+ Assert.assertEquals(testString, value);
+ }
+ else
+ {
+ Assert.assertNotEquals(testString, value);
+ }
+ }
+
+ @Test(
+ groups = "Functional",
+ dataProvider = "argAutoIndexAndSubstitutions")
+ public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
+ String linkedId, Arg a, String filename)
+ {
+ // { "--append=filename0 --new --append=filename1", "JALVIEW:1",
+ // Arg.OPEN, "filename1" },
+ String[] args = commandLineArgs.split("\\s+");
+ ArgParser argparser = new ArgParser(args);
+ ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
+ ArgValue av = avm.getArgValue(a);
+ Assert.assertEquals(av.getValue(), filename);
+ }
+
+ @Test(groups = "Functional", dataProvider = "argLines")
+ public void bootstrapArgsTest(String commandLineArgs, Arg a, String other)
+ {
+ String[] args = commandLineArgs.split("\\s+");
+ BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
+
+ Assert.assertTrue(b.contains(a));
+ if (a == 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.getValueList(a);
+ boolean found = false;
+ for (String s : filenames)
+ {
+ File f = new File(s);
+ File fo = new File(other);
+ try
+ {
+ if (fo.getCanonicalPath().equals(f.getCanonicalPath()))
+ {
+ found = true;
+ break;
+ }
+ } catch (IOException e)
+ {
+ }
+ }
+ Assert.assertTrue(found,
+ "File '" + other + "' not found in shell expanded glob '"
+ + commandLineArgs + "'");
+ }
+ }
+
+ @Test(groups = "Functional", dataProvider = "argFiles")
+ public void argFilesTest(String commandLineArgs, Arg a, String other)
+ {
+ String[] args = commandLineArgs.split("\\s+");
+ BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
+
+ Assert.assertTrue(b.contains(a));
+ Assert.assertFalse(b.contains(Arg.APPEND));
+ if (a == Arg.PROPS)
+ {
+ Properties bP = Cache.bootstrapProperties(b.getValue(Arg.PROPS));
+ Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
+ }
+ }
+
+ @DataProvider(name = "argLinesNotworking")
+ public Object[][] argLinesTest()
+ {
+ return new Object[][] {
+ // can't use this one yet as it doesn't get shell glob expanded by the
+ // test
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile*.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile0.txt" }, };
+ }
+
+ @DataProvider(name = "argLines")
+ public Object[][] argLines()
+ {
+ 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 },
+ { "--append=test/jalview/bin/argparser/testfiles/test1.fa --headless",
+ Arg.HEADLESS, null },
+
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+ // these next three are what a shell glob expansion would look like
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile1.txt" },
+ { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile2.txt" },
+ { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+ { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile1.txt" },
+ { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+ Arg.ARGFILE,
+ "test/jalview/bin/argparser/testfiles/argfile2.txt" } };
+ }
+
+ @DataProvider(name = "argSubValsAndLinkedIds")
+ public Object[][] argSubValsAndLinkedIds()
+ {
+ 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[][] {
+ //
+ /*
+ */
+ { "--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 --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",
+ "linkD-0", Arg.IMAGE, "outputD0.txt" },
+ { "--open[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" },
+ { "--open[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" },
+ { "--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" },
+ /*
+ */
+
+ //
+ };
+ }
+
+ @DataProvider(name = "argFiles")
+ public Object[][] argFiles()
+ {
+ return new Object[][] { {
+ "--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 commandLineArgs, Arg a,
+ String[] values, String[] nonvalues)
+ {
+ 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).getAbsolutePath();
+ Assert.assertEquals(v, value, "Arg value for " + a.argString()
+ + " not applied correctly to linkedId '" + linkedId + "'");
+ }
+ }
+
+ }
+
+ @DataProvider(name = "allLinkedIdsData")
+ public Object[][] allLinkedIdsData()
+ {
+ return new Object[][] {
+ //
+ /*
+ */
+ { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+ Arg.CLOSE, new String[]
+ { 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 },
+ { "--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 },
+ //
+ };
+ }
+
+ @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 },
+ //
+ };
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff