spoonlabs/astor

Automatic program repair for Java with generate-and-validate techniques :v::v:: jGenProg (2014) - jMutRepair (2016) - jKali (2016) - DeepRepair (2017) - Cardumen (2018) - 3sfix (2018)

astor's Issues

arguments of MainjGenProg add "[mandatory]" or "[optional]"

In the arguments of MainjGenProg , add "[mandatory]" or "[optional]" to clarify usage.

Wrong patches proposed for math-44

Test prioritization

Ingredient for replace operator

Take in account ct hierarchy. i.e., ctassignment, ctopassig

IntroClass

Some code transformations fail:

ERROR main - Error: the model was not the same from the original after this generation
2016-02-04 10:18:08,367 ERROR main - Parent diferent to block
2016-02-04 10:18:08,411 ERROR main - Parent diferent to block
2016-02-04 10:18:08,474 ERROR main - Parent diferent to block
2016-02-04 10:18:08,503 ERROR main - Parent diferent to block
2016-02-04 10:18:08,591 ERROR main - Error: parent not found

Command:

java -cp /Users/matias/develop/code/astor/target/astor-0.0.2-SNAPSHOT-jar-with-dependencies.jar fr.inria.main.evolution.AstorMain -location /Users/matias/develop/IntroClassJava/dataset/median/3b2376ab97bb5d1a5dbbf2b45cf062db320757549c761936d19df05e856de894e45695014cd8063cdc22148b13fa1803b3c9e77356931d66f4fbec0efacf7829/003/ -failing introclassJava.median_3b2376ab_003BlackboxTest:introclassJava.median_3b2376ab_003WhiteboxTest -dependencies /Users/matias/develop/code/astor/examples/libs/junit-4.11.jar

rename Gen in ModificationPoint

Results

Operation Type property sometimes is Null

Statement Parent is a Case

Check example Math-288.
We required a parent is a CtBlock

Classpath in Process

Filter classpath by including junit dependency

Duplicate remove

Variables

Check variables related to a ModPoint.
Create a Test Case

Compilation output

Check the compilation output.

Code source folders

Avoid merge src and test code in one folder

Problems handling package-info when compiling Hadoop-submodule

I am using Astor to do some automated bug repair work. Now I have problems compiling Hadoop submodule (i.e. hadoop/hadoop-common-project/hadoop-auth).

Seems that Spoon can NOT get the declared type from package-info.java file. Is there anyone knowing how to fix this issue? Thanks a lot!

The command line argument I use:
java -cp $(cat /tmp/astor-classpath.txt):target/classes fr.inria.main.evolution.MainjGenProg -loglevel debug -hadoop11859

I add an option in AbstractMain.java to run this bug, the folder 11859hadp is the a submodule of Hadoop project (hadoop/hadoop-common-project/hadoop-auth), which can be compiled and tested separately:

if (cmd.hasOption("hadoop11859")) {
	dependenciespath = gatherDependencies(
			"libBugs/11859hadp/lib/");
	folder = "11859hadp";
	failing = "org.apache.hadoop.security.authentication.server.TestPseudoAuthenticationHandler";
	location = ("libBugs/11859hadp/");
	packageToInstrument = "org.apache.hadoop.security.authentication.server";
	faultLocalizationThreshold = 0.5;
}

As for other configuration, I just use the configuration.properties file, only change the alternativecompliancelevel from 4 to 7.

the log information is listed below:

2017-08-30 17:59:15,128 INFO main - building model: /Users/someone/git/astor/./outputMutation/AstorMain-11859hadp//src//default, compliance level: 8
2017-08-30 17:59:15,136 INFO main - Classpath for building SpoonModel [too long to list all of them]
2017-08-30 17:59:16,885 ERROR main - Problem compiling the model with compliance level 8
2017-08-30 17:59:16,885 ERROR main - inconsistent compilation unit: '/Users/someone/git/astor/outputMutation/AstorMain-11859hadp/src/default/org/apache/hadoop/security/authentication/server/package-info.java': declared types are []
2017-08-30 17:59:16,885 INFO main - building model: /Users/someone/git/astor/./outputMutation/AstorMain-11859hadp//src//default, compliance level: 7
2017-08-30 17:59:16,887 INFO main - Classpath for building SpoonModel [too long to list all of them]
Exception in thread "main" java.lang.RuntimeException: inconsistent compilation unit: '/Users/someone/git/astor/outputMutation/AstorMain-11859hadp/src/default/org/apache/hadoop/security/authentication/server/package-info.java': declared types are []
    at spoon.support.reflect.cu.CompilationUnitImpl.getMainType(CompilationUnitImpl.java:68)
    at spoon.support.compiler.jdt.JDTBasedSpoonCompiler.generateProcessedSourceFilesUsingCUs(JDTBasedSpoonCompiler.java:498)
    at spoon.support.compiler.jdt.JDTBasedSpoonCompiler.generateProcessedSourceFiles(JDTBasedSpoonCompiler.java:203)
    at spoon.support.compiler.jdt.JDTBasedSpoonCompiler.generateProcessedSourceFiles(JDTBasedSpoonCompiler.java:192)
    at fr.inria.astor.core.manipulation.MutationSupporter.buildModel(MutationSupporter.java:90)
    at fr.inria.astor.core.manipulation.MutationSupporter.buildModel(MutationSupporter.java:71)
    at fr.inria.astor.approaches.jgenprog.JGenProg.initModel(JGenProg.java:152)
    at fr.inria.astor.approaches.jgenprog.JGenProg.createInitialPopulation(JGenProg.java:62)
    at fr.inria.main.evolution.AstorMain.createEngine(AstorMain.java:97)
    at fr.inria.main.evolution.AstorMain.run(AstorMain.java:142)
    at fr.inria.main.AbstractMain.executeExample(AbstractMain.java:708)
    at fr.inria.main.evolution.AstorMain.execute(AstorMain.java:209)
    at fr.inria.main.evolution.AstorMain.main(AstorMain.java:199)
    at fr.inria.main.evolution.MainjGenProg.main(MainjGenProg.java:14)

Call to printSolutions

Excluding throws

Execution mode

Define better arguments for execution jGP mode

Configuration

From Reviewer:
it seems there are a lot of settings regarding the structure of the project
that needs to be provided by the user. You might want to consider to implement a Maven plugin, as to avoid all this overhead (eg resolution of classpath). Furthermore, it is
unclear whether multi­module Maven projects are supported (from your description, I would guess not, but I might be mistaken of course).

when a argument is missing, MainjGenProg does not say which one

Hi Matias,

We're trying to run the Math-issue-280 directly with all arguments (and not with "-bug280").

One argument is missing but we don't know the one.

 fr.inria.main.evolution.MainjGenProg  -srcjavafolder examples/Math-issue-280/src/java/ -srctestfolder examples/Math-issue-280/src/test/  -binjavafolder examples/Math-issue-280/target/classes/ -bintestfolder  examples/Math-issue-280/target/test-classes/

What's the missing argument?

Time

In a program variant that is solution, we store the generation but not the time

Remove ProgramValidator class

update to Spoon 4.3.0

we should update to Spoon 4.3.0 (hence remove dependency to CtSimpleType)

add support for multiple test suite

srctestfolder can take several test folders separated by ":"

the output json files give the kinds of number of failures for each different test folder.

this would be used for playing with different "extended tests" (beyond manual tests)

Improve calculation of Regression Test

See ProjectRepairFacade#calculateRegression and FaultLocalizationFacade.

1. we calculate tests that conform regression parsing classes
2. We preprocess the previous result (Stored in ProjectProperties)
3. We send to Gzoltar to execute the regression
   4)We analyze the test that Gzoltar could analyze. (Stored in ConfigurationProperties and)

Problem: when FL is not executed.

Output folder

We could separate the "workingFolder" and "output". Right now It's the same....

Duplicates elements

output += java.lang.String.format("%d is the median\n", n3.value)
output += java.lang.String.format("%d is the median\n", n1.value)
Signature:

java.lang.String introclassJava.median_3b2376ab_003#outputPLUS(java.lang.String#format(java.lang.String, java.lang.Object[])("%d is the median\n",int introclassJava.IntObj#value))

Remove hardcoded string

String hardcode:
-folder name of variants stored
-solution folders

Extension Point for Operators

Repair Tests

testExample340CommandLine
Ne passe pas

testExample309CommandLine
Ne passe pas

testExample288CommandLine
Ne passe pas

Class Clone in VariantFactory

add extension point IngredientChooser

interface IngredientChooser {
  CtElement chooseIngredient(IngredientSpace ingredients, MutationLocation x, RepairContext/ProgramVariant y);
}

Improve VariantFactory

remove hard coded path from MutRepairTest and jKaliTest

Path too long

Is it possible to rename the directory astor/examples/introclass/3b2376... using a shorter name? Otherwise paths in that subtree are too long for some systems when extracting or cloning.

Undefined cases

Running example bug288 produces the following errors:

[ERROR] fr.inria.astor.core.manipulation.sourcecode.VariableResolver.fitInPlace(VariableResolver.java:308) -
Undefined case spoon.support.reflect.code.CtThisAccessImpl
[ERROR] fr.inria.astor.core.manipulation.sourcecode.VariableResolver.fitInPlace(VariableResolver.java:308) -
Undefined case spoon.support.reflect.code.CtNewArrayImpl
[ERROR] fr.inria.astor.core.manipulation.sourcecode.VariableResolver.fitInPlace(VariableResolver.java:308) -
Undefined case spoon.support.reflect.code.CtConditionalImpl

My environment references spoon-core-5.1.0.jar.

Improve Operator Hierarchy

Astor in Java8

When we use java 8 (jdk and maven pom change) we have 2 failing test.
Results :

Failed tests:
JGenProgTest.testExample280CommandLine:66->BaseEvolutionaryTest.validatePatchExistence:92 null [UPDATE: OK, it works, changing the nr of generations]
jKaliTest.testMath2ExampleRemoveModeOneSolution:102 expected:<1> but was:<0>

Tests run: 24, Failures: 2, Errors: 0, Skipped: 3

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE

Classpath format

There are URL[], String[], List<...>
Unify

add method getModifiedClasses::List<CtClass> in ProgramVariant

Math-70 Flaky?

Missing dependence "org.eclipse.jdt.core:3.12.0.v20150913-1717"

When using spoon(5.1.0), I am not able to build it because the "org.eclipse.jdt.core:3.12.0.v20150913-1717" has been removed, which has been reported(INRIA/spoon#688).

After changing the version of spoon to 5.2.0-snapshot, I can build it.

build failure: Could not resolve dependencies

[ERROR] Failed to execute goal on project astor: Could not resolve dependencies for project org.inria.sacha.automaticRepair:astor:jar:0.0.2-SNAPSHOT: Could not find artifact fr.spoonlab:jte:jar:0.0.1 in inria (http://spoon.gforge.inria.fr/repositories/releases/)

Arguments

Improving management of command line arguments

mode arguments

Rename argument values

NPE when Astor aims printing some ingredient

Gzoltar migration to 1.5

Arguments used to the experiment

I read astor's paper and the readme, and succeeded to repair some bugs contained at examples folder.However I couldn't generate patches reported in docs/bugs_repaired.md to some bugs(Math-5,7) downloaded from defects4j manually.
Could you give me more information about how to execute astor on defects4j (or the bugs not contained in the examples folder of astor)?

For example, I executed astor to math-5 in the following arguments:

-location ../defects4j/tmp/math-5-buggy
-mode jgenprog -scope local -srcjavafolder /src/java -srctestfolder /src/test/
-binjavafolder /target/classes -bintestfolder /target/test-classes -flthreshold 0.5 -seed 10 -maxtime 100 -stopfirst true

-failing org.apache.commons.math3.complex.ComplexTest:org.apache.commons.math3.util.FastMathTest
(obteined by mvn test

-dependencies ./examples/libs/junit-4.10.jar:./examples/libs/hamcrest-core-1.1.jar
(obteined by mvn dependency:build-classpath

-javacompliancelevel 8 ##how should we determine this argument?

NPE in jsoup

bug reported by Johnson K.
stacktrace.txt

Test cases to create

-Maxtime property

Access to Factory

We have to "Kill" mutation supporter class