Weekly release

.gitmodules

@@ -58,3 +58,18 @@
 [submodule "benchmark/aprcompaijs"]
 	path = benchmark/aprcompaijs
 	url = https://github.com/RepairComp/autocodejs.git
+[submodule "benchmark/aprcompvulnjava"]
+	path = benchmark/aprcompvulnjava
+	url = https://github.com/apR-Comp/vulnerabilities-java
+[submodule "benchmark/aprcompedupython"]
+	path = benchmark/aprcompedupython
+	url = https://github.com/APR-Comp/education-python-benchmark.git
+[submodule "benchmark/aprcompfuncc"]
+	path = benchmark/aprcompfuncc
+	url = https://github.com/APR-Comp/functional-c
+[submodule "benchmark/aprcompfuncjava"]
+	path = benchmark/aprcompfuncjava
+	url = https://github.com/apr-comp/functional-java
+[submodule "benchmark/aprcompeduc"]
+	path = benchmark/aprcompeduc
+	url = https://github.com/APR-Comp/education-c-benchmark.git

app/core/container.py

@@ -127,6 +127,10 @@ def build_image(dockerfile_path: str, image_name: str):
                         emitter.build("\t\t[docker-api] {}".format(line_stream))
                     if "Successfully built" in line["stream"]:
                         id = line["stream"].split(" ")[-1]
+            if id is None:
+                utilities.error_exit(
+                    "[error] Image was not build successfully. Please check whether the file builds outside of Cerberus"
+                )
             return id
         except docker.errors.BuildError as ex:  # type: ignore
             emitter.error(ex)
@@ -426,7 +430,7 @@ def stop_container(container_id: str):
     emitter.normal("\t\t\t[framework] stopping docker container")
     try:
         container = client.containers.get(container_id)
-        container.stop(timeout=20)  # type: ignore
+        container.stop(timeout=120)  # type: ignore
     except docker.errors.APIError as exp:  # type: ignore
         emitter.warning(exp)
         emitter.warning(

app/core/task/repair.py

@@ -278,6 +278,7 @@ def repair_wrapped(
         # give 5 min grace period for threads to finish
         wait_time = wait_time + 60.0 * 5
         tool_thread.join(wait_time)
+
         if tool_thread.is_alive():
             emitter.highlight(
                 "\t\t\t[framework] {}: thread is not done, setting event to kill thread.".format(

app/drivers/benchmarks/AbstractBenchmark.py

@@ -51,6 +51,10 @@ class AbstractBenchmark(AbstractDriver):
     key_build_system = definitions.KEY_BUILD_SYSTEM
     key_fail_mod_dir = definitions.KEY_FAILING_MODULE_DIRECTORY
     key_test_all_cmd = definitions.KEY_TEST_ALL_CMD
+    key_dir_class = definitions.KEY_CLASS_DIRECTORY
+    key_dir_source = definitions.KEY_SOURCE_DIRECTORY
+    key_dir_tests = definitions.KEY_TEST_DIRECTORY
+    key_dir_test_class = definitions.KEY_TEST_CLASS_DIRECTORY
     key_subject = definitions.KEY_SUBJECT
     has_standard_name: bool = False
 

app/drivers/benchmarks/c/APRCompEduC.py

@@ -0,0 +1,82 @@
+import os
+from datetime import datetime
+
+from app.drivers.benchmarks.AbstractBenchmark import AbstractBenchmark
+
+
+class APRCompEduC(AbstractBenchmark):
+    def __init__(self):
+        self.name = os.path.basename(__file__)[:-3].lower()
+        super(APRCompEduC, self).__init__()
+
+    def setup_experiment(self, bug_index, container_id, test_all):
+        is_error = super(APRCompEduC, self).setup_experiment(
+            bug_index, container_id, test_all
+        )
+        return is_error
+
+    def deploy(self, bug_index, container_id):
+        self.emit_normal("downloading experiment subject")
+        self.run_command(
+            container_id, "cp -rf {} {}/src".format(self.dir_setup, self.dir_expr)
+        )
+        return True
+
+    def config(self, bug_index, container_id):
+        self.emit_normal("configuring experiment subject")
+        return True
+
+    def build(self, bug_index, container_id):
+        self.emit_normal("building experiment subject")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_build_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-build.log"
+        )
+        time = datetime.now()
+        command_str = "bash build_subject"
+
+        status = self.run_command(
+            container_id, command_str, self.log_build_path, self.dir_setup
+        )
+        self.emit_debug(
+            "setup took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status == 0
+
+    def test(self, bug_index, container_id):
+        self.emit_normal("testing experiment subject")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_test_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-test.log"
+        )
+        time = datetime.now()
+        failing_test_list = experiment_item[self.key_failing_tests]
+        command_str = f"bash run_test {failing_test_list[0]}"
+        status = self.run_command(
+            container_id, command_str, self.log_test_path, self.dir_setup
+        )
+        self.emit_debug(
+            " Test took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status != 0
+
+    def verify(self, bug_index, container_id):
+        self.emit_normal("verify dev patch and test-oracle")
+        return True
+
+    def transform(self, bug_index, container_id):
+        self.emit_normal("transform fix-file")
+        return True
+
+    def clean(self, exp_dir_path, container_id):
+        self.emit_normal("[framework] removing experiment subject")
+        command_str = "rm -rf " + exp_dir_path
+        self.run_command(container_id, command_str)
+        return
+
+    def save_artifacts(self, dir_info, container_id):
+        self.list_artifact_dirs = []  # path should be relative to experiment directory
+        self.list_artifact_files = []  # path should be relative to experiment directory
+        super(APRCompEduC, self).save_artifacts(dir_info, container_id)

app/drivers/benchmarks/c/APRCompFuncC.py

@@ -0,0 +1,172 @@
+import os
+from datetime import datetime
+
+from app.drivers.benchmarks.AbstractBenchmark import AbstractBenchmark
+
+
+class APRCompFuncC(AbstractBenchmark):
+    def __init__(self):
+        self.name = os.path.basename(__file__)[:-3].lower()
+        super(APRCompFuncC, self).__init__()
+
+    def setup_experiment(self, bug_index, container_id, test_all):
+        if not container_id:
+            self.error_exit(
+                "unimplemented functionality: this benchmark only runs on docker"
+            )
+
+        is_error = True
+        if self.install_deps(bug_index, container_id):
+            is_error = super(APRCompFuncC, self).setup_experiment(
+                bug_index, container_id, test_all
+            )
+        if not is_error:
+            if self.verify(bug_index, container_id):
+                self.emit_success("verified successfully")
+                if self.transform(bug_index, container_id):
+                    self.emit_success("transformation successful")
+                else:
+                    self.emit_error("transformation failed")
+                    is_error = True
+            else:
+                self.emit_error("verification failed")
+                is_error = True
+        return is_error
+
+    def install_deps(self, bug_index, container_id):
+        self.emit_normal("installing experiment dependencies")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_deps_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-deps.log"
+        )
+        time = datetime.now()
+        command_str = "bash install_deps"
+        status = self.run_command(
+            container_id, command_str, self.log_deps_path, self.dir_setup
+        )
+        self.emit_debug(
+            "installing dependencies took {} second(s)".format(
+                (datetime.now() - time).total_seconds()
+            )
+        )
+        return status == 0
+
+    def deploy(self, bug_index, container_id):
+        self.emit_normal("downloading experiment subject")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_deploy_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-deploy.log"
+        )
+        time = datetime.now()
+        command_str = "bash setup_subject"
+        status = self.run_command(
+            container_id, command_str, self.log_deploy_path, self.dir_setup
+        )
+        self.emit_debug(
+            "setup took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status == 0
+
+    def config(self, bug_index, container_id):
+        self.emit_normal("configuring experiment subject")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_config_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-config.log"
+        )
+        time = datetime.now()
+        command_str = "bash config_subject"
+        status = self.run_command(
+            container_id, command_str, self.log_config_path, self.dir_setup
+        )
+        self.emit_debug(
+            "config took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status == 0
+
+    def build(self, bug_index, container_id):
+        self.emit_normal("building experiment subject")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_build_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-build.log"
+        )
+        time = datetime.now()
+        command_str = "bash build_subject"
+
+        status = self.run_command(
+            container_id, command_str, self.log_build_path, self.dir_setup
+        )
+        self.emit_debug(
+            "build took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status == 0
+
+    def test(self, bug_index, container_id):
+        self.emit_normal("testing experiment subject")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_test_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-test.log"
+        )
+        time = datetime.now()
+        failing_test_list = experiment_item[self.key_failing_tests]
+        command_str = f"bash run_test {failing_test_list[0]}"
+        status = self.run_command(
+            container_id, command_str, self.log_test_path, self.dir_setup
+        )
+        self.emit_debug(
+            "test took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status != 0
+
+    def verify(self, bug_index, container_id):
+        self.emit_normal("verify dev patch and test-oracle")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_test_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-verify.log"
+        )
+        time = datetime.now()
+        failing_test_list = experiment_item[self.key_failing_tests]
+        command_str = f"bash verify_dev {failing_test_list[0]}"
+        status = self.run_command(
+            container_id, command_str, self.log_test_path, self.dir_setup
+        )
+
+        self.emit_debug(
+            "verify took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status == 0
+
+    def transform(self, bug_index, container_id):
+        self.emit_normal("transforming source code")
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_test_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-transform.log"
+        )
+        time = datetime.now()
+        command_str = "echo 'transformation complete'"
+        status = self.run_command(
+            container_id, command_str, self.log_test_path, self.dir_setup
+        )
+        self.emit_debug(
+            "transform took {} second(s)".format(
+                (datetime.now() - time).total_seconds()
+            )
+        )
+        return status == 0
+
+    def clean(self, exp_dir_path, container_id):
+        self.emit_normal("removing experiment subject")
+        command_str = "rm -rf " + exp_dir_path
+        self.run_command(container_id, command_str)
+        return
+
+    def save_artifacts(self, dir_info, container_id):
+        self.list_artifact_dirs = []  # path should be relative to experiment directory
+        self.list_artifact_files = []  # path should be relative to experiment directory
+        super(APRCompFuncC, self).save_artifacts(dir_info, container_id)

app/drivers/benchmarks/c/APRCompVulnC.py

@@ -100,7 +100,7 @@ def build(self, bug_index, container_id):
             container_id, command_str, self.log_build_path, self.dir_setup
         )
         self.emit_debug(
-            "setup took {} second(s)".format((datetime.now() - time).total_seconds())
+            "build took {} second(s)".format((datetime.now() - time).total_seconds())
         )
         return status == 0
 
@@ -117,7 +117,7 @@ def test(self, bug_index, container_id):
             container_id, command_str, self.log_test_path, self.dir_setup
         )
         self.emit_debug(
-            " Test took {} second(s)".format((datetime.now() - time).total_seconds())
+            "test took {} second(s)".format((datetime.now() - time).total_seconds())
         )
         return status != 0
 

app/drivers/benchmarks/c/ITSP.py

@@ -1,4 +1,5 @@
 import os
+from datetime import datetime
 
 from app.drivers.benchmarks.AbstractBenchmark import AbstractBenchmark
 
@@ -14,6 +15,9 @@ def setup_experiment(self, bug_index, container_id, test_all):
 
     def deploy(self, bug_index, container_id):
         self.emit_normal("downloading experiment subject")
+        self.run_command(
+            container_id, "cp -rf {} {}/src".format(self.dir_setup, self.dir_expr)
+        )
         return True
 
     def config(self, bug_index, container_id):
@@ -22,11 +26,39 @@ def config(self, bug_index, container_id):
 
     def build(self, bug_index, container_id):
         self.emit_normal("building experiment subject")
-        return True
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_build_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-build.log"
+        )
+        time = datetime.now()
+        command_str = "bash build_subject"
+
+        status = self.run_command(
+            container_id, command_str, self.log_build_path, self.dir_setup
+        )
+        self.emit_debug(
+            "setup took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status == 0
 
     def test(self, bug_index, container_id):
         self.emit_normal("testing experiment subject")
-        return True
+        experiment_item = self.experiment_subjects[bug_index - 1]
+        bug_id = str(experiment_item[self.key_bug_id])
+        self.log_test_path = (
+            self.dir_logs + "/" + self.name + "-" + bug_id + "-test.log"
+        )
+        time = datetime.now()
+        failing_test_list = experiment_item[self.key_failing_tests]
+        command_str = f"bash run_test {failing_test_list[0]}"
+        status = self.run_command(
+            container_id, command_str, self.log_test_path, self.dir_setup
+        )
+        self.emit_debug(
+            " Test took {} second(s)".format((datetime.now() - time).total_seconds())
+        )
+        return status != 0
 
     def verify(self, bug_index, container_id):
         self.emit_normal("verify dev patch and test-oracle")