Fixed gcovr report reading and added coverage method to bug manager (…

…fixes #158) (#168)

* fixed API migration bugs

* added files_to_instrument parameter to Bug.coverage method

* added missing imports

* added mktemp method to container manager

* bug fix: tweaked gcovr to write to temporary file; avoids corrupted XML outputs

* bumped version to 2.0.4

bugzoo/core/coverage.py

@@ -98,10 +98,10 @@ class TestSuiteCoverage(object):
     @staticmethod
     def from_dict(d: dict) -> 'TestSuiteCoverage':
         coverage_by_test = {}
-        for test_coverage_dict in d:
+        for test_coverage_dict in d.values():
             test_coverage = TestCoverage.from_dict(test_coverage_dict)
             coverage_by_test[test_coverage.test] = test_coverage
-        return ProjectCoverageMap(coverage_by_test)
+        return TestSuiteCoverage(coverage_by_test)
 
     @staticmethod
     def from_file(fn: str) -> 'TestSuiteCoverage':

bugzoo/mgr/bug.py

@@ -1,4 +1,5 @@
-from typing import Iterator
+from typing import Iterator, Optional, List
+import os
 
 import docker
 import textwrap
@@ -185,10 +186,21 @@ def validate(self, bug: Bug, verbose: bool = True) -> bool:
 
         return validated
 
-    def coverage(self, bug: Bug) -> TestSuiteCoverage:
+    def coverage(self,
+                 bug: Bug,
+                 files_to_instrument: Optional[List[str]] = None
+                 ) -> TestSuiteCoverage:
         """
         Provides coverage information for each test within the test suite
         for the program associated with this bug.
+
+        Parameters:
+            bug: the bug for which to compute coverage.
+            files_to_instrument: an optional list of files that should be
+                instrumented before generating the coverage report.
+
+        Returns:
+            a test suite coverage report for the given bug.
         """
         # determine the location of the coverage map on disk
         fn = os.path.join(self.__installation.coverage_path,
@@ -201,9 +213,12 @@ def coverage(self, bug: Bug) -> TestSuiteCoverage:
         # if we don't have coverage information, compute it
         try:
             mgr_ctr = self.__installation.containers
+            mgr_cov = self.__installation.coverage
             container = None
             container = mgr_ctr.provision(bug)
-            coverage = mgr_ctr.coverage(container)
+            coverage = mgr_cov.coverage(container,
+                                        bug.tests,
+                                        files_to_instrument=files_to_instrument)
 
             # save to disk
             with open(fn, 'w') as f:

bugzoo/mgr/container.py

@@ -153,6 +153,20 @@ def provision(self,
         self.__containers[uid] = container
         return container
 
+    def mktemp(self,
+               container: Container
+               ) -> str:
+        """
+        Creates a named temporary file within a given container.
+
+        Returns:
+            the absolute path to the created temporary file.
+        """
+        response = self.command(container, "mktemp")
+        assert response.code == 0, "failed to create temporary file"
+        fn = response.output.strip()
+        return fn
+
     def ip_address(self,
                    container: Container,
                    raise_error: bool = False

bugzoo/mgr/coverage.py

@@ -56,8 +56,7 @@ def _from_gcovr_xml_string(self,
         dir_source = container.bug.source_dir # TODO port
         # getting a list of all files in source directory to later use for resolving path
         resp = mgr_ctr.command(container, "find {} -type f".format(dir_source))
-        all_files = resp.output.split('\n')
-
+        all_files = [fn.strip() for fn in resp.output.split('\n')]
 
         def has_file(fn_rel: str) -> bool:
             fn_abs = os.path.join(dir_source, fn_rel)
@@ -233,7 +232,7 @@ def extract(self,
         """
         logger = self.__logger.getChild(container.id)
         mgr_ctr = self.__installation.containers
-        logger.debug("Starting to extract coverage info")
+        logger.debug("Extracting coverage information")
 
         if not instrumented_files:
             instrumented_files = set()
@@ -243,17 +242,29 @@ def extract(self,
         dir_source = container.bug.source_dir # TODO port
         t_start = timer()
         logger.debug("Running gcovr.")
+        fn_temp_ctr = mgr_ctr.mktemp(container)
+        cmd = 'gcovr -o "{}" -x -d -r .'.format(fn_temp_ctr)
         response = mgr_ctr.command(container,
-                                   'gcovr -x -d -r .',
-                                   context=dir_source)
-        logger.debug("gcovr returned. Seconds passed: %.2f", timer() - t_start)
-        assert response.code == 0
-        response = response.output
+                                   cmd,
+                                   context=dir_source,
+                                   verbose=True)
+        logger.debug("Finished running gcovr (took %.2f seconds).", timer() - t_start)
+        assert response.code == 0, "failed to run gcovr"
+
+        # copy the contents of the temporary file to the host machine
+        (_, fn_temp_host) = tempfile.mkstemp(suffix='.bugzoo')
+        try:
+            mgr_ctr.copy_from(container, fn_temp_ctr, fn_temp_host)
+            with open(fn_temp_host, 'r') as fh:
+                report = fh.read()
+        finally:
+            os.remove(fn_temp_host)
 
         t_start = timer()
-        logger.debug("Parsing gcovr xml.")
-        res = self._from_gcovr_xml_string(response,
-                                           instrumented_files,
-                                           container)
-        logger.debug("Finished parsing gcovr xml. Seconds passed: %.2f", timer() - t_start)
+        logger.debug("Parsing gcovr XML report.")
+        res = self._from_gcovr_xml_string(report,
+                                          instrumented_files,
+                                          container)
+        logger.debug("Finished parsing gcovr XML report (took %.2f seconds).", timer() - t_start)
+        logger.debug("Finished extracting coverage information")
         return res

bugzoo/version.py

@@ -1 +1 @@
-__version__ = '2.0.3'
+__version__ = '2.0.4'