diff --git a/mx.fastr/mx_fastr_pkgs.py b/mx.fastr/mx_fastr_pkgs.py
index b9d793c9e732d7421654b920bd18245e09525410..9f27c6205616daeb2f0899a62c8148d37b98fd95 100644
--- a/mx.fastr/mx_fastr_pkgs.py
+++ b/mx.fastr/mx_fastr_pkgs.py
@@ -320,6 +320,7 @@ class TestFileStatus:
def __init__(self, status, abspath):
self.status = status
self.abspath = abspath
+ self.report = 0, 1, 0
class TestStatus:
'''Records the test status of a package. status ends up as either "OK" or "FAILED",
@@ -456,6 +457,8 @@ def _set_test_status(fastr_test_info):
if fastr_testfile_status.status == "FAILED":
break
+ print "Comparing {0} to {1}\n".format(gnur_testfile_status.abspath, fastr_testfile_status.abspath)
+
gnur_content = None
with open(gnur_testfile_status.abspath) as f:
gnur_content = f.readlines()
@@ -463,38 +466,100 @@ def _set_test_status(fastr_test_info):
with open(fastr_testfile_status.abspath) as f:
fastr_content = f.readlines()
- result = _fuzzy_compare(gnur_content, fastr_content, gnur_testfile_status.abspath, fastr_testfile_status.abspath)
- if result == -1:
- print "{0}: content malformed: {1}".format(pkg, gnur_test_output_relpath)
- fastr_test_status.status = "INDETERMINATE"
- break
- if result != 0:
- fastr_test_status.status = "FAILED"
- fastr_testfile_status.status = "FAILED"
- print "{0}: FastR output mismatch: {1}".format(pkg, gnur_test_output_relpath)
- break
+ # first, parse file and see if a known test framework has been used
+ ok, skipped, failed = handle_output_file(fastr_content)
+ if ok is not None:
+ fastr_testfile_status.report = ok, skipped, failed
+ else:
+ result, n_tests_passed, n_tests_failed = _fuzzy_compare(gnur_content, fastr_content, gnur_testfile_status.abspath, fastr_testfile_status.abspath)
+ print "result={0}, passed={1}, failed={2}\n".format(result, n_tests_passed, n_tests_failed)
+ if result == -1:
+ print "{0}: content malformed: {1}".format(pkg, gnur_test_output_relpath)
+ fastr_test_status.status = "INDETERMINATE"
+ # we don't know how many tests are in there, so consider the whole file to be one big skipped test
+ fastr_testfile_status.report = 0, 1, 0
+ #break
+ elif result != 0:
+ fastr_test_status.status = "FAILED"
+ fastr_testfile_status.status = "FAILED"
+ fastr_testfile_status.report = n_tests_passed, 0, n_tests_failed
+ print "{0}: FastR output mismatch: {1}".format(pkg, gnur_test_output_relpath)
+ #break
+ else:
+ fastr_testfile_status.status = "OK"
+ fastr_testfile_status.report = n_tests_passed, 0, n_tests_failed
+
+
# we started out as UNKNOWN
if not (fastr_test_status.status == "INDETERMINATE" or fastr_test_status.status == "FAILED"):
fastr_test_status.status = "OK"
# write out a file with the test status for each output (that exists)
with open(join(_pkg_testdir('fastr', pkg), 'testfile_status'), 'w') as f:
+ f.write('# <file path> <tests passed> <tests skipped> <tests failed>\n')
for fastr_relpath, fastr_testfile_status in fastr_outputs.iteritems():
if fastr_testfile_status.status == "FAILED":
relpath = fastr_relpath + ".fail"
else:
relpath = fastr_relpath
- if os.path.exists(join(_pkg_testdir('fastr', pkg), relpath)):
- f.write('# <file path> <tests passed> <tests skipped> <tests failed>')
- # TODO
- f.write(relpath)
- f.write(' ')
- f.write(fastr_testfile_status.status)
- f.write('\n')
+ test_output_file = join(_pkg_testdir('fastr', pkg), relpath)
+ if os.path.exists(test_output_file):
+ print "Generating testfile_status for {0}".format(str(test_output_file))
+ #ok, skipped, failed = handle_output_file(test_output_file, fastr_testfile_status)
+ ok, skipped, failed = fastr_testfile_status.report
+ f.write("{0} {1} {2} {3}\n".format(relpath, ok, skipped, failed))
print 'END checking ' + pkg
+
+def handle_output_file(test_output_file_contents):
+ """
+ R package tests are usually distributed over several files. Each file can be interpreted as a test suite.
+ This function parses the output file of all test suites and tries to detect if it used the testthat or RUnit.
+ In this case, it parses the summary (number of passed, skipped, failed tests) of these test frameworks.
+ If none of the frameworks is used, it performs an output diff and tries to determine, how many statements
+ produces different output, i.e., every statement is considered to be a unit test.
+ :param test_output_file_contents: the lines of the output file
+ :return: A 3-tuple with the number of passed, skipped, and failed tests.
+ """
+ for i in range(0, len(test_output_file_contents)):
+ if test_output_file_contents[i].startswith("testthat results"):
+ return _parse_testthat_result(test_output_file_contents, i)
+
+ # TODO parse RUnit test protocol
+
+ # if this test did not use one of the known test frameworks, take the report from the fuzzy compare
+ return None, None, None
+
+
+def _parse_testthat_result(lines, i):
+ '''
+ OK: 2 SKIPPED: 0 FAILED: 0
+ '''
+ if i+1 < len(lines) and lines[i+1].startswith("OK"):
+ result_line = lines[i+1]
+ idx_ok = 0
+ idx_skipped = result_line.find("SKIPPED")
+ idx_failed = result_line.find("FAILED")
+ if idx_ok != -1 and idx_skipped != -1 and idx_failed != -1:
+ ok_part = result_line[idx_ok:idx_skipped]
+ skipped_part = result_line[idx_skipped:idx_failed]
+ failed_part = result_line[idx_failed:]
+ return (_testthat_parse_part(ok_part), _testthat_parse_part(skipped_part), _testthat_parse_part(failed_part))
+ raise Exception("Could not parse testthat status line {0}".format(result_line))
+
+def _testthat_parse_part(part):
+ '''
+ parses a part like "OK: 2"
+ '''
+ parts = part.split(":")
+ if len(parts) == 2:
+ assert parts[0] == "OK" or parts[0] == "SKIPPED" or parts[0] == "FAILED"
+ return int(parts[1])
+ raise Exception("could not parse testthat status part {0}".format(part))
+
+
def _find_start(content):
marker = "Type 'q()' to quit R."
for i in range(len(content)):
@@ -509,14 +574,16 @@ def _find_start(content):
j = j + 1
return None
+
def _find_end(content):
marker = "Time elapsed:"
for i in range(len(content)):
line = content[i]
if marker in line:
- return i - 1
+ return i
# not all files have a Time elapsed:
- return len(content) - 1
+ return len(content)
+
def _find_line(gnur_line, fastr_content, fastr_i):
'''
@@ -532,6 +599,7 @@ def _find_line(gnur_line, fastr_content, fastr_i):
fastr_i = fastr_i + 1
return -1
+
def _replace_engine_references(output):
for idx, val in enumerate(output):
if "RUNIT TEST PROTOCOL -- " in val:
@@ -542,6 +610,14 @@ def _replace_engine_references(output):
output[idx] = val.replace('fastr', '<engine>').replace('gnur', '<engine>')
def _fuzzy_compare(gnur_content, fastr_content, gnur_filename, fastr_filename):
+ '''
+ Compares the test output of GnuR and FastR by ignoring implementation-specific differences like header, error,
+ and warning messages.
+ It returns a 3-tuple (<status>, <statements passed>, <statements failed>), where status=0 if files are equal,
+ status=1 if the files are different, status=-1 if the files could not be compared. In case of status=1,
+ statements passed and statements failed give the numbers on how many statements produced the same or a different
+ output, respectively.
+ '''
_replace_engine_references(gnur_content)
_replace_engine_references(fastr_content)
gnur_start = _find_start(gnur_content)
@@ -549,17 +625,40 @@ def _fuzzy_compare(gnur_content, fastr_content, gnur_filename, fastr_filename):
fastr_start = _find_start(fastr_content)
fastr_len = len(fastr_content)
if not gnur_start or not gnur_end or not fastr_start:
- return -1
+ return -1, 0, 0
gnur_i = gnur_start
fastr_i = fastr_start
+ # the overall result for comparing the file
+ overall_result = 0
+ # the local result, i.e., for the current statement
result = 0
+ statements_passed = set()
+ statements_failed = set()
+
+ # the first line must start with the prompt, so capture it
+ gnur_prompt = _capture_prompt(gnur_content, gnur_i)
+ fastr_prompt = _capture_prompt(fastr_content, fastr_i)
+
+ gnur_cur_statement_start = -1
+ fastr_cur_statement_start = -1
while gnur_i < gnur_end:
gnur_line = gnur_content[gnur_i]
if fastr_i >= fastr_len:
- result = 1
+ overall_result = 1
break
fastr_line = fastr_content[fastr_i]
+
+ # check if the current line starts a statement
+ if _is_statement_begin(gnur_prompt, gnur_line) and gnur_cur_statement_start != gnur_i:
+ gnur_cur_statement_start = gnur_i
+
+ # if we find a new statement begin
+ if _is_statement_begin(fastr_prompt, fastr_line) and fastr_cur_statement_start != fastr_i:
+ fastr_cur_statement_start = fastr_i
+
+ # flag indicating that we want to synchronize
+ sync = False
if gnur_line != fastr_line:
if fastr_line.startswith('Warning') and 'FastR does not support graphics package' in fastr_content[fastr_i + 1]:
# ignore warning about FastR not supporting the graphics package
@@ -578,7 +677,7 @@ def _fuzzy_compare(gnur_content, fastr_content, gnur_filename, fastr_filename):
fastr_i = fastr_i + 1
continue
# we are fuzzy on Error/Warning as FastR often differs
- # in the context/format of the error/warniong message AND GnuR is sometimes
+ # in the context/format of the error/warning message AND GnuR is sometimes
# inconsistent over which error message it uses. Unlike the unit test environment,
# we cannot tag tests in any way, so we simply check that FastR does report
# an error. We then scan forward to try to get the files back in sync, as the
@@ -587,43 +686,86 @@ def _fuzzy_compare(gnur_content, fastr_content, gnur_filename, fastr_filename):
to_match = 'Error' if 'Error' in gnur_line else 'Warning'
if to_match not in fastr_line:
result = 1
- break
+ # XXX do not break
+ # break
else:
- # skip until lines match (or not)
- gnur_i = gnur_i + 1
- fastr_i = fastr_i + 1
- if gnur_i == gnur_end - 1:
- # at end (there is always a blank line)
- break
- ni = -1
- while gnur_i < gnur_end:
- ni = _find_line(gnur_content[gnur_i], fastr_content, fastr_i)
- if ni > 0:
- break
- gnur_i = gnur_i + 1
- if ni > 0:
- fastr_i = ni
- continue
- else:
- result = 1
- break
+ # accept differences in the error/warning messages but we need to synchronize
+ sync = True
+
else:
# genuine difference (modulo whitespace)
if not _ignore_whitespace(gnur_line, fastr_line):
result = 1
- break
- gnur_i = gnur_i + 1
- fastr_i = fastr_i + 1
- if result == 1:
+ # XXX do not break, but we might need to synchronize indices
+ # break
+
+
+ # report a mismatch or success
+ if result == 1:
+ # we need to synchronize the indices such that we can continue
+ sync = True
+ # report the last statement to produce different output
+ assert fastr_cur_statement_start != -1
+ if fastr_cur_statement_start in statements_passed:
+ statements_passed.remove(fastr_cur_statement_start)
+ statements_failed.add(fastr_cur_statement_start)
+ else:
+ assert result == 0
+ if fastr_cur_statement_start not in statements_failed:
+ statements_passed.add(fastr_cur_statement_start)
+
+ # synchronize: skip until lines match (or file end reached)
+ if sync:
+ gnur_i = gnur_i + 1
+ fastr_i = fastr_i + 1
+ if gnur_i == gnur_end - 1:
+ # at end (there is always a blank line)
+ break
+ ni = -1
+ # find next statement line (i.e. starting with a prompt)
+
+
+ while gnur_i < gnur_end:
+ if _is_statement_begin(gnur_prompt, gnur_content[gnur_i]):
+ ni = _find_line(gnur_content[gnur_i], fastr_content, fastr_i)
+ if ni > 0:
+ break
+ gnur_i = gnur_i + 1
+ if ni > 0:
+ fastr_i = ni
+
+ overall_result = 1
+ result = 0
+ else:
+ # just advance by one line in FastR and GnuR
+ gnur_i = gnur_i + 1
+ fastr_i = fastr_i + 1
+
+ if overall_result == 1:
print gnur_filename + ':%d' % gnur_i + ' vs. ' + fastr_filename + ':%d' % fastr_i
print gnur_line.strip()
print "vs."
print fastr_line.strip()
- return result
+ return overall_result, len(statements_passed), len(statements_failed)
+
def _ignore_whitespace(gnur_line, fastr_line):
return gnur_line.translate(None, ' \t') == fastr_line.translate(None, ' \t')
+
+def _capture_prompt(lines, idx):
+ # The prompt can be anything, so it is hard to determine it in general.
+ # We will therefore just consider the default prompt.
+ DEFAULT_PROMPT = "> "
+ if idx < len(lines) and lines[idx].startswith(DEFAULT_PROMPT):
+ return DEFAULT_PROMPT
+ return None
+
+
+def _is_statement_begin(captured_prompt, line):
+ return line.startswith(captured_prompt) and line.replace(captured_prompt, "").strip() is not ""
+
+
def pkgtest_cmp(args):
with open(args[0]) as f:
gnur_content = f.readlines()
@@ -631,6 +773,7 @@ def pkgtest_cmp(args):
fastr_content = f.readlines()
return _fuzzy_compare(gnur_content, fastr_content, args[0], args[1])
+
def find_top100(args):
libinstall = join(_fastr_suite_dir(), "top100.tmp")
if not os.path.exists(libinstall):
@@ -638,6 +781,7 @@ def find_top100(args):
os.environ['R_LIBS_USER'] = libinstall
_installpkgs(['--find-top100', '--use-installed-pkgs'])
+
def remove_dup_pkgs(args):
pkgs = args[0].split(",")
x = dict()
@@ -648,6 +792,7 @@ def remove_dup_pkgs(args):
result += p
return result
+
def computeApiChecksum(includeDir):
'''
Computes a checksum of the header files found in the provided directory (recursively).