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Steve Goldhaber
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Add unit tests for SDF reading
Fix xmllint checking (some xmllint versions do not return error codes) Update regex usage for fortran_conditional
1 parent e0d375b commit 62ae9da

35 files changed

Lines changed: 947 additions & 12 deletions

‎scripts/parse_tools/fortran_conditional.py‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,10 @@
77

88
import re
99

10-
FORTRAN_CONDITIONAL_REGEX_WORDS = [' ', '(', ')', '==', '/=', '<=', '>=', '<', '>', '.eqv.', '.neqv.',
10+
fortran_conditional_regex_tokens = ['==', '/=', '<=', '>=', '<', '>', '.eqv.', '.neqv.',
1111
'.true.', '.false.', '.lt.', '.le.', '.eq.', '.ge.', '.gt.', '.ne.',
1212
'.not.', '.and.', '.or.', '.xor.']
13-
FORTRAN_CONDITIONAL_REGEX = re.compile(r"[\w']+|" + "|".join([word.replace('(','\(').replace(')', '\)') for word in FORTRAN_CONDITIONAL_REGEX_WORDS]))
13+
14+
FORTRAN_CONDITIONAL_REGEX_WORDS = [' ', '[(]', '[)]'] + fortran_conditional_regex_tokens
15+
16+
FORTRAN_CONDITIONAL_REGEX = re.compile(r"[\w']+|[ ()]|" + "|".join([word for word in FORTRAN_CONDITIONAL_REGEX_WORDS]))

‎scripts/parse_tools/parse_checkers.py‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -13,13 +13,14 @@
1313
########################################################################
1414

1515
_UNITLESS_REGEX = "1"
16-
_NON_LEADING_ZERO_NUM = "[1-9]\d*"
16+
_NON_LEADING_ZERO_NUM = r"[1-9]\d*"
1717
_CHAR_WITH_UNDERSCORE = "([a-zA-Z]+_[a-zA-Z]+)+"
1818
_NEGATIVE_NON_LEADING_ZERO_NUM = f"[-]{_NON_LEADING_ZERO_NUM}"
1919
_POSITIVE_NON_LEADING_ZERO_NUM = f"[+]{_NON_LEADING_ZERO_NUM}"
2020
_UNIT_EXPONENT = f"({_NEGATIVE_NON_LEADING_ZERO_NUM}|{_POSITIVE_NON_LEADING_ZERO_NUM}|{_NON_LEADING_ZERO_NUM})"
2121
_UNIT_REGEX = f"[a-zA-Z]+{_UNIT_EXPONENT}?"
22-
_UNITS_REGEX = f"^({_CHAR_WITH_UNDERSCORE}|{_UNIT_REGEX}(\s{_UNIT_REGEX})*|{_UNITLESS_REGEX})$"
22+
_UNIT_REGEXES = f"{_UNIT_REGEX}(" r"\s" f"{_UNIT_REGEX})"
23+
_UNITS_REGEX = f"^({_CHAR_WITH_UNDERSCORE}|{_UNIT_REGEXES}*|{_UNITLESS_REGEX})$"
2324
_UNITS_RE = re.compile(_UNITS_REGEX)
2425
_MAX_MOLAR_MASS = 10000.0
2526

‎scripts/parse_tools/xml_tools.py‎

Lines changed: 36 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -38,10 +38,14 @@ def __init__(self, message):
3838
super().__init__(message)
3939

4040
###############################################################################
41-
def call_command(commands, logger, silent=False):
41+
def call_command(commands, logger, silent=False, return_proc=False):
4242
###############################################################################
4343
"""
44-
Try a command line and return the output on success (None on failure)
44+
Try a command line and return True only for a zero return code
45+
If silent==True, do not log output and simply return False on an exception
46+
If return_proc==True, return the CompletedProcess instance instead of a boolean
47+
If silent==True and return_proc==True, return None in the case of an exception
48+
4549
>>> _LOGGER = init_log('xml_tools')
4650
>>> set_log_to_null(_LOGGER)
4751
>>> call_command(['ls', 'really__improbable_fffilename.foo'], _LOGGER) #doctest: +IGNORE_EXCEPTION_DETAIL
@@ -50,6 +54,8 @@ def call_command(commands, logger, silent=False):
5054
[Errno 2] No such file or directory
5155
>>> call_command(['ls', 'really__improbable_fffilename.foo'], _LOGGER, silent=True)
5256
False
57+
>>> call_command(['ls'], _LOGGER, silent=True, return_proc=True).returncode
58+
0
5359
>>> call_command(['ls'], _LOGGER)
5460
True
5561
>>> try:
@@ -75,11 +81,22 @@ def call_command(commands, logger, silent=False):
7581
capture_output=True)
7682
if not silent:
7783
logger.debug(cproc.stdout)
84+
if cproc.stderr:
85+
logger.warning(cproc.stderr)
86+
# end if
87+
# end if
88+
if return_proc:
89+
result = cproc
90+
else:
91+
result = cproc.returncode == 0
7892
# end if
79-
result = cproc.returncode == 0
8093
except (OSError, CCPPError, subprocess.CalledProcessError) as err:
8194
if silent:
82-
result = False
95+
if return_proc:
96+
result = None
97+
else:
98+
result = False
99+
# end if
83100
else:
84101
cmd = ' '.join(commands)
85102
outstr = f"Execution of '{cmd}' failed with code: {err.returncode}\n"
@@ -213,7 +230,15 @@ def validate_xml_file(filename, schema_root, version, logger,
213230
logger.debug("Checking file {} against schema {}".format(filename,
214231
schema_file))
215232
cmd = [_XMLLINT, '--noout', '--schema', schema_file, filename]
216-
result = call_command(cmd, logger)
233+
result = call_command(cmd, logger, return_proc=True)
234+
if result.returncode == 0:
235+
## We got a pass return code but some versions of xmllint do not
236+
## correctly return an error code on non-validation so double check
237+
## the result
238+
result = b'validates' in result.stdout or b'validates' in result.stderr
239+
else:
240+
result = True
241+
# end if
217242
return result
218243
# end if
219244
lmsg = "xmllint not found, could not validate file {}"
@@ -411,11 +436,14 @@ def replace_nested_suite(element, nested_suite, default_path, logger):
411436
suite_name = nested_suite.attrib.get("name")
412437
group_name = nested_suite.attrib.get("group")
413438
file = nested_suite.attrib.get("file")
439+
if not file:
440+
raise CCPPError("file attribute required for nested_suite tag")
441+
# end if
414442
if not os.path.isabs(file):
415443
file = os.path.join(default_path, file)
416444
referenced_suite = load_suite_by_name(suite_name, group_name, file,
417445
logger=logger)
418-
imported_content = [ET.fromstring(ET.tostring(child))
446+
imported_content = [ET.fromstring(ET.tostring(child))
419447
for child in referenced_suite]
420448
# Swap nested suite with imported content
421449
for item in imported_content:
@@ -581,7 +609,7 @@ def expand_nested_suites(suite, default_path, logger=None):
581609
return
582610
raise CCPPError("Exceeded number of iterations while expanding nested suites:" + \
583611
"check for inifite recursion or adjust limit max_iterations")
584-
612+
585613
###############################################################################
586614
def write_xml_file(root, file_path, logger=None):
587615
###############################################################################
@@ -598,7 +626,7 @@ def remove_whitespace_nodes(node):
598626

599627
# Convert ElementTree to a byte string
600628
byte_string = ET.tostring(root, 'us-ascii')
601-
629+
602630
# Parse string using minidom for pretty printing
603631
reparsed = xml.dom.minidom.parseString(byte_string)
604632

‎test/unit_tests/sample_suite_files/another_suite.xml‎

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@@ -0,0 +1,10 @@
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<?xml version="1.0" encoding="UTF-8"?>
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3+
<suite name="another_suite" version="2.0">
4+
<group name="another_group">
5+
<subcycle loop="num_subcycles_for_ag">
6+
<scheme>another_scheme</scheme>
7+
</subcycle>
8+
<scheme>more_scheme</scheme>
9+
</group>
10+
</suite>

‎test/unit_tests/sample_suite_files/another_suite2.xml‎

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@@ -0,0 +1,16 @@
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<?xml version="1.0" encoding="UTF-8"?>
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3+
<suite name="another_suite2" version="2.0">
4+
<group name="another_group2">
5+
<subcycle loop="num_subcycles_for_ag2">
6+
<scheme>another_scheme</scheme>
7+
</subcycle>
8+
<scheme>more_scheme</scheme>
9+
</group>
10+
<group name="another_group3">
11+
<subcycle loop="num_subcycles_for_ag3">
12+
<scheme>another_scheme</scheme>
13+
</subcycle>
14+
<scheme>more_scheme</scheme>
15+
</group>
16+
</suite>

‎test/unit_tests/sample_suite_files/nested_full_suite.xml‎

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@@ -0,0 +1,10 @@
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<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<suite name="nested_suite" version="2.0" >
4+
<group name="nested_group1">
5+
<scheme>g1_scheme1</scheme>
6+
</group>
7+
<group name="nested_group2">
8+
<nested_suite name="subsuite_1" group="group1" file="subsuite1.xml"/>
9+
</group>
10+
</suite>

‎test/unit_tests/sample_suite_files/subsuite1.xml‎

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@@ -0,0 +1,7 @@
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<?xml version="1.0" encoding="UTF-8"?>
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3+
<suite name="subsuite_1" version="2.0">
4+
<group name="group1">
5+
<scheme>scheme_subsuite1</scheme>
6+
</group>
7+
</suite>

‎test/unit_tests/sample_suite_files/subsuite_inline.xml‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,9 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<suite name="subsuite_inline" version="1.0">
4+
<group name="group2">
5+
<scheme>scheme1i</scheme>
6+
<scheme>scheme2i</scheme>
7+
<scheme>scheme1i</scheme>
8+
</group>
9+
</suite>

‎test/unit_tests/sample_suite_files/suite_bad_v2_duplicate_group.xml‎

Lines changed: 16 additions & 0 deletions
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@@ -0,0 +1,16 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<suite name="main_suite" version="2.0">
4+
<group name="group1">
5+
<subcycle loop="num_subcycles_for_scheme9">
6+
<scheme>effr_pre</scheme>
7+
<subcycle loop="2">
8+
<subcycle loop="2">
9+
<scheme>scheme9</scheme>
10+
</subcycle>
11+
</subcycle>
12+
<scheme>scheme3</scheme>
13+
</subcycle>
14+
</group>
15+
<nested_suite name="subsuite_1" file="subsuite1.xml"/>
16+
</suite>

‎test/unit_tests/sample_suite_files/suite_bad_v2_suite_tag.xml‎

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@@ -0,0 +1,7 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<suite name="ver_test_suite" version="2.0">
4+
<group name="group1">
5+
<suite>subsuite_inline</suite>
6+
</group>
7+
</suite>

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