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Source code for galaxy.tool_util.verify
"""Module of utilities for verifying test results."""
import difflib
import filecmp
import hashlib
import json
import logging
import os
import os.path
import re
import shutil
import tempfile
try:
import pysam
except ImportError:
pysam = None
from galaxy.tool_util.parser.util import (
DEFAULT_DELTA,
DEFAULT_DELTA_FRAC
)
from galaxy.util import unicodify
from galaxy.util.compression_utils import get_fileobj
from .asserts import verify_assertions
from .test_data import TestDataResolver
log = logging.getLogger(__name__)
DEFAULT_TEST_DATA_RESOLVER = TestDataResolver()
[docs]def verify(
item_label,
output_content,
attributes,
filename=None,
get_filecontent=None,
get_filename=None,
keep_outputs_dir=None,
verify_extra_files=None,
mode='file',
):
"""Verify the content of a test output using test definitions described by attributes.
Throw an informative assertion error if any of these tests fail.
"""
if get_filename is None:
if get_filecontent is None:
get_filecontent = DEFAULT_TEST_DATA_RESOLVER.get_filecontent
def get_filename(filename):
file_content = get_filecontent(filename)
local_name = make_temp_fname(fname=filename)
with open(local_name, 'wb') as f:
f.write(file_content)
return local_name
# Check assertions...
assertions = attributes.get("assert_list", None)
if attributes is not None and assertions is not None:
try:
verify_assertions(output_content, attributes["assert_list"])
except AssertionError as err:
errmsg = f'{item_label} different than expected\n'
errmsg += unicodify(err)
raise AssertionError(errmsg)
# Verify checksum attributes...
# works with older Galaxy style md5=<expected_sum> or cwltest
# style checksum=<hash_type>$<hash>.
expected_checksum_type = None
expected_checksum = None
if attributes is not None and attributes.get("md5", None) is not None:
expected_checksum_type = "md5"
expected_checksum = attributes.get("md5")
elif attributes is not None and attributes.get("checksum", None) is not None:
checksum_value = attributes.get("checksum", None)
expected_checksum_type, expected_checksum = checksum_value.split("$", 1)
if expected_checksum_type:
try:
_verify_checksum(output_content, expected_checksum_type, expected_checksum)
except AssertionError as err:
errmsg = f'{item_label} different than expected\n'
errmsg += unicodify(err)
raise AssertionError(errmsg)
if attributes is None:
attributes = {}
# expected object might be None, so don't pull unless available
has_expected_object = 'object' in attributes
if has_expected_object:
assert filename is None
expected_object = attributes.get('object')
actual_object = json.loads(output_content)
expected_object_type = type(expected_object)
actual_object_type = type(actual_object)
if expected_object_type != actual_object_type:
message = f"Type mismatch between expected object ({expected_object_type}) and actual object ({actual_object_type})"
raise AssertionError(message)
if expected_object != actual_object:
message = f"Expected object ({expected_object}) does not match actual object ({actual_object})"
raise AssertionError(message)
elif filename is not None:
temp_name = make_temp_fname(fname=filename)
with open(temp_name, 'wb') as f:
f.write(output_content)
# If the server's env has GALAXY_TEST_SAVE, save the output file to that
# directory.
# This needs to be done before the call to `get_filename()` because that
# may raise an exception if `filename` does not exist (e.g. when
# generating a tool output file from scratch with
# `planemo test --update_test_data`).
if keep_outputs_dir:
ofn = os.path.join(keep_outputs_dir, filename)
out_dir = os.path.dirname(ofn)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
log.debug('keep_outputs_dir: %s, ofn: %s', keep_outputs_dir, ofn)
try:
shutil.copy(temp_name, ofn)
except Exception:
log.exception('Could not save output file %s to %s', temp_name, ofn)
else:
log.debug('## GALAXY_TEST_SAVE=%s. saved %s', keep_outputs_dir, ofn)
if mode == 'directory':
# if verifying a file inside a extra_files_path directory
# filename already point to a file that exists on disk
local_name = filename
else:
local_name = get_filename(filename)
compare = attributes.get('compare', 'diff')
try:
if attributes.get('ftype', None) in ['bam', 'qname_sorted.bam', 'qname_input_sorted.bam', 'unsorted.bam', 'cram']:
try:
local_fh, temp_name = _bam_to_sam(local_name, temp_name)
local_name = local_fh.name
except Exception as e:
log.warning("%s. Will compare BAM files", unicodify(e))
if compare == 'diff':
files_diff(local_name, temp_name, attributes=attributes)
elif compare == 're_match':
files_re_match(local_name, temp_name, attributes=attributes)
elif compare == 're_match_multiline':
files_re_match_multiline(local_name, temp_name, attributes=attributes)
elif compare == 'sim_size':
files_delta(local_name, temp_name, attributes=attributes)
elif compare == "contains":
files_contains(local_name, temp_name, attributes=attributes)
else:
raise Exception(f'Unimplemented Compare type: {compare}')
except AssertionError as err:
errmsg = f'{item_label} different than expected, difference (using {compare}):\n'
errmsg += f"( {local_name} v. {temp_name} )\n"
errmsg += unicodify(err)
raise AssertionError(errmsg)
finally:
if 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
os.remove(temp_name)
if verify_extra_files:
extra_files = attributes.get('extra_files', None)
if extra_files:
verify_extra_files(extra_files)
[docs]def make_temp_fname(fname=None):
"""Safe temp name - preserve the file extension for tools that interpret it."""
suffix = os.path.split(fname)[-1] # ignore full path
with tempfile.NamedTemporaryFile(prefix='tmp', suffix=suffix, delete=False) as temp:
return temp.name
def _bam_to_sam(local_name, temp_name):
temp_local = tempfile.NamedTemporaryFile(suffix='.sam', prefix='local_bam_converted_to_sam_')
with tempfile.NamedTemporaryFile(suffix='.sam', prefix='history_bam_converted_to_sam_', delete=False) as temp:
try:
pysam.view('-h', '--no-PG', '-o', temp_local.name, local_name, catch_stdout=False)
except Exception as e:
msg = f"Converting local (test-data) BAM to SAM failed: {unicodify(e)}"
raise Exception(msg)
try:
pysam.view('-h', '--no-PG', '-o', temp.name, temp_name, catch_stdout=False)
except Exception as e:
msg = f"Converting history BAM to SAM failed: {unicodify(e)}"
raise Exception(msg)
os.remove(temp_name)
return temp_local, temp.name
def _verify_checksum(data, checksum_type, expected_checksum_value):
if checksum_type not in ["md5", "sha1", "sha256", "sha512"]:
raise Exception(f"Unimplemented hash algorithm [{checksum_type}] encountered.")
h = hashlib.new(checksum_type)
h.update(data)
actual_checksum_value = h.hexdigest()
if expected_checksum_value != actual_checksum_value:
template = "Output checksum [%s] does not match expected [%s] (using hash algorithm %s)."
message = template % (actual_checksum_value, expected_checksum_value, checksum_type)
raise AssertionError(message)
[docs]def files_delta(file1, file2, attributes=None):
"""Check the contents of 2 files for size differences."""
if attributes is None:
attributes = {}
delta = attributes.get('delta', DEFAULT_DELTA)
delta_frac = attributes.get('delta_frac', DEFAULT_DELTA_FRAC)
s1 = os.path.getsize(file1)
s2 = os.path.getsize(file2)
if abs(s1 - s2) > delta:
raise AssertionError('Files %s=%db but %s=%db - compare by size (delta=%s) failed' % (file1, s1, file2, s2, delta))
if delta_frac is not None and not (s1 - (s1 * delta_frac) <= s2 <= s1 + (s1 * delta_frac)):
raise AssertionError('Files %s=%db but %s=%db - compare by size (delta_frac=%s) failed' % (file1, s1, file2, s2, delta_frac))
[docs]def get_compressed_formats(attributes):
attributes = attributes or {}
decompress = attributes.get("decompress")
# None means all compressed formats are allowed
return None if decompress else []
[docs]def files_diff(file1, file2, attributes=None):
"""Check the contents of 2 files for differences."""
attributes = attributes or {}
def get_lines_diff(diff):
count = 0
for line in diff:
if (line.startswith('+') and not line.startswith('+++')) or (line.startswith('-') and not line.startswith('---')):
count += 1
return count
if not filecmp.cmp(file1, file2, shallow=False):
compressed_formats = get_compressed_formats(attributes)
is_pdf = False
try:
with get_fileobj(file2, compressed_formats=compressed_formats) as fh:
history_data = fh.readlines()
with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
local_file = fh.readlines()
except UnicodeDecodeError:
if file1.endswith('.pdf') or file2.endswith('.pdf'):
is_pdf = True
# Replace non-Unicode characters using unicodify(),
# difflib.unified_diff doesn't work on list of bytes
history_data = [unicodify(line) for line in get_fileobj(file2, mode='rb', compressed_formats=compressed_formats)]
local_file = [unicodify(line) for line in get_fileobj(file1, mode='rb', compressed_formats=compressed_formats)]
else:
raise AssertionError("Binary data detected, not displaying diff")
if attributes.get('sort', False):
local_file.sort()
history_data.sort()
allowed_diff_count = int(attributes.get('lines_diff', 0))
diff = list(difflib.unified_diff(local_file, history_data, "local_file", "history_data"))
diff_lines = get_lines_diff(diff)
if diff_lines > allowed_diff_count:
if 'GALAXY_TEST_RAW_DIFF' in os.environ:
diff_slice = diff
else:
if len(diff) < 60:
diff_slice = diff[0:40]
else:
diff_slice = diff[:25] + ["********\n", "*SNIP *\n", "********\n"] + diff[-25:]
# FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff
# due to unknown desired behavior when used in conjunction with a non-zero lines_diff
# PDF forgiveness can probably be handled better by not special casing by __extension__ here
# and instead using lines_diff or a regular expression matching
# or by creating and using a specialized pdf comparison function
if is_pdf:
# PDF files contain creation dates, modification dates, ids and descriptions that change with each
# new file, so we need to handle these differences. As long as the rest of the PDF file does
# not differ we're ok.
valid_diff_strs = ['description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator']
valid_diff = False
invalid_diff_lines = 0
for line in diff_slice:
# Make sure to lower case strings before checking.
line = line.lower()
# Diff lines will always start with a + or - character, but handle special cases: '--- local_file \n', '+++ history_data \n'
if (line.startswith('+') or line.startswith('-')) and line.find('local_file') < 0 and line.find('history_data') < 0:
for vdf in valid_diff_strs:
if line.find(vdf) < 0:
valid_diff = False
else:
valid_diff = True
# Stop checking as soon as we know we have a valid difference
break
if not valid_diff:
invalid_diff_lines += 1
log.info("## files diff on '%s' and '%s': lines_diff = %d, found diff = %d, found pdf invalid diff = %d" % (file1, file2, allowed_diff_count, diff_lines, invalid_diff_lines))
if invalid_diff_lines > allowed_diff_count:
# Print out diff_slice so we can see what failed
log.info("###### diff_slice ######")
raise AssertionError("".join(diff_slice))
else:
log.info("## files diff on '%s' and '%s': lines_diff = %d, found diff = %d" % (file1, file2, allowed_diff_count, diff_lines))
raise AssertionError("".join(diff_slice))
[docs]def files_re_match(file1, file2, attributes=None):
"""Check the contents of 2 files for differences using re.match."""
attributes = attributes or {}
join_char = ''
to_strip = os.linesep
compressed_formats = get_compressed_formats(attributes)
try:
with get_fileobj(file2, compressed_formats=compressed_formats) as fh:
history_data = fh.readlines()
with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
local_file = fh.readlines()
except UnicodeDecodeError:
join_char = b''
to_strip = os.linesep.encode('utf-8')
with open(file2, 'rb') as fh:
history_data = fh.readlines()
with open(file1, 'rb') as fh:
local_file = fh.readlines()
assert len(local_file) == len(history_data), 'Data File and Regular Expression File contain a different number of lines (%d != %d)\nHistory Data (first 40 lines):\n%s' % (len(local_file), len(history_data), join_char.join(history_data[:40]))
if attributes.get('sort', False):
history_data.sort()
lines_diff = int(attributes.get('lines_diff', 0))
line_diff_count = 0
diffs = []
for regex_line, data_line in zip(local_file, history_data):
regex_line = regex_line.rstrip(to_strip)
data_line = data_line.rstrip(to_strip)
if not re.match(regex_line, data_line):
line_diff_count += 1
diffs.append(f'Regular Expression: {regex_line}, Data file: {data_line}\n')
if line_diff_count > lines_diff:
raise AssertionError("Regular expression did not match data file (allowed variants=%i):\n%s" % (lines_diff, "".join(diffs)))
[docs]def files_re_match_multiline(file1, file2, attributes=None):
"""Check the contents of 2 files for differences using re.match in multiline mode."""
attributes = attributes or {}
join_char = ''
compressed_formats = get_compressed_formats(attributes)
try:
with get_fileobj(file2, compressed_formats=compressed_formats) as fh:
history_data = fh.readlines()
with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
local_file = fh.read()
except UnicodeDecodeError:
join_char = b''
with open(file2, 'rb') as fh:
history_data = fh.readlines()
with open(file1, 'rb') as fh:
local_file = fh.read()
if attributes.get('sort', False):
history_data.sort()
history_data = join_char.join(history_data)
# lines_diff not applicable to multiline matching
assert re.match(local_file, history_data, re.MULTILINE), "Multiline Regular expression did not match data file"
[docs]def files_contains(file1, file2, attributes=None):
"""Check the contents of file2 for substrings found in file1, on a per-line basis."""
# TODO: allow forcing ordering of contains
attributes = attributes or {}
to_strip = os.linesep
compressed_formats = get_compressed_formats(attributes)
try:
with get_fileobj(file2, compressed_formats=compressed_formats) as fh:
history_data = fh.read()
with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
local_file = fh.readlines()
except UnicodeDecodeError:
to_strip = os.linesep.encode('utf-8')
with open(file2, 'rb') as fh:
history_data = fh.read()
with open(file1, 'rb') as fh:
local_file = fh.readlines()
lines_diff = int(attributes.get('lines_diff', 0))
line_diff_count = 0
for contains in local_file:
contains = contains.rstrip(to_strip)
if contains not in history_data:
line_diff_count += 1
if line_diff_count > lines_diff:
raise AssertionError(f"Failed to find '{contains}' in history data. (lines_diff={lines_diff}).")