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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 math
import os
import os.path
import re
import shutil
import tempfile
from typing import (
Any,
Callable,
Dict,
List,
Optional,
TYPE_CHECKING,
)
try:
import numpy
except ImportError:
pass
try:
import pysam
except ImportError:
pass
try:
from PIL import Image
except ImportError:
Image = None # type: ignore[assignment]
from galaxy.tool_util.parser.util import (
DEFAULT_DELTA,
DEFAULT_DELTA_FRAC,
DEFAULT_EPS,
DEFAULT_METRIC,
)
from galaxy.util import unicodify
from galaxy.util.compression_utils import get_fileobj
from .asserts import verify_assertions
from .test_data import TestDataResolver
if TYPE_CHECKING:
import numpy.typing
log = logging.getLogger(__name__)
DEFAULT_TEST_DATA_RESOLVER = TestDataResolver()
[docs]def verify(
item_label: str,
output_content: bytes,
attributes: Optional[Dict[str, Any]],
filename: Optional[str] = None,
get_filecontent: Optional[Callable[[str], bytes]] = None,
get_filename: Optional[Callable[[str], str]] = None,
keep_outputs_dir: Optional[str] = None,
verify_extra_files: Optional[Callable] = 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.
"""
attributes = attributes or {}
if get_filename is None:
get_filecontent_: Callable[[str], bytes]
if get_filecontent is None:
get_filecontent_ = DEFAULT_TEST_DATA_RESOLVER.get_filecontent
else:
get_filecontent_ = get_filecontent
def get_filename(filename: str) -> str:
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 assertions is not None:
try:
verify_assertions(output_content, attributes["assert_list"], attributes.get("decompress", False))
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)
# 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:
filename_ = get_filename(filename)
assert filename_, f"Failed to find output target for test {filename_}"
local_name = 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)
elif compare == "image_diff":
files_image_diff(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()
local_file.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}).")
def _multiobject_intersection_over_union(
mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray", repeat_reverse: bool = True
) -> List["numpy.floating"]:
iou_list: List[numpy.floating] = []
for label1 in numpy.unique(mask1):
cc1 = mask1 == label1
cc1_iou_list: List[numpy.floating] = []
for label2 in numpy.unique(mask2[cc1]):
cc2 = mask2 == label2
cc1_iou_list.append(intersection_over_union(cc1, cc2))
iou_list.append(max(cc1_iou_list)) # type: ignore[type-var, unused-ignore] # https://github.com/python/typeshed/issues/12562
if repeat_reverse:
iou_list.extend(_multiobject_intersection_over_union(mask2, mask1, repeat_reverse=False))
return iou_list
[docs]def intersection_over_union(mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray") -> "numpy.floating":
assert mask1.dtype == mask2.dtype
assert mask1.ndim == mask2.ndim == 2
assert mask1.shape == mask2.shape
if mask1.dtype == bool:
return numpy.logical_and(mask1, mask2).sum() / numpy.logical_or(mask1, mask2).sum()
else:
return min(_multiobject_intersection_over_union(mask1, mask2)) # type: ignore[type-var, unused-ignore] # https://github.com/python/typeshed/issues/12562
[docs]def get_image_metric(
attributes: Dict[str, Any]
) -> Callable[["numpy.typing.NDArray", "numpy.typing.NDArray"], "numpy.floating"]:
metric_name = attributes.get("metric", DEFAULT_METRIC)
metrics = {
"mae": lambda arr1, arr2: numpy.abs(arr1 - arr2).mean(),
# Convert to float before squaring to prevent overflows
"mse": lambda arr1, arr2: numpy.square((arr1 - arr2).astype(float)).mean(),
"rms": lambda arr1, arr2: math.sqrt(numpy.square((arr1 - arr2).astype(float)).mean()),
"fro": lambda arr1, arr2: numpy.linalg.norm((arr1 - arr2).reshape(1, -1), "fro"),
"iou": lambda arr1, arr2: 1 - intersection_over_union(arr1, arr2),
}
try:
return metrics[metric_name]
except KeyError:
raise ValueError(f'No such metric: "{metric_name}"')
[docs]def files_image_diff(file1: str, file2: str, attributes: Optional[Dict[str, Any]] = None) -> None:
"""Check the pixel data of 2 image files for differences."""
attributes = attributes or {}
with Image.open(file1) as im1:
arr1 = numpy.array(im1)
with Image.open(file2) as im2:
arr2 = numpy.array(im2)
if arr1.dtype != arr2.dtype:
raise AssertionError(f"Image data types did not match ({arr1.dtype}, {arr2.dtype}).")
if arr1.shape != arr2.shape:
raise AssertionError(f"Image dimensions did not match ({arr1.shape}, {arr2.shape}).")
distance = get_image_metric(attributes)(arr1, arr2)
distance_eps = attributes.get("eps", DEFAULT_EPS)
if distance > distance_eps:
raise AssertionError(f"Image difference {distance} exceeds eps={distance_eps}.")