New upstream version 1.0.20180302231433 (9c74d157) · Commits · Debian Med / cwltool

Makefile

+1 −2

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@ PYSOURCES=$(wildcard ${MODULE}/*.py tests/.py) setup.py
		DEVPKGS=pep8 diff_cover autopep8 pylint coverage pydocstyle flake8 pytest isort mock
		DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
		python-flake8 python-mock shellcheck
		VERSION=1.0.$(shell date +%Y%m%d%H%M%S --date=`git log --first-parent \
		VERSION=1.0.$(shell date +%Y%m%d%H%M%S --utc --date=`git log --first-parent \
		--max-count=1 --format=format:%cI`)
		mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))

		@@ -190,4 +190,3 @@ FORCE:
		# Example `make print-VERSION`
		# From https://www.cmcrossroads.com/article/printing-value-makefile-variable
		print-% : ; @echo $* = $($*)

PKG-INFO

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Original line number	Diff line number	Diff line
		Metadata-Version: 1.1
		Name: cwltool
		Version: 1.0.20180225105849
		Version: 1.0.20180302231433
		Summary: Common workflow language reference implementation
		Home-page: https://github.com/common-workflow-language/cwltool
		Author: Common workflow language working group
		@@ -616,7 +616,6 @@ Classifier: Operating System :: Microsoft :: Windows :: Windows 8.1
		Classifier: Programming Language :: Python :: 2
		Classifier: Programming Language :: Python :: 2.7
		Classifier: Programming Language :: Python :: 3
		Classifier: Programming Language :: Python :: 3.3
		Classifier: Programming Language :: Python :: 3.4
		Classifier: Programming Language :: Python :: 3.5
		Classifier: Programming Language :: Python :: 3.6

cwltool.egg-info/PKG-INFO

+1 −2

Original line number	Diff line number	Diff line
		Metadata-Version: 1.1
		Name: cwltool
		Version: 1.0.20180225105849
		Version: 1.0.20180302231433
		Summary: Common workflow language reference implementation
		Home-page: https://github.com/common-workflow-language/cwltool
		Author: Common workflow language working group
		@@ -616,7 +616,6 @@ Classifier: Operating System :: Microsoft :: Windows :: Windows 8.1
		Classifier: Programming Language :: Python :: 2
		Classifier: Programming Language :: Python :: 2.7
		Classifier: Programming Language :: Python :: 3
		Classifier: Programming Language :: Python :: 3.3
		Classifier: Programming Language :: Python :: 3.4
		Classifier: Programming Language :: Python :: 3.5
		Classifier: Programming Language :: Python :: 3.6

cwltool/expression.py

+51 −30

Original line number	Diff line number	Diff line
		@@ -120,54 +120,75 @@ def scanner(scan): # type: (Text) -> List[int]
		return None


		def next_seg(remain, obj): # type: (Text, Any) -> Any
		if remain:
		m = segment_re.match(remain)
		def next_seg(parsed_string, remaining_string, current_value): # type: (Text, Text, Any) -> Any
		if remaining_string:
		m = segment_re.match(remaining_string)
		next_segment_str = m.group(0)

		key = None # type: Union[Text, int]
		if m.group(0)[0] == '.':
		key = m.group(0)[1:]
		elif m.group(0)[1] in ("'", '"'):
		key = m.group(0)[2:-2].replace("\\'", "'").replace('\\"', '"')
		if next_segment_str[0] == '.':
		key = next_segment_str[1:]
		elif next_segment_str[1] in ("'", '"'):
		key = next_segment_str[2:-2].replace("\\'", "'").replace('\\"', '"')

		if key:
		if isinstance(obj, list) and key == "length" and not remain[m.end(0):]:
		return len(obj)
		if not isinstance(obj, dict):
		raise WorkflowException(" is a %s, cannot index on string '%s'" % (type(obj).__name__, key))
		if key not in obj:
		raise WorkflowException(" does not contain key '%s'" % key)
		if isinstance(current_value, list) and key == "length" and not remaining_string[m.end(0):]:
		return len(current_value)
		if not isinstance(current_value, dict):
		raise WorkflowException("%s is a %s, cannot index on string '%s'" % (parsed_string, type(current_value).__name__, key))
		if key not in current_value:
		raise WorkflowException("%s does not contain key '%s'" % (parsed_string, key))
		else:
		try:
		key = int(m.group(0)[1:-1])
		key = int(next_segment_str[1:-1])
		except ValueError as v:
		raise WorkflowException(u(str(v)))
		if not isinstance(obj, list):
		raise WorkflowException(" is a %s, cannot index on int '%s'" % (type(obj).__name__, key))
		if key >= len(obj):
		raise WorkflowException(" list index %i out of range" % key)
		if not isinstance(current_value, list):
		raise WorkflowException("%s is a %s, cannot index on int '%s'" % (parsed_string, type(current_value).__name__, key))
		if key >= len(current_value):
		raise WorkflowException("%s list index %i out of range" % (parsed_string, key))

		try:
		return next_seg(remain[m.end(0):], obj[key])
		except WorkflowException as w:
		raise WorkflowException("%s%s" % (m.group(0), w))
		return next_seg(parsed_string + remaining_string, remaining_string[m.end(0):], current_value[key])
		except KeyError:
		raise WorkflowException("%s doesn't have property %s" % (parsed_string, key))
		else:
		return obj
		return current_value


		def evaluator(ex, jslib, obj, fullJS=False, timeout=None, force_docker_pull=False, debug=False, js_console=False):
		# type: (Text, Text, Dict[Text, Any], bool, int, bool, bool, bool) -> JSON
		m = param_re.match(ex)

		expression_parse_exception = None
		expression_parse_succeeded = False

		if m:
		if m.end(1)+1 == len(ex) and m.group(1) == "null":
		first_symbol = m.group(1)
		first_symbol_end = m.end(1)

		if first_symbol_end + 1 == len(ex) and first_symbol == "null":
		return None
		try:
		return next_seg(m.group(0)[m.end(1) - m.start(0):-1], obj[m.group(1)])
		except Exception as w:
		raise WorkflowException("%s%s" % (m.group(1), w))
		elif fullJS:
		if obj.get(first_symbol) is None:
		raise WorkflowException("%s is not defined" % first_symbol)

		return next_seg(first_symbol, ex[first_symbol_end:-1], obj[first_symbol])
		except WorkflowException as w:
		expression_parse_exception = w
		else:
		expression_parse_succeeded = True

		if fullJS and not expression_parse_succeeded:
		return sandboxjs.execjs(ex, jslib, timeout=timeout, force_docker_pull=force_docker_pull, debug=debug, js_console=js_console)
		else:
		if expression_parse_exception is not None:
		raise sandboxjs.JavascriptException(
		"Syntax error in parameter reference '%s': %s. This could be due to using Javascript code without specifying InlineJavascriptRequirement." % \
		(ex[1:-1], expression_parse_exception))
		else:
		raise sandboxjs.JavascriptException(
		"Syntax error in parameter reference '%s' or used Javascript code without specifying InlineJavascriptRequirement.",
		"Syntax error in parameter reference '%s'. This could be due to using Javascript code without specifying InlineJavascriptRequirement." % \
		ex)

cwltool/sandboxjs.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -292,7 +292,8 @@ def execjs(js, jslib, timeout=None, force_docker_pull=False, debug=False, js_con
		info = u"returncode was: %s\nscript was:\n%s\nstdout was: %s\nstderr was: %s\n" %\
		(nodejs.returncode, fn_linenum(), stdfmt(stdoutdata.decode('utf-8')), stdfmt(stderrdata.decode('utf-8')))
		else:
		info = stdfmt(stderrdata.decode('utf-8'))
		info = u"Javascript expression was: %s\nstdout was: %s\nstderr was: %s" %\
		(js, stdfmt(stdoutdata.decode('utf-8')), stdfmt(stderrdata.decode('utf-8')))

		if nodejs.poll() not in (None, 0):
		if killed: