[med-svn] [Git][med-team/cwltool][master] 3 commits: New upstream version 1.0.20180302231433
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Mar 5 16:43:20 UTC 2018
Michael R. Crusoe pushed to branch master at Debian Med / cwltool
Commits:
9c74d157 by Michael R. Crusoe at 2018-03-05T06:33:41-08:00
New upstream version 1.0.20180302231433
- - - - -
403fd75c by Michael R. Crusoe at 2018-03-05T06:33:43-08:00
Update upstream source from tag 'upstream/1.0.20180302231433'
Update to upstream version '1.0.20180302231433'
with Debian dir 019242afe88799d5f0c5d8cfbd3b9b7107e9f94c
- - - - -
81cf88a2 by Michael R. Crusoe at 2018-03-05T06:44:46-08:00
New upstream release
- - - - -
8 changed files:
- Makefile
- PKG-INFO
- cwltool.egg-info/PKG-INFO
- cwltool/expression.py
- cwltool/sandboxjs.py
- debian/changelog
- setup.cfg
- setup.py
Changes:
=====================================
Makefile
=====================================
--- a/Makefile
+++ b/Makefile
@@ -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
=====================================
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
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
=====================================
--- a/cwltool.egg-info/PKG-INFO
+++ b/cwltool.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
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
=====================================
--- a/cwltool/expression.py
+++ b/cwltool/expression.py
@@ -120,55 +120,76 @@ 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:
- raise sandboxjs.JavascriptException(
- "Syntax error in parameter reference '%s' or used Javascript code without specifying InlineJavascriptRequirement.",
- ex)
+ 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'. This could be due to using Javascript code without specifying InlineJavascriptRequirement." % \
+ ex)
def interpolate(scan, rootvars,
=====================================
cwltool/sandboxjs.py
=====================================
--- a/cwltool/sandboxjs.py
+++ b/cwltool/sandboxjs.py
@@ -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:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+cwltool (1.0.20180302231433-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 05 Mar 2018 06:44:41 -0800
+
cwltool (1.0.20180225105849-2) unstable; urgency=medium
* Fix FTBFS. (Closes: #891752)
=====================================
setup.cfg
=====================================
--- a/setup.cfg
+++ b/setup.cfg
@@ -13,6 +13,6 @@ addopts = --ignore cwltool/schemas
testpaths = tests
[egg_info]
-tag_build = .20180225105849
+tag_build = .20180302231433
tag_date = 0
=====================================
setup.py
=====================================
--- a/setup.py
+++ b/setup.py
@@ -88,7 +88,6 @@ setup(name='cwltool',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
- 'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
View it on GitLab: https://salsa.debian.org/med-team/cwltool/compare/9c1bd76a8598898dea22f2f81d3b51860ad17148...81cf88a2cb4414337cbb55780e66cefd7a5ba15a
---
View it on GitLab: https://salsa.debian.org/med-team/cwltool/compare/9c1bd76a8598898dea22f2f81d3b51860ad17148...81cf88a2cb4414337cbb55780e66cefd7a5ba15a
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-commit/attachments/20180305/2e7fa20b/attachment-0001.html>
More information about the debian-med-commit
mailing list