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Unexpected section title or transition error in refinery_test tools #5

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hackdna opened this issue Apr 19, 2018 · 0 comments
Open

Unexpected section title or transition error in refinery_test tools #5

hackdna opened this issue Apr 19, 2018 · 0 comments

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@hackdna
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hackdna commented Apr 19, 2018

Installing revision https://testtoolshed.g2.bx.psu.edu/view/refinery-platform/refinery_test/b87749d7a24c results in the following error messages in Galaxy (v17.05) log:

docutils WARNING 2018-04-19 15:31:47,266 <string>:8: (SEVERE/4) Unexpected section title or transition.

-----

galaxy.tools ERROR 2018-04-19 15:31:47,266 error in help for tool Refinery test tool N-1
Traceback (most recent call last):
  File "/Users/isytchev/code/galaxy/live/lib/galaxy/tools/__init__.py", line 1111, in __inititalize_help
    self.__help = Template( rst_to_html(help_text), input_encoding='utf-8',
  File "/Users/isytchev/code/galaxy/live/lib/galaxy/util/__init__.py", line 794, in rst_to_html
    settings_overrides=settings_overrides ) )
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 414, in publish_string
    enable_exit_status=enable_exit_status)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 662, in publish_programmatically
    output = pub.publish(enable_exit_status=enable_exit_status)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 217, in publish
    self.settings)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/readers/__init__.py", line 72, in read
    self.parse()
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/__init__.py", line 172, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 170, in run
    input_source=document['source'])
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 1135, in indent
    elements = self.block_quote(indented, line_offset)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 1150, in block_quote
    self.nested_parse(blockquote_lines, line_offset, blockquote)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse
    node=node, match_titles=match_titles)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2371, in line
    line=self.state_machine.abs_line_number())
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 235, in severe
    return self.system_message(self.SEVERE_LEVEL, *args, **kwargs)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 193, in system_message
    raise SystemMessage(msg, level)
SystemMessage: <string>:8: (SEVERE/4) Unexpected section title or transition.

-----
docutils WARNING 2018-04-19 15:31:47,358 <string>:8: (SEVERE/4) Unexpected section title or transition.

-----

galaxy.tools ERROR 2018-04-19 15:31:47,359 error in help for tool Refinery test tool 1-N
Traceback (most recent call last):
  File "/Users/isytchev/code/galaxy/live/lib/galaxy/tools/__init__.py", line 1111, in __inititalize_help
    self.__help = Template( rst_to_html(help_text), input_encoding='utf-8',
  File "/Users/isytchev/code/galaxy/live/lib/galaxy/util/__init__.py", line 794, in rst_to_html
    settings_overrides=settings_overrides ) )
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 414, in publish_string
    enable_exit_status=enable_exit_status)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 662, in publish_programmatically
    output = pub.publish(enable_exit_status=enable_exit_status)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 217, in publish
    self.settings)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/readers/__init__.py", line 72, in read
    self.parse()
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/__init__.py", line 172, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 170, in run
    input_source=document['source'])
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 1135, in indent
    elements = self.block_quote(indented, line_offset)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 1150, in block_quote
    self.nested_parse(blockquote_lines, line_offset, blockquote)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse
    node=node, match_titles=match_titles)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2371, in line
    line=self.state_machine.abs_line_number())
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 235, in severe
    return self.system_message(self.SEVERE_LEVEL, *args, **kwargs)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 193, in system_message
    raise SystemMessage(msg, level)
SystemMessage: <string>:8: (SEVERE/4) Unexpected section title or transition.

-----
docutils WARNING 2018-04-19 15:31:47,389 <string>:8: (SEVERE/4) Unexpected section title or transition.

-----

galaxy.tools ERROR 2018-04-19 15:31:47,389 error in help for tool Refinery test tool N-1
Traceback (most recent call last):
  File "/Users/isytchev/code/galaxy/live/lib/galaxy/tools/__init__.py", line 1111, in __inititalize_help
    self.__help = Template( rst_to_html(help_text), input_encoding='utf-8',
  File "/Users/isytchev/code/galaxy/live/lib/galaxy/util/__init__.py", line 794, in rst_to_html
    settings_overrides=settings_overrides ) )
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 414, in publish_string
    enable_exit_status=enable_exit_status)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 662, in publish_programmatically
    output = pub.publish(enable_exit_status=enable_exit_status)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 217, in publish
    self.settings)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/readers/__init__.py", line 72, in read
    self.parse()
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/__init__.py", line 172, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 170, in run
    input_source=document['source'])
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 1135, in indent
    elements = self.block_quote(indented, line_offset)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 1150, in block_quote
    self.nested_parse(blockquote_lines, line_offset, blockquote)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse
    node=node, match_titles=match_titles)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2371, in line
    line=self.state_machine.abs_line_number())
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 235, in severe
    return self.system_message(self.SEVERE_LEVEL, *args, **kwargs)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 193, in system_message
    raise SystemMessage(msg, level)
SystemMessage: <string>:8: (SEVERE/4) Unexpected section title or transition.

-----
docutils WARNING 2018-04-19 15:31:47,677 <string>:8: (SEVERE/4) Unexpected section title or transition.

-----

galaxy.tools ERROR 2018-04-19 15:31:47,677 error in help for tool Refinery test tool 1-N
Traceback (most recent call last):
  File "/Users/isytchev/code/galaxy/live/lib/galaxy/tools/__init__.py", line 1111, in __inititalize_help
    self.__help = Template( rst_to_html(help_text), input_encoding='utf-8',
  File "/Users/isytchev/code/galaxy/live/lib/galaxy/util/__init__.py", line 794, in rst_to_html
    settings_overrides=settings_overrides ) )
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 414, in publish_string
    enable_exit_status=enable_exit_status)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 662, in publish_programmatically
    output = pub.publish(enable_exit_status=enable_exit_status)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/core.py", line 217, in publish
    self.settings)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/readers/__init__.py", line 72, in read
    self.parse()
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/__init__.py", line 172, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 170, in run
    input_source=document['source'])
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 1135, in indent
    elements = self.block_quote(indented, line_offset)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 1150, in block_quote
    self.nested_parse(blockquote_lines, line_offset, blockquote)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse
    node=node, match_titles=match_titles)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run
    context, state, transitions)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line
    return method(match, context, next_state)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2371, in line
    line=self.state_machine.abs_line_number())
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 235, in severe
    return self.system_message(self.SEVERE_LEVEL, *args, **kwargs)
  File "/Users/isytchev/code/galaxy/live/.venv/lib/python2.7/site-packages/docutils/utils/__init__.py", line 193, in system_message
    raise SystemMessage(msg, level)
SystemMessage: <string>:8: (SEVERE/4) Unexpected section title or transition.

-----
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