def lint_help(tool_xml, lint_ctx):
root = tool_xml.getroot()
helps = root.findall("help")
if len(helps) > 1:
lint_ctx.error("More than one help section found, behavior undefined.")
return
if len(helps) == 0:
lint_ctx.warn("No help section found, consider adding a help section to your tool.")
return
help = helps[0].text or ''
if not help.strip():
lint_ctx.warn("Help section appears to be empty.")
return
lint_ctx.valid("Tool contains help section.")
invalid_rst = False
try:
rst_to_html(help)
except Exception as e:
invalid_rst = str(e)
if "TODO" in help:
lint_ctx.warn("Help contains TODO text.")
if invalid_rst:
lint_ctx.warn("Invalid reStructuredText found in help - [%s]." % invalid_rst)
else:
lint_ctx.valid("Help contains valid reStructuredText.")
def lint_help(tool_xml, lint_ctx):
root = tool_xml.getroot()
helps = root.findall("help")
if len(helps) > 1:
lint_ctx.error("More than one help section found, behavior undefined.")
return
if len(helps) == 0:
lint_ctx.warn("No help section found, consider adding a help section to your tool.")
return
help = helps[0].text
if not help.strip():
lint_ctx.warn("Help section appears to be empty.")
return
lint_ctx.valid("Tool contains help section.")
invalid_rst = False
try:
rst_to_html(help)
except Exception as e:
invalid_rst = str(e)
if "TODO" in help:
lint_ctx.warn("Help contains TODO text.")
if invalid_rst:
lint_ctx.warn("Invalid reStructuredText found in help - [%s]." % invalid_rst)
else:
lint_ctx.valid("Help contains valid reStructuredText.")
def rst_invalid(text):
invalid_rst = False
try:
rst_to_html(text)
except Exception as e:
invalid_rst = str(e)
return invalid_rst
def rst_invalid(text):
"""Predicate to determine if text is invalid reStructuredText.
Return False if the supplied text is valid reStructuredText or
a string indicating the problem.
"""
invalid_rst = False
try:
rst_to_html(text)
except Exception as e:
invalid_rst = str(e)
return invalid_rst
def build_readme_files_dict( app, repository, changeset_revision, metadata, tool_path=None ):
"""
Return a dictionary of valid readme file name <-> readme file content pairs for all readme files defined in the received metadata. Since the
received changeset_revision (which is associated with the received metadata) may not be the latest installable changeset revision, the README
file contents may not be available on disk. This method is used by both Galaxy and the Tool Shed.
"""
if app.name == 'galaxy':
can_use_disk_files = True
else:
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
latest_downloadable_changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo )
can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
readme_files_dict = {}
if metadata:
if 'readme_files' in metadata:
for relative_path_to_readme_file in metadata[ 'readme_files' ]:
readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ]
if can_use_disk_files:
if tool_path:
full_path_to_readme_file = os.path.abspath( os.path.join( tool_path, relative_path_to_readme_file ) )
else:
full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file )
text = None
try:
f = open( full_path_to_readme_file, 'r' )
text = unicodify( f.read() )
f.close()
except Exception, e:
log.exception( "Error reading README file '%s' from disk: %s" % ( str( relative_path_to_readme_file ), str( e ) ) )
text = None
if text:
text_of_reasonable_length = basic_util.size_string( text )
if text_of_reasonable_length.find( '.. image:: ' ) >= 0:
# Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy.
lock = threading.Lock()
lock.acquire( True )
try:
text_of_reasonable_length = suc.set_image_paths( app,
app.security.encode_id( repository.id ),
text_of_reasonable_length )
except Exception, e:
log.exception( "Exception in build_readme_files_dict, so images may not be properly displayed:\n%s" % str( e ) )
finally:
lock.release()
if readme_file_name.endswith( '.rst' ):
text_of_reasonable_length = Template( rst_to_html( text_of_reasonable_length ),
input_encoding='utf-8',
output_encoding='utf-8',
default_filters=[ 'decode.utf8' ],
encoding_errors='replace' )
text_of_reasonable_length = text_of_reasonable_length.render( static_path=web.url_for( '/static' ),
host_url=web.url_for( '/', qualified=True ) )
text_of_reasonable_length = unicodify( text_of_reasonable_length )
else:
text_of_reasonable_length = basic_util.to_html_string( text_of_reasonable_length )
readme_files_dict[ readme_file_name ] = text_of_reasonable_length
def build_readme_files_dict( app, repository, changeset_revision, metadata, tool_path=None ):
"""
Return a dictionary of valid readme file name <-> readme file content pairs for all readme files defined in the received metadata. Since the
received changeset_revision (which is associated with the received metadata) may not be the latest installable changeset revision, the README
file contents may not be available on disk. This method is used by both Galaxy and the Tool Shed.
"""
if app.name == 'galaxy':
can_use_disk_files = True
else:
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
latest_downloadable_changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo )
can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
readme_files_dict = {}
if metadata:
if 'readme_files' in metadata:
for relative_path_to_readme_file in metadata[ 'readme_files' ]:
readme_file_name = os.path.split( relative_path_to_readme_file )[ 1 ]
if can_use_disk_files:
if tool_path:
full_path_to_readme_file = os.path.abspath( os.path.join( tool_path, relative_path_to_readme_file ) )
else:
full_path_to_readme_file = os.path.abspath( relative_path_to_readme_file )
text = None
try:
f = open( full_path_to_readme_file, 'r' )
text = unicodify( f.read() )
f.close()
except Exception, e:
log.exception( "Error reading README file '%s' from disk: %s" % ( str( relative_path_to_readme_file ), str( e ) ) )
text = None
if text:
text_of_reasonable_length = basic_util.size_string( text )
if text_of_reasonable_length.find( '.. image:: ' ) >= 0:
# Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy.
lock = threading.Lock()
lock.acquire( True )
try:
text_of_reasonable_length = suc.set_image_paths( app,
app.security.encode_id( repository.id ),
text_of_reasonable_length )
except Exception, e:
log.exception( "Exception in build_readme_files_dict, so images may not be properly displayed:\n%s" % str( e ) )
finally:
lock.release()
if readme_file_name.endswith( '.rst' ):
text_of_reasonable_length = Template( rst_to_html( text_of_reasonable_length ),
input_encoding='utf-8',
output_encoding='utf-8',
default_filters=[ 'decode.utf8' ],
encoding_errors='replace' )
text_of_reasonable_length = text_of_reasonable_length.render( static_path=web.url_for( '/static' ),
host_url=web.url_for( '/', qualified=True ) )
text_of_reasonable_length = unicodify( text_of_reasonable_length )
else:
text_of_reasonable_length = basic_util.to_html_string( text_of_reasonable_length )
readme_files_dict[ readme_file_name ] = text_of_reasonable_length
def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_path=None):
"""
Return a dictionary of valid readme file name <-> readme file content pairs for all readme files defined in the received metadata. Since the
received changeset_revision (which is associated with the received metadata) may not be the latest installable changeset revision, the README
file contents may not be available on disk. This method is used by both Galaxy and the Tool Shed.
"""
if app.name == 'galaxy':
can_use_disk_files = True
else:
latest_downloadable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision(app, repository)
can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
readme_files_dict = {}
if metadata:
if 'readme_files' in metadata:
for relative_path_to_readme_file in metadata['readme_files']:
readme_file_name = os.path.split(relative_path_to_readme_file)[1]
if can_use_disk_files:
if tool_path:
full_path_to_readme_file = os.path.abspath(os.path.join(tool_path, relative_path_to_readme_file))
else:
full_path_to_readme_file = os.path.abspath(relative_path_to_readme_file)
text = None
try:
with open(full_path_to_readme_file, encoding='utf-8') as f:
text = f.read()
except Exception:
log.exception("Error reading README file '%s' from disk", relative_path_to_readme_file)
text = None
if text:
text_of_reasonable_length = basic_util.size_string(text)
if text_of_reasonable_length.find('.. image:: ') >= 0:
# Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy.
try:
text_of_reasonable_length = suc.set_image_paths(app,
text_of_reasonable_length,
encoded_repository_id=app.security.encode_id(repository.id))
except Exception:
log.exception("Exception in build_readme_files_dict, so images may not be properly displayed")
if readme_file_name.endswith('.rst'):
text_of_reasonable_length = Template(rst_to_html(text_of_reasonable_length),
input_encoding='utf-8',
default_filters=['decode.utf8'],
encoding_errors='replace')
text_of_reasonable_length = text_of_reasonable_length.render(static_path=web.url_for('/static'),
host_url=web.url_for('/', qualified=True))
text_of_reasonable_length = unicodify(text_of_reasonable_length)
else:
text_of_reasonable_length = basic_util.to_html_string(text_of_reasonable_length)
readme_files_dict[readme_file_name] = text_of_reasonable_length
else:
# We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest.
repo = repository.hg_repo
ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
if ctx:
fctx = hg_util.get_file_context_from_ctx(ctx, readme_file_name)
if fctx and fctx not in ['DELETED']:
try:
text = unicodify(fctx.data())
readme_files_dict[readme_file_name] = basic_util.size_string(text)
except Exception:
log.exception("Error reading README file '%s' from repository manifest", relative_path_to_readme_file)
return readme_files_dict