def handle_command( self, tool_dependency, cmd, return_output=False ):
"""Handle a command and log the results."""
context = self.app.install_model.context
command = str( cmd )
output = self.handle_complex_command( command )
self.log_results( cmd, output, os.path.join( self.install_dir, basic_util.INSTALLATION_LOG ) )
stdout = output.stdout
stderr = output.stderr
if len( stdout ) > DATABASE_MAX_STRING_SIZE:
print "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY )
stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
if len( stderr ) > DATABASE_MAX_STRING_SIZE:
print "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY )
stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
if output.return_code not in [ 0 ]:
tool_dependency.status = self.app.install_model.ToolDependency.installation_status.ERROR
if stderr:
tool_dependency.error_message = unicodify( stderr )
elif stdout:
tool_dependency.error_message = unicodify( stdout )
else:
# We have a problem if there was no stdout and no stderr.
tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \
( str( cmd ), str( output.return_code ) )
context.add( tool_dependency )
context.flush()
if return_output:
return output
return output.return_code
def handle_command( self, tool_dependency, cmd, return_output=False, job_name="" ):
"""Handle a command and log the results."""
command = str( cmd )
output = self.handle_complex_command( command, job_name=job_name )
self.log_results( cmd, output, os.path.join( self.install_dir, basic_util.INSTALLATION_LOG ) )
stdout = output.stdout
stderr = output.stderr
if len( stdout ) > DATABASE_MAX_STRING_SIZE:
log.warn( "Length of stdout > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) )
stdout = shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
if len( stderr ) > DATABASE_MAX_STRING_SIZE:
log.warn( "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) )
stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
if output.return_code not in [ 0 ]:
status = self.app.install_model.ToolDependency.installation_status.ERROR
if stderr:
error_message = unicodify( stderr )
elif stdout:
error_message = unicodify( stdout )
else:
# We have a problem if there was no stdout and no stderr.
error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \
( str( cmd ), str( output.return_code ) )
tool_dependency_util.set_tool_dependency_attributes(self.app,
tool_dependency=tool_dependency,
status=status,
error_message=error_message)
if return_output:
return output
return output.return_code
def get_repository_file_contents(app,
file_path,
repository_id,
is_admin=False):
"""Return the display-safe contents of a repository file for display in a browser."""
safe_str = ''
if not is_path_browsable(app, file_path, repository_id, is_admin):
log.warning(
'Request tries to access a file outside of the repository location. File path: %s',
file_path)
return 'Invalid file path'
# Symlink targets are checked by is_path_browsable
if os.path.islink(file_path):
safe_str = 'link to: ' + basic_util.to_html_string(
os.readlink(file_path))
return safe_str
elif checkers.is_gzip(file_path):
return '<br/>gzip compressed file<br/>'
elif checkers.is_bz2(file_path):
return '<br/>bz2 compressed file<br/>'
elif checkers.check_zip(file_path):
return '<br/>zip compressed file<br/>'
elif checkers.check_binary(file_path):
return '<br/>Binary file<br/>'
else:
for i, line in enumerate(open(file_path)):
safe_str = '%s%s' % (safe_str, basic_util.to_html_string(line))
# Stop reading after string is larger than MAX_CONTENT_SIZE.
if len(safe_str) > MAX_CONTENT_SIZE:
large_str = \
'<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>' % \
util.nice_size( MAX_CONTENT_SIZE )
safe_str = '%s%s' % (safe_str, large_str)
break
if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
# Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
# This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
join_by_str = \
"<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>" % \
util.nice_size( basic_util.MAX_DISPLAY_SIZE )
safe_str = util.shrink_string_by_size(safe_str,
basic_util.MAX_DISPLAY_SIZE,
join_by=join_by_str,
left_larger=True,
beginning_on_size_error=True)
return safe_str
def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
"""Return the display-safe contents of a repository file for display in a browser."""
safe_str = ''
if not is_path_browsable(app, file_path, repository_id, is_admin):
log.warning('Request tries to access a file outside of the repository location. File path: %s', file_path)
return 'Invalid file path'
# Symlink targets are checked by is_path_browsable
if os.path.islink(file_path):
safe_str = 'link to: ' + basic_util.to_html_string(os.readlink(file_path))
return safe_str
elif checkers.is_gzip(file_path):
return '<br/>gzip compressed file<br/>'
elif checkers.is_bz2(file_path):
return '<br/>bz2 compressed file<br/>'
elif checkers.is_zip(file_path):
return '<br/>zip compressed file<br/>'
elif checkers.check_binary(file_path):
return '<br/>Binary file<br/>'
else:
for i, line in enumerate(open(file_path)):
safe_str = '%s%s' % (safe_str, basic_util.to_html_string(line))
# Stop reading after string is larger than MAX_CONTENT_SIZE.
if len(safe_str) > MAX_CONTENT_SIZE:
large_str = \
'<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>' % \
util.nice_size(MAX_CONTENT_SIZE)
safe_str = '%s%s' % (safe_str, large_str)
break
if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
# Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
# This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
join_by_str = \
"<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>" % \
util.nice_size(basic_util.MAX_DISPLAY_SIZE)
safe_str = util.shrink_string_by_size(safe_str,
basic_util.MAX_DISPLAY_SIZE,
join_by=join_by_str,
left_larger=True,
beginning_on_size_error=True)
return safe_str