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Source code for galaxy.util.biostar

"""
Support for integration with the Biostar application
"""

import hmac
import logging
import re
import urlparse

from unicodedata import normalize

from six import text_type

from galaxy.tools.errors import ErrorReporter
from galaxy.web.base.controller import url_for

from . import smart_str

log = logging.getLogger( __name__ )

_punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?@\[\\\]^_`{|},.]+')

DEFAULT_GALAXY_TAG = ''

# Default values for new posts to Biostar
DEFAULT_PAYLOAD = {
    'title': '',
    'tag_val': DEFAULT_GALAXY_TAG,
    'content': '',
}

BIOSTAR_ACTIONS = {
    None: { 'url': lambda x: '', 'uses_payload': False },
    'new_post': { 'url': lambda x: 'p/new/external/post/', 'uses_payload': True, 'hmac_values': {'content': 'digest'} },
    'show_tags': { 'url': lambda x: 't/%s/' % ( "+".join( ( x.get( 'tag_val' ) or DEFAULT_GALAXY_TAG ).split( ',' ) ) ), 'uses_payload': False },
    'log_out': { 'url': lambda x: 'site/logout/', 'uses_payload': False }
}

DEFAULT_BIOSTAR_COOKIE_AGE = 1


[docs]def biostar_enabled( app ): return bool( app.config.biostar_url )
# Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/)
[docs]def slugify(text, delim=u'-'): """Generates an slightly worse ASCII-only slug.""" if not isinstance( text, text_type ): text = text_type( text ) result = [] for word in _punct_re.split(text.lower()): word = normalize('NFKD', word).encode('ascii', 'ignore') if word: result.append(word) return text_type(delim.join(result))
[docs]def get_biostar_url( app, payload=None, biostar_action=None ): # Ensure biostar integration is enabled if not biostar_enabled( app ): raise Exception( "Biostar integration is not enabled" ) if biostar_action not in BIOSTAR_ACTIONS: raise Exception( "Invalid action specified (%s)." % ( biostar_action ) ) biostar_action = BIOSTAR_ACTIONS[ biostar_action ] # Start building up the payload payload = payload or {} payload = dict( DEFAULT_PAYLOAD, **payload ) payload[ 'name' ] = app.config.biostar_key_name for hmac_value_name, hmac_parameter_name in biostar_action.get( 'hmac_values', {} ).items(): # Biostar requires ascii only on HMAC'd things payload[ hmac_value_name ] = smart_str( payload.get( hmac_value_name, '' ), encoding='ascii', errors='replace' ) payload[ hmac_parameter_name ] = hmac.new( app.config.biostar_key, payload[ hmac_value_name ] ).hexdigest() # generate url, can parse payload info url = str( urlparse.urljoin( app.config.biostar_url, biostar_action.get( 'url' )( payload ) ) ) if not biostar_action.get( 'uses_payload' ): payload = {} url = url_for( url ) return url, payload
[docs]def tag_for_tool( tool ): """ Generate a reasonable biostar tag for a tool. """ # Biostar can now handle tags with spaces, do we want to generate tags differently now? return slugify( tool.name, delim='-' )
[docs]def populate_tag_payload( payload=None, tool=None ): if payload is None: payload = {} if DEFAULT_GALAXY_TAG: tag_val = [ DEFAULT_GALAXY_TAG ] else: tag_val = [] if tool: tag_val.append( tag_for_tool( tool ) ) payload[ 'tag_val' ] = ','.join( tag_val ) return payload
[docs]def populate_tool_payload( payload=None, tool=None ): payload = populate_tag_payload( payload=payload, tool=tool ) payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name ) tool_url = None if tool.tool_shed_repository: tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) if tool_url: tool_url = '</br>ToolShed URL: <a href="%s">%s</a>' % ( tool_url, tool_url ) if not tool_url: tool_url = '' payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s%s</p></br>' % ( tool.name, tool.version, tool.id, tool_url ) return payload
[docs]def biostar_logged_in( trans ): if biostar_enabled( trans.app ): if trans.app.config.biostar_key_name in trans.request.cookies: return True return False
[docs]def biostar_logout( trans ): if biostar_enabled( trans.app ): delete_cookie( trans, trans.app.config.biostar_key_name ) return get_biostar_url( trans.app, biostar_action='log_out' )[0] return None
[docs]class BiostarErrorReporter( ErrorReporter ): def _send_report( self, user, email=None, message=None, **kwd ): assert biostar_enabled( self.app ), ValueError( "Biostar is not configured for this galaxy instance" ) assert self.app.config.biostar_enable_bug_reports, ValueError( "Biostar is not configured to allow bug reporting for this galaxy instance" ) assert self._can_access_dataset( user ), Exception( "You are not allowed to access this dataset." ) tool_version_select_field, tools, tool = \ self.app.toolbox.get_tool_components( self.tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True ) payload = { 'title': 'Bug report on "%s" tool' % ( tool.name ), 'content': self.report.replace( '\n', '<br />' ).replace( '\r', '' ), 'tag_val': slugify( 'bug report' ) } # Get footer for email from here payload2 = populate_tool_payload( tool=tool ) if 'content' in payload2: payload[ 'content' ] = "%s<br />%s" % ( payload['content'], payload2['content'] ) if 'tag_val' in payload2: payload[ 'tag_val' ] = ','.join( [ payload2[ 'tag_val' ], payload[ 'tag_val' ] ] ) if 'action' not in payload: payload[ 'action' ] = 1 # Automatically post bug reports to biostar return payload