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Source code for galaxy.util.biostar

Support for integration with the Biostar application
from __future__ import absolute_import

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 values for new posts to Biostar
    'title': '',
    'tag_val': DEFAULT_GALAXY_TAG,
    'content': '',

    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}


[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) # Strip out unwanted HTML characters html_remove = ['<html>', '<body>', '</body>', '</html>', '\n', '\r'] report = self.html_report for tag in html_remove: report = report.replace(tag, '') # Must lstrip spaces or it isn't recognised as HTML report = report.lstrip() payload = { 'title': 'Bug report on "%s" tool' % (tool.name), 'content': report, '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