Source code for galaxy.util.biostar

"""
Support for integration with the Biostar application
"""
from __future__ import absolute_import

import hmac
import logging
import re
from unicodedata import normalize

from six import text_type
from six.moves.urllib.parse import (
    urljoin,
    urlsplit
)

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(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 determine_cookie_domain(galaxy_hostname, biostar_hostname):
    if galaxy_hostname == biostar_hostname:
        return galaxy_hostname

    sub_biostar_hostname = biostar_hostname.split('.', 1)[-1]
    if sub_biostar_hostname == galaxy_hostname:
        return galaxy_hostname

    sub_galaxy_hostname = galaxy_hostname.split('.', 1)[-1]
    if sub_biostar_hostname == sub_galaxy_hostname:
        return sub_galaxy_hostname

    return galaxy_hostname


[docs]def create_cookie(trans, key_name, key, email, age=DEFAULT_BIOSTAR_COOKIE_AGE, override_never_authenticate=False):
    if trans.app.config.biostar_never_authenticate and not override_never_authenticate:
        log.debug('A BioStar link was clicked, but never authenticate has been enabled, so we will not create the login cookie.')
        return
    digest = hmac.new(key, email).hexdigest()
    value = "%s:%s" % (email, digest)
    trans.set_cookie(value, name=key_name, path='/', age=age, version='1')
    # We need to explicitly set the domain here, in order to allow for biostar in a subdomain to work
    galaxy_hostname = urlsplit(url_for('/', qualified=True)).hostname
    biostar_hostname = urlsplit(trans.app.config.biostar_url).hostname
    trans.response.cookies[key_name]['domain'] = determine_cookie_domain(galaxy_hostname, biostar_hostname)


[docs]def delete_cookie(trans, key_name):
    # Set expiration of Cookie to time in past, to cause browser to delete
    if key_name in trans.request.cookies:
        create_cookie(trans, trans.app.config.biostar_key_name, '', '', age=-90, override_never_authenticate=True)


[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