Switch biostars to using HTML submission

lib/galaxy/tools/error_reports/sinks/biostars.py

@@ -0,0 +1,44 @@
+"""The module describes the ``biostars`` error sink plugin."""
+from __future__ import absolute_import
+
+import logging
+
+from galaxy.tools.errors import EmailErrorReporter
+from galaxy.util import string_as_bool
+from galaxy.util import biostar
+from galaxy.web.base.controller import url_for
+
+
+from ..sinks import ErrorSinkPlugin
+
+log = logging.getLogger( __name__ )
+
+
+class BiostarsPlugin( ErrorSinkPlugin ):
+    """Send error report as an issue on Biostars
+    """
+    plugin_type = "biostars"
+
+    def __init__( self, **kwargs ):
+        self.app = kwargs['app']
+        self.verbose = string_as_bool(kwargs.get('verbose', True))
+        self.user_submission = string_as_bool(kwargs.get('user_submission', True))
+
+    def submit_report( self, dataset, job, tool, **kwargs ):
+        """Send report as an email
+        """
+        try:
+            assert biostar.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" )
+            print(kwargs)
+
+            url = url_for(controller='biostar',
+                          action='biostar_tool_bug_report',
+                          hda=self.app.security.encode_id(dataset.id),
+                          email=kwargs['email'], message=kwargs['message'])
+            return ( 'Click <a href="%s">here</a> to submit to BioStars' % url, 'success' )
+        except Exception as e:
+            return ( "An error occurred submitting the report to biostars: %s" % str( e ), "danger" )
+
+
+__all__ = ( 'BiostarsPlugin', )

lib/galaxy/util/biostar.py

@@ -169,7 +169,20 @@ class BiostarErrorReporter( ErrorReporter ):
         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' ) }
+
+        # 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: