Merge branch 'release_21.09' into dev

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -98,6 +98,7 @@ class MockApp(di.Container, GalaxyDataTestApp):
         self.file_sources = Bunch(to_dict=lambda *args, **kwargs: {})
         self.interactivetool_manager = Bunch(create_interactivetool=lambda *args, **kwargs: None)
         self.is_job_handler = False
+        self.biotools_metadata_source = None
         rebind_container_to_task(self)
 
         def url_for(*args, **kwds):

lib/galaxy/job_execution/actions/post.py

@@ -58,7 +58,7 @@ class EmailAction(DefaultJobAction):
                 else:
                     host = socket.getfqdn()
                 frm = f'galaxy-no-reply@{host}'
-            to = job.user.email
+            to = job.get_user_email()
             subject = f"Galaxy job completion notification from history '{job.history.name}'"
             outdata = ',\n'.join(ds.dataset.display_name() for ds in job.output_datasets)
             body = f"Your Galaxy job generating dataset(s):\n\n{outdata}\n\nis complete as of {datetime.datetime.now().strftime('%I:%M')}. Click the link below to access your data: \n{link}"

lib/galaxy/jobs/__init__.py

@@ -2151,12 +2151,9 @@ class JobWrapper(HasResourceParameters):
     @property
     def user(self):
         job = self.get_job()
-        if job.user is not None:
-            return job.user.email
-        elif job.galaxy_session is not None and job.galaxy_session.user is not None:
-            return job.galaxy_session.user.email
-        elif job.history is not None and job.history.user is not None:
-            return job.history.user.email
+        user_email = job.get_user_email()
+        if user_email:
+            return user_email
         elif job.galaxy_session is not None:
             return f"anonymous@{job.galaxy_session.remote_addr.split()[-1]}"
         else:

lib/galaxy/managers/jobs.py

@@ -411,11 +411,7 @@ def view_show_job(trans, job, full: bool) -> typing.Dict:
         ))
 
         if is_admin:
-            if job.user:
-                job_dict['user_email'] = job.user.email
-            else:
-                job_dict['user_email'] = None
-
+            job_dict['user_email'] = job.get_user_email()
             job_dict['job_metrics'] = summarize_job_metrics(trans, job)
     return job_dict
 

lib/galaxy/model/__init__.py

@@ -1147,6 +1147,15 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     def set_tool_id(self, tool_id):
         self.tool_id = tool_id
 
+    def get_user_email(self):
+        if self.user is not None:
+            return self.user.email
+        elif self.galaxy_session is not None and self.galaxy_session.user is not None:
+            return self.galaxy_session.user.email
+        elif self.history is not None and self.history.user is not None:
+            return self.history.user.email
+        return None
+
     def set_tool_version(self, tool_version):
         self.tool_version = tool_version
 

lib/galaxy/tools/__init__.py

@@ -1029,8 +1029,9 @@ class Tool(Dictifiable):
         has_missing_data = len(edam_operations) == 0 or len(edam_topics) == 0
         if has_missing_data:
             biotools_reference = self.biotools_reference
-            if biotools_reference:
-                biotools_entry = self.app.biotools_metadata_source.get_biotools_metadata(biotools_reference)
+            metadata_source = self.app.biotools_metadata_source
+            if biotools_reference and metadata_source:
+                biotools_entry = metadata_source.get_biotools_metadata(biotools_reference)
                 if biotools_entry:
                     edam_info = biotools_entry.edam_info
                     if len(edam_operations) == 0:

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -210,7 +210,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
             if view == 'admin_job_list':
                 j['decoded_job_id'] = job.id
             if user_details:
-                j['user_email'] = job.user.email
+                j['user_email'] = job.get_user_email()
             out.append(j)
 
         return out

lib/galaxy/webapps/reports/controllers/jobs.py

@@ -154,7 +154,7 @@ class SpecifiedDateListGrid(grids.Grid):
 
         def get_value(self, trans, grid, job):
             if job.user:
-                return escape(job.user.email)
+                return escape(job.get_user_email())
             return 'anonymous'
 
     class EmailColumn(grids.GridColumn):
@@ -303,10 +303,7 @@ class Jobs(BaseUIController, ReportQueryBuilder):
                 # that submitted the job.
                 job_id = kwd.get('id', None)
                 job = get_job(trans, job_id)
-                if job.user:
-                    kwd['email'] = job.user.email
-                else:
-                    kwd['email'] = None  # For anonymous users
+                kwd['email'] = job.get_user_email()
                 return trans.response.send_redirect(web.url_for(controller='jobs',
                                                                 action='user_per_month',
                                                                 **kwd))

templates/webapps/reports/job_info.mako

@@ -37,8 +37,8 @@
             <tr>
                 <td colspan="2">${job.tool_id}</td>
                 <td>
-                    %if job.user and job.user.email:
-                        ${job.user.email}
+                    %if job.get_user_email():
+                        ${job.get_user_email()}
                     %else:
                         anonymous
                     %endif