diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py index 192e144079e..98e3574b028 100644 --- a/lib/galaxy/app_unittest_utils/galaxy_mock.py +++ b/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): diff --git a/lib/galaxy/job_execution/actions/post.py b/lib/galaxy/job_execution/actions/post.py index eb34662d7f6..ede02a4a0ca 100644 --- a/lib/galaxy/job_execution/actions/post.py +++ b/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}" diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index 4c47dadea16..7524e216adb 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/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: diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py index 2d24fbf784d..37cd15debbb 100644 --- a/lib/galaxy/managers/jobs.py +++ b/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 diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 6e4e70452c8..6e7b6ff84bb 100644 --- a/lib/galaxy/model/__init__.py +++ b/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 diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index af3405daae7..088696a853e 100644 --- a/lib/galaxy/tools/__init__.py +++ b/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: diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py index a63f2efcdae..b70837c8012 100644 --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/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 diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 8b9c2b755c5..e85cb5d1b1e 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/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)) diff --git a/templates/webapps/reports/job_info.mako b/templates/webapps/reports/job_info.mako index 8f246bb5039..53461b1066f 100644 --- a/templates/webapps/reports/job_info.mako +++ b/templates/webapps/reports/job_info.mako @@ -37,8 +37,8 @@ ${job.tool_id} - %if job.user and job.user.email: - ${job.user.email} + %if job.get_user_email(): + ${job.get_user_email()} %else: anonymous %endif