heliport.cwl_execution package
Subpackages
- heliport.cwl_execution.cwl_helpers package
- Submodules
- heliport.cwl_execution.cwl_helpers.cwl2rdf module
- heliport.cwl_execution.cwl_helpers.cwl_execution module
CWLExecutorManager
CWLExecutorManager.absolute_job_folder
CWLExecutorManager.append_job_output_text()
CWLExecutorManager.build_ssh_shell()
CWLExecutorManager.config_invalid()
CWLExecutorManager.configure_job_error()
CWLExecutorManager.configure_job_running()
CWLExecutorManager.configure_job_stopped()
CWLExecutorManager.data_source_filename()
CWLExecutorManager.data_source_path()
CWLExecutorManager.datasource_has_native_cwl_support()
CWLExecutorManager.download_data_with_curl()
CWLExecutorManager.execute()
CWLExecutorManager.execution_directory
CWLExecutorManager.executor
CWLExecutorManager.extract_data_source_from_cwl_parameter()
CWLExecutorManager.extract_inputs_from_tags()
CWLExecutorManager.extract_pure_executable_cwl_and_token_inputs()
CWLExecutorManager.extract_pure_job_cwl_and_data_sources()
CWLExecutorManager.get_inputs_dict()
CWLExecutorManager.job
CWLExecutorManager.job_config
CWLExecutorManager.job_folder
CWLExecutorManager.load_cwltool()
CWLExecutorManager.load_node_js()
CWLExecutorManager.load_venv()
CWLExecutorManager.login
CWLExecutorManager.make_parameter_pure_and_extract_data_source_to_copy()
CWLExecutorManager.prepare_job_folder()
CWLExecutorManager.run()
CWLExecutorManager.run_cwl_tool()
CWLExecutorManager.save_connect()
CWLExecutorManager.save_metadata()
CWLExecutorManager.save_profiling()
CWLExecutorManager.set_tokens()
CWLExecutorManager.srun
CWLExecutorManager.strip_comments()
CWLExecutorManager.test_directory_cwl_class()
CWLExecutorManager.test_node_requirement()
CWLExecutorManager.transfer_cwl()
CWLExecutorManager.transfer_data_source()
CWLExecutorManager.transfer_ssh_data_source()
CWLExecutorManager.update_renamed_workflow_steps()
CWLExecutorManager.user
save()
- heliport.cwl_execution.cwl_helpers.cwl_generation module
- heliport.cwl_execution.cwl_helpers.cwl_job module
- heliport.cwl_execution.cwl_helpers.cwl_parameter module
- heliport.cwl_execution.cwl_helpers.cwl_tool module
- heliport.cwl_execution.cwl_helpers.cwl_workflow module
- Module contents
- heliport.cwl_execution.management package
- heliport.cwl_execution.migrations package
Submodules
heliport.cwl_execution.admin module
Registers Django admin pages.
See django.contrib.admin.ModelAdmin
from Django documentation.
heliport.cwl_execution.apps module
Django app configuration.
Some HELIPORT hooks can be registered in app config django.apps.AppConfig.ready()
.
See also Django documentation
heliport.cwl_execution.conf module
Additional settings for this app.
See also django appconf
- class heliport.cwl_execution.conf.CwlExecutionAppConf(**kwargs)
Bases:
AppConf
Settings of the
heliport.cwl_execution
app.All settings in this class can be overwritten in settings.py
- DEFAULT_JOB_OPTIONS = '--time=10 # min or day-hour:min\n#--partition=gpu # part of cluster\n#--nodes=8 # number compute nodes\n# ... many more options possible'
- DEFAULT_JOB_PATH = '~/heliport_jobs_3_9'
- DEFAULT_JOB_SETUP_COMMAND = 'ml python/3.9\n@HELIPORT load venv # or conda activate, ...'
- SSH_DATA_TRANSFER_BATCH_SIZE = 10000
- USE_SRUN = True
heliport.cwl_execution.interface module
Module with special name “interface” hooks into HELIPORT.
Some functions and heliport.core.app_interaction.Module
subclasses are detected
by HELIPORT and control how HELIPORT uses this app.
Note that this module must be imported in __init__.py of the django app.
- class heliport.cwl_execution.interface.ArbitraryCWLModule
Bases:
Module
- get_url(project)
Return the URL for the entry point of this module.
- is_configured(project)
Return whether the module is configured, i.e. to show it in the graph.
- module_id = 'arbitrary_cwl'
- name = 'CWL File'
- class heliport.cwl_execution.interface.JobModule
Bases:
Module
- get_url(project)
Return the URL for the entry point of this module.
- is_configured(project)
Return whether the module is configured, i.e. to show it in the graph.
- module_id = 'job'
- name = 'CWL Jobs'
- class heliport.cwl_execution.interface.ToolModule
Bases:
Module
- get_url(project)
Return the URL for the entry point of this module.
- is_configured(project)
Return whether the module is configured, i.e. to show it in the graph.
- module_id = 'tool'
- name = 'Tool'
- class heliport.cwl_execution.interface.WorkflowModule
Bases:
Module
- get_url(project)
Return the URL for the entry point of this module.
- is_configured(project)
Return whether the module is configured, i.e. to show it in the graph.
- module_id = 'workflow'
- name = 'Workflow'
- heliport.cwl_execution.interface.get_search_url()
Return the search URL for this app.
This URL is used to implement the global HELIPORT string search.
heliport.cwl_execution.models module
Contains django.db.models.Model
classes for Django ORM.
See Quick example from Django documentation.
In HELIPORT the heliport.core.models.DigitalObject
can be subclassed for models
containing metadata in a project.
- class heliport.cwl_execution.models.Executable(digital_object_id, persistent_id, generated_persistent_id, category, label, label_is_public, description, description_is_public, created, last_modified, last_modified_is_public, deleted, permission, special_heliport_role, is_helper, projects_is_public, owner, members_is_public, digitalobject_ptr, executable_id, cwl_json, cwl_is_public, cwl_type, type, download_url_is_public, original_id)
Bases:
DigitalObject
- exception DoesNotExist
Bases:
DoesNotExist
- class ExecutableTypes(value)
Bases:
IntegerChoices
An enumeration.
- ARBITRARY_CWL = 3
- TOOL = 1
- WORKFLOW = 2
- exception MultipleObjectsReturned
Bases:
MultipleObjectsReturned
- property cwl
- cwl_is_public
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- cwl_json
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- cwl_type
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- digitalobject_ptr
Accessor to the related object on the forward side of a one-to-one relation.
In the example:
class Restaurant(Model): place = OneToOneField(Place, related_name='restaurant')
Restaurant.place
is aForwardOneToOneDescriptor
instance.
- digitalobject_ptr_id
- download_url_is_public
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- executable_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- get_cwl_type_display(*, field=<django.db.models.fields.IntegerField: cwl_type>)
- get_type_display(*, field=<django.db.models.fields.IntegerField: type>)
- property job_count
- job_set
Accessor to the related objects manager on the reverse side of a many-to-one relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Parent.children
is aReverseManyToOneDescriptor
instance.Most of the implementation is delegated to a dynamically defined manager class built by
create_forward_many_to_many_manager()
defined below.
- original_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- property parameters
- type
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- uses_files()
- class heliport.cwl_execution.models.ExecutionLog(execution_log_id, config, start_time, end_time, memory_usage, execution_id, aborted, step_times, output_code, error_message, user, original_id)
Bases:
Model
- exception DoesNotExist
Bases:
ObjectDoesNotExist
- exception MultipleObjectsReturned
Bases:
MultipleObjectsReturned
- aborted
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- config
Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Child.parent
is aForwardManyToOneDescriptor
instance.
- config_id
- property duration
- property duration_str
- end_time
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- error_message
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- execution_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- execution_log_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- get_next_by_start_time(*, field=<django.db.models.fields.DateTimeField: start_time>, is_next=True, **kwargs)
- get_output_code_display(*, field=<django.db.models.fields.IntegerField: output_code>)
- get_previous_by_start_time(*, field=<django.db.models.fields.DateTimeField: start_time>, is_next=False, **kwargs)
- get_user()
- memory_usage
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- property memory_usage_bytes
- property memory_usage_dict
- objects = <django.db.models.manager.Manager object>
- original_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- output_code
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- static parse_memory_units(memory_with_unit)
- property profiling
- property seconds_since_start
- start(execution_id=None)
- start_time
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- step_times
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- stop(kill=False)
- user
Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Child.parent
is aForwardManyToOneDescriptor
instance.
- user_id
- class heliport.cwl_execution.models.Job(digital_object_id, persistent_id, generated_persistent_id, category, label, label_is_public, description, description_is_public, created, last_modified, last_modified_is_public, deleted, permission, special_heliport_role, is_helper, projects_is_public, owner, members_is_public, digitalobject_ptr, job_id, status, output_text, output_code, cwl_json, repeat, interval, base_executable, setup_command, cmd_options, original_id)
Bases:
DigitalObject
- exception DoesNotExist
Bases:
DoesNotExist
- exception MultipleObjectsReturned
Bases:
MultipleObjectsReturned
- class OutputCodes(value)
Bases:
IntegerChoices
An enumeration.
- ERROR = 2
- MESSAGE = 0
- UNDEFINED = -1
- WARNING = 1
- class StatusCodes(value)
Bases:
TextChoices
An enumeration.
- PAUSED = 'Paused'
- RUNNING = 'Running'
- STOPPED = 'Stopped'
- base_executable
Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Child.parent
is aForwardManyToOneDescriptor
instance.
- base_executable_id
- cmd_options
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- property cwl
- cwl_json
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- digitalobject_ptr
Accessor to the related object on the forward side of a one-to-one relation.
In the example:
class Restaurant(Model): place = OneToOneField(Place, related_name='restaurant')
Restaurant.place
is aForwardOneToOneDescriptor
instance.
- digitalobject_ptr_id
- get_output_code_display(*, field=<django.db.models.fields.IntegerField: output_code>)
- get_status_display(*, field=<django.db.models.fields.CharField: status>)
- interval
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- job_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- original_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- output_code
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- output_text
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- repeat
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- setup_command
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- status
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- userjobconfig_set
Accessor to the related objects manager on the reverse side of a many-to-one relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Parent.children
is aReverseManyToOneDescriptor
instance.Most of the implementation is delegated to a dynamically defined manager class built by
create_forward_many_to_many_manager()
defined below.
- class heliport.cwl_execution.models.UserJobConfig(user_job_config_id, job, ssh_login, directory, original_id)
Bases:
Model
- exception DoesNotExist
Bases:
ObjectDoesNotExist
- exception MultipleObjectsReturned
Bases:
MultipleObjectsReturned
- directory
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- executionlog_set
Accessor to the related objects manager on the reverse side of a many-to-one relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Parent.children
is aReverseManyToOneDescriptor
instance.Most of the implementation is delegated to a dynamically defined manager class built by
create_forward_many_to_many_manager()
defined below.
- job
Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Child.parent
is aForwardManyToOneDescriptor
instance.
- job_id
- objects = <django.db.models.manager.Manager object>
- original_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- property projects
- ssh_login
Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.
In the example:
class Child(Model): parent = ForeignKey(Parent, related_name='children')
Child.parent
is aForwardManyToOneDescriptor
instance.
- ssh_login_id
- user_job_config_id
A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.
- heliport.cwl_execution.models.json_load_dict(json_string, error_dict=None)
heliport.cwl_execution.serializers module
This module is for serialization into Datacite, RDF and JSON.
The JSON format is used for API endpoints via Django rest framework. Using this, it is typical to put the serializer classes into a “serializers.py” file.
For the serialization into RDF, attributes are described.
See heliport.core.attribute_description.BaseAttribute
for more detail.
- class heliport.cwl_execution.serializers.ExecutableDATACITESerializer
Bases:
DigitalObjectDATACITESerializer
- resource_type(exe)
- class heliport.cwl_execution.serializers.ExecutableRDFSerializer
Bases:
DigitalObjectRDFSerializer
- static_triples(exe, user)
- class heliport.cwl_execution.serializers.ExecutableSerializer(*args, **kwargs)
Bases:
ModelSerializer
- class Meta
Bases:
object
- fields = ['executable_id', 'cwl_type', 'projects', 'type', 'cwl', 'cwl_json', 'namespace_str']
- model
alias of
Executable
- class heliport.cwl_execution.serializers.ExecutionLogSerializer(*args, **kwargs)
Bases:
ModelSerializer
- class Meta
Bases:
object
- fields = ['execution_log_id', 'config', 'start_time', 'end_time', 'memory_usage', 'execution_id', 'aborted', 'step_times', 'output_code', 'error_message', 'user']
- model
alias of
ExecutionLog
- class heliport.cwl_execution.serializers.JobDATACITESerializer
Bases:
DigitalObjectDATACITESerializer
- resource_type(job)
- class heliport.cwl_execution.serializers.JobSerializer(*args, **kwargs)
Bases:
ModelSerializer
- class heliport.cwl_execution.serializers.UserJobConfigSerializer(*args, **kwargs)
Bases:
ModelSerializer
- class Meta
Bases:
object
- fields = ['user_job_config_id', 'job', 'ssh_login', 'directory']
- model
alias of
UserJobConfig
heliport.cwl_execution.tasks module
heliport.cwl_execution.tests module
Test the behaviour of this app.
This follows the Writing tests guide in Django.
- class heliport.cwl_execution.tests.ArbitraryCWLTests(methodName='runTest')
Bases:
TestCase
- setUp()
Set up project and logged-in heliport users.
- test_list()
- test_post_fail()
- test_post_success()
- test_remove()
- test_update_list()
- test_update_show()
- class heliport.cwl_execution.tests.ToolTests(methodName='runTest')
Bases:
TestCase
- setUp()
Set up project and logged-in heliport users.
- test_concat_base_command()
- test_create_tool_and_update_tool()
- test_json_description()
- test_list_and_delete()
- test_split_base_command()
- class heliport.cwl_execution.tests.WorkflowTests(methodName='runTest')
Bases:
TestCase
- build_url(action, pk=None, no_project=False)
- static generate_cwl()
- setUp()
Set up project and logged-in heliport users.
- test_create_tool_and_update_tool()
- test_cwl_to_workflow()
- test_generate_port_data()
- test_id_generation()
- test_label_index()
- test_list_and_delete()
- test_node_categorization()
- test_node_visualization_data()
- test_unique_labels()
- test_workflow_to_cwl()
heliport.cwl_execution.urls module
Map django views to urls.
See this Example including explanation from the Django documentation.
heliport.cwl_execution.views module
Contains Django View classes to handle HTTP requests.
See Using class-based views from Django
documentation.
In HELIPORT heliport.core.mixins
are used to create uniform views. Also
heliport.core.views.generic.HeliportObjectListView
is used to quicly create a
typical HELIPORT list view.
- class heliport.cwl_execution.views.ArbitraryCWLListView(**kwargs)
Bases:
HeliportProjectMixin
,ListView
- context_object_name = 'arbitrary_cwls'
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
- get_queryset()
- model
alias of
Executable
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/arbitrary_cwl.html'
- class heliport.cwl_execution.views.ArbitraryCWLUpdateView(**kwargs)
Bases:
HeliportObjectMixin
,UpdateView
- fields = ['cwl_json', 'cwl_type']
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes the CWL.
- model
alias of
Executable
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/arbitrary_cwl.html'
- class heliport.cwl_execution.views.ExecutableRawJsonView(**kwargs)
Bases:
DetailView
URLs of this view also used in cwl identifiers.
- get(request, *args, **kwargs)
- model
alias of
Executable
- class heliport.cwl_execution.views.ExecutableRawYamlView(**kwargs)
Bases:
DetailView
- static check_permission(exe, request)
- get(request, *args, **kwargs)
- model
alias of
Executable
- static redirect_part(exe, kwargs)
- class heliport.cwl_execution.views.ExecutableViewSet(**kwargs)
Bases:
HeliportModelViewSet
Tools, Workflows and Arbitrary CWL.
- filterset_fields = ['executable_id', 'cwl_type', 'type']
- get_queryset()
- serializer_class
alias of
ExecutableSerializer
- class heliport.cwl_execution.views.ExecutionLogPermission
Bases:
BasePermission
Permission class to be used for execution logs. See
ExecutionLogViewSet
.- has_object_permission(request, view, obj: ExecutionLog)
Permission is granted if user
heliport.core.permissions.has_permission_for()
the job this log belongs to.
- class heliport.cwl_execution.views.ExecutionLogViewSet(**kwargs)
Bases:
HeliportModelViewSet
Concrete executions of a UserJobConfig.
- filterset_fields = ['execution_log_id', 'config', 'execution_id', 'aborted', 'output_code', 'user']
- get_queryset()
- permission_classes = [<class 'heliport.cwl_execution.views.ExecutionLogPermission'>]
Make sure user is authenticated and is allowed to access the DigitalObject
- serializer_class
alias of
ExecutionLogSerializer
- class heliport.cwl_execution.views.JobCreateView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- add_tags(tag_dict, cwl, job)
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes the job to edit if it exists.
- get_default_tag(already_saved_job)
- model
alias of
Executable
- pk_url_kwarg = 'executable'
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/job_create.html'
- class heliport.cwl_execution.views.JobDebugView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get(request, *args, **kwargs)
- model
alias of
UserJobConfig
- class heliport.cwl_execution.views.JobDetailView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes the job output in html format.
- template_name = 'cwl_execution/job_detail.html'
- class heliport.cwl_execution.views.JobListView(**kwargs)
Bases:
HeliportProjectMixin
,ListView
- context_object_name = 'userjobconfigs'
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes the default login calculated from statistics of past executions for the user.
- get_queryset()
- model
alias of
UserJobConfig
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/job_list.html'
- class heliport.cwl_execution.views.JobOutputView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get(request, *args, **kwargs)
- class heliport.cwl_execution.views.JobParameterValueView(**kwargs)
Bases:
HeliportProjectMixin
,TemplateView
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
- static serialize(tag_obj)
- template_name = 'cwl_execution/job_parameter_input.html'
- class heliport.cwl_execution.views.JobProfilingJsonView(**kwargs)
Bases:
HeliportProjectMixin
,DetailView
- get(request, *args, **kwargs)
- pk_url_kwarg = 'project'
- class heliport.cwl_execution.views.JobRawYamlView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get(request, *args, **kwargs)
- class heliport.cwl_execution.views.JobStartView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get(request, *args, **kwargs)
- model
alias of
UserJobConfig
- class heliport.cwl_execution.views.JobStopView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get(request, *args, **kwargs)
- model
alias of
UserJobConfig
- class heliport.cwl_execution.views.JobViewSet(**kwargs)
Bases:
HeliportModelViewSet
Jobs. To execute a job go to its UserJobConfig like …/user_job_config/user_job_config id/execute/.
- filterset_fields = ['job_id', 'label', 'status', 'output_code', 'repeat', 'interval', 'base_executable', 'setup_command']
- get_queryset()
- serializer_class
alias of
JobSerializer
- class heliport.cwl_execution.views.PublicationWorkflowCreateView(**kwargs)
Bases:
HeliportProjectMixin
,TemplateView
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/publication_workflow.html'
- class heliport.cwl_execution.views.RunningJobsView(**kwargs)
Bases:
HeliportProjectMixin
,DetailView
- get(request, *args, **kwargs)
- pk_url_kwarg = 'project'
- class heliport.cwl_execution.views.SearchView(**kwargs)
Bases:
HeliportLoginRequiredMixin
,TemplateView
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes the search results.
- template_name = 'cwl_execution/search.html'
- class heliport.cwl_execution.views.ToolCreateView(**kwargs)
Bases:
HeliportProjectMixin
,TemplateView
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/tool_edit.html'
- class heliport.cwl_execution.views.ToolJsonDescriptionView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get(request, *args, **kwargs)
- model
alias of
Executable
- class heliport.cwl_execution.views.ToolListView(**kwargs)
Bases:
HeliportProjectMixin
,ListView
- context_object_name = 'tools'
- get_queryset()
- model
alias of
Executable
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/tool_list.html'
- class heliport.cwl_execution.views.ToolUpdateView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes to render template for editing.
- model
alias of
Executable
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/tool_edit.html'
- class heliport.cwl_execution.views.UserJobConfigViewSet(**kwargs)
Bases:
ModelViewSet
User specific config for a job.
You can Execute your config by appending /execute/ to the URL. For example: …/user_job_config/123/execute/.
- execute(request, pk=None)
- filterset_fields = ['user_job_config_id', 'job', 'ssh_login', 'directory']
- get_queryset()
- permission_classes = [<class 'rest_framework.permissions.IsAuthenticated'>, <class 'heliport.core.permissions.HeliportObjectPermission'>]
- serializer_class
alias of
UserJobConfigSerializer
- class heliport.cwl_execution.views.VisualizationDataView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- get(request, *args, **kwargs)
- model
alias of
Executable
- class heliport.cwl_execution.views.WorkflowCreateView(**kwargs)
Bases:
HeliportProjectMixin
,TemplateView
- context_object_name = 'workflow'
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes executables that can be added to workflow.
- model
alias of
Executable
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/workflow_edit.html'
- class heliport.cwl_execution.views.WorkflowListView(**kwargs)
Bases:
HeliportProjectMixin
,ListView
- context_object_name = 'workflows'
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes the data sources to warn about if no exist and the Workflow uses some.
- get_queryset()
- model
alias of
Executable
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/workflow_list.html'
- class heliport.cwl_execution.views.WorkflowUpdateView(**kwargs)
Bases:
HeliportObjectMixin
,DetailView
- context_object_name = 'workflow'
- get_context_data(**kwargs)
Add extra context for rendering template (Called by django base view).
The extra context includes executables that can be added to workflow.
- model
alias of
Executable
- post(request, *args, **kwargs)
- template_name = 'cwl_execution/workflow_edit.html'
- heliport.cwl_execution.views.start_job(job_config, request, project_pk=None, debug=False)
Module contents
App to run, manage and record metadata related to CWL workflows.
The interface
module is imported to the top level of the package for HELIPORT app
interface discovery (see heliport.core.app_interaction.get_heliport_apps()
).