controllers Package

controllers Package

Galaxy reports controllers.

jobs Module

class galaxy.webapps.reports.controllers.jobs.Jobs(app)

Bases: galaxy.web.base.controller.BaseUIController

Class contains functions for querying data requested by user via the webapp. It exposes the functions and responds to requests with the filled .mako templates.

job_info(trans, **kwd)

per_month_all(trans, **kwd)

Queries the DB for all jobs. Avoids monitor jobs.

per_month_in_error(trans, **kwd)

Queries the DB for user jobs in error. Filters out monitor jobs.

per_tool(trans, **kwd)

per_user(trans, **kwd)

specified_date_handler(trans, **kwd)

specified_date_list_grid = <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid object>

specified_month_all(trans, **kwd)

Queries the DB for all jobs in given month, defaults to current month.

specified_month_in_error(trans, **kwd)

Queries the DB for the user jobs in error.

tool_per_month(trans, **kwd)

user_per_month(trans, **kwd)

class galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class CreateTimeColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.DateTimeColumn

get_value(trans, grid, job)

class SpecifiedDateListGrid.EmailColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

filter(trans, user, query, column_filter)

class SpecifiedDateListGrid.JobIdColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.IntegerColumn

get_value(trans, grid, job)

class SpecifiedDateListGrid.SpecifiedDateColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

filter(trans, user, query, column_filter)

class SpecifiedDateListGrid.StateColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

filter(trans, user, query, column_filter)

get_value(trans, grid, job)

class SpecifiedDateListGrid.ToolColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, job)

class SpecifiedDateListGrid.UserColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, job)

SpecifiedDateListGrid.build_initial_query(trans, **kwd)

SpecifiedDateListGrid.columns = [<galaxy.webapps.reports.controllers.jobs.JobIdColumn object at 0x7f92e3c1e110>, <galaxy.webapps.reports.controllers.jobs.StateColumn object at 0x7f92eb0aec50>, <galaxy.webapps.reports.controllers.jobs.ToolColumn object at 0x7f92e9a22790>, <galaxy.webapps.reports.controllers.jobs.CreateTimeColumn object at 0x7f92ec0f4e50>, <galaxy.webapps.reports.controllers.jobs.UserColumn object at 0x7f92e94a9150>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateColumn object at 0x7f92ee7f50d0>, <galaxy.webapps.reports.controllers.jobs.EmailColumn object at 0x7f92f43d10d0>, <galaxy.web.framework.helpers.grids.StateColumn object at 0x7f92f43d12d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92ec11cf50>]

SpecifiedDateListGrid.default_filter = {'specified_date': 'All'}

SpecifiedDateListGrid.default_sort_key = 'id'

SpecifiedDateListGrid.model_class

alias of Job

SpecifiedDateListGrid.num_rows_per_page = 50

SpecifiedDateListGrid.preserve_state = False

SpecifiedDateListGrid.standard_filters = []

SpecifiedDateListGrid.template = '/webapps/reports/grid.mako'

SpecifiedDateListGrid.title = 'Jobs'

SpecifiedDateListGrid.use_async = False

SpecifiedDateListGrid.use_paging = True

galaxy.webapps.reports.controllers.jobs.get_job(trans, id)

galaxy.webapps.reports.controllers.jobs.get_monitor_id(trans, monitor_email)

A convenience method to obtain the monitor job id.

root Module

class galaxy.webapps.reports.controllers.root.Report(app)

Bases: galaxy.web.base.controller.BaseUIController

index(trans, **kwd)

sample_tracking Module

class galaxy.webapps.reports.controllers.sample_tracking.SampleTracking(app)

Bases: galaxy.web.base.controller.BaseUIController

per_month_all(trans, **kwd)

per_user(trans, **kwd)

specified_date_handler(trans, **kwd)

specified_date_list_grid = <galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid object>

user_per_month(trans, **kwd)

class galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class CreateTimeColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.DateTimeColumn

get_value(trans, grid, request)

class SpecifiedDateListGrid.EmailColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

filter(trans, user, query, column_filter)

class SpecifiedDateListGrid.RequestNameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, request)

class SpecifiedDateListGrid.SpecifiedDateColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

filter(trans, user, query, column_filter)

class SpecifiedDateListGrid.UserColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, request)

SpecifiedDateListGrid.build_initial_query(trans, **kwd)

SpecifiedDateListGrid.columns = [<galaxy.webapps.reports.controllers.sample_tracking.RequestNameColumn object at 0x7f92e1fc7990>, <galaxy.webapps.reports.controllers.sample_tracking.CreateTimeColumn object at 0x7f92e1c057d0>, <galaxy.webapps.reports.controllers.sample_tracking.UserColumn object at 0x7f92e217d410>, <galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateColumn object at 0x7f92e1c05750>, <galaxy.webapps.reports.controllers.sample_tracking.EmailColumn object at 0x7f92e1c05810>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e1c05850>]

SpecifiedDateListGrid.default_filter = {'specified_date': 'All'}

SpecifiedDateListGrid.default_sort_key = 'name'

SpecifiedDateListGrid.model_class

alias of Request

SpecifiedDateListGrid.num_rows_per_page = 50

SpecifiedDateListGrid.preserve_state = False

SpecifiedDateListGrid.standard_filters = []

SpecifiedDateListGrid.template = '/webapps/reports/grid.mako'

SpecifiedDateListGrid.title = 'Sequencing Requests'

SpecifiedDateListGrid.use_async = False

SpecifiedDateListGrid.use_paging = True

galaxy.webapps.reports.controllers.sample_tracking.get_request(trans, id)

system Module

class galaxy.webapps.reports.controllers.system.System(app)

Bases: galaxy.web.base.controller.BaseUIController

dataset_info(trans, **kwd)

deleted_datasets(trans, **kwd)

The number of datasets that were deleted more than the specified number of days ago, but have not yet been purged.

deleted_histories(trans, **kwd)

The number of histories that were deleted more than the specified number of days ago, but have not yet been purged. Also included is the number of datasets associated with the histories.

disk_usage(trans, **kwd)

get_disk_usage(file_path)

index(trans, **kwd)

userless_histories(trans, **kwd)

The number of userless histories and associated datasets that have not been updated for the specified number of days.

galaxy.webapps.reports.controllers.system.nice_size(size, include_bytes=False)

Returns a readably formatted string with the size

users Module

class galaxy.webapps.reports.controllers.users.Users(app)

Bases: galaxy.web.base.controller.BaseUIController

last_access_date(trans, **kwd)

registered_users(trans, **kwd)

registered_users_per_month(trans, **kwd)

specified_date(trans, **kwd)

specified_month(trans, **kwd)

user_disk_usage(trans, **kwd)

workflows Module

class galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class CreateTimeColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.DateTimeColumn

get_value(trans, grid, stored_workflow)

class SpecifiedDateListGrid.EmailColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

filter(trans, user, query, column_filter)

class SpecifiedDateListGrid.SpecifiedDateColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

filter(trans, user, query, column_filter)

class SpecifiedDateListGrid.UserColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, stored_workflow)

class SpecifiedDateListGrid.WorkflowNameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, stored_workflow)

SpecifiedDateListGrid.build_initial_query(trans, **kwd)

SpecifiedDateListGrid.columns = [<galaxy.webapps.reports.controllers.workflows.WorkflowNameColumn object at 0x7f92e185ea10>, <galaxy.webapps.reports.controllers.workflows.CreateTimeColumn object at 0x7f92e851ef90>, <galaxy.webapps.reports.controllers.workflows.UserColumn object at 0x7f92e181e990>, <galaxy.webapps.reports.controllers.workflows.SpecifiedDateColumn object at 0x7f92e181e910>, <galaxy.webapps.reports.controllers.workflows.EmailColumn object at 0x7f92e181e9d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e181ea10>]

SpecifiedDateListGrid.default_filter = {'specified_date': 'All'}

SpecifiedDateListGrid.default_sort_key = 'name'

SpecifiedDateListGrid.model_class

alias of StoredWorkflow

SpecifiedDateListGrid.num_rows_per_page = 50

SpecifiedDateListGrid.preserve_state = False

SpecifiedDateListGrid.standard_filters = []

SpecifiedDateListGrid.template = '/webapps/reports/grid.mako'

SpecifiedDateListGrid.title = 'Workflows'

SpecifiedDateListGrid.use_async = False

SpecifiedDateListGrid.use_paging = True

class galaxy.webapps.reports.controllers.workflows.Workflows(app)

Bases: galaxy.web.base.controller.BaseUIController

per_month_all(trans, **kwd)

per_user(trans, **kwd)

specified_date_handler(trans, **kwd)

specified_date_list_grid = <galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid object>

user_per_month(trans, **kwd)

galaxy.webapps.reports.controllers.workflows.get_workflow(trans, id)