controllers Package

controllers Package

Galaxy reports controllers.

jobs Module

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

Bases: galaxy.web.base.controller.BaseUIController, galaxy.webapps.reports.controllers.query.ReportQueryBuilder

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 0x7f85c93d4590>, <galaxy.webapps.reports.controllers.jobs.StateColumn object at 0x7f85c9d3f950>, <galaxy.webapps.reports.controllers.jobs.ToolColumn object at 0x7f85c950df90>, <galaxy.webapps.reports.controllers.jobs.CreateTimeColumn object at 0x7f85c94799d0>, <galaxy.webapps.reports.controllers.jobs.UserColumn object at 0x7f85c9479490>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateColumn object at 0x7f85c946a450>, <galaxy.webapps.reports.controllers.jobs.EmailColumn object at 0x7f85c946a110>, <galaxy.web.framework.helpers.grids.StateColumn object at 0x7f85d71df810>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85d71df510>]

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, galaxy.webapps.reports.controllers.query.ReportQueryBuilder

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 0x7f85c946a7d0>, <galaxy.webapps.reports.controllers.sample_tracking.CreateTimeColumn object at 0x7f85c9a78c10>, <galaxy.webapps.reports.controllers.sample_tracking.UserColumn object at 0x7f85c9d8aa10>, <galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateColumn object at 0x7f85c9a8e150>, <galaxy.webapps.reports.controllers.sample_tracking.EmailColumn object at 0x7f85c9d79dd0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85c91284d0>]

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, galaxy.webapps.reports.controllers.query.ReportQueryBuilder

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 0x7f85c8d105d0>, <galaxy.webapps.reports.controllers.workflows.CreateTimeColumn object at 0x7f85c8d10290>, <galaxy.webapps.reports.controllers.workflows.UserColumn object at 0x7f85c923c4d0>, <galaxy.webapps.reports.controllers.workflows.SpecifiedDateColumn object at 0x7f85c8cd6690>, <galaxy.webapps.reports.controllers.workflows.EmailColumn object at 0x7f85c8cd6610>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85c8cd66d0>]

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, galaxy.webapps.reports.controllers.query.ReportQueryBuilder

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)