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galaxy.webapps.reports.controllers package

Galaxy reports controllers.

Submodules

galaxy.webapps.reports.controllers.home module

class galaxy.webapps.reports.controllers.home.HomePage(app)[source]

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

run_stats(trans, **kwd)[source]

galaxy.webapps.reports.controllers.jobs module

class galaxy.webapps.reports.controllers.jobs.Timer[source]

Bases: object

__init__()[source]
start()[source]
stop()[source]
time_elapsed()[source]
galaxy.webapps.reports.controllers.jobs.sorter(default_sort_id, kwd)[source]

Initialize sorting variables

galaxy.webapps.reports.controllers.jobs.get_spark_time(time_period)[source]
class galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid[source]

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

class 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, target=None)[source]

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

get_value(trans, grid, job)[source]
class 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, target=None)[source]

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

get_value(trans, grid, job)[source]
filter(trans, user, query, column_filter)[source]
class 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, target=None)[source]

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

get_value(trans, grid, job)[source]
filter(trans, user, query, column_filter)[source]
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, target=None)[source]

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

get_value(trans, grid, job)[source]
class 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, target=None)[source]

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

get_value(trans, grid, job)[source]
class 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, target=None)[source]

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

filter(trans, user, query, column_filter)[source]
class 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, target=None)[source]

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

filter(trans, user, query, column_filter)[source]
use_async = False
model_class

alias of galaxy.model.Job

title = 'Jobs'
template = '/webapps/reports/grid.mako'
default_sort_key = 'id'
columns = [<galaxy.webapps.reports.controllers.jobs.JobIdColumn object>, <galaxy.webapps.reports.controllers.jobs.StateColumn object>, <galaxy.webapps.reports.controllers.jobs.ToolColumn object>, <galaxy.webapps.reports.controllers.jobs.CreateTimeColumn object>, <galaxy.webapps.reports.controllers.jobs.UserColumn object>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateColumn object>, <galaxy.webapps.reports.controllers.jobs.EmailColumn object>, <galaxy.web.framework.helpers.grids.StateColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
standard_filters = []
default_filter = {'specified_date': 'All'}
num_rows_per_page = 50
preserve_state = False
use_paging = True
build_initial_query(trans, **kwd)[source]
class galaxy.webapps.reports.controllers.jobs.Jobs(app)[source]

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.

specified_date_list_grid = <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid object>
specified_date_handler(trans, **kwd)[source]
specified_month_all(trans, **kwd)[source]

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

specified_month_in_error(trans, **kwd)[source]

Queries the DB for the user jobs in error.

per_month_all(trans, **kwd)[source]

Queries the DB for all jobs. Avoids monitor jobs.

per_month_in_error(trans, **kwd)[source]

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

per_user(trans, **kwd)[source]
user_per_month(trans, **kwd)[source]
per_tool(trans, **kwd)[source]
errors_per_tool(trans, **kwd)[source]

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

tool_per_month(trans, **kwd)[source]
job_info(trans, **kwd)[source]
galaxy.webapps.reports.controllers.jobs.get_job(trans, id)[source]
galaxy.webapps.reports.controllers.jobs.get_monitor_id(trans, monitor_email)[source]

A convenience method to obtain the monitor job id.

galaxy.webapps.reports.controllers.query module

Mixin to help build advanced queries for reports interface.

class galaxy.webapps.reports.controllers.query.ReportQueryBuilder[source]
group_by_month(column)[source]
select_month(column)[source]
group_by_day(column)[source]
select_day(column)[source]

galaxy.webapps.reports.controllers.root module

class galaxy.webapps.reports.controllers.root.Report(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

index(trans, **kwd)[source]

galaxy.webapps.reports.controllers.sample_tracking module

class galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid[source]

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

class 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, target=None)[source]

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

get_value(trans, grid, request)[source]
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, target=None)[source]

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

get_value(trans, grid, request)[source]
class 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, target=None)[source]

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

get_value(trans, grid, request)[source]
class 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, target=None)[source]

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

filter(trans, user, query, column_filter)[source]
class 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, target=None)[source]

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

filter(trans, user, query, column_filter)[source]
use_async = False
model_class

alias of galaxy.model.Request

title = 'Sequencing Requests'
template = '/webapps/reports/grid.mako'
default_sort_key = 'name'
columns = [<galaxy.webapps.reports.controllers.sample_tracking.RequestNameColumn object>, <galaxy.webapps.reports.controllers.sample_tracking.CreateTimeColumn object>, <galaxy.webapps.reports.controllers.sample_tracking.UserColumn object>, <galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateColumn object>, <galaxy.webapps.reports.controllers.sample_tracking.EmailColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
standard_filters = []
default_filter = {'specified_date': 'All'}
num_rows_per_page = 50
preserve_state = False
use_paging = True
build_initial_query(trans, **kwd)[source]
class galaxy.webapps.reports.controllers.sample_tracking.SampleTracking(app)[source]

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

specified_date_list_grid = <galaxy.webapps.reports.controllers.sample_tracking.SpecifiedDateListGrid object>
specified_date_handler(trans, **kwd)[source]
per_month_all(trans, **kwd)[source]
per_user(trans, **kwd)[source]
user_per_month(trans, **kwd)[source]
galaxy.webapps.reports.controllers.sample_tracking.get_request(trans, id)[source]

galaxy.webapps.reports.controllers.system module

class galaxy.webapps.reports.controllers.system.System(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

index(trans, **kwd)[source]
userless_histories(trans, **kwd)[source]

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

deleted_histories(trans, **kwd)[source]

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.

deleted_datasets(trans, **kwd)[source]

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

dataset_info(trans, **kwd)[source]
get_disk_usage(file_path)[source]
disk_usage(trans, **kwd)[source]
galaxy.webapps.reports.controllers.system.nice_size(size, include_bytes=False)[source]

Returns a readably formatted string with the size

galaxy.webapps.reports.controllers.users module

class galaxy.webapps.reports.controllers.users.Users(app)[source]

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

registered_users(trans, **kwd)[source]
registered_users_per_month(trans, **kwd)[source]
specified_month(trans, **kwd)[source]
specified_date(trans, **kwd)[source]
last_access_date(trans, **kwd)[source]
user_disk_usage(trans, **kwd)[source]
history_per_user(trans, **kwd)[source]

galaxy.webapps.reports.controllers.workflows module

class galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid[source]

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

class 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, target=None)[source]

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

get_value(trans, grid, stored_workflow)[source]
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, target=None)[source]

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

get_value(trans, grid, stored_workflow)[source]
class 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, target=None)[source]

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

get_value(trans, grid, stored_workflow)[source]
class 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, target=None)[source]

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

filter(trans, user, query, column_filter)[source]
class 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, target=None)[source]

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

filter(trans, user, query, column_filter)[source]
use_async = False
model_class

alias of galaxy.model.StoredWorkflow

title = 'Workflows'
template = '/webapps/reports/grid.mako'
default_sort_key = 'name'
columns = [<galaxy.webapps.reports.controllers.workflows.WorkflowNameColumn object>, <galaxy.webapps.reports.controllers.workflows.CreateTimeColumn object>, <galaxy.webapps.reports.controllers.workflows.UserColumn object>, <galaxy.webapps.reports.controllers.workflows.SpecifiedDateColumn object>, <galaxy.webapps.reports.controllers.workflows.EmailColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
standard_filters = []
default_filter = {'specified_date': 'All'}
num_rows_per_page = 50
preserve_state = False
use_paging = True
build_initial_query(trans, **kwd)[source]
class galaxy.webapps.reports.controllers.workflows.Workflows(app)[source]

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

specified_date_list_grid = <galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid object>
specified_date_handler(trans, **kwd)[source]
per_month_all(trans, **kwd)[source]
per_user(trans, **kwd)[source]
user_per_month(trans, **kwd)[source]
per_workflow(trans, **kwd)[source]
galaxy.webapps.reports.controllers.workflows.get_workflow(trans, id)[source]