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galaxy.webapps.reports.controllers package¶

Galaxy reports controllers.

Submodules¶

galaxy.webapps.reports.controllers.history module¶

class galaxy.webapps.reports.controllers.history.History(app)[source]¶

Bases: galaxy.webapps.base.controller.BaseUIController

Class defining functions used by reports to make requests to get informations and fill templates before being displayed. The name of function must be the same as as the field “action” of the “href” dict, in .mako templates (templates/webapps/reports).

history_and_dataset_per_user(trans, **kwd)[source]¶

fill history_and_dataset_per_user.mako template with:

user email
the number of history and their size
the number of dataset

history_and_dataset_type(trans, **kwd)[source]¶

fill history_and_dataset_type.mako template with:

the name of history
the number of dataset foreach type

galaxy.webapps.reports.controllers.history.int_to_octet(size)[source]¶

galaxy.webapps.reports.controllers.home module¶

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

Bases: galaxy.webapps.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.Jobs(app)[source]¶

Bases: galaxy.webapps.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.

errors_per_tool(trans, **kwd)[source]¶: Queries the DB for user jobs in error. Filters out monitor jobs.

job_info(trans, **kwd)[source]¶

per_month_all(trans, **kwd)[source]¶: Queries the DB for all jobs. Avoids monitor jobs. The by_destination param will group by User.email and Job.destination_id.

per_month_in_error(trans, **kwd)[source]¶: Queries the DB for user jobs in error. Filters out monitor jobs.

per_tool(trans, **kwd)[source]¶

per_user(trans, **kwd)[source]¶: Queries the DB for jobs per user. The by_destination param will group by Job.destination_id.

specified_date_handler(trans, **kwd)[source]¶

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

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.

tool_per_month(trans, **kwd)[source]¶

user_per_month(trans, **kwd)[source]¶: Queries the DB for jobs per user per month. The by_destination param will group by Job.destination_id.

class galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid[source]¶

Bases: galaxy.web.legacy_framework.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, target=None)[source]¶

Bases: galaxy.web.legacy_framework.grids.DateTimeColumn

get_value(trans, grid, job)[source]¶

class DestinationIdColumn(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.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)[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.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)[source]¶

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.legacy_framework.grids.IntegerColumn

get_value(trans, grid, job)[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.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)[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.legacy_framework.grids.TextColumn

filter(trans, user, query, column_filter)[source]¶

get_value(trans, grid, job)[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.legacy_framework.grids.TextColumn

filter(trans, user, query, column_filter)[source]¶

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.legacy_framework.grids.GridColumn

get_value(trans, grid, job)[source]¶

build_initial_query(trans, **kwd)[source]¶

columns = [<galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.JobIdColumn object>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.StateColumn object>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.DestinationIdColumn object>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.ToolColumn object>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.CreateTimeColumn object>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.UserColumn object>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.SpecifiedDateColumn object>, <galaxy.webapps.reports.controllers.jobs.SpecifiedDateListGrid.EmailColumn object>, <galaxy.web.legacy_framework.grids.StateColumn object>, <galaxy.web.legacy_framework.grids.MulticolFilterColumn object>]¶

default_filter = {'specified_date': 'All'}¶

default_sort_key = 'id'¶

model_class¶: alias of galaxy.model.Job

num_rows_per_page = 50¶

title = 'Jobs'¶

use_async = False¶

use_paging = True¶

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

Bases: object

__init__()[source]¶

start()[source]¶

stop()[source]¶

time_elapsed()[source]¶

galaxy.webapps.reports.controllers.jobs.get_curr_item(check_item, unique_items)[source]¶: When rendering by item and destination_id, render the item uniquely.

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.jobs.get_spark_time(time_period)[source]¶

galaxy.webapps.reports.controllers.jobs.sorter(default_sort_id, kwd)[source]¶: Initialize sorting variables

galaxy.webapps.reports.controllers.query module¶

Mixin to help build advanced queries for reports interface.

class galaxy.webapps.reports.controllers.query.ReportQueryBuilder[source]¶

Bases: object

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.webapps.base.controller.BaseUIController

index(trans, **kwd)[source]¶

galaxy.webapps.reports.controllers.system module¶

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

Bases: galaxy.webapps.base.controller.BaseUIController

dataset_info(trans, **kwd)[source]¶

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.

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.

disk_usage(trans, **kwd)[source]¶

get_disk_usage(file_path)[source]¶

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.

galaxy.webapps.reports.controllers.system.nice_size(size, include_bytes=False)[source]¶: Returns a readably formatted string with the size

galaxy.webapps.reports.controllers.tools module¶

class galaxy.webapps.reports.controllers.tools.Tools(app)[source]¶

Bases: galaxy.webapps.base.controller.BaseUIController

Class defining functions used by reports to make requests to get informations and fill templates before being displayed. The name of function must be the same as as the field “action” of the “href” dict, in .mako templates (templates/webapps/reports).

formatted(date, colored=False)[source]¶

tool_error_messages(trans, **kwd)[source]¶

tool_execution_time(trans, **kwd)[source]¶

Fill the template tool_execution_time.mako with informations:

Tool name
Tool average execution time
last job execution time
min and max execution time

tool_execution_time_per_month(trans, **kwd)[source]¶

Fill the template tool_execution_time_per_month.mako with informations:

Tool average execution time
last job execution time
min and max execution time

tools_and_job_state(trans, **kwd)[source]¶

fill tools_and_job_state.mako template with

the name of the tool
the number of jobs using this tool in state ‘ok’
the number of jobs using this tool in error

tools_and_job_state_per_month(trans, **kwd)[source]¶

fill tools_and_job_state_per_month.mako template with

the name of the tool
the number of jobs using this tool in state ‘ok’
the number of jobs using this tool in error

galaxy.webapps.reports.controllers.tools.int_to_octet(size)[source]¶

galaxy.webapps.reports.controllers.users module¶

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

Bases: galaxy.webapps.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.legacy_framework.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.legacy_framework.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.legacy_framework.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.legacy_framework.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.legacy_framework.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.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)[source]¶

use_async = False¶

model_class¶: alias of galaxy.model.StoredWorkflow

title = 'Workflows'¶

default_sort_key = 'name'¶

columns = [<galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.WorkflowNameColumn object>, <galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.CreateTimeColumn object>, <galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.UserColumn object>, <galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.SpecifiedDateColumn object>, <galaxy.webapps.reports.controllers.workflows.SpecifiedDateListGrid.EmailColumn object>, <galaxy.web.legacy_framework.grids.MulticolFilterColumn object>]¶

default_filter = {'specified_date': 'All'}¶

num_rows_per_page = 50¶

use_paging = True¶

build_initial_query(trans, **kwd)[source]¶

class galaxy.webapps.reports.controllers.workflows.Workflows(app)[source]¶

Bases: galaxy.webapps.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]¶