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galaxy.webapps.reports.controllers package

Galaxy reports controllers.

Submodules

galaxy.webapps.reports.controllers.history module

galaxy.webapps.reports.controllers.history.int_to_octet(size)

class galaxy.webapps.reports.controllers.history.History(app)

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)

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)

fill history_and_dataset_type.mako template with:

• the name of history

• the number of dataset foreach type

galaxy.webapps.reports.controllers.home module

class galaxy.webapps.reports.controllers.home.HomePage(app)

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

run_stats(trans, **kwd)

galaxy.webapps.reports.controllers.jobs module

class galaxy.webapps.reports.controllers.jobs.Timer

Bases: object

__init__()

start()

stop()

time_elapsed()

galaxy.webapps.reports.controllers.jobs.sorter(default_sort_id, kwd)

Initialize sorting variables

galaxy.webapps.reports.controllers.jobs.get_spark_time(time_period)

galaxy.webapps.reports.controllers.jobs.get_curr_item(check_item, unique_items)

When rendering by item and destination_id, render the item uniquely.

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

Bases: galaxy.web.legacy_framework.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)

Bases: galaxy.web.legacy_framework.grids.IntegerColumn

get_value(trans, grid, job)

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)

Bases: galaxy.web.legacy_framework.grids.TextColumn

get_value(trans, grid, job)

filter(trans, user, query, column_filter)

Modify query to filter using free text, case independence.

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)

Bases: galaxy.web.legacy_framework.grids.TextColumn

get_value(trans, grid, job)

filter(trans, user, query, column_filter)

Modify query to filter using free text, case independence.

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)

Bases: galaxy.web.legacy_framework.grids.DateTimeColumn

get_value(trans, grid, job)

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)

Bases: galaxy.web.legacy_framework.grids.GridColumn

get_value(trans, grid, job)

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)

Bases: galaxy.web.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)

Modify query to reflect the column filter.

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)

Bases: galaxy.web.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)

Modify query to reflect the column filter.

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)

Bases: galaxy.web.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)

Modify query to reflect the column filter.

use_async = False

model_class

alias of galaxy.model.Job

title = 'Jobs'

default_sort_key: Optional[str] = 'id'

columns: List[galaxy.web.legacy_framework.grids.GridColumn] = [<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: Dict[str, str] = {'specified_date': 'All'}

num_rows_per_page = 50

use_paging = True

build_initial_query(trans, **kwd)

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

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.

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

specified_date_handler(trans, **kwd)

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.

per_month_all(trans, **kwd)

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)

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

per_user(trans, **kwd)

Queries the DB for jobs per user. The by_destination param will group by Job.destination_id.

user_per_month(trans, **kwd)

Queries the DB for jobs per user per month. The by_destination param will group by Job.destination_id.

per_tool(trans, **kwd)

errors_per_tool(trans, **kwd)

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

tool_per_month(trans, **kwd)

job_info(trans, **kwd)

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.

galaxy.webapps.reports.controllers.query module

Mixin to help build advanced queries for reports interface.

class galaxy.webapps.reports.controllers.query.ReportQueryBuilder

Bases: object

group_by_month(column)

select_month(column)

group_by_day(column)

select_day(column)

galaxy.webapps.reports.controllers.root module

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

Bases: galaxy.webapps.base.controller.BaseUIController

index(trans, **kwd)

galaxy.webapps.reports.controllers.system module

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

Bases: galaxy.webapps.base.controller.BaseUIController

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.

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.

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.

dataset_info(trans, **kwd)

get_disk_usage(file_path)

disk_usage(trans, **kwd)

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

Returns a readably formatted string with the size

galaxy.webapps.reports.controllers.tools module

galaxy.webapps.reports.controllers.tools.int_to_octet(size)

class galaxy.webapps.reports.controllers.tools.Tools(app)

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)

tools_and_job_state(trans, **kwd)

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)

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

tool_execution_time(trans, **kwd)

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)

Fill the template tool_execution_time_per_month.mako with informations:

• Tool average execution time

• last job execution time

• min and max execution time

tool_error_messages(trans, **kwd)

galaxy.webapps.reports.controllers.users module

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

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

registered_users(trans, **kwd)

registered_users_per_month(trans, **kwd)

specified_month(trans, **kwd)

specified_date(trans, **kwd)

last_access_date(trans, **kwd)

user_disk_usage(trans, **kwd)

history_per_user(trans, **kwd)

galaxy.webapps.reports.controllers.workflows module

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

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)

Bases: galaxy.web.legacy_framework.grids.TextColumn

get_value(trans, grid, stored_workflow)

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)

Bases: galaxy.web.legacy_framework.grids.DateTimeColumn

get_value(trans, grid, stored_workflow)

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)

Bases: galaxy.web.legacy_framework.grids.TextColumn

get_value(trans, grid, stored_workflow)

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)

Bases: galaxy.web.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)

Modify query to reflect the column filter.

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)

Bases: galaxy.web.legacy_framework.grids.GridColumn

filter(trans, user, query, column_filter)

Modify query to reflect the column filter.

use_async = False

model_class

alias of galaxy.model.StoredWorkflow

title = 'Workflows'

default_sort_key: Optional[str] = 'name'

columns: List[galaxy.web.legacy_framework.grids.GridColumn] = [<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: Dict[str, str] = {'specified_date': 'All'}

num_rows_per_page = 50

use_paging = True

build_initial_query(trans, **kwd)

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

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)

per_month_all(trans, **kwd)

per_user(trans, **kwd)

user_per_month(trans, **kwd)

per_workflow(trans, **kwd)

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