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Source code for galaxy.webapps.reports.controllers.workflows

import calendar
import logging
import re
from collections import namedtuple
from datetime import (
    date,
    datetime,
    timedelta,
)
from math import (
    ceil,
    floor,
)

import sqlalchemy as sa
from markupsafe import escape
from sqlalchemy import and_

from galaxy import (
    model,
    util,
)
from galaxy.util import UNKNOWN
from galaxy.web.legacy_framework import grids
from galaxy.webapps.base.controller import (
    BaseUIController,
    web,
)
from galaxy.webapps.reports.controllers.jobs import (
    get_spark_time,
    sorter,
)
from galaxy.webapps.reports.controllers.query import ReportQueryBuilder

log = logging.getLogger(__name__)


[docs]class SpecifiedDateListGrid(grids.Grid):
[docs] class WorkflowNameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, stored_workflow): return escape(stored_workflow.name)
[docs] class CreateTimeColumn(grids.DateTimeColumn):
[docs] def get_value(self, trans, grid, stored_workflow): return stored_workflow.create_time
[docs] class UserColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, stored_workflow): if stored_workflow.user: return escape(stored_workflow.user.email) return UNKNOWN
[docs] class EmailColumn(grids.GridColumn):
[docs] def filter(self, trans, user, query, column_filter): if column_filter == "All": return query return query.filter( and_( model.StoredWorkflow.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter, ) )
[docs] class SpecifiedDateColumn(grids.GridColumn):
[docs] def filter(self, trans, user, query, column_filter): if column_filter == "All": return query # We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM, # so we need to figure out which type of date we have if column_filter.count("-") == 2: # We are filtering on a date like YYYY-MM-DD year, month, day = map(int, column_filter.split("-")) start_date = date(year, month, day) end_date = start_date + timedelta(days=1) return query.filter( and_( self.model_class.table.c.create_time >= start_date, self.model_class.table.c.create_time < end_date, ) ) if column_filter.count("-") == 1: # We are filtering on a month like YYYY-MM year, month = map(int, column_filter.split("-")) start_date = date(year, month, 1) end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1]) return query.filter( and_( self.model_class.table.c.create_time >= start_date, self.model_class.table.c.create_time < end_date, ) )
# Grid definition use_async = False model_class = model.StoredWorkflow title = "Workflows" default_sort_key = "name" columns = [ WorkflowNameColumn("Name", key="name", attach_popup=False, filterable="advanced"), CreateTimeColumn("Creation Time", key="create_time", attach_popup=False), UserColumn( "User", key="email", model_class=model.User, link=(lambda item: dict(operation="user_per_month", id=item.id, webapp="reports")), attach_popup=False, ), # Columns that are valid for filtering but are not visible. SpecifiedDateColumn("Specified Date", key="specified_date", visible=False), EmailColumn("Email", key="email", model_class=model.User, visible=False), ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[columns[0], columns[2]], key="free-text-search", visible=False, filterable="standard", ) ) default_filter = {"specified_date": "All"} num_rows_per_page = 50 use_paging = True
[docs] def build_initial_query(self, trans, **kwd): return trans.sa_session.query(self.model_class).join(model.User).enable_eagerloads(False)
[docs]class Workflows(BaseUIController, ReportQueryBuilder): specified_date_list_grid = SpecifiedDateListGrid()
[docs] @web.expose def specified_date_handler(self, trans, **kwd): # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have # to take this approach because the "-" character is illegal in HTTP requests. if "f-specified_date" in kwd and "specified_date" not in kwd: # The user clicked a State link in the Advanced Search box, so 'specified_date' # will have been eliminated. pass elif "specified_date" not in kwd: kwd["f-specified_date"] = "All" else: kwd["f-specified_date"] = kwd["specified_date"] if "operation" in kwd: operation = kwd["operation"].lower() if operation == "workflow_per_month": # The received id is the stored_workflow id. return trans.response.send_redirect( web.url_for(controller="workflows", action="workflow_per_month", **kwd) ) elif operation == "user_per_month": stored_workflow_id = kwd.get("id", None) workflow = get_workflow(trans, stored_workflow_id) if workflow.user: kwd["email"] = workflow.user.email else: kwd["email"] = None # For anonymous users ( shouldn't happen with workflows ) return trans.response.send_redirect(web.url_for(controller="workflows", action="user_per_month", **kwd)) return self.specified_date_list_grid(trans, **kwd)
[docs] @web.expose def per_month_all(self, trans, **kwd): message = "" PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"]) specs = sorter("date", kwd) sort_id = specs.sort_id order = specs.order arrow = specs.arrow _order = specs.exc_order offset = 0 limit = 10 if "entries" in kwd: entries = int(kwd.get("entries")) else: entries = 10 limit = entries * 4 if "offset" in kwd: offset = int(kwd.get("offset")) else: offset = 0 if "page" in kwd: page = int(kwd.get("page")) else: page = 1 q = sa.select( ( self.select_month(model.StoredWorkflow.table.c.create_time).label("date"), sa.func.count(model.StoredWorkflow.table.c.id).label("total_workflows"), ), from_obj=[sa.outerjoin(model.StoredWorkflow.table, model.User.table)], group_by=self.group_by_month(model.StoredWorkflow.table.c.create_time), order_by=[_order], offset=offset, limit=limit, ) all_workflows = sa.select( (self.select_day(model.StoredWorkflow.table.c.create_time).label("date"), model.StoredWorkflow.table.c.id) ) trends = dict() for workflow in trans.sa_session.execute(all_workflows): workflow_day = int(workflow.date.strftime("%-d")) - 1 workflow_month = int(workflow.date.strftime("%-m")) workflow_month_name = workflow.date.strftime("%B") workflow_year = workflow.date.strftime("%Y") key = str(workflow_month_name + workflow_year) try: trends[key][workflow_day] += 1 except KeyError: workflow_year = int(workflow_year) wday, day_range = calendar.monthrange(workflow_year, workflow_month) trends[key] = [0] * day_range trends[key][workflow_day] += 1 workflows = [] for row in trans.sa_session.execute(q): month_name = row.date.strftime("%B") year = int(row.date.strftime("%Y")) workflows.append((row.date.strftime("%Y-%m"), row.total_workflows, month_name, year)) pages_found = ceil(len(workflows) / float(entries)) page_specs = PageSpec(entries, offset, page, pages_found) return trans.fill_template( "/webapps/reports/workflows_per_month_all.mako", order=order, arrow=arrow, sort_id=sort_id, trends=trends, workflows=workflows, message=message, page_specs=page_specs, )
[docs] @web.expose def per_user(self, trans, **kwd): message = "" PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"]) specs = sorter("user_email", kwd) sort_id = specs.sort_id order = specs.order arrow = specs.arrow _order = specs.exc_order time_period = kwd.get("spark_time") time_period, _time_period = get_spark_time(time_period) spark_limit = 30 offset = 0 limit = 10 if "entries" in kwd: entries = int(kwd.get("entries")) else: entries = 10 limit = entries * 4 if "offset" in kwd: offset = int(kwd.get("offset")) else: offset = 0 if "page" in kwd: page = int(kwd.get("page")) else: page = 1 workflows = [] q = sa.select( ( model.User.table.c.email.label("user_email"), sa.func.count(model.StoredWorkflow.table.c.id).label("total_workflows"), ), from_obj=[sa.outerjoin(model.StoredWorkflow.table, model.User.table)], group_by=["user_email"], order_by=[_order], offset=offset, limit=limit, ) all_workflows_per_user = sa.select( ( model.User.table.c.email.label("user_email"), self.select_day(model.StoredWorkflow.table.c.create_time).label("date"), model.StoredWorkflow.table.c.id, ), from_obj=[sa.outerjoin(model.StoredWorkflow.table, model.User.table)], ) currday = datetime.today() trends = dict() for workflow in trans.sa_session.execute(all_workflows_per_user): curr_user = re.sub(r"\W+", "", workflow.user_email) try: day = currday - workflow.date except TypeError: day = datetime.date(currday) - datetime.date(workflow.date) day = day.days container = floor(day / _time_period) container = int(container) try: if container < spark_limit: trends[curr_user][container] += 1 except KeyError: trends[curr_user] = [0] * spark_limit if container < spark_limit: trends[curr_user][container] += 1 for row in trans.sa_session.execute(q): workflows.append((row.user_email, row.total_workflows)) pages_found = ceil(len(workflows) / float(entries)) page_specs = PageSpec(entries, offset, page, pages_found) return trans.fill_template( "/webapps/reports/workflows_per_user.mako", order=order, arrow=arrow, sort_id=sort_id, spark_limit=spark_limit, trends=trends, time_period=time_period, workflows=workflows, message=message, page_specs=page_specs, )
[docs] @web.expose def user_per_month(self, trans, **kwd): params = util.Params(kwd) message = "" specs = sorter("date", kwd) sort_id = specs.sort_id order = specs.order arrow = specs.arrow _order = specs.exc_order email = util.restore_text(params.get("email", "")) user_id = trans.security.decode_id(params.get("id", "")) q = sa.select( ( self.select_month(model.StoredWorkflow.table.c.create_time).label("date"), sa.func.count(model.StoredWorkflow.table.c.id).label("total_workflows"), ), whereclause=model.StoredWorkflow.table.c.user_id == user_id, from_obj=[model.StoredWorkflow.table], group_by=self.group_by_month(model.StoredWorkflow.table.c.create_time), order_by=[_order], ) all_workflows_user_month = sa.select( (self.select_day(model.StoredWorkflow.table.c.create_time).label("date"), model.StoredWorkflow.table.c.id), whereclause=model.StoredWorkflow.table.c.user_id == user_id, from_obj=[model.StoredWorkflow.table], ) trends = dict() for workflow in trans.sa_session.execute(all_workflows_user_month): workflow_day = int(workflow.date.strftime("%-d")) - 1 workflow_month = int(workflow.date.strftime("%-m")) workflow_month_name = workflow.date.strftime("%B") workflow_year = workflow.date.strftime("%Y") key = str(workflow_month_name + workflow_year) try: trends[key][workflow_day] += 1 except KeyError: workflow_year = int(workflow_year) wday, day_range = calendar.monthrange(workflow_year, workflow_month) trends[key] = [0] * day_range trends[key][workflow_day] += 1 workflows = [] for row in trans.sa_session.execute(q): workflows.append( (row.date.strftime("%Y-%m"), row.total_workflows, row.date.strftime("%B"), row.date.strftime("%Y")) ) return trans.fill_template( "/webapps/reports/workflows_user_per_month.mako", email=util.sanitize_text(email), order=order, arrow=arrow, sort_id=sort_id, trends=trends, workflows=workflows, message=message, )
[docs] @web.expose def per_workflow(self, trans, **kwd): message = "" PageSpec = namedtuple("PageSpec", ["entries", "offset", "page", "pages_found"]) specs = sorter("workflow_name", kwd) sort_id = specs.sort_id order = specs.order arrow = specs.arrow _order = specs.exc_order time_period = kwd.get("spark_time") time_period, _time_period = get_spark_time(time_period) spark_limit = 30 offset = 0 limit = 10 if "entries" in kwd: entries = int(kwd.get("entries")) else: entries = 10 limit = entries * 4 if "offset" in kwd: offset = int(kwd.get("offset")) else: offset = 0 if "page" in kwd: page = int(kwd.get("page")) else: page = 1 # In case we don't know which is the monitor user we will query for all jobs q = sa.select( ( model.Workflow.table.c.id.label("workflow_id"), sa.func.min(model.Workflow.table.c.name).label("workflow_name"), sa.func.count(model.WorkflowInvocation.table.c.id).label("total_runs"), ), from_obj=[model.Workflow.table, model.WorkflowInvocation.table], whereclause=sa.and_(model.WorkflowInvocation.table.c.workflow_id == model.Workflow.table.c.id), group_by=[model.Workflow.table.c.id], order_by=[_order], offset=offset, limit=limit, ) all_runs_per_workflow = sa.select( ( model.Workflow.table.c.id.label("workflow_id"), model.Workflow.table.c.name.label("workflow_name"), self.select_day(model.WorkflowInvocation.table.c.create_time).label("date"), ), from_obj=[model.Workflow.table, model.WorkflowInvocation.table], whereclause=sa.and_(model.WorkflowInvocation.table.c.workflow_id == model.Workflow.table.c.id), ) currday = date.today() trends = dict() for run in trans.sa_session.execute(all_runs_per_workflow): curr_tool = re.sub(r"\W+", "", str(run.workflow_id)) try: day = currday - run.date except TypeError: day = currday - datetime.date(run.date) day = day.days container = floor(day / _time_period) container = int(container) try: if container < spark_limit: trends[curr_tool][container] += 1 except KeyError: trends[curr_tool] = [0] * spark_limit if container < spark_limit: trends[curr_tool][container] += 1 runs = [] for row in trans.sa_session.execute(q): runs.append((row.workflow_name, row.total_runs, row.workflow_id)) pages_found = ceil(len(runs) / float(entries)) page_specs = PageSpec(entries, offset, page, pages_found) return trans.fill_template( "/webapps/reports/workflows_per_workflow.mako", order=order, arrow=arrow, sort_id=sort_id, spark_limit=spark_limit, time_period=time_period, trends=trends, runs=runs, message=message, page_specs=page_specs, )
# ---- Utility methods -------------------------------------------------------
[docs]def get_workflow(trans, id): return trans.sa_session.query(trans.model.Workflow).get(trans.security.decode_id(id))