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

import calendar
from datetime import datetime, date, timedelta
import logging
from collections import namedtuple
import sqlalchemy as sa
from sqlalchemy import and_
from markupsafe import escape

from galaxy import model, util
from math import floor
from galaxy.web.base.controller import BaseUIController, web
from galaxy.web.framework.helpers import grids
import re
from math import ceil
from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
from galaxy.webapps.reports.controllers.jobs import sorter, get_spark_time

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" template = '/webapps/reports/grid.mako' 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")) standard_filters = [] default_filter = {'specified_date': 'All'} num_rows_per_page = 50 preserve_state = False 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 all_workflows.execute(): 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 q.execute(): 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 all_workflows_per_user.execute(): 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 q.execute(): 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 all_workflows_user_month.execute(): 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 q.execute(): 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 all_runs_per_workflow.execute(): 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 q.execute(): 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))