Fix where days/weeks/... reverted to days when sorting columns.

Refactored time_period code into function.
Applied sparklines to workflows pages.

lib/galaxy/webapps/reports/controllers/jobs.py

@@ -52,6 +52,22 @@ def sorter(default_sort_id, kwd):
 
     return SortSpec(sort_id, order, arrow, _order)
 
+def get_spark_time( time_period ):
+    _time_period = 0
+
+    if time_period == "days":
+        _time_period = 1.0
+    elif time_period == "weeks":
+        _time_period = 7.0
+    elif time_period == "months":
+        _time_period = 30.0
+    elif time_period == "years":
+        _time_period = 365.0
+    else:
+        time_period = "days"
+        _time_period = 1.0
+
+    return time_period, _time_period
 
 class SpecifiedDateListGrid( grids.Grid ):
 
@@ -454,10 +470,8 @@ def per_month_all( self, trans, **kwd ):
 
         jobs = []
         for row in jobs_by_month.execute():
-            month = int(row.date.strftime("%-m"))
             month_name = row.date.strftime("%B")
             year = int(row.date.strftime("%Y"))
-            wday, day_range = calendar.monthrange(year, month)
 
             jobs.append( (
                 row.date.strftime( "%Y-%m" ),
@@ -557,17 +571,7 @@ def per_user( self, trans, **kwd ):
         arrow = specs.arrow
         _order = specs.exc_order
         time_period = kwd.get('spark_time')
-        if time_period == "days":
-            _time_period = 1.0
-        elif time_period == "weeks":
-            _time_period = 7.0
-        elif time_period == "months":
-            _time_period = 30.0
-        elif time_period == "years":
-            _time_period = 365.0
-        else:
-            time_period = "days"
-            _time_period = 1.0
+        time_period, _time_period = get_spark_time( time_period )
         limit = 30
 
         jobs = []
@@ -689,18 +693,7 @@ def per_tool( self, trans, **kwd ):
         arrow = specs.arrow
         _order = specs.exc_order
         time_period = kwd.get('spark_time')
-        if time_period == "days":
-            _time_period = 1.0
-        elif time_period == "weeks":
-            _time_period = 7.0
-        elif time_period == "months":
-            _time_period = 30.0
-        elif time_period == "years":
-            _time_period = 365.0
-        else:
-            time_period = "days"
-            _time_period = 1.0
-
+        time_period, _time_period = get_spark_time( time_period )
         limit = 30
 
         # In case we don't know which is the monitor user we will query for all jobs
@@ -770,19 +763,9 @@ def errors_per_tool( self, trans, **kwd ):
         arrow = specs.arrow
         _order = specs.exc_order
         time_period = kwd.get('spark_time')
-        if time_period == "days":
-            _time_period = 1.0
-        elif time_period == "weeks":
-            _time_period = 7.0
-        elif time_period == "months":
-            _time_period = 30.0
-        elif time_period == "years":
-            _time_period = 365.0
-        else:
-            time_period = "days"
-            _time_period = 1.0
-
+        time_period, _time_period = get_spark_time( time_period )
         limit = 30
+
         # In case we don't know which is the monitor user we will query for all jobs
         monitor_user_id = get_monitor_id( trans, monitor_email )
 

lib/galaxy/webapps/reports/controllers/workflows.py

@@ -1,14 +1,16 @@
 import calendar
-from datetime import date, timedelta
+from datetime import datetime, date, timedelta
 from galaxy import eggs
 from galaxy import model, util
 from galaxy.model.orm import and_
+from math import floor
 from galaxy.web.base.controller import BaseUIController, web
 from galaxy.web.framework.helpers import grids
 eggs.require( "SQLAlchemy >= 0.4" )
+import re
 import sqlalchemy as sa
 from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
-from galaxy.webapps.reports.controllers.jobs import sorter
+from galaxy.webapps.reports.controllers.jobs import sorter, get_spark_time
 
 import logging
 log = logging.getLogger( __name__ )
@@ -152,20 +154,46 @@ def per_month_all( self, trans, **kwd ):
         order = specs.order
         arrow = specs.arrow
         _order = specs.exc_order
-        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' ) ),
+
+        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 ] )
+
+        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,
-                                row.date.strftime( "%B" ),
-                                row.date.strftime( "%Y" ) ) )
+                                month_name,
+                                year ) )
         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 )
 
@@ -177,19 +205,52 @@ def per_user( self, trans, **kwd ):
         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 )
+        limit=30
+
         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 ] )
+
+        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 < limit:
+                    trends[curr_user][container] += 1
+            except KeyError:
+                trends[curr_user] = [0] * limit
+                if container < limit:
+                    trends[curr_user][container] += 1
+
         for row in q.execute():
             workflows.append( ( row.user_email,
                                 row.total_workflows ) )
         return trans.fill_template( '/webapps/reports/workflows_per_user.mako',
                                     order=order,
                                     arrow=arrow,
                                     sort_id=sort_id,
+                                    limit=limit,
+                                    trends=trends,
+                                    time_period=time_period,
                                     workflows=workflows,
                                     message=message )
 
@@ -204,12 +265,35 @@ def user_per_month( self, trans, **kwd ):
         _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" ),
@@ -221,6 +305,7 @@ def user_per_month( self, trans, **kwd ):
                                     order=order,
                                     arrow=arrow,
                                     sort_id=sort_id,
+                                    trends=trends,
                                     workflows=workflows,
                                     message=message )
 

templates/webapps/reports/index.mako

@@ -53,7 +53,7 @@
                         <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_month_in_error', sort_id='default', order='default' )}">Jobs in error per month</a></div>
                         <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_user', sort_id='default', order='default' )}">Jobs per user</a></div>
                         <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='per_tool', sort_id='default', order='default' )}">Jobs per tool</a></div>
-                        <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='errors_per_tool', sort_id='default', order='default')}">Errors per tool</a></div>
+                        <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='jobs', action='errors_per_tool', sort_id='default', order='default', spark_time='')}">Errors per tool</a></div>
                     </div>
                 </div>
                 <div class="toolSectionPad"></div>

templates/webapps/reports/jobs_errors_per_tool.mako

@@ -28,17 +28,17 @@ ${get_css()}
             %else:
                 <tr class="header">
                     <td>
-                        ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'errors_per_tool', 'Tool ID')}
+                        ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'errors_per_tool', 'Tool ID', spark_time=time_period)}
                         <span class='dir_arrow tool_id'>${arrow}</span>
                     </td>
                     %if is_user_jobs_only:
     					<td>
-                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User Jobs in Error')}
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User Jobs in Error', spark_time=time_period)}
                             <span class='dir_arrow total_jobs'>${arrow}</span>
                         </td>
 					%else:
 	                    <td>
-                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User and Monitor Jobs in Error')}
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User and Monitor Jobs in Error', spark_time=time_period)}
                             <span class='dir_arrow total_jobs'>${arrow}</span>
                         </td>
 	                %endif

templates/webapps/reports/jobs_per_tool.mako

@@ -27,17 +27,17 @@ ${get_css()}
             %else:
                 <tr class="header">
                     <td>
-                        ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'per_tool', 'Tool ID')}
+                        ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'per_tool', 'Tool ID', spark_time=time_period)}
                         <span class='dir_arrow tool_id'>${arrow}</span>
                     </td>
                     %if is_user_jobs_only:
                         <td>
-                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User Jobs')}
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User Jobs', spark_time=time_period)}
                             <span class='dir_arrow total_jobs'>${arrow}</span>
                         </td>
 					%else:
                         <td>
-                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User and Monitor Jobs')}
+                            ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User and Monitor Jobs', spark_time=time_period)}
                             <span class='dir_arrow total_jobs'>${arrow}</span>
                         </td>
 	                %endif

templates/webapps/reports/jobs_per_user.mako

@@ -27,11 +27,11 @@ ${get_css()}
             %else:
                 <tr class="header">
                     <td>
-                        ${get_sort_url(sort_id, order, 'user_email', 'jobs', 'per_user', 'User')}
+                        ${get_sort_url(sort_id, order, 'user_email', 'jobs', 'per_user', 'User', spark_time=time_period)}
                         <span class='dir_arrow user_email'>${arrow}</span>
                     </td>
                     <td>
-                        ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_user', 'Total Jobs')}
+                        ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_user', 'Total Jobs', spark_time=time_period)}
                         <span class='dir_arrow total_jobs'>${arrow}</span>
                     </td>
                 </tr>

templates/webapps/reports/jobs_user_per_month.mako

@@ -3,7 +3,9 @@
 <%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" />
 <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" />
 
-<% from galaxy import util %>
+<% 
+   from galaxy import util 
+%>
 
 %if message:
     ${render_msg( message, 'done' )}

templates/webapps/reports/workflows_per_month_all.mako

@@ -1,11 +1,14 @@
 <%inherit file="/base.mako"/>
 <%namespace file="/message.mako" import="render_msg" />
 <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" />
+<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" />
 
 %if message:
     ${render_msg( message, 'done' )}
 %endif
 
+${spark_css()}
+${jqs_style()}
 ${get_css()}
 
 <div class="toolForm">
@@ -27,6 +30,7 @@ ${get_css()}
                 </tr>
                 <% ctr = 0 %>
                 %for workflow in workflows:
+                    <% key = str(workflow[2]) + str(workflow[3]) %>
                     <%
                         month = workflow[0]
                         total = workflow[1]
@@ -38,6 +42,11 @@ ${get_css()}
                     %endif
                         <td>${month}</td>
                         <td>${total}</td>
+                        %try:
+                            ${make_sparkline(key, trends[key], "bar", "/ day")}
+                        %except KeyError:
+                        %endtry
+                        <td id=${key}></td>
                     </tr>
                     <% ctr += 1 %>
                 %endfor