[galaxy-dev] [hg] galaxy 1607: Fix jobs report to display jobs in deleted and...

5 Nov 2008

details:   http://www.bx.psu.edu/hg/galaxy/rev/4e2ad77de095
changeset: 1607:4e2ad77de095
user:      Greg Von Kuster <greg@bx.psu.edu>
date:      Wed Nov 05 10:35:06 2008 -0500
description:
Fix jobs report to display jobs in deleted and waiting states.

10 file(s) affected in this change:

lib/galaxy/jobs/__init__.py
lib/galaxy/webapps/reports/controllers/jobs.py
lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css
lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako
lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako
lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako
lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako
lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako
lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako
lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako

diffs (181 lines):

diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/jobs/__init__.py

--- a/lib/galaxy/jobs/__init__.py	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/jobs/__init__.py	Wed Nov 05 10:35:06 2008 -0500
@@ -403,11 +403,11 @@
             idata.dataset.refresh() #we need to refresh the base Dataset, since that is where 'state' is stored
             # don't run jobs for which the input dataset was deleted
             if idata.deleted:
-                self.fail( "input data %d was deleted before this job started" % idata.hid )
+                self.fail( "input data %d (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) )
                 return JOB_INPUT_DELETED
             # an error in the input data causes us to bail immediately
             elif idata.state == idata.states.ERROR:
-                self.fail( "input data %d is in an error state" % idata.hid )
+                self.fail( "input data %d (file: %s) is in an error state" % ( idata.hid, idata.file_name ) )
                 return JOB_INPUT_ERROR
             elif idata.state != idata.states.OK:
                 # need to requeue
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/controllers/jobs.py
--- a/lib/galaxy/webapps/reports/controllers/jobs.py	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py	Wed Nov 05 10:35:06 2008 -0500
@@ -91,7 +91,8 @@
         year_label = start_date.strftime( "%Y" )
         q = sa.select( ( sa.func.date( galaxy.model.Job.table.c.create_time ).label( 'date' ),
                          sa.func.count( galaxy.model.Job.table.c.id ).label( 'total_jobs' ) ),
-                       whereclause = sa.and_( galaxy.model.Job.table.c.state == 'error', 
+                       whereclause = sa.and_( sa.or_( galaxy.model.Job.table.c.state == 'error', 
+                                                      galaxy.model.Job.table.c.state == 'deleted' ),
                                               galaxy.model.Job.table.c.create_time >= start_date, 
                                               galaxy.model.Job.table.c.create_time < end_date ),
                        from_obj = [ sa.outerjoin( galaxy.model.Job.table, 
@@ -133,7 +134,8 @@
                          galaxy.model.Job.table.c.info,
                          ( galaxy.model.User.table.c.email ).label( 'user_email' ),
                          galaxy.model.GalaxySession.table.c.remote_addr ),
-                       whereclause = sa.and_( galaxy.model.Job.table.c.state == 'error', 
+                       whereclause = sa.and_( sa.or_( galaxy.model.Job.table.c.state == 'error', 
+                                                      galaxy.model.Job.table.c.state == 'deleted' ),
                                               galaxy.model.Job.table.c.create_time >= start_date, 
                                               galaxy.model.Job.table.c.create_time < end_date ),
                        from_obj = [ sa.outerjoin( galaxy.model.Job.table, 
@@ -245,6 +247,7 @@
                          galaxy.model.GalaxySession.table.c.remote_addr ),
                        whereclause = sa.or_( galaxy.model.Job.table.c.state == 'running', 
                                              galaxy.model.Job.table.c.state == 'queued',
+                                             galaxy.model.Job.table.c.state == 'waiting', 
                                              galaxy.model.Job.table.c.state == 'new' ),
                        from_obj = [ sa.outerjoin( galaxy.model.Job.table, 
                                                   galaxy.model.History.table ).outerjoin( galaxy.model.User.table ).outerjoin( galaxy.model.GalaxySession.table,
@@ -297,7 +300,8 @@
         msg = ''
         q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.Job.table.c.create_time ) ).label( 'date' ),
                          sa.func.count( galaxy.model.Job.table.c.id ).label( 'total_jobs' ) ),
-                       whereclause = galaxy.model.Job.table.c.state == 'error', 
+                       whereclause = sa.or_( galaxy.model.Job.table.c.state == 'error', 
+                                             galaxy.model.Job.table.c.state == 'deleted' ),
                        from_obj = [ galaxy.model.Job.table ],
                        group_by = [ sa.func.date_trunc( 'month', sa.func.date( galaxy.model.Job.table.c.create_time ) ) ],
                        order_by = [ sa.desc( 'date' ) ] )
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css
--- a/lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css	Wed Nov 05 10:35:06 2008 -0500
@@ -267,6 +267,14 @@
   border-bottom: solid #d8b365 1px;
   font-weight: bold;
 }
+table.colored tr.headerwaiting
+{ 
+  background: #ebd9b2;
+  background-repeat: repeat-x;
+  background-position: top;
+  border-bottom: solid #d8b365 1px;
+  font-weight: bold;
+}
 table.colored tr.headerqueued
 { 
   background: #ee82ee;
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako	Wed Nov 05 10:35:06 2008 -0500
@@ -17,6 +17,8 @@
             state = job[0]
             if state == 'new':
               rowdef = '<tr class="headernew">'
+            elif state == 'waiting':
+              rowdef = '<tr class="headerwaiting">'
             elif state == 'queued':
               rowdef = '<tr class="headerqueued">'
             elif state == 'running':
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako	Wed Nov 05 10:35:06 2008 -0500
@@ -2,7 +2,7 @@
 
 <%def name="main_body()">
   <div class="reportBody">
-    <h3 align="center">Jobs In Error Per Month</h3>
+    <h3 align="center">Jobs In Error Per Month ( includes jobs deleted before finishing )</h3>
     <h4 align="center">Click Month to view the number of jobs in error for each day of that month</h4>
     %if msg:
       <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5">
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako	Wed Nov 05 10:35:06 2008 -0500
@@ -17,11 +17,15 @@
             state = job[0]
             if state == 'new':
               rowdef = '<tr class="headernew">'
+            elif state == 'waiting':
+              rowdef = '<tr class="headerwaiting">'
             elif state == 'queued':
               rowdef = '<tr class="headerqueued">'
             elif state == 'running':
               rowdef = '<tr class="headerrunning">'
             elif state == 'error':
+              rowdef = '<tr class="headererror">'
+            elif state == 'deleted':
               rowdef = '<tr class="headererror">'
             elif state == 'ok':
               rowdef = '<tr class="headerok">'
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako	Wed Nov 05 10:35:06 2008 -0500
@@ -2,7 +2,7 @@
 
 <%def name="main_body()">
   <div class="reportBody">
-    <h3 align="center">All Jobs in Error for ${day_label}, ${month_label} ${day_of_month}, ${year_label}</h3>
+    <h3 align="center">All Jobs in Error for ${day_label}, ${month_label} ${day_of_month}, ${year_label} ( includes jobs deleted before finishing )</h3>
     %if msg:
       <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5">
         <tr><td class="ok_bgr">${msg}</td></tr>
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako	Wed Nov 05 10:35:06 2008 -0500
@@ -2,7 +2,7 @@
 
 <%def name="main_body()">
   <div class="reportBody">
-    <h3 align="center">Jobs in Error for ${month_label} ${year_label}</h3>
+    <h3 align="center">Jobs in Error for ${month_label} ${year_label} ( includes jobs deleted before finishing )</h3>
     <h4 align="center">Click Jobs in Error to view jobs in error for that day</h4>
     %if msg:
       <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5">
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako	Wed Nov 05 10:35:06 2008 -0500
@@ -17,11 +17,15 @@
             state = job[0]
             if state == 'new':
               rowdef = '<tr class="headernew">'
+            elif state == 'waiting':
+              rowdef = '<tr class="headerwaiting">'
             elif state == 'queued':
               rowdef = '<tr class="headerqueued">'
             elif state == 'running':
               rowdef = '<tr class="headerrunning">'
             elif state == 'error':
+              rowdef = '<tr class="headererror">'
+            elif state == 'deleted':
               rowdef = '<tr class="headererror">'
             elif state == 'ok':
               rowdef = '<tr class="headerok">'
diff -r 72252f33edd1 -r 4e2ad77de095 lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako
--- a/lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako	Wed Nov 05 09:28:48 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako	Wed Nov 05 10:35:06 2008 -0500
@@ -17,11 +17,15 @@
             state = job[0]
             if state == 'new':
               rowdef = '<tr class="headernew">'
+            elif state == 'waiting':
+              rowdef = '<tr class="headerwaiting">'
             elif state == 'queued':
               rowdef = '<tr class="headerqueued">'
             elif state == 'running':
               rowdef = '<tr class="headerrunning">'
             elif state == 'error':
+              rowdef = '<tr class="headererror">'
+            elif state == 'deleted':
               rowdef = '<tr class="headererror">'
             elif state == 'ok':
               rowdef = '<tr class="headerok">'

    