Script to fetch gops jobs that might have produced incorrect/empty oUtput due to the bug in BitsetSafeReaderWrapper.

2026-09-24 16:30:27 +08:00 · 2008-11-11 15:20:36 -05:00
parent fe0c619856
commit 2f5e0c58ae
2 changed files with 84 additions and 0 deletions
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+"""
+Fetch jobs using gops_intersect, gops_merge, gops_subtract, gops_complement, gops_coverage wherein the second dataset doesn't have chr, start and end in standard columns 1,2 and 3.
+"""
+
+from galaxy import eggs
+import sys, os, ConfigParser
+import galaxy.app
+#from galaxy.util.bunch import Bunch
+
+import galaxy.model.mapping
+import pkg_resources
+        
+pkg_resources.require( "SQLAlchemy >= 0.4" )
+import sqlalchemy as sa
+#from sqlalchemy.orm import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+class TestApplication( object ):
+    """Encapsulates the state of a Universe application"""
+    def __init__( self, database_connection=None, file_path=None ):
+        print >> sys.stderr, "python path is: " + ", ".join( sys.path )
+        if database_connection is None:
+            raise Exception( "CleanupDatasetsApplication requires a database_connection value" )
+        if file_path is None:
+            raise Exception( "CleanupDatasetsApplication requires a file_path value" )
+        self.database_connection = database_connection
+        self.file_path = file_path
+        # Setup the database engine and ORM
+        self.model = galaxy.model.mapping.init( self.file_path, self.database_connection, engine_options={}, create_tables=False )
+
+def main():
+    ini_file = sys.argv[1]
+    conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
+    conf_parser.read( ini_file )
+    configuration = {}
+    for key, value in conf_parser.items( "app:main" ):
+        configuration[key] = value
+    database_connection = configuration['database_connection']
+    file_path = configuration['file_path']
+    app = TestApplication( database_connection=database_connection, file_path=file_path )
+    jobs = {}
+    for job in app.model.Job.filter(
+        sa.and_(
+             app.model.Job.table.c.create_time.between('2008-05-23','2008-11-29'),
+             app.model.Job.table.c.state == 'ok',
+             sa.or_(app.model.Job.table.c.tool_id == 'gops_intersect_1',
+                 app.model.Job.table.c.tool_id == 'gops_subtract_1',
+                 app.model.Job.table.c.tool_id == 'gops_merge_1',
+                 app.model.Job.table.c.tool_id == 'gops_coverage_1',
+                 app.model.Job.table.c.tool_id == 'gops_complement_1',
+                ),
+             sa.not_(app.model.Job.table.c.command_line.like('%-2 1,2,3%'))
+            )).all():
+	for od in job.output_datasets:
+            ds = app.model.Dataset.get(od.dataset_id)
+            if not ds.deleted:
+                hda = app.model.HistoryDatasetAssociation.filter(app.model.HistoryDatasetAssociation.table.c.dataset_id == ds.id)[0]
+                hist = app.model.History.get(hda.history_id)
+                if hist.user_id:
+                    user = app.model.User.get(hist.user_id)
+                    jobs[job.id] = {}
+                    jobs[job.id]['dataset_id'] = ds.id
+                    jobs[job.id]['dataset_create_time'] = ds.create_time 
+                    jobs[job.id]['dataset_name'] = hda.name 
+                    jobs[job.id]['hda_id'] = hda.id 
+                    jobs[job.id]['hist_id'] = hist.id 
+                    jobs[job.id]['hist_name'] = hist.name 
+                    jobs[job.id]['hist_modified_time'] = hist.update_time
+		    jobs[job.id]['user_email'] = user.email 
+    
+    print "Number of Incorrect Jobs: %d\n"%(len(jobs))
+    print "#job_id\tdataset_id\tdataset_create_time\thda_id\thistory_id\thistory_name\thistory_modified_time\tuser_email"
+    for jid in jobs:
+        print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %(jid,jobs[jid]['dataset_id'],jobs[jid]['dataset_create_time'],jobs[jid]['dataset_name'],jobs[jid]['hda_id'],jobs[jid]['hist_id'],jobs[jid]['hist_name'],jobs[jid]['hist_modified_time'],jobs[jid]['user_email'] )
+    sys.exit(0)
+
+if __name__ == "__main__":
+    main()
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+cd `dirname $0`/../..
+python ./scripts/others/incorrect_gops_jobs.py ./universe_wsgi.ini