[hg] galaxy 1637: Fix job recovery
by Nate Coraor
details: http://www.bx.psu.edu/hg/galaxy/rev/c141cb89aa45
changeset: 1637:c141cb89aa45
user: Nate Coraor <nate(a)bx.psu.edu>
date: Thu Nov 20 16:15:39 2008 -0500
description:
Fix job recovery
2 file(s) affected in this change:
lib/galaxy/jobs/__init__.py
universe_wsgi.ini.sample
diffs (27 lines):
diff -r 8412e0cbe7f0 -r c141cb89aa45 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py Tue Nov 18 16:04:41 2008 -0500
+++ b/lib/galaxy/jobs/__init__.py Thu Nov 20 16:15:39 2008 -0500
@@ -107,7 +107,7 @@
self.monitor_thread = threading.Thread( target=self.monitor )
self.monitor_thread.start()
log.info( "job manager started" )
- if self.track_jobs_in_database:
+ if app.config.get_bool( 'enable_job_recovery', True ):
self.check_jobs_at_startup()
def check_jobs_at_startup( self ):
diff -r 8412e0cbe7f0 -r c141cb89aa45 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample Tue Nov 18 16:04:41 2008 -0500
+++ b/universe_wsgi.ini.sample Thu Nov 20 16:15:39 2008 -0500
@@ -24,6 +24,11 @@
# Should jobs be tracked through the database, rather than in memory
## track_jobs_in_database = true
+
+# Enable job recovery (if Galaxy is restarted while cluster jobs are running,
+# it can "recover" them when it starts). This is not safe to use if you are
+# running more than one Galaxy server using the same database.
+#enable_job_recovery = True
# Number of concurrent jobs to run (local runner)
local_job_queue_workers = 5
10 years, 12 months
Galaxy question
by Fu, Yi-Ping
Hi,
I just learned Galaxy in this ASHG meeting, but I wonder how I can use
my own plink-format binary data. The tool side from
http://main.g2.bx.psu.edu/ does not look like the one we had in class,
and it keeps giving me error if I try to upload my *.bed data.
Also, I would suggest Galaxy to provide a pdf manual to look things up,
just like all the other genetic program/software. The screencasts takes
too much time.
Many thanks in advance!
Regards,
Yi-Ping
------------------------------------------------------------------------
------
Yi-Ping Fu, MS, PhD candidate
Human Genetics Center
School of Public Health
The University of Texas Health Science Center at Houston
1200 Hermann Pressler, Suite RAS-E427
Houston TX 77030
Office: 713-500-9898
Fax: 713-500-0900
10 years, 12 months
[hg] galaxy 1634: (no commit message)
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/ad26fd305881
changeset: 1634:ad26fd305881
user: wychung
date: Tue Nov 18 11:23:09 2008 -0500
description:
(no commit message)
3 file(s) affected in this change:
lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
tools/fasta_tools/fasta_compute_length.py
tools/fasta_tools/fasta_to_tabular.py
diffs (36 lines):
diff -r 950a71339420 -r ad26fd305881 lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py Fri Nov 14 13:21:02 2008 -0500
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py Tue Nov 18 11:23:09 2008 -0500
@@ -27,7 +27,7 @@
else:
if line:
sequence += line
- if line.split()[0].isdigit():
+ if line.split() and line.split()[0].isdigit():
sequence += ' '
if sequence:
seq_hash[( sequence_count, title )] = sequence
diff -r 950a71339420 -r ad26fd305881 tools/fasta_tools/fasta_compute_length.py
--- a/tools/fasta_tools/fasta_compute_length.py Fri Nov 14 13:21:02 2008 -0500
+++ b/tools/fasta_tools/fasta_compute_length.py Tue Nov 18 11:23:09 2008 -0500
@@ -34,7 +34,7 @@
tmp_seq = ''
else:
tmp_seq = "%s%s" % ( tmp_seq, line )
- if line.split()[0].isdigit():
+ if line.split() and line.split()[0].isdigit():
tmp_seq = "%s " % tmp_seq
if len( tmp_seq ) > 0:
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
diff -r 950a71339420 -r ad26fd305881 tools/fasta_tools/fasta_to_tabular.py
--- a/tools/fasta_tools/fasta_to_tabular.py Fri Nov 14 13:21:02 2008 -0500
+++ b/tools/fasta_tools/fasta_to_tabular.py Tue Nov 18 11:23:09 2008 -0500
@@ -35,7 +35,7 @@
sequence = ''
else:
sequence = "%s%s" % ( sequence, line )
- if line.split()[0].isdigit():
+ if line.split() and line.split()[0].isdigit():
sequence += ' '
if sequence:
seq_hash[( sequence_count, title )] = sequence
10 years, 12 months
[hg] galaxy 1636: bugfix to last commit
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/8412e0cbe7f0
changeset: 1636:8412e0cbe7f0
user: James Taylor <james(a)jamestaylor.org>
date: Tue Nov 18 16:04:41 2008 -0500
description:
bugfix to last commit
1 file(s) affected in this change:
lib/galaxy/model/custom_types.py
diffs (13 lines):
diff -r 2302d3914843 -r 8412e0cbe7f0 lib/galaxy/model/custom_types.py
--- a/lib/galaxy/model/custom_types.py Tue Nov 18 15:47:13 2008 -0500
+++ b/lib/galaxy/model/custom_types.py Tue Nov 18 16:04:41 2008 -0500
@@ -32,6 +32,9 @@
def compare_values( self, x, y ):
return json_encoder.encode( x ) == json_encoder.encode( y )
+
+ def is_mutable( self ):
+ return True
metadata_pickler = AliasPickleModule( {
( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" )
10 years, 12 months
[hg] galaxy 1635: Always write keys in order when creating json ...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/2302d3914843
changeset: 1635:2302d3914843
user: James Taylor <james(a)jamestaylor.org>
date: Tue Nov 18 15:47:13 2008 -0500
description:
Always write keys in order when creating json strings. Also removed a bunch of unused stuff from JSONType -- if you don't need it...
1 file(s) affected in this change:
lib/galaxy/model/custom_types.py
diffs (89 lines):
diff -r ad26fd305881 -r 2302d3914843 lib/galaxy/model/custom_types.py
--- a/lib/galaxy/model/custom_types.py Tue Nov 18 11:23:09 2008 -0500
+++ b/lib/galaxy/model/custom_types.py Tue Nov 18 15:47:13 2008 -0500
@@ -6,6 +6,10 @@
from galaxy.util.bunch import Bunch
from galaxy.util.aliaspickler import AliasPickleModule
+# Default JSON encoder and decoder
+json_encoder = simplejson.JSONEncoder( sort_keys=True )
+json_decoder = simplejson.JSONDecoder( )
+
class JSONType( TypeDecorator ):
"""
Defines a JSONType for SQLAlchemy. Takes a primitive as input and
@@ -13,63 +17,42 @@
"""
impl = Binary
- def __init__( self, jsonifyer=None, mutable=True ):
- self.jsonifyer = jsonifyer or simplejson
- self.mutable = mutable
- super( JSONType, self).__init__()
-
def process_bind_param( self, value, dialect ):
if value is None:
return None
- return self.jsonifyer.dumps( value )
+ return json_encoder.encode( value )
def process_result_value( self, value, dialect ):
if value is None:
return None
- return self.jsonifyer.loads( str( value ) )
+ return json_decoder.decode( str( value ) )
def copy_value( self, value ):
- if self.mutable:
- return self.jsonifyer.loads( self.jsonifyer.dumps(value) )
- else:
- return value
+ return json_decoder.decode( json_encoder.encode( value ) )
def compare_values( self, x, y ):
- if self.mutable:
- return self.jsonifyer.dumps( x ) == self.jsonifyer.dumps( y )
- else:
- return x is y
+ return json_encoder.encode( x ) == json_encoder.encode( y )
- def is_mutable( self ):
- return self.mutable
-
-MetadataPickler = AliasPickleModule( {
+metadata_pickler = AliasPickleModule( {
( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" )
} )
class MetadataType( JSONType ):
"""
- Mixture between JSONType and PickleType...can read in either, and
- writes JSON.
+ Backward compatible metadata type. Can read pickles or JSON, but always
+ writes in JSON.
"""
-
- def __init__( self, pickler=MetadataPickler, jsonifyer=None, mutable=True ):
- self.jsonifyer = jsonifyer or simplejson
- self.pickler = pickler or pickle
- self.mutable = mutable
- super( MetadataType, self).__init__()
-
def process_result_value( self, value, dialect ):
if value is None:
return None
- buf = value
ret = None
try:
- ret = self.pickler.loads( str(buf) )
- if ret: ret = dict( ret.__dict__ )
+ ret = metadata_pickler.loads( str( value ) )
+ if ret:
+ ret = dict( ret.__dict__ )
except:
try:
- ret = self.jsonifyer.loads( str(buf) )
+ ret = json_decoder.decode( str( value ) )
except:
ret = None
return ret
10 years, 12 months
[hg] galaxy 1633: update poisson test tool for R warnings.
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/950a71339420
changeset: 1633:950a71339420
user: wychung
date: Fri Nov 14 13:21:02 2008 -0500
description:
update poisson test tool for R warnings.
2 file(s) affected in this change:
tools/taxonomy/poisson2test.py
tools/taxonomy/poisson2test.xml
diffs (40 lines):
diff -r a5ec5ab6144b -r 950a71339420 tools/taxonomy/poisson2test.py
--- a/tools/taxonomy/poisson2test.py Thu Nov 13 19:19:03 2008 -0500
+++ b/tools/taxonomy/poisson2test.py Fri Nov 14 13:21:02 2008 -0500
@@ -5,7 +5,7 @@
from rpy import *
-if ((len(sys.argv)-1) != 5):
+if ((len(sys.argv)-1) != 6):
print 'too few parameters'
print 'usage: inputfile, col1, col2, d-value(not 0), p-val correction method(0 or 1)'
sys.exit()
@@ -21,6 +21,7 @@
j = int(sys.argv[3]) #second colum to compare
d = float(sys.argv[4]) #correction factor
k = int(sys.argv[5]) #p-val correction method
+ outfile = open(sys.argv[6],'w') # output data
if (i>j):
print 'column order not correct col1 < col2'
@@ -114,7 +115,7 @@
#printing all columns
for n in range(fsize):
- print "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n])
+ print >> outfile, "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n])
diff -r a5ec5ab6144b -r 950a71339420 tools/taxonomy/poisson2test.xml
--- a/tools/taxonomy/poisson2test.xml Thu Nov 13 19:19:03 2008 -0500
+++ b/tools/taxonomy/poisson2test.xml Fri Nov 14 13:21:02 2008 -0500
@@ -1,6 +1,6 @@
<tool id="poisson2test" name="Poisson two-sample test" version="1.0.0">
<description></description>
- <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 > $output1 </command>
+ <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 $output1 2>/dev/null </command>
<inputs>
<param name="input1" format="tabular" type="data" label="Input File"/>
<param name="input2" type="integer" size="5" value="2" label="First Column"/>
10 years, 12 months
[hg] galaxy 1632: Some job runner fixes.
by Nate Coraor
details: http://www.bx.psu.edu/hg/galaxy/rev/a5ec5ab6144b
changeset: 1632:a5ec5ab6144b
user: Nate Coraor <nate(a)bx.psu.edu>
date: Thu Nov 13 19:19:03 2008 -0500
description:
Some job runner fixes.
2 file(s) affected in this change:
lib/galaxy/jobs/__init__.py
lib/galaxy/jobs/runners/pbs.py
diffs (37 lines):
diff -r a39afe99b3bd -r a5ec5ab6144b lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py Thu Nov 13 15:17:42 2008 -0500
+++ b/lib/galaxy/jobs/__init__.py Thu Nov 13 19:19:03 2008 -0500
@@ -64,7 +64,7 @@
"""Start the job manager"""
self.app = app
# Should we use IPC to communicate (needed if forking)
- self.track_jobs_in_database = app.config.get( 'track_jobs_in_database', False )
+ self.track_jobs_in_database = app.config.get_bool( 'track_jobs_in_database', False )
# Check if any special scheduling policy should be used. If not, default is FIFO.
sched_policy = app.config.get('job_scheduler_policy', 'FIFO')
@@ -107,7 +107,8 @@
self.monitor_thread = threading.Thread( target=self.monitor )
self.monitor_thread.start()
log.info( "job manager started" )
- self.check_jobs_at_startup()
+ if self.track_jobs_in_database:
+ self.check_jobs_at_startup()
def check_jobs_at_startup( self ):
"""
diff -r a39afe99b3bd -r a5ec5ab6144b lib/galaxy/jobs/runners/pbs.py
--- a/lib/galaxy/jobs/runners/pbs.py Thu Nov 13 15:17:42 2008 -0500
+++ b/lib/galaxy/jobs/runners/pbs.py Thu Nov 13 19:19:03 2008 -0500
@@ -267,7 +267,10 @@
except Empty:
pass
# Iterate over the list of watched jobs and check state
- self.check_watched_items()
+ try:
+ self.check_watched_items()
+ except:
+ log.exception( "Uncaught exception checking jobs" )
# Sleep a bit before the next state check
time.sleep( 1 )
11 years
[hg] galaxy 1631: Missed translating the primaryTable data type ...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/a39afe99b3bd
changeset: 1631:a39afe99b3bd
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Thu Nov 13 15:17:42 2008 -0500
description:
Missed translating the primaryTable data type from UCSC in my last commit.
3 file(s) affected in this change:
tools/data_source/ucsc_tablebrowser.xml
tools/data_source/ucsc_tablebrowser_archaea.xml
tools/data_source/ucsc_tablebrowser_test.xml
diffs (33 lines):
diff -r 311ee61dc989 -r a39afe99b3bd tools/data_source/ucsc_tablebrowser.xml
--- a/tools/data_source/ucsc_tablebrowser.xml Thu Nov 13 14:56:33 2008 -0500
+++ b/tools/data_source/ucsc_tablebrowser.xml Thu Nov 13 15:17:42 2008 -0500
@@ -23,6 +23,7 @@
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
<data_type_translation>
+ <format galaxy_format="tabular" remote_format="primaryTable" />
<format galaxy_format="tabular" remote_format="selectedFields" />
</data_type_translation>
</request_param>
diff -r 311ee61dc989 -r a39afe99b3bd tools/data_source/ucsc_tablebrowser_archaea.xml
--- a/tools/data_source/ucsc_tablebrowser_archaea.xml Thu Nov 13 14:56:33 2008 -0500
+++ b/tools/data_source/ucsc_tablebrowser_archaea.xml Thu Nov 13 15:17:42 2008 -0500
@@ -23,6 +23,7 @@
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
<data_type_translation>
+ <format galaxy_format="tabular" remote_format="primaryTable" />
<format galaxy_format="tabular" remote_format="selectedFields" />
</data_type_translation>
</request_param>
diff -r 311ee61dc989 -r a39afe99b3bd tools/data_source/ucsc_tablebrowser_test.xml
--- a/tools/data_source/ucsc_tablebrowser_test.xml Thu Nov 13 14:56:33 2008 -0500
+++ b/tools/data_source/ucsc_tablebrowser_test.xml Thu Nov 13 15:17:42 2008 -0500
@@ -23,6 +23,7 @@
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
<data_type_translation>
+ <format galaxy_format="tabular" remote_format="primaryTable" />
<format galaxy_format="tabular" remote_format="selectedFields" />
</data_type_translation>
</request_param>
11 years
[hg] galaxy 1630: Add a new <data_type_translation> tag set to d...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/311ee61dc989
changeset: 1630:311ee61dc989
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Thu Nov 13 14:56:33 2008 -0500
description:
Add a new <data_type_translation> tag set to data_source tools that enable the translation of an unsupported data type to a supported one in Galaxy ( currently only used in UCSC ). Also some tweaks to the jobs reports.
9 file(s) affected in this change:
lib/galaxy/tools/__init__.py
lib/galaxy/util/__init__.py
lib/galaxy/webapps/reports/controllers/jobs.py
lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako
lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako
lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako
tools/data_source/ucsc_tablebrowser.xml
tools/data_source/ucsc_tablebrowser_archaea.xml
tools/data_source/ucsc_tablebrowser_test.xml
diffs (188 lines):
diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py Wed Nov 12 15:42:46 2008 -0500
+++ b/lib/galaxy/tools/__init__.py Thu Nov 13 14:56:33 2008 -0500
@@ -242,6 +242,19 @@
remote_name = req_param.get( "remote_name" )
trans_list.append( req_param.get( "galaxy_name" ) )
trans_list.append( req_param.get( "missing" ) )
+ if req_param.get( "galaxy_name" ) == "data_type":
+ # The req_param tag for data_type is special in that it can contain another tag set like
+ # <data_type_translation>
+ # <format galaxy_format="tabular" remote_format="selectedFields" />
+ # </data_type_translation>
+ format_trans = req_param.find( "data_type_translation" )
+ if format_trans is not None:
+ format_trans_dict = {}
+ for format in format_trans.findall( "format" ):
+ remote_format = format.get( "remote_format" )
+ galaxy_format = format.get( "galaxy_format" )
+ format_trans_dict[ remote_format ] = galaxy_format
+ trans_list.append( format_trans_dict )
self.param_trans_dict[ remote_name ] = trans_list
# Command line (template). Optional for tools that do not invoke a local program
command = root.find("command")
diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py Wed Nov 12 15:42:46 2008 -0500
+++ b/lib/galaxy/util/__init__.py Thu Nov 13 14:56:33 2008 -0500
@@ -155,7 +155,17 @@
if tool and tool.tool_type == 'data_source':
if key in tool.param_trans_dict:
new_key = tool.param_trans_dict[ key ][0]
- if not value:
+ if new_key == 'data_type':
+ try:
+ # The Galaxy "data_type entry is special in that it can include the ability
+ # to translate the format to a Galaxy supported format. In the dict, this entry
+ # looks something like: {'hgta_outputType': ['data_type', 'bed', {'selectedFields': 'tabular'}] }
+ format_trans_dict = tool.param_trans_dict[ key ][2]
+ if value in format_trans_dict:
+ new_value = format_trans_dict[ value ]
+ except:
+ pass
+ if not value and not new_value:
new_value = tool.param_trans_dict[ key ][1]
if key not in self.NEVER_SANITIZE and sanitize:
self.__dict__[ new_key ] = sanitize_param( new_value )
diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/webapps/reports/controllers/jobs.py
--- a/lib/galaxy/webapps/reports/controllers/jobs.py Wed Nov 12 15:42:46 2008 -0500
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py Thu Nov 13 14:56:33 2008 -0500
@@ -91,8 +91,7 @@
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_( sa.or_( galaxy.model.Job.table.c.state == 'error',
- galaxy.model.Job.table.c.state == 'deleted' ),
+ whereclause = sa.and_( galaxy.model.Job.table.c.state == 'error',
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,
@@ -134,8 +133,7 @@
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_( sa.or_( galaxy.model.Job.table.c.state == 'error',
- galaxy.model.Job.table.c.state == 'deleted' ),
+ whereclause = sa.and_( galaxy.model.Job.table.c.state == 'error',
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,
@@ -305,8 +303,7 @@
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 = sa.or_( galaxy.model.Job.table.c.state == 'error',
- galaxy.model.Job.table.c.state == 'deleted' ),
+ whereclause = galaxy.model.Job.table.c.state == 'error',
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 df23879dec70 -r 311ee61dc989 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 12 15:42:46 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako Thu Nov 13 14:56:33 2008 -0500
@@ -2,7 +2,7 @@
<%def name="main_body()">
<div class="reportBody">
- <h3 align="center">Jobs In Error Per Month ( includes jobs deleted before finishing )</h3>
+ <h3 align="center">Jobs In Error Per Month</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">
@@ -11,7 +11,7 @@
%endif
<table align="center" width="60%" class="colored">
%if len( jobs ) == 0:
- <tr><td colspan="2">There are no jobs in the deleted or error state</td></tr>
+ <tr><td colspan="2">There are no jobs in the error state</td></tr>
%else:
<tr class="header">
<td>Month</td>
diff -r df23879dec70 -r 311ee61dc989 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 12 15:42:46 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Thu Nov 13 14:56:33 2008 -0500
@@ -10,15 +10,13 @@
%endif
<table align="center" width="60%" class="colored">
%if len( jobs ) == 0:
- <tr><td colspan="5">There are no jobs in the deleted or error state for ${day_label}, ${month_label} ${day_of_month}, ${year_label}</td></tr>
+ <tr><td colspan="5">There are no jobs in the error state for ${day_label}, ${month_label} ${day_of_month}, ${year_label}</td></tr>
%else:
%for job in jobs:
<%
state = job[0]
if state == 'error':
rowdef = '<tr class="headererror">'
- elif state == 'deleted':
- rowdef = '<tr class="headerdeleted">'
else:
rowdef = '<tr class="headerunknown">'
%>
diff -r df23879dec70 -r 311ee61dc989 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 12 15:42:46 2008 -0500
+++ b/lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako Thu Nov 13 14:56:33 2008 -0500
@@ -2,7 +2,7 @@
<%def name="main_body()">
<div class="reportBody">
- <h3 align="center">Jobs in Error for ${month_label} ${year_label} ( includes jobs deleted before finishing )</h3>
+ <h3 align="center">Jobs in Error for ${month_label} ${year_label}</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">
@@ -11,7 +11,7 @@
%endif
<table align="center" width="60%" class="colored">
%if len( jobs ) == 0:
- <tr><td colspan="3">There are no jobs in error for ${month_label} ${year_label}</td></tr>
+ <tr><td colspan="3">There are no jobs in the error state for ${month_label} ${year_label}</td></tr>
%else:
<tr class="header">
<td>Day</td>
diff -r df23879dec70 -r 311ee61dc989 tools/data_source/ucsc_tablebrowser.xml
--- a/tools/data_source/ucsc_tablebrowser.xml Wed Nov 12 15:42:46 2008 -0500
+++ b/tools/data_source/ucsc_tablebrowser.xml Thu Nov 13 14:56:33 2008 -0500
@@ -21,7 +21,11 @@
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
<request_param galaxy_name="table" remote_name="hgta_track" missing="unknown table" />
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
- <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
+ <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
+ <data_type_translation>
+ <format galaxy_format="tabular" remote_format="selectedFields" />
+ </data_type_translation>
+ </request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
diff -r df23879dec70 -r 311ee61dc989 tools/data_source/ucsc_tablebrowser_archaea.xml
--- a/tools/data_source/ucsc_tablebrowser_archaea.xml Wed Nov 12 15:42:46 2008 -0500
+++ b/tools/data_source/ucsc_tablebrowser_archaea.xml Thu Nov 13 14:56:33 2008 -0500
@@ -21,7 +21,11 @@
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
<request_param galaxy_name="table" remote_name="hgta_track" missing="" />
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
- <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
+ <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
+ <data_type_translation>
+ <format galaxy_format="tabular" remote_format="selectedFields" />
+ </data_type_translation>
+ </request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
diff -r df23879dec70 -r 311ee61dc989 tools/data_source/ucsc_tablebrowser_test.xml
--- a/tools/data_source/ucsc_tablebrowser_test.xml Wed Nov 12 15:42:46 2008 -0500
+++ b/tools/data_source/ucsc_tablebrowser_test.xml Thu Nov 13 14:56:33 2008 -0500
@@ -21,7 +21,11 @@
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
<request_param galaxy_name="table" remote_name="hgta_track" missing="" />
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
- <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
+ <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
+ <data_type_translation>
+ <format galaxy_format="tabular" remote_format="selectedFields" />
+ </data_type_translation>
+ </request_param>
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
11 years
[hg] galaxy 1629: Fix a bug I missed in my last commit.
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/df23879dec70
changeset: 1629:df23879dec70
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Nov 12 15:42:46 2008 -0500
description:
Fix a bug I missed in my last commit.
1 file(s) affected in this change:
scripts/others/incorrect_gops_jobs.py
diffs (19 lines):
diff -r 54f12bb6cb29 -r df23879dec70 scripts/others/incorrect_gops_jobs.py
--- a/scripts/others/incorrect_gops_jobs.py Wed Nov 12 15:19:27 2008 -0500
+++ b/scripts/others/incorrect_gops_jobs.py Wed Nov 12 15:42:46 2008 -0500
@@ -77,11 +77,12 @@
print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) )
print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email"
for jid in jobs:
- print "%s\t%s\t%s\t%s\t%s\t%s\t%s" % \
- ( jid, jobs[ jid ][ 'hda_id' ],
+ print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % \
+ ( str( jid ),
+ str( jobs[ jid ][ 'hda_id' ] ),
jobs[ jid ][ 'hda_name' ],
jobs[ jid ][ 'hda_info' ],
- jobs[ jid ][ 'history_id' ],
+ str( jobs[ jid ][ 'history_id' ] ),
jobs[ jid ][ 'history_name' ],
jobs[ jid ][ 'history_update_time' ],
jobs[ jid ][ 'user_email' ]
11 years
