mirror of
https://github.com/galaxyproject/galaxy.git
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merging from next-stable
This commit is contained in:
Greg Von Kuster
+69
-73
@@ -2,24 +2,22 @@
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Support for running a tool in Galaxy via an internal job management system
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"""
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import os
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import sys
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import pwd
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import time
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import copy
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import random
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import logging
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import datetime
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import logging
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import os
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import pwd
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import random
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import re
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import shutil
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import subprocess
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import sys
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import threading
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import traceback
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import subprocess
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import galaxy
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from galaxy import util, model
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from galaxy.util.bunch import Bunch
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from galaxy.datatypes.tabular import *
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from galaxy.datatypes.interval import *
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# tabular/interval imports appear to be unused. Clean up?
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from galaxy.datatypes import metadata
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from galaxy.util.json import from_json_string
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from galaxy.util.expressions import ExpressionContext
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@@ -86,7 +84,7 @@ class JobToolConfiguration( Bunch ):
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class JobConfiguration( object ):
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"""A parser and interface to advanced job management features.
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These features are configured in the job configuration, by default, ``job_conf.xml``
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"""
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DEFAULT_NWORKERS = 4
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@@ -611,7 +609,7 @@ class JobWrapper( object ):
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Calling this method for the first time causes the dynamic runner to do
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its calculation, if any.
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:returns: ``JobDestination``
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"""
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return self.job_runner_mapper.get_job_destination(self.params)
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@@ -675,7 +673,7 @@ class JobWrapper( object ):
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special = self.sa_session.query( model.GenomeIndexToolData ).filter_by( job=job ).first()
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if special:
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out_data[ "output_file" ] = FakeDatasetAssociation( dataset=special.dataset )
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# These can be passed on the command line if wanted as $__user_*__
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if job.history and job.history.user:
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user_id = '%d' % job.history.user.id
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@@ -779,11 +777,11 @@ class JobWrapper( object ):
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if ( len( stdout ) > 32768 ):
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stdout = stdout[:32768]
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log.info( "stdout for job %d is greater than 32K, only first part will be logged to database" % job.id )
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job.stdout = stdout
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job.stdout = stdout
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if ( len( stderr ) > 32768 ):
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stderr = stderr[:32768]
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log.info( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id )
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job.stderr = stderr
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job.stderr = stderr
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# Let the exit code be Null if one is not provided:
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if ( exit_code != None ):
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job.exit_code = exit_code
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@@ -865,7 +863,7 @@ class JobWrapper( object ):
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self.sa_session.expunge_all()
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job = self.get_job()
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# TODO: After failing here, consider returning from the function.
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# TODO: After failing here, consider returning from the function.
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try:
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self.reclaim_ownership()
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except:
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@@ -882,13 +880,16 @@ class JobWrapper( object ):
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return self.fail( job.info, stderr=stderr, stdout=stdout, exit_code=tool_exit_code )
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# Check the tool's stdout, stderr, and exit code for errors, but only
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# if the job has not already been marked as having an error.
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# if the job has not already been marked as having an error.
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# The job's stdout and stderr will be set accordingly.
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# We set final_job_state to use for dataset management, but *don't* set
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# job.state until after dataset collection to prevent history issues
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if job.states.ERROR != job.state:
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if ( self.check_tool_output( stdout, stderr, tool_exit_code, job )):
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job.state = job.states.OK
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final_job_state = job.states.OK
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else:
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job.state = job.states.ERROR
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final_job_state = job.states.ERROR
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if self.version_string_cmd:
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version_filename = self.get_version_string_path()
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@@ -908,9 +909,11 @@ class JobWrapper( object ):
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if os.path.exists( dataset_path.real_path ) and os.stat( dataset_path.real_path ).st_size > 0:
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log.warning( "finish(): %s not found, but %s is not empty, so it will be used instead" % ( dataset_path.false_path, dataset_path.real_path ) )
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else:
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# Prior to fail we need to set job.state
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job.state = final_job_state
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return self.fail( "Job %s's output dataset(s) could not be read" % job.id )
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job_context = ExpressionContext( dict( stdout = job.stdout, stderr = job.stderr ) )
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job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None )
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for dataset_assoc in job.output_datasets + job.output_library_datasets:
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context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset )
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@@ -926,10 +929,7 @@ class JobWrapper( object ):
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# Update (non-library) job output datasets through the object store
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if dataset not in job.output_library_datasets:
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self.app.object_store.update_from_file(dataset.dataset, create=True)
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# TODO: The context['stderr'] holds stderr's contents. An error
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# only really occurs if the job also has an error. So check the
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# job's state:
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if job.states.ERROR == job.state:
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if job.states.ERROR == final_job_state:
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dataset.blurb = "error"
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dataset.mark_unhidden()
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elif dataset.has_data():
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@@ -945,13 +945,7 @@ class JobWrapper( object ):
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( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) \
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and self.app.config.retry_metadata_internally ):
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dataset.datatype.set_meta( dataset, overwrite = False ) #call datatype.set_meta directly for the initial set_meta call during dataset creation
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# TODO: The context['stderr'] used to indicate that there
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# was an error. Now we must rely on the job's state instead;
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# that indicates whether the tool relied on stderr to indicate
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# the state or whether the tool used exit codes and regular
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# expressions to do so. So we use
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# job.state == job.states.ERROR to replace this same test.
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elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and job.states.ERROR != job.state:
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elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and job.states.ERROR != final_job_state:
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dataset._state = model.Dataset.states.FAILED_METADATA
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else:
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#load metadata from file
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@@ -981,10 +975,7 @@ class JobWrapper( object ):
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if dataset.ext == 'auto':
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dataset.extension = 'txt'
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self.sa_session.add( dataset )
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# TODO: job.states.ERROR == job.state now replaces checking
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# stderr for a problem:
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#if context['stderr']:
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if job.states.ERROR == job.state:
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if job.states.ERROR == final_job_state:
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log.debug( "setting dataset state to ERROR" )
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# TODO: This is where the state is being set to error. Change it!
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dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR
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@@ -1015,7 +1006,7 @@ class JobWrapper( object ):
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job.stderr = job.stderr[:32768]
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# The exit code will be null if there is no exit code to be set.
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# This is so that we don't assign an exit code, such as 0, that
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# is either incorrect or has the wrong semantics.
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# is either incorrect or has the wrong semantics.
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if None != tool_exit_code:
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job.exit_code = tool_exit_code
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# custom post process setup
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@@ -1054,7 +1045,12 @@ class JobWrapper( object ):
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# fix permissions
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for path in [ dp.real_path for dp in self.get_mutable_output_fnames() ]:
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util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid )
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# Finally set the job state. This should only happen *after* all
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# dataset creation, and will allow us to eliminate force_history_refresh.
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job.state = final_job_state
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self.sa_session.flush()
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log.debug( 'job %d ended' % self.job_id )
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if self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ):
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self.cleanup()
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@@ -1062,26 +1058,26 @@ class JobWrapper( object ):
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def check_tool_output( self, stdout, stderr, tool_exit_code, job ):
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"""
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Check the output of a tool - given the stdout, stderr, and the tool's
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exit code, return True if the tool exited succesfully and False
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exit code, return True if the tool exited succesfully and False
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otherwise. No exceptions should be thrown. If this code encounters
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an exception, it returns True so that the workflow can continue;
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otherwise, a bug in this code could halt workflow progress.
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otherwise, a bug in this code could halt workflow progress.
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Note that, if the tool did not define any exit code handling or
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any stdio/stderr handling, then it reverts back to previous behavior:
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if stderr contains anything, then False is returned.
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Note that the job id is just for messages.
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"""
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# By default, the tool succeeded. This covers the case where the code
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# By default, the tool succeeded. This covers the case where the code
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# has a bug but the tool was ok, and it lets a workflow continue.
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success = True
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success = True
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try:
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# Check exit codes and match regular expressions against stdout and
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# Check exit codes and match regular expressions against stdout and
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# stderr if this tool was configured to do so.
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# If there is a regular expression for scanning stdout/stderr,
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# then we assume that the tool writer overwrote the default
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# then we assume that the tool writer overwrote the default
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# behavior of just setting an error if there is *anything* on
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# stderr.
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# stderr.
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if ( len( self.tool.stdio_regexes ) > 0 or
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len( self.tool.stdio_exit_codes ) > 0 ):
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# Check the exit code ranges in the order in which
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@@ -1092,9 +1088,9 @@ class JobWrapper( object ):
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max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR
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if tool_exit_code != None:
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for stdio_exit_code in self.tool.stdio_exit_codes:
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if ( tool_exit_code >= stdio_exit_code.range_start and
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if ( tool_exit_code >= stdio_exit_code.range_start and
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tool_exit_code <= stdio_exit_code.range_end ):
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# Tack on a generic description of the code
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# Tack on a generic description of the code
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# plus a specific code description. For example,
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# this might prepend "Job 42: Warning (Out of Memory)\n".
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code_desc = stdio_exit_code.desc
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@@ -1106,21 +1102,21 @@ class JobWrapper( object ):
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code_desc ) )
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log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) )
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stderr = tool_msg + "\n" + stderr
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max_error_level = max( max_error_level,
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max_error_level = max( max_error_level,
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stdio_exit_code.error_level )
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if ( max_error_level >=
|
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if ( max_error_level >=
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galaxy.tools.StdioErrorLevel.FATAL ):
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break
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if max_error_level < galaxy.tools.StdioErrorLevel.FATAL:
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# We'll examine every regex. Each regex specifies whether
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# it is to be run on stdout, stderr, or both. (It is
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# it is to be run on stdout, stderr, or both. (It is
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# possible for neither stdout nor stderr to be scanned,
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# but those regexes won't be used.) We record the highest
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# error level, which are currently "warning" and "fatal".
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# If fatal, then we set the job's state to ERROR.
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# If warning, then we still set the job's state to OK
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# but include a message. We'll do this if we haven't seen
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# but include a message. We'll do this if we haven't seen
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# a fatal error yet
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for regex in self.tool.stdio_regexes:
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# If ( this regex should be matched against stdout )
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@@ -1130,16 +1126,16 @@ class JobWrapper( object ):
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# Repeat the stdout stuff for stderr.
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# TODO: Collapse this into a single function.
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if ( regex.stdout_match ):
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regex_match = re.search( regex.match, stdout,
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regex_match = re.search( regex.match, stdout,
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re.IGNORECASE )
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if ( regex_match ):
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rexmsg = self.regex_err_msg( regex_match, regex)
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log.info( "Job %s: %s"
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log.info( "Job %s: %s"
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% ( job.get_id_tag(), rexmsg ) )
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stdout = rexmsg + "\n" + stdout
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max_error_level = max( max_error_level,
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max_error_level = max( max_error_level,
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regex.error_level )
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if ( max_error_level >=
|
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if ( max_error_level >=
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galaxy.tools.StdioErrorLevel.FATAL ):
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break
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@@ -1148,33 +1144,33 @@ class JobWrapper( object ):
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re.IGNORECASE )
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if ( regex_match ):
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rexmsg = self.regex_err_msg( regex_match, regex)
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log.info( "Job %s: %s"
|
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log.info( "Job %s: %s"
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% ( job.get_id_tag(), rexmsg ) )
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stderr = rexmsg + "\n" + stderr
|
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max_error_level = max( max_error_level,
|
||||
max_error_level = max( max_error_level,
|
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regex.error_level )
|
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if ( max_error_level >=
|
||||
if ( max_error_level >=
|
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galaxy.tools.StdioErrorLevel.FATAL ):
|
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break
|
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|
||||
|
||||
# If we encountered a fatal error, then we'll need to set the
|
||||
# job state accordingly. Otherwise the job is ok:
|
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if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL:
|
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success = False
|
||||
success = False
|
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else:
|
||||
success = True
|
||||
|
||||
success = True
|
||||
|
||||
# When there are no regular expressions and no exit codes to check,
|
||||
# default to the previous behavior: when there's anything on stderr
|
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# the job has an error, and the job is ok otherwise.
|
||||
# the job has an error, and the job is ok otherwise.
|
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else:
|
||||
# TODO: Add in the tool and job id:
|
||||
# TODO: Add in the tool and job id:
|
||||
log.debug( "Tool did not define exit code or stdio handling; "
|
||||
+ "checking stderr for success" )
|
||||
if stderr:
|
||||
success = False
|
||||
success = False
|
||||
else:
|
||||
success = True
|
||||
success = True
|
||||
|
||||
# On any exception, return True.
|
||||
except:
|
||||
@@ -1182,7 +1178,7 @@ class JobWrapper( object ):
|
||||
log.warning( "Tool check encountered unexpected exception; "
|
||||
+ "assuming tool was successful: " + tb )
|
||||
success = True
|
||||
|
||||
|
||||
# Store the modified stdout and stderr in the job:
|
||||
if None != job:
|
||||
job.stdout = stdout
|
||||
@@ -1196,7 +1192,7 @@ class JobWrapper( object ):
|
||||
ToolStdioRegex regex object. The regex_match is a MatchObject
|
||||
that will contain the string matched on.
|
||||
"""
|
||||
# Get the description for the error level:
|
||||
# Get the description for the error level:
|
||||
err_msg = galaxy.tools.StdioErrorLevel.desc( regex.error_level ) + ": "
|
||||
# If there's a description for the regular expression, then use it.
|
||||
# Otherwise, we'll take the first 256 characters of the match.
|
||||
@@ -1210,7 +1206,7 @@ class JobWrapper( object ):
|
||||
if mend - mstart > 256:
|
||||
err_msg += match.string[ mstart : mstart+256 ] + "..."
|
||||
else:
|
||||
err_msg += match.string[ mstart: mend ]
|
||||
err_msg += match.string[ mstart: mend ]
|
||||
return err_msg
|
||||
|
||||
def cleanup( self ):
|
||||
@@ -1489,7 +1485,7 @@ class TaskWrapper(JobWrapper):
|
||||
self.status = task.states.NEW
|
||||
|
||||
def can_split( self ):
|
||||
# Should the job handler split this job up? TaskWrapper should
|
||||
# Should the job handler split this job up? TaskWrapper should
|
||||
# always return False as the job has already been split.
|
||||
return False
|
||||
|
||||
@@ -1631,8 +1627,8 @@ class TaskWrapper(JobWrapper):
|
||||
the contents of the output files.
|
||||
"""
|
||||
# This may have ended too soon
|
||||
log.debug( 'task %s for job %d ended; exit code: %d'
|
||||
% (self.task_id, self.job_id,
|
||||
log.debug( 'task %s for job %d ended; exit code: %d'
|
||||
% (self.task_id, self.job_id,
|
||||
tool_exit_code if tool_exit_code != None else -256 ) )
|
||||
# default post job setup_external_metadata
|
||||
self.sa_session.expunge_all()
|
||||
@@ -1647,12 +1643,12 @@ class TaskWrapper(JobWrapper):
|
||||
self.fail( task.info )
|
||||
return
|
||||
|
||||
# Check what the tool returned. If the stdout or stderr matched
|
||||
# Check what the tool returned. If the stdout or stderr matched
|
||||
# regular expressions that indicate errors, then set an error.
|
||||
# The same goes if the tool's exit code was in a given range.
|
||||
if ( self.check_tool_output( stdout, stderr, tool_exit_code, task ) ):
|
||||
task.state = task.states.OK
|
||||
else:
|
||||
else:
|
||||
task.state = task.states.ERROR
|
||||
|
||||
# Save stdout and stderr
|
||||
|
||||
@@ -29,7 +29,7 @@ def slugify(text, delim=u'-'):
|
||||
# Biostar requires all keys to be present, so we start with a template
|
||||
DEFAULT_PAYLOAD = {
|
||||
'email': "",
|
||||
'title': "Question about Galaxy",
|
||||
'title': "",
|
||||
'tags': 'galaxy',
|
||||
'tool_name': '',
|
||||
'tool_version': '',
|
||||
@@ -72,14 +72,16 @@ class BiostarController( BaseUIController ):
|
||||
payload = dict( DEFAULT_PAYLOAD, **payload )
|
||||
# Do the best we can of providing user information for the payload
|
||||
if trans.user:
|
||||
payload['username'] = "user-" + trans.security.encode_id( trans.user.id )
|
||||
payload['email'] = trans.user.email
|
||||
if trans.user.username:
|
||||
payload['username'] = trans.user.username
|
||||
payload['display_name'] = trans.user.username
|
||||
else:
|
||||
payload['display_name'] = "Galaxy User"
|
||||
payload['display_name'] = trans.user.email.split( "@" )[0]
|
||||
else:
|
||||
payload['username'] = payload['display_name'] = "Anonymous Galaxy User %d" % trans.galaxy_session.id
|
||||
encoded = trans.security.encode_id( trans.galaxy_session.id )
|
||||
payload['username'] = "anon-" + encoded
|
||||
payload['display_name'] = "Anonymous Galaxy User %d" % encoded[0:8]
|
||||
data, digest = encode_data( trans.app.config.biostar_key, payload )
|
||||
return trans.response.send_redirect( url_for( trans.app.config.biostar_url, data=data, digest=digest, name=trans.app.config.biostar_key_name, action=biostar_action ) )
|
||||
|
||||
@@ -107,8 +109,7 @@ class BiostarController( BaseUIController ):
|
||||
if not tool:
|
||||
return error( "No tool found matching '%s'" % tool_id )
|
||||
# Tool specific information for payload
|
||||
payload = { 'title': "Question about Galaxy tool '%s'" % tool.name,
|
||||
'tool_name': tool.name,
|
||||
payload = { 'tool_name': tool.name,
|
||||
'tool_version': tool.version,
|
||||
'tool_id': tool.id,
|
||||
'tags': 'galaxy ' + tag_for_tool( tool ) }
|
||||
|
||||
@@ -239,6 +239,14 @@ function naturalSort(a, b) {
|
||||
return 0;
|
||||
}
|
||||
|
||||
$.fn.refresh_select2 = function() {
|
||||
var select_elt = $(this);
|
||||
var options = { width: "resolve",
|
||||
closeOnSelect: !select_elt.is("[MULTIPLE]"),
|
||||
};
|
||||
return select_elt.select2( options );
|
||||
}
|
||||
|
||||
// Replace select box with a text input box + autocomplete.
|
||||
function replace_big_select_inputs(min_length, max_length, select_elts) {
|
||||
// To do replace, the select2 plugin must be loaded.
|
||||
@@ -276,9 +284,7 @@ function replace_big_select_inputs(min_length, max_length, select_elts) {
|
||||
*
|
||||
* - should we still sort dbkey fields here?
|
||||
*/
|
||||
|
||||
select_elt.select2( { width: "resolve" } );
|
||||
|
||||
select_elt.refresh_select2();
|
||||
});
|
||||
}
|
||||
|
||||
|
||||
@@ -73,7 +73,7 @@
|
||||
});
|
||||
$(this).append(select_link).append(" ").append(unselect_link);
|
||||
});
|
||||
|
||||
|
||||
$(".add-librarydataset").live("click", function() {
|
||||
var link = $(this);
|
||||
$.ajax({
|
||||
@@ -311,7 +311,7 @@
|
||||
|
||||
%if trans.app.config.biostar_url:
|
||||
<!-- BioStar links -->
|
||||
<span class="pull-right"><a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" target="galaxy_main" class="fa-icon-question-sign tooltip" data-original-title="Ask a question about this tool"></a></span>
|
||||
<span class="pull-right"><a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" target="_blank" class="fa-icon-question-sign tooltip" data-original-title="Ask a question about this tool"></a></span>
|
||||
<!-- End of BioStar links -->
|
||||
%endif
|
||||
</div>
|
||||
|
||||
@@ -8,7 +8,7 @@
|
||||
|
||||
<%def name="javascripts()">
|
||||
${parent.javascripts()}
|
||||
${h.js( "libs/jquery/jquery.autocomplete" )}
|
||||
${h.js( "libs/jquery/select2" )}
|
||||
<script type="text/javascript">
|
||||
$( function() {
|
||||
function show_tool_body(title){
|
||||
@@ -40,12 +40,12 @@
|
||||
select.val($('option:last', select).val());
|
||||
}
|
||||
select.closest('.form-row').children('label').children('span.mode-icon').hide();
|
||||
select.removeAttr('multiple').removeAttr('size');
|
||||
select.removeAttr('multiple').refresh_select2().removeAttr('size');
|
||||
placeholder = 'type to filter';
|
||||
} else {
|
||||
$('.multiinput', select.closest('.form-row')).removeClass('disabled');
|
||||
select.closest('.form-row').children('label').children('span.mode-icon').show();
|
||||
select.attr('multiple', 'multiple').attr('size', 8);
|
||||
select.attr('multiple', 'multiple').refresh_select2().attr('size', 8);
|
||||
placeholder = 'type to filter, [enter] to select all';
|
||||
}
|
||||
$('input.multiinput-filter', select.parent()).attr(
|
||||
@@ -79,7 +79,7 @@
|
||||
$("#new_history_cbx").click(function(){
|
||||
$("#new_history_input").toggle(this.checked);
|
||||
});
|
||||
$('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').each(function(i, s) {
|
||||
$('span.multiinput_wrap select[name*="|input"]').removeAttr('multiple').refresh_select2().each(function(i, s) {
|
||||
var select = $(s);
|
||||
var new_width = Math.max(200, select.width()) + 20;
|
||||
// Find the label for this element.
|
||||
|
||||
@@ -281,8 +281,7 @@ def json_from_url( url ):
|
||||
|
||||
def register_test_result( url, metadata_id, test_results_dict, tests_passed=False ):
|
||||
'''
|
||||
Set do_not_test = True if the repository fails functional tests. Set do_not_test = False
|
||||
if the repository passes functional tests, so that the repository will always be re-tested
|
||||
This script should never set do_not_test = True, because the repositories should always be re-tested
|
||||
against the most recent code.
|
||||
'''
|
||||
params = {}
|
||||
@@ -291,7 +290,7 @@ def register_test_result( url, metadata_id, test_results_dict, tests_passed=Fals
|
||||
params[ 'do_not_test' ] = 'false'
|
||||
else:
|
||||
params[ 'tools_functionally_correct' ] = 'false'
|
||||
params[ 'do_not_test' ] = 'true'
|
||||
params[ 'do_not_test' ] = 'false'
|
||||
params[ 'tool_test_errors' ] = test_results_dict
|
||||
return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False )
|
||||
|
||||
|
||||
Reference in New Issue
Block a user