1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/af8a76870774/ Changeset: af8a76870774 User: dan Date: 2013-04-09 19:00:47 Summary: Change database logging of stderr and stdout to take text from start and end of the string (instead of just the start) when the size exceeds the set character limit (32k). Affected #: 2 files

diff -r 2cfc5c8223ef102c320472cb84f197ca28a064d6 -r af8a76870774ee664331dc018c4ad85cfe06b871 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -34,6 +34,9 @@ # and should eventually become API'd TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json'

+DATABASE_MAX_STRING_SIZE = 32768 +DATABASE_MAX_STRING_SIZE_PRETTY = '32K' + class Sleeper( object ): """ Provides a 'sleep' method that sleeps for a number of seconds *unless* @@ -774,13 +777,13 @@ job.info = message # TODO: Put setting the stdout, stderr, and exit code in one place # (not duplicated with the finish method). - if ( len( stdout ) > 32768 ): - stdout = stdout[:32768] - log.info( "stdout for job %d is greater than 32K, only first part will be logged to database" % job.id ) + if ( len( stdout ) > DATABASE_MAX_STRING_SIZE ): + stdout = util.shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + log.info( "stdout for job %d is greater than %s, only a portion will be logged to database" % ( job.id, DATABASE_MAX_STRING_SIZE_PRETTY ) ) job.stdout = stdout - if ( len( stderr ) > 32768 ): - stderr = stderr[:32768] - log.info( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id ) + if ( len( stderr ) > DATABASE_MAX_STRING_SIZE ): + stderr = util.shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + log.info( "stderr for job %d is greater than %s, only a portion will be logged to database" % ( job.id, DATABASE_MAX_STRING_SIZE_PRETTY ) ) job.stderr = stderr # Let the exit code be Null if one is not provided: if ( exit_code != None ): @@ -998,12 +1001,12 @@ # will now be seen by the user. self.sa_session.flush() # Save stdout and stderr - if len( job.stdout ) > 32768: - log.info( "stdout for job %d is greater than 32K, only first part will be logged to database" % job.id ) - job.stdout = job.stdout[:32768] - if len( job.stderr ) > 32768: - log.info( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id ) - job.stderr = job.stderr[:32768] + if len( job.stdout ) > DATABASE_MAX_STRING_SIZE: + log.info( "stdout for job %d is greater than %s, only a portion will be logged to database" % ( job.id, DATABASE_MAX_STRING_SIZE_PRETTY ) ) + job.stdout = util.shrink_string_by_size( job.stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if len( job.stderr ) > DATABASE_MAX_STRING_SIZE: + log.info( "stderr for job %d is greater than %s, only a portion will be logged to database" % ( job.id, DATABASE_MAX_STRING_SIZE_PRETTY ) ) + job.stderr = util.shrink_string_by_size( job.stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) # The exit code will be null if there is no exit code to be set. # This is so that we don't assign an exit code, such as 0, that # is either incorrect or has the wrong semantics. @@ -1652,12 +1655,12 @@ task.state = task.states.ERROR

# Save stdout and stderr - if len( stdout ) > 32768: - log.error( "stdout for task %d is greater than 32K, only first part will be logged to database" % task.id ) - task.stdout = stdout[:32768] - if len( stderr ) > 32768: - log.error( "stderr for job %d is greater than 32K, only first part will be logged to database" % task.id ) - task.stderr = stderr[:32768] + if len( stdout ) > DATABASE_MAX_STRING_SIZE: + log.error( "stdout for task %d is greater than %s, only a portion will be logged to database" % ( task.id, DATABASE_MAX_STRING_SIZE_PRETTY ) ) + task.stdout = util.shrink_string_by_size( stdout, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if len( stderr ) > DATABASE_MAX_STRING_SIZE: + log.error( "stderr for task %d is greater than %s, only a portion will be logged to database" % ( task.id, DATABASE_MAX_STRING_SIZE_PRETTY ) ) + task.stderr = util.shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) task.exit_code = tool_exit_code task.command_line = self.command_line self.sa_session.flush()

diff -r 2cfc5c8223ef102c320472cb84f197ca28a064d6 -r af8a76870774ee664331dc018c4ad85cfe06b871 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -152,6 +152,25 @@ elem.tail = i + pad return elem

+def shrink_string_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ): + if len( value ) > size: + len_join_by = len( join_by ) + min_size = len_join_by + 2 + if size < min_size: + if beginning_on_size_error: + return value[:size] + elif end_on_size_error: + return value[-size:] + raise ValueError( 'With the provided join_by value (%s), the minimum size value is %i.' % ( join_by, min_size ) ) + left_index = right_index = int( ( size - len_join_by ) / 2 ) + if left_index + right_index + len_join_by < size: + if left_larger: + left_index += 1 + else: + right_index += 1 + value = "%s%s%s" % ( value[:left_index], join_by, value[-right_index:] ) + return value + # characters that are valid valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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