1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1edc3c13a7a2/ Changeset: 1edc3c13a7a2 User: greg Date: 2014-02-25 20:37:44 Summary: A bit of cleanup and some important fixes in re-engineered code for eliminating fabric.local when installing tool dependencies along with repositories from the tool shed. Affected #: 1 file
diff -r 451b411b4b19ca34ed154352b07b3f49983d1197 -r 1edc3c13a7a272102a2a9c178440466ba7ab5525 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -14,6 +14,8 @@ import shlex
from contextlib import contextmanager +from galaxy.util import DATABASE_MAX_STRING_SIZE +from galaxy.util import shrink_string_by_size from galaxy.util import unicodify from galaxy.util.template import fill_template from galaxy import eggs @@ -34,7 +36,7 @@ log = logging.getLogger( __name__ )
INSTALLATION_LOG = 'INSTALLATION.log' -NO_CMD_OUTPUT_TIMEOUT = 600 +NO_CMD_OUTPUT_TIMEOUT = 600.0 VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz'
@@ -159,12 +161,12 @@ is printed and saved to that thread's queue. The calling thread can then retrieve the data using thread.stdout and thread.stderr. """ - for line in iter( stdout.readline, b'' ): + for line in iter( stdout.readline, '' ): output = line.rstrip() print output stdout_queue.put( output ) stdout_queue.put( None ) - for line in iter( stderr.readline, b'' ): + for line in iter( stderr.readline, '' ): output = line.rstrip() print output stderr_queue.put( output ) @@ -222,14 +224,26 @@ context = app.install_model.context output = run_local_command( cmd ) log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) - if output.return_code not in [ None, env.ok_ret_codes ]: + stdout = output.stdout + stderr = output.stderr + if len( stdout ) > DATABASE_MAX_STRING_SIZE: + print "Process id %s stdout > %s, so only a portion will be saved in the database." % \ + ( str( pid ), str( DATABASE_MAX_STRING_SIZE_PRETTY ) ) + stdout = 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: + print "Process id %s stderr > %s, so only a portion will be saved in the database." % \ + ( str( pid ), str( DATABASE_MAX_STRING_SIZE_PRETTY ) ) + stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) + if output.return_code not in [ 0 ]: tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR - if output.stderr: - tool_dependency.error_message = unicodify( str( output.stderr )[ :32768 ] ) - elif output.stdout: - tool_dependency.error_message = unicodify( str( output.stdout )[ :32768 ] ) + if stderr: + tool_dependency.error_message = unicodify( stderr ) + elif stdout: + tool_dependency.error_message = unicodify( stdout ) else: - tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % ( str( cmd ), str( output.return_code ) ) + # We have a problem if there was no stdout and no stderr. + tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \ + ( str( cmd ), str( output.return_code ) ) context.add( tool_dependency ) context.flush() if return_output: @@ -833,7 +847,6 @@ stdout_queue, process_handle.stderr, stderr_queue ) ) - stdio_thread.daemon = True stdio_thread.start() # Check the queues for output until there is nothing more to get. start_timer = time.time() @@ -884,9 +897,11 @@ current_wait_time = time.time() - start_timer if stdout_queue.empty() and stderr_queue.empty() and current_wait_time < NO_CMD_OUTPUT_TIMEOUT: break - # Let's be tidy and join the threads we've started. - stdout_reader.join() - stderr_reader.join() + # Wait until each of the threads we've started terminate. The following calls will block each thread + # until it terminates either normally, through an unhandled exception, or until the timeout occurs. + stdio_thread.join( NO_CMD_OUTPUT_TIMEOUT ) + stdout_reader.join( NO_CMD_OUTPUT_TIMEOUT ) + stderr_reader.join( NO_CMD_OUTPUT_TIMEOUT ) # Close subprocess' file descriptors. process_handle.stdout.close() process_handle.stderr.close() @@ -895,6 +910,7 @@ # Handle error condition (deal with stdout being None, too) output = _AttributeString( stdout.strip() if stdout else "" ) errors = _AttributeString( stderr.strip() if stderr else "" ) + process_handle.poll() output.return_code = process_handle.returncode output.stderr = errors return output
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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