jmchilton

def merge_sorted_iterables( operator, *iterables ):
    """

    >>> operator = lambda x: x
    >>> list( merge_sorted_iterables( operator, [1,2,3], [4,5] ) )
    [1, 2, 3, 4, 5]
    >>> list( merge_sorted_iterables( operator, [4, 5], [1,2,3] ) )
    [1, 2, 3, 4, 5]
    >>> list( merge_sorted_iterables( operator, [1, 4, 5], [2], [3] ) )
    [1, 2, 3, 4, 5]

jmchilton

Traceback (most recent call last):
  File "/home/john/workspace/galaxy-central/lib/galaxy/jobs/runners/lwr.py", line 161, in __prepare_job
    client = self.get_client_from_wrapper(job_wrapper)
  File "/home/john/workspace/galaxy-central/lib/galaxy/jobs/runners/lwr.py", line 221, in get_client_from_wrapper
    return self.get_client( params, job_id )
  File "/home/john/workspace/galaxy-central/lib/galaxy/jobs/runners/lwr.py", line 231, in get_client
    files_endpoint = url_for( controller="job_files", job_id=encoded_job_id )
  File "/home/john/workspace/galaxy-central/eggs/Routes-1.12.3-py2.7.egg/routes/util.py", line 189, in url_for
    encoding = config.mapper.encoding
  File "/home/john/workspace/galaxy-central/eggs/Routes-1.12.3-py2.7.egg/routes/__init__.py", line 14, in __getattr__

jmchilton

""" API for asynchronous job running mechanisms can use to fetch or put files
related to running and queued jobs.
"""
import os
import shutil

from galaxy import exceptions
from galaxy import util
from galaxy import model
from galaxy.web.base.controller import BaseAPIController

jmchilton

diff -r fac578cca758 lib/galaxy/webapps/galaxy/controllers/library_common.py
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py   Fri Feb 21 22:09:57 2014 -0600
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py   Wed Feb 26 08:34:28 2014 -0600
@@ -2001,6 +2001,7 @@
                 status = 'error'
             else:
                 if new_history_name:
+                    log.info("Handling new history.")
                     new_history = trans.app.model.History()
                     new_history.name = new_history_name

jmchilton

diff -r c80947795972 lib/galaxy/jobs/runners/lwr_client/staging/up.py
--- a/lib/galaxy/jobs/runners/lwr_client/staging/up.py  Fri Feb 21 16:57:59 2014 -0500
+++ b/lib/galaxy/jobs/runners/lwr_client/staging/up.py  Wed Feb 26 08:52:07 2014 -0600
@@ -149,7 +149,9 @@
 
     def __upload_input_extra_files(self, input_file):
         files_path = "%s_files" % input_file[0:-len(".dat")]
+        log.info( "Extra files path guess is %s, exists? %s" % ( files_path, exists( files_path ) ) )
         if exists(files_path) and self.__stage_input(files_path):
+            log.info( "Going to stage extra files - %s" % str(directory_files(files_path)) )

jmchilton

diff -r c80947795972 lib/galaxy/jobs/runners/lwr_client/client.py
--- a/lib/galaxy/jobs/runners/lwr_client/client.py      Fri Feb 21 16:57:59 2014 -0500
+++ b/lib/galaxy/jobs/runners/lwr_client/client.py      Wed Feb 26 10:55:11 2014 -0600
@@ -9,6 +9,9 @@
 MAX_RETRY_COUNT = 5
 RETRY_SLEEP_TIME = 0.1
 
+import logging
+log = logging.getLogger(__name__)
+

jmchilton

diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index 6fd577a..22f12a5 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -5,6 +5,7 @@ import traceback
 from datetime import timedelta
 
 from galaxy import model
+from galaxy import util
 from galaxy.util.bunch import Bunch

jmchilton

<tool id="pbsdebug" name="PBS DEBUG">
  <command>                                                                                                               
    echo \$GALAXY_SLOTS > $out1;                                                                                          
    env > $out3;                                                                                                          
    echo "No PBS_NODEFILE defined." > $out2;                                                                              
    if [ -f "\$PBS_NODEFILE" ]; then cp \$PBS_NODEFILE $out2; fi                                                          
  </command>
  <inputs>
  </inputs>
  <outputs>

jmchilton

--- a/getalleleseq.xml  Fri Jul 19 17:49:30 2013 -0400
+++ b/getalleleseq.xml  Mon Mar 17 10:09:45 2014 -0500
@@ -4,7 +4,6 @@
                                    $alleles
                                 -l $seq_length
                                 -j $major_seq
-                                -d $__new_file_path__
                                 -p $major_seq.id
 </command>
   <inputs>

jmchilton

Open Model Questions:

Key:
  HDCA - HistoryDatasetCollectionAssociation (connects history and dataset collection)
  DC - DatasetCollection 
   -or-
  HDC - HistoryDatasetCollection - combine concepts of HDCA and DC into one.

  DCE - DatasetCollectionElement (connects dataset instance or some kind of collection to 
          a some kind of collection, was called DatasetAssociationDatasetCollectionAssociation