1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b172ca94e169/
Changeset: b172ca94e169
User: jmchilton
Date: 2014-04-24 03:33:41
Summary: Fix Python 3 incompat in galaxy.jobs.runners.util.
Module shared with LWR so hoping for Python 3 compat.
Affected #: 2 files
diff -r 776e13962bbc861a94242e142e73278c9499dc70 -r b172ca94e169ccf2450432398d67623f79c5588f lib/galaxy/jobs/runners/util/__init__.py
--- a/lib/galaxy/jobs/runners/util/__init__.py
+++ b/lib/galaxy/jobs/runners/util/__init__.py
@@ -3,7 +3,5 @@
processes and interfacing with job managers. This module should contain
functionality shared between Galaxy and the LWR.
"""
-try:
- from galaxy.util.bunch import Bunch
-except ImportError:
- from lwr.util import Bunch
+
+from galaxy.util.bunch import Bunch
diff -r 776e13962bbc861a94242e142e73278c9499dc70 -r b172ca94e169ccf2450432398d67623f79c5588f lib/galaxy/jobs/runners/util/condor/__init__.py
--- a/lib/galaxy/jobs/runners/util/condor/__init__.py
+++ b/lib/galaxy/jobs/runners/util/condor/__init__.py
@@ -20,7 +20,8 @@
def submission_params(prefix=SUBMIT_PARAM_PREFIX, **kwds):
submission_params = {}
- for key, value in kwds.iteritems():
+ for key in kwds:
+ value = kwds[key]
key = key.lower()
if key.startswith(prefix):
condor_key = key[len(prefix):]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/51643642564f/
Changeset: 51643642564f
User: dannon
Date: 2014-04-23 23:07:39
Summary: Add mock, poster eggs. Both may go away depending on which way bioblend goes w/ deps, but it keeps things working for now.
Affected #: 1 file
diff -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f -r 51643642564f214f09c2eff32307360f5e09dfaf eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -46,6 +46,7 @@
kombu = 3.0.12
lrucache = 0.2
Mako = 0.4.1
+mock = 1.0.1
nose = 0.11.1
NoseHTML = 0.4.1
NoseTestDiff = 0.1
@@ -54,6 +55,7 @@
Paste = 1.7.5.1
PasteDeploy = 1.5.0
pexpect = 2.4
+poster = 0.8.1
python_openid = 2.2.5
python_daemon = 1.5.5
pytz = 2013.9
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b801d178c90c/
Changeset: b801d178c90c
User: carlfeberhard
Date: 2014-04-23 17:59:21
Summary: Visualization framework: remove deprecated 'template_root' element left from when visualizations were loaded from galaxy's template directory
Affected #: 5 files
diff -r 1d1292f5b4ab6da6863f845ec538389c1e8659a9 -r b801d178c90c0ca22d4fe9c219af7f9ae603b8c9 config/plugins/visualizations/circster/config/circster.xml
--- a/config/plugins/visualizations/circster/config/circster.xml
+++ b/config/plugins/visualizations/circster/config/circster.xml
@@ -21,8 +21,6 @@
<param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier><param type="dbkey">dbkey</param></params>
- <!-- template_root and template are currently ignored for the 'built-in' visualizations -->
- <template_root>webapps/galaxy/visualization</template_root><template>circster.mako</template><render_target>_top</render_target></visualization>
diff -r 1d1292f5b4ab6da6863f845ec538389c1e8659a9 -r b801d178c90c0ca22d4fe9c219af7f9ae603b8c9 config/plugins/visualizations/phyloviz/config/phyloviz.xml
--- a/config/plugins/visualizations/phyloviz/config/phyloviz.xml
+++ b/config/plugins/visualizations/phyloviz/config/phyloviz.xml
@@ -14,8 +14,6 @@
<param type="dataset" var_name_in_template="hda" required="true">dataset_id</param><param type="integer" default="0">tree_index</param></params>
- <!-- template_root and template are currently ignored for the 'built-in' visualizations -->
- <template_root>webapps/galaxy/visualization</template_root><template>phyloviz.mako</template><render_target>_top</render_target></visualization>
diff -r 1d1292f5b4ab6da6863f845ec538389c1e8659a9 -r b801d178c90c0ca22d4fe9c219af7f9ae603b8c9 config/plugins/visualizations/sweepster/config/sweepster.xml
--- a/config/plugins/visualizations/sweepster/config/sweepster.xml
+++ b/config/plugins/visualizations/sweepster/config/sweepster.xml
@@ -20,8 +20,6 @@
<param type="hda_or_ldda" var_name_in_template="dataset">dataset_id</param><param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier></params>
- <!-- template_root and template are currently ignored for the 'built-in' visualizations -->
- <template_root>webapps/galaxy/visualization</template_root><template>sweepster.mako</template><render_target>_top</render_target></visualization>
diff -r 1d1292f5b4ab6da6863f845ec538389c1e8659a9 -r b801d178c90c0ca22d4fe9c219af7f9ae603b8c9 config/plugins/visualizations/trackster/config/trackster.xml
--- a/config/plugins/visualizations/trackster/config/trackster.xml
+++ b/config/plugins/visualizations/trackster/config/trackster.xml
@@ -23,8 +23,6 @@
<param type="genome_region">genome_region</param><param type="dbkey">dbkey</param></params>
- <!-- template_root and template are currently ignored for the 'built-in' visualizations -->
- <template_root>webapps/galaxy/visualization/tracks</template_root><template>browser.mako</template><render_target>_top</render_target></visualization>
diff -r 1d1292f5b4ab6da6863f845ec538389c1e8659a9 -r b801d178c90c0ca22d4fe9c219af7f9ae603b8c9 config/plugins/visualizations/visualization.dtd
--- a/config/plugins/visualizations/visualization.dtd
+++ b/config/plugins/visualizations/visualization.dtd
@@ -126,10 +126,6 @@
var_name_in_template CDATA #IMPLIED
>
-<!-- template_root: the directory to search for the template relative to templates/webapps/galaxy
- (optional) DEFAULT: visualizations
--->
-<!ELEMENT template_root (#PCDATA)><!-- template: the template used to render the visualization. REQUIRED --><!ELEMENT template (#PCDATA)><!-- render_target: used as the target attribute of the link to the visualization.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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