1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/3f12abbd2394/
changeset: 3f12abbd2394
user: dannon
date: 2012-04-11 15:16:20
summary: Cloud Launch - Password Field for AWS Secret instead of plain text input
affected #: 1 file
diff -r 37c43980034e744d05647c3aad3631f5a1dd9c1c -r 3f12abbd23941683e44b34a21f0cf82d14bf02ad templates/cloud/index.mako
--- a/templates/cloud/index.mako
+++ b/templates/cloud/index.mako
@@ -71,7 +71,7 @@
</div><div class="form-row"><label for="id_secret">Secret Key</label>
- <input type="text" size="120" name="secret" id="id_secret"/><br/>
+ <input type="password" size="120" name="secret" id="id_secret"/><br/></div><div class="form-row"><label for="id_instance_type">Instance Type</label>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/dae7eefe2f71/
changeset: dae7eefe2f71
user: dannon
date: 2012-04-10 22:46:49
summary: New config option, and change in default behavior regarding dataset path display in View Details. Administrators can now *always* see the full path, and if the expose_dataset_path option is True, so can regular users.
affected #: 3 files
diff -r d59674927a521dec8619441ac8801807e150392d -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -106,6 +106,7 @@
self.smtp_username = kwargs.get( 'smtp_username', None )
self.smtp_password = kwargs.get( 'smtp_password', None )
self.start_job_runners = kwargs.get( 'start_job_runners', None )
+ self.expose_dataset_path = string_as_bool( kwargs.get( 'expose_dataset_path', 'False' ) )
# External Service types used in sample tracking
self.external_service_type_config_file = resolve_path( kwargs.get( 'external_service_type_config_file', 'external_service_types_conf.xml' ), self.root )
self.external_service_type_path = resolve_path( kwargs.get( 'external_service_type_path', 'external_service_types' ), self.root )
diff -r d59674927a521dec8619441ac8801807e150392d -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 templates/show_params.mako
--- a/templates/show_params.mako
+++ b/templates/show_params.mako
@@ -52,6 +52,9 @@
<tr><td>Tool Version:</td><td>${hda.tool_version}</td></tr><tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr><tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr>
+ %if trans.user_is_admin() or trans.app.config.expose_dataset_path:
+ <tr><td>Full Path:</td><td>${hda.file_name}</td></tr>
+ %endif
</table><br /><table class="tabletip">
diff -r d59674927a521dec8619441ac8801807e150392d -r dae7eefe2f710313ed5bb9e19cd484cbc395bab8 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -678,6 +678,10 @@
#pbs_stage_path =
#pbs_dataset_server =
+# This option allows users to see the full path of datasets via the "View
+# Details" option in the history. Administrators can always see this.
+#expose_dataset_path = False
+
# ---- Per-Tool Job Management ----------------------------------------------
# Per-tool job handler and runner overrides. Parameters can be included to define multiple
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/25edd75ca72f/
changeset: 25edd75ca72f
user: dan
date: 2012-04-10 22:08:15
summary: Fix inconsequential warning about when tag when loading FreeBayes.
affected #: 1 file
diff -r b148fcea038fa00867a3c0e260e8d255a0a08ecb -r 25edd75ca72fd9c276476203e05c093e949b37eb tools/variant_detection/freebayes.xml
--- a/tools/variant_detection/freebayes.xml
+++ b/tools/variant_detection/freebayes.xml
@@ -241,7 +241,7 @@
<option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param>
- <when value="do_no_set">
+ <when value="do_not_set"><!-- do nothing here --></when><when value="set">
@@ -257,7 +257,7 @@
<option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param>
- <when value="do_no_set">
+ <when value="do_not_set"><!-- do nothing here --></when><when value="set">
@@ -289,7 +289,7 @@
<option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param>
- <when value="do_no_set">
+ <when value="do_not_set"><!-- do nothing here --></when><when value="set">
@@ -311,7 +311,7 @@
<option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param>
- <when value="do_no_set">
+ <when value="do_not_set"><!-- do nothing here --></when><when value="set">
@@ -352,7 +352,7 @@
<option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param>
- <when value="do_no_set">
+ <when value="do_not_set"><!-- do nothing here --></when><when value="set">
@@ -368,7 +368,7 @@
<option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param>
- <when value="do_no_set">
+ <when value="do_not_set"><!-- do nothing here --></when><when value="set">
@@ -384,7 +384,7 @@
<option value="do_not_set" selected="True">Do not set</option><option value="set">Set</option></param>
- <when value="do_no_set">
+ <when value="do_not_set"><!-- do nothing here --></when><when value="set">
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b148fcea038f/
changeset: b148fcea038f
user: dan
date: 2012-04-10 22:07:19
summary: Fix inconsequential warning about when tag when loading samtools mpileup.
affected #: 1 file
diff -r 09ce2f09585514d6ce60ef3cd3dc56d9edd526e4 -r b148fcea038fa00867a3c0e260e8d255a0a08ecb tools/samtools/samtools_mpileup.xml
--- a/tools/samtools/samtools_mpileup.xml
+++ b/tools/samtools/samtools_mpileup.xml
@@ -97,7 +97,7 @@
<when value="perform_indel_calling"><param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" /></when>
- <when value="do_no_perform_indel_calling" />
+ <when value="do_not_perform_indel_calling" /></conditional><param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" /><repeat name="platform_list_repeat" title="Platform for INDEL candidates">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/09ce2f095855/
changeset: 09ce2f095855
user: dannon
date: 2012-04-10 20:41:26
summary: Whitespace cleanup.
affected #: 1 file
diff -r b9c0762a09db90952ebd51ce123927f097cd68ff -r 09ce2f09585514d6ce60ef3cd3dc56d9edd526e4 lib/galaxy/web/api/history_contents.py
--- a/lib/galaxy/web/api/history_contents.py
+++ b/lib/galaxy/web/api/history_contents.py
@@ -21,12 +21,11 @@
"""
GET /api/histories/{encoded_history_id}/contents
Displays a collection (list) of history contents
- """
+ """
try:
history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True )
except Exception, e:
return str( e )
-
rval = []
try:
for dataset in history.datasets:
@@ -67,7 +66,7 @@
item = self.encode_all_ids( trans, item )
except Exception, e:
item = "Error in history API at listing dataset"
- log.error( item + ": %s" % str(e) )
+ log.error( item + ": %s" % str(e) )
trans.response.status = 500
return item
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b9c0762a09db/
changeset: b9c0762a09db
user: dannon
date: 2012-04-10 20:32:13
summary: Fix history_contents API adding the HDA to the history twice (resulting in skipped hids)
affected #: 1 file
diff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 -r b9c0762a09db90952ebd51ce123927f097cd68ff lib/galaxy/web/api/history_contents.py
--- a/lib/galaxy/web/api/history_contents.py
+++ b/lib/galaxy/web/api/history_contents.py
@@ -95,7 +95,6 @@
except Exception, e:
return str( e )
hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True )
- history.add_dataset( hda )
trans.sa_session.flush()
return hda.get_api_value()
else:
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