2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2a1459ef5bc4/
Changeset: 2a1459ef5bc4
Branch: stable
User: natefoo
Date: 2013-06-05 21:25:19
Summary: Fix a couple bugs in job recovery in the Condor runner found by Branden Timm.
Affected #: 1 file
diff -r 47b86d6a9077facb54804576be49ca545d18bd4e -r 2a1459ef5bc402c585f24c904e0d5ad82a7326db lib/galaxy/jobs/runners/condor.py
--- a/lib/galaxy/jobs/runners/condor.py
+++ b/lib/galaxy/jobs/runners/condor.py
@@ -232,6 +232,7 @@
"""Recovers jobs stuck in the queued/running state when Galaxy started"""
# TODO Check if we need any changes here
job_id = job.get_job_runner_external_id()
+ galaxy_id_tag = job_wrapper.get_id_tag()
if job_id is None:
self.put( job_wrapper )
return
@@ -252,7 +253,7 @@
cjs.running = False
self.monitor_queue.put( cjs )
- def __old_state_paths( self, cjs, job ):
+ def __old_state_paths( self, cjs ):
"""For recovery of jobs started prior to standardizing the naming of
files in the AsychronousJobState object
"""
https://bitbucket.org/galaxy/galaxy-central/commits/af91c734dbb7/
Changeset: af91c734dbb7
User: natefoo
Date: 2013-06-05 21:25:30
Summary: Merge stable
Affected #: 1 file
diff -r 89d391f23c1bfb9a745b03095dbcf0459b830e19 -r af91c734dbb76b8c0e3166c7471370f9ba8260b5 lib/galaxy/jobs/runners/condor.py
--- a/lib/galaxy/jobs/runners/condor.py
+++ b/lib/galaxy/jobs/runners/condor.py
@@ -232,6 +232,7 @@
"""Recovers jobs stuck in the queued/running state when Galaxy started"""
# TODO Check if we need any changes here
job_id = job.get_job_runner_external_id()
+ galaxy_id_tag = job_wrapper.get_id_tag()
if job_id is None:
self.put( job_wrapper )
return
@@ -252,7 +253,7 @@
cjs.running = False
self.monitor_queue.put( cjs )
- def __old_state_paths( self, cjs, job ):
+ def __old_state_paths( self, cjs ):
"""For recovery of jobs started prior to standardizing the naming of
files in the AsychronousJobState object
"""
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a6e2e099e89a/
Changeset: a6e2e099e89a
User: greg
Date: 2013-06-05 15:58:11
Summary: Fix for handling multiple repository installations simultaneously when handle repository dependencies is checked and at least 1 selected repository for installation has no repository dependencies while at least one selected repository for installation does. This scenario occurs only when searching the tool shed for tools rather than browssing it for repositories.
Affected #: 1 file
diff -r 583f5edfc5977d92f884d86eb9f1af22294fe4c7 -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -252,6 +252,8 @@
# We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids.
required_repository_tups = []
for repo_info_dict in repo_info_dicts:
+ if repo_info_dict not in all_repo_info_dicts:
+ all_repo_info_dicts.append( repo_info_dict )
for repository_name, repo_info_tup in repo_info_dict.items():
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tup )
https://bitbucket.org/galaxy/galaxy-central/commits/7f26e0efb93b/
Changeset: 7f26e0efb93b
Branch: stable
User: greg
Date: 2013-06-05 15:58:11
Summary: Fix for handling multiple repository installations simultaneously when handle repository dependencies is checked and at least 1 selected repository for installation has no repository dependencies while at least one selected repository for installation does. This scenario occurs only when searching the tool shed for tools rather than browssing it for repositories.
Affected #: 1 file
diff -r 2dd18c7198ad7ff1c354dbefa0715b2344360487 -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -252,6 +252,8 @@
# We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids.
required_repository_tups = []
for repo_info_dict in repo_info_dicts:
+ if repo_info_dict not in all_repo_info_dicts:
+ all_repo_info_dicts.append( repo_info_dict )
for repository_name, repo_info_tup in repo_info_dict.items():
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tup )
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/583f5edfc597/
Changeset: 583f5edfc597
User: Dave Bouvier
Date: 2013-06-04 21:54:28
Summary: Add information on why a repository was not tested, if it has been configured not to be tested.
Affected #: 1 file
diff -r 393b3d86fbf1b8c1471faef828de31110d3a90f5 -r 583f5edfc5977d92f884d86eb9f1af22294fe4c7 test/install_and_test_tool_shed_repositories/functional_tests.py
--- a/test/install_and_test_tool_shed_repositories/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/functional_tests.py
@@ -743,6 +743,10 @@
skip_because = reason
break
if skip_this_repository:
+ repository_status[ 'not_tested' ] = dict( reason=skip_because )
+ params[ 'tools_functionally_correct' ] = False
+ params[ 'do_not_test' ] = False
+ register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, repository_info_dict, params )
log.info( "Not testing revision %s of repository %s owned by %s.", changeset_revision, name, owner )
continue
else:
@@ -854,6 +858,10 @@
# "missing_components": "Which components are missing, e.g. the test data filename, or the test-data directory."
# },
# ]
+ # "not_tested":
+ # {
+ # "reason": "The Galaxy development team has determined that this repository should not be installed and tested by the automated framework."
+ # }
# }
failed_tool_dependencies = repository.includes_tool_dependencies and repository.tool_dependencies_with_installation_errors
failed_repository_dependencies = repository.repository_dependencies_with_installation_errors
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/4466b12313cc/
Changeset: 4466b12313cc
User: afgane
Date: 2013-06-04 20:24:10
Summary: Add tabindex to cloudlaunch and set the width for select boxes
Affected #: 1 file
diff -r a28faa6ac188594a60cd495327661a15efd37ea5 -r 4466b12313cc7e22e941c1255ba989e3adbbadf1 templates/webapps/galaxy/cloud/index.mako
--- a/templates/webapps/galaxy/cloud/index.mako
+++ b/templates/webapps/galaxy/cloud/index.mako
@@ -186,16 +186,16 @@
<div class="form-row"><label for="id_key_id">Key ID</label>
- <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value=""/><br/>
+ <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value="" tabindex="1"/><br/><div class="toolParamHelp">
- This is the text string that uniquely identifies your account, found in the
+ This is the text string that uniquely identifies your account, found in the
<a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS Console</a>.
</div></div><div class="form-row"><label for="id_secret">Secret Key</label>
- <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value=""/><br/>
+ <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value="" tabindex="2"/><br/><div class="toolParamHelp">
This is your AWS Secret Key, also found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security
Credentials section of the AWS Console</a>. </div>
@@ -205,7 +205,7 @@
%if not share_string:
<div id='existing_instance_wrapper' style="display:none;" class="form-row"><label for="id_existing_instance">Instances in your account</label>
- <select name="existing_instance" id="id_existing_instance">
+ <select name="existing_instance" id="id_existing_instance" style="min-width: 228px"></select><input id='id_zone' type='hidden' name='zone' value=''/></div>
@@ -231,7 +231,7 @@
<div class="form-row"><label for="id_keypair">Key Pair</label>
- <select name="keypair" id="id_keypair">
+ <select name="keypair" id="id_keypair" style="min-width: 228px"><option name="Create" value="cloudman_keypair">cloudman_keypair</option></select></div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2dd18c7198ad/
Changeset: 2dd18c7198ad
Branch: stable
User: Dave Bouvier
Date: 2013-06-04 18:02:55
Summary: Fix missing import.
Affected #: 1 file
diff -r 2a116647d7d75d5088c43fe3ac1d10bd9e66a08c -r 2dd18c7198ad7ff1c354dbefa0715b2344360487 lib/tool_shed/util/shed_util_common.py
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -8,6 +8,7 @@
from time import strftime
from galaxy import util
from galaxy.util import json
+from galaxy.util import unicodify
from galaxy.web import url_for
from galaxy.web.form_builder import SelectField
from galaxy.datatypes import checkers
https://bitbucket.org/galaxy/galaxy-central/commits/f3cfd3936759/
Changeset: f3cfd3936759
User: Dave Bouvier
Date: 2013-06-04 18:02:55
Summary: Fix missing import.
Affected #: 1 file
diff -r ef3816ca5e0cc88616c34144af00b4fcce5bf0d0 -r f3cfd3936759aa70f3a3b772ecf469e1a059d7cb lib/tool_shed/util/shed_util_common.py
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -8,6 +8,7 @@
from time import strftime
from galaxy import util
from galaxy.util import json
+from galaxy.util import unicodify
from galaxy.web import url_for
from galaxy.web.form_builder import SelectField
from galaxy.datatypes import checkers
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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