1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ad9cb3bde1ee/
Changeset: ad9cb3bde1ee
User: inithello
Date: 2014-01-27 16:44:24
Summary: Fix description for find_diag_hits.
Affected #: 1 file
diff -r 74392b32685f35aa146cd5b66da098eb78eb77be -r ad9cb3bde1ee3aace42ed16dca5e40ac537eee6d scripts/migrate_tools/0009_tools.xml
--- a/scripts/migrate_tools/0009_tools.xml
+++ b/scripts/migrate_tools/0009_tools.xml
@@ -75,7 +75,7 @@
<repository owner="devteam" changeset_revision="31154ff9f5e1" name="filter_transcripts_via_tracking" description="Filter Combined Transcripts"><tool id="filter_combined_via_tracking" version="0.1" file="filter_transcripts_via_tracking.xml" /></repository>
- <repository owner="devteam" changeset_revision="acf51ff24c7d" name="find_diag_hits" description="find_diag_hits">
+ <repository owner="devteam" changeset_revision="acf51ff24c7d" name="find_diag_hits" description="Identify sequence reads corresponding to a particular taxonomic group"><tool id="find_diag_hits" version="1.0.0" file="find_diag_hits.xml" /></repository><repository owner="devteam" changeset_revision="33a0e6aca936" name="freebayes_wrapper" description="Call SNPS with Freebayes">
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/6c5913a4b701/
Changeset: 6c5913a4b701
Branch: stable
User: dan
Date: 2014-01-27 15:54:34
Summary: Fix for aggregate_scores_in_intervals.py broken in 95bf71620d50c6d81248eef2001a7dc156ae1088.
Affected #: 1 file
diff -r 03f7d79212ecf626af4940296e663c376b9cd2ee -r 6c5913a4b701813e823638125fff8bf9fda7354b tools/stats/aggregate_scores_in_intervals.py
--- a/tools/stats/aggregate_scores_in_intervals.py
+++ b/tools/stats/aggregate_scores_in_intervals.py
@@ -201,7 +201,7 @@
continue
# Get the score, only count if not 'nan'
score = scores_by_chrom[chrom][j]
- if not isNaN( score ):
+ if not isnan( score ):
total += score
count += 1
max_score = max( score, max_score )
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/04bce95d8fd2/
Changeset: 04bce95d8fd2
User: dan
Date: 2014-01-27 15:54:34
Summary: Fix for aggregate_scores_in_intervals.py broken in 95bf71620d50c6d81248eef2001a7dc156ae1088.
Affected #: 1 file
diff -r bbd852d8ed7c125844aac9f38a85d5246bbd845b -r 04bce95d8fd21ae597ba839936dd644870450051 tools/stats/aggregate_scores_in_intervals.py
--- a/tools/stats/aggregate_scores_in_intervals.py
+++ b/tools/stats/aggregate_scores_in_intervals.py
@@ -201,7 +201,7 @@
continue
# Get the score, only count if not 'nan'
score = scores_by_chrom[chrom][j]
- if not isNaN( score ):
+ if not isnan( score ):
total += score
count += 1
max_score = max( score, max_score )
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/03f7d79212ec/
Changeset: 03f7d79212ec
Branch: stable
User: jmchilton
Date: 2014-01-27 03:47:59
Summary: Bugfix: Disallow shared workflows from being inappropriately deletable...
... by user workflow is shared with via workflow API.
Affected #: 1 file
diff -r 87b586afb05428a3b0ae37d68c79241994a27021 -r 03f7d79212ecf626af4940296e663c376b9cd2ee lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -296,9 +296,8 @@
# check to see if user has permissions to selected workflow
if stored_workflow.user != trans.user and not trans.user_is_admin():
- if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
- trans.response.status = 403
- return("Workflow is not owned by or shared with current user")
+ trans.response.status = 403
+ return("Workflow is not owned by current user")
#Mark a workflow as deleted
stored_workflow.deleted = True
https://bitbucket.org/galaxy/galaxy-central/commits/a7ac443f9c9b/
Changeset: a7ac443f9c9b
User: jmchilton
Date: 2014-01-27 03:48:23
Summary: Merge latest stable.
Affected #: 1 file
diff -r e410940a015c5245f2d065b8f7a9eda8da56d966 -r a7ac443f9c9b7b5383284149db4bcc6a99e4b124 lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -325,9 +325,8 @@
# check to see if user has permissions to selected workflow
if stored_workflow.user != trans.user and not trans.user_is_admin():
- if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
- trans.response.status = 403
- return("Workflow is not owned by or shared with current user")
+ trans.response.status = 403
+ return("Workflow is not owned by current user")
#Mark a workflow as deleted
stored_workflow.deleted = True
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/e410940a015c/
Changeset: e410940a015c
User: greg
Date: 2014-01-26 23:41:11
Summary: Timing and statistics improvements in the tool shed's install and test framework.
Affected #: 1 file
diff -r d658d4ec711d0c778b9ce07d700c3d3fee9aeca0 -r e410940a015c5245f2d065b8f7a9eda8da56d966 test/install_and_test_tool_shed_repositories/base/util.py
--- a/test/install_and_test_tool_shed_repositories/base/util.py
+++ b/test/install_and_test_tool_shed_repositories/base/util.py
@@ -878,24 +878,25 @@
else:
# The assumption is that the Tool SHed's install and test framework is executed no more than once per 24 hour
# period, so check the required repository's time_last_tested value to see if its tool_test_results column
- # has been updated within the past 24 hours. The RepositoryMetadata class's to_dict() method returns the value
- # of time_last_tested in datetime.isoformat().
+ # has been updated within the past 20 hours to allow for differing test run times (some may be slower than
+ # others). The RepositoryMetadata class's to_dict() method returns the value of time_last_tested in
+ # datetime.isoformat().
time_last_tested, error_message = get_time_last_tested( galaxy_tool_shed_url, required_repository_metadata_id )
print 'Value of time_last_tested: %s' % str( time_last_tested )
if time_last_tested is None:
print 'The time_last_tested column value is None for version %s of repository dependency %s owned by %s.' % \
( changeset_revision, name, owner )
else:
- twenty_four_hours_ago = ( datetime.utcnow() - timedelta( hours=24 ) ).isoformat()
- print 'Value of twenty_four_hours_ago: %s' % str( twenty_four_hours_ago )
+ twenty_hours_ago = ( datetime.utcnow() - timedelta( hours=20 ) ).isoformat()
+ print 'Value of twenty_hours_ago: %s' % str( twenty_hours_ago )
# This is counter intuitive because the following check is on strings like this: '2014-01-21T19:46:06.953741',
- # so if "time_last_tested > twenty_four_hours_ago" is True, then it implies that the time_last_tested column
- # was actually updated less than 24 hours ago, and should not be updated again because we're likely processing
+ # so if "time_last_tested > twenty_hours_ago" is True, then it implies that the time_last_tested column
+ # was actually updated less than 20 hours ago, and should not be updated again because we're likely processing
# another dependent repository, many of which can have the same repository dependency.
try:
# Be very conservative here. Our default behavior will be to assume containers have not been populated
# during the current test run.
- already_populated = time_last_tested > twenty_four_hours_ago
+ already_populated = time_last_tested > twenty_hours_ago
except Exception, e:
log.exception( 'Error attempting to set already_populated: %s' % str( e ) )
already_populated = False
@@ -903,10 +904,10 @@
if already_populated:
print 'The install containers for version %s of repository dependency %s owned by %s have been ' % \
( changeset_revision, name, owner )
- print 'populated within the past 24 hours (likely in this test run), so skipping this check.'
+ print 'populated within the past 20 hours (likely in this test run), so skipping this check.'
continue
else:
- print 'Version %s of repository dependency %s owned by %s was last tested more than 24 hours ago.' % \
+ print 'Version %s of repository dependency %s owned by %s was last tested more than 20 hours ago.' % \
( changeset_revision, name, owner )
# Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated.
if len( tool_test_results_dicts ) == 0:
@@ -996,27 +997,27 @@
print "# Repository revisions processed: %s" % str( total_repositories_processed )
if successful_repository_installations:
print "# ----------------------------------------------------------------------------------"
- print "# The following revisions were successfully installed:"
+ print "# The following %d revisions were successfully installed:" % len( successful_repository_installations )
display_repositories_by_owner( successful_repository_installations )
if repositories_with_installation_error:
print "# ----------------------------------------------------------------------------------"
- print "# The following revisions have installation errors:"
+ print "# The following %d revisions have installation errors:" % len( repositories_with_installation_error )
display_repositories_by_owner( repositories_with_installation_error )
if successful_tool_dependency_installations:
print "# ----------------------------------------------------------------------------------"
- print "# The following tool dependencies were successfully installed:"
+ print "# The following %d tool dependencies were successfully installed:" % len( successful_tool_dependency_installations )
display_tool_dependencies_by_name( successful_tool_dependency_installations )
if tool_dependencies_with_installation_error:
print "# ----------------------------------------------------------------------------------"
- print "# The following tool dependencies have installation errors:"
+ print "# The following %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error )
display_tool_dependencies_by_name( tool_dependencies_with_installation_error )
if all_tests_passed:
print '# ----------------------------------------------------------------------------------'
- print "# The following revisions successfully passed all functional tests:"
+ print "# The following %d revisions successfully passed all functional tests:" % len( all_tests_passed )
display_repositories_by_owner( all_tests_passed )
if at_least_one_test_failed:
print '# ----------------------------------------------------------------------------------'
- print "# The following revisions failed at least 1 functional test:"
+ print "# The following %d revisions failed at least 1 functional test:" % len( at_least_one_test_failed )
display_repositories_by_owner( at_least_one_test_failed )
print "####################################################################################"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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