1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/165927888055/
Changeset: 165927888055
User: greg
Date: 2014-04-10 17:35:37
Summary: Display repository dependency definition attributes for repositories being installed into Galaxy where the dependency hierarchy cannot be determined likely due to invalid dependency definitions.
Affected #: 5 files
diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -276,7 +276,7 @@
@web.expose_api
def repository_ids_for_setting_metadata( self, trans, my_writable=False, **kwd ):
"""
- GET /api/get_repository_ids_for_setting_metadata
+ GET /api/repository_ids_for_setting_metadata
Displays a collection (list) of repository ids ordered for setting metadata.
diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/galaxy/webapps/tool_shed/api/repository_revisions.py
--- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
+++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
@@ -26,7 +26,7 @@
Creates and saves a gzip compressed tar archive of a repository and optionally all of it's repository dependencies.
The following parameters are included in the payload.
- :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed
+ :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository is to be exported
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
:param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository
diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -2570,11 +2570,8 @@
invalid = True
break
if invalid:
- message += 'The repository dependency definitions for this repository are invalid and will be ignored. '
- message += 'The complete dependency hierarchy could not be determined. The cause of repository dependency '
- message += 'definition errors like this can usually be seen when viewing the repository directly from the '
- message += 'Tool Shed. The exact cause cannot be determined when visiting the Tool Shed from Galaxy to '
- message += 'install the repository.'
+ message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata,
+ error_from_tuple=False )
status = 'error'
else:
repository_metadata_id = None
diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/galaxy/webapps/tool_shed/controllers/upload.py
--- a/lib/galaxy/webapps/tool_shed/controllers/upload.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py
@@ -288,7 +288,8 @@
status = 'error'
# Handle messaging for invalid repository dependencies.
invalid_repository_dependencies_message = \
- repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict )
+ repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict,
+ error_from_tuple=True )
if invalid_repository_dependencies_message:
message += invalid_repository_dependencies_message
status = 'error'
diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/tool_shed/util/repository_dependency_util.py
--- a/lib/tool_shed/util/repository_dependency_util.py
+++ b/lib/tool_shed/util/repository_dependency_util.py
@@ -225,18 +225,46 @@
build_repository_dependency_relationships( trans, all_repo_info_dicts, all_created_or_updated_tool_shed_repositories )
return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts
-def generate_message_for_invalid_repository_dependencies( metadata_dict ):
- """Return the error message associated with an invalid repository dependency for display in the caller."""
+def generate_message_for_invalid_repository_dependencies( metadata_dict, error_from_tuple=False ):
+ """Get or generate and return an error message associated with an invalid repository dependency."""
message = ''
if metadata_dict:
- invalid_repository_dependencies_dict = metadata_dict.get( 'invalid_repository_dependencies', None )
- if invalid_repository_dependencies_dict:
- invalid_repository_dependencies = invalid_repository_dependencies_dict.get( 'invalid_repository_dependencies', [] )
- for repository_dependency_tup in invalid_repository_dependencies:
- toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \
- common_util.parse_repository_dependency_tuple( repository_dependency_tup, contains_error=True )
- if error:
- message = '%s ' % str( error )
+ if error_from_tuple:
+ # Return the error messages associated with a set of one or more invalid repository dependency tuples.
+ invalid_repository_dependencies_dict = metadata_dict.get( 'invalid_repository_dependencies', None )
+ if invalid_repository_dependencies_dict is not None:
+ invalid_repository_dependencies = invalid_repository_dependencies_dict.get( 'invalid_repository_dependencies', [] )
+ for repository_dependency_tup in invalid_repository_dependencies:
+ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \
+ common_util.parse_repository_dependency_tuple( repository_dependency_tup, contains_error=True )
+ if error:
+ message += '%s ' % str( error )
+ else:
+ # The complete dependency hierarchy could not be determined for a repository being installed into
+ # Galaxy. This is likely due to invalid repository dependency definitions, so we'll get them from
+ # the metadata and parse them for display in an error message. This will hopefully communicate the
+ # problem to the user in such a way that a resolution can be determined.
+ message += 'The complete dependency hierarchy could not be determined for this repository, so no required '
+ message += 'repositories will not be installed. This is likely due to invalid repository dependency definitions. '
+ repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', None )
+ if repository_dependencies_dict is not None:
+ rd_tups = repository_dependencies_dict.get( 'repository_dependencies', None )
+ if rd_tups is not None:
+ message += 'Here are the attributes of the dependencies defined for this repository to help determine the '
+ message += 'cause of this problem.<br/>'
+ message += '<table cellpadding="2" cellspacing="2">'
+ message += '<tr><th>Tool shed</th><th>Repository name</th><th>Owner</th><th>Changeset revision</th>'
+ message += '<th>Prior install required</th></tr>'
+ for rd_tup in rd_tups:
+ tool_shed, name, owner, changeset_revision, pir, oicct = \
+ common_util.parse_repository_dependency_tuple( rd_tup )
+ if asbool( pir ):
+ pir_str = 'True'
+ else:
+ pir_str = ''
+ message += '<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>' % \
+ ( tool_shed, name, owner, changeset_revision, pir_str )
+ message += '</table>'
return message
def get_key_for_repository_changeset_revision( trans, toolshed_base_url, repository, repository_metadata, all_repository_dependencies ):
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/11624c8dfc6c/
Changeset: 11624c8dfc6c
Branch: trevorw/job_directory-jobs_directory-1397077266550
User: jmchilton
Date: 2014-04-10 15:51:47
Summary: Close branch trevorw/job_directory-jobs_directory-1397077266550
Affected #: 0 files
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/a146d1007651/
Changeset: a146d1007651
User: jmchilton
Date: 2014-04-10 15:51:47
Summary: Thanks Trevor!
Merged in trevorw/galaxy-central-5/trevorw/job_directory-jobs_directory-1397077266550 (pull request #360)
job_directory -> jobs_directory
Affected #: 1 file
diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r a146d1007651d7f08240d39f0ac18a2491207bc7 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -110,7 +110,7 @@
<!-- Traditionally, the LWR client sends request to LWR
server to populate various system properties. This
extra step can be disabled and these calculated here
- on client by uncommenting job_directory and
+ on client by uncommenting jobs_directory and
specifying any additional remote_property_ of
interest. When using message queues this is nessecary
not optional.
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/7f1aa2813345/
Changeset: 7f1aa2813345
Branch: trevorw/job_directory-jobs_directory-1397077266550
User: trevorw
Date: 2014-04-09 23:02:33
Summary: job_directory -> jobs_directory
Affected #: 1 file
diff -r 63a81f21363325ebbefc321350315804b15bc79e -r 7f1aa2813345f8671948bbce0a14ca1638e57d9b job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -110,7 +110,7 @@
<!-- Traditionally, the LWR client sends request to LWR
server to populate various system properties. This
extra step can be disabled and these calculated here
- on client by uncommenting job_directory and
+ on client by uncommenting jobs_directory and
specifying any additional remote_property_ of
interest. When using message queues this is nessecary
not optional.
https://bitbucket.org/galaxy/galaxy-central/commits/a146d1007651/
Changeset: a146d1007651
User: jmchilton
Date: 2014-04-10 15:51:47
Summary: Thanks Trevor!
Merged in trevorw/galaxy-central-5/trevorw/job_directory-jobs_directory-1397077266550 (pull request #360)
job_directory -> jobs_directory
Affected #: 1 file
diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r a146d1007651d7f08240d39f0ac18a2491207bc7 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -110,7 +110,7 @@
<!-- Traditionally, the LWR client sends request to LWR
server to populate various system properties. This
extra step can be disabled and these calculated here
- on client by uncommenting job_directory and
+ on client by uncommenting jobs_directory and
specifying any additional remote_property_ of
interest. When using message queues this is nessecary
not optional.
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/febeffc4787e/
Changeset: febeffc4787e
User: greg
Date: 2014-04-10 13:20:27
Summary: Fix in the tool shed install and test framework for a recently relocated function.
Affected #: 1 file
diff -r b887ef428f8f99685878df3cfe61531e3b4a26a2 -r febeffc4787e625f3687c7d24298d5b2d3fa6241 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
@@ -40,6 +40,7 @@
import galaxy.webapps.tool_shed.model.mapping
from nose.plugins import Plugin
+from tool_shed.util import common_util
from tool_shed.util import tool_dependency_util
from tool_shed.util.xml_util import parse_xml
@@ -1093,7 +1094,7 @@
params[ 'tool_test_results' ] = tool_test_results_dicts
# Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed.
params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.'
- url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) )
+ url = '%s' % ( common_util.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) )
print 'url: ', url
print 'params: ', params
try:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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