1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/76a8795d3a7e/
changeset: 76a8795d3a7e
user: greg
date: 2013-01-14 23:15:46
summary: Fixes for discovering repository dependencies when resinstalling a tool shed repository when the repository dependencies were added to updated revisions of a repository after it was uninstalled.
affected #: 3 files
diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -952,12 +952,16 @@
update_dict = encoding_util.tool_shed_decode( encoded_update_dict )
changeset_revision = update_dict[ 'changeset_revision' ]
ctx_rev = update_dict[ 'ctx_rev' ]
+ includes_tools = update_dict.get( 'includes_tools', False )
+ has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False )
response.close()
except Exception, e:
log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) )
+ includes_tools = False
+ has_repository_dependencies = False
changeset_revision = None
ctx_rev = None
- return changeset_revision, ctx_rev
+ return changeset_revision, ctx_rev, includes_tools, has_repository_dependencies
def handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ):
"""
Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the
diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1256,6 +1256,21 @@
@web.expose
def get_changeset_revision_and_ctx_rev( self, trans, **kwd ):
"""Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated."""
+ def has_tools_and_repository_dependencies( repository_metadata ):
+ includes_tools = False
+ has_repository_dependencies = False
+ if repository_metadata:
+ metadata = repository_metadata.metadata
+ if metadata:
+ if 'tools' in metadata:
+ includes_tools = True
+ else:
+ includes_tools = False
+ if 'repository_dependencies' in metadata:
+ has_repository_dependencies = True
+ else:
+ has_repository_dependencies = False
+ return includes_tools, has_repository_dependencies
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
@@ -1264,20 +1279,24 @@
owner = params.get( 'owner', None )
changeset_revision = params.get( 'changeset_revision', None )
repository = suc.get_repository_by_name_and_owner( trans, name, owner )
+ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
+ trans.security.encode_id( repository.id ),
+ changeset_revision )
+ includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( repository_metadata )
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
# Default to the received changeset revision and ctx_rev.
update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
ctx_rev = str( update_to_ctx.rev() )
latest_changeset_revision = changeset_revision
- update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev )
+ update_dict = dict( changeset_revision=changeset_revision,
+ ctx_rev=ctx_rev,
+ includes_tools=includes_tools,
+ has_repository_dependencies=has_repository_dependencies )
if changeset_revision == repository.tip( trans.app ):
# If changeset_revision is the repository tip, there are no additional updates.
return encoding_util.tool_shed_encode( update_dict )
else:
- repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
- trans.security.encode_id( repository.id ),
- changeset_revision )
if repository_metadata:
# If changeset_revision is in the repository_metadata table for this repository, there are no additional updates.
return encoding_util.tool_shed_encode( update_dict )
@@ -1286,10 +1305,16 @@
# repository was installed. We need to find the changeset_revision to which we need to update.
update_to_changeset_hash = None
for changeset in repo.changelog:
+ includes_tools = False
+ has_repository_dependencies = False
changeset_hash = str( repo.changectx( changeset ) )
ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
if update_to_changeset_hash:
- if suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ):
+ update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
+ trans.security.encode_id( repository.id ),
+ changeset_hash )
+ if update_to_repository_metadata:
+ includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( update_to_repository_metadata )
# We found a RepositoryMetadata record.
if changeset_hash == repository.tip( trans.app ):
# The current ctx is the repository tip, so use it.
@@ -1302,6 +1327,8 @@
elif not update_to_changeset_hash and changeset_hash == changeset_revision:
# We've found the changeset in the changelog for which we need to get the next update.
update_to_changeset_hash = changeset_hash
+ update_dict[ 'includes_tools' ] = includes_tools
+ update_dict[ 'has_repository_dependencies' ] = has_repository_dependencies
update_dict[ 'changeset_revision' ] = str( latest_changeset_revision )
update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() )
return encoding_util.tool_shed_encode( update_dict )
diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -372,27 +372,15 @@
if operation == "activate or reinstall":
repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
if repository.uninstalled:
- # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated so that we
+ # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated so that we
# can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies
# will be current.
- current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository )
- if current_ctx_rev != repository.ctx_rev:
- repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( repository.repo_path( trans.app ) ) )
- repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
- shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision )
- suc.update_repository( repo, ctx_rev=current_ctx_rev )
- shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
- shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf )
- metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app,
- repository=repository,
- repository_clone_url=repository_clone_url,
- shed_config_dict=shed_config_dict,
- relative_install_dir=relative_install_dir,
- repository_files_dir=None,
- resetting_all_metadata_on_repository=False,
- updating_installed_repository=True,
- persist=True )
- if repository.includes_tools or repository.has_repository_dependencies:
+ current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \
+ shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository )
+ if current_ctx_rev == repository.ctx_rev:
+ includes_tools = repository.includes_tools
+ has_repository_dependencies = repository.has_repository_dependencies
+ if includes_tools or has_repository_dependencies:
# Only allow selecting a different section in the tool panel if the repository was uninstalled.
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='reselect_tool_panel_section',
@@ -859,12 +847,12 @@
if cloned_ok:
if reinstalling:
# Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated.
- current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository )
+ current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \
+ shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository )
if current_ctx_rev != ctx_rev:
repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) )
shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision )
suc.update_repository( repo, ctx_rev=current_ctx_rev )
-
self.handle_repository_contents( trans,
tool_shed_repository=tool_shed_repository,
tool_path=tool_path,
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/dc575517a5f2/
changeset: dc575517a5f2
user: jgoecks
date: 2013-01-14 20:14:41
summary: Add tool id for when clause warnings that are output when tool XML is parsed.
affected #: 1 file
diff -r 7b30a0fd0a042eb6db92e43e005ccd6634184e66 -r dc575517a5f2d3081e1795c5d5e91c77e4488bc5 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1600,9 +1600,11 @@
try:
possible_cases.remove( case.value )
except:
- log.warning( "A when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( group.name, group.test_param.name, case.value ) )
+ log.warning( "Tool %s: a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." %
+ ( self.id, group.name, group.test_param.name, case.value ) )
for unspecified_case in possible_cases:
- log.warning( "A when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( group.name, group.test_param.name, unspecified_case ) )
+ log.warning( "Tool %s: a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." %
+ ( self.id, group.name, group.test_param.name, unspecified_case ) )
case = ConditionalWhen()
case.value = unspecified_case
case.inputs = odict()
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/f57b2bfb2365/
changeset: f57b2bfb2365
user: greg
date: 2013-01-14 17:22:07
summary: Ensure each repository dependency container contains only unique entries.
affected #: 1 file
diff -r 937966b77a10fb229ee265f2a85eac6634fb7d08 -r f57b2bfb2365bef93b7974d990d663a0660a67d9 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -235,11 +235,8 @@
for name, repo_info_tuple 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_tuple )
- clone_dir = os.path.join( tool_path, generate_tool_path( repository_clone_url, changeset_revision ) )
- relative_install_dir = os.path.join( clone_dir, name )
# Make sure the repository was not already installed.
- installed_tool_shed_repository, installed_changeset_revision = \
- repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, clone_dir )
+ installed_tool_shed_repository, installed_changeset_revision = repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple )
if installed_tool_shed_repository:
tool_section, new_tool_panel_section, tool_panel_section_key = handle_tool_panel_selection( trans=trans,
metadata=installed_tool_shed_repository.metadata,
@@ -602,8 +599,7 @@
installed_rd, missing_rd = \
get_installed_and_missing_repository_dependencies( trans, repository )
else:
- installed_rd, missing_rd = \
- get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies )
+ installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
# Discover all repository dependencies and retrieve information for installing them.
required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) )
# Display tool dependencies defined for each of the repository dependencies.
@@ -697,7 +693,7 @@
missing_repository_dependencies[ root_key ] = missing_rd_tups
missing_repository_dependencies[ 'description' ] = description
return installed_repository_dependencies, missing_repository_dependencies
-def get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies ):
+def get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ):
"""
Parse the received repository_dependencies dictionary that is associated with a repository being installed into Galaxy for the first time
and attempt to determine repository dependencies that are already installed and those that are not.
@@ -706,28 +702,32 @@
installed_repository_dependencies = {}
missing_rd_tups = []
installed_rd_tups = []
- description = repository_dependencies[ 'description' ]
- root_key = repository_dependencies[ 'root_key' ]
- # The repository dependencies container will include only the immediate repository dependencies of this repository, so the container will be
- # only a single level in depth.
- for key, rd_tups in repository_dependencies.items():
- if key in [ 'description', 'root_key' ]:
- continue
- for rd_tup in rd_tups:
- tool_shed, name, owner, changeset_revision = rd_tup
- # This is tricky because updates to installed repository revisions may have occurred making it difficult to discover installed repository
- # revisions. If installed repositories are not discovered in this method, they will be returned in the list of missing_repository_dependencies,
- # but should be discovered later during the installation process since that process inspects all appropriate changeset revisions.
- repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed, name, owner, changeset_revision )
- if repository:
- new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ]
- if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED:
- installed_rd_tups.append( new_rd_tup )
+ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
+ suc.get_repo_info_tuple_contents( repo_info_tuple )
+ if repository_dependencies:
+ description = repository_dependencies[ 'description' ]
+ root_key = repository_dependencies[ 'root_key' ]
+ # The repository dependencies container will include only the immediate repository dependencies of this repository, so the container will be
+ # only a single level in depth.
+ for key, rd_tups in repository_dependencies.items():
+ if key in [ 'description', 'root_key' ]:
+ continue
+ for rd_tup in rd_tups:
+ tool_shed, name, owner, changeset_revision = rd_tup
+ # Updates to installed repository revisions may have occurred, so make sure to locate the appropriate repository revision if one exists.
+ repository, current_changeset_revision = repository_was_previously_installed( trans, tool_shed, name, repo_info_tuple )
+ if repository:
+ new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ]
+ if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED:
+ if new_rd_tup not in installed_rd_tups:
+ installed_rd_tups.append( new_rd_tup )
+ else:
+ if new_rd_tup not in missing_rd_tups:
+ missing_rd_tups.append( new_rd_tup )
else:
- missing_rd_tups.append( new_rd_tup )
- else:
- new_rd_tup = [ tool_shed, name, owner, changeset_revision, None, 'Never installed' ]
- missing_rd_tups.append( new_rd_tup )
+ new_rd_tup = [ tool_shed, name, owner, changeset_revision, None, 'Never installed' ]
+ if new_rd_tup not in missing_rd_tups:
+ missing_rd_tups.append( new_rd_tup )
if installed_rd_tups:
installed_repository_dependencies[ 'root_key' ] = root_key
installed_repository_dependencies[ root_key ] = installed_rd_tups
@@ -1415,16 +1415,11 @@
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if tool_dependencies:
- clone_dir = os.path.join( tool_path, generate_tool_path( repository_clone_url, changeset_revision ) )
# Add the install_dir attribute to the tool_dependencies.
tool_dependencies = suc.add_installation_directories_to_tool_dependencies( trans=trans,
tool_dependencies=tool_dependencies )
# The required_repository may have been installed with a different changeset revision.
- required_repository, installed_changeset_revision = repository_was_previously_installed( trans,
- tool_shed_url,
- name,
- repo_info_tuple,
- clone_dir )
+ required_repository, installed_changeset_revision = repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple )
if required_repository:
required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \
get_installed_and_missing_tool_dependencies( trans, required_repository, tool_dependencies )
@@ -1610,7 +1605,7 @@
trans.sa_session.add( tool_dependency )
trans.sa_session.flush()
return removed, error_message
-def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple, clone_dir ):
+def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ):
"""
Handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated
in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one
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/937966b77a10/
changeset: 937966b77a10
user: clements
date: 2013-01-12 01:00:01
summary: Reindented license text to make it render better at bitbucket.
Also dropped non-informative link from outside the license.
affected #: 1 file
diff -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 -r 937966b77a10fb229ee265f=
2a85eac6634fb7d08 LICENSE.txt
--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -2,49 +2,178 @@
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Work, thereby creating derivative works ("Derivative Works") based upon the=
Original Work;
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nal=20
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+14) Definition of "You" in This License. "You" throughout this License,=20
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+16) Modification of This License. This License is Copyright =C2=A9 2005 La=
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