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Merge pull request #1909 from mvdbeek/backport_repository_for_dependency_relationship

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[16.01] Backport  PR #1868
This commit is contained in:
Nicola Soranzo
2016-03-11 14:49:06 +00:00
parent 3abd2c213a d6e38c7d48
commit 5a50a4691c
1 changed files with 6 additions and 38 deletions
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lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+6 -38
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@@ -2,8 +2,6 @@ import logging
import os
import tempfile
from sqlalchemy import and_
from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY
from galaxy.util import listify
from tool_shed.util import basic_util
@@ -360,34 +358,6 @@ class Repository( RecipeTag, SyncDatabase ):
env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' )
return env_sh_file_path
def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( self, tool_shed_url, name, owner, changeset_revision ):
sa_session = self.app.install_model.context
# The protocol is not stored, but the port is if it exists.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \
.filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
self.app.install_model.ToolShedRepository.table.c.name == name,
self.app.install_model.ToolShedRepository.table.c.owner == owner,
self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
.first()
if tool_shed_repository:
return tool_shed_repository
# The tool_shed_repository must have been updated to a newer changeset revision than the one defined in the repository_dependencies.xml file,
# so call the tool shed to get all appropriate newer changeset revisions.
text = suc.get_updated_changeset_revisions_from_tool_shed( self.app, tool_shed_url, name, owner, changeset_revision )
if text:
changeset_revisions = listify( text )
for changeset_revision in changeset_revisions:
tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \
.filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
self.app.install_model.ToolShedRepository.table.c.name == name,
self.app.install_model.ToolShedRepository.table.c.owner == owner,
self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
.first()
if tool_shed_repository:
return tool_shed_repository
return None
def handle_complex_repository_dependency_for_package( self, elem, package_name, package_version, tool_shed_repository,
from_tool_migration_manager=False ):
"""
@@ -398,17 +368,15 @@ class Repository( RecipeTag, SyncDatabase ):
and package_version is being installed.
"""
handled_tool_dependencies = []
tool_shed = elem.attrib[ 'toolshed' ]
# The protocol is not stored, but the port is if it exists.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
tool_shed_url = elem.attrib[ 'toolshed' ]
required_repository_name = elem.attrib[ 'name' ]
required_repository_owner = elem.attrib[ 'owner' ]
default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ]
required_repository = \
self.get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( tool_shed,
required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision )
required_repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed_url,
required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision )
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
tmp_filename = None
if required_repository:
required_repository_changeset_revision = required_repository.installed_changeset_revision