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Merged in BjoernGruening/galaxy-central-bgruening/action_type_misc (pull request #216)

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Move the evaluate_template function to the td_common_util file.
This commit is contained in:
Dave Bouvier
2013-10-15 11:15:57 -04:00
parent 73670bd2dc 237a86715d
commit dc950c15dd
3 changed files with 66 additions and 34 deletions
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lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+53 -25
View File
@@ -199,6 +199,54 @@ def install_virtualenv( app, venv_dir ):
shutil.move( full_path_to_dir, venv_dir )
return True
class InstallEnvironment( object ):
"""
Object describing the environment built up as part of the process of building
and installing a package.
"""
def __init__( self ):
self.env_shell_file_paths = []
def build_command( self, command, action_type='shell_command' ):
"""
Build command line for execution from simple command, but
configuring environment described by this object.
"""
env_cmds = self.environment_commands(action_type)
return '\n'.join(env_cmds + [command])
def environment_commands(self, action_type):
"""
Build a list of commands used to construct the environment described by
this object.
"""
cmds = []
for env_shell_file_path in self.env_shell_file_paths:
if os.path.exists( env_shell_file_path ):
for env_setting in open( env_shell_file_path ):
cmds.append( env_setting.strip( '\n' ) )
else:
log.debug( 'Invalid file %s specified, ignoring %s action.', env_shell_file_path, action_type )
return cmds
def environment_dict(self, action_type='template_command'):
env_vars = dict()
for env_shell_file_path in self.env_shell_file_paths:
if os.path.exists( env_shell_file_path ):
for env_setting in open( env_shell_file_path ):
env_string = env_setting.split( ';' )[ 0 ]
env_name, env_path = env_string.split( '=' )
env_vars[ env_name ] = env_path
else:
log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path )
return env_vars
def add_env_shell_file_paths(self, paths):
self.env_shell_file_paths.extend(paths)
def install_and_build_package( app, tool_dependency, actions_dict ):
"""Install a Galaxy tool dependency package either via a url or a mercurial or git clone command."""
sa_session = app.model.context.current
@@ -206,7 +254,7 @@ def install_and_build_package( app, tool_dependency, actions_dict ):
package_name = actions_dict[ 'package_name' ]
actions = actions_dict.get( 'actions', None )
filtered_actions = []
env_shell_file_paths = []
install_environment = InstallEnvironment()
if actions:
with make_tmp_dir() as work_dir:
with lcd( work_dir ):
@@ -326,13 +374,7 @@ def install_and_build_package( app, tool_dependency, actions_dict ):
# Currently the only action supported in this category is "environment_variable".
# Build a command line from the prior_installation_required, in case an environment variable is referenced
# in the set_environment action.
cmds = []
for env_shell_file_path in env_shell_file_paths:
if os.path.exists( env_shell_file_path ):
for env_setting in open( env_shell_file_path ):
cmds.append( env_setting.strip( '\n' ) )
else:
log.debug( 'Invalid file %s specified, ignoring set_environment action.', env_shell_file_path )
cmds = install_environment.environment_commands( 'set_environment' )
env_var_dicts = action_dict[ 'environment_variable' ]
for env_var_dict in env_var_dicts:
# Check for the presence of the $ENV[] key string and populate it if possible.
@@ -345,7 +387,7 @@ def install_and_build_package( app, tool_dependency, actions_dict ):
# Currently the only action supported in this category is a list of paths to one or more tool dependency env.sh files,
# the environment setting in each of which will be injected into the environment for all <action type="shell_command">
# tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file.
env_shell_file_paths = action_dict[ 'env_shell_file_paths' ]
install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] )
elif action_type == 'setup_virtualenv':
# TODO: maybe should be configurable
venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) )
@@ -391,27 +433,13 @@ def install_and_build_package( app, tool_dependency, actions_dict ):
return
elif action_type == 'shell_command':
with settings( warn_only=True ):
cmd = ''
for env_shell_file_path in env_shell_file_paths:
if os.path.exists( env_shell_file_path ):
for env_setting in open( env_shell_file_path ):
cmd += '%s\n' % env_setting
else:
log.debug( 'Invalid file %s specified, ignoring shell_command action.', env_shell_file_path )
cmd += action_dict[ 'command' ]
cmd = install_environment.build_command( action_dict[ 'command' ] )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
if return_code:
return
elif action_type == 'template_command':
env_vars = dict()
for env_shell_file_path in env_shell_file_paths:
if os.path.exists( env_shell_file_path ):
for env_setting in open( env_shell_file_path ):
env_string = env_setting.split( ';' )[ 0 ]
env_name, env_path = env_string.split( '=' )
env_vars[ env_name ] = env_path
else:
log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path )
env_vars = install_environment.environment_dict()
env_vars.update( td_common_util.get_env_var_values( install_dir ) )
language = action_dict[ 'language' ]
with settings( warn_only=True, **env_vars ):
lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+8 -9
View File
@@ -445,10 +445,6 @@ def install_package( app, elem, tool_shed_repository, tool_dependencies=None ):
def install_via_fabric( app, tool_dependency, install_dir, package_name=None, proprietary_fabfile_path=None, actions_elem=None, action_elem=None, **kwd ):
"""Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric."""
def evaluate_template( text ):
""" Substitute variables defined in XML blocks from dependencies file."""
return Template( text ).safe_substitute( td_common_util.get_env_var_values( install_dir ) )
sa_session = app.model.context.current
if not os.path.exists( install_dir ):
os.makedirs( install_dir )
@@ -493,7 +489,7 @@ def install_via_fabric( app, tool_dependency, install_dir, package_name=None, pr
action_dict[ 'target_directory' ] = action_elem.get( 'target_directory', None )
elif action_type == 'shell_command':
# <action type="shell_command">make</action>
action_elem_text = evaluate_template( action_elem.text )
action_elem_text = td_common_util.evaluate_template( action_elem.text, install_dir )
if action_elem_text:
action_dict[ 'command' ] = action_elem_text
else:
@@ -541,7 +537,7 @@ def install_via_fabric( app, tool_dependency, install_dir, package_name=None, pr
elif action_type == 'make_directory':
# <action type="make_directory">$INSTALL_DIR/lib/python</action>
if action_elem.text:
action_dict[ 'full_path' ] = evaluate_template( action_elem.text )
action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir )
else:
continue
elif action_type == 'change_directory':
@@ -556,7 +552,7 @@ def install_via_fabric( app, tool_dependency, install_dir, package_name=None, pr
# <destination_directory>$INSTALL_DIR/bin</destination_directory>
# </action>
for move_elem in action_elem:
move_elem_text = evaluate_template( move_elem.text )
move_elem_text = td_common_util.evaluate_template( move_elem.text, install_dir )
if move_elem_text:
action_dict[ move_elem.tag ] = move_elem_text
elif action_type == 'move_file':
@@ -609,9 +605,12 @@ def install_via_fabric( app, tool_dependency, install_dir, package_name=None, pr
# <action type="setup_virtualenv">pyyaml==3.2.0
# lxml==2.3.0</action>
## Manually specify contents of requirements.txt file to create dynamically.
action_dict[ 'requirements' ] = evaluate_template( action_elem.text or 'requirements.txt' )
action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir )
elif action_type == 'chmod':
# Change the read, write, and execute bits on a file.
# <action type="chmod">
# <file mode="750">$INSTALL_DIR/bin/faToTwoBit</file>
# </action>
file_elems = action_elem.findall( 'file' )
chmod_actions = []
# A unix octal mode is the sum of the following values:
@@ -627,7 +626,7 @@ def install_via_fabric( app, tool_dependency, install_dir, package_name=None, pr
received_mode = int( file_elem.get( 'mode', 600 ), base=8 )
# For added security, ensure that the setuid and setgid bits are not set.
mode = received_mode & ~( stat.S_ISUID | stat.S_ISGID )
file = evaluate_template( file_elem.text )
file = td_common_util.evaluate_template( file_elem.text, install_dir )
chmod_tuple = ( file, mode )
chmod_actions.append( chmod_tuple )
action_dict[ 'change_modes' ] = chmod_actions
lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py
+5
View File
@@ -7,6 +7,7 @@ import tarfile
import traceback
import urllib2
import zipfile
from string import Template
import tool_shed.util.shed_util_common as suc
from galaxy.datatypes import checkers
@@ -470,3 +471,7 @@ def zipfile_ok( path_to_archive ):
def __shellquote(s):
"""Quote and escape the supplied string for use in shell expressions."""
return "'" + s.replace( "'", "'\\''" ) + "'"
def evaluate_template( text, install_dir ):
""" Substitute variables defined in XML blocks from dependencies file."""
return Template( text ).safe_substitute( get_env_var_values( install_dir ) )