Add support for 3 new tool dependency installation recipe action tag types: assert_directory_exists, assert_file_exists and assert_file_executable.

lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py

@@ -4,6 +4,8 @@ import os
 from galaxy import eggs
 
 eggs.require( 'Fabric' )
+eggs.require( 'ssh' )
+eggs.require( 'paramiko' )
 
 from fabric.api import env
 from fabric.api import lcd

lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py

@@ -13,6 +13,8 @@ from contextlib import contextmanager
 # TODO: eliminate the use of fabric here.
 from galaxy import eggs
 eggs.require( 'Fabric' )
+eggs.require( 'ssh' )
+eggs.require( 'paramiko' )
 
 from fabric.operations import _AttributeString
 from fabric import state
@@ -412,7 +414,10 @@ class RecipeManager( object ):
         return tool_dependency, filtered_actions, dir
 
     def load_step_handlers( self ):
-        step_handlers_by_type = dict( autoconf=step_handler.Autoconf(),
+        step_handlers_by_type = dict( assert_directory_exists=step_handler.AssertDirectoryExists(),
+                                      assert_file_executable=step_handler.AssertFileExecutable(),
+                                      assert_file_exists=step_handler.AssertFileExists(),
+                                      autoconf=step_handler.Autoconf(),
                                       change_directory=step_handler.ChangeDirectory(),
                                       chmod=step_handler.Chmod(),
                                       download_binary=step_handler.DownloadBinary(),

lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py

@@ -14,6 +14,9 @@ from tool_shed.galaxy_install.tool_dependencies import td_common_util
 # TODO: eliminate the use of fabric here.
 from galaxy import eggs
 eggs.require( 'Fabric' )
+eggs.require( 'ssh' )
+eggs.require( 'paramiko' )
+
 from fabric.api import settings
 from fabric.api import lcd
 
@@ -33,6 +36,105 @@ class RecipeStep( object ):
         raise "Unimplemented Method"
 
 
+class AssertDirectoryExists( RecipeStep ):
+
+    def __init__( self ):
+        self.type = 'assert_directory_exists'
+
+    def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+                      install_environment, work_dir, install_dir, current_dir=None, initial_download=False ):
+        """
+        Make sure a directory on disk exists.  Since this class is not used in the initial download stage,
+        no recipe step filtering is performed here, and None values are always returned for filtered_actions
+        and dir.
+        """
+        if os.path.isabs( action_dict[ 'full_path' ] ):
+            full_path = action_dict[ 'full_path' ]
+        else:
+            full_path = os.path.join( current_dir, action_dict[ 'full_path' ] )
+        if not td_common_util.assert_directory_exists( full_path=full_path ):
+            status = app.install_model.ToolDependency.installation_status.ERROR
+            error_message = 'The required directory %s does not exist.' % str( full_path )
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+                                                                                   tool_dependency,
+                                                                                   status=status,
+                                                                                   error_message=error_message,
+                                                                                   remove_from_disk=False )
+        return tool_dependency, None, None
+
+    def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_download ):
+        # <action type="make_directory">$INSTALL_DIR/mira</action>
+        if action_elem.text:
+            action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir )
+        return action_dict
+
+
+class AssertFileExecutable( RecipeStep ):
+
+    def __init__( self ):
+        self.type = 'assert_file_executable'
+
+    def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+                      install_environment, work_dir, install_dir, current_dir=None, initial_download=False ):
+        """
+        Make sure a file on disk exists and is executable.  Since this class is not used in the initial
+        download stage, no recipe step filtering is performed here, and None values are always returned
+        for filtered_actions and dir.
+        """
+        if os.path.isabs( action_dict[ 'full_path' ] ):
+            full_path = action_dict[ 'full_path' ]
+        else:
+            full_path = os.path.join( current_dir, action_dict[ 'full_path' ] )
+        if not td_common_util.assert_file_executable( full_path=full_path ):
+            status = app.install_model.ToolDependency.installation_status.ERROR
+            error_message = 'The file %s is not executable by the owner.' % str( full_path )
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+                                                                                   tool_dependency,
+                                                                                   status=status,
+                                                                                   error_message=error_message,
+                                                                                   remove_from_disk=False )
+        return tool_dependency, None, None
+
+    def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_download ):
+        # <action type="assert_executable">$INSTALL_DIR/mira/my_file</action>
+        if action_elem.text:
+            action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir )
+        return action_dict
+
+
+class AssertFileExists( RecipeStep ):
+
+    def __init__( self ):
+        self.type = 'assert_file_exists'
+
+    def execute_step( self, app, tool_dependency, package_name, actions, action_dict, filtered_actions, env_file_builder,
+                      install_environment, work_dir, install_dir, current_dir=None, initial_download=False ):
+        """
+        Make sure a file on disk exists.  Since this class is not used in the initial download stage,
+        no recipe step filtering is performed here, and None values are always returned for
+        filtered_actions and dir.
+        """
+        if os.path.isabs( action_dict[ 'full_path' ] ):
+            full_path = action_dict[ 'full_path' ]
+        else:
+            full_path = os.path.join( current_dir, action_dict[ 'full_path' ] )
+        if not td_common_util.assert_file_exists( full_path=full_path ):
+            status = app.install_model.ToolDependency.installation_status.ERROR
+            error_message = 'The required file %s does not exist.' % str( full_path )
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
+                                                                                   tool_dependency,
+                                                                                   status=status,
+                                                                                   error_message=error_message,
+                                                                                   remove_from_disk=False )
+        return tool_dependency, None, None
+
+    def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_dir, is_binary_download ):
+        # <action type="assert_on_path">$INSTALL_DIR/mira/my_file</action>
+        if action_elem.text:
+            action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir )
+        return action_dict
+
+
 class Autoconf( RecipeStep ):
 
     def __init__( self ):

lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py

@@ -2,6 +2,7 @@ import logging
 import os
 import re
 import shutil
+import stat
 import sys
 import tarfile
 import time
@@ -110,6 +111,31 @@ class CompressedFile( object ):
     def open_zip( self, filepath, mode ):
         return zipfile.ZipFile( filepath, mode )
 
+def assert_directory_exists( full_path ):
+    """Return True if a directory exists and is not a symbolic link."""
+    if os.path.islink( full_path ):
+        return False
+    if os.path.is_dir( full_path ):
+        return True
+    return False
+
+def assert_file_exists( full_path ):
+    """Return True if a file exists.  This will work for both symbolic linke and files."""
+    if os.path.exists( full_path ):
+        return True
+    return False
+
+def assert_file_executable( full_path ):
+    """Return True if a file exists and is executable."""
+    if os.path.islink( full_path ):
+        return False
+    if os.path.is_file( full_path ):
+        # Make sure the owner has execute permission on the file.
+        # See http://docs.python.org/2/library/stat.html
+        if stat.S_IXUSR & os.stat( full_path )[ stat.ST_MODE ] == 64:
+            return True
+    return False
+
 def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ):
     env_var_name = elem.get( 'name', 'PATH' )
     env_var_action = elem.get( 'action', 'prepend_to' )
@@ -155,6 +181,10 @@ def egrep_escape( text ):
     regex = regex.replace( r"\'", "'" )
     return regex
 
+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 ) )
+
 def format_traceback():
     ex_type, ex, tb = sys.exc_info()
     return ''.join( traceback.format_tb( tb ) )
@@ -444,6 +474,10 @@ def parse_package_elem( package_elem, platform_info_dict=None, include_after_ins
             continue
     return actions_elem_tuples
 
+def __shellquote( s ):
+    """Quote and escape the supplied string for use in shell expressions."""
+    return "'" + s.replace( "'", "'\\''" ) + "'"
+
 def url_download( install_dir, downloaded_file_name, download_url, extract=True ):
     file_path = os.path.join( install_dir, downloaded_file_name )
     src = None
@@ -494,11 +528,3 @@ def zipfile_ok( path_to_archive ):
         if not member_path.startswith( basename ):
             return False
     return True
-
-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 ) )