Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo…

…_queue_sharing

lib/galaxy/jobs/__init__.py

@@ -755,6 +755,7 @@ def __init__( self, job, queue, use_persisted_destination=False ):
         self.sa_session = self.app.model.context
         self.extra_filenames = []
         self.command_line = None
+        self.dependencies = []
         # Tool versioning variables
         self.write_version_cmd = None
         self.version_string = ""
@@ -902,6 +903,7 @@ def get_special( ):
         # We need command_line persisted to the db in order for Galaxy to re-queue the job
         # if the server was stopped and restarted before the job finished
         job.command_line = unicodify(self.command_line)
+        job.dependencies = self.tool.dependencies
         self.sa_session.add( job )
         self.sa_session.flush()
         # Return list of all extra files

lib/galaxy/model/__init__.py

@@ -393,6 +393,7 @@ def __init__( self ):
         self.tool_id = None
         self.tool_version = None
         self.command_line = None
+        self.dependencies = []
         self.param_filename = None
         self.parameters = []
         self.input_datasets = []
@@ -450,6 +451,9 @@ def get_tool_version( self ):
     def get_command_line( self ):
         return self.command_line
 
+    def get_dependencies(self):
+        return self.dependencies
+
     def get_param_filename( self ):
         return self.param_filename
 
@@ -530,6 +534,9 @@ def set_tool_version( self, tool_version ):
     def set_command_line( self, command_line ):
         self.command_line = command_line
 
+    def set_dependencies( self, dependencies ):
+        self.dependencies = dependencies
+
     def set_param_filename( self, param_filename ):
         self.param_filename = param_filename
 

lib/galaxy/model/mapping.py

@@ -445,6 +445,7 @@
     Column( "state", String( 64 ), index=True ),
     Column( "info", TrimmedString( 255 ) ),
     Column( "command_line", TEXT ),
+    Column( "dependencies", JSONType, nullable=True),
     Column( "param_filename", String( 1024 ) ),
     Column( "runner_name", String( 255 ) ),
     Column( "stdout", TEXT ),

lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py

@@ -0,0 +1,49 @@
+"""
+Add dependencies column to jobs table
+"""
+from __future__ import print_function
+
+import logging
+
+from sqlalchemy import Column, MetaData, Table
+
+from galaxy.model.custom_types import JSONType
+
+log = logging.getLogger( __name__ )
+jobs_dependencies_column = Column( "dependencies", JSONType, nullable=True )
+
+
+def display_migration_details():
+    print("")
+    print("This migration adds dependencies column to job table")
+
+
+def upgrade(migrate_engine):
+    print(__doc__)
+    metadata = MetaData()
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    # Add the dependencies column to the job table
+    try:
+        jobs_table = Table( "job", metadata, autoload=True )
+        jobs_dependencies_column.create( jobs_table )
+        assert jobs_dependencies_column is jobs_table.c.dependencies
+    except Exception as e:
+        print(str(e))
+        log.error( "Adding column 'dependencies' to job table failed: %s" % str( e ) )
+        return
+
+
+def downgrade(migrate_engine):
+    metadata = MetaData()
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    # Drop the job table's dependencies column.
+    try:
+        jobs_table = Table( "job", metadata, autoload=True )
+        jobs_dependencies = jobs_table.c.dependencies
+        jobs_dependencies.drop()
+    except Exception as e:
+        log.debug( "Dropping 'dependencies' column from job table failed: %s" % ( str( e ) ) )

lib/galaxy/tools/__init__.py

@@ -304,6 +304,7 @@ def __init__( self, config_file, tool_source, app, guid=None, repository_id=None
         self.guid = guid
         self.old_id = None
         self.version = None
+        self.dependencies = []
         # Enable easy access to this tool's version lineage.
         self.lineage_ids = []
         # populate toolshed repository info, if available
@@ -1284,13 +1285,15 @@ def validate_inputs( input, value, error, parent, context, prefixed_name, prefix
 
     def build_dependency_shell_commands( self, job_directory=None, metadata=False ):
         """Return a list of commands to be run to populate the current environment to include this tools requirements."""
-        return self.app.toolbox.dependency_manager.dependency_shell_commands(
+        requirements_to_dependencies = self.app.toolbox.dependency_manager.requirements_to_dependencies(
             self.requirements,
             installed_tool_dependencies=self.installed_tool_dependencies,
             tool_dir=self.tool_dir,
             job_directory=job_directory,
             metadata=metadata,
         )
+        self.dependencies = [dep.to_dict() for dep in requirements_to_dependencies.values()]
+        return [dep.shell_commands(req) for req, dep in requirements_to_dependencies.items()]
 
     @property
     def installed_tool_dependencies(self):

lib/galaxy/tools/deps/__init__.py

@@ -88,21 +88,25 @@ def __init__( self, default_base_path, conf_file=None, **extra_config ):
         self.dependency_resolvers = self.__build_dependency_resolvers( conf_file )
 
     def dependency_shell_commands( self, requirements, **kwds ):
-        commands = []
+        requirement_to_dependency = self.requirements_to_dependencies(requirements, **kwds)
+        return [dependency.shell_commands(requirement) for requirement, dependency in requirement_to_dependency.items()]
+
+    def requirements_to_dependencies(self, requirements, **kwds):
+        """
+        Takes a list of requirements and returns a dictionary
+        with requirements as key and dependencies as value.
+        """
+        requirement_to_dependency = dict()
         for requirement in requirements:
-            log.debug( "Building dependency shell command for dependency '%s'", requirement.name )
-            dependency = NullDependency(version=requirement.version, name=requirement.name)
             if requirement.type in [ 'package', 'set_environment' ]:
                 dependency = self.find_dep( name=requirement.name,
                                             version=requirement.version,
                                             type=requirement.type,
                                             **kwds )
-            dependency_commands = dependency.shell_commands( requirement )
-            if not dependency_commands:
-                log.warning( "Failed to resolve dependency on '%s', ignoring", requirement.name )
-            else:
-                commands.append( dependency_commands )
-        return commands
+                log.debug(dependency.resolver_msg)
+                if dependency.dependency_type:
+                    requirement_to_dependency[requirement] = dependency
+        return requirement_to_dependency
 
     def uses_tool_shed_dependencies(self):
         return any( map( lambda r: isinstance( r, ToolShedPackageDependencyResolver ), self.dependency_resolvers ) )

lib/galaxy/tools/deps/resolvers/__init__.py

@@ -91,6 +91,13 @@ def exact( self ):
         the dependency.
         """
 
+    @property
+    def resolver_msg(self):
+        """
+        Return a message describing this dependency
+        """
+        return "Using dependency %s version %s of type %s" % (self.name, self.version, self.dependency_type)
+
 
 class NullDependency( Dependency ):
     dependency_type = None
@@ -100,5 +107,12 @@ def __init__(self, version=None, name=None):
         self.version = version
         self.name = name
 
+    @property
+    def resolver_msg(self):
+        """
+        Return a message describing this dependency
+        """
+        return "Dependency %s not found." % self.name
+
     def shell_commands( self, requirement ):
         return None

templates/show_params.mako

@@ -205,6 +205,30 @@
     ${ render_msg( 'One or more of your original parameters may no longer be valid or displayed properly.', status='warning' ) }
 %endif
 
+%if job and job.dependencies:
+    <br>
+    <table class="tabletip">
+        <thead>
+        <tr>
+            <th>Dependency</th>
+            <th>Dependency Type</th>
+            <th>Version</th>
+        </tr>
+        </thead>
+        <tbody>
+
+            %for dependency in job.dependencies:
+                <tr><td>${ dependency['name'] | h }</td>
+                    <td>${ dependency['dependency_type'] | h }</td>
+                    <td>${ dependency['version'] | h }</td>
+                </tr>
+            %endfor
+
+        </tbody>
+    </table>
+    <br />
+%endif
+
 <script type="text/javascript">
 $(function(){
     $( '.input-dataset-show-params' ).on( 'click', function( ev ){

test/unit/jobs/test_job_wrapper.py

@@ -157,6 +157,7 @@ class MockTool(object):
 
     def __init__(self, app):
         self.version_string_cmd = TEST_VERSION_COMMAND
+        self.dependencies = []
 
     def build_dependency_shell_commands(self, job_directory):
         return TEST_DEPENDENCIES_COMMANDS