root/galaxy-central/lib/galaxy/webapps/community/controllers/tool.py

import os, logging, urllib, tarfile

from galaxy.web.base.controller import *
from galaxy.webapps.community import model
from galaxy.web.framework.helpers import time_ago, iff, grids
from galaxy.model.orm import *
from common import *

log = logging.getLogger( __name__ )

class StateColumn( grids.StateColumn ):
    def get_value( self, trans, grid, tool ):
        state = tool.state
        if state == trans.model.Tool.states.APPROVED:
            state_color = 'ok'
        elif state == trans.model.Tool.states.REJECTED:
            state_color = 'error'
        elif state == trans.model.Tool.states.ARCHIVED:
            state_color = 'upload'
        else:
            state_color = state
        return '<div class="count-box state-color-%s">%s</div>' % ( state_color, state )

class ToolStateColumn( grids.StateColumn ):
    def filter( self, trans, user, query, column_filter ):
        """Modify query to filter self.model_class by state."""
        if column_filter == "All":
            pass
        elif column_filter in [ v for k, v in self.model_class.states.items() ]:
            # Get all of the latest Events associated with the current version of each tool
            latest_event_id_for_current_versions_of_tools = [ tool.latest_event.id for tool in get_latest_versions_of_tools( trans ) ]
            # Filter query by the latest state for the current version of each tool
            return query.filter( and_( model.Event.table.c.state == column_filter,
                                       model.Event.table.c.id.in_( latest_event_id_for_current_versions_of_tools ) ) )
        return query
        
class ApprovedToolListGrid( ToolListGrid ):
    columns = [ col for col in ToolListGrid.columns ]
    columns.append(
        StateColumn( "Status",
                     link=( lambda item: dict( operation="tools_by_state", id=item.id, webapp="community" ) ),
                     visible=False,
                     attach_popup=False )
    )
    columns.append(
        ToolStateColumn( "State",
                         key="state",
                         visible=False,
                         filterable="advanced" )
    )

class MyToolsListGrid( ApprovedToolListGrid ):
    columns = [ col for col in ToolListGrid.columns ]
    columns.append(
        StateColumn( "Status",
                     link=( lambda item: dict( operation="tools_by_state", id=item.id, webapp="community" ) ),
                     visible=True,
                     attach_popup=False )
    )
    columns.append(
        ToolStateColumn( "State",
                         key="state",
                         visible=False,
                         filterable="advanced" )
    )

class ToolCategoryListGrid( CategoryListGrid ):
    """
    Replaces the tools column in the Category grid with a similar column,
    but displaying the number of APPROVED tools in the category.
    """
    class ToolsColumn( grids.TextColumn ):
        def get_value( self, trans, grid, category ):
            if category.tools:
                viewable_tools = 0
                for tca in category.tools:
                    tool = tca.tool
                    if tool.is_approved:
                        viewable_tools += 1
                return viewable_tools
            return 0

    columns = []
    for col in CategoryListGrid.columns:
        if not isinstance( col, CategoryListGrid.ToolsColumn ):
            columns.append( col )
    columns.append(
        ToolsColumn( "Tools",
                     model_class=model.Tool,
                     attach_popup=False )
    )

class ToolController( BaseController ):

    tool_list_grid = ApprovedToolListGrid()
    my_tools_list_grid = MyToolsListGrid()
    category_list_grid = ToolCategoryListGrid()
    
    @web.expose
    def index( self, trans, **kwd ):
        params = util.Params( kwd )
        message = util.restore_text( params.get( 'message', ''  ) )
        status = params.get( 'status', 'done' )
        return trans.fill_template( '/webapps/community/index.mako', message=message, status=status )
    @web.expose
    def browse_categories( self, trans, **kwd ):
        if 'operation' in kwd:
            operation = kwd['operation'].lower()
            if operation in [ "tools_by_category", "tools_by_state", "tools_by_user" ]:
                # Eliminate the current filters if any exist.
                for k, v in kwd.items():
                    if k.startswith( 'f-' ):
                        del kwd[ k ]
                return trans.response.send_redirect( web.url_for( controller='tool',
                                                                  action='browse_tools',
                                                                  **kwd ) )
        # Render the list view
        return self.category_list_grid( trans, **kwd )
    @web.expose
    def browse_tools( self, trans, **kwd ):
        # We add params to the keyword dict in this method in order to rename the param
        # with an "f-" prefix, simulating filtering by clicking a search link.  We have
        # to take this approach because the "-" character is illegal in HTTP requests.
        if 'operation' in kwd:
            operation = kwd['operation'].lower()
            if operation == "view_tool":
                return trans.response.send_redirect( web.url_for( controller='common',
                                                                  action='view_tool',
                                                                  cntrller='tool',
                                                                  **kwd ) )
            elif operation == "edit_tool":
                return trans.response.send_redirect( web.url_for( controller='common',
                                                                  action='edit_tool',
                                                                  cntrller='tool',
                                                                  **kwd ) )
            elif operation == "download tool":
                return trans.response.send_redirect( web.url_for( controller='common',
                                                                  action='download_tool',
                                                                  cntrller='tool',
                                                                  **kwd ) )
            elif operation == "tools_by_user":
                # Eliminate the current filters if any exist.
                for k, v in kwd.items():
                    if k.startswith( 'f-' ):
                        del kwd[ k ]
                if 'user_id' in kwd:
                    user = get_user( trans, kwd[ 'user_id' ] )
                    kwd[ 'f-email' ] = user.email
                    del kwd[ 'user_id' ]
                else:
                    # The received id is the tool id, so we need to get the id of the user
                    # that uploaded the tool.
                    tool_id = kwd.get( 'id', None )
                    tool = get_tool( trans, tool_id )
                    kwd[ 'f-email' ] = tool.user.email
            elif operation == "my_tools":
                # Eliminate the current filters if any exist.
                for k, v in kwd.items():
                    if k.startswith( 'f-' ):
                        del kwd[ k ]
                kwd[ 'f-email' ] = trans.user.email
                return self.my_tools_list_grid( trans, **kwd )
            elif operation == "approved_tools":
                # Eliminate the current filters if any exist.
                for k, v in kwd.items():
                    if k.startswith( 'f-' ):
                        del kwd[ k ]
                # Make sure only the latest version of a tool whose state is APPROVED are displayed.
                kwd[ 'f-state' ] = trans.model.Tool.states.APPROVED
                return self.tool_list_grid( trans, **kwd )
            elif operation == "tools_by_category":
                # Eliminate the current filters if any exist.
                for k, v in kwd.items():
                    if k.startswith( 'f-' ):
                        del kwd[ k ]
                category_id = kwd.get( 'id', None )
                category = get_category( trans, category_id )
                kwd[ 'f-Category.name' ] = category.name
                # Make sure only the latest version of a tool whose state is APPROVED are displayed.
                kwd[ 'f-state' ] = trans.model.Tool.states.APPROVED
        # Render the list view
        return self.tool_list_grid( trans, **kwd )
    @web.expose
    def view_tool_file( self, trans, **kwd ):
        params = util.Params( kwd )
        id = params.get( 'id', None )
        if not id:
            return trans.response.send_redirect( web.url_for( controller='tool',
                                                              action='browse_tools',
                                                              message='Select a tool to download',
                                                              status='error' ) )
        tool = get_tool( trans, id )
        tool_file_name = urllib.unquote_plus( kwd['file_name'] )
        tool_file = tarfile.open( tool.file_name ).extractfile( tool_file_name )
        trans.response.set_content_type( 'text/plain' )
        return tool_file
    @web.expose
    def help( self, trans, **kwd ):
        params = util.Params( kwd )
        message = util.restore_text( params.get( 'message', ''  ) )
        status = params.get( 'status', 'done' )
        return trans.fill_template( '/webapps/community/tool/help.mako', message=message, status=status, **kwd )