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Several miscellaneous fixes for the tool shed.

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This commit is contained in:
Greg Von Kuster
2010-11-23 15:09:49 -05:00
parent 5f26d1a84b
commit 3a5caa755c
4 changed files with 47 additions and 12 deletions
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lib/galaxy/webapps/community/controllers/common.py
+25 -10
View File
@@ -205,6 +205,7 @@ class CommonController( BaseController, ItemRatings ):
if not id:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='Select a tool to edit',
status='error' ) )
tool = get_tool( trans, id )
@@ -212,6 +213,7 @@ class CommonController( BaseController, ItemRatings ):
if not can_edit:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='You are not allowed to edit this tool',
status='error' ) )
if params.get( 'edit_tool_button', False ):
@@ -306,6 +308,7 @@ class CommonController( BaseController, ItemRatings ):
if not id:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='Select a tool to view',
status='error' ) )
tool = get_tool( trans, id )
@@ -313,6 +316,7 @@ class CommonController( BaseController, ItemRatings ):
if not can_view:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='You are not allowed to view this tool',
status='error' ) )
avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, tool, webapp_model=trans.model )
@@ -368,6 +372,7 @@ class CommonController( BaseController, ItemRatings ):
if not trans.app.security_agent.can_delete( trans.user, trans.user_is_admin(), cntrller, tool ):
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='You are not allowed to delete this tool',
status='error' ) )
# Create a new event
@@ -382,10 +387,11 @@ class CommonController( BaseController, ItemRatings ):
trans.sa_session.add_all( ( tool, tea ) )
trans.sa_session.flush()
# TODO: What if the tool has versions, should they all be deleted?
message = "Tool '%s' has been marked deleted" % tool.name
message = "Tool '%s' version %s has been marked deleted" % ( tool.name, tool.version )
status = 'done'
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message=message,
status=status ) )
@web.expose
@@ -395,12 +401,14 @@ class CommonController( BaseController, ItemRatings ):
if not id:
return trans.response.send_redirect( web.url_for( controller='tool',
action='browse_tools',
cntrller=cntrller,
message='Select a tool to download',
status='error' ) )
tool = get_tool( trans, id )
if not trans.app.security_agent.can_download( trans.user, trans.user_is_admin(), cntrller, tool ):
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='You are not allowed to download this tool',
status='error' ) )
trans.response.set_content_type( tool.mimetype )
@@ -416,12 +424,14 @@ class CommonController( BaseController, ItemRatings ):
if not id:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='Select a tool to upload a new version',
status='error' ) )
tool = get_tool( trans, id )
if not trans.app.security_agent.can_upload_new_version( trans.user, tool ):
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='You are not allowed to upload a new version of this tool',
status='error' ) )
return trans.response.send_redirect( web.url_for( controller='upload',
@@ -439,6 +449,7 @@ class CommonController( BaseController, ItemRatings ):
if not id:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='Select a tool to view its history',
status='error' ) )
tool = get_tool( trans, id )
@@ -446,6 +457,7 @@ class CommonController( BaseController, ItemRatings ):
if not can_view:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message="You are not allowed to view this tool's history",
status='error' ) )
can_approve_or_reject = trans.app.security_agent.can_approve_or_reject( trans.user, trans.user_is_admin(), cntrller, tool )
@@ -476,6 +488,7 @@ class CommonController( BaseController, ItemRatings ):
if not id:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message='Select a tool to rate',
status='error' ) )
tool = get_tool( trans, id )
@@ -483,6 +496,7 @@ class CommonController( BaseController, ItemRatings ):
if not can_rate:
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_tools',
cntrller=cntrller,
message="You are not allowed to rate this tool",
status='error' ) )
if params.get( 'rate_button', False ):
@@ -539,15 +553,16 @@ def get_tool( trans, id ):
def get_latest_versions_of_tools( trans ):
"""Get only the latest version of each tool from the database"""
return trans.sa_session.query( trans.model.Tool ) \
.filter( trans.model.Tool.newer_version_id == None ) \
.order_by( trans.model.Tool.name )
def get_approved_tools( trans ):
"""Get the tools from the database whose state is APPROVED"""
approved_tools = []
for tool in get_latest_versions_of_tools( trans ):
if tool.state == trans.model.Tool.states.APPROVED:
approved_tools.append( tool )
return approved_tools
.filter( trans.model.Tool.table.c.newer_version_id == None ) \
.order_by( trans.model.Tool.table.c.name )
def get_latest_versions_of_tools_by_state( trans, state ):
"""Get only the latest version of each tool whose state is the received state from the database"""
tools = []
for tool in trans.sa_session.query( trans.model.Tool ) \
.order_by( trans.model.Tool.table.c.name ):
if tool.state == state:
tools.append( tool )
return tools
def get_event( trans, id ):
"""Get an event from the databse"""
return trans.sa_session.query( trans.model.Event ).get( trans.security.decode_id( id ) )
lib/galaxy/webapps/community/controllers/tool.py
+12 -1
View File
@@ -28,7 +28,7 @@ class ToolStateColumn( grids.StateColumn ):
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 ) ]
latest_event_id_for_current_versions_of_tools = [ tool.latest_event.id for tool in get_latest_versions_of_tools_by_state( trans, column_filter ) ]
# 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 ) ) )
@@ -113,6 +113,7 @@ class ToolController( BaseController ):
del kwd[ k ]
return trans.response.send_redirect( web.url_for( controller='tool',
action='browse_tools',
cntrller='tool',
**kwd ) )
# Render the list view
return self.category_list_grid( trans, **kwd )
@@ -121,6 +122,15 @@ class ToolController( BaseController ):
# 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' not in kwd:
# We may have been redirected here after performing an action. If we were
# redirected from the tool controller, we have to add the default tools_by_category
# operation to kwd so only tools we should see are displayed. This implies that
# all redirectes from the tool controller added the cntrller value to kwd when
# redirecting.
cntrller = kwd.get( 'cntrller', None )
if cntrller == 'tool':
kwd[ 'operation' ] = 'approved_tools'
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "view_tool":
@@ -187,6 +197,7 @@ class ToolController( BaseController ):
if not id:
return trans.response.send_redirect( web.url_for( controller='tool',
action='browse_tools',
cntrller='tool',
message='Select a tool to download',
status='error' ) )
tool = get_tool( trans, id )
lib/galaxy/webapps/community/controllers/upload.py
+9
View File
@@ -115,6 +115,15 @@ class UploadController( BaseController ):
if replace_version and replace_id:
replace_version.newer_version_id = obj.id
trans.sa_session.add( replace_version )
# TODO: should the state be changed to archived? We'll leave it alone for now
# because if the newer version is deleted, we'll need to add logic to reset the
# the older version back to it's previous state ( possible approved ).
comment = "Replaced by new version %s" % obj.version
event = trans.app.model.Event( state=replace_version.state, comment=comment )
# Flush to get an event id
trans.sa_session.add( event )
trans.sa_session.flush()
tea = trans.app.model.ToolEventAssociation( replace_version, event )
trans.sa_session.flush()
try:
os.link( uploaded_file.name, obj.file_name )
lib/galaxy/webapps/community/security/__init__.py
+1 -1
View File
@@ -223,7 +223,7 @@ class CommunityRBACAgent( RBACAgent ):
# or if the item's state is APPROVED.
if user and user_is_admin and cntrller == 'admin':
return True
if cntrller in [ 'tool' ] and item.is_approved:
if cntrller in [ 'tool' ] and item.is_approved or item.is_archived or item.is_deleted:
return True
return user and user==item.user
def get_all_action_permissions( self, user, user_is_admin, cntrller, item ):