mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fixes for uploading a tool to the community space, and keep None from being displayed if there is no user_description.
This commit is contained in:
Greg Von Kuster
@@ -28,8 +28,11 @@ class CommonController( BaseController ):
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else:
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# There must not be any categories associated with the tool
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trans.app.security_agent.set_entity_category_associations( tools=[ tool ], categories=[] )
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if params.get( 'description', False ):
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tool.user_description = util.restore_text( params.get( 'description', '' ) )
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user_description = util.restore_text( params.get( 'user_description', '' ) )
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if user_description:
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tool.user_description = user_description
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else:
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tool.user_description = ''
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trans.sa_session.add( tool )
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trans.sa_session.flush()
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message="Tool '%s' description and category associations have been saved" % tool.name
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@@ -236,7 +239,10 @@ def set_categories( trans, obj, category_ids, delete_existing_assocs=True ):
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def get_tool( trans, id ):
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return trans.sa_session.query( trans.model.Tool ).get( trans.app.security.decode_id( id ) )
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def get_tools( trans ):
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return trans.sa_session.query( trans.model.Tool ).order_by( trans.model.Tool.name )
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# Return only the latest version of each tool
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return trans.sa_session.query( trans.model.Tool ) \
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.filter( trans.model.Tool.newer_version_id == None ) \
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.order_by( trans.model.Tool.name )
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def get_approved_tools( trans, category=None ):
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# TODO: write this as a query using eagerload - will be much faster.
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ids = []
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@@ -26,112 +26,119 @@ class UploadController( BaseController ):
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replace_version = None
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uploaded_file = None
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categories = get_categories( trans )
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if not get_categories( trans ):
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if not categories:
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return trans.response.send_redirect( web.url_for( controller='tool',
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action='browse_tools',
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cntrller='tool',
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message='No categories have been configured in this instance of the Galaxy Community. An administrator needs to create some via the Administrator control panel before anything can be uploaded',
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status='error' ) )
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elif params.file_data == '' and params.url.strip() == '':
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message = 'No files were entered on the upload form.'
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status = 'error'
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elif params.file_data == '':
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try:
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uploaded_file = urllib2.urlopen( params.url.strip() )
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except ( ValueError, urllib2.HTTPError ), e:
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message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e
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if params.get( 'upload_button', False ):
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url_paste = params.get( 'url', '' ).strip()
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file_data = params.get( 'file_data', '' )
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if file_data == '' and url_paste == '':
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message = 'No files were entered on the upload form.'
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status = 'error'
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except urllib2.URLError, e:
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message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e.reason
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status = 'error'
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elif params.file_data not in ( '', None ):
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uploaded_file = params.file_data.file
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if params.upload_button and uploaded_file:
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datatype = trans.app.datatypes_registry.get_datatype_by_extension( params.upload_type )
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if datatype is None:
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message = 'An unknown file type was selected. This should not be possible, please report the error.'
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status = 'error'
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else:
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elif file_data == '':
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try:
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# Initialize the tool object
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meta = datatype.verify( uploaded_file )
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meta.user = trans.user
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meta.guid = trans.app.security.get_new_guid()
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obj = datatype.create_model_object( meta )
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trans.sa_session.add( obj )
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if isinstance( obj, trans.app.model.Tool ):
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existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).first()
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if existing and replace_id is None:
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raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' )
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elif existing:
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replace_version = trans.sa_session.query( trans.app.model.Tool ).get( trans.security.decode_id( replace_id ) )
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if replace_version.newer_version:
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# If the user has picked an old version, switch to the newest version
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replace_version = get_versions( trans, replace_version )[0]
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if replace_version.tool_id != meta.id:
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raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Check the tool XML file' % ( meta.id, replace_version.tool_id ) )
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for old_version in get_versions( trans, replace_version ):
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if old_version.version == meta.version:
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raise UploadError( 'The new version (%s) matches an old version. Check your version in the tool XML file' % meta.version )
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if old_version.is_new():
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raise UploadError( 'There is an existing version of this tool which has not yet been submitted for approval, so either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common',
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action='view_tool',
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cntrller='tool',
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id=trans.security.encode_id( old_version.id ) ) )
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if old_version.is_waiting():
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raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' )
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# Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed
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if category_ids:
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for category_id in category_ids:
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category = trans.app.model.Category.get( trans.security.decode_id( category_id ) )
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# Initialize the tool category
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tca = trans.app.model.ToolCategoryAssociation( obj, category )
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trans.sa_session.add( tca )
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# Initialize the tool event
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event = trans.app.model.Event( state=trans.app.model.Tool.states.NEW )
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# Flush to get an event id
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trans.sa_session.add( event )
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trans.sa_session.flush()
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tea = trans.app.model.ToolEventAssociation( obj, event )
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trans.sa_session.add( tea )
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if replace_version and replace_id:
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replace_version.newer_version_id = obj.id
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trans.sa_session.add( replace_version )
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trans.sa_session.flush()
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try:
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os.link( uploaded_file.name, obj.file_name )
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except OSError:
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shutil.copy( uploaded_file.name, obj.file_name )
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# We're setting cntrller to 'tool' since that is the only controller from which we can upload
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return trans.response.send_redirect( web.url_for( controller='common',
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action='edit_tool',
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cntrller='tool',
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id=trans.app.security.encode_id( obj.id ),
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message='Uploaded %s' % meta.message,
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status='done' ) )
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except ( datatypes.DatatypeVerificationError, UploadError ), e:
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message = str( e )
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uploaded_file = urllib2.urlopen( url_paste )
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except ( ValueError, urllib2.HTTPError ), e:
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message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e
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status = 'error'
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uploaded_file.close()
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elif replace_id is not None:
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replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) )
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old_version = None
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for old_version in get_versions( trans, replace_version ):
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if old_version.is_new():
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message = 'There is an existing version of this tool which has not been submitted for approval, so either submit or delete it before uploading a new version.'
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break
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if old_version.is_waiting():
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message = 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.'
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break
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else:
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except urllib2.URLError, e:
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message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e.reason
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status = 'error'
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elif file_data not in ( '', None ):
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uploaded_file = file_data.file
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if uploaded_file:
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# TODO: tool should no longer be the default when we upload histories and workflows
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upload_type = params.get( 'upload_type', 'tool' )
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datatype = trans.app.datatypes_registry.get_datatype_by_extension( upload_type )
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if datatype is None:
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message = 'An unknown file type was selected. This should not be possible, please report the error.'
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status = 'error'
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else:
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try:
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# Initialize the tool object
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meta = datatype.verify( uploaded_file )
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meta.user = trans.user
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meta.guid = trans.app.security.get_new_guid()
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obj = datatype.create_model_object( meta )
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trans.sa_session.add( obj )
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if isinstance( obj, trans.app.model.Tool ):
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existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).first()
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if existing and replace_id is None:
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raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' )
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elif existing:
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replace_version = trans.sa_session.query( trans.app.model.Tool ).get( trans.security.decode_id( replace_id ) )
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if replace_version.newer_version:
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# If the user has picked an old version, switch to the newest version
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replace_version = get_versions( trans, replace_version )[0]
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if replace_version.tool_id != meta.id:
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raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Check the tool XML file' % ( meta.id, replace_version.tool_id ) )
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for old_version in get_versions( trans, replace_version ):
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if old_version.version == meta.version:
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raise UploadError( 'The new version (%s) matches an old version. Check your version in the tool XML file' % meta.version )
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if old_version.is_new():
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raise UploadError( 'There is an existing version of this tool which has not yet been submitted for approval, so either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common',
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action='view_tool',
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cntrller='tool',
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id=trans.security.encode_id( old_version.id ) ) )
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if old_version.is_waiting():
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raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' )
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# Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed
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if category_ids:
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for category_id in category_ids:
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category = trans.app.model.Category.get( trans.security.decode_id( category_id ) )
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# Initialize the tool category
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tca = trans.app.model.ToolCategoryAssociation( obj, category )
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trans.sa_session.add( tca )
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# Initialize the tool event
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event = trans.app.model.Event( state=trans.app.model.Tool.states.NEW )
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# Flush to get an event id
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trans.sa_session.add( event )
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trans.sa_session.flush()
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tea = trans.app.model.ToolEventAssociation( obj, event )
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trans.sa_session.add( tea )
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if replace_version and replace_id:
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replace_version.newer_version_id = obj.id
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trans.sa_session.add( replace_version )
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trans.sa_session.flush()
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try:
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os.link( uploaded_file.name, obj.file_name )
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except OSError:
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shutil.copy( uploaded_file.name, obj.file_name )
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# We're setting cntrller to 'tool' since that is the only controller from which we can upload
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# TODO: this will need tweaking when we can upload histories or workflows
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return trans.response.send_redirect( web.url_for( controller='common',
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action='edit_tool',
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cntrller='tool',
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id=trans.app.security.encode_id( obj.id ),
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message='Uploaded %s' % meta.message,
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status='done' ) )
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except ( datatypes.DatatypeVerificationError, UploadError ), e:
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message = str( e )
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status = 'error'
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uploaded_file.close()
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elif replace_id is not None:
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replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) )
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old_version = None
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if old_version is not None:
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return trans.response.send_redirect( web.url_for( controller='common',
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action='view_tool',
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cntrller='tool',
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id=trans.app.security.encode_id( old_version.id ),
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message=message,
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status='error' ) )
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for old_version in get_versions( trans, replace_version ):
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if old_version.is_new():
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message = 'There is an existing version of this tool which has not been submitted for approval, so either submit or delete it before uploading a new version.'
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break
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if old_version.is_waiting():
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message = 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.'
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break
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else:
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old_version = None
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if old_version is not None:
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return trans.response.send_redirect( web.url_for( controller='common',
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action='view_tool',
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cntrller='tool',
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id=trans.app.security.encode_id( old_version.id ),
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message=message,
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status='error' ) )
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selected_upload_type = params.get( 'type', 'tool' )
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selected_categories = [ trans.security.decode_id( id ) for id in category_ids ]
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return trans.fill_template( '/webapps/community/upload/upload.mako',
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@@ -120,11 +120,13 @@ class Tool( object ):
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rval.version = root.attrib['version']
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except KeyError, e:
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raise DatatypeVerificationError( 'Tool XML file does not conform to the specification. Missing required <tool> tag attribute: %s' % e )
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rval.description = None
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rval.description = ''
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desc_tag = root.find( 'description' )
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if desc_tag is not None:
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rval.description = desc_tag.text.strip()
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rval.message = 'Tool: %s %s, Version: %s, ID: %s' % ( rval.name, rval.description or '', rval.version, rval.id )
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if desc_tag:
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description = desc_tag.text
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if description:
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rval.description = description.strip()
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rval.message = 'Tool: %s %s, Version: %s, ID: %s' % ( str( rval.name ), str( rval.description ), str( rval.version ), str( rval.id ) )
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return rval
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else:
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raise DatatypeVerificationError( 'Unable to find a properly formatted tool XML file' )
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@@ -82,7 +82,11 @@ $().ready(function() {
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</div>
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<div class="form-row">
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<label>Description:</label>
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<div class="form-row-input"><textarea name="description" rows="5" cols="35">${tool.user_description}</textarea></div>
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%if tool.user_description:
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<div class="form-row-input"><textarea name="user_description" rows="5" cols="35">${tool.user_description}</textarea></div>
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%else:
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<div class="form-row-input"><textarea name="user_description" rows="5" cols="35"></textarea></div>
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%endif
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<div style="clear: both"></div>
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</div>
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<div class="form-row">
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@@ -4,8 +4,12 @@
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from galaxy.web.framework.helpers import time_ago
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from urllib import quote_plus
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menu_label = 'Edit information'
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if cntrller in [ 'tool' ]:
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can_edit = trans.app.security_agent.can_edit_item( trans.user, tool )
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if can_edit:
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menu_label = 'Edit information or submit for approval'
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can_upload_new_version = trans.app.security_agent.can_upload_new_version( trans.user, tool, versions )
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visible_versions = []
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@@ -89,7 +93,7 @@
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<a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a>
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<div popupmenu="tool-${tool.id}-popup">
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%if cntrller=='admin' or can_edit:
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<a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a>
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<a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">${menu_label}</a>
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%endif
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<a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a>
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%if cntrller=='admin' or trans.user==tool.user:
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@@ -114,7 +118,9 @@
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</div>
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<div class="form-row">
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<label>Description:</label>
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${tool.user_description}
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%if tool.user_description:
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${tool.user_description}
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%endif
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<div style="clear: both"></div>
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</div>
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<div class="form-row">
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Block a user