def delete_repository_metadata(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
for repository_metadata_id in ids:
repository_metadata = suc.get_repository_metadata_by_id(
trans, repository_metadata_id)
trans.sa_session.delete(repository_metadata)
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % (
count, inflector.cond_plural(len(ids), "record"))
else:
message = "No repository metadata ids received for deleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repository_metadata',
message=util.sanitize_text(message),
status=status))
def browse_repository_metadata( self, trans, **kwd ):
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if operation == "delete":
return self.delete_repository_metadata( trans, **kwd )
if operation == "view_or_manage_repository_revision":
# The received id is a RepositoryMetadata object id, so we need to get the
# associated Repository and redirect to view_or_manage_repository with the
# changeset_revision.
repository_metadata = suc.get_repository_metadata_by_id( trans, kwd[ 'id' ] )
repository = repository_metadata.repository
kwd[ 'id' ] = trans.security.encode_id( repository.id )
kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
kwd[ 'operation' ] = 'view_or_manage_repository'
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories',
**kwd ) )
return self.repository_metadata_grid( trans, **kwd )
def browse_repository_metadata(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "delete":
return self.delete_repository_metadata(trans, **kwd)
if operation == "view_or_manage_repository_revision":
# The received id is a RepositoryMetadata object id, so we need to get the
# associated Repository and redirect to view_or_manage_repository with the
# changeset_revision.
repository_metadata = suc.get_repository_metadata_by_id(
trans, kwd['id'])
repository = repository_metadata.repository
kwd['id'] = trans.security.encode_id(repository.id)
kwd['changeset_revision'] = repository_metadata.changeset_revision
kwd['operation'] = 'view_or_manage_repository'
return trans.response.send_redirect(
web.url_for(controller='repository',
action='browse_repositories',
**kwd))
return self.repository_metadata_grid(trans, **kwd)
def delete_repository_metadata( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
ids = util.listify( id )
count = 0
for repository_metadata_id in ids:
repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id )
trans.sa_session.delete( repository_metadata )
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural( len( ids ), "record" ) )
else:
message = "No repository metadata ids received for deleting."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='browse_repository_metadata',
message=util.sanitize_text( message ),
status=status ) )
def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode( workflow_name )
if trans.webapp.name == 'community':
# We're in the tool shed.
repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id )
repository_id = trans.security.encode_id( repository_metadata.repository_id )
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id( trans, repository_id )
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata[ 'workflows' ]:
workflow_dict = workflow_tup[1]
if workflow_dict[ 'name' ] == workflow_name:
break
if 'tools' in metadata:
tools_metadata = metadata[ 'tools' ]
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict( trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision )
data = []
canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" )
text = svgfig.SVG( "g" )
connectors = svgfig.SVG( "g" )
boxes = svgfig.SVG( "g" )
svgfig.Text.defaults[ "font-size" ] = "10px"
in_pos = {}
out_pos = {}
margin = 5
# Spacing between input/outputs.
line_px = 16
# Store px width for boxes of each step.
widths = {}
max_width, max_x, max_y = 0, 0, 0
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
tool_errors = module.type == 'tool' and not module.tool
module_data_inputs = get_workflow_data_inputs( step, module )
module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps )
step_dict = {
'id' : step.order_index,
'data_inputs' : module_data_inputs,
'data_outputs' : module_data_outputs,
'position' : step.position,
'tool_errors' : tool_errors
}
input_conn_dict = {}
for conn in step.input_connections:
input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name )
step_dict[ 'input_connections' ] = input_conn_dict
data.append( step_dict )
x, y = step.position[ 'left' ], step.position[ 'top' ]
count = 0
module_name = get_workflow_module_name( module, missing_tool_tups )
max_len = len( module_name ) * 1.5
text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() )
y += 45
for di in module_data_inputs:
cur_y = y + count * line_px
if step.order_index not in in_pos:
in_pos[ step.order_index ] = {}
in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y )
text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() )
count += 1
max_len = max( max_len, len( di[ 'label' ] ) )
if len( module.get_data_inputs() ) > 0:
y += 15
for do in module_data_outputs:
cur_y = y + count * line_px
if step.order_index not in out_pos:
out_pos[ step.order_index ] = {}
out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y )
text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() )
count += 1
max_len = max( max_len, len( do['name' ] ) )
widths[ step.order_index ] = max_len * 5.5
max_x = max( max_x, step.position[ 'left' ] )
max_y = max( max_y, step.position[ 'top' ] )
max_width = max( max_width, widths[ step.order_index ] )
for step_dict in data:
tool_unavailable = step_dict[ 'tool_errors' ]
width = widths[ step_dict[ 'id' ] ]
x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ]
# Only highlight missing tools if displaying in the tool shed.
if trans.webapp.name == 'community' and tool_unavailable:
fill = "#EBBCB2"
else:
fill = "#EBD9B2"
boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() )
box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin
# Draw separator line.
if len( step_dict[ 'data_inputs' ] ) > 0:
box_height += 15
sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40
text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() )
# Define an input/output box.
boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() )
for conn, output_dict in step_dict[ 'input_connections' ].iteritems():
in_coords = in_pos[ step_dict[ 'id' ] ][ conn ]
# out_pos_index will be a step number like 1, 2, 3...
out_pos_index = output_dict[ 'id' ]
# out_pos_name will be a string like 'o', 'o2', etc.
out_pos_name = output_dict[ 'output_name' ]
if out_pos_index in out_pos:
# out_conn_index_dict will be something like:
# 7: {'o': (824.5, 618)}
out_conn_index_dict = out_pos[ out_pos_index ]
if out_pos_name in out_conn_index_dict:
out_conn_pos = out_pos[ out_pos_index ][ out_pos_name ]
else:
# Take any key / value pair available in out_conn_index_dict.
# A problem will result if the dictionary is empty.
if out_conn_index_dict.keys():
key = out_conn_index_dict.keys()[0]
out_conn_pos = out_pos[ out_pos_index ][ key ]
adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] )
text.append( svgfig.SVG( "circle",
cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin,
cy=out_conn_pos[ 1 ] - margin,
r = 5,
fill="#ffffff" ) )
connectors.append( svgfig.Line( adjusted[ 0 ],
adjusted[ 1 ] - margin,
in_coords[ 0 ] - 10,
in_coords[ 1 ],
arrow_end = "true" ).SVG() )
canvas.append( connectors )
canvas.append( boxes )
canvas.append( text )
width, height = ( max_x + max_width + 50 ), max_y + 300
canvas[ 'width' ] = "%s px" % width
canvas[ 'height' ] = "%s px" % height
canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height )
trans.response.set_content_type( "image/svg+xml" )
return canvas.standalone_xml()
def generate_workflow_image(trans, workflow_name, repository_metadata_id=None, repository_id=None):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode(workflow_name)
if trans.webapp.name == "community":
# We're in the tool shed.
repository_metadata = suc.get_repository_metadata_by_id(trans, repository_metadata_id)
repository_id = trans.security.encode_id(repository_metadata.repository_id)
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id(trans, repository_id)
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata["workflows"]:
workflow_dict = workflow_tup[1]
if workflow_dict["name"] == workflow_name:
break
if "tools" in metadata:
tools_metadata = metadata["tools"]
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict(
trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision,
)
data = []
canvas = svgfig.canvas(style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left")
text = svgfig.SVG("g")
connectors = svgfig.SVG("g")
boxes = svgfig.SVG("g")
svgfig.Text.defaults["font-size"] = "10px"
in_pos = {}
out_pos = {}
margin = 5
# Spacing between input/outputs.
line_px = 16
# Store px width for boxes of each step.
widths = {}
max_width, max_x, max_y = 0, 0, 0
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step(trans, repository_id, changeset_revision, tools_metadata, step)
tool_errors = module.type == "tool" and not module.tool
module_data_inputs = get_workflow_data_inputs(step, module)
module_data_outputs = get_workflow_data_outputs(step, module, workflow.steps)
step_dict = {
"id": step.order_index,
"data_inputs": module_data_inputs,
"data_outputs": module_data_outputs,
"position": step.position,
"tool_errors": tool_errors,
}
input_conn_dict = {}
for conn in step.input_connections:
input_conn_dict[conn.input_name] = dict(id=conn.output_step.order_index, output_name=conn.output_name)
step_dict["input_connections"] = input_conn_dict
data.append(step_dict)
x, y = step.position["left"], step.position["top"]
count = 0
module_name = get_workflow_module_name(module, missing_tool_tups)
max_len = len(module_name) * 1.5
text.append(svgfig.Text(x, y + 20, module_name, **{"font-size": "14px"}).SVG())
y += 45
for di in module_data_inputs:
cur_y = y + count * line_px
if step.order_index not in in_pos:
in_pos[step.order_index] = {}
in_pos[step.order_index][di["name"]] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, di["label"]).SVG())
count += 1
max_len = max(max_len, len(di["label"]))
if len(module.get_data_inputs()) > 0:
y += 15
for do in module_data_outputs:
cur_y = y + count * line_px
if step.order_index not in out_pos:
out_pos[step.order_index] = {}
out_pos[step.order_index][do["name"]] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, do["name"]).SVG())
count += 1
max_len = max(max_len, len(do["name"]))
widths[step.order_index] = max_len * 5.5
max_x = max(max_x, step.position["left"])
max_y = max(max_y, step.position["top"])
max_width = max(max_width, widths[step.order_index])
for step_dict in data:
tool_unavailable = step_dict["tool_errors"]
width = widths[step_dict["id"]]
x, y = step_dict["position"]["left"], step_dict["position"]["top"]
# Only highlight missing tools if displaying in the tool shed.
if trans.webapp.name == "community" and tool_unavailable:
fill = "#EBBCB2"
else:
fill = "#EBD9B2"
boxes.append(svgfig.Rect(x - margin, y, x + width - margin, y + 30, fill=fill).SVG())
box_height = (len(step_dict["data_inputs"]) + len(step_dict["data_outputs"])) * line_px + margin
# Draw separator line.
if len(step_dict["data_inputs"]) > 0:
box_height += 15
sep_y = y + len(step_dict["data_inputs"]) * line_px + 40
text.append(svgfig.Line(x - margin, sep_y, x + width - margin, sep_y).SVG())
# Define an input/output box.
boxes.append(svgfig.Rect(x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff").SVG())
for conn, output_dict in step_dict["input_connections"].iteritems():
in_coords = in_pos[step_dict["id"]][conn]
# out_pos_index will be a step number like 1, 2, 3...
out_pos_index = output_dict["id"]
# out_pos_name will be a string like 'o', 'o2', etc.
out_pos_name = output_dict["output_name"]
if out_pos_index in out_pos:
# out_conn_index_dict will be something like:
# 7: {'o': (824.5, 618)}
out_conn_index_dict = out_pos[out_pos_index]
if out_pos_name in out_conn_index_dict:
out_conn_pos = out_pos[out_pos_index][out_pos_name]
else:
# Take any key / value pair available in out_conn_index_dict.
# A problem will result if the dictionary is empty.
if out_conn_index_dict.keys():
key = out_conn_index_dict.keys()[0]
out_conn_pos = out_pos[out_pos_index][key]
adjusted = (out_conn_pos[0] + widths[output_dict["id"]], out_conn_pos[1])
text.append(
svgfig.SVG(
"circle",
cx=out_conn_pos[0] + widths[output_dict["id"]] - margin,
cy=out_conn_pos[1] - margin,
r=5,
fill="#ffffff",
)
)
connectors.append(
svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true").SVG()
)
canvas.append(connectors)
canvas.append(boxes)
canvas.append(text)
width, height = (max_x + max_width + 50), max_y + 300
canvas["width"] = "%s px" % width
canvas["height"] = "%s px" % height
canvas["viewBox"] = "0 0 %s %s" % (width, height)
trans.response.set_content_type("image/svg+xml")
return canvas.standalone_xml()
