def add_connection( self, step_dict, conn, output_dict):
margin = MARGIN
in_coords = self.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 self.out_pos:
# out_conn_index_dict will be something like:
# 7: {'o': (824.5, 618)}
out_conn_index_dict = self.out_pos[ out_pos_index ]
if out_pos_name in out_conn_index_dict:
out_conn_pos = out_conn_index_dict[ 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 = self.out_pos[ out_pos_index ][ key ]
adjusted = ( out_conn_pos[ 0 ] + self.widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] )
self.text.append( svgfig.SVG( "circle",
cx=out_conn_pos[ 0 ] + self.widths[ output_dict[ 'id' ] ] - margin,
cy=out_conn_pos[ 1 ] - margin,
r=5,
fill="#ffffff" ) )
self.connectors.append( svgfig.Line( adjusted[ 0 ],
adjusted[ 1 ] - margin,
in_coords[ 0 ] - 10,
in_coords[ 1 ],
arrow_end="true" ).SVG() )
def draw_cell(cell_data):
out = []
if cell_data == 0:
out.append(svgfig.Rect(0, 0, CELL_WIDTH, CELL_HEIGHT,
fill="black"))
elif type(cell_data) == type(1):
out.append(svgfig.Rect(0, 0, CELL_WIDTH, CELL_HEIGHT))
out.append(
svgfig.Text(
10,
10,
cell_data,
text_anchor="middle",
font_size=12,
font_weight=600,
dominant_baseline="middle",
fill="brown",
))
elif type(cell_data) == type(()):
across = cell_data[0]
down = cell_data[1]
out.append(svgfig.Rect(0, 0, CELL_WIDTH, CELL_HEIGHT))
out.append(
svgfig.Line(
0,
0,
CELL_WIDTH,
CELL_HEIGHT,
stroke_width=1,
))
if down == 0:
points = ((0, 0), (0, CELL_HEIGHT), (CELL_WIDTH, CELL_HEIGHT))
out.append(svgfig.Poly(points, "lines", fill="black"))
else:
out.append(
svgfig.Text(
2,
18,
down,
text_anchor="start",
font_size=7,
alignment_baseline="middle",
))
if across == 0:
points = ((0, 0), (CELL_WIDTH, 0), (CELL_WIDTH, CELL_HEIGHT))
out.append(svgfig.Poly(points, "lines", fill="black"))
else:
out.append(
svgfig.Text(
19,
7,
across,
text_anchor="end",
font_size=7,
))
else:
raise Exception("")
return out
def add_boxes( self, step_dict, width, name_fill ):
x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ]
self.boxes.append( svgfig.Rect( x - MARGIN, y, x + width - MARGIN, y + 30, fill=name_fill ).SVG() )
box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * LINE_SPACING + MARGIN
# Draw separator line.
if len( step_dict[ 'data_inputs' ] ) > 0:
box_height += 15
sep_y = y + len( step_dict[ 'data_inputs' ] ) * LINE_SPACING + 40
self.text.append( svgfig.Line( x - MARGIN, sep_y, x + width - MARGIN, sep_y ).SVG() )
# Define an input/output box.
self.boxes.append( svgfig.Rect( x - MARGIN, y + 30, x + width - MARGIN, y + 30 + box_height, fill="#ffffff" ).SVG() )
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 _line(self, x1, y1, x2, y2, w): return [svgfig.Line(x1, y1, x2, y2, stroke_width=w*self.q, stroke=self.color).SVG(trans=self.trans)]
import svgfig
svgfig.canvas(svgfig.Frame(-0.2,
1.2,
0,
3,
svgfig.Line(0, 0.20, 1, 1.65),
svgfig.Line(0, 1.7, 1, 2.26),
xticks={
0: "tuned APEs",
1: "infinite APEs"
},
xminiticks=[],
height=35,
yticks=-7).SVG(),
viewBox="0 0 100 35").save("statsyst.svg")
def _draw_line(self, x, y, new_x, new_y):
if self.pen:
self.lines.append(svg.Line(x, y, new_x, new_y, stroke_width=0.2))
