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Source code for galaxy.workflow.render
import svgwrite
MARGIN = 5
LINE_SPACING = 15
STANDALONE_SVG_TEMPLATE = """<?xml version="1.0" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
%s"""
[docs]class WorkflowCanvas:
[docs] def __init__(self):
self.canvas = svgwrite.Drawing(profile="full")
self.connectors = []
self.boxes = []
self.text = []
self.in_pos = {}
self.out_pos = {}
self.widths = {}
self.max_x = 0
self.max_y = 0
self.max_width = 0
self.data = []
[docs] def finish(self, for_embed=False):
# max_x, max_y, max_width = self.max_x, self.max_y, self.max_width
for box in self.boxes:
self.canvas.add(box)
for connector in self.connectors:
self.canvas.add(connector)
text_style_layer = self.canvas.g(style="font-family: Helvetica, Arial, FreeSans, Sans, sans, sans-serif;")
for text in self.text:
text_style_layer.add(text)
self.canvas.add(text_style_layer)
# if we're embedding this in HTML - setup a viewbox and preserve aspect ratio
# https://css-tricks.com/scale-svg/#aa-the-viewbox-attribute
if for_embed:
self.canvas.viewbox(-5, -5, self.max_x + self.max_width, self.max_y + 150)
self.canvas.fit()
return self.canvas
[docs] def add_boxes(self, step_dict, width, name_fill):
x, y = step_dict["position"]["left"], step_dict["position"]["top"]
self.boxes.append(svgwrite.shapes.Rect((x - MARGIN, y), (width, 30), fill=name_fill, stroke="#000000"))
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 += LINE_SPACING
sep_y = y + len(step_dict["data_inputs"]) * LINE_SPACING + 40
self.text.append(
svgwrite.shapes.Line((x - MARGIN, sep_y), (x + width - MARGIN, sep_y), stroke=svgwrite.rgb(0, 0, 0))
)
# Define an input/output box.
self.boxes.append(
svgwrite.shapes.Rect(
(x - MARGIN, y + 30), (width, box_height), fill="#ffffff", stroke=svgwrite.rgb(0, 0, 0)
)
)
[docs] def add_text(self, module_data_inputs, module_data_outputs, step, module_name):
left, top = step.position["left"], step.position["top"]
x, y = left, top
order_index = step.order_index
max_len = len(module_name) * 1.5
self.text.append(svgwrite.text.Text(module_name, (x, y + 20), style="font-size:14px"))
y += 45
count = 0
in_pos = self.in_pos
out_pos = self.out_pos
for di in module_data_inputs:
cur_y = y + count * LINE_SPACING
if order_index not in in_pos:
in_pos[order_index] = {}
in_pos[order_index][di["name"]] = (x, cur_y)
self.text.append(svgwrite.text.Text(di["label"], (x, cur_y), style="font-size:10px"))
count += 1
max_len = max(max_len, len(di["label"]))
if len(module_data_inputs) > 0:
y += LINE_SPACING
for do in module_data_outputs:
cur_y = y + count * LINE_SPACING
if order_index not in out_pos:
out_pos[order_index] = {}
out_pos[order_index][do["name"]] = (x, cur_y)
self.text.append(svgwrite.text.Text(do["name"], (x, cur_y), style="font-size:10px"))
count += 1
max_len = max(max_len, len(do["name"]))
self.widths[order_index] = max_len * 5.5
self.max_x = max(self.max_x, left)
self.max_y = max(self.max_y, top)
self.max_width = max(self.max_width, self.widths[order_index])
[docs] def add_connection(self, step_dict, conn, output_dict):
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:
key = next(iter(out_conn_index_dict.keys()))
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(
svgwrite.shapes.Circle(
center=(out_conn_pos[0] + self.widths[output_dict["id"]] - MARGIN, out_conn_pos[1] - MARGIN),
r=5,
fill="#ffffff",
stroke="#000000",
)
)
marker = self.canvas.marker(
overflow="visible",
refX="0",
refY="5",
viewBox="0 0 10 5",
markerWidth="8",
markerHeight="10",
markerUnits="strokeWidth",
orient="auto",
stroke="none",
fill="black",
)
marker.add(self.canvas.path(d="M 0 0 L 10 5 L 0 10 z"))
self.canvas.defs.add(marker)
conn = svgwrite.shapes.Line(
(adjusted[0], adjusted[1] - MARGIN), (in_coords[0] - 10, in_coords[1]), stroke="#000000"
)
conn["marker-end"] = marker.get_funciri()
self.connectors.append(conn)
[docs] def add_steps(self, highlight_errors=False):
# Only highlight missing tools if displaying in the tool shed.
for step_dict in self.data:
tool_unavailable = step_dict.get("tool_errors", False)
if highlight_errors and tool_unavailable:
fill = "#EBBCB2"
else:
fill = "#EBD9B2"
width = self.widths[step_dict["id"]]
self.add_boxes(step_dict, width, fill)
for conn, output_dict in step_dict["input_connections"].items():
self.add_connection(step_dict, conn, output_dict)
[docs] def populate_data_for_step(self, step, module_name, module_data_inputs, module_data_outputs, tool_errors=None):
step_dict = {
"id": step.order_index,
"data_inputs": module_data_inputs,
"data_outputs": module_data_outputs,
"position": step.position,
}
if tool_errors:
step_dict["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
self.data.append(step_dict)
self.add_text(module_data_inputs, module_data_outputs, step, module_name)