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Merged in fbacall/galaxy-central-myexp-integration (pull request #49)

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Jeremy Goecks
2012-06-20 14:59:37 -04:00
parent 1c6f425659 fd8e12cadd
commit b9a64ec113
2 changed files with 111 additions and 104 deletions
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lib/galaxy/web/controllers/workflow.py
+107 -101
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@@ -505,107 +505,8 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
stored = self.get_stored_workflow( trans, id, check_ownership=True )
session = trans.sa_session
workflow = stored.latest_workflow
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
line_px = 16 # how much spacing between input/outputs
widths = {} # store px width for boxes of each step
max_width, max_x, max_y = 0, 0, 0
for step in workflow.steps:
# Load from database representation
module = module_factory.from_workflow_step( trans, step )
# Pack attributes into plain dictionary
step_dict = {
'id': step.order_index,
'data_inputs': module.get_data_inputs(),
'data_outputs': module.get_data_outputs(),
'position': step.position
}
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
max_len = len(module.get_name()) * 1.5
text.append( svgfig.Text(x, y + 20, module.get_name(), **{"font-size": "14px"} ).SVG() )
y += 45
for di in module.get_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.get_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:
width = widths[step_dict['id']]
x, y = step_dict['position']['left'], step_dict['position']['top']
boxes.append( svgfig.Rect(x-margin, y, x+width-margin, y+30, fill="#EBD9B2").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() ) #
# 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_conn_pos = out_pos[output_dict['id']][output_dict['output_name']]
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()
return self._workflow_to_svg_canvas( trans, stored ).standalone_xml()
@web.expose
@@ -1056,7 +957,8 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
request_raw = trans.fill_template( "workflow/myexp_export.mako", \
workflow_name=workflow_dict['name'], \
workflow_description=workflow_dict['annotation'], \
workflow_content=workflow_content
workflow_content=workflow_content, \
workflow_svg=self._workflow_to_svg_canvas( trans, stored ).standalone_xml()
)
# strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters.
request = unicode( request_raw.strip(), 'utf-8' )
@@ -1929,6 +1831,110 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
trans.sa_session.flush()
return stored, missing_tool_tups
def _workflow_to_svg_canvas( self, trans, stored ):
workflow = stored.latest_workflow
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
line_px = 16 # how much spacing between input/outputs
widths = {} # store px width for boxes of each step
max_width, max_x, max_y = 0, 0, 0
for step in workflow.steps:
# Load from database representation
module = module_factory.from_workflow_step( trans, step )
# Pack attributes into plain dictionary
step_dict = {
'id': step.order_index,
'data_inputs': module.get_data_inputs(),
'data_outputs': module.get_data_outputs(),
'position': step.position
}
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
max_len = len(module.get_name()) * 1.5
text.append( svgfig.Text(x, y + 20, module.get_name(), **{"font-size": "14px"} ).SVG() )
y += 45
for di in module.get_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.get_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:
width = widths[step_dict['id']]
x, y = step_dict['position']['left'], step_dict['position']['top']
boxes.append( svgfig.Rect(x-margin, y, x+width-margin, y+30, fill="#EBD9B2").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() ) #
# 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_conn_pos = out_pos[output_dict['id']][output_dict['output_name']]
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)
return canvas
## ---- Utility methods -------------------------------------------------------
templates/workflow/myexp_export.mako
+4 -3
View File
@@ -15,6 +15,7 @@
<content encoding="base64" type="binary">
${textwrap.fill( base64.b64encode( workflow_content ), 64 )}
</content>
<preview encoding="base64" type="binary">
</preview>
</workflow>
<svg encoding="base64">
${textwrap.fill( base64.b64encode( workflow_svg ), 64 )}
</svg>
</workflow>