Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/gxformat2/cytoscape.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1:75ca89e9b81c 2:6af9afd405e9
1 """Build standalone visualization for Galaxy workflows."""
2 import json
3 import os
4 import string
5 import sys
6
7 import pkg_resources
8
9 from gxformat2._scripts import ensure_format2
10 from gxformat2._yaml import ordered_load
11 from gxformat2.converter import convert_inputs_to_steps, ensure_step_position, steps_as_list
12
13 CYTOSCAPE_JS_TEMPLATE = pkg_resources.resource_filename(__name__, 'cytoscape.html')
14 MAIN_TS_PREFIX = "toolshed.g2.bx.psu.edu/repos/"
15
16
17 def main(argv=None):
18 """Entry point for building Cytoscape visualizations of Galaxy workflows."""
19 if argv is None:
20 argv = sys.argv[1:]
21
22 workflow_path = argv[0]
23 with open(workflow_path, "r") as f:
24 workflow_dict = ordered_load(f)
25
26 workflow_dict = ensure_format2(workflow_dict)
27 elements = []
28
29 steps = steps_as_list(workflow_dict)
30 convert_inputs_to_steps(workflow_dict, steps)
31
32 for i, step in enumerate(steps):
33 step_id = step.get("id") or step.get("label") or str(i)
34 step_type = step.get("type") or 'tool'
35 classes = ["type_%s" % step_type]
36 if step_type in ['tool', 'subworkflow']:
37 classes.append("runnable")
38 else:
39 classes.append("input")
40
41 tool_id = step.get("tool_id")
42 if tool_id and tool_id.startswith(MAIN_TS_PREFIX):
43 tool_id = tool_id[len(MAIN_TS_PREFIX):]
44 label = step.get("id") or step.get("label") or ("tool:%s" % tool_id) or str(i)
45 ensure_step_position(step, i)
46 node_position = dict(x=int(step["position"]["left"]), y=int(step["position"]["top"]))
47 repo_link = None
48 if "tool_shed_repository" in step:
49 repo = step["tool_shed_repository"]
50 repo_link = "https://" + repo["tool_shed"] + "/view/" + repo["owner"] + "/" + repo["name"] + "/" + repo["changeset_revision"]
51 node_data = {
52 "id": step_id,
53 "label": label,
54 "doc": step.get("doc"),
55 "tool_id": step.get("tool_id"),
56 "step_type": step_type,
57 "repo_link": repo_link
58 }
59 elements.append({"group": "nodes", "data": node_data, "classes": classes, "position": node_position})
60 for key, value in (step.get("in") or {}).items():
61 # handle lists?
62 if isinstance(value, dict) and 'source' in value:
63 value = value["source"]
64 elif isinstance(value, dict):
65 continue
66 if "/" in value:
67 from_step, output = value.split("/", 1)
68 else:
69 from_step, output = value, None
70 edge_id = "%s__to__%s" % (step_id, from_step)
71 edge_data = {"id": edge_id, "source": from_step, "target": step_id, "input": key, "output": output}
72 elements.append({"group": "edges", "data": edge_data})
73
74 if len(argv) > 1:
75 output_path = argv[1]
76 else:
77 output_path, _ = os.path.splitext(workflow_path)
78 output_path += ".html"
79
80 if output_path.endswith(".html"):
81 with open(CYTOSCAPE_JS_TEMPLATE, "r") as f:
82 template = f.read()
83 viz = string.Template(template).safe_substitute(elements=json.dumps(elements))
84 with open(output_path, "w") as f:
85 f.write(viz)
86 else:
87 with open(output_path, "w") as f:
88 json.dump(elements, f)
89
90
91 if __name__ == "__main__":
92 main()