Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/gxformat2/cytoscape.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 """Build standalone visualization for Galaxy workflows."""
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2 import json
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3 import os
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4 import string
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5 import sys
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6
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7 import pkg_resources
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8
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9 from gxformat2._scripts import ensure_format2
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10 from gxformat2._yaml import ordered_load
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11 from gxformat2.converter import convert_inputs_to_steps, ensure_step_position, steps_as_list
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12
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13 CYTOSCAPE_JS_TEMPLATE = pkg_resources.resource_filename(__name__, 'cytoscape.html')
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14 MAIN_TS_PREFIX = "toolshed.g2.bx.psu.edu/repos/"
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15
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16
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17 def main(argv=None):
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18 """Entry point for building Cytoscape visualizations of Galaxy workflows."""
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19 if argv is None:
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20 argv = sys.argv[1:]
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21
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22 workflow_path = argv[0]
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23 with open(workflow_path, "r") as f:
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24 workflow_dict = ordered_load(f)
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25
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26 workflow_dict = ensure_format2(workflow_dict)
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27 elements = []
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28
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29 steps = steps_as_list(workflow_dict)
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30 convert_inputs_to_steps(workflow_dict, steps)
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31
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32 for i, step in enumerate(steps):
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33 step_id = step.get("id") or step.get("label") or str(i)
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34 step_type = step.get("type") or 'tool'
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35 classes = ["type_%s" % step_type]
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36 if step_type in ['tool', 'subworkflow']:
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37 classes.append("runnable")
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38 else:
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39 classes.append("input")
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40
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41 tool_id = step.get("tool_id")
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42 if tool_id and tool_id.startswith(MAIN_TS_PREFIX):
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43 tool_id = tool_id[len(MAIN_TS_PREFIX):]
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44 label = step.get("id") or step.get("label") or ("tool:%s" % tool_id) or str(i)
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45 ensure_step_position(step, i)
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46 node_position = dict(x=int(step["position"]["left"]), y=int(step["position"]["top"]))
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47 repo_link = None
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48 if "tool_shed_repository" in step:
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49 repo = step["tool_shed_repository"]
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50 repo_link = "https://" + repo["tool_shed"] + "/view/" + repo["owner"] + "/" + repo["name"] + "/" + repo["changeset_revision"]
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51 node_data = {
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52 "id": step_id,
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53 "label": label,
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54 "doc": step.get("doc"),
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55 "tool_id": step.get("tool_id"),
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56 "step_type": step_type,
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57 "repo_link": repo_link
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58 }
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59 elements.append({"group": "nodes", "data": node_data, "classes": classes, "position": node_position})
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60 for key, value in (step.get("in") or {}).items():
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61 # handle lists?
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62 if isinstance(value, dict) and 'source' in value:
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63 value = value["source"]
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64 elif isinstance(value, dict):
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65 continue
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66 if "/" in value:
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67 from_step, output = value.split("/", 1)
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68 else:
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69 from_step, output = value, None
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70 edge_id = "%s__to__%s" % (step_id, from_step)
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71 edge_data = {"id": edge_id, "source": from_step, "target": step_id, "input": key, "output": output}
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72 elements.append({"group": "edges", "data": edge_data})
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73
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74 if len(argv) > 1:
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75 output_path = argv[1]
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76 else:
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77 output_path, _ = os.path.splitext(workflow_path)
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78 output_path += ".html"
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79
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80 if output_path.endswith(".html"):
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81 with open(CYTOSCAPE_JS_TEMPLATE, "r") as f:
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82 template = f.read()
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83 viz = string.Template(template).safe_substitute(elements=json.dumps(elements))
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84 with open(output_path, "w") as f:
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85 f.write(viz)
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86 else:
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87 with open(output_path, "w") as f:
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88 json.dump(elements, f)
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89
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90
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91 if __name__ == "__main__":
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92 main()