Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/gxformat2/cytoscape.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """Build standalone visualization for Galaxy workflows."""
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2 import argparse
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3 import json
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4 import os
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5 import string
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6 import sys
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7
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8 import pkg_resources
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9
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10 from gxformat2.model import ensure_step_position
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11 from gxformat2.normalize import steps_normalized
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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 SCRIPT_DESCRIPTION = """
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16 This script converts the an executable Galaxy workflow (in either format -
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17 Format 2 or native .ga) into a format for visualization with Cytoscape
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18 (https://cytoscape.org/).
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19
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20 If the target output path ends with .html this script will output a HTML
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21 page with the workflow visualized using cytoscape.js. Otherwise, this script
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22 will output a JSON description of the workflow elements for consumption by
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23 Cytoscape.
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24 """
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25
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26
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27 def to_cytoscape(workflow_path: str, output_path=None):
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28 """Produce cytoscape output for supplied workflow path."""
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29 if output_path is None:
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30 output_path, _ = os.path.splitext(workflow_path)
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31 output_path += ".html"
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32
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33 steps = steps_normalized(workflow_path=workflow_path)
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34 elements = []
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35 for i, step in enumerate(steps):
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36 step_id = step.get("id") or step.get("label") or str(i)
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37 step_type = step.get("type") or 'tool'
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38 classes = ["type_%s" % step_type]
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39 if step_type in ['tool', 'subworkflow']:
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40 classes.append("runnable")
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41 else:
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42 classes.append("input")
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43
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44 tool_id = step.get("tool_id")
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45 if tool_id and tool_id.startswith(MAIN_TS_PREFIX):
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46 tool_id = tool_id[len(MAIN_TS_PREFIX):]
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47 label = step.get("id") or step.get("label") or ("tool:%s" % tool_id) or str(i)
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48 ensure_step_position(step, i)
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49 node_position = dict(x=int(step["position"]["left"]), y=int(step["position"]["top"]))
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50 repo_link = None
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51 if "tool_shed_repository" in step:
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52 repo = step["tool_shed_repository"]
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53 repo_link = "https://" + repo["tool_shed"] + "/view/" + repo["owner"] + "/" + repo["name"] + "/" + repo["changeset_revision"]
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54 node_data = {
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55 "id": step_id,
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56 "label": label,
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57 "doc": step.get("doc"),
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58 "tool_id": step.get("tool_id"),
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59 "step_type": step_type,
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60 "repo_link": repo_link
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61 }
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62 elements.append({"group": "nodes", "data": node_data, "classes": classes, "position": node_position})
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63 for key, value in (step.get("in") or {}).items():
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64 # handle lists?
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65 if isinstance(value, dict) and 'source' in value:
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66 value = value["source"]
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67 elif isinstance(value, dict):
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68 continue
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69 if "/" in value:
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70 from_step, output = value.split("/", 1)
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71 else:
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72 from_step, output = value, None
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73 edge_id = "%s__to__%s" % (step_id, from_step)
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74 edge_data = {"id": edge_id, "source": from_step, "target": step_id, "input": key, "output": output}
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75 elements.append({"group": "edges", "data": edge_data})
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76
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77 if output_path.endswith(".html"):
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78 with open(CYTOSCAPE_JS_TEMPLATE, "r") as f:
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79 template = f.read()
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80 viz = string.Template(template).safe_substitute(elements=json.dumps(elements))
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81 with open(output_path, "w") as f:
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82 f.write(viz)
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83 else:
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84 with open(output_path, "w") as f:
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85 json.dump(elements, f)
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86
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87
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88 def main(argv=None):
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89 """Entry point for building Cytoscape visualizations of Galaxy workflows."""
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90 if argv is None:
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91 argv = sys.argv[1:]
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92
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93 args = _parser().parse_args(argv)
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94
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95 workflow_path = args.input_path
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96 output_path = args.output_path
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97 to_cytoscape(workflow_path, output_path)
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98
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99
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100 def _parser():
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101 parser = argparse.ArgumentParser(description=SCRIPT_DESCRIPTION)
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102 parser.add_argument('input_path', metavar='INPUT', type=str,
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103 help='input workflow path (.ga/gxwf.yml)')
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104 parser.add_argument('output_path', metavar='OUTPUT', type=str, nargs="?",
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105 help='output viz path (.json/.html)')
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106 return parser
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107
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108
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109 if __name__ == "__main__":
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110 main()