ipycytoscape.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ipycytoscape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "\n",
    "import wic\n",
    "import sophios.cli\n",
    "import sophios.plugins\n",
    "\n",
    "args = sophios.cli.get_args()\n",
    "\n",
    "tools_cwl = sophios.plugins.get_tools_cwl(args.homedir)\n",
    "yml_paths = sophios.plugins.get_yml_paths(args.homedir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import graphviz\n",
    "import networkx as nx\n",
    "import yaml\n",
    "\n",
    "import sophios.ast, sophios.utils, sophios.utils_graphs\n",
    "from sophios.schemas import wic_schema\n",
    "from sophios.utils_yaml import wic_loader\n",
    "from sophios.wic_types import Yaml, YamlTree, GraphReps, NodeData, GraphData, StepId\n",
    "\n",
    "yml_path_str = 'tutorial'\n",
    "yml_namespace = 'global'\n",
    "yml_path = yml_paths[yml_namespace][yml_path_str]\n",
    "\n",
    "# Generate schemas for validation and vscode IntelliSense code completion\n",
    "yaml_stems = sophios.utils.flatten([list(p) for p in yml_paths.values()])\n",
    "validator = wic_schema.get_validator(tools_cwl, yaml_stems, write_to_disk=True)\n",
    "\n",
    "# Load the high-level yaml workflow file.\n",
    "with open(yml_path, mode='r', encoding='utf-8') as y:\n",
    "    root_yaml_tree: Yaml = yaml.load(y.read(), Loader=wic_loader())\n",
    "Path('autogenerated/').mkdir(parents=True, exist_ok=True)\n",
    "wic_tag = {'wic': root_yaml_tree.get('wic', {})}\n",
    "plugin_ns = wic_tag['wic'].get('namespace', 'global')\n",
    "step_id = StepId(yml_path_str, plugin_ns)\n",
    "y_t = YamlTree(step_id, root_yaml_tree)\n",
    "yaml_tree_raw = sophios.ast.read_ast_from_disk(args.homedir, y_t, yml_paths, tools_cwl, validator)\n",
    "with open(f'autogenerated/{Path(yml_path).stem}_tree_raw.wic', mode='w', encoding='utf-8') as f:\n",
    "    f.write(yaml.dump(yaml_tree_raw.yml))\n",
    "yaml_tree = sophios.ast.merge_yml_trees(yaml_tree_raw, {}, tools_cwl)\n",
    "with open(f'autogenerated/{Path(yml_path).stem}_tree_merged.wic', mode='w', encoding='utf-8') as f:\n",
    "    f.write(yaml.dump(yaml_tree.yml))\n",
    "root_yml_dir_abs = Path(yml_path).parent.absolute()\n",
    "yaml_tree = sophios.ast.python_script_generate_cwl(yaml_tree, root_yml_dir_abs, tools_cwl)\n",
    "with open(f'autogenerated/{Path(yml_path).stem}_tree_python_script.wic', mode='w', encoding='utf-8') as f:\n",
    "    f.write(yaml.dump(yaml_tree.yml))\n",
    "\n",
    "\n",
    "yaml_forest = sophios.ast.tree_to_forest(yaml_tree, tools_cwl)\n",
    "yaml_forest_lst =  sophios.utils.flatten_forest(yaml_forest)\n",
    "yaml_subtrees_lst = [subforest.yaml_tree for subforest in yaml_forest_lst]\n",
    "yaml_subtrees = {t.step_id.stem:t.yml for t in yaml_subtrees_lst}\n",
    "#print(yaml_subtrees.keys())\n",
    "\n",
    "\n",
    "graph_gv = graphviz.Digraph(name=f'cluster_{yml_path}')\n",
    "graph_gv.attr(newrank='True')\n",
    "graph_nx = nx.DiGraph()\n",
    "graphdata = GraphData(yml_path)\n",
    "graph = GraphReps(graph_gv, graph_nx, graphdata)\n",
    "compiler_info = sophios.compiler.compile_workflow(yaml_tree, args, [], [graph], {}, {}, tools_cwl, True, relative_run_path=True, testing=False)\n",
    "rose_tree = compiler_info.rose\n",
    "sub_node_data: NodeData = rose_tree.data\n",
    "yaml_stem = sub_node_data.name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "gd = sub_node_data.graph.graphdata\n",
    "gd_flat = sophios.utils_graphs.flatten_graphdata(gd)\n",
    "#print(len(gd_flat.nodes))\n",
    "#print(len(gd_flat.edges))\n",
    "json_cyto = sophios.utils_graphs.graphdata_to_cytoscape(gd_flat)\n",
    "#import json\n",
    "#json.dumps(json_cyto)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cyto = ipycytoscape.CytoscapeWidget()\n",
    "\n",
    "cyto.graph.add_graph_from_json(json_cyto, directed=True)\n",
    "\n",
    "import json\n",
    "with open(\"wicStyle.json\", mode='r', encoding='utf-8') as f:\n",
    "    s = json.load(f)\n",
    "\n",
    "cyto.set_style(s)\n",
    "cyto.set_layout(name='cola')\n",
    "cyto.box_selection_enabled = False"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ipywidgets\n",
    "import yaml\n",
    "\n",
    "textarea = ipywidgets.Textarea(layout=ipywidgets.Layout(height=\"auto\", width=\"auto\"))\n",
    "out = ipywidgets.Output()\n",
    "\n",
    "def node_name(node):\n",
    "    textarea.description = node['data'].get('label', '')\n",
    "    id = node['data'].get('id', '')\n",
    "    #with out:\n",
    "    #    print('id', id, id in yaml_subtrees)\n",
    "    #    print(yaml_subtrees.get(id))\n",
    "    textarea.value = yaml.dump(yaml_subtrees.get(id, ''))\n",
    "\n",
    "# TODO: Round tripping: After user edits AST in textarea, re-compile.\n",
    "\n",
    "cyto.on('node', 'click', node_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from IPython.display import display\n",
    "display(cyto, textarea)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "display(out)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.8"
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  "vscode": {
   "interpreter": {
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