[GIN] Generate maDMP

maDMP.ipynb

@@ -0,0 +1,191 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# ようこそ\n",
+    "\n",
+    "maDMPへようこそ。ここでは、DMPに入力いただいた研究分野等情報に基づき、研究活動の支援、およびデータ管理品質向上のためにデータガバナンス機能が提供するワークフローを最適化します。\n",
+    "\n",
+    "![maDMP_to_workflow](https://raw.githubusercontent.com/NII-DG/maDMP-template/main/images/maDMP_to_workflow.jpg)\n",
+    "\n",
+    "このmaDMPには、データガバナンス機能で作成いただいたDMPの情報の中で、ワークフローの最適化に必要な情報が既に埋め込まれています。以下を順番に実行することで、システムがDMP情報を活用した最適化処理を行います。"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "# DMP情報\n",
+    "field = 'basic'\n",
+    "dataSize = '1GB'\n",
+    "datasetStructure = 'RCOS_with_code'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "# ワークフローテンプレート取得\n",
+    "clone_url = 'https://github.com/NII-DG/workflow-template'+'.git'\n",
+    "workflow_path = '/home/jovyan/WORKFLOW'\n",
+    "!git clone $clone_url $workflow_path\n",
+    "!rm -rf $workflow_path/.git"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "# dmp.jsonに\"fields\"プロパティがある想定\n",
+    "import os\n",
+    "import glob\n",
+    "import shutil\n",
+    "\n",
+    "path_flows = os.path.join('WORKFLOW', 'FLOW')\n",
+    "\n",
+    "templates = glob.glob(os.path.join(path_flows, '**'), recursive=True)\n",
+    "\n",
+    "# 選択外の分野のセクション群を削除\n",
+    "for tmpl in templates:\n",
+    "    file = os.path.basename(tmpl)\n",
+    "    if not os.path.isdir(tmpl) and os.path.splitext(file)[1] == '.ipynb':\n",
+    "        if 'base_' not in file and field not in file:\n",
+    "            os.remove(tmpl)\n",
+    "            \n",
+    "print('最適化処理が完了しました。次の手順へお進みください。')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# モニタリング準備\n",
+    "import os\n",
+    "import json\n",
+    "\n",
+    "path_params = os.path.join('WORKFLOW', 'FLOW', 'param_files', 'monitoring_params.json')\n",
+    "monitoring_dict = {\n",
+    "    'dataSize': dataSize,\n",
+    "    'datasetStructure': datasetStructure\n",
+    "    # モニタリング項目を追加する場合は以下に追記してください\n",
+    "    # e.g. 'dirStructure': 'withCode'\n",
+    "}\n",
+    "\n",
+    "with open(path_params, 'w') as f:\n",
+    "    json.dump(monitoring_dict, f, indent=4)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# ワークフロー全体の関連図と目次を生成する\n",
+    "\n",
+    "次に、最適化したワークフロー全体が俯瞰できる図を生成します。  \n",
+    "以下を実行することで、システムがワークフロー関連図、および目次を作成します。\n",
+    "\n",
+    "◆◆◆開発メモ◆◆◆\n",
+    "\n",
+    "*.diagに分野固有のセクションはまだ反映されていない？"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import nbformat\n",
+    "\n",
+    "flow_path = 'WORKFLOW/FLOW/base_FLOW.ipynb'\n",
+    "rcos_binder_url = 'https://jupyter.cs.rcos.nii.ac.jp/'\n",
+    "flow_path_notebook = 'notebooks/WORKFLOW/FLOW/base_FLOW.ipynb'\n",
+    "# flow_path_lab = 'lab/tree/WORKFLOW/FLOW/base_FLOW.ipynb'\n",
+    "\n",
+    "nb = nbformat.read(flow_path, 4)\n",
+    "\n",
+    "title1 = \"\"\"## ワークフロー図を作成する\n",
+    "\n",
+    "以下のセルを実行してワークフロー図を作成できます。  \n",
+    "すでに実行したワークフローを確認したい場合は再度実行してください。\"\"\"\n",
+    "\n",
+    "code1 = \"\"\"import os\n",
+    "from IPython.display import SVG\n",
+    "\n",
+    "nb_utils_path   = os.path.join(os.environ['HOME'], 'WORKFLOW/FLOW/util/scripts/nb_utils.py')\n",
+    "\n",
+    "basic_path      = os.path.join(os.environ['HOME'], 'WORKFLOW/images')\n",
+    "basic_path_diag = os.path.join(basic_path, 'notebooks.diag')\n",
+    "basic_path_svg  = os.path.join(basic_path, 'notebooks.svg')\n",
+    "\n",
+    "os.chdir(os.environ['HOME'])\n",
+    "!python3 $nb_utils_path $basic_path_diag\n",
+    "\n",
+    "SVG(filename=basic_path_svg)\"\"\"\n",
+    "\n",
+    "title2 = \"\"\"ワークフロー図の左のノードはワークフローのフェーズとその流れを表しており、フェーズの右側にあるノードは個々のワークフローを表しています。  \n",
+    "各ワークフローを実行するには、ワークフローの各ノードのリンクをクリックしてください。\"\"\"\n",
+    "\n",
+    "title3 = \"\"\"## データガバナンス機能へ戻る\n",
+    "\n",
+    "以下のセルを実行し、表示されるURLをクリックするとデータガバナンス機能へアクセスできます。\"\"\"\n",
+    "\n",
+    "code2 = \"\"\"!git config --get remote.origin.url\"\"\"\n",
+    "\n",
+    "\n",
+    "nb[\"cells\"] += [\n",
+    "    nbformat.v4.new_markdown_cell(title1),\n",
+    "    nbformat.v4.new_code_cell(code1),\n",
+    "    nbformat.v4.new_markdown_cell(title2),\n",
+    "    nbformat.v4.new_markdown_cell(title3),\n",
+    "    nbformat.v4.new_code_cell(code2)\n",
+    "]\n",
+    "\n",
+    "with open(flow_path, \"w\") as f:\n",
+    "    nbformat.write(nb, f)\n",
+    "\n",
+    "print('ワークフローの生成が完了しました。以下のURLをクリックすることで')\n",
+    "print('ワークフロー全体図を閲覧できるページに遷移します。')\n",
+    "print(rcos_binder_url + os.environ['JUPYTERHUB_SERVICE_PREFIX'] + flow_path_notebook)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}