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@@ -11,7 +11,6 @@
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]
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},
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{
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- "attachments": {},
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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@@ -93,15 +92,143 @@
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},
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{
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"cell_type": "code",
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- "execution_count": null,
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+ "execution_count": 2,
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"metadata": {},
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- "outputs": [],
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+ "outputs": [
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+ {
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+ "data": {
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+ "image/svg+xml": [
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+ "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:inkspace=\"http://www.inkscape.org/namespaces/inkscape\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" viewBox=\"0 0 946 595\">\n",
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+ " <defs id=\"defs_block\">\n",
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+ " <filter height=\"1.504\" id=\"filter_blur\" inkspace:collect=\"always\" width=\"1.1575\" x=\"-0.07875\" y=\"-0.252\">\n",
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+ " <feGaussianBlur id=\"feGaussianBlur3780\" inkspace:collect=\"always\" stdDeviation=\"4.2\"/>\n",
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+ " </filter>\n",
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+ " </defs>\n",
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+ " <title>blockdiag</title>\n",
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+ " <desc>\n",
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+ " blockdiag {\n",
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+ " node_width = 230;\n",
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+ " node_height = 145;\n",
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+ "\n",
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+ " group {\n",
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+ " orientation = portrait;\n",
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+ " shape = line;\n",
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+ " style = none;\n",
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+ "\n",
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+ " group {\n",
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+ " shape = line;\n",
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+ " style = none;\n",
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+ " orientation = portrait;\n",
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+ " group {\n",
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+ " orientation = portrait;\n",
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+ " color = "#ffeed9";\n",
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+ " "0. 実験ワークフロー実行準備"[label = "0. 実験ワークフロー実行準備", fontsize = 14];\n",
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+ " "required_every_time";\n",
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+ " }\n",
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+ " }\n",
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+ "\n",
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+ " group {\n",
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+ " shape = line;\n",
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+ " style = none;\n",
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+ " orientation = portrait;\n",
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+ " group {\n",
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+ " orientation = portrait;\n",
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+ " color = "#fcdcb1";\n",
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+ " "1. 実験ワークフロー"[label = "1. 実験ワークフロー", fontsize = 14];\n",
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+ " "enter_metadata";\n",
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+ " "save";\n",
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+ " "finish";\n",
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+ " }\n",
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+ " }\n",
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+ " }\n",
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+ "\n",
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+ " "0. 実験ワークフロー実行準備" -> "1. 実験ワークフロー";\n",
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+ " "enter_metadata","save" -> "finish";\n",
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+ "\n",
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+ " }\n",
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+ "</desc>\n",
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+ " <rect fill=\"rgb(255,238,217)\" height=\"165\" style=\"filter:url(#filter_blur)\" width=\"540\" x=\"56\" y=\"30\"/>\n",
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+ " <rect fill=\"rgb(252,220,177)\" height=\"350\" style=\"filter:url(#filter_blur)\" width=\"834\" x=\"56\" y=\"215\"/>\n",
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+ " <rect fill=\"rgb(0,0,0)\" height=\"145\" stroke=\"rgb(0,0,0)\" style=\"filter:url(#filter_blur);opacity:0.7;fill-opacity:1\" width=\"230\" x=\"67\" y=\"46\"/>\n",
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+ " <rect fill=\"rgb(0,0,0)\" height=\"145\" stroke=\"rgb(0,0,0)\" style=\"filter:url(#filter_blur);opacity:0.7;fill-opacity:1\" width=\"230\" x=\"361\" y=\"46\"/>\n",
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+ " <rect fill=\"rgb(0,0,0)\" height=\"145\" stroke=\"rgb(0,0,0)\" style=\"filter:url(#filter_blur);opacity:0.7;fill-opacity:1\" width=\"230\" x=\"67\" y=\"231\"/>\n",
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+ " <rect fill=\"rgb(0,0,0)\" height=\"145\" stroke=\"rgb(0,0,0)\" style=\"filter:url(#filter_blur);opacity:0.7;fill-opacity:1\" width=\"230\" x=\"361\" y=\"231\"/>\n",
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+ " <rect fill=\"rgb(0,0,0)\" height=\"145\" stroke=\"rgb(0,0,0)\" style=\"filter:url(#filter_blur);opacity:0.7;fill-opacity:1\" width=\"230\" x=\"655\" y=\"231\"/>\n",
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+ " <rect fill=\"rgb(0,0,0)\" height=\"145\" stroke=\"rgb(0,0,0)\" style=\"filter:url(#filter_blur);opacity:0.7;fill-opacity:1\" width=\"230\" x=\"361\" y=\"416\"/>\n",
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+ " <rect fill=\"rgb(255,255,255)\" height=\"145\" stroke=\"rgb(0,0,0)\" width=\"230\" x=\"64\" y=\"40\"/>\n",
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+ " <text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"14\" font-style=\"normal\" font-weight=\"normal\" text-anchor=\"middle\" textLength=\"189\" x=\"179.5\" y=\"120\">0. 実験ワークフロー実行準備</text>\n",
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+ " <rect fill=\"rgb(255,255,255)\" height=\"145\" stroke=\"rgb(0,0,0)\" width=\"230\" x=\"358\" y=\"40\"/>\n",
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+ " <text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"140\">6. 実行結果を実験リポジトリに同期する</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"129\">5. 高性能実験環境利用のために必要な設定をする</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"118\">4. データ同期のための設定をする</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"107\">3. ユーザー認証を行う</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"96\">2. READMEに実験実行環境へのリンクを追加する</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"85\">1. Git管理対象外ファイルを.gitignoreで設定する</text><a xlink:href=\"WORKFLOW/util/required_every_time.ipynb\"><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"11\" font-style=\"normal\" font-weight=\"bold\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"62\">必要な準備を行う</text></a><rect fill=\"rgb(255,255,255)\" height=\"145\" stroke=\"rgb(0,0,0)\" width=\"230\" x=\"64\" y=\"225\"/>\n",
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+ " <text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"14\" font-style=\"normal\" font-weight=\"normal\" text-anchor=\"middle\" textLength=\"133\" x=\"179.5\" y=\"305\">1. 実験ワークフロー</text>\n",
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+ " <rect fill=\"rgb(255,255,255)\" height=\"145\" stroke=\"rgb(0,0,0)\" width=\"230\" x=\"358\" y=\"225\"/>\n",
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+ " <text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"292\">3. 実行結果をデータガバナンス機能に同期する</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"281\">2.メタ情報をファイルに保存する</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"270\">1. メタデータを入力する</text><a xlink:href=\"WORKFLOW/enter_metadata.ipynb\"><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"11\" font-style=\"normal\" font-weight=\"bold\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"247\">実験メタデータを入力する</text></a><rect fill=\"rgb(255,255,255)\" height=\"145\" stroke=\"rgb(0,0,0)\" width=\"230\" x=\"652\" y=\"225\"/>\n",
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+ " <text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"654\" width=\"226\" y=\"292\">3. 途中保存する</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"654\" width=\"226\" y=\"281\">2. 高性能実験環境から実験記録を取得する</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"654\" width=\"226\" y=\"270\">1. コミットメッセージを変数に入力する</text><a xlink:href=\"WORKFLOW/save.ipynb\"><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"11\" font-style=\"normal\" font-weight=\"bold\" font-anchor=\"middle\" x=\"654\" width=\"226\" y=\"247\">実験を途中保存する</text></a><rect fill=\"rgb(255,255,255)\" height=\"145\" stroke=\"rgb(0,0,0)\" width=\"230\" x=\"358\" y=\"410\"/>\n",
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+ " <text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"477\">3. 実験記録をデータガバナンス機能に同期する</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"466\">2. 高性能実験環境から実験記録を取得する</text><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"9\" font-style=\"normal\" font-weight=\"normal\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"455\">1.実行環境構成を記録する</text><a xlink:href=\"WORKFLOW/finish.ipynb\"><text fill=\"rgb(0,0,0)\" font-family=\"sans-serif\" font-size=\"11\" font-style=\"normal\" font-weight=\"bold\" font-anchor=\"middle\" x=\"360\" width=\"226\" y=\"432\">実験を終了する</text></a><path d=\"M 179 185 L 179 217\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"179,224 175,217 183,217 179,224\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 179 185 L 179 217\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"179,224 175,217 183,217 179,224\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 370 L 473 402\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"473,409 469,402 477,402 473,409\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 767 370 L 767 390\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 390 L 767 390\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 390 L 473 402\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"473,409 469,402 477,402 473,409\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 370 L 473 402\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"473,409 469,402 477,402 473,409\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 767 370 L 767 390\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 390 L 767 390\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 390 L 473 402\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"473,409 469,402 477,402 473,409\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 179 185 L 179 217\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"179,224 175,217 183,217 179,224\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 179 185 L 179 217\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"179,224 175,217 183,217 179,224\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 370 L 473 402\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"473,409 469,402 477,402 473,409\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 767 370 L 767 390\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 390 L 767 390\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 390 L 473 402\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"473,409 469,402 477,402 473,409\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 370 L 473 402\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"473,409 469,402 477,402 473,409\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 767 370 L 767 390\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 390 L 767 390\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <path d=\"M 473 390 L 473 402\" fill=\"none\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <polygon fill=\"rgb(0,0,0)\" points=\"473,409 469,402 477,402 473,409\" stroke=\"rgb(0,0,0)\"/>\n",
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+ " <rect fill=\"none\" height=\"535\" stroke=\"rgb(243,152,0)\" stroke-dasharray=\"0 196605\" stroke-width=\"3\" width=\"834\" x=\"56\" y=\"30\"/>\n",
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+ " <rect fill=\"none\" height=\"165\" stroke=\"rgb(243,152,0)\" stroke-dasharray=\"0 196605\" stroke-width=\"3\" width=\"540\" x=\"56\" y=\"30\"/>\n",
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+ " <rect fill=\"none\" height=\"350\" stroke=\"rgb(243,152,0)\" stroke-dasharray=\"0 196605\" stroke-width=\"3\" width=\"834\" x=\"56\" y=\"215\"/>\n",
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+ "</svg>"
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+ ],
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+ "text/plain": [
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+ "<IPython.core.display.SVG object>"
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+ ]
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+ },
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+ "execution_count": 2,
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+ "metadata": {},
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+ "output_type": "execute_result"
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+ }
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+ ],
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"source": [
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"from IPython.display import SVG\n",
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- "%cd ~/\n",
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- "%run /home/jovyan/WORKFLOW/scripts/nb_utils.py\n",
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- "SVG(filename=generate_svg_diag(diag='WORKFLOW/images/notebooks.diag'))"
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+ "import os\n",
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+ "\n",
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+ "nb_utils_path = os.path.join(os.environ['HOME'], 'WORKFLOW/util/scripts/nb_utils.py')\n",
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+ "basic_path = os.path.join(os.environ['HOME'], 'WORKFLOW/images')\n",
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+ "basic_path_svg = os.path.join(basic_path, 'notebooks.svg')\n",
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+ "basic_path_diag = os.path.join(basic_path, 'notebooks.diag')\n",
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+ "os.chdir(os.environ['HOME'])\n",
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+ "!python3 $nb_utils_path $basic_path_diag\n",
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+ "\n",
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+ "SVG(filename=basic_path_svg)"
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]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": []
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}
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],
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"metadata": {
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@@ -120,7 +247,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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- "version": "3.7.10"
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+ "version": "3.9.7"
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}
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},
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"nbformat": 4,
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