コード作成

PACKAGE/experiment.ipynb

@@ -20,24 +20,40 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "    1. 変数にメタデータ情報を入力し、入力後セルを実行する"
+    "1. 変数にメタデータ情報を入力し、入力後セルを実行する"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
-    "Experiment_date = \"2021/12/15\" \n",
-    "Experimenter = \"yamada taro\""
+    "import json\n",
+    "meta_data = {\n",
+    "    \"experiment_date\": \"2021/12/16\",\n",
+    "    \"experimenter\": \"tanaka taro\"\n",
+    "}"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "    2. meta_data.jsonに保存する"
+    "2. meta_data.jsonに保存する"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import json\n",
+    "from collections import OrderedDict\n",
+    "\n",
+    "with open('./meta_data.json', 'w') as jf:\n",
+    "    json.dump(meta_data, jf, ensure_ascii=False, indent=2)"
    ]
   },
   {
@@ -51,23 +67,23 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "    1. コミットメッセージを変数に入力する"
+    "1. コミットメッセージを変数に入力する"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
-    "save_message = \"\""
+    "save_message = \" \""
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "    2. 一部のファイルのみ保存したい場合は、変数に保存したいファイル名を入力する"
+    "2. 途中保存する"
    ]
   },
   {
@@ -76,14 +92,73 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "save_files = \"\""
+    "from datalad import api\n",
+    "\n",
+    "api.save(message=save_message)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "- ## 実験を終了する\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "1. 実行環境構成を記録する"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%sh\n",
+    "conda env export > environment.yaml"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%sh\n",
+    "pip freeze > requirements.txt"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "2. パイプラインを作成する（検討中）"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "3. 実験単体の再現性をモニタリングする（コード付帯機能で行うか検討中）"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "    3. 途中保存する"
+    "4. コミットメッセージを変数に入力し、実験記録の書き戻し準備をする"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "SAVE_MESSAGE = ''"
    ]
   },
   {
@@ -94,27 +169,74 @@
    "source": [
     "from datalad import api\n",
     "\n",
-    "api.save(message=save_message, path=save_files)"
+    "api.save(message=SAVE_MESSAGE)"
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "- ## 実験を終了する\n"
+    "import os\n",
+    "\n",
+    "os.chdir(\"/home/jovyan\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%sh\n",
+    "chmod 600 /home/jovyan/.ssh/id_rsa"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%sh\n",
+    "mkdir ./tmp\n",
+    "git remote show origin > ./tmp/remote.txt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open('./tmp/remote.txt', 'r') as f:\n",
+    "    lines = [s.strip() for s in f.readlines()]\n",
+    "    ssh_push_url = lines[2].replace('Push  URL: https://github.com/', 'ssh://root@dg02.dg.rcos.nii.ac.jp:3001/')"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "option: 実験メタデータを入力する\n",
-    "1. 実行環境構成を記録する\n",
-    "2. パイプラインを作成する（検討中）\n",
-    "3. 実験単体の再現性をモニタリングする（コード付帯機能で行うか検討中）\n",
-    "4. 実験記録の書き戻し準備\n",
     "5. 実験記録を書き戻す"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from datalad import api\n",
+    "\n",
+    "try:\n",
+    "    api.siblings(action='add', name=SIBLING_NAME, url=SSH_PUSH_URL)\n",
+    "except:\n",
+    "    pass\n",
+    "\n",
+    "api.push(to=SIBLING_NAME, result_renderer='default')"
+   ]
   }
  ],
  "metadata": {