update プロトコルをssh->httpに変更

WORKFLOW/SECTIONS/base/02_experimental_phase/launch_an_experiment.ipynb

@@ -73,6 +73,20 @@
     "2. 空リポジトリ名のフォルダを作成し、実験パッケージをコピーします。"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%sh\n",
+    "echo \"\n",
+    "machine dg02.dg.rcos.nii.ac.jp\n",
+    "login 【ユーザ名】\n",
+    "password 【パスワード】\n",
+    "\" > ~/.netrc"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -82,9 +96,11 @@
     "!mkdir ~/.tmp/\n",
     "!git init ~/.tmp/$repository_title\n",
     "!cp -r ~/WORKFLOW/PACKAGE/* ~/.tmp/$repository_title/\n",
+    "%cd ~/.tmp/$repository_title\n",
+    "!git add ~/.tmp/$repository_title\n",
     "!git commit -m '1st commit'\n",
-    "!git remote add $ssh_url\n",
-    "!git push"
+    "!git remote add $repository_title $ssh_url\n",
+    "!git push $repository_title master"
    ]
   },
   {
@@ -100,6 +116,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%cd ~/\n",
     "!git submodule add $ssh_url ~/experiments/repository_title"
    ]
   },
@@ -134,42 +151,16 @@
     "## 5. 変更内容を書き戻す"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "1. 書き戻しメッセージを変更したい場合は以下のセルでsave_messageに代入する値を編集してください。"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "save_message = '実験の作成'"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "2. 変更内容を書き戻す"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import papermill as pm\n",
-    "\n",
-    "pm.execute_notebook(\n",
-    "    '../util/datalad_save_push.ipynb',\n",
-    "    '-',\n",
-    "    parameters = dict(SAVE_MESSAGE = save_message)\n",
-    ")"
+    "%cd ~/\n",
+    "!git add ~/\n",
+    "!git commit -m '実験の作成'\n",
+    "!git push origin master"
    ]
   },
   {

WORKFLOW/SECTIONS/base/util/prepare_for_workflow.ipynb

@@ -14,84 +14,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 1. SSH鍵を準備する"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "1. SSH鍵を生成し、秘密鍵を.ssh/id_rsaに配置します。"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%sh\n",
-    "cd ~/\n",
-    "mkdir .ssh\n",
-    "ssh-keygen -f .ssh/id_rsa -t rsa -N \"\""
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "2. 以下のセルで出力された公開鍵を[こちら](http://dg02.dg.rcos.nii.ac.jp/user/settings/ssh)からGINリポジトリに登録してください。"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%sh\n",
-    "cat ~/.ssh/id_rsa.pub"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## 2. SSH接続で書き戻しを行うためにssh鍵に権限を与える（ssh鍵は.sshディレクトリの中にid_rsaとして保存する）"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%sh\n",
-    "chmod 600 ~/.ssh/id_rsa"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## 3. SSH鍵の利用確認をオフにする"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%sh\n",
-    "echo \"host *\\n\\tStrictHostKeyChecking no\\n\\tUserKnownHostsFile /dev/null\" >> ~/.ssh/config"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## 4. .gitconfigにユーザー名とメールアドレスを登録する"
+    "## 1. .gitconfigにユーザー名とメールアドレスを登録する"
    ]
   },
   {
@@ -143,7 +66,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 5. Dataladを使用するため、このリポジトリをデータセットとする"
+    "## 2. Dataladを使用するため、このリポジトリをデータセットとする"
    ]
   },
   {
@@ -161,7 +84,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 6. ワークフロー実行結果をGINリポジトリに反映させるため、GINリポジトリをリモートリポジトリに設定する"
+    "## 3. ワークフロー実行結果をGINリポジトリに反映させるため、GINリポジトリをリモートリポジトリに設定する"
    ]
   },
   {
@@ -217,7 +140,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 7. Git管理対象外ファイルを.gitignoreで設定する"
+    "## 4. Git管理対象外ファイルを.gitignoreで設定する"
    ]
   },
   {
@@ -235,18 +158,20 @@
     "/.ipython/\n",
     "/.local/\n",
     "/.tmp/\n",
+    "/.WORKFLOW/\n",
     "/.bashrc\n",
     "/.bash_logout\n",
     "/.profile\n",
+    "/.netrc\n",
     ".ipynb_checkpoints/\n",
-    "\" >> ~/.gitignore"
+    "\" > ~/.gitignore"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 8. 実験用フォルダを作成し、その中にpipeline.jsonを用意する"
+    "## 5. 実験用フォルダを作成し、その中にpipeline.jsonを用意する"
    ]
   },
   {
@@ -257,14 +182,14 @@
    "source": [
     "%%sh\n",
     "mkdir ~/experiments\n",
-    "echo \"[]\" >> ~/experiments/pipeline.json"
+    "echo \"[]\" > ~/experiments/pipeline.json"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 9. 必要なファイルをPACKAGEテンプレートに複製する"
+    "## 6. 必要なファイルをPACKAGEテンプレートに複製する"
    ]
   },
   {
@@ -275,9 +200,6 @@
    "source": [
     "%%sh\n",
     "cd ~/\n",
-    "mkdir WORKFLOW/PACKAGE/.ssh\n",
-    "cp .ssh/id_rsa WORKFLOW/PACKAGE/.ssh/id_rsa\n",
-    "cp .ssh/config WORKFLOW/PACKAGE/.ssh/config\n",
     "cp .gitconfig WORKFLOW/PACKAGE/.gitconfig\n",
     "cp environment.yml WORKFLOW/PACKAGE/environment.yml"
    ]
@@ -286,7 +208,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 10. 変更内容を書き戻す"
+    "## 7. 変更内容を書き戻す"
    ]
   },
   {
@@ -295,13 +217,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import papermill as pm\n",
+    "%%sh\n",
+    "\n",
+    "echo \"\n",
+    "machine dg02.dg.rcos.nii.ac.jp\n",
+    "login 【ユーザ名】\n",
+    "password 【パスワード】\n",
+    "\" > ~/.netrc\n",
     "\n",
-    "pm.execute_notebook(\n",
-    "    '../util/datalad_save_push.ipynb',\n",
-    "    '-',\n",
-    "    parameters = dict(SAVE_MESSAGE = 'ワークフロー実行準備')\n",
-    ")"
+    "cd ~/\n",
+    "git add .\n",
+    "git commit -m 'save'\n",
+    "git push origin master"
    ]
   }
  ],