pipeline.py now imports Equipment & minor fixes

kushalbakshi · Aug 31, 2022 · 814a380 · 814a380
1 parent 6600942
commit 814a380
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Showing 7 changed files with 69 additions and 34,089 deletions.
diff --git a/notebooks/01-configure.ipynb b/notebooks/01-configure.ipynb
@@ -17,32 +17,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
-    "os.chdir('..')"
+    "if os.path.basename(os.getcwd()) == \"notebooks\": os.chdir(\"..\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
     "pwd"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import datajoint as dj"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -54,7 +45,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -73,7 +64,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,16 +83,17 @@
     "\n",
     "+ Giving a prefix to schema could help on the configuration of privilege settings. For example, if we set prefix `neuro_`, every schema created with the current workflow will start with `neuro_`, e.g. `neuro_lab`, `neuro_subject`, `neuro_imaging` etc.\n",
     "\n",
-    "+ The prefix could be configurated as follows in `dj.config`:"
+    "+ The prefix could be configurated in `dj.config` as follows. CodeBook users should keep their username as the prefix for schema for declaration permissions."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
-    "dj.config['custom'] = {'database.prefix': 'neuro_'}"
+    "username_as_prefix = dj.config[\"database.user\"] + \"_\"\n",
+    "dj.config[\"custom\"] = {\"database.prefix\": username_as_prefix}"
    ]
   },
   {
@@ -130,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,7 +134,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -160,7 +152,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -169,7 +161,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -206,8 +198,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.7.9 64-bit ('workflow-calcium-imaging': conda)",
-   "name": "python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c"
+   "display_name": "Python 3.9.12 ('elementsPractice')",
+   "language": "python",
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -219,7 +212,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.12"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "28657e2c4c8fc87d9c51bab987cae00550904d22e795ba7dc84df7e29d09653b"
+   }
   }
  },
  "nbformat": 4,