Notebook edits (#144)

* demo service wip

* Fixed notebooks

* cleanup for PR

* styling & cleanup

* Replace %openadd with %openad in Generation.ipynb

Author: themoenen

openad/notebooks/Bio_Medical_Properties.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 43,
+   "execution_count": 1,
    "id": "6b8a0da0-f81c-4872-8ac0-081189c73d35",
    "metadata": {
     "tags": []
@@ -941,7 +941,7 @@
     "# %openad clear sessions\n",
     "# %openad create workspace foobar\n",
     "# %openad set workspace default\n",
-    "%openad copy file 'imported_molecules.csv' to '~/foobar'"
+    "%openad copy 'imported_molecules.csv' to '~/foobar'"
    ]
   },
   {
@@ -1148,9 +1148,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "ad-venv",
+   "display_name": "test_venv",
    "language": "python",
-   "name": "ad-venv"
+   "name": "test_venv"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1162,7 +1162,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.11"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

openad/notebooks/Common_Client_Intro.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 47,
+   "execution_count": 1,
    "id": "cfd86401-463d-4ba2-92ba-d4764ef72ee4",
    "metadata": {
     "tags": []
@@ -1107,9 +1107,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "ad-venv",
+   "display_name": "test_venv",
    "language": "python",
-   "name": "ad-venv"
+   "name": "test_venv"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1121,7 +1121,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.11"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

openad/notebooks/Demonstration.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 1,
    "id": "684f2227-0d30-4f9f-88b2-08eade6ae0ac",
    "metadata": {
     "tags": []
@@ -466,9 +466,9 @@
     "patented_molecules = []\n",
     "for result in datasets:\n",
     "    for mol in result[\"0\"].to_list():\n",
-    "        x = %openadd search for patents containing molecule '{mol}'\n",
+    "        x = %openadd ds search for patents containing molecule '{mol}'\n",
     "        if isinstance(x, DataFrame):\n",
-    "            patents_to_search.extend(x[\"PATENT ID\"].to_list())\n",
+    "            patents_to_search.extend(x[\"application_id\"].to_list())\n",
     "            patented_molecules.append(mol)\n",
     "\n",
     "str(patents_to_search)"
@@ -522,10 +522,10 @@
     "    \"esol\",\n",
     "]\n",
     "\n",
-    "new_props = %openadd propd get molecule property {properties_all} for {patented_molecules}\n",
+    "new_props = %openadd prop get molecule property {properties_all} for {patented_molecules}\n",
     "\n",
     "for x in patented_molecules:\n",
-    "    %openad add molecule {x} Force\n",
+    "    %openad add molecule {x} force\n",
     "\n",
     "%openad merge molecules data using dataframe new_props\n",
     "%openad enrich molecules with analysis"
@@ -579,9 +579,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "ad-venv",
+   "display_name": "test_venv",
    "language": "python",
-   "name": "ad-venv"
+   "name": "test_venv"
   },
   "language_info": {
    "codemirror_mode": {

openad/notebooks/End_to_End.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 1,
    "id": "93aa997a-e74f-4412-915f-68a4ba8cd536",
    "metadata": {
     "tags": []
@@ -322,9 +322,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "ad-venv",
+   "display_name": "test_venv",
    "language": "python",
-   "name": "ad-venv"
+   "name": "test_venv"
   },
   "language_info": {
    "codemirror_mode": {
@@ -336,7 +336,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.11"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,