Updated notebook documentation and included an example metadata annotation notebook.

workflow_data_integration.ipynb

@@ -4,7 +4,17 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Import libraries and modules"
+    "# Data integration workflow of experimental campaign\n",
+    "\n",
+    "In this notebook, we will go through a our data integration workflow. This involves the following steps:\n",
+    "\n",
+    "1. Specify data integration file through YAML configuration file.\n",
+    "2. Create an integrated HDF5 file of experimental campaign from configuration file.\n",
+    "3. Display the created HDF5 file using a treemap\n",
+    "\n",
+    "## Import libraries and modules\n",
+    "\n",
+    "* Excecute (or Run) the Cell below"
    ]
   },
   {
@@ -20,14 +30,15 @@
     "sys.path.append(root_dir)\n",
     "\n",
     "import src.hdf5_vis as hdf5_vis\n",
-    "import src.data_integration_lib as dilib\n"
+    "import src.data_integration_lib as dilib\n",
+    "import pathlib"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Specify data integration task through yaml configuration file\n",
+    "## Step 1: Specify data integration task through YAML configuration file\n",
     "\n",
     "* Create your configuration file (i.e., *.yaml file) adhering to the example yaml file in the input folder.\n",
     "* Set up input directory and output directory paths and Excecute Cell.\n",
@@ -41,15 +52,33 @@
    "outputs": [],
    "source": [
     "#output_filename_path = 'output_files/unified_file_smog_chamber_2024-04-07_UTC-OFST_+0200_NG.h5'\n",
-    "yaml_config_file_path = 'input_files/data_integr_config_file_LI.yaml'\n",
-    "output_filename_path = dilib.integrate_data_sources(yaml_config_file_path)\n"
+    "yaml_config_file_path = 'input_files/data_integr_config_file_TBR.yaml'\n"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Display integrated HDF5 file using a treemap\n",
+    "## Step 2: Create an integrated HDF5 file of experimental campaign.\n",
+    "\n",
+    "* Excecute Cell. Here we run the function `integrate_data_sources` with input argument as the previously specified YAML config file."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "hdf5_file_path = dilib.integrate_data_sources(yaml_config_file_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Display integrated HDF5 file using a treemap\n",
     "\n",
     "* Excecute Cell. A visual representation in html format of the integrated file should be displayed and stored in the output directory folder"
    ]
@@ -60,13 +89,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hdf5_vis.display_group_hierarchy_on_a_treemap(output_filename_path)"
+    "if isinstance(hdf5_file_path ,list):\n",
+    "    for path_item in hdf5_file_path :\n",
+    "        hdf5_vis.display_group_hierarchy_on_a_treemap(path_item)\n",
+    "else:\n",
+    "    hdf5_vis.display_group_hierarchy_on_a_treemap(hdf5_file_path)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "test_atmos_chem_env",
+   "display_name": "multiphase_chemistry_env",
    "language": "python",
    "name": "python3"
   },
@@ -84,5 +117,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }