From 005e855e480e39c827bdff862853ed60f4e791c4 Mon Sep 17 00:00:00 2001
From: Florez Ospina Juan Felipe <juan.florez-ospina@psi.ch>
Date: Fri, 24 May 2024 11:15:05 +0200
Subject: [PATCH] Updated configuration file organization and workflow
 description.

---
 input_files/data_integr_config_file_LI.yaml | 18 +++++++++++-------
 workflow_data_integration.ipynb             | 11 ++++++-----
 2 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/input_files/data_integr_config_file_LI.yaml b/input_files/data_integr_config_file_LI.yaml
index 4d03f70..5d75dde 100644
--- a/input_files/data_integr_config_file_LI.yaml
+++ b/input_files/data_integr_config_file_LI.yaml
@@ -1,13 +1,15 @@
-project_name:  'scientific question' # beamtime, smog_chamber, lab_experiment   
-experiment_name: 'kinetic_flowtube_study' # 'flowtube' beamtime, smog_chamber, lab_experiment   
+input_file_directory: '//fs101/5505/Data'
+output_file_directory: 'output_files/'
+
+# Define 
+project_name:  'Photoenhanced uptake of NO2 driven by Fe(III)-carboxylate'
+experiment_name: 'kinetic_flowtube_study' # 'beamtime', 'smog_chamber_study'   
 user_name: 'LuciaI'
 group_id: '5505'
 experiment_date: 
 data_level: 'level_0'
 
-input_file_directory: '//fs101/5505/Data'
-output_file_directory: 'output_files/'
-
+# 
 instrument_datafolder: # analytical_methods: 
   - 'Lopap'
   - 'Humidity_Sensors'
@@ -16,10 +18,12 @@ instrument_datafolder: # analytical_methods:
   - 'T200_NOx'
   - 'T360U_CO2'
 
-integration_mode: 'collection' #'experimental_step # 'collection' # or experimental_step
+# Define data_integration mode as either 'collection' or 'experimental_step'
+integration_mode: 'collection' 
 # Specify datetimes (YYYY-MM-DD HH-MM-SS) at which experimental steps were created. 
 datetime_steps:
     - '2022-11-22 00-00-00'
     - '2022-01-31 00-00-00'
+    - '2023-06-22 00-00-00'
     - '2023-06-29 00-00-00'
-    - '2023-06-22 00-00-00'
\ No newline at end of file
+    
\ No newline at end of file
diff --git a/workflow_data_integration.ipynb b/workflow_data_integration.ipynb
index 715489c..87a4728 100644
--- a/workflow_data_integration.ipynb
+++ b/workflow_data_integration.ipynb
@@ -20,8 +20,7 @@
     "sys.path.append(root_dir)\n",
     "\n",
     "import src.hdf5_vis as hdf5_vis\n",
-    "import src.data_integration_lib as dilib\n",
-    "import yaml\n"
+    "import src.data_integration_lib as dilib\n"
    ]
   },
   {
@@ -31,7 +30,7 @@
     "# 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 the path and Excecute Cell.\n",
+    "* Set up input directory and output directory paths and Excecute Cell.\n",
     "\n"
    ]
   },
@@ -43,14 +42,16 @@
    "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, output_yml_filename_path = dilib.integrate_data_sources(yaml_config_file_path)\n"
+    "output_filename_path = dilib.integrate_data_sources(yaml_config_file_path)\n"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Display integrated file using a treemap"
+    "# 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"
    ]
   },
   {