{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# ACSM Data Chain Workflow\n",
    "\n",
    "In this notebook, we will go through our **ACSM Data Chain**. This involves the following steps:\n",
    "\n",
    "1. Run the data integration pipeline to retrieve ACSM input data and prepare it for processing.  \n",
    "2. Perform QC/QA analysis.  \n",
    "3. (Optional) Conduct visual analysis for flag validation.  \n",
    "4. Prepare input data and QC/QA analysis results for submission to the EBAS database.  \n",
    "\n",
    "## Import Libraries and Data Chain Steps\n",
    "\n",
    "* Execute (or Run) the cell below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "import os\n",
    "# Set up project root directory\n",
    "\n",
    "\n",
    "notebook_dir = os.getcwd()  # Current working directory (assumes running from notebooks/)\n",
    "project_path = os.path.normpath(os.path.join(notebook_dir, \"..\"))  # Move up to project root\n",
    "dima_path = os.path.normpath(os.path.join(project_path, \"dima\"))  # Move up to project root\n",
    "\n",
    "if project_path not in sys.path:  # Avoid duplicate entries\n",
    "    sys.path.append(project_path)\n",
    "if dima_path not in sys.path:\n",
    "    sys.path.insert(0,dima_path)\n",
    "#sys.path.append(os.path.join(root_dir,'dima','instruments'))\n",
    "#sys.path.append(os.path.join(root_dir,'dima','src'))\n",
    "#sys.path.append(os.path.join(root_dir,'dima','utils'))\n",
    "\n",
    "#import dima.visualization.hdf5_vis as hdf5_vis\n",
    "#import dima.pipelines.data_integration as data_integration\n",
    "import subprocess\n",
    "\n",
    "\n",
    "for item in sys.path:\n",
    "    print(item)\n",
    "\n",
    "from dima.pipelines.data_integration import run_pipeline as get_campaign_data\n",
    "from pipelines.steps.apply_calibration_factors import main as apply_calibration_factors\n",
    "from pipelines.steps.generate_flags import main as generate_flags\n",
    "from pipelines.steps.prepare_ebas_submission import main as prepare_ebas_submission "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 1: Retrieve Input Data from a Network Drive\n",
    "\n",
    "* Create a configuration file (i.e., a `.yaml` file) following the example provided in the input folder.\n",
    "* Set up the input and output directory paths.\n",
    "* Execute the cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "path_to_config_file = '../campaignDescriptor.yaml'\n",
    "paths_to_hdf5_files = get_campaign_data(path_to_config_file)\n",
    "\n",
    "# Select campaign data file and append directory\n",
    "CAMPAIGN_DATA_FILE = paths_to_hdf5_files[0]\n",
    "APPEND_DATA_DIR = os.path.splitext(CAMPAIGN_DATA_FILE)[0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 2: Calibrate Input Campaign Data and Save Data Products\n",
    "\n",
    "* Set up the input and output directory paths.\n",
    "* Execute the cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "path_to_data_file = CAMPAIGN_DATA_FILE\n",
    "path_to_calibration_file = '../pipelines/params/calibration_factors.yaml'\n",
    "dataset_name = 'ACSM_TOFWARE/2024/ACSM_JFJ_2024_timeseries.txt/data_table'\n",
    "#command = ['python', 'pipelines/steps/apply_calibration_factors.py', path_to_data_file, dataset_name, path_to_calibration_file]\n",
    "#status = subprocess.run(command, capture_output=True, check=True)\n",
    "#print(status.stdout.decode())\n",
    "\n",
    "apply_calibration_factors(path_to_data_file,path_to_calibration_file)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 3: Perform QC/QA Analysis\n",
    "\n",
    "* Generate automated flags based on validity thresholds for diagnostic channels.\n",
    "* (Optional) Generate manual flags using the **Data Flagging App**, accessible at:  \n",
    "  [http://localhost:8050/](http://localhost:8050/)\n",
    "* Execute the cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset_name = 'ACSM_TOFWARE/2024/ACSM_JFJ_2024_meta.txt/data_table'\n",
    "path_to_config_file = 'pipelines/params/validity_thresholds.yaml'\n",
    "#command = ['python', 'pipelines/steps/compute_automated_flags.py', path_to_data_file, dataset_name, path_to_config_file]\n",
    "#status = subprocess.run(command, capture_output=True, check=True)\n",
    "#print(status.stdout.decode())\n",
    "generate_flags(path_to_data_file, 'diagnostics')\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## (Optional) Step 3.1: Inspect Previously Generated Flags for Correctness\n",
    "\n",
    "* Perform flag validation using the Jupyter Notebook workflow available at:  \n",
    "  [../notebooks/demo_visualize_diagnostic_flags_from_hdf5_file.ipynb](demo_visualize_diagnostic_flags_from_hdf5_file.ipynb)\n",
    "* Follow the notebook steps to visually inspect previously generated flags."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 4: Apply Diagnostic and Manual Flags to Variables of Interest\n",
    "\n",
    "* Generate flags for species based on previously collected QC/QA flags.\n",
    "* Execute the cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "path_to_data_file = CAMPAIGN_DATA_FILE\n",
    "dataset_name = 'ACSM_TOFWARE/2024/ACSM_JFJ_2024_meta.txt/data_table'\n",
    "path_to_config_file = 'pipelines/params/validity_thresholds.yaml'\n",
    "#command = ['python', 'pipelines/steps/compute_automated_flags.py', path_to_data_file, dataset_name, path_to_config_file]\n",
    "#status = subprocess.run(command, capture_output=True, check=True)\n",
    "#print(status.stdout.decode())\n",
    "generate_flags(path_to_data_file, 'species')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 5: Generate Campaign Data in EBAS Format\n",
    "\n",
    "* Gather and set paths to the required data products produced in the previous steps.\n",
    "* Execute the cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "PATH1=\"../data/collection_JFJ_2024_2025-03-14_2025-03-14/ACSM_TOFWARE_processed/2024/ACSM_JFJ_2024_timeseries_calibrated.csv\"\n",
    "PATH2=\"../data/collection_JFJ_2024_2025-03-14_2025-03-14/ACSM_TOFWARE_processed/2024/ACSM_JFJ_2024_timeseries_calibrated_err.csv\"\n",
    "PATH3=\"../data/collection_JFJ_2024_2025-03-14_2025-03-14/ACSM_TOFWARE_processed/2024/ACSM_JFJ_2024_timeseries_calibration_factors.csv\"\n",
    "PATH4=\"../data/collection_JFJ_2024_2025-03-14_2025-03-14/ACSM_TOFWARE_flags/2024/ACSM_JFJ_2024_timeseries_flags.csv\"\n",
    "month = 4\n",
    "prepare_ebas_submission([PATH1,PATH2,PATH3], PATH4, month)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 6: Save Data Products to an HDF5 File\n",
    "\n",
    "* Gather and set paths to the required data products produced in the previous steps.\n",
    "* Execute the cell.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import dima.src.hdf5_ops as dataOps \n",
    "#print(os.curdir)\n",
    "\n",
    "\n",
    "dataManager = dataOps.HDF5DataOpsManager(CAMPAIGN_DATA_FILE)\n",
    "print(dataManager.file_path)\n",
    "print(APPEND_DATA_DIR)\n",
    "dataManager.update_file(APPEND_DATA_DIR)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataManager = dataOps.HDF5DataOpsManager(path_to_data_file)\n",
    "dataManager.load_file_obj()\n",
    "dataManager.extract_and_load_dataset_metadata()\n",
    "df = dataManager.dataset_metadata_df\n",
    "print(df.head(10))\n",
    "dataManager.unload_file_obj()"
   ]
  }
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