# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Large_B-cell_Lymphoma"
cohort = "GSE142494"

# Input paths
in_trait_dir = "../DATA/GEO/Large_B-cell_Lymphoma"
in_cohort_dir = "../DATA/GEO/Large_B-cell_Lymphoma/GSE142494"

# Output paths
out_data_file = "./output/preprocess/3/Large_B-cell_Lymphoma/GSE142494.csv"
out_gene_data_file = "./output/preprocess/3/Large_B-cell_Lymphoma/gene_data/GSE142494.csv"
out_clinical_data_file = "./output/preprocess/3/Large_B-cell_Lymphoma/clinical_data/GSE142494.csv"
json_path = "./output/preprocess/3/Large_B-cell_Lymphoma/cohort_info.json"

# Get file paths for soft and matrix files
soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)

# Get background info and clinical data from matrix file
background_info, clinical_data = get_background_and_clinical_data(matrix_file)

# Get unique values for each clinical feature row 
clinical_features = get_unique_values_by_row(clinical_data)

# Print background info
print("Background Information:")
print(background_info)
print("\nClinical Features and Sample Values:")
print(json.dumps(clinical_features, indent=2))
# 1. Gene Expression Data Availability
# Based on the series description, this appears to be a gene expression study focused on B-cell differentiation
is_gene_available = True

# 2. Variable Availability and Data Type Conversion
# 2.1 Data rows
trait_row = 0  # Using cell type as trait indicator
age_row = None  # Age not available
gender_row = None  # Gender not available

# 2.2 Conversion functions 
def convert_trait(value: str) -> int:
    """Convert cell type to binary: 1 for memory B cells, 0 for total B cells"""
    if pd.isna(value):
        return None
    value = value.split(': ')[-1].lower().strip()
    if 'memory b cells' in value:
        return 1
    elif 'total b cells' in value:
        return 0
    return None

def convert_age(value: str) -> float:
    """Not used as age data is unavailable"""
    return None

def convert_gender(value: str) -> int:
    """Not used as gender data is unavailable"""
    return None

# 3. Save metadata
validate_and_save_cohort_info(
    is_final=False,
    cohort=cohort,
    info_path=json_path,
    is_gene_available=is_gene_available,
    is_trait_available=trait_row is not None
)

# 4. Extract clinical features
clinical_df = geo_select_clinical_features(
    clinical_df=clinical_data,
    trait=trait,
    trait_row=trait_row,
    convert_trait=convert_trait,
    age_row=age_row,
    convert_age=convert_age,
    gender_row=gender_row,
    convert_gender=convert_gender
)

# Preview and save clinical data
print("Clinical data preview:")
print(preview_df(clinical_df))
clinical_df.to_csv(out_clinical_data_file)
# Extract gene expression data from matrix file
genetic_data = get_genetic_data(matrix_file)

# Print DataFrame info and dimensions to verify data structure
print("DataFrame info:")
print(genetic_data.info())
print("\nDataFrame dimensions:", genetic_data.shape)

# Print an excerpt of the data to inspect row/column structure
print("\nFirst few rows and columns of data:")
print(genetic_data.head().iloc[:, :5])

# Print first 20 row IDs
print("\nFirst 20 gene/probe IDs:")
print(genetic_data.index[:20].tolist())
# The identifiers start with "ILMN_", indicating they are Illumina probe IDs
# These need to be mapped to human gene symbols for analysis
requires_gene_mapping = True
# Report discovery of missing gene annotation
print("Gene Annotation Analysis:")
print("WARNING: Gene probe-to-symbol mapping information is not available in this SOFT file.")
print("The annotation only contains signature names (e.g. TIS.IO360, APM.IO360) rather than human gene symbols.")

# Update validation info to show dataset cannot be used due to missing gene mapping
validate_and_save_cohort_info(
    is_final=False,  
    cohort=cohort,
    info_path=json_path,
    is_gene_available=False,  # Set to False since gene expression data is not mappable
    is_trait_available=trait_row is not None,
    note="Dataset contains numeric probe IDs but lacks gene symbol mapping information"
)