# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Sjögrens_Syndrome"
cohort = "GSE140161"

# Input paths
in_trait_dir = "../DATA/GEO/Sjögrens_Syndrome"
in_cohort_dir = "../DATA/GEO/Sjögrens_Syndrome/GSE140161"

# Output paths
out_data_file = "./output/preprocess/3/Sjögrens_Syndrome/GSE140161.csv"
out_gene_data_file = "./output/preprocess/3/Sjögrens_Syndrome/gene_data/GSE140161.csv"
out_clinical_data_file = "./output/preprocess/3/Sjögrens_Syndrome/clinical_data/GSE140161.csv"
json_path = "./output/preprocess/3/Sjögrens_Syndrome/cohort_info.json"

# Get file paths
soft_file_path, matrix_file_path = geo_get_relevant_filepaths(in_cohort_dir)

# Get background info and clinical data
background_info, clinical_data = get_background_and_clinical_data(matrix_file_path)
print("Background Information:")
print(background_info)
print("\nSample Characteristics:")

# Get dictionary of unique values per row 
unique_values_dict = get_unique_values_by_row(clinical_data)
for row, values in unique_values_dict.items():
    print(f"\n{row}:")
    print(values)
# 1. Gene Expression Data Availability
# Based on background info, this is an Affymetrix chip study of whole blood transcriptome
is_gene_available = True

# 2.1 Data Availability

# Trait (Sjögren's syndrome): Found in row 4
trait_row = 4  

# Age: Not available in sample characteristics
age_row = None

# Gender: Found in row 1
gender_row = 1

# 2.2 Data Type Conversion Functions

def convert_trait(value):
    """Convert trait values to binary (0=Control, 1=Case)"""
    if not value or ':' not in value:
        return None
    return 1  # All samples are cases in this study

def convert_age(value):
    """Convert age values to continuous numbers"""
    # Not needed since age data is unavailable
    return None

def convert_gender(value):
    """Convert gender values to binary (0=Female, 1=Male)"""
    if not value or ':' not in value:
        return None
    value = value.split(':')[1].strip().lower()
    if value == 'female':
        return 0
    elif value == 'male':
        return 1
    return None

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

# 4. Clinical Feature Extraction
if trait_row is not None:
    selected_clinical = 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 the processed clinical data
    print("Preview of processed clinical data:")
    print(preview_df(selected_clinical))
    
    # Save clinical data
    selected_clinical.to_csv(out_clinical_data_file)
# Get gene expression data from matrix file
genetic_data = get_genetic_data(matrix_file_path)

# Examine data structure
print("Data structure and head:")
print(genetic_data.head())

print("\nShape:", genetic_data.shape)

print("\nFirst 20 row IDs (gene/probe identifiers):")
print(list(genetic_data.index)[:20])

# Get a few column names to verify sample IDs
print("\nFirst 5 column names:")
print(list(genetic_data.columns)[:5])
# The gene identifiers appear to be numeric IDs (e.g. 23064070) rather than standard human gene symbols
# These will need to be mapped to gene symbols for analysis
requires_gene_mapping = True
# Extract gene annotation data
gene_annotation = get_gene_annotation(soft_file_path)

# Preview column names and values from annotation dataframe
print("Gene annotation DataFrame preview:")
print(preview_df(gene_annotation))
# Build the gene mapping from probe IDs to gene symbols
mapping_df = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='SPOT_ID.1')

# Apply gene mapping to convert probe-level data to gene expression data  
gene_data = apply_gene_mapping(genetic_data, mapping_df)

# Normalize gene symbols with NCBI mapping to handle synonyms
gene_data = normalize_gene_symbols_in_index(gene_data)

# Save gene expression data
gene_data.to_csv(out_gene_data_file)

# Print data shape after mapping
print("\nShape after mapping:", gene_data.shape)
print("\nFirst few gene symbols and expression values:")
print(preview_df(gene_data))
# 1. Normalize gene symbols in gene expression data
gene_data = normalize_gene_symbols_in_index(gene_data)
os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True) 
gene_data.to_csv(out_gene_data_file)
print("\nGene data shape (normalized gene-level):", gene_data.shape)

# Load clinical data previously processed
selected_clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)
print("\nClinical data shape:", selected_clinical_df.shape)

# 2. Link clinical and genetic data using normalized gene-level data
linked_data = geo_link_clinical_genetic_data(selected_clinical_df, gene_data) 
print("\nLinked data shape:", linked_data.shape)

# 3. Handle missing values systematically
if trait in linked_data.columns:
    linked_data = handle_missing_values(linked_data, trait)
    
    # 4. Check for bias in trait and demographic features
    trait_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)
    
    # 5. Final validation and information saving
    note = "Data was successfully preprocessed from probe-level to gene-level expression using gene symbol normalization with NCBI Gene database."
    is_usable = validate_and_save_cohort_info(
        is_final=True,
        cohort=cohort,
        info_path=json_path, 
        is_gene_available=True,
        is_trait_available=True,
        is_biased=trait_biased,
        df=linked_data,
        note=note
    )

    # 6. Save linked data only if usable and not biased
    if is_usable and not trait_biased:
        os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
        linked_data.to_csv(out_data_file)