# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Mesothelioma"
cohort = "GSE163721"

# Input paths
in_trait_dir = "../DATA/GEO/Mesothelioma"
in_cohort_dir = "../DATA/GEO/Mesothelioma/GSE163721"

# Output paths
out_data_file = "./output/preprocess/3/Mesothelioma/GSE163721.csv"
out_gene_data_file = "./output/preprocess/3/Mesothelioma/gene_data/GSE163721.csv"
out_clinical_data_file = "./output/preprocess/3/Mesothelioma/clinical_data/GSE163721.csv"
json_path = "./output/preprocess/3/Mesothelioma/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 Analysis
is_gene_available = True  # Background info indicates microarray data analysis

# 2. Variable Analysis
trait_row = 0  # All samples are tumor, indicating mesothelioma
age_row = None  # Age data not available
gender_row = None  # Gender data not available

# 2.2 Conversion Functions
def convert_trait(x):
    if not isinstance(x, str):
        return None
    if "tumor" in x.lower():
        return 1
    return None
    
convert_age = None
convert_gender = 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_features = 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("Preview of clinical features:")
print(preview_df(clinical_features))
clinical_features.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])
# Examining the row IDs which are just numeric strings without any gene/probe identifiers
# This indicates the need for mapping from probe IDs to gene symbols
requires_gene_mapping = True
# Extract gene annotation data
gene_annotation = get_gene_annotation(soft_file_path)

# Display column names and preview data
print("Column names:")
print(gene_annotation.columns)

print("\nPreview of gene annotation data:")
print(preview_df(gene_annotation))
# Extract gene mapping from annotation
# 'ID' column in gene_annotation matches numeric IDs in gene expression data
# 'Gene Symbol' column contains the target gene symbols
mapping_data = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Gene Symbol')

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

# Preview the mapped gene data
print("\nMapped gene expression data shape:", gene_data.shape)
print("\nFirst few rows of mapped gene expression data:")
print(gene_data.head())
# 1. Normalize gene symbols
genetic_data = normalize_gene_symbols_in_index(gene_data)
genetic_data.to_csv(out_gene_data_file)

# 2. Link clinical and genetic data 
linked_data = geo_link_clinical_genetic_data(clinical_features, genetic_data)

# 3. Handle missing values systematically
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 = "Dataset contains only tumor samples without a control group, making it unsuitable for associational studies."
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=True,  # Force biased=True since all samples are tumor samples
    df=linked_data,
    note=note
)

# 6. Save linked data only if usable (which won't happen since is_biased=True)
if is_usable:
    os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
    linked_data.to_csv(out_data_file)