# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Pancreatic_Cancer"
cohort = "GSE222788"

# Input paths
in_trait_dir = "../DATA/GEO/Pancreatic_Cancer"
in_cohort_dir = "../DATA/GEO/Pancreatic_Cancer/GSE222788"

# Output paths
out_data_file = "./output/preprocess/3/Pancreatic_Cancer/GSE222788.csv"
out_gene_data_file = "./output/preprocess/3/Pancreatic_Cancer/gene_data/GSE222788.csv"
out_clinical_data_file = "./output/preprocess/3/Pancreatic_Cancer/clinical_data/GSE222788.csv"
json_path = "./output/preprocess/3/Pancreatic_Cancer/cohort_info.json"

# Get file paths
soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)

# Extract background info and clinical data 
background_info, clinical_data = get_background_and_clinical_data(matrix_file)

# Get unique values per clinical feature
sample_characteristics = get_unique_values_by_row(clinical_data)

# Print background info
print("Dataset Background Information:")
print(f"{background_info}\n")

# Print sample characteristics
print("Sample Characteristics:")
for feature, values in sample_characteristics.items():
    print(f"Feature: {feature}")
    print(f"Values: {values}\n")
# 1. Gene Expression Data Availability
# From background info, this is a NanoString gene profiling study with 730 genes panel
is_gene_available = True

# 2.1 Data Availability & Row Keys
# From sample characteristics, only treatment group info is available (row 0)
# Can infer trait (cancer vs control) from treatment - patients are all cancer cases
trait_row = 0
age_row = None  # Age not recorded
gender_row = None  # Gender not recorded

# 2.2 Data Type Conversion Functions
def convert_trait(value):
    # Extract value after colon and strip whitespace
    if ':' in value:
        value = value.split(':')[1].strip()
    # All samples are cancer cases - convert to binary 1
    return 1

def convert_age(value):
    return None  # Not used since age data not available

def convert_gender(value):
    return None  # Not used since gender data not available

# 3. Save metadata about data availability
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. Extract clinical features if trait data available
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 data
    preview = preview_df(selected_clinical)
    print("Preview of selected clinical features:")
    print(preview)
    
    # Save to CSV
    selected_clinical.to_csv(out_clinical_data_file)
# Extract gene expression data from matrix file
gene_data = get_genetic_data(matrix_file)

# Print first 20 row IDs and shape of data to help debug
print("Shape of gene expression data:", gene_data.shape)
print("\nFirst few rows of data:")
print(gene_data.head())
print("\nFirst 20 gene/probe identifiers:")
print(gene_data.index[:20])

# Inspect a snippet of raw file to verify identifier format
import gzip
with gzip.open(matrix_file, 'rt', encoding='utf-8') as f:
    lines = []
    for i, line in enumerate(f):
        if "!series_matrix_table_begin" in line:
            # Get the next 5 lines after the marker
            for _ in range(5):
                lines.append(next(f).strip())
            break
print("\nFirst few lines after matrix marker in raw file:")
for line in lines:
    print(line)
# Looking at gene identifiers like "A2M-mRNA", "ABCB1-mRNA", etc.
# These are already human gene symbols with "-mRNA" suffix
# No mapping needed, just need to remove the "-mRNA" suffix
requires_gene_mapping = False
# 1. Normalize gene symbols and save normalized gene data
# Remove "-mRNA" suffix from gene symbols before normalization
gene_data.index = gene_data.index.str.replace('-mRNA', '')
gene_data = normalize_gene_symbols_in_index(gene_data)
gene_data.to_csv(out_gene_data_file)

# 2. Link clinical and genetic data and trait
# First get selected clinical features using the extraction function from previous step
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
)

# Debug data structures before linking
print("\nPre-linking data shapes:")
print("Clinical data shape:", selected_clinical.shape)
print("Gene data shape:", gene_data.shape)
print("\nClinical data preview:")
print(selected_clinical.head())

# Transpose gene data to match clinical data orientation
gene_data_t = gene_data.T
linked_data = pd.concat([selected_clinical.T, gene_data_t], axis=1)

# 3. Handle missing values systematically
linked_data = handle_missing_values(linked_data, trait)

# 4. Check for biased features and remove them if needed
is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)

# 5. Validate data quality and save metadata
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=is_biased,
    df=linked_data,
    note="Gene expression data from pancreatic cancer study. All samples are cancer cases (no controls)."
)

# 6. Save linked data if usable
if is_usable:
    linked_data.to_csv(out_data_file)