upload_log.py

#!/usr/bin/env python3

###########################	Description	##################################
# Functions for handling update log
################################################################################

import file_handler
import pandas as pd
from config.seqsender.upload_log_schema import schema as upload_schema
from typing import List, Optional, Dict, Any, Tuple, Union
from pandera import pandera, DataFrameSchema, Column, Check, Index, MultiIndex
import os
import sys
import genbank_handler
import gisaid_handler
from datetime import datetime
import biosample_sra_handler
import ncbi_handler
import tools

from config.seqsender.submission_status_report.biosample_submission_status_report_schema import schema as status_report_bs_schema
from config.seqsender.submission_status_report.sra_submission_status_report_schema import schema as status_report_sra_schema
from config.seqsender.submission_status_report.genbank_submission_status_report_schema import schema as status_report_gb_schema
from config.seqsender.submission_status_report.gisaid_submission_status_report_schema import schema as status_report_gs_schema

from settings import SAMPLE_NAME_DATABASE_PREFIX, BIOSAMPLE_SUBMISSION_STATUS_COLUMNS, SRA_SUBMISSION_STATUS_COLUMNS, GENBANK_SUBMISSION_STATUS_COLUMNS, GISAID_SUBMISSION_STATUS_COLUMNS, SUBMISSION_LOG_COLUMNS

# create new submission_status.csv based on databases submitting to
def create_submission_status_csv(database: List[str], metadata: pd.DataFrame, submission_dir: str) -> None:
	submission_status_file = os.path.join(submission_dir, "submission_status_report.csv")
	database_columns: List[str]  = []
	sample_name_columns: List[str] = []
	ordered_database_columns: List[str]  = []
	if "BIOSAMPLE" in database:
		database_columns += BIOSAMPLE_SUBMISSION_STATUS_COLUMNS
		sample_name_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['BIOSAMPLE']}sample_name"]
		ordered_database_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['BIOSAMPLE']}sample_name"] + BIOSAMPLE_SUBMISSION_STATUS_COLUMNS
	if "SRA" in database:
		database_columns += SRA_SUBMISSION_STATUS_COLUMNS
		sample_name_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['SRA']}sample_name"]
		ordered_database_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['SRA']}sample_name"] + SRA_SUBMISSION_STATUS_COLUMNS
	if "GENBANK" in database:
		database_columns += GENBANK_SUBMISSION_STATUS_COLUMNS
		sample_name_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['GENBANK']}sample_name"]
		ordered_database_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['GENBANK']}sample_name"] + GENBANK_SUBMISSION_STATUS_COLUMNS
	if "GISAID" in database:
		database_columns += GISAID_SUBMISSION_STATUS_COLUMNS
		sample_name_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['GISAID']}sample_name"]
		if f"{SAMPLE_NAME_DATABASE_PREFIX['GISAID']}Isolate_Name" in metadata:
			sample_name_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['GISAID']}Isolate_Name"]
			ordered_database_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['GISAID']}Isolate_Name", f"{SAMPLE_NAME_DATABASE_PREFIX['GISAID']}sample_name"] + GISAID_SUBMISSION_STATUS_COLUMNS
		else:
			ordered_database_columns += [f"{SAMPLE_NAME_DATABASE_PREFIX['GISAID']}sample_name"] + GISAID_SUBMISSION_STATUS_COLUMNS
	sample_name_df = metadata[sample_name_columns].copy()
	sample_name_df = sample_name_df.assign(**{col: "" for col in database_columns})
	sample_name_df = sample_name_df.reindex(columns = ordered_database_columns)
	if "gs-Isolate_Name" in sample_name_df:
		sample_name_df = sample_name_df.rename(columns={"gs-Isolate_Name":"gs-sample_name", "gs-sample_name":"gs-segment_name"})
	file_handler.save_csv(df=sample_name_df, file_path=submission_status_file)

# Validate data in submission_status.csv file is correctly formatted
def validate_submission_status_df(metadata: pd.DataFrame, database: List[str]) -> None:
	error_msg_list: List[pandera.errors.SchemaErrors] = []
	if "BIOSAMPLE" in database:
		try:
			status_report_bs_schema.validate(metadata, lazy = True)
		except pandera.errors.SchemaErrors as schema_error:
			error_msg_list.append(schema_error)
	if "SRA" in database:
		try:
			status_report_sra_schema.validate(metadata, lazy = True)
		except pandera.errors.SchemaErrors as schema_error:
			error_msg_list.append(schema_error)
	if "GENBANK" in database:
		try:
			status_report_gb_schema.validate(metadata, lazy = True)
		except pandera.errors.SchemaErrors as schema_error:
			error_msg_list.append(schema_error)
	if "GISAID" in database:
		try:
			status_report_gs_schema.validate(metadata, lazy = True)
		except pandera.errors.SchemaErrors as schema_error:
			error_msg_list.append(schema_error)
	if error_msg_list:
		print(metadata.head())
		tools.pretty_print_pandera_errors(file="submission_status_report.csv", error_msgs=error_msg_list)
		sys.exit(1)

# Update values of existing submission_status.csv file
def update_submission_status_csv(submission_dir: str, update_database: str, update_df: pd.DataFrame) -> None:
	# Check if there are updates to be made
	if update_df.empty:
		print(f"Error: Unable to update 'submission_status.csv' for '{update_database}' at '{submission_dir}'. The log file may be empty.", file=sys.stderr)
	# Pop off directory if inside database directory
	if os.path.split(submission_dir)[-1] in ["BIOSAMPLE", "SRA", "GENBANK", "GISAID"]:
		submission_dir = os.path.dirname(submission_dir)
	submission_status_file = os.path.join(submission_dir, "submission_status_report.csv")
	file_handler.validate_file(file_type="submission status report", file_path=submission_status_file)
	df = file_handler.load_csv(file_path=submission_status_file)
	# Identify database schemas based on <database_prefix>_sample_name
	all_databases = [database_name for database_name, database_prefix in SAMPLE_NAME_DATABASE_PREFIX.items() if (database_prefix + "sample_name") in df.columns]
	validate_submission_status_df(metadata=df, database=all_databases)
	if f"{SAMPLE_NAME_DATABASE_PREFIX[update_database]}sample_name" in update_df:
		sample_column = (SAMPLE_NAME_DATABASE_PREFIX[update_database] + "sample_name")
	elif f"{SAMPLE_NAME_DATABASE_PREFIX[update_database]}segment_name" in update_df:
		sample_column = (SAMPLE_NAME_DATABASE_PREFIX[update_database] + "segment_name")
	df = df.set_index(sample_column, drop = False)
	update_df = update_df.set_index(sample_column)
	df.update(update_df)
	df = df.reset_index(drop = True)
	validate_submission_status_df(metadata=df, database=all_databases)
	file_handler.save_csv(df=df, file_path=submission_status_file)

# Create new row in submission_log.csv for database submission
def create_submission_log(database: str, organism: str, submission_name: str, submission_dir: str, database_dir: str, config_file: str, submission_status: str, submission_id: str, submission_type: str) -> None:
	# if log exists load existing one
	if os.path.isfile(os.path.join(submission_dir, "submission_log.csv")):
		df = load_submission_log(submission_dir=submission_dir)
	else:
		# If log doesn't exist create it
		df = pd.DataFrame(columns = SUBMISSION_LOG_COLUMNS)
	# Create new field
	new_entry = {'Submission_Name': submission_name,
				 'Organism': organism,
				 'Database': database,
				 'Submission_Type': submission_type,
				 'Submission_Date': datetime.now().strftime("%Y-%m-%d"),
				 'Submission_ID': submission_id,
				 'Submission_Status': submission_status,
				 'Submission_Directory': database_dir,
				 'Config_File': config_file,
				 'Update_Date': datetime.now().strftime("%Y-%m-%d")
				}
	df.loc[len(df)] = new_entry # type: ignore
	# Remove duplicates and keep latest update
	df = df.drop_duplicates(subset = ["Submission_Name", "Organism", "Database", "Submission_Type", "Config_File"], keep = "last", ignore_index = True)
	file_handler.save_csv(df=df, file_path=submission_dir, file_name="submission_log.csv")

# Update values of existing submission_log.csv file
def update_submission_log(database: str, organism: str, submission_name: str, submission_log_dir: str, submission_dir: str, submission_status: str, submission_id: str, submission_type: str) -> None:
	df = load_submission_log(submission_dir=submission_log_dir)
	# Select correct fields
	df_partial = df.loc[(df["Organism"] == organism) & (df["Database"] == database) & (df["Submission_Directory"] == submission_dir) & (df["Submission_Name"] == submission_name) & (df["Submission_Type"] == submission_type)]
	# Update existing field
	if df_partial.shape[0] > 0:
		df.loc[df_partial.index.values, "Submission_ID"] = submission_id
		df.loc[df_partial.index.values, "Submission_Status"] = submission_status
		df.loc[df_partial.index.values, "Update_Date"] = datetime.now().strftime("%Y-%m-%d")
	else:
		print(f"Error: '{submission_name}' '{database}' is not present in the submission log at '{submission_log_dir}'.", file=sys.stderr)
		sys.exit(1)
	file_handler.save_csv(df=df, file_path=submission_log_dir, file_name="submission_log.csv")

# Validate submission_dir and log exists and then validate syntax is correct
def load_submission_log(submission_dir: str) -> pd.DataFrame:
	submission_log_file = os.path.join(submission_dir, "submission_log.csv")
	file_handler.validate_file(file_type = "submission_log", file_path = submission_log_file)
	df = file_handler.load_csv(file_path = submission_log_file)
	# Drop no longer used columns if present
	df = df.drop(columns=["Submission_Position", "Table2asn", "GFF_File"], errors="ignore")
	# Remove duplicates and keep latest update
	df = df.drop_duplicates(subset = ["Submission_Name", "Organism", "Database", "Submission_Type", "Config_File"], keep = "last", ignore_index = True)
	try:
		upload_schema.validate(df, lazy = True)
	except pandera.errors.SchemaErrors as schema_error:
		print("Error: Upload log columns are incorrect. Cannot process submissions.", file=sys.stderr)
		tools.pretty_print_pandera_errors(file=submission_log_file, error_msgs=[schema_error])
		sys.exit(1)
	return df

# Validate files listed inside submission_log.csv
def validate_fields_exist(df: pd.DataFrame):
	submission_dir = df["Submission_Directory"].iloc[0]
	submission_status_file = os.path.join(os.path.dirname(submission_dir), "submission_status_report.csv")
	config_file = df["Config_File"].iloc[0]
	file_handler.validate_directory(name = "directory", path = submission_dir)
	file_handler.validate_file(file_type = "submission_status_report", file_path = submission_status_file)
	file_handler.validate_file(file_type = "config file", file_path = config_file)

# Process submission status of existing biosample/sra database submission
def process_biosample_sra(submission_name: str, database: str, organism: str, submission_log_dir: str, submission_dir: str, curr_status: str, config_dict: Dict[str, Any], submission_type: str) -> Tuple[bool, str]:
	if curr_status == "PROCESSED":
		return True, curr_status
	report_file = ncbi_handler.get_ncbi_report(database=database, submission_name=submission_name, submission_dir=submission_dir, config_dict=config_dict, submission_type=submission_type)
	if report_file:
		new_submission_status, submission_id = biosample_sra_handler.process_biosample_sra_report(report_file=report_file, database=database, submission_dir=submission_dir)
	else:
		new_submission_status = curr_status
		submission_id = "PENDING"
	update_submission_log(database=database, organism=organism, submission_name=submission_name, submission_log_dir=submission_log_dir, submission_dir=submission_dir, submission_status=new_submission_status, submission_id=submission_id, submission_type=submission_type)
	if new_submission_status == "PROCESSED":
		return True, new_submission_status
	return False, new_submission_status

# Upload log submit GenBank database submission after previous required database submission
def upload_log_submit_genbank(genbank_type: str, submission_name: str, organism: str, submission_log_dir: str, submission_dir: str, config_dict: Dict[str, Any], submission_type:str) -> str:
	if genbank_type == "GENBANK-TBL2ASN":
		submission_id = genbank_handler.create_table2asn(submission_name=submission_name, submission_dir=submission_dir)
		if submission_id == "VALIDATED":
			submission_status = ncbi_handler.email_table2asn(submission_name=submission_name, submission_dir=submission_dir, config_dict=config_dict, submission_type=submission_type)
		else:
			submission_status = "PENDING"
	elif genbank_type == "GENBANK-FTP":
		genbank_handler.create_zip(submission_name=submission_name, submission_dir=submission_dir)
		ncbi_handler.submit_ncbi(database="GENBANK", submission_name=submission_name, submission_dir=submission_dir, config_dict=config_dict, submission_type=submission_type)
		submission_id, submission_status = "PENDING", "SUBMITTED"
	else:
		print(f"Error: {genbank_type} is not a valid GenBank submission option.", file=sys.stderr)
		sys.exit(1)
	update_submission_log(database=genbank_type, organism=organism, submission_name=submission_name, submission_log_dir=submission_log_dir, submission_dir=submission_dir, submission_status=submission_status, submission_id=submission_id, submission_type=submission_type)
	return submission_status

# Process submission status of existing genbank database submission
def process_genbank(genbank_type: str, submission_name: str, submission_log_dir: str, submission_dir: str, curr_status: str, organism: str, config_dict: Dict[str, Any], submission_type: str, linking_databases: Dict[str, bool]) -> Tuple[bool, str]:
	if curr_status in ["PROCESSED", "EMAILED"]:
		return True, curr_status
	elif curr_status == "WAITING" and submission_ready(submission_requirements=linking_databases, config_dict=config_dict, database="GENBANK"):
		if config_dict["Link_Sample_Between_NCBI_Databases"]:
			genbank_handler.update_genbank_files(linking_databases=linking_databases, organism=organism, submission_dir=submission_dir)
		new_submission_status = upload_log_submit_genbank(genbank_type=genbank_type, submission_name=submission_name, organism=organism, submission_log_dir=submission_log_dir, submission_dir=submission_dir, config_dict=config_dict, submission_type=submission_type)
		return False, new_submission_status
	elif curr_status == "WAITING":
		return False, curr_status
	else:
		report_file = ncbi_handler.get_ncbi_report("GENBANK", submission_name, submission_dir, config_dict, submission_type)
		if report_file:
			new_submission_status, submission_id = genbank_handler.process_genbank_report(report_file=report_file, submission_dir=submission_dir)
		else:
			new_submission_status = curr_status
			submission_id = "PENDING"
		update_submission_log(database=genbank_type, organism=organism, submission_name=submission_name, submission_log_dir=submission_log_dir, submission_dir=submission_dir, submission_status=new_submission_status, submission_id=submission_id, submission_type=submission_type)
		if new_submission_status == "PROCESSED":
			return True, new_submission_status
		return False, new_submission_status

# Process submission status of GISAID status
def process_gisaid(submission_name: str, submission_log_dir: str, submission_dir: str, organism: str, curr_status: str, config_dict: Dict[str, Any], submission_type: str, submission_requirements: Dict[str, bool]) -> Tuple[bool, str]:
	if curr_status == "PROCESSED":
		return True, curr_status
	elif curr_status == "WAITING" and not submission_ready(submission_requirements=submission_requirements, config_dict=config_dict, database="GISAID"):
		return False, curr_status
	else:
		submission_id = "SUBMITTED"
		new_submission_status = gisaid_handler.submit_gisaid(organism=organism, submission_dir=submission_dir, submission_name=submission_name, config_dict=config_dict, submission_type=submission_type)
		update_submission_log(database='GISAID', organism=organism, submission_name=submission_name, submission_log_dir=submission_log_dir, submission_dir=submission_dir, submission_status=new_submission_status, submission_id=submission_id, submission_type=submission_type)
		if new_submission_status == "PROCESSED":
			return True, new_submission_status
		else:
			return False, new_submission_status

# Determine if upload log can submission to database
def submission_ready(submission_requirements: Dict[str,bool], config_dict: Dict[str, Any], database: str) -> bool:
	opposite_database = {"GENBANK":"GISAID", "GISAID":"GENBANK"}
	position = tools.get_submission_position(config_dict=config_dict, database=database)
	if position is None:
		return True
	elif position == 1 and submission_requirements["BIOSAMPLE"] and submission_requirements["SRA"]:
		return True
	elif position == 2 and submission_requirements["BIOSAMPLE"] and submission_requirements["SRA"] and submission_requirements[opposite_database[database]]:
		return True
	else:
		return False

# Create SeqSender dict of the status for each DB under one submission name
def create_submission_requirements_dict(group_df: pd.DataFrame) -> Dict[str, bool]:
	submission_requirements = dict()
	database_list = group_df["Database"].tolist()
	for database in ["BIOSAMPLE", "SRA", "GISAID"]:
		if database in database_list:
			if group_df.loc[group_df["Database"] == database, "Submission_Status"].iloc[0] == "PROCESSED":
				submission_requirements[database] = True
			else:
				submission_requirements[database] = False
		else:
			submission_requirements[database] = True
	if "GENBANK-FTP" in database_list:
		if group_df.loc[group_df["Database"] == "GENBANK-FTP", "Submission_Status"].iloc[0] == "PROCESSED":
			submission_requirements["GENBANK"] = True
		else:
			submission_requirements["GENBANK"] = False
	elif "GENBANK-TBL2ASN" in database_list:
		if group_df.loc[group_df["Database"] == "GENBANK-TBL2ASN", "Submission_Status"].iloc[0] == "PROCESSED":
			submission_requirements["GENBANK"] = True
		else:
			submission_requirements["GENBANK"] = False
	else:
		submission_requirements["GENBANK"] = True
	return submission_requirements

# Update all databases listed under one submission_name
def update_grouped_submission(group_df: pd.DataFrame, submission_log_dir: str):
	validate_fields_exist(df=group_df)
	submission_requirements = create_submission_requirements_dict(group_df=group_df)
	# Reset index
	group_df = group_df.reset_index()
	submission_name = group_df.at[0, "Submission_Name"]
	submission_type = group_df.at[0, "Submission_Type"]
	submission_organism = group_df.at[0, "Organism"]
	submission_dir = group_df.at[0, "Submission_Directory"]
	databases = group_df["Database"].tolist()
	config_dict = tools.get_config(config_file=group_df.at[0, "Config_File"], database=databases)
	if "BIOSAMPLE" in databases:
		biosample_status = group_df.loc[group_df["Database"] == "BIOSAMPLE", "Submission_Status"].iloc[0]
		submission_dir = group_df.loc[group_df["Database"] == "BIOSAMPLE", "Submission_Directory"].iloc[0]
		submission_requirements["BIOSAMPLE"], biosample_status = process_biosample_sra(submission_name=submission_name, organism=submission_organism, database="BIOSAMPLE", curr_status=biosample_status, submission_log_dir=submission_log_dir, submission_dir=submission_dir, config_dict=config_dict["NCBI"], submission_type=submission_type)
		print(f"\tBioSample: {biosample_status}", file=sys.stdout)
	if "SRA" in databases:
		sra_status = group_df.loc[group_df["Database"] == "SRA", "Submission_Status"].iloc[0]
		submission_dir = group_df.loc[group_df["Database"] == "SRA", "Submission_Directory"].iloc[0]
		submission_requirements["SRA"], sra_status = process_biosample_sra(submission_name=submission_name, organism=submission_organism, database="SRA", curr_status=sra_status, submission_log_dir=submission_log_dir, submission_dir=submission_dir, config_dict=config_dict["NCBI"], submission_type=submission_type)
		print(f"\tSRA: {sra_status}", file=sys.stdout)
	# If GISAID submitted to first, check it now
	if "GISAID" in databases and tools.get_submission_position(config_dict=config_dict, database="GISAID") == 1:
		gisaid_status = group_df.loc[group_df["Database"] == "GISAID", "Submission_Status"].iloc[0]
		submission_dir = group_df.loc[group_df["Database"] == "GISAID", "Submission_Directory"].iloc[0]
		submission_requirements["GISAID"], gisaid_status = process_gisaid(submission_name=submission_name, submission_log_dir=submission_log_dir, submission_dir=submission_dir, organism=submission_organism, curr_status=gisaid_status, config_dict=config_dict["GISAID"], submission_type=submission_type, submission_requirements=submission_requirements)
		print(f"\tGISAID: {gisaid_status}", file=sys.stdout)
	# Same requirements for GENBANK-FTP and GENBANK-TBL2ASN
	if any("GENBANK" in database for database in databases):
		if "GENBANK-FTP" in databases:
			genbank_type = "GENBANK-FTP"
		elif "GENBANK-TBL2ASN" in databases:
			genbank_type = "GENBANK-TBL2ASN"
		else:
			print(f"Error: Incorrect database option for GenBank in 'submission_log.csv' databases '{databases}' for '{submission_name}'.")
			sys.exit(1)
		genbank_status = group_df.loc[group_df["Database"] == genbank_type, "Submission_Status"].iloc[0]
		submission_dir = group_df.loc[group_df["Database"] == genbank_type, "Submission_Directory"].iloc[0]
		submission_requirements["GENBANK"], genbank_status = process_genbank(genbank_type=genbank_type, submission_name=submission_name, submission_log_dir=submission_log_dir, submission_dir=submission_dir, curr_status=genbank_status, organism=submission_organism, config_dict=config_dict["NCBI"], submission_type=submission_type, linking_databases=submission_requirements)
		print(f"\tGenBank: {genbank_status}", file=sys.stdout)
	# If GISAID was not previously submitted to, try again
	if "GISAID" in databases and tools.get_submission_position(config_dict=config_dict, database="GISAID") != 1:
		gisaid_status = group_df.loc[group_df["Database"] == "GISAID", "Submission_Status"].iloc[0]
		submission_dir = group_df.loc[group_df["Database"] == "GISAID", "Submission_Directory"].iloc[0]
		submission_requirements["GISAID"], gisaid_status = process_gisaid(submission_name=submission_name, submission_log_dir=submission_log_dir, submission_dir=submission_dir, organism=submission_organism, curr_status=gisaid_status, config_dict=config_dict["GISAID"], submission_type=submission_type, submission_requirements=submission_requirements)
		print(f"\tGISAID: {gisaid_status}", file=sys.stdout)

# Update submission log, if given submission_name only update that specific submission
def update_submission_status(submission_dir: str, submission_name: Optional[str]) -> None:
	df = load_submission_log(submission_dir)
	grouped_submissions = df.groupby(["Submission_Name", "Organism", "Submission_Type", "Config_File"])
	print("Checking Submissions:", file=sys.stdout)
	for name, group in grouped_submissions:
		if not group["Submission_Status"].isin(["PROCESSED", "EMAILED"]).all() and submission_name is None or name[0] == submission_name:
			print(f"Submission: {name[0]}", file=sys.stdout)
			update_grouped_submission(group_df=group, submission_log_dir=submission_dir)
			# try:
			# 	print(f"Submission: {name[0]}", file=sys.stdout)
			# 	update_grouped_submission(group_df=group, submission_log_dir=submission_dir)
			# except Exception as e:
			# 	print(f"Error: Unable to process {name} because:\n{e}", file=sys.stderr)
	print("\nUpdating submissions complete.", file=sys.stdout)