run_apollo_report.py

"""
Copyright [2017-2020] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
     http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""
import argparse
import configparser
import sys
from module.apollo_reporter import ApolloReporter

sys.setrecursionlimit(1500)

if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Check annotations and send reports based on a config file."
    )
    parser.add_argument("config_file", help="Config file to use")
    parser.add_argument(
        "--nosend", action="store_true", help="Do not send emails (for testing)"
    )
    args = parser.parse_args()

    send_email = not args.nosend
    config_file = args.config_file

    # Parse config
    report_config = configparser.ConfigParser()
    report_config.read(config_file)
    apollo_reporter = ApolloReporter(report_config)

    # Summary annotations
    if report_config["PIPELINE"]["summary_annotation"] == "yes":
        gene_to_organism, master_gff = apollo_reporter.prepare_summary_gff()

        emails = apollo_reporter.prepare_summary_emails(
            master_gff, gene_to_organism, "summary"
        )
        if send_email:
            apollo_reporter.send_emails("summary", emails)
        else:
            for email in emails:
                user_id, email_message = email
                print(f"Summary email not sent to {user_id}")

        error_emails = apollo_reporter.prepare_error_emails(
            master_gff, gene_to_organism, "error"
        )
        if send_email:
            apollo_reporter.send_emails("error", error_emails)
        else:
            for email in error_emails:
                user_id, email_message = email
                print(f"Error email not sent to {user_id}")

    # Recent annotations
    if report_config["PIPELINE"]["recent_annotation"] == "yes":
        recent_genes, recent_gff = apollo_reporter.prepare_recent_gff()

        # Write error emails
        error_emails = apollo_reporter.prepare_error_emails(
            recent_gff, recent_genes, "error"
        )
        if send_email:
            apollo_reporter.send_emails("error", error_emails)
        else:
            for email in error_emails:
                user_id, email_message = email
                print(f"Error email not sent to {user_id}")