Merge pull request #169 from apriltuesday/EVA-3538

EVA-3538 - Move accession monitoring script from eva-accession

accession-monitoring/__init__.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+
+# Copyright 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 configparser
+import logging
+import os
+import subprocess
+import sys
+
+
+def init_logger():
+    logging.basicConfig(stream=sys.stdout, level=logging.INFO, format='%(asctime)-15s %(levelname)s %(message)s')
+    result_logger = logging.getLogger(__name__)
+    return result_logger
+
+
+def get_args_from_properties_file(properties_file):
+    parser = configparser.ConfigParser()
+    parser.optionxform = str
+
+    with open(properties_file, "r") as properties_file_handle:
+        # Dummy section is needed because
+        # ConfigParser is not clever enough to read config files without section headers
+        properties_section_name = "pipeline_properties"
+        properties_string = '[{0}]\n{1}'.format(properties_section_name, properties_file_handle.read())
+        parser.read_string(properties_string)
+        config = dict(parser.items(section=properties_section_name))
+        return config
+
+
+def get_mongo_connection_details_from_properties_file(properties_file):
+    properties_file_args = get_args_from_properties_file(properties_file)
+    mongo_connection_properties = {"mongo_host": properties_file_args["spring.data.mongodb.host"],
+                                   "mongo_port": properties_file_args["spring.data.mongodb.port"],
+                                   "mongo_db": properties_file_args["spring.data.mongodb.database"],
+                                   "mongo_username": properties_file_args["spring.data.mongodb.username"],
+                                   "mongo_password": properties_file_args["spring.data.mongodb.password"],
+                                   "mongo_auth_db": properties_file_args["spring.data.mongodb.authentication-database"]}
+    return mongo_connection_properties
+
+
+def run_command_with_output(command_description, command, return_process_output=False):
+    process_output = ""
+
+    logger.info("Starting process: " + command_description)
+    logger.info("Running command: " + command)
+
+    with subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1, universal_newlines=True,
+                          shell=True) as process:
+        for line in iter(process.stdout.readline, ''):
+            line = str(line).rstrip()
+            logger.info(line)
+            if return_process_output:
+                process_output += line
+        for line in iter(process.stderr.readline, ''):
+            line = str(line).rstrip()
+            logger.error(line)
+    if process.returncode != 0:
+        logger.error(command_description + " failed! Refer to the error messages for details.")
+        raise subprocess.CalledProcessError(process.returncode, process.args)
+    else:
+        logger.info(command_description + " - completed successfully")
+    if return_process_output:
+        return process_output
+
+
+logger = init_logger()

accession-monitoring/monitor_duplicate_accessions.py

@@ -0,0 +1,114 @@
+#!/usr/bin/env python3
+
+# Copyright 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 click
+from datetime import datetime
+import getpass
+import smtplib
+from __init__ import *
+from urllib.parse import quote_plus
+
+
+def get_mongo_uri(mongo_connection_properties):
+    return "mongodb://{0}:{1}@{2}/{3}?authSource={4}".format(mongo_connection_properties["mongo_username"],
+                                                             quote_plus(mongo_connection_properties["mongo_password"]),
+                                                             mongo_connection_properties["mongo_host"],
+                                                             mongo_connection_properties["mongo_db"],
+                                                             mongo_connection_properties["mongo_auth_db"])
+
+
+def export_mongo_accessions(mongo_connection_properties, collection_name, export_output_filename):
+    export_command = 'mongoexport --uri {0} ' \
+                     '--collection {1} --type=csv --fields accession ' \
+                     "--query  '{{\"remappedFrom\": {{\"$exists\": false}}}}' " \
+                     '-o "{2}" 2>&1' \
+                    .format(get_mongo_uri(mongo_connection_properties), collection_name, export_output_filename)
+    run_command_with_output("Exporting accessions in the {0} collection in the {1} database at {2}..."
+                            .format(collection_name, mongo_connection_properties["mongo_db"],
+                                    mongo_connection_properties["mongo_host"]), export_command)
+
+
+def notify_by_email(mongo_connection_properties, collection_name, duplicates_output_filename,
+                    number_of_duplicate_accessions, email_recipients):
+    error_message = "{0} DUPLICATE ACCESSIONS !!! in the {1} collection in the {2} database at {3}"\
+                    .format(number_of_duplicate_accessions, collection_name, mongo_connection_properties["mongo_db"],
+                            mongo_connection_properties["mongo_host"])
+    logger.error(error_message)
+    email_message = "Subject: {0}\n\n" \
+                    "Please see {1} for the list of duplicates.".format(error_message, duplicates_output_filename)
+    smtplib.SMTP('localhost').sendmail(getpass.getuser(), email_recipients, email_message)
+
+
+def report_duplicates_in_exported_accessions_file(mongo_connection_properties, collection_name, export_output_filename,
+                                                  duplicates_output_filename, email_recipients):
+    sorted_export_output_filename = export_output_filename.replace(".csv", "_sorted.csv")
+    run_command_with_output("Sorting {0}...".format(duplicates_output_filename),
+                            'sort -S 4G -T {0} -o "{1}" "{2}"'
+                            .format(os.path.dirname(export_output_filename), sorted_export_output_filename,
+                                    export_output_filename))
+    run_command_with_output("Exporting duplicates to {0}...".format(duplicates_output_filename),
+                            'uniq -d "{0}" > {1}'.format(sorted_export_output_filename, duplicates_output_filename))
+    number_of_duplicate_accessions = run_command_with_output("Find duplicate accessions in the exported file...",
+                                                             'wc -l < "{0}"'.format(duplicates_output_filename),
+                                                             return_process_output=True)
+    if int(number_of_duplicate_accessions) > 0:
+        notify_by_email(mongo_connection_properties, collection_name, duplicates_output_filename,
+                        number_of_duplicate_accessions, email_recipients)
+        return 1
+    else:
+        logger.info("NO duplicate accessions were found in the {0} collection in the {1} database at {2}..."
+                    .format(collection_name, mongo_connection_properties["mongo_db"],
+                            mongo_connection_properties["mongo_host"]))
+        return 0
+
+
+def report_duplicate_accessions_in_mongo(pipeline_properties_file, accessions_export_output_dir,
+                                         collection_name, email_recipients):
+    mongo_connection_properties = get_mongo_connection_details_from_properties_file(pipeline_properties_file)
+    export_output_filename = os.path.sep.join([accessions_export_output_dir,
+                                               "accessions_in_{0}_{1}_at_{2}_as_of_{3}.csv"
+                                              .format(mongo_connection_properties["mongo_db"], collection_name,
+                                                      mongo_connection_properties["mongo_host"],
+                                                      datetime.today().strftime('%Y%m%d%H%M%S'))])
+    duplicates_output_filename = export_output_filename.replace("accessions_in", "duplicate_accessions_in")
+
+    logger.info("Checking duplicate accessions in the {0} collection in the {1} database at {2}..."
+                .format(collection_name, mongo_connection_properties["mongo_db"],
+                        mongo_connection_properties["mongo_host"]))
+
+    export_mongo_accessions(mongo_connection_properties, collection_name, export_output_filename)
+
+    return report_duplicates_in_exported_accessions_file(mongo_connection_properties, collection_name,
+                                                         export_output_filename, duplicates_output_filename,
+                                                         email_recipients)
+
+
+@click.option("-p", "--pipeline-properties-file", required=True)
+@click.option("-o", "--accessions-export-output-dir", required=True)
+@click.option("-e", "--email-recipients", multiple=True, required=True)
+@click.argument("collection-names", nargs=-1, required=True)
+@click.command()
+def main(pipeline_properties_file, accessions_export_output_dir,  email_recipients, collection_names):
+    exit_code = 0
+    for collection_name in collection_names:
+        exit_code = exit_code or \
+                    report_duplicate_accessions_in_mongo(pipeline_properties_file, accessions_export_output_dir,
+                                                         collection_name, email_recipients)
+    sys.exit(exit_code)
+
+
+if __name__ == '__main__':
+    main()

accession-monitoring/requirements.txt

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+click