EVA-3632 - Script to go through multiple ELOADs and report the naming convention found

tasks/eva_3632/gather_naming_conventions.py

@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+
+# 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 logging
+from argparse import ArgumentParser
+
+from ebi_eva_common_pyutils.logger import logging_config as log_cfg
+
+from eva_submission.eload_submission import Eload
+from eva_submission.submission_config import load_config
+
+logger = log_cfg.get_logger(__name__)
+
+
+def report_per_files(eloads):
+    for eload in eloads:
+        eload_obj = Eload(eload_number=eload)
+        vcf_files_2_naming_conv = eload_obj.eload_cfg.query('validation', 'naming_convention_check', 'files')
+        if vcf_files_2_naming_conv:
+            for vcf_file in vcf_files_2_naming_conv:
+                if vcf_files_2_naming_conv[vcf_file]['naming_convention']:
+                    print(f"ELOAD_{eload}: {vcf_file} {vcf_files_2_naming_conv[vcf_file]['naming_convention']}")
+                elif vcf_files_2_naming_conv[vcf_file]['naming_convention_map']:
+                    nc_map = vcf_files_2_naming_conv[vcf_file]['naming_convention_map']
+                    if 'Not found' in nc_map:
+                        print(f"ELOAD_{eload}: {vcf_file} Missing {len(nc_map['Not found'])} chromosome")
+                    else:
+                        print(f"ELOAD_{eload}: {vcf_file} Found {len(nc_map)} naming conventions")
+                else:
+                    print(f"ELOAD_{eload}: {vcf_file} naming conventions not assessed")
+
+
+def report_per_eload(eloads):
+    for eload in eloads:
+        eload_obj = Eload(eload_number=eload)
+        vcf_files_2_naming_conv = eload_obj.eload_cfg.query('validation', 'naming_convention_check', 'files')
+        naming_conv = eload_obj.eload_cfg.query('validation', 'naming_convention_check', 'naming_convention')
+        if naming_conv:
+            pass
+        elif vcf_files_2_naming_conv:
+            for vcf_file in vcf_files_2_naming_conv:
+                file_naming_convention = vcf_files_2_naming_conv[vcf_file]['naming_convention']
+                if file_naming_convention and naming_conv not in ['Multiple', 'Not calculated', 'Not found']:
+                    # If we get here it means that different files use different naming convention
+                    naming_conv = 'Different per files'
+                nc_map = vcf_files_2_naming_conv[vcf_file]['naming_convention_map']
+                if vcf_files_2_naming_conv[vcf_file]['naming_convention']:
+                    pass
+                elif vcf_files_2_naming_conv[vcf_file]['naming_convention_map']:
+                    if naming_conv not in ['Not calculated'] and 'Not found' in nc_map:
+                        naming_conv = 'Not found'
+                    elif naming_conv not in ['Not calculated', 'Not found']:
+                        naming_conv = 'Multiple'
+                else:
+                    naming_conv = 'Not calculated'
+        else:
+            naming_conv = 'Not calculated'
+
+        print(f"ELOAD_{eload}: {naming_conv}")
+
+
+def main():
+    argparse = ArgumentParser(description='Validate an ELOAD by checking the data and metadata format and semantics.')
+    argparse.add_argument('--eloads', required=True, type=int, nargs='+',
+                          help='The ELOAD numbers of the submissions to summarise')
+    argparse.add_argument('--per_files', action='store_true', default=False,
+                          help='Report the naming convention per file rather than per eload')
+    argparse.add_argument('--debug', action='store_true', default=False,
+                          help='Set the script to output logging information at debug level')
+
+    args = argparse.parse_args()
+
+    log_cfg.add_stdout_handler()
+    if args.debug:
+        log_cfg.set_log_level(logging.DEBUG)
+
+    # Load the config_file from default location
+    load_config()
+    if args.per_files:
+        report_per_files(args.eloads)
+    else:
+        report_per_eload(args.eloads)
+
+
+if __name__ == "__main__":
+    main()