some fixes after review

EBI-Metagenomics · Feb 6, 2024 · bfb1b54 · bfb1b54
1 parent 18d4641
commit bfb1b54
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Showing 4 changed files with 11 additions and 32 deletions.
diff --git a/emgapi/management/commands/populate_metagenomics_exchange.py b/emgapi/management/commands/populate_metagenomics_exchange.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2017-2022 EMBL - European Bioinformatics Institute
+# Copyright 2017-2024 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.
@@ -96,7 +96,7 @@ def handle(self, *args, **options):
     def process_to_index_and_update_records(self, analyses_to_index_and_update):
         logging.info(f"Indexing {len(analyses_to_index_and_update)} new analyses")
 
-        for page in Paginator(analyses_to_index_and_update, 100):
+        for page in Paginator(analyses_to_index_and_update, settings.METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER):
             jobs_to_update = []
             for ajob in page:
                 metadata = self.mgx_api.generate_metadata(
@@ -152,7 +152,7 @@ def process_to_index_and_update_records(self, analyses_to_index_and_update):
                         logging.debug(f"No edit for {ajob}, metadata is correct")
 
             AnalysisJob.objects.bulk_update(
-                jobs_to_update, ["last_mgx_indexed", "mgx_accession"], batch_size=100
+                jobs_to_update, ["last_mgx_indexed", "mgx_accession"], batch_size=settings.METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER
             )
 
     def process_to_delete_records(self, analyses_to_delete):
@@ -161,7 +161,7 @@ def process_to_delete_records(self, analyses_to_delete):
         """
         logging.info(f"Processing {len(analyses_to_delete)} analyses to remove")
 
-        for page in Paginator(analyses_to_delete, 100):
+        for page in Paginator(analyses_to_delete, settings.METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER):
             jobs_to_update = []
 
             for ajob in page:
@@ -192,5 +192,5 @@ def process_to_delete_records(self, analyses_to_delete):
 
             # BULK UPDATE #
             AnalysisJob.objects.bulk_update(
-                jobs_to_update, ["last_mgx_indexed"], batch_size=100
+                jobs_to_update, ["last_mgx_indexed"], batch_size=settings.METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER
             )
diff --git a/emgapi/metagenomics_exchange.py b/emgapi/metagenomics_exchange.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2018-2023 EMBL - European Bioinformatics Institute
+# Copyright 2018-2024 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.
@@ -25,7 +25,7 @@ class MetagenomicsExchangeAPI:
     """Metagenomics Exchange API Client"""
 
     def __init__(self, base_url=None):
-        self.base_url = base_url if base_url else settings.METAGENOMICS_EXCHANGE_API
+        self.base_url = base_url or settings.METAGENOMICS_EXCHANGE_API
         self.__token = settings.METAGENOMICS_EXCHANGE_API_TOKEN
         self.broker = settings.METAGENOMICS_EXCHANGE_MGNIFY_BROKER
 

diff --git a/emgapi/models.py b/emgapi/models.py
@@ -1687,27 +1687,6 @@ def __str__(self):
         return 'Assembly:{} - Sample:{}'.format(self.assembly, self.sample)
 
 
-class MetagenomicsExchangeModel(models.Model):
-    """Model to track Metagenomics Exchange population
-    https://www.ebi.ac.uk/ena/registry/metagenome/api/
-    """
-    last_updated_me = models.DateTimeField(
-        db_column='LAST_UPDATED_ME',
-        auto_now=True
-    )
-    last_populated_me = models.DateTimeField(
-        db_column='LAST_POPULATED_ME',
-        null=True,
-        blank=True,
-        help_text="Date at which this model was last appeared in Metagenomics Exchange"
-    )
-
-    objects_for_population = MetagenomicsExchangeQueryset.as_manager()
-
-    class Meta:
-        abstract = True
-
-
 class AnalysisJobQuerySet(BaseQuerySet, MySQLQuerySet, SuppressQuerySet, SelectRelatedOnlyQuerySetMixin):
 
     def __init__(self, *args, **kwargs):

diff --git a/emgcli/settings.py b/emgcli/settings.py
@@ -687,11 +687,11 @@ def create_secret_key(var_dir):
 METAGENOMICS_EXCHANGE_MGNIFY_BROKER = "EMG"
 METAGENOMICS_EXCHANGE_API = ""
 METAGENOMICS_EXCHANGE_API_TOKEN = ""
+METAGENOMICS_EXCHANGE_PAGINATOR_NUMBER = 100
 try:
     METAGENOMICS_EXCHANGE_API = EMG_CONF['emg']['me_api']
-    if EMG_CONF['emg'].get('me_api_token'):
+    METAGENOMICS_EXCHANGE_API_TOKEN = os.getenv('METAGENOMICS_EXCHANGE_API_TOKEN')
+    if not METAGENOMICS_EXCHANGE_API_TOKEN:
         METAGENOMICS_EXCHANGE_API_TOKEN = EMG_CONF['emg']['me_api_token']
-    else:
-        METAGENOMICS_EXCHANGE_API_TOKEN = os.getenv('METAGENOMICS_EXCHANGE_API_TOKEN')
 except KeyError:
-    warnings.warn("The metagenomics exchange API and Token are not configured properly")
+    warnings.warn("The metagenomics exchange API and Token are not configured properly")