Fix error in map creation

EBIvariation · Jul 3, 2024 · e2f1d05 · e2f1d05
1 parent 370c08a
commit e2f1d05
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/eva-accession-release-automation/gather_clustering_counts/gather_release_counts.py b/eva-accession-release-automation/gather_clustering_counts/gather_release_counts.py
@@ -443,7 +443,7 @@ def generate_per_taxonomy_counts(self):
         species_annotations = defaultdict(dict)
         for count_groups in self.all_counts_grouped:
             taxonomy_and_types = set([(count_dict['taxonomy'], count_dict['idtype']) for count_dict in count_groups])
-            release_folder_map = dict((count_dict['taxonomy'], count_dict['release_folder'] for count_dict in count_groups))
+            release_folder_map = dict((count_dict['taxonomy'], count_dict['release_folder']) for count_dict in count_groups)
             for taxonomy, rstype in taxonomy_and_types:
                 if taxonomy not in species_annotations:
                     species_annotations[taxonomy] = {'assemblies': set(), 'release_folder': None}
@@ -464,7 +464,6 @@ def generate_per_assembly_counts(self):
         assembly_annotations = {}
         for count_groups in self.all_counts_grouped:
             assembly_and_types = set([(count_dict['assembly'], count_dict['idtype']) for count_dict in count_groups])
-            release_folder_map = dict((count_dict['taxonomy'], count_dict['release_folder'] for count_dict in count_groups))
             for assembly_accession, rstype in assembly_and_types:
                 if assembly_accession not in assembly_annotations:
                     assembly_annotations[assembly_accession] = {'taxonomies': set(), 'release_folder': None}
@@ -485,7 +484,7 @@ def generate_per_taxonomy_and_assembly_counts(self):
         species_assembly_annotations = defaultdict(dict)
         for count_groups in self.all_counts_grouped:
             taxonomy_assembly_and_types = set([(count_dict['taxonomy'], count_dict['assembly'], count_dict['idtype']) for count_dict in count_groups])
-            release_folder_map = dict((count_dict['taxonomy'], count_dict['release_folder'] for count_dict in count_groups))
+            release_folder_map = dict((count_dict['taxonomy'], count_dict['release_folder']) for count_dict in count_groups)
             for taxonomy, assembly, rstype in taxonomy_assembly_and_types:
                 if (taxonomy, assembly) not in species_assembly_annotations:
                     species_assembly_annotations[(taxonomy, assembly)] = {'release_folder': None}

diff --git a/...accession-release-automation/gather_clustering_counts/tests/test_gather_release_counts.py b/...accession-release-automation/gather_clustering_counts/tests/test_gather_release_counts.py
@@ -94,6 +94,7 @@ def test_write_counts_to_db(self):
         assert rs_assembly_count.release_folder == 'GCA_000003205.6'
 
     def test_write_counts_to_db2(self):
+        """This test require a postgres database running on localhost. See config_xml_file.xml for detail."""
         log_files_release = [os.path.join(self.resource_folder, 'count_for_haplochromini_oreochromis_niloticus.log')]
         folder_to_taxonomy = {'oreochromis_niloticus': 8128, 'haplochromini': 319058}