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ena-submission/ENA_submission.md

@@ -35,7 +35,7 @@ We require the following components:
 
 - Analysis: An analysis contains secondary analysis results derived from sequence reads (e.g. a genome assembly).
 
-At the time of writing (October 2023), in contrast to ENA, Pathoplexus has no hierarchy of study/sample/sequence: every sequence is its own study and sample. Thus, each sequence will have to be submitted to ENA as its own study and sample. Alternatively, each submitter could have exactly _one_ study pre organism (this is the approach we are currently taking).
+At the time of writing (October 2023), in contrast to ENA, Pathoplexus has no hierarchy of study/sample/sequence: every sequence is its own study and sample. Therefore we need to figure out how to map sequences to projects, each submitter could have exactly _one_ study pre organism (this is the approach we are currently taking), or each sequence could be associated with its own study.
 
 ### Mapping sequences and studies
 

ena-submission/scripts/get_ena_submission_list.py

@@ -74,14 +74,16 @@ def get_db_config(config: Config):
     type=click.Path(),
 )
 def get_ena_submission_list(log_level, config_file, output_file):
+    """
+    Get a list of all sequences in state APPROVED_FOR_RELEASE without insdc-specific
+    metadata fields and not already in the ena_submission.submission_table.
+    """
     logger.setLevel(log_level)
     logging.getLogger("requests").setLevel(logging.WARNING)
 
     with open(config_file) as file:
         full_config = yaml.safe_load(file)
-        relevant_config = {
-            key: full_config.get(key, []) for key in Config.__annotations__
-        }
+        relevant_config = {key: full_config.get(key, []) for key in Config.__annotations__}
         config = Config(**relevant_config)
     logger.info(f"Config: {config}")
 
@@ -93,9 +95,7 @@ def get_ena_submission_list(log_level, config_file, output_file):
             value["name"] for value in config.organisms[organism]["externalMetadata"]
         ]
         logging.info(f"Getting released sequences for organism: {organism}")
-        entries = get_released_data(
-            config, organism, remove_if_has_ena_specific_metadata=True
-        )
+        entries = get_released_data(config, organism, remove_if_has_ena_specific_metadata=True)
 
         for key, item in entries.items():
             accession, version = key.split(".")