EVA-3528: Refactor release tracker creation script #433
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| def _insert_entry_for_taxonomy_and_assembly(self, tax, asm_acc, sources, sc_name=None, fasta_path=None, | ||
| report_path=None, release_folder_name=None): | ||
| sc_name = sc_name if sc_name else get_scientific_name_from_ensembl(tax) | ||
| sc_name = sc_name.replace("'", "\''") |
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change to accommodate our good friend Ambystoma 'unisexual hybrid'
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Ticket to remove scientific name where it's not needed: EVA-3405
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| def create_table_if_not_exists(self): | ||
| query_create_table = ( | ||
| 'create table if not exists eva_progress_tracker.clustering_release_tracker(' |
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have left this table as-is but made a note of which fields we could get rid of
| return get_metadata_connection_handle(self.maven_profile, self.private_config_xml_file) | ||
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| @cached_property | ||
| def mongo_conn(self): |
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Previously the mongo database being used was always production, even if you were creating the table in development - this seemed messy/confusing to me so I've unified it to use a single profile, but it did have the advantage that you could create a table in dev based on real production data for should_be_released. I don't think it matters much for how we use the table now (e.g. we don't actually compute any counts that need to be checked), but let me know if you think this functionality should be restored.
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That should be an incentive to keep one species in mongoDEV so we can test properly.
It's a good change.
| return get_metadata_connection_handle(self.maven_profile, self.private_config_xml_file) | ||
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| @cached_property | ||
| def mongo_conn(self): |
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That should be an incentive to keep one species in mongoDEV so we can test properly.
It's a good change.
ReleaseTrackerclassI've noted the only functional changes in the script, otherwise only refactoring.