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patch to add species routine to work with new updates #1671

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merged 1 commit into from
Jan 24, 2025
Merged

patch to add species routine to work with new updates #1671

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30 changes: 21 additions & 9 deletions maintenance/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -222,6 +222,11 @@ def write_catalog_stub(*, path, sps_id, ensembl_id, species_data, genome_data):
scientific_name = species_data["scientific_name"]
common_name = species_data["display_name"]
logger.info(f"{sps_id}: name={scientific_name}, common_name={common_name}")

# Get assembly information from genome_data
assembly_source = genome_data.get("assembly_source", "ensembl")
assembly_build_version = genome_data.get("assembly_build_version", "unknown")

chr_names = genome_data["chromosomes"].keys()
chromosome_rate_template = {name: -1 for name in chr_names}
species_code = species_template.substitute(
Expand All @@ -242,6 +247,8 @@ def write_catalog_stub(*, path, sps_id, ensembl_id, species_data, genome_data):
scientific_name=scientific_name,
common_name=common_name,
chromosome_rate_dict=chromosome_rate_template,
assembly_source=assembly_source,
assembly_build_version=assembly_build_version,
)
test_path = pathlib.Path("tests") / f"test_{sps_id}.py"
logger.info(f"Writing species test stub to {test_path}")
Expand Down Expand Up @@ -272,14 +279,19 @@ def add_species(self, ensembl_id, force=False):
shutil.rmtree(root, ignore_errors=True)
root.mkdir()
genome_data = self.write_genome_data(ensembl_id)
species_data = self.ensembl_client.get_species_data(ensembl_id)
write_catalog_stub(
path=root,
sps_id=sps_id,
ensembl_id=ensembl_id,
species_data=species_data,
genome_data=genome_data,
)
if genome_data[0] == "updated":
species_data = self.ensembl_client.get_species_data(ensembl_id)
write_catalog_stub(
path=root,
sps_id=sps_id,
ensembl_id=ensembl_id,
species_data=species_data,
genome_data=genome_data[1],
)
else:
raise ValueError(
f"Failed to get genome data for {sps_id}: {genome_data[0]}"
)

def add_species_ncbi(self, ncbi_id, force=False):
species_name = ncbi.get_species_name(ncbi_id)
Expand Down Expand Up @@ -375,7 +387,7 @@ def write_genome_data(self, ensembl_id):
# Format the code with Black so we don't get noisy diffs
with self.write(genome_data_path) as f:
f.write(black_format(code))
return ("updated", None)
return ("updated", data)

def write_genome_data_ncbi(self, ncbi_id, sps_id):
path = catalog_path(sps_id)
Expand Down
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