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Check before creating by_assembly directories #459

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merged 2 commits into from
Sep 23, 2024
Merged

Check before creating by_assembly directories #459

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9efd90c
Only create a symlink in the by assembly directory if the correspondi…
tcezard Jul 17, 2024
56771ca
Update eva-accession-release-automation/publish_release_to_ftp/publis…
tcezard Jul 29, 2024
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24 changes: 14 additions & 10 deletions eva-accession-release-automation/publish_release_to_ftp/publish_release_files_to_ftp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -129,13 +129,16 @@ def create_symlink_to_species_folder_from_assembly_folder(current_release_assemb
public_release_species_assembly_folder = os.path.join(release_properties.public_ftp_current_release_folder,
by_species_folder_name, species_release_folder_name,
assembly_accession)
run_command_with_output(f"""Creating symlink from assembly folder {public_release_assembly_species_folder} to
species folder {public_release_species_assembly_folder}""",
'bash -c "cd {0} && ln -sfT {1} {2}"'.format(
public_release_assembly_folder,
os.path.relpath(public_release_species_assembly_folder,
public_release_assembly_folder),
public_release_assembly_species_folder))
if os.path.isdir(public_release_assembly_species_folder):
run_command_with_output(f"""Creating symlink from assembly folder {public_release_assembly_species_folder} to
species folder {public_release_species_assembly_folder}""",
'bash -c "cd {0} && ln -sfT {1} {2}"'.format(
public_release_assembly_folder,
os.path.relpath(public_release_species_assembly_folder,
public_release_assembly_folder),
public_release_assembly_species_folder))
else:
raise Exception(f'The species folder {public_release_assembly_species_folder} we're linking to does not exist')


def recreate_public_release_species_assembly_folder(assembly_accession, public_release_species_assembly_folder):
Expand Down Expand Up @@ -198,9 +201,10 @@ def publish_assembly_release_files_to_ftp(current_release_assembly_info, release
)
)

# Create a link from assembly folder to species_folder ex: by_assembly/GCA_000005005.5/zea_mays to by_species/zea_mays/GCA_000005005.5
create_symlink_to_species_folder_from_assembly_folder(current_release_assembly_info, release_properties,
public_release_assembly_folder)
if current_release_assembly_info["num_rs_to_release"] > 0:
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Debatable whether this is even a good idea, but elsewhere we check both num_rs_to_release and should_be_released... should we do the same here to be consistent?

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I think you're right that this is inconsistent with what is done elsewhere.
The reason I've only used the num_rs_to_release is because originally the should_be_released flag really meant that the release pipeline should be run not that the data should be copied and in previous version of the release automation should_be_released=false and num_rs_to_release>0 was used to denote release that had not changed since the previous release and could be hard-linked.

# Create a link from assembly folder to species_folder ex: by_assembly/GCA_000005005.5/zea_mays to by_species/zea_mays/GCA_000005005.5
create_symlink_to_species_folder_from_assembly_folder(current_release_assembly_info, release_properties,
public_release_assembly_folder)


def get_release_assemblies_for_release_version(assemblies_to_process, release_version):
Expand Down
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