Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bugfix/run accession for assembly #372

Merged
merged 2 commits into from
Mar 7, 2025
Merged

Bugfix/run accession for assembly #372

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
b0d388a
fixes retrieval of run accession for assemblies
SandyRogers Mar 7, 2025
8226c1e
version bump
SandyRogers Mar 7, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 1 addition & 2 deletions emgapianns/management/lib/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,7 @@ def get_run_accession(path):
match = re.search(pattern, path)
if match:
if len(match.groups()) > 0:
end_pos = match.end()
return path[0:end_pos]
return match.groups()[0]
else:
raise Exception("Could not identify run accession from {}".format(path))
else:
Expand Down
9 changes: 9 additions & 0 deletions tests/webuploader/test_import_assembly.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@

from model_bakery import baker

from emgapianns.management.lib.utils import get_run_accession


def bake_models(coverage=None, min_gap_length=None):
"""Build the required models for import_assembly
Expand Down Expand Up @@ -109,3 +111,10 @@ def test_import_assembly_with_cov(self, mock_get_assembly):
assert emg_assembly.is_private == False
assert emg_assembly.wgs_accession == ena_assembly.wgs_accession
assert emg_assembly.legacy_accession == ena_assembly.gc_id

def test_run_accession_getter(self):
assert get_run_accession("ERR1111111") == "ERR1111111"
assert get_run_accession("ERR1111111;ERR1111112") == "ERR1111111" # first only
assert get_run_accession("PREFIX_ERR1111111") == "ERR1111111" # only accession part
assert get_run_accession("ERR1111111_SUFFIX") == "ERR1111111"
assert get_run_accession("NOPE;PREFIX_ERR1111111_SUFFIX;PREFIX_ERR1111112_SUFFIX;ALSONOPE") == "ERR1111111" # complete edge case