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two small bugfixes #6

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Merged
NicolasCARPi merged 2 commits into from
Nov 24, 2025
Merged

two small bugfixes #6

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360535d
make sure archiving respects the --out_dir parameter
phue Nov 24, 2025
6a9b1a2
fix TextIOWrapper.write() call when exporting csv
phue Nov 24, 2025
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15 changes: 7 additions & 8 deletions any2eln/labfolder/labfolder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@ def extract(self) -> Path:
SelfNode = TypedDict('SelfNode', {'@id': str, '@type': str, 'hasPart': list[dict[str, str]]})

now = datetime.now().strftime('%Y-%m-%d-%H-%M-%S')
main_dir = Path(self.out_dir).joinpath(f'export-{now}')
main_dir = Path(self.out_dir).joinpath(f'export-{now}').resolve()
main_dir.mkdir()

with tqdm(total=len(entries_by_author)) as superpbar:
Expand Down Expand Up @@ -220,7 +220,7 @@ def extract(self) -> Path:
csv_id = self.__get_unique_enough_id()
node = self.__get_node_from_csv(csv_id, csv, entry_folder)
with entry_folder.joinpath(csv_id).open('w') as file:
file.write(csv[1], 'w', 'utf-8')
file.write(csv[1])
node['sha256'] = hashlib.sha256(csv[1].encode()).hexdigest()
crate_metadata['@graph'].append(node)
files.append(node['@id'])
Expand Down Expand Up @@ -270,15 +270,14 @@ def extract(self) -> Path:
json.dump(crate_metadata, json_file, indent=2)

# create a container directory because shutil will gobble up the folder
# don't use joinpath here because the endslash of the author_dir is kept
container = Path(f'{author_dir}-container')
container = main_dir.joinpath(f'{author_dir.name}-container')
container.mkdir()
author_dir.rename(container.joinpath(author_dir.name))
eln_name = 'tmp.eln'
shutil.make_archive(eln_name, 'zip', container)
eln_name = main_dir.joinpath(f'{author_dir.name}.eln')
eln_zip = shutil.make_archive(eln_name, 'zip', container)
# shutil will add a .zip extension but we want a .eln
Path(f'{eln_name}.zip').rename(f'{author_dir}.eln')
print(f'Created {author_dir}.eln')
Path(eln_zip).rename(eln_name)
print(f'Created {eln_name}')
superpbar.update(1)

# write the summary.txt file with authors names
Expand Down