housekeeper does not list file present in bundle

[seallard]

Description

housekeeper add file fails, stating that the file already exists. However, when the specific bundle is retrieved with housekeeper get bundle it is shown to be empty. When looking at the bundle directory, the file is present in a version - so it should be listed for the bundle. It cannot be retrieved with housekeeper get file either.

The command below was run in the /home/proj/production/housekeeper-bundles/ADM1091A3/2018-06-05 directory:

for f in *; do housekeeper add file -t fastq -t H9GA6ADXX -b ADM1091A3 ./${f}; done
2023-06-13 09:47:51 [hasta.scilifelab.se](http://hasta.scilifelab.se/) housekeeper.cli.core[37109] INFO Use root path /home/proj/production/housekeeper-bundles
2023-06-13 09:47:51 [hasta.scilifelab.se](http://hasta.scilifelab.se/) housekeeper.cli.add[37109] INFO Running add file
2023-06-13 09:47:51 [hasta.scilifelab.se](http://hasta.scilifelab.se/) housekeeper.store.api.handlers.read[37109] INFO Fetching bundle with name: ADM1091A3
Traceback (most recent call last):
 File "/home/proj/production/bin/miniconda3/envs/P_main/bin/housekeeper", line 8, in <module>
  sys.exit(base())
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/click/core.py", line 722, in __call__
  return self.main(*args, **kwargs)
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/click/core.py", line 697, in main
  rv = self.invoke(ctx)
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
  return _process_result(sub_ctx.command.invoke(sub_ctx))
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
  return _process_result(sub_ctx.command.invoke(sub_ctx))
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/click/core.py", line 895, in invoke
  return ctx.invoke(self.callback, **ctx.params)
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/click/core.py", line 535, in invoke
  return callback(*args, **kwargs)
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/click/decorators.py", line 17, in new_func
  return f(get_current_context(), *args, **kwargs)
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/housekeeper/cli/add.py", line 124, in file_cmd
  link_to_relative_path(version=version, file_path=file_path, root_path=context.obj[ROOT])
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/housekeeper/include.py", line 63, in link_to_relative_path
  link_file(file_path=file_path, new_path=housekeeper_path, hardlink=True)
 File "/home/proj/production/bin/miniconda3/envs/P_main/lib/python3.7/site-packages/housekeeper/include.py", line 19, in link_file
  os.link(file_path.resolve(), new_path)
FileExistsError: [Errno 17] File exists: '/home/proj/production/housekeeper-bundles/ADM1091A3/2018-06-05/ADM1091A3_L001_R1_001.fastq.gz' -> '/home/proj/production/housekeeper-bundles/ADM1091A3/2018-06-05/ADM1091A3_L001_R1_001.fastq.gz'

Suggested solution

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[seallard]

It is possible that the file was manually deleted from the bundle/version in the database.

[ChrOertlin]

duplicate of: https://github.com/Clinical-Genomics/housekeeper/issues/129