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Not all landing zones listed with cubi-tk sodar list-landingzones #234

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your-highness opened this issue Aug 15, 2024 · 1 comment
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@your-highness
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Describe the bug
When using cubi-tk sodar landing-zone-list only a subset of all landing zones is listed, i.e. only ones marked as "ACTIVE". Version 0.4.0

To Reproduce
Steps to reproduce the behavior:

  1. Run cubi-tk sodar landing-zone-list
>cubi-tk sodar landing-zone-list f2acceb7-067d-41a4-8e39-236c022678f1
[I 240815 15:19:04] Starting cubi-tk sodar landing-zone-list
[I 240815 15:19:04]   args: Namespace(verbose=False, config=None, sodar_server_url=None, sodar_api_token='87a94aa011bf1d6a524f53f17e4d06f609e723e39a0e6e96d4d7181b329325cc', cmd='sodar', sodar_cmd=<bound method ListLandingZoneCommand.run of <class 'cubi_tk.sodar.lz_list.ListLandingZoneCommand'>>, sodar_url='https://sodar.bihealth.org/', unless_exists=False, dry_run=False, format_string=None, project_uuid='f2acceb7-067d-41a4-8e39-236c022678f1')
{"sodar_uuid": "509fb34a-3803-4015-a532-9105a40413b3", "date_modified": "2024-08-14T16:02:52.299700+02:00", "status": "ACTIVE", "project": "f2acceb7-067d-41a4-8e39-236c022678f1", "title": "20240813_182919", "description": "", "user": {"sodar_uuid": "e1441046-2727-41cb-a620-6453201f811e", "username": "svc-bih-lb-upload@CHARITE", "name": "svc-bih-lb-upload", "email": ""}, "assay": "928c4658-fa58-4486-b6ec-862911c160ab", "status_info": "Successfully validated 89 files", "configuration": null, "config_data": {}, "irods_path": "/sodarZone/projects/f2/f2acceb7-067d-41a4-8e39-236c022678f1/landing_zones/svc-bih-lb-upload@CHARITE/cads_exomes_diagnostics/cads_exomes_diagnostics_genome_sequencing_nucleotide_sequencing/20240813_182919"}
{"sodar_uuid": "38d56493-a984-443e-94d2-1269b07fdfb7", "date_modified": "2024-08-15T03:09:24.721818+02:00", "status": "ACTIVE", "project": "f2acceb7-067d-41a4-8e39-236c022678f1", "title": "20240814_033122", "description": "", "user": {"sodar_uuid": "e1441046-2727-41cb-a620-6453201f811e", "username": "svc-bih-lb-upload@CHARITE", "name": "svc-bih-lb-upload", "email": ""}, "assay": "928c4658-fa58-4486-b6ec-862911c160ab", "status_info": "Successfully validated 287 files", "configuration": null, "config_data": {}, "irods_path": "/sodarZone/projects/f2/f2acceb7-067d-41a4-8e39-236c022678f1/landing_zones/svc-bih-lb-upload@CHARITE/cads_exomes_diagnostics/cads_exomes_diagnostics_genome_sequencing_nucleotide_sequencing/20240814_033122"}
[I 240815 15:19:04] All done. Have a nice day!
  1. Check landing zones in SODAR web
    grafik

Expected behavior
cubi-tk sodar landing-zone-list should list all landing zones available to the user. If only landing zones marked as "ACTIVE" are requested, the output can be filtered or an additional flag can be introduced.

Additional context

@your-highness
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Any fix for this, @Nicolai-vKuegelgen @sellth @tedil ?

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