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BU-ISCIII / iskylims

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
https://github.com/BU-ISCIII/iSkyLIMS/wiki
GNU General Public License v3.0
71 stars 34 forks source link

Problem with test data for docker install #255

Closed saramonzon closed 8 months ago

saramonzon commented 8 months ago

Description of the bug

  File "/usr/local/lib/python3.10/dist-packages/MySQLdb/cursors.py", line 206, in execute
    res = self._query(query)
  File "/usr/local/lib/python3.10/dist-packages/MySQLdb/cursors.py", line 319, in _query
    db.query(q)
  File "/usr/local/lib/python3.10/dist-packages/MySQLdb/connections.py", line 259, in query
    _mysql.connection.query(self, query)
django.db.utils.OperationalError: Problem installing fixture '/opt/iskylims/test/test_data.json': Could not load core.SampleType(pk=1): (1054, "Unknown column 'mandatory_fields' in 'field list'")
Download testing files and copy it to samba container
--2024-01-03 16:31:09--  https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz
Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.184.103.159, 188.185.79.172, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.
HTTP request sent, awaiting response... 301 MOVED PERMANENTLY
Location: /records/8091169/files/iskylims_demo_data.tar.gz [following]
--2024-01-03 16:31:09--  https://zenodo.org/records/8091169/files/iskylims_demo_data.tar.gz
Reusing existing connection to zenodo.org:443.
HTTP request sent, awaiting response... 200 OK
Length: 3029160079 (2,8G) [application/octet-stream]
Saving to: ‘iskylims_demo_data.tar.gz’

iskylims_demo_data.tar.gz                            100%[===================================================================================================================>]   2,82G  1,33MB/s    in 34m 5s

Command used and terminal output

No response

Relevant files

No response

System information

iSkyLIMS v.3.0.0

saramonzon commented 8 months ago

There was a conflict with previous database, after cleaning docker env for clean installation everything worked just fine:

docker compose down                                                                                                                               [11:23:57]
docker volume rm iskylims_db_data_vol 
docker volume rm iskylims_ngs_data_vol 
docker image rm iskylims-app
docker image rm mysql:8.0    
docker image rm dperson/samba