[Loris-dev] Pipeline Launch for BIDS datasets

[Morales Pinzon, Alfredo]

Hi Cécile,

Thank you for pointing me to the template. Is there something else to be changed/set besides the mysql information?

Best,
Alfredo.

On Apr 19, 2021, at 5:53 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

You will find an example of the config file in the following link: https://github.com/aces/Loris-MRI/blob/main/dicom-archive/database_config_template.py<https://secure-web.cisco.com/14v9fDWJRa9ZMgF-c6sX4RVfdAEWb_znxnoMUUc0WPqPd_b_HimePfVJozn3mw53yD9Hucc__VfucNqdnp5TIeA47y5ceixh5ozU-NPEuFZ2XB1so3uOCQPKUgnDXnuninUzvjIbsaxsk-mviXcG7zyi-qSb_Xr8QVdzMqpMbC4PGJxgWsn-axkNtCPyecEZqPRNN47HsFC6ReyJA8QQMMt1n0g_EhPRP1lTEVA5UmdxXEMvtjqhxCjz4-8HPo__aI6y73i1_5p-iHntelYAa_Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2Fdicom-archive%2Fdatabase_config_template.py>

Indeed, this is a python-based config file, which is different from the prod file that is perl-based.

Hope this helps,

Cécile

On Mon, Apr 19, 2021 at 4:38 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,

In the section “5.2 - Pipeline Launch for BIDS datasets<https://secure-web.cisco.com/1baxhZvvaU0jSJOoyrJ9G2KofU_VeNAw5OsUE8lsMQJrZlNrDvMPRM1fSAVpu1AgXYR9MlZmhQwNdsHEZ94iEAY_GPZMwvRWxE7SpXqf-620lbhKdWDzOSFVjBCk5_w1ioTjpSSHZKouo5gYz6cFJy-KngOc0byf2dmHwsXZLOHI1bjsN4t1VVi1FH77psTswq-8GVIBIeZi0TEFmmF8AXOXFLbxZFSU5ci1cM7UD--16yMhwGe2Dli_ky-EkYrWYgyFH-PkDTOmdCQtIBjHFiw/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2Fdocs%2F05-PipelineLaunchOptions.md%2352---pipeline-launch-for-bids-datasets>” the command line bids_import.py requires the option -p which is defined as

-p, --profile        : name of the python database config file in dicom-archive/.loris-mri

In the example provided this option has the value “database_config.py”, is this actually a python file? Where can I find it? How can I create it? The only file I have always had in .loris-mri is prod.

Thank you in advance for your help.

Regards,
Alfredo.
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