Improve env object for more flexible lifecyle - #1478
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* move the sourcing of the python environment up as this erase the PATH configuration when done at the end of the file * Update comment for the python environment sourcingg
…#1455) * remove update of session scan done field from the delete script now that the Scan_done field has been removed from the DB * update MD file --------- Co-authored-by: lorisadmin <lorisadmin@cbrain.mcgill.ca>
* Validate config-provided CenterID against the psc table in getPSC * Validate config CenterID and finish removing MRI_alias from Perl * shorten comment section * address Nics comments: generate associated .md file for documentation changes in MRI.pm file. better validation strategy with PSCOB class rather than database check. Improved order of code for readability in tarchiveLoader.pl
* add a few test plans * fix typo
* add dicom and bids importer documentation * fix whoopsie
Co-authored-by: cmadjar <lorisadmin@cbrain.mcgill.ca>
… generate Python config file. (aces#1477) * fix old file name * fix macos
* fix PosixPath error when running push to s3 script * fix startswith s3:/ and return from remove empty directory if path does not exists on the file system * check if directory exists before calling remove_empty_directory instead of inside the function
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This is a preparatory PR for the LORIS Python server, but that is still valuable on its own.
Description
Improve the flexibility of the
Envobject with the following two changes:env.close()method to manually close anenvobject, which closes its database connections and delete its temporary directory. It is not necessary to manually call this method in the current LORIS Python pipelines as they only use a single long-lived environment, but it is required for the Python server that manages many short-livedenvobjects (one per request).log_file: bool = Trueparameter tomake_env(), which determines if the environment should create its own log file. We currently do so for our pipelines, but we certainly don't want to for the Python server, where we likely prefer to rely on the more standard Linux system logs.