Assay protection

Assays are protected by default. This means their run directories on disk are owned by the LabID UNIX technical user and kept read-only for users. Protecting the run directory prevents accidental modifications and/or deletion of the data.

Example of assay directory tree

Default permissions set on a run directory and files

Unprotecting an assay run directory

Unprotection is only a available for Electron Microscopy (EM) assays

In certain cases, it is needed to make the data directory of an assay writable. This is done by unprotecting the assay. This changes the UNIX rights of the directory to grant write permission for the UNIX group owning the data (your group). Practically, with UNIX write rights, any member of the group can add data to the directory as well as modify and delete existing data. Modification or deletion of data is never the intended effect of assay unprotection, but this may be an undesired side-effect.

Example 1: Bioinformatics tools that need to write its output alongside input files

Some bioinformatics tools need to write their output alongside the input files. Such tools should be avoided when possible in favor of tools that can write output to a different chosen location. However, there is sometimes no other option available.

Example 2: The data was transfered to its final location before its registration

In some cases, the data was transfered to its final location before finalising its registration. The assay directory can be unprotected to massage the data (reorganise and rename files and folders) before its registration.

The integrity of data stored within an unprotected assay directory cannot be guaranted. We advise unprotection to always happen when strictly necessary (due to e.g. data processing tool limitation) and to always remain a temporary measure.

Unprotecting the assay after data registration

When the datasets inside the assay directory have normally been registered in LabID, we advise to keep the assay protected in order to guarantee the integrity of the data. However, as stated in Example 1 above, certain bioinformatics tools that process data require to write their output alongside input files. In such cases, the assay can be unprotected for the time the said tool needs to run.

Please note that any data added to an unprotected assay directory past assay registration time

1. will not be automatically registered by LabID
2. will prevent the assay reprotection as long as it remains in the directory.
3. still need to undergo the standard registration process

The data that already have been registered inside the assay directory should not be modified/deleted

• The registered data files/folders should not be modified nor deleted.
• The registered data files/folders content should not be modified.
• The registered data files/folders should not be renamed.
• The registered data files/folders should not be moved.

In unprotected assay directories, all the above operations are possible but should strictly be avoided to prevent data integrity and traceability issues. For example, if a file is renamed, LabID will not be able to find it anymore.

Any new data added to an unprotected assay directory needs to be exctracted and manually registered.

Unprotecting the assay before data registration

Sometimes, automated processes do place the data at its final location (assay data directory) before it is effectively registered in LabID (Example 2 above). In such cases, we encourage you to reorganise files and folders as it pleases you. The data itself (content of files) should not be modified, but files and folders names as well as their hierarchical organisation, could be changed if necessary.