Permission on files created by secondary analysis for external samples

[Nicklas Nordborg]

Files that are created as part of secondary analysis are usually created with only permission for the 'scanb' user. In #863 we implemented support for checking the consent to also give read permission to the 'scanb' group.

This doesn't work for external samples since we have no upstreams information for them. However, it would nice if the administrator could configure the server so that data files for external samples can be assigned a group and give that group read permission.

Since we typically give all external samples a name with a prefix we could, for example, configure the server to map a given prefix to a group name. If a mapping exists the script should set the umask with g=rx option. Note that the scripts also need to change the group name of files that are created. This can be done with chgrp <groupname> <filename> to change the group on one or more files or chgrp -R <groupname> <folder> to change the group on a folder and all files and subfolders in it.

[Nicklas Nordborg]

In 5593:

References #1174: Permission on files created by secondary analysis for external samples

Added configuration section <external-samples> with options to specify a prefix->groupname mapping.

[Nicklas Nordborg]

In 5594:

References #1174: Permission on files created by secondary analysis for external samples

Added helper functions for reading prefix->groupname mapping from the configuration file.

[Nicklas Nordborg]

In 5595:

References #1174: Permission on files created by secondary analysis for external samples

Implemented in the MIPs demux. If an external group has been configured the umask will be set according to the specification in FilePermission.EXTERNAL_GROUP_READABLE. The final step in the script adds chgrp command that sets the group on the fastq-folder.

[Nicklas Nordborg]

In 5596:

References #1174: Permission on files created by secondary analysis for external samples

Implemented in all other secondary analysis scripts.