#1174 closed enhancement (fixed)

Permission on files created by secondary analysis for external samples

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: minor Milestone: Reggie v4.23
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

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.

Change History (5)

comment:1 Changed 15 months ago by 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.

comment:2 Changed 15 months ago by 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.

comment:3 Changed 15 months ago by 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.

comment:4 Changed 15 months ago by Nicklas Nordborg

In 5596:

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

Implemented in all other secondary analysis scripts.

comment:5 Changed 15 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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