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Question:

Can I archive data files stored in the GSLE database to the filesystem?

 

Answer:

Can I archive data files stored in the GSLE database to the file system?

Yes, chromatograms (.AB1), fragment files (.FSA), and generic files (.png, .txt, etc) can be taken out of folders and stored onto the server’s files system. All file metadata will remain in GSLE, and the files can be optionally restored at a later date provided they remain visible to GSLE in the same spot they were exported to.

The following tutorial will walk you through on how to create an archive and handling the files in GeneSifter Laboratory Edition.

    Creating a new archive:

  1. Log in as an administrator user or laboratory manager. Go to your system tab, Left side panel under "Data Archiving" tab and click on add archive.

    You can select two types of archive: 1. Project: This will include all the folders related to this project and his files. 2.Folder: This will include just the files related to this folder.

    Missing:
  Creating a new archive.
    Figure 1 - Creating a new archive.
  2. Archiving the files:

  3. For archiving the files you need to select the folder and select an action (Archive Chromats,Fragment files or Other type of files).

    Please see below for guidance.

    Missing:
  Archiving the files.
    Figure 2 - Archiving the files.

    Now you need to give the archive a name and it will be created. See below

    Missing:
  Archiving the files.
    Figure 3 - Archiving the files.
  4. Deleting/Restoring the files from an archive:

  5. Go to your system tab, Left side panel under "Data Archiving" tab and click on Archives.

    Select the archive you want to restore or delete the files and from the drop-down list pick the action to perform.

    Missing:
  Deleting/Restoring the files from an archive.
    Figure 4 - Deleting/Restoring the files from an archive.
  6. Technical Details:

  7. Before using the data archive feature a new directory should be created.

    The $ARCHIVE_PATH is set by default as: "/usr/local/geospiza/archived_files"

    This can be changed by going into the "System tab", in the left side panel, "preferences sub-tab", click on all, and select core options.

    Missing:
  Archive Settings.
    Figure 5 - Archive Settings.

    To properly create the "archived_files" directory you should have in consideration the following:

    1. The directory permissions should be set to "770".

    2. The owner should be changed to "geospiza:geospiza".

    3. Please see below for example:

      Missing:
  Archive Settings.
      Figure 6 - Archive Settings.

    When an archive is created, the directories hierarchy will be: /archived_files/archive_name/Project_LabGroup/Project_Name/Folder_name/File_type/Files

    This is an example of how the files should look when exported to the filesystem:

    The file name structure is created as: "File_Id:File_Type:MD5"

    Missing:
  File Structure.
    Figure 7 - File Structure.

TROUBLESHOOTING/Additional Information


Q: Can the file system be a mount?

A: Yes, It can be any mount you like to use as : GlusterFS, S3 Buckets, NFS mount, Samba mount.


Q: If I move the files elsewhere for long term storage can I move them back and re-import them?


A: Yes, While the files preserves his integrity and the same permissions which he was first imported with to the file system.




Created on: 5/15/2015
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