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## Retrieve a specific file
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## Retrieve everything under the current directory (not recommended) Retrieve everything under the current directory (not recommended)
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== Modifying a data file ==

To modify the contents of a data file, first unlock it (which eliminates the symlink), than modify it, then re-add to the annex:
{{{
git annex unlock mri_em_register/testdata.tar.gz
<modify contents of tar file>
git annex add mri_em_register/testdata.tar.gz
git commit -am "New test data"
git push
git annex sync
}}}

Contents

  1. Initial Setup
  2. Adding a data file
  3. Getting a data file
  4. Modifying a data file
  5. Tagging a data file
    1. Display metadata
    2. Assign metadata
    3. List all files with a given tag
    4. Retrieve all files with a given tag

This page describes how to deal with adding and tagging data files in the freesurfer source code repository.

Initial Setup

Based in the information included in the Freesurfer_github page, the remotes of your freesurfer repo working directory should look something like: 

git remote -v 
 
  datasrc       file:///space/freesurfer/repo/annex.git (fetch)
  datasrc       file:///space/freesurfer/repo/annex.git (push)
  origin        git@github.com:zkaufman/freesurfer.git (fetch)
  origin        git@github.com:zkaufman/freesurfer.git (push)
  upstream      git@github.com:freesurfer/freesurfer.git (fetch)
  upstream      git@github.com:freesurfer/freesurfer.git (push)

Adding a data file

The following example assumes we want to add a data file called 'testdata.tar.gz' to the 'distribution' directory: 



Getting a data file


To retrieve the contents of a data file: 
git annex get mri_em_register/testdata.tar.gz
Retrieve everything under the current directory (not recommended) 
git annex get .


Modifying a data file


To modify the contents of a data file, first unlock it (which eliminates the symlink), than modify it, then re-add to the annex: 
git annex unlock mri_em_register/testdata.tar.gz
<modify contents of tar file>
git annex add mri_em_register/testdata.tar.gz
git commit -am "New test data"
git push
git annex sync


Tagging a data file


The data files have been broken down into the following 3 categories, and it is essential that data files get the proper tag(s) so that our servers and diskspace is not overwhelmed when only a known subset of the data is required.: 
  1. Those being required for build time checks (tagged makecheck) 
  2. Those required for a local installation (tagged makeinstall) 
  3. Everything else (untagged) 


Display metadata


To show all the metadata associated with a file: 
git annex metadata mri_em_register/testdata.tar.gz


Assign metadata


To assign a tag to an existing datafile.  
git annex metadata mri_em_register/testdata.tar.gz -s fstags=makecheck
git annex sync
We can also append tags: 
git annex metadata mri_em_register/testdata.tar.gz -s fstags+=makeinstall
git annex sync


List all files with a given tag


git annex find --metadata fstags=makecheck


Retrieve all files with a given tag


Get only the data files required for build time checks (1.9 GB) 
git annex get --metadata fstags=makecheck .
Get only the data files required for local installation (4.3 GB) 
git annex get --metadata fstags=makeinstall .