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<<TableOfContents>>

This page describes how to work with

== Initial Setup ==

Based in the information included in the [[Freesurfer_github|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)
}}}

Users outside the Martinos Center, who do not have access to the local filesystem, should instead have the '''datasrc''' repo pointed to the public facing server:

{{{
git remote -v

  datasrc https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git (fetch)
  datasrc https://surfer.nmr.mgh.harvard.edu/pub/dist/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:

{{{
git annex add <filename>
git commit -a -m "Added new file"
git annex copy --to datasrc
}}}

== Getting a data file ==

To retrieve the contents of a data file:
{{{
git fetch datasrc (maybe could do 'git annex sync')
git annex get mri_em_register/testdata.tar.gz
}}}

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 .
}}}

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 copy --to datasrc
}}}

== Tagging ==

Git -annex provides the ability to to tag data files. Freesurfer utilizes tags so that subsets of the data can be retrieved without having to download everything. The data files have been broken down into the following 3 categories:

 1. Those being required for build time checks (tagged '''makecheck''')
 1. Those required for a local installation (tagged '''makeinstall''')
 1. Everything else (untagged)

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.

=== 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
}}}