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== Tagging a data file == | == Tagging == |
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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.: | 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: |
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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. |
Contents
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:
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
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:
Those being required for build time checks (tagged makecheck)
Those required for a local installation (tagged makeinstall)
- 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
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 .