Name:           freesurfer-data-fetch
Version:        1.0
Release:        1%{?dist}
Summary:        Fetch FreeSurfer's atlases, template subjects and models on demand

# The tool and the manifests are ours (MIT). The data they fetch is MGH's, under the
# FreeSurfer licence, and is not rehosted: every URL is MGH's public git-annex. This lives
# in neurofedora-nonfree because it exists only to serve freesurfer7/freesurfer8.
License:        MIT
URL:            https://gitlab.com/morgan.hough/neurofedora
Source0:        freesurfer-data-install
# Generated by ci/freesurfer-data-manifest.py from the v8.2.0 / v7.4.1 source tarballs and
# checked against MGH's official installs of the same versions (no size disagreement).
Source1:        freesurfer-data-manifest-8.2.0.tsv
Source2:        freesurfer-data-manifest-7.4.1.tsv
BuildArch:      noarch
BuildRequires:  python3-devel
Requires:       python3

%description
FreeSurfer keeps the data recon-all reads (the average/ atlases and colortables,
the fsaverage subject, the SynthMorph models, ...) in git-annex rather than in
its source release, so no RPM carries it: about 11 GB per version. This tool
downloads each file from MGH's public annex, checks it against the sha256 and
size in its annex key, and installs it under /var/lib/freesurfer-data/VERSION,
linked into /usr/lib/freesurfer-VERSION where FreeSurfer reads it.

    freesurfer-data-install --list
    sudo freesurfer-data-install recon-all      # core + synthmorph, about 7.6 GB
    sudo freesurfer-data-install --fs 7.4.1 core

Nothing is downloaded when this package is installed or upgraded.

%prep

%build

%install
install -D -m 0755 %{SOURCE0} %{buildroot}%{_bindir}/freesurfer-data-install
install -D -m 0644 %{SOURCE1} %{buildroot}%{_datadir}/%{name}/8.2.0/manifest.tsv
install -D -m 0644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/7.4.1/manifest.tsv
install -d -m 0755 %{buildroot}%{_sharedstatedir}/freesurfer-data

%check
# The full offline suite is tests/freesurfer-data-fetch.bats (14 tests). Here: one
# synthetic file through the real code path (file:// URL, sha256 and size check, link
# into FREESURFER_HOME), and a corrupted copy that must be refused with exit 65.
t=%{_builddir}/fdtest; rm -rf $t; mkdir -p $t/fs $t/st
echo atlas > $t/a.gca
sha=$(sha256sum $t/a.gca | cut -d' ' -f1); size=$(stat -c %s $t/a.gca)
printf 'set\tname\tdest\taction\tbytes\tsha256\tkey\turl\ncore\ta.gca\taverage/a.gca\tplace\t%s\t%s\tSHA256E-s%s--%s.gca\tfile://%s\n' \
    $size $sha $size $sha $t/a.gca > $t/m.tsv
%{buildroot}%{_bindir}/freesurfer-data-install --manifest $t/m.tsv --state $t/st --fshome $t/fs core
test "$(cat $t/fs/average/a.gca)" = atlas
%{buildroot}%{_bindir}/freesurfer-data-install --manifest $t/m.tsv --state $t/st --fshome $t/fs --status core
rm -rf $t/st $t/fs; echo tampered > $t/a.gca; sed -i "s/\t$size\t/\t9\t/" $t/m.tsv
rc=0; %{buildroot}%{_bindir}/freesurfer-data-install --manifest $t/m.tsv --state $t/st --fshome $t/fs core || rc=$?
test $rc -eq 65 && test ! -e $t/fs/average/a.gca
# Both shipped manifests load, list their sets, and name only MGH's annex.
for v in 8.2.0 7.4.1; do
    FREESURFER_DATA_MANIFESTS=%{buildroot}%{_datadir}/%{name} \
        %{buildroot}%{_bindir}/freesurfer-data-install --fs $v --state %{_builddir}/st-$v \
        --fshome %{_builddir}/fs-$v --list | grep -q '^core '
    if awk -F'\t' 'NF==8 && $1!="set" && $8 !~ /^https:\/\/surfer\.nmr\.mgh\.harvard\.edu\/pub\/dist\/freesurfer\/repo\/annex\.git\/annex\/objects\//' \
        %{buildroot}%{_datadir}/%{name}/$v/manifest.tsv | grep -q .; then
        echo "ERROR: $v manifest has a URL outside MGH's annex" >&2; exit 1
    fi
done

%files
%{_bindir}/freesurfer-data-install
%{_datadir}/%{name}/
%dir %{_sharedstatedir}/freesurfer-data

%changelog
* Sat Oct 10 2026 Morgan Hough <morgan.hough@gmail.com> - 1.0-1
- Initial package: freesurfer-data-install and manifests for 8.2.0 and 7.4.1,
  fetching FreeSurfer's annexed data from MGH on demand, sha256- and
  size-verified. A separate tool for now (Morgan, 2026-10-10); merging with
  fsl-data-install is fsk-dual's proposal for later. Includes the 4dfp atlases
  talairach_avi reads, which MGH's own 8.2.0 build omits. Tests:
  tests/freesurfer-data-fetch.bats (14, two mutation-checked).