Re: Mail archives in Git using ssoma (Docker image)

Re: Mail archives in Git using ssoma (Docker image)

[Eric Wong]

+Cc meta@public-inbox.org

"W. Trevor King" <wking@tremily.us> wrote:
> On Sat, Aug 20, 2016 at 09:36:31PM -0700, W. Trevor King wrote:
> > [2]: git://tremily.us/notmuch-archives.git

Cool!

> This is the ssoma archive (with the data in it).  I just set up a
> basic HTTP archive (following [1]) based on a Docker image [2] (Gentoo
> doesn't package all the Perl dependencies public-inbox needs).

Ugh, that sucks (sorry, not a fan of Docker).

What's missing from Gentoo?

It should be easy to copy just the necessary .pm files and use
PERL5LIB environment to point to the correct path (man perlrun).

I'm conciously avoiding XS (compiled) extensions to make
installation/distribution easier.

> Dockerfile for rebuilding the image is in [2].  I'm currently hosting
> the archives (HTTP only) at [3].  Spinning that up from the Docker
> image looks like:
> 
>   $ mkdir srv
>   $ git clone --bare git://tremily.us/notmuch-archives.git srv/notmuch
>   $ echo 'Notmuch -- Just an email system' >srv/notmuch.git/description
>   $ git config -f srv/notmuch.git/config publicinbox.http http://tremily.us
>   $ git config -f srv/notmuch.git/config publicinbox.email notmuch@notmuchmail.org

That should probably be:

	; based on your [3]
	git config -f srv/notmuch.git/config \
		publicinbox.notmuch.url http://tremily.us/notmuch

	git config -f srv/notmuch.git/config \
		publicinbox.notmuch.address notmuch@notmuchmail.org

	; this is crucial for all the public-inbox-* tools
	git config -f srv/notmuch.git/config \
		publicinbox.notmuch.mainrepo /path/to/notmuch.git

I'm sorry that most of this is still undocumented at the moment,
but it's my first priority once I'm done sorting out some
non-computing-related stuff.

>   $ docker run --name notmuch-archives -d -p 80:8080 -v ${PWD}/srv/:/srv/ wking/public-inbox
> 
> (although I'm using -p ###:8080 and have an Nginx reverse-proxy in
> front).  It's not updating automatically yet, but that will probably
> look like:
> 
> 1. Pull new mbox [4].
> 2. Import into notmuch-archives [5].
> 3. Re-run public-inbox-index (this could probably be via ‘docker exec …’.
> 
> But I'll have to test that to confirm.  And ideally we'd be using
> ssoma-mda or similar directly, instead of going through mbox, but I'd
> rather get the official headers on the stored mail than be efficient
> ;).

For mirroring existing lists, I started using public-inbox-watch
which currently watches Maildirs.  The config knobs are sorta
documented from my announcement to git@vger:

https://public-inbox.org/git/20160710004813.GA20210@dcvr.yhbt.net/
http://hjrcffqmbrq6wope.onion/git/20160710004813.GA20210@dcvr.yhbt.net/

Initial import (w/o spamassassin) was done with
scripts/import_vger_from_mbox in the source:

        torsocks git clone http://hjrcffqmbrq6wope.onion/public-inbox
        git clone https://public-inbox.org/ public-inbox
        git clone git://repo.or.cz/public-inbox

I recommend public-inbox-watch for mirroring existing lists
(such as what I did with git@vger) but public-inbox-mda for
self-hosted lists (such as meta@public-inbox.org).

> One shift from Gmane's mid.gmane.org/… is that the public-inbox UI
> Message-ID lookup is per-bucket, and public-inbox seems to be
> encouraging per-list buckets.

The public-inbox-nntpd interface supports mid lookups across all
inboxes in that instance; so it should be doable in the WWW
interface, too.  Either way, I think it has to be O(n) where (n)
is the number of Xapian DBs, though.

I already have news.public-inbox.org hooked up to both
NNTP and HTTP(*), so I plan on making

	http://news.public-inbox.org/<Message-ID>

to work like:

	nntp://news.public-inbox.org/<Message-ID>

(*) Right now, it just redirects $GROUP to the HTTP interface:
    http://news.public-inbox.org/$NEWSGROUP -> http://...


And the WWW interface already has fallbacks to scan + link
across inboxes, so s/git/meta/ the above URLs and you'll get
a link to the message on /git/ instead of /meta/

http://hjrcffqmbrq6wope.onion/meta/20160710004813.GA20210@dcvr.yhbt.net/

> And while I feel like I had a good grasp of the ssoma format two years
> ago, I know very little about Perl and public-inbox.  I'm sure you
> could setup a public-inbox host that is more efficient than what's
> currently in my Docker image.

Feel free to ask me + meta@public-inbox.org if you have any
questions or need help.  Writing documentation doesn't come
naturally to me, so it's easier for me to answer emails.

I try to make it not very Perly.  I don't think I'll bother with
CPAN, for example  (I don't think I successfully got my PAUSE
account activated; not a fan of registrations, either).

But there will definitely be tarball releases for distros
soonish.  (mainly targeting Debian at the moment, but FreeBSD is
on the table).

> Cheers,
> Trevor
> 
> [1]: http://public-inbox.org/INSTALL
> [2]: https://hub.docker.com/r/wking/public-inbox/
> [3]: http://tremily.us/notmuch/
> [4]: https://notmuchmail.org/archives/notmuch.mbox
> [5]: id:20160821043631.GA2338@odin.tremily.us

Re: Mail archives in Git using ssoma (Docker image)

[W. Trevor King]

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On Sun, Aug 21, 2016 at 12:08:52PM +0000, Eric Wong wrote:
> "W. Trevor King" <wking@tremily.us> wrote:
> > This is the ssoma archive (with the data in it).  I just set up a
> > basic HTTP archive (following [1]) based on a Docker image [2] (Gentoo
> > doesn't package all the Perl dependencies public-inbox needs).
> 
> Ugh, that sucks (sorry, not a fan of Docker).
> 
> What's missing from Gentoo?

Gentoo doesn't package (or I couldn't find the package for)
Encode::MIME::Header or Mail::Thread.  I tried installing things from
CPAN, but ran into a compile-time error from the ‘cpan’ invocationand
gave up ;).  I can try and reproduce the error if you're curious, but
I don't have it handy at the moment.

> >   $ git config -f srv/notmuch.git/config publicinbox.http http://tremily.us
> >   $ git config -f srv/notmuch.git/config publicinbox.email notmuch@notmuchmail.org
> 
> That should probably be:
> 
> 	; based on your [3]
> 	git config -f srv/notmuch.git/config \
> 		publicinbox.notmuch.url http://tremily.us/notmuch
> 
> 	git config -f srv/notmuch.git/config \
> 		publicinbox.notmuch.address notmuch@notmuchmail.org
> 
> 	; this is crucial for all the public-inbox-* tools
> 	git config -f srv/notmuch.git/config \
> 		publicinbox.notmuch.mainrepo /path/to/notmuch.git

I was using these in the Dockerfile's CMD:

  (cd /srv;
   for NAME in *;
   do
     CONF="/srv/${NAME}/config";
     public-inbox-init "${NAME}" "/srv/${NAME}" $(git config -f "${CONF}" publicinbox.http) $(git config -f "${CONF}" publicinbox.email);
   done) && …

Are you saying that I can skip the ~/.public-inbox/config entries
setup by public-inbox-init if I set publicinbox.{name}.* in the ssoma
repository's config?  That would be nice.

I don't see a point to having {name} in ssoma-config settings though,
since you're already in a single bucket by that point (using
publicinbox.{name}.* makes sense in the multi-bucket
~/.public-inbox/config).

> > It's not updating automatically yet, but that will probably look
> > like:
> > 
> > 1. Pull new mbox [4].
> > 2. Import into notmuch-archives [5].
> > 3. Re-run public-inbox-index (this could probably be via ‘docker exec …’.
> > 
> > But I'll have to test that to confirm.  And ideally we'd be using
> > ssoma-mda or similar directly, instead of going through mbox, but I'd
> > rather get the official headers on the stored mail than be efficient
> > ;).
> 
> For mirroring existing lists, I started using public-inbox-watch
> which currently watches Maildirs.

If I had a Maildir locally, I'd just use procmail and push new
messages into ssoma-mda.  I'm using the import script because my local
mail has “how we delivered this to Trevor” headers (which I don't want
to add) but the downloaded mbox has “how we delivered this to
notmuch@notmuchmail.org” (which seems like a better fit for a shared
ssoma repo).

> I recommend public-inbox-watch for mirroring existing lists (such as
> what I did with git@vger) but public-inbox-mda for self-hosted lists
> (such as meta@public-inbox.org).

Why is that?  Procmail + public-inbox-mda (or my Python ssoma-mda fork
[1,2]) seems simpler and equally effective if you want to insert a
message that your mail system is delivering locally.

> > One shift from Gmane's mid.gmane.org/… is that the public-inbox UI
> > Message-ID lookup is per-bucket, and public-inbox seems to be
> > encouraging per-list buckets.
> 
> The public-inbox-nntpd interface supports mid lookups across all
> inboxes in that instance; so it should be doable in the WWW
> interface, too.  Either way, I think it has to be O(n) where (n) is
> the number of Xapian DBs, though.

I'm more concerned about the interface, and less about the
implementation (which can be improved later).  The (n) lookups are
trivially parallelizable, and you can always add a Message-ID →
buckets lookup table if (n) lookups turns out to be too slow.

Cheers,
Trevor

[1]: id:20141107190321.GL23609@odin.tremily.us
[2]: id:af679af8257e250ac606e35a1307ad02907b8426.1413663212.git.wking@tremily.us
     http://public-inbox.org/meta/af679af8257e250ac606e35a1307ad02907b8426.1413663212.git.wking@tremily.us/t/#u

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Re: Mail archives in Git using ssoma (Docker image)

[Eric Wong]

"W. Trevor King" <wking@tremily.us> wrote:
> On Sun, Aug 21, 2016 at 12:08:52PM +0000, Eric Wong wrote:
> > "W. Trevor King" <wking@tremily.us> wrote:
> > > This is the ssoma archive (with the data in it).  I just set up a
> > > basic HTTP archive (following [1]) based on a Docker image [2] (Gentoo
> > > doesn't package all the Perl dependencies public-inbox needs).
> > 
> > Ugh, that sucks (sorry, not a fan of Docker).
> > 
> > What's missing from Gentoo?
> 
> Gentoo doesn't package (or I couldn't find the package for)
> Encode::MIME::Header or Mail::Thread.  I tried installing things from
> CPAN, but ran into a compile-time error from the ‘cpan’ invocationand
> gave up ;).  I can try and reproduce the error if you're curious, but
> I don't have it handy at the moment.

Encode::MIME::Header is distributed with perl itself on Debian and also
the stock upstream install.  Not sure if there's an option you missed or
disabled.

Which perl version do you use?

perl on 5.14 Debian wheezy even seems to have it.  I actually
still want everything to work on 5.8, since that seems to be
the de-facto baseline in the wild.


Mail::Thread is one .pm, and I'll probably replace it with
something (same algorithm) which can use half the memory by
avoiding wrapper object abstractions (it's probably the biggest
memory hog at the moment).

lib/PublicInbox/Thread.pm already has 3 monkey patches to workaround
upstream bugs in Mail::Thread.  It's dead upstream, and not available on
FreeBSD, either.

> > >   $ git config -f srv/notmuch.git/config publicinbox.http http://tremily.us
> > >   $ git config -f srv/notmuch.git/config publicinbox.email notmuch@notmuchmail.org
> > 
> > That should probably be:
> > 
> > 	; based on your [3]
> > 	git config -f srv/notmuch.git/config \
> > 		publicinbox.notmuch.url http://tremily.us/notmuch
> > 
> > 	git config -f srv/notmuch.git/config \
> > 		publicinbox.notmuch.address notmuch@notmuchmail.org
> > 
> > 	; this is crucial for all the public-inbox-* tools
> > 	git config -f srv/notmuch.git/config \
> > 		publicinbox.notmuch.mainrepo /path/to/notmuch.git
> 
> I was using these in the Dockerfile's CMD:
> 
>   (cd /srv;
>    for NAME in *;
>    do
>      CONF="/srv/${NAME}/config";
>      public-inbox-init "${NAME}" "/srv/${NAME}" $(git config -f "${CONF}" publicinbox.http) $(git config -f "${CONF}" publicinbox.email);
>    done) && …
> 
> Are you saying that I can skip the ~/.public-inbox/config entries
> setup by public-inbox-init if I set publicinbox.{name}.* in the ssoma
> repository's config?  That would be nice.

Erm, sorry, no, I mean ~/.public-inbox/config as the "git config -f"
arg in the above commands.  Your original config was
meaningless in the context of public-inbox itself; I don't
recall public-inbox relies on $GIT_DIR/config much (if at all)
outside of standard git things.

Using ~/.public-inbox/config is required for multi-inbox lookups
(since you normally run MDA w/o args)

You can also override ~/.public-inbox/config by setting the
PI_CONFIG env (like GIT_CONFIG).

> I don't see a point to having {name} in ssoma-config settings though,
> since you're already in a single bucket by that point (using
> publicinbox.{name}.* makes sense in the multi-bucket
> ~/.public-inbox/config).
> 
> > > It's not updating automatically yet, but that will probably look
> > > like:
> > > 
> > > 1. Pull new mbox [4].
> > > 2. Import into notmuch-arcives [5].
> > > 3. Re-run public-inbox-index (this could probably be via ‘docker exec …’.
> > > 
> > > But I'll have to test that to confirm.  And ideally we'd be using
> > > ssoma-mda or similar directly, instead of going through mbox, but I'd
> > > rather get the official headers on the stored mail than be efficient
> > > ;).
> > 
> > For mirroring existing lists, I started using public-inbox-watch
> > which currently watches Maildirs.
> 
> If I had a Maildir locally, I'd just use procmail and push new
> messages into ssoma-mda.  I'm using the import script because my local
> mail has “how we delivered this to Trevor” headers (which I don't want
> to add) but the downloaded mbox has “how we delivered this to
> notmuch@notmuchmail.org” (which seems like a better fit for a shared
> ssoma repo).

I don't mind extra/different headers.   The majority of messages in
public-inbox.org/git/ has messages that were delivered to gmane;
recent ones are delivered to me, and some holes were filled in by
Jeff King's archives.  All of our mail systems add different
headers.

> > I recommend public-inbox-watch for mirroring existing lists (such as
> > what I did with git@vger) but public-inbox-mda for self-hosted lists
> > (such as meta@public-inbox.org).
> 
> Why is that?  Procmail + public-inbox-mda (or my Python ssoma-mda fork
> [1,2]) seems simpler and equally effective if you want to insert a
> message that your mail system is delivering locally.

-watch is usable for importing big archives or bursts of traffic
since it doesn't have to reload Perl/python on every mail (this
is probably not a problem for notmuch; but is for vger lists).
The defaults are also less-opinionated so it won't reject
attachments that passed through the list server.

Maildir with your MUA (in case you missed some earlier, and got
them from another user or archive).

There's also a Filter inferface I added (see
lib/PublicInbox/Filter/Vger.pm as an example) for dropping
list trailers before SA, so those trailers don't influence
Bayes, but you can do that in the MDA stage, too.


But *-mda is fine, too :>

> [1]: id:20141107190321.GL23609@odin.tremily.us
> [2]: id:af679af8257e250ac606e35a1307ad02907b8426.1413663212.git.wking@tremily.us
>      http://public-inbox.org/meta/af679af8257e250ac606e35a1307ad02907b8426.1413663212.git.wking@tremily.us/t/#u

Re: Mail archives in Git using ssoma

[W. Trevor King]

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On Sun, Aug 21, 2016 at 06:37:04PM +0000, Eric Wong wrote:
> "W. Trevor King" <wking@tremily.us> wrote:
> > On Fri, Nov 07, 2014 at 11:03:21AM -0800, W. Trevor King wrote:
> > > Eric Wong has been working on some tools to store email in a Git
> > > repository, and his client-side code is ssoma [1].  I wanted a bit
> > > more metadata than the stock ssoma-mda [2], and ended up just
> > > writing a ssoma-mda in Python [3]…
>
> Btw, for public-inbox, I'm using git-fast-import now, so imports are
> a bit faster and $GIT_DIR/ssoma.index is no longer used.  This was
> crucial for getting git@vger archives imported in a reasonable time.
>
> public-inbox-* still keeps ssoma.index up-to-date for backwards
> compatibility with ssoma, and will probably do so until 2020 or
> later (there'll be a few years of deprecation notices)
>
> So I or someone else needs to update Perl ssoma to use fast-import
> at some point, too; and I suggest your python version do the same.

ssoma-mda imports 22k notmuch messages in around 15 minutes (with
profiling enabled), and:

  $ python -m cProfile -o profile import.py notmuch.mbox
  $ python -c "import pstats; p=pstats.Stats('profile'); p.sort_stats('cumulative').print_stats(10)"
  Sun Aug 21 12:56:49 2016    profile

           101823722 function calls (99078415 primitive calls) in 885.069 seconds

     Ordered by: cumulative time
     List reduced from 1145 to 10 due to restriction <10>

     ncalls  tottime  percall  cumtime  percall filename:lineno(function)
       70/1    0.002    0.000  885.069  885.069 {built-in method exec}
          1    0.111    0.111  885.069  885.069 /home/wking/src/notmuch/notmuch-archives.git/import.py:9(<module>)
          1    0.400    0.400  884.915  884.915 /home/wking/src/notmuch/notmuch-archives.git/import.py:17(import_mbox)
      22875    0.601    0.000  863.371    0.038 /home/wking/src/notmuch/notmuch-archives.git/ssoma_mda.py:362(deliver)
      22875    8.943    0.000  810.459    0.035 /home/wking/src/notmuch/notmuch-archives.git/ssoma_mda.py:207(append)
      22875    0.418    0.000  308.353    0.013 /home/wking/.local/lib64/python3.4/site-packages/pygit2/index.py:146(write_tree)
      22875  307.855    0.013  307.855    0.013 {built-in method git_index_write_tree}
      22874    0.575    0.000  279.293    0.012 /home/wking/.local/lib64/python3.4/site-packages/pygit2/index.py:238(diff_to_tree)
      22874  278.501    0.012  278.501    0.012 {built-in method git_diff_tree_to_index}
      22875    0.088    0.000   80.413    0.004 /home/wking/.local/lib64/python3.4/site-packages/pygit2/index.py:99(read)

38 ms per ssoma delivery is probably fast enough, especially if you
are invoking ssoma-mda once per message, since process setup will take a similar amount of time:

  $ time python -c 'print("hello")'
  hello

  real    0m0.016s
  user    0m0.013s
  sys     0m0.003s

It's possible that fast-import would shave a few ms off the pygit2
addition (I'm not sure, and maybe pygit2 is faster than fast-import).
But I doubt it matters enough either way to be worth changing unless
you are dealing with a really large corpus.

Cheers,
Trevor

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Re: Mail archives in Git using ssoma

[Eric Wong]

"W. Trevor King" <wking@tremily.us> wrote:
> On Sun, Aug 21, 2016 at 06:37:04PM +0000, Eric Wong wrote:
> > Btw, for public-inbox, I'm using git-fast-import now, so imports are
> > a bit faster and $GIT_DIR/ssoma.index is no longer used.  This was
> > crucial for getting git@vger archives imported in a reasonable time.
> 
> ssoma-mda imports 22k notmuch messages in around 15 minutes (with
> profiling enabled), and:

In contrast, git@vger is around 300K messages.  LKML is well
into the millions, and I hope public-inbox (and git!) can handle
that one day, even on cheap hardware (haven't tried).

One problem I noticed with ssoma-mda is that it gets slower as
more messages get imported, since all those files sit in the
index, and the git index format is bad for incremental updates
with big, flat trees.  Big trees are a general problem with git:

    I'm now storing blob IDs directly in Xapian and will be
    using them more to avoid tree lookups.  tree creation
    lookups degrade the same way the index does as they
    get bigger.

    Currently it's using 2/38 of the SHA-1 like git loose
    objects; a goal might be to move towards supporting 2/2/36
    (or deeper) as Jeff noted substantial object traversal
    improvements:

https://public-inbox.org/git/20160805092805.w3nwv2l6jkbuwlzf@sigill.intra.peff.net/

    Of course, support for 2/38 will be retained for old
    archives/messages.

>   $ python -m cProfile -o profile import.py notmuch.mbox
>   $ python -c "import pstats; p=pstats.Stats('profile'); p.sort_stats('cumulative').print_stats(10)"
>   Sun Aug 21 12:56:49 2016    profile
> 
>            101823722 function calls (99078415 primitive calls) in 885.069 seconds
> 
>      Ordered by: cumulative time
>      List reduced from 1145 to 10 due to restriction <10>
> 
>      ncalls  tottime  percall  cumtime  percall filename:lineno(function)
>        70/1    0.002    0.000  885.069  885.069 {built-in method exec}
>           1    0.111    0.111  885.069  885.069 /home/wking/src/notmuch/notmuch-archives.git/import.py:9(<module>)
>           1    0.400    0.400  884.915  884.915 /home/wking/src/notmuch/notmuch-archives.git/import.py:17(import_mbox)
>       22875    0.601    0.000  863.371    0.038 /home/wking/src/notmuch/notmuch-archives.git/ssoma_mda.py:362(deliver)
>       22875    8.943    0.000  810.459    0.035 /home/wking/src/notmuch/notmuch-archives.git/ssoma_mda.py:207(append)
>       22875    0.418    0.000  308.353    0.013 /home/wking/.local/lib64/python3.4/site-packages/pygit2/index.py:146(write_tree)
>       22875  307.855    0.013  307.855    0.013 {built-in method git_index_write_tree}
>       22874    0.575    0.000  279.293    0.012 /home/wking/.local/lib64/python3.4/site-packages/pygit2/index.py:238(diff_to_tree)
>       22874  278.501    0.012  278.501    0.012 {built-in method git_diff_tree_to_index}

It looks like writing the index is already the slowest, here, in
terms of total time, too.  It might be interesting if you
profiled each *-mda invocation to see the degradation from the
first to last message.

>       22875    0.088    0.000   80.413    0.004 /home/wking/.local/lib64/python3.4/site-packages/pygit2/index.py:99(read)
> 
> 38 ms per ssoma delivery is probably fast enough, especially if you

Not even close for me :)

> are invoking ssoma-mda once per message, since process setup will take a similar amount of time:
> 
>   $ time python -c 'print("hello")'
>   hello
> 
>   real    0m0.016s
>   user    0m0.013s
>   sys     0m0.003s
> 
> It's possible that fast-import would shave a few ms off the pygit2
> addition (I'm not sure, and maybe pygit2 is faster than fast-import).
> But I doubt it matters enough either way to be worth changing unless
> you are dealing with a really large corpus.

One key feature is fast-import avoids writing an index entirely.
I think pygit2 would have to learn that, too.