Articles from Software

  • DaCHS 2.2 is out

    2020-10-13 Markus Demleitner
    Image: DaCHS "entails" 2.2

    DaCHS 2.2 adds support for what simple semantics we currently do in the VO. Which is a welcome excuse to abuse one of the funny symbols semanticians love so much.

    Today, I've released DaCHS 2.2, the second stable version of DaCHS running on Python 3. Indeed, we have ironed out a few sore spots that have put that “stable” into question, especially if you didn't run things on Debian Buster. Mind you, playing it safe and just going for Debian is still recommended: Compared to the Python 2 world, where things largely didn't break for a decade, the Python 3 universe is still shaking out, and so the versions of dependencies do matter. It's actually fairly gruesome how badly pyparsing 2.4 will break DaCHS. But that's for another day.

    Despite this piece of fearmongering, it'd be great if you could upgrade your installations if you are running DaCHS, and it's pretty safe if you're on Debian buster anyway (and if you're running Debian in the first place, you should be running buster by now).

    Here are the more notable changes in this release:

    • DaCHS can now (relatively easily) write time series in the form of what Ada Nebot's Time Series Annotation note proposes. See the tutorial chapter on building time series for how to do that in practice. Seriously: If you have time series to publish, by all means try this out. The specification can still be fixed, and so this is the perfect time to find problems with the plan.
    • The 2.2 release contains support for the MOC ADQL functions mentioned in the last post on this blog. Of course, to make them work, you will still have to acquaint your database with the new functionality.
    • DaCHS has learned to use IVOA vocabularies as per the current draft for Vocabularies in the VO 2. The most visible effect for you probably is that DaCHS now warns if your subject keywords are not taken from the Unified Astronomy Thesaurus (UAT) – which they almost certainly are not, because the actual format of these keywords is a bit funky. On the other hand, if you employ the “plain” root page template (see the root template in our templating guide if you are not sure what I am talking about here), you will get nice, human-friendly labels for the computer-friendly terms you ought to put into subjects. In case you don't bother: Given I'm currently serving as chair of the semantics working group of the IVOA, the whole topic will certainly come up again soon, and at that point I will probably also talk about another semantics-related newcomer to DaCHS, the gavo_vocmatch ADQL UDF.
    • There is a new command dachs datapack for interacting with frictionless data packages. The idea is that you can say dachs datapack create myres/q myres.pack and obtain an archive of all that is necessary to re-create myres on another DaCHS installation, where you would say dachs datapack load myres.pack. Frankly, this isn't much different from just tarring up the resource directory at this point, except that any cruft that may have accumulated in the directory is skipped and there is a bit of structured metadata. But then interoperability always starts slowly. Note, by the way, that this certainly does not teach DaCHS to do anything sensible with third-party data packages; while I've not thought hard about this, as it seems a remote use case, I am pretty sure that even the “tabular data packages” that refine the rough general metadata quite a bit simply have nowhere near enough metadata to create a useful VO resource or TAP table.
    • As part of my never-ending struggle against bitrot (in case you've always wondered what “curation” means: that, essentially), I'm running dachs val -vc ALL in my own data center once every month. This used to traverse the file system to locate all RDs defined on a box and then make sure they are still ok and their definitions match the database schema. That behaviour has now changed a bit: It will only check published RDs now. I cannot lie: the main reason for the change is because on my production machine the file system traversal has taken longer and longer as data accumulated. But then beyond that there is much less to worry when unpublished gets a little bit mouldy. To get back the old behaviour of validating all RDs that are reachable by the server, use ALL_RECURSE instead of ALL.
    • DaCHS has traditionally assumed that you are running multiple services on one site, which is why its root page is rendered over a service that exposes metadata on local resources. If that doesn't quite work for how you use DaCHS – perhaps because you want to have your own custom renderers and data functions on your root page, perhaps because you only have one browser-based service and that should be the root page right away –, you can now override what is shown when people access the root URI of your DaCHS installation by setting the [web]root config item to the path of the resource you want as root (e.g., myres/q/s/fixed when the root page should be made by the fixed renderer on the service s within the RD myres/q).
    • Scripting in DaCHS is a powerful way to execute python or SQL code when certain things happen. That seems an odd thing to want until you need it; then you need it badly. Since DaCHS 2.2, scripts executed before or after the creation of a table, before its deletion, or after its meta data has been updated, can sit on tables (where they have always belonged). Before, they could only be on makes (where they can still sit, but of course they are then only executed if the table is operated through that particular make) and RDs (from where they could be copied). That latter location is now forbidden in order to free up RD scripts for later sanitation. Use STREAM and FEED instead if you really used something like that (and I'd bet you don't).
    • Minor behavioural changes:
      1. Due to a bug, you could write things like <schema foo="bar">my_schema<schema>, i.e., have attributes on attributes written in element form. That is now flagged as an error. Since that attribute was fed to the embedding element, you might need to add it there.
      2. If you have custom flot plots in one of your templates (and you don't if you don't know what I'm talking about), you now have to set style to Points or Lines where you had usingIndex 0 or 1 before.
      3. The sidebar template no longer has links to a privacy policy (that few bothered to fill out). See extra sidebar items in the tutorial on how to get them back or add something else.

    The most important change comes last: The default logo DaCHS shows unless you override it is no longer the GAVO logo. That's, really, been inappropriate from the start. It's now the DaCHS logo, the thing that's in this posts's article image. Which isn't quite as tasteful as the GAVO one, true. But I trust we'll all get used to it.

  • Tutorial Renewal

    2020-06-25 Markus Demleitner
    The DaCHS Tutorial among other seminal works

    DaCHS' documentation (readthedocs mirror) has two fat pieces and a lot of smaller read-as-you-go pieces. One of the behmoths, the reference documentation, at roughly 350 PDF pages, has large parts generated from source code, and there is no expectation that anyone would ever read it linearly. Hence, I wasn't terribly worried about unreadable^Wpassages of questionable entertainment value in there.

    That's a bit different with the tutorial (also available as 150 page PDF; epub on request): I think serious DaCHS deployers ought to read the DaCHS Basics and the chapters on configuring DaCHS and the interaction with the VO Registry, and they should skim the remaining material so they are at least aware of what's there.

    Ok. I give you that is a bit utopian. But given that pious wish I felt rather bad that the tutorial has become somewhat incoherent in the years since I had started the piece in April 2009 (perhaps graciously, the early history is not visible at the documentation's current github home). Hence, when applying for funds under our current e-inf-astro project, I had promised to give the tutorial a solid makeover as, hold your breath, Milestone B1-5, due in the 10th quarter. In human terms: last December.

    When it turned out the Python 3 migration was every bit as bad as I had feared, it became clear that other matters had to take priority and that we might miss this part of that “milestone” (sorry, I can't resist these quotes). And given e-inf-astro only had two quarters to go after that, I prepared for having to confess I couldn't make good on my promise of fixing the tutorial.

    But then along came Corona, and reworking prose seemed the ideal pastime for the home office. So, on April 4, I forked off a new-tutorial branch and started a rather large overhaul that, among others, resulted in the operators' guide with its precarious position between tutorial and reference being largely absorbed into the tutorial. In all, off and on over the last few months I accumulated (according to git diff --shortstat 6372 inserted and 3453 deleted lines in the tutorial's source. Since that source currently is 7762 lines, I'd say that's the complete makeover I had promised. Which is good as e-inf-astro will be over next Wednesday (but don't worry, our work is still funded).

    So – whether you are a DaCHS expert, think about running it, or if you're just curious what it takes to build VO services, let me copy from index.html: Tutorial on importing data (tutorial.html,tutorial.pdf,tutorial.rstx). The ideal company for your vacation!

    And if you find typos, boring pieces, overly radical advocacy or anything else you don't like: there's a bug tracker for you (not to mention PRs are welcome).

  • DaCHS 2.1: Say hello to Python 3

    2020-05-29 Markus Demleitner
    DaCHS and python logos

    Today, I have released DaCHS 2.1, the first stable DaCHS running on Python 3. I have tried hard to make the major version move painless and easy, and indeed “pure DaCHS” RDs should just continue to work. But wherever there's Python in your RDs or near them, things may break, since Python 3 is different from Python 2 in some rather fundamental ways.

    Hence, the Debian package even has a new name: gavodachs2-server. Unless you install that, things will keep running as they do. I will keep fixing serious DaCHS 1 bugs for a while, so there's no immediate urgency to migrate. But unless you migrate, you will not see any new features, so one of these days you will have to migrate anyway. Why not do it today?

    Migrating to DaCHS 2

    In principle, just say apt install gavodachs2-server and hope for the best. If you have a development machine and regression tests defined, this is actually what we recommend, and we'd be very grateful to learn of any problems you may encounter.

    If you'd rather be a little more careful, Carlos Henrique Brandt has kindly updated his Docker files in order to let you spot problems before you mess up your production server. See Test Migration for a quick intro on how to do that. If you spot any problems that are not related to the Python 3 pitfalls mentioned in the howto linked below or nevow exodus, please tell me or (preferably) the dachs-support mailing list.

    A longer, more or less permanent piece elaborating possible migration pains, is in our how-to documentation: How do I go from DaCHS1 to DaCHS2?

    What's new in DaCHS2?

    I've used the opportunity of the major version change to remove a few (mis-) features that I'm rather sure nobody uses; and there are a few new features, too. Here's a rundown of the more notable changes:

    • DaCHS now produces VOTable 1.4 by default. This is particularly notable when you provide TIMESYS metadata (on which I'll report some other time).
    • When doing spatial indices, prefer the new //scs#pgs-pos-index to //scs#q3cindex. While q3c is still faster and more compact than pgsphere when just indexing points, on the longer run I'd like to shed the extra dependency (note, however, that the pgsphere index limits the cone search to a maximum radius of 90 degrees at this point).
    • Talking about Cone Search: For custom parameters, DaCHS has so far used SSA-like syntax, so you could say, for instance, vmag=12/13 (for “give me rows where vmag is between 12 and 13”). Since I don't think this was widely used, I've taken the liberty to migrate to DALI-compliant syntax, where intervals are written as they would be in VOTable PARAM values: vmag=12 13.
    • In certain situations, DaCHS tries to enable parallel queries (previously on this blog).
    • Some new ADQL user defined functions: gavo_random_normal, gavo_mocintersect, and gavo_mocunion. See the TAP capabilities for details, and note that the moc functions will fail until we put out a new pgsphere package that has support for the MOC-MOC operations.
    • dachs info (highly recommended after an import) now takes a --sample-percent option that helps when doing statistics on large tables.
    • For SSA services serving something other than spectra (in all likelihood, timeseries), you can now set a productType meta as per the upcoming SimpleDALRegExt 1.2.
    • If you have large, obscore-published SIAP tables, re-index them (dachs imp -I q) so queries over s_ra and s_dec get index support, too.
    • Since we now maintain RD state in the database, you can remove the files /var/gavo/state/updated* after upgrading.
    • When writing datalink metaMakers returning links, you can (and should, for new RDs) define the semantics in an attribute to the element rather in the LinkDef constructor.
    • Starting with this version, it's a good idea to run dachs limits after an import. This, right now, will mainly set an estimate for the number of rows in a table, but that's already relevant because the ADQL translator uses it to help the postgres query planner. It will later also update various kinds of column metadata that, or so I hope, will become relevant in VODataService 1.3.
    • forceUnique on table elements is now a no-op (and should be removed); just define a dupePolicy as before.
    • If you write bad obscore mappings, it could so far be hard to figure out the reason of the failure and, between lots of confusing error messages, to fix it. Instead, you can now run ``dachs imp //obscore recover`` in such a situation. It will re-create the obscore table and throw out all stanzas that fail; after that, you can fix the obscore declarations that were thrown out one by one.
    • If you run DaCHS behind a reverse proxy that terminates https, you can now set [web]adaptProtocol in /etc/gavo.rc to False. This will make that setup work for form-based services, too.
    • If you have custom OAI set name (i.e., anything but local and ivo_managed in the sets attribute of publish elements), you now have to declare them in [ivoa]validOAISets.
    • Removed things: the docform renderer (use form instead), the soap renderer (well, it's not actually removed, it's just that the code it depends on doesn't exist on python3 any more), sortKey on services (use the defaultSortKey property), //scs#q3cpositions (port the table to have ra and dec and one of the SCS index mixins), the (m)img.jpeg renderers (if you were devious enough to use these, let me know), and quite a few even more exotic things.

    Some Breaking Changes

    Python 3 was released in 2008, not long after DaCHS' inception, but since quite a few of the libraries it uses to do its job haven't been available for Python 3, we have been reluctant to make the jump over the past then years (and actually, the stability of the python2 platform was a very welcome thing).

    Indeed, the most critical of our dependencies, twisted, only became properly usable with python3 in, roughly, 2017. Indeed, large parts of DaCHS weren't even using twisted directly, but rather a nice add-on to it called nevow. Significant parts of nevow bled through to DaCHS operators; for instance, the render functions or the entire HTML templating.

    Nevow, unfortunately, fell out of fashion, and so nobody stepped forward to port it. And when I started porting it myself I realised that I'm mainly using the relatively harmless parts of nevow, and hence after a while I figured that I could replace the entire dependency by something like a 1000 lines in DaCHS, which, given significant aches when porting the whole of nevow, seemed like a good deal.

    The net effect is that if you built code on top of nevow – most likely in the form of a custom renderer – that will break now, and porting will probably be rather involved (having ported ~5 custom renderers, I think I can tell). If this concerns you, have a look at the README in gavo.formal (and then complain because it's mainly notes to myself at this point). I feel a bit bad about having to break things that are not totally unreasonable in this drastic way and thus offer any help I can give to port legacy DaCHS code.

    Outside of these custom renderers, there should just be a single visible change: If you have used n:data="some_key" in nevow templates to pull data from dictionaries, that won't work any longer. Use n:data="key some_key" n:render="str" instead. And it turns out that this very construct was used in the default root template, which you may have derived from. So – see if you have /var/gavo/web/templates/root.html and if so, whether there is <ul n:data="chunk" in there. If you have that, change it to <ul n:data="key chunk".

    Update (2020-11-19): Two only loosely related problems have surfaced during updates. In particular if you are updating on rather old installations, you may want to look at the points on Invalid script type preIndex and function spoint_in already exists in our list of common problems.

  • DaCHS 1.4 is out

    2019-10-15 Markus Demleitner
    Dachs logo with "version 1.4" superposed

    Since the Groningen Interop is over, it's time for a DaCHS release, and so, roughly half a year after the release of DaCHS 1.3, today I've pushed DaCHS 1.4 into our Debian repository.

    As usual, you should upgrade as soon as you find time to do so, because upgrades become more difficult if they span large version gaps; and one of these days you will need some new feature or run into one of the odd bugs. Upgrading is a good opportunity to also get your DaCHS ready for buster by adding the repos mentioned there.

    The list of new features is rather short this time around. Here are some noteworthy ones:

    • There's now an XML grammar that can be used when you have to parse smallish snippets of XML as, for instance, in VOEvent.
    • You can now use TABLESAMPLE(1) after a table specification in DaCHS' ADQL to tell the database engine to just use 1% of a table for a query. While this isn't a precise way to sample tables, it's great when developing queries.
    • Also among new features I'd like to see in ADQL and have therefore put into DaCHS is GENERATE_SERIES(a,b), which is what is known as table-generating function in SQL . If you know SDSS CasJobs, you'll have seen lots of those already. GENERATE_SERIES, however, is really plain: it just spits out a table with a column with integers between a and b. For an example of why one might what to have that, check out the poster I'm linking to in my ADASS report.
    • If you have an updating data descriptor (usually, because you keep feeding data into a data collection), DaCHS will no longer automatically re-make its dependencies (like, say, views). That's because that's not necessary in general, and it's a pain if every update on an obscore-published table tears down and rebuilds the obscore view. For the rare cases when you do need to rebuild dependencies, there's now a remakeOnDataChange attribute on data.
    • At the interop, I've mentioned a few use cases for knowing which server software you're talking to, and I've said that people should set their server headers to informative values. DaCHS does that now.

    To conclude on a low note: This is probably going to be the last release of DaCHS for python 2. Even though we will have to shed a dependency or two that simply will not be ported to python 3, and even though I'm rather unhappy with a few properties of the python 3 port of twisted, there's probably no way to escape this, given that Debian is purging out python 2 packages quickly already.

    So, when we meet again for the next release, you'll probably be looking at DaCHS 2.0, and where you have custom code in your RDs, it's rather likely that you'll see a minor amount of breakage. I promise I'll do everything I can to make the migration easy for deployers, but I can't do higher magic, so: If there's ever been a time to add regression tests to your RDs, it's now.

  • DaCHS is Bustered

    2019-08-01 Markus Demleitner

    DaCHS is developed on Debian, and Debian is the recommended deployment platform. Hence, a new major release of Debian (where major means for them: We may break stuff) is always a big thing for me. And so it was with the release that came in July, codenamed “buster”. Both on the “big thing” and on the “break” counts. This posting gives DaCHS deployers some background for their buster upgrades. Astronomers not running Debian themselves won't risk missing anything if they skip this post.

    So, after I upgraded the first thing I noticed is that DaCHS would no longer even start because astropy (which it needs, in particular, because that's where pyfits sits these days) was gone. Simple explanation: Upstream astropy doesn't support python2 any more, and so Debian buster only has python3-astropy.

    Moving DaCHS to python3, unfortunately, isn't that easy; a major dependency, nevow (essentially, a web framework), isn't ported yet, and porting it is a major thing. Believe me, I've tried. The nasty thing, in particular, is that twisted, which lies below nevow still, hands up lots of byte strings. And in python3, b"a"!="a". You wouldn't believe how many interesting bugs that simple truth introduces when you got a library that handed out “just strings” in python2 and now byte strings in python3. Yikes.

    Update (2019-08-28): After quite a bit of experimentation, I finally gave up on providing a python2 version of astropy through release, because for a complicated set of reasons (including numpy declaring a conflict with existing astropys in buster) it is impossible to provide a package that works in buster and doesn't break stretch. So, for buster only you'll have to have a second (or, if running beta, third) gavo line in your sources.list (or equivalent):

    deb http://vo.ari.uni-heidelberg.de/debian buster-foreports main

    The instructions at our APT repository have been updated, so you won't have to bookmark this particular page.

    But that wasn't the end of it. Buster comes with Postgres 11, which I look forward to in particular because it supports parallel query execution. That could help us quite a bit, given out large catalogs that quite often we want to run sequential scans on. But of course this means upgrading postgres. And attempting to do that on my development machine immediately hit a wall. What's nice is that the q3c and pgsphere extensions that we've had to push out ourselves so far are now part of Debian main. What's rather fatal is that our pgsphere extensions dealing with HEALPixes and MOCs aren't part of the buster pgsphere package (the reasons for that are tedious and arcane and have to do with OpenSSL and the GPL).

    Also, the pgsphere package coming with buster is called postgres-pgsphere, which is rather unfortunate as it's missing the version indication. So: If you find it on your system, remove it right away. It will conflict with the one true pgsphere package (postgresql-11-pgsphere). That one you'll get from us, and it has the HEALPix stuff built in. TL;DR: run apt install postgresql-q3c postgresql-11-pgsphere before following the postgres update recipe linked above.

    There's a bit more to upgrading the database this time. Because of fairly low-level cleanup in Postgres itself. you're risking index corruption on string indices. Realistically, for almost anything you'll have, it's unlikely that you're affected (it's essentially about non-ASCII in strings), but then it's better to be safe than sorry, and hence you should say:

    reindex database gavo

    first thing after you've upgraded to Postgres 11 (which you should really do once the box is on buster). Only if you have very large tables it might be worth it to restrict the index regeneration to indices that could actually need it; see the postgres link above for how to do that.

    One last thing on Postgres upgrades: I've not quite tried to work out why, but probably depending on your /etc/hosts DaCHS on buster is much more likely to connect to your database using IPv6 than it was before. Many older Postgres configurations won't let you in then. If that happens to you, just edit /etc/postgresql/11/main/pg_hba.conf and add a line:

    host    all         all         ::1/32          md5

    (or something less permissive if you prefer).

    The next buster-related shock was when TOPCAT's TAP uploads stopped working while my regression tests didn't find anything wrong. After a bit of cursing I eventually figured out that that's not actually buster's fault but twisted's, which in a commit from May 2018 broke chunked uploads (essentially, that's when you're not saying up front how large your upload will be). I've filed a bug report on twisted, but we can't really wait until any sort of fix will be ready and have a broken TOPCAT-DaCHS relationship until then, so for now we're also shipping a fixed twisted package. If you're running DaCHS without our repository enabled, you will have to patch your the twisted code itself. The bug report tells what to do (no warranties, though, because I'm not entriely sure why they changed it in the first place; it's a very small change, though).

    [Update (2019-08-14) scratch the part with the fixed twisted packages. They're too much trouble on stretch systems. You can keep using them on buster boxes if you want, though. The most recent stable release monkeypatches the problem out of presumably broken twisteds, and so will the next beta.]

    I hope you're not totally discouraged now, because upgrade you should (though perhaps not right before going on vacation) – distribution upgrades are unavoidable if you want to run services for decades, and that's definitely a goal within the VO. See the Debian release note for Debian's take on dist upgrades, which arguably is a bit more alarmist than it would need to; a lean, server-only system typically is really simple to upgrade.

    Given the relatively large number of Debian packages we override in buster, I'll be particularly grateful if you complain early about breakage you observe (ideally use the dachs-support mailing list, but see Support for alternatives), and as usual you are encouraged to try the upgrade first on a development system if you have one. Which you should.

« Page 3 / 4 »