--- Log opened Wed Aug 29 00:00:10 2012
00:09 < foucist> delinquentme: 11:19 < nmz787> delinquentme: I would use SCP
00:13 < delinquentme> that was the last activity??
00:13 < foucist> delinquentme: right after you asked how to send a 2gb file
00:14 < delinquentme> Ohhh
00:16 < foucist> delinquentme: personally i use the alias: scpresume
00:16 < foucist> scpresume='rsync --partial --progress --rsh=ssh'
00:16 < foucist> just in case the file gets interrupted
00:16 < foucist> scp doesn't have resume itself
00:16 < foucist> though wget -c is pretty good too
00:16 < foucist> asuming the file was on a webserver :P
00:17 < foucist> funny how ftp clients already solved the problem a long time ago
00:17 < foucist> but i havne't used ftp in YEARS
00:18 < foucist> well, probably not since i used windows
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01:07 < delinquentme> NIGHT!
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01:54 < archels> http://www.urbandictionary.com/define.php?term=Hacker%20Spaces
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02:00 < Utopiah> looks accurate
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04:49 < strangewarp> P2P Foundation has a maddive hard-on for Carrico, all of a sudden... Looks like their main blogger has been captured by the "social justice before technology" thing
04:49 < strangewarp> massive*
04:49  * strangewarp unfollows that blog
05:04 < strangewarp> I was momentarily tempted to write an essay about how Carrico's opposition of globalization technologies impedes the formation of international workers' solidarity, which means his leftist credentials are short-sighted at best... but then I remembered he's a dang troll
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05:46 < nmz787> kanzure: jrayhawk: i have this dir... d-wx-ws--x  5 root staff      4096 Apr 20 01:33 djangoApps
05:46 < nmz787> when i type groups, two things show up, staff and sudo
05:46 < nmz787> so why can't I even ls the dir as my user?
05:48 < chris_99> don't you need read permissions
05:50 < nmz787> derr
05:50 < nmz787> yes
05:50 < nmz787> thx
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06:33 < OldCoder> minimoose, Good nick
06:41 < minimoose> tx, OldCoder
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08:19 < nmz787> anyone here know SVN?
08:29 < bkero> for a certain definition of know
08:30 < bkero> nmz787: chmod g+x djangoApps
08:30 < bkero> s-s-s-sticky bit
08:30 < nmz787> bkero: that was already done
08:31 < nmz787> svn status says the dir is locked tho
08:31  * bkero doesn't deal with svn locks
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09:08 <@kanzure> death to svn
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09:25 <@kanzure> "A hundred billion or so humans have ever lived, but only seven billion are alive now (which gives the human condition a 93% mortality rate)."
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10:18 < nmz787> soo ACS Synthetic Biology is now offered in print
10:18 < nmz787> that's stupid
10:19 < nmz787> how am i suppoesd to be a synBio fanboy if i can't get some physical instruments
10:19 < nmz787> but members get to choose 5 titles with their subscription
10:20 < nmz787> so 25 bucks a year for some ACS journals isn't too bad
10:20 < nmz787> but i really wanted print
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10:25 <@kanzure> http://coding.fm/ i like the "angry dev coding" mode (it's just "sounds of angry coders typing on keyboard")
10:25 <@kanzure> they need to throw in some "FUCK"s and "SHIIIT"s
10:25 < chido> I have that live at home
10:28 <@kanzure> the at-home version exhausts your resources of food and drink
10:29 < nmz787> any opinions on http://phabricator.org
10:29 <@kanzure> i'd look at redmine first probably
10:30 <@kanzure> i'm not too hawt on running php
10:30 <@kanzure> a lot of people just use github or unfuddle or something
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10:44 < chris_99> if i'm going to get a book on microbiology
10:44 < chris_99> what would you guys recommend
10:45 < chris_99> *molecular biology
10:48 < nmz787> why doesnt this work find / -name svn2|grep -v 'denied'
10:49 < nmz787> mol bio of the gene
10:49 < nmz787> mol bio of the cell is supposed to be good too
10:50 <@kanzure> nmz787: do you mean "find ./"
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10:51 < nmz787> no
10:51 <@kanzure> chris_99: the wikibook on microbiology is surprisingly awful http://en.wikibooks.org/wiki/Microbiology
10:51 < nmz787> grep isn't finding denied
10:51 <@kanzure> -v is to exclude
10:51 < nmz787> chris_99 this is better prob http://www.google.com/url?sa=t&rct=j&q=microbio%20book&source=web&cd=13&cad=rja&ved=0CGUQFjAM&url=http%3A%2F%2Ftextbookofbacteriology.net%2F&ei=p1Y-UJ-wFMHW0QGs-oDICw&usg=AFQjCNFNPmWiNaFLBuTdBWxcAJOctFU0lg
10:51 <@kanzure> and this sounds like you want "locate". your system is probably running locatedb. this would be faster than running find on your whole file system.
10:52 < nmz787> google sucks
10:52 < nmz787> textbookofbacteriology.net/
10:52 < nmz787> yes i want to exclude
10:52 < nmz787> that is why i give -v
10:52 < nmz787> but it doesnt exclude 'denied'
10:52 < nmz787> it still shows up on STDOUT
10:52 <@kanzure> because of how find works, i think
10:52 < nmz787> :/
10:52 < nmz787> grr
10:52 <@kanzure> locate svn2 | grep -v denied
10:53 < nmz787> that immediately returns with no results
10:53 < nmz787> i just installed svn2git
10:53 < nmz787> and it cant find it
10:53 < nmz787> and i wanna search for the sv2git file
10:53 <@kanzure> what is svn2git?
10:53 <@kanzure> git-svn is provided by default with git i think
10:53 <@kanzure> type: man git-svn
10:54 <@kanzure> that textbook doesn't look very thorough.. it goes over some metabolism stuff but it doesn't seem to mention streaking, plating, or things like that
10:55 < nmz787> https://github.com/nirvdrum/svn2git
10:55 < nmz787> there is nothing called git-svn
10:55 < nmz787> after installing some stuff git svn works
10:56 < nmz787> with a space
10:56 < nmz787> not dash
10:57 < nmz787> is streaking really microbiology though?
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11:00 < jrayhawk> '2|' is not a valid stream redirection
11:01 < jrayhawk> you can use |& as shorthand for 2>&1 |
11:01 < jrayhawk> at least, in bash
11:01 < nmz787> no i want to search for 'svn2'
11:01 < nmz787> i didnt think a space was rewuired
11:01 < nmz787> required
11:01 < jrayhawk> oh, well, use 2>&1 | to get stderr into stdout
11:01 < jrayhawk> It isn't.
11:01 < nmz787> why is find going to put results in stderr?
11:02 < jrayhawk> you seemed to be grepping for 'permission denied', which is, notably, an error.
11:02 <@kanzure> what is the "ncbi C++ toolbox"? http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ seems to have BLAST, fastcgi, some weird xml crap.. bleh
11:02 < nmz787> oh
11:02 < nmz787> kanzure: yes
11:02 < nmz787> its just bindings
11:02 <@kanzure> i see
11:02 < nmz787> i use it through biopython
11:03 <@kanzure> so um, hey, what's the point of ncbi.nlm.nih.gov/books if the book contents can't be displayed? http://www.ncbi.nlm.nih.gov/books/NBK21154/ "By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed"
11:04 < jrayhawk> presumably so that you can find them with searches?
11:04 < nmz787> you can see stuff if you search
11:04 < nmz787> so you could prob search streaking
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11:10 <@kanzure> jrayhawk: when i try to clone a private repo on gnusha i get "fatal: failed to open '/srv/git/enzyme-filter.git/objects/17': Permission denied"
11:10 <@kanzure> (i addaccess'd myself)
11:12 < jrayhawk> You may need to relogin in order to get the new groups
11:14 <@kanzure> doh
11:15 <@kanzure> nmz787: the only commit message in there is "Convert svn:ignore properties to .gitignore."
11:16 < nmz787> can you delete everything, i guess i'll jus push the files
11:16 < nmz787> this git to svn seems to not work
11:16 <@kanzure> you can do "git push -f" if you want to override the crap already there
11:16 <@kanzure> you don't want git->svn.. you want svn->git
11:16 < jrayhawk> receive.denynonfastforwards might be on
11:16 < nmz787> well there arent any files in the dir the stupid git svn command made
11:17 < nmz787> oh, right
11:17 < nmz787> well it sucks no matter
11:17 <@kanzure> jrayhawk: stat( /srv/git/enzmye-filter.git/objects ) failed: No such file or directory at /usr/share/perl5/Piny/Repo.pm line 601.
11:17 < nmz787> i just want something that easily does diff/patch
11:17 < nmz787> geez
11:18 < jrayhawk> 'enzmye'
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11:26 <@kanzure> oh fooey
11:26 <@kanzure> nmz787: ok i made a terrible typo
11:26 < nmz787> oh
11:27 <@kanzure> nmz787: ok now "git push -f" will work
11:27 <@kanzure> what did you do to convert it?
11:29 < chris_99> it's £185 for 100ug of GFP, isn't that rather expensive?!
11:31 < nmz787> git svn clone 'svn+ssh://secretrepo'  --no-metadata -A authors-transform.txt --stdlayout ~/temp
11:31 < jrayhawk> looks like he's following http://john.albin.net/git/convert-subversion-to-git but something is going wrong with git svn
11:31 < nmz787> the shit here http://john.albin.net/git/convert-subversion-to-git
11:32 < nmz787> yes
11:32 < nmz787> so in Oregon you can ask a doctor to sterilize you without parental consent at 15
11:32 < nmz787> pretty cool
11:33 < nmz787> there are no files in the resulting temp dir
11:33 < nmz787> except for a .git dir
11:33 < jrayhawk> Which kind of sterilization?
11:33 < nmz787> sexual
11:33 < jrayhawk> i mean, more specifically
11:33 < nmz787>       (4) “Sterilization” means any medical  procedure, treatment or operation for the purpose of rendering an individual  permanently incapable of procreating. [1983 c.460 §3; 1991 c.67  §116]
11:34 < nmz787> from Definitions here http://www.leg.state.or.us/ors/436.html
11:34 < nmz787> wait
11:34 < nmz787> .us
11:34 < nmz787> same as diyhpl.us
11:34 < jrayhawk> holy moses
11:34 < nmz787> kanzure are you posing as Oregon?
11:34 <@kanzure> .us is a generic "united states" domain
11:34 <@kanzure> *gtld
11:34 < jrayhawk> i don't think even planned parenthood would give a 15 year old a hysterectemy
11:34 < nmz787> go Oregon
11:35 < jrayhawk> or a tubal ligation
11:35 < nmz787> though I suspect Oregon is not on the top of the over-populators list
11:35 <@kanzure> so do they have to be a resident?
11:35 < jrayhawk> well, if they cross state lines, then it becomes a federal issue
11:36 <@kanzure> jrayhawk: maybe you know an easier way for nmz787 to convert his svn repository
11:36 <@kanzure> nmz787: what's that molecular biology protocols book that everyone keeps recommending?
11:37 < jrayhawk> i suspect it's the wrong path or permissions are still wrong or something and git-svn doesn't give sufficient error messages
11:38 < nmz787> wish this was on android https://www.facebook.com/TheSimpsonsTappedOut
11:38 < nmz787> no this http://itunes.apple.com/us/app/id497595276?mt=8
11:38 < jrayhawk> i need to take off, so i probably won't be of much help for at least a couple hours
11:38 < nmz787> maniatas
11:39 < nmz787> molecular cloning a lab manual... by sambrook and russel
11:39 < nmz787> i guess maniatis was on older editions
11:40 < nmz787> this sounds like a PITA http://codeascraft.etsy.com/2011/12/02/moving-from-svn-to-git-in-1000-easy-steps/
11:40 < nmz787> i want 1 or 2 steps
11:40 <@kanzure> oh it's sambrook
11:40 <@kanzure> "Molecular Cloning: A Laboratory Manual"
11:41 <@kanzure> right
11:41 <@kanzure> ok thanks
11:44 < nmz787> yeah i think the git svn is silently failing
11:44 <@kanzure> does "svn log" work?
11:46 < nmz787> ok looks like removing the -A authors-transform.txt --stdlayout is working
11:46 < nmz787> i actually see files being downloaded
11:47 <@kanzure> did you make authors-transform.txt?
11:47 <@kanzure> or did you neglect that part :P
11:48 < nmz787> yes
11:48 < nmz787> i made it
11:48 <@kanzure> hrrm
11:48 <@kanzure> well ok
11:49 < nmz787> it was a 1 line file
11:49 < nmz787> nathan = nathan <nathan>
11:49 <@kanzure> haha i think you should've used "Nathan McCorkle <nmz787@gmail.com>"
11:53 < nmz787> well i'm not using it at all now
12:00 < nmz787> gah, it died
12:00 < nmz787> r16 = 94559e0d1272d17d0fa5f800855c89cc4071fe54 (refs/remotes/git-svn)
12:00 < nmz787> fatal: refs/remotes/trunk: not a valid SHA1
12:00 < nmz787> update-ref refs/heads/master refs/remotes/trunk: command returned error: 128
12:03 <@kanzure> that looks like a valid SHA1 to me..
12:07 < nmz787> rf -Rfing and trying again
12:09 < gnusha> diyhpluswiki.git: 641e37c links to actual books
12:10 < nmz787> why do some of the files it shows during check say D
12:10 < gnusha> diyhpluswiki.git: 101c23a remove pesky inconsistency in book labelling
12:10 < nmz787> if i made them D (deleted) why are they showing up in a new checkout???
12:10 <@kanzure> because you didn't svn commit your deletions
12:11 < nmz787> wtf
12:11 <@kanzure> (probably)
12:11 < nmz787> i said commit
12:11 <@kanzure> i don't know how svn works
12:11 <@kanzure> the only time i use it is when i'm converting it to git
12:11 <@kanzure> i have added some possibly-useful files here http://diyhpl.us/wiki/diybio/faq/books
12:12 <@kanzure> as far as i can tell there's no actually-useful free molecular biology book out there on the interwebs
12:13 < nmz787> the ones i like are free outside US copyright law
12:14 < nmz787> you should add mol bio of the gene
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12:18 <@kanzure> ok grabbing
12:23 < gnusha> diyhpluswiki.git: 095952d add a link to Molecular Biology of the Gene
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12:31 <@kanzure> actually i think my copy of mbotg is bad.. doesn't seem to be a pdf, can't figure out what type of file it is
12:31 < nmz787> so i tried again, this time adding --username myusername
12:31 < nmz787> i dunno if the rm -Rf did it, or that
12:31 < nmz787> but it worked
12:32 < nmz787> so now
12:33 < nmz787> shit, just boiled a pot of water dry
12:36 < nmz787> ok kanzure the repo should be all pushed
12:38 < nmz787> hmm, beer or coffee
12:40 <@kanzure> sambrooks is pretty awesome, why haven't i read this yet?
12:45 < nmz787> dunno
12:46 < nmz787> late to the game
12:46 < nmz787> found that PDF after being in school maybe 6 months
12:46 < nmz787> referred to it quite often for background research
12:46 < nmz787> one lab i worked in actually had a paper copy, that was nice too
12:47 < nmz787> i doubt most other students used it much
12:48 < nmz787> kanzure: did you ever make an equipment auction  app?
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12:48 <@kanzure> nope not yet
12:48 < nmz787> i wonder if there is cheap stuff within an hour of NYC
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12:50 <@kanzure> i want to find a book like sambrooks except for motion control automation things
12:51 <@kanzure> (and not something insulting like "here's some gear equations, now piss off")
12:51 < nmz787> hmm
12:51 < nmz787> i can email someone
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13:15 <@kanzure> nmz787: do you have a pdf copy of cathal's wikibook?
13:15 <@kanzure> every time i try to render it on wikipedia it ends up with an error
13:15 <@kanzure> i've told cathal about this, but he can't fix it
13:16 <@kanzure> http://pastebin.com/raw.php?i=AdJg9gwv
13:16 < nmz787> no
13:17 < nmz787> can you complain?
13:17 < nmz787> submit bug?
13:18 <@kanzure> not sure where to submit this bug
13:19 <@kanzure> i guess i should complain to aran dunkley
13:20 <@kanzure> "Multibyte characters not working"
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13:39 < nmz787> kanzure: when do you have time to look at that enzymeFilter code?
13:39 < nmz787> with me
13:41 <@kanzure> i can look at it in a few minutes (it's downloading but i'm on a slow connection)
13:42 < nmz787> cool
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13:47 <@kanzure> nmz787: so what are all these multi-megabyte files in the main directory?
13:47 <@kanzure> like CAZyall.faa
13:48 <@kanzure> whog
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13:48 <@kanzure> KEGG_KO_list
13:49 <@kanzure> nmz787: i've pushed a minor change (git pull it)
13:49 < nmz787> they are... lists
13:49 < nmz787> what you do?
13:49 < nmz787> CAZy is carbohydrate active enzymes or something like that
13:49 <@kanzure> i removed a small svn file
13:49 < nmz787> KEGG is some japanese database/ontology AFAIK
13:50 < nmz787> KO is KEGG ORTHOLOG
13:50 <@kanzure> what is the difference between enzymeFilter/views.py.new and enzymeFilter/views.py.old ?
13:50 <@kanzure> and enzymeFilter/views.py
13:50 < nmz787> umm
13:51 < nmz787> i dunno if the dates are there or not
13:51 < nmz787> but the .new .old are both not active
13:51 < nmz787> so I'm not sure but they can be deleted most likely
13:51 < nmz787> i stopped using svn after I forgot it last summer
13:51 <@kanzure> ok pushed
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13:52 < nmz787> brb, lemme switch to linux pidgin in VM
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13:57 <@kanzure> nmz787: i think your first step is to switch out postgresql in settings.py with sqlite
13:57 <@kanzure> second step is to assemble a requirements.txt file to list out the dependencies
13:58 <@kanzure> this way you can re-install this app in different environments
13:58 < nmz787> why go to sqlite?
13:58 <@kanzure> well, unless you want to install postgresql on your system
13:58 < nmz787> well isn't it faster and more robust?
13:58 <@kanzure> requirements.txt is necessary so that you know which version of django you're using, or which version of the other packages
13:59 < nmz787> oh, its the newest version of django, 3 something i think
13:59 <@kanzure> postgresql is definitely better for production, but sqlite is really nice for development (unless you're dealing with huge databases..)
13:59 < nmz787> grr, i had that all written somewhere, once
13:59 <@kanzure> i thought you said it was from last year?
13:59 < nmz787> well i upgraded to the newest django about 5 months ago
14:00 <@kanzure> do you have virtualenv stuff already installed?
14:00 < nmz787> never use virtualenc
14:00 < nmz787> env
14:00 < nmz787> never saw the reason
14:00 <@kanzure> i suggest doing this:
14:00 <@kanzure> curl -s https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | bash
14:00 <@kanzure> this way you can switch into a virtualenv just for this project
14:00 < nmz787> why?
14:00 <@kanzure> and keep track of the dependencies
14:00 < nmz787> the VM i'm on is only for doing this
14:00 <@kanzure> because then you can commit requirements.txt and just push your git repository around
14:00 <@kanzure> when you want to deploy.
14:01 < nmz787> likewise, the server its on is only for this app
14:01 <@kanzure> yes, but you're not going to push this back to jbei
14:01 <@kanzure> presumably you will want to deploy this elsewhere
14:01 < nmz787> if you help me get it working i will
14:01 < nmz787> hmm
14:01 < nmz787> well, sure
14:01 <@kanzure> exactly. so using requirements.txt is how you're going to get it to work.
14:01 < nmz787> but why use virtualenv?
14:01 < nmz787> why should the app be as easy to install along whatever system?
14:02 <@kanzure> because then you don't need me in the future
14:02 <@kanzure> brownies: help me :(
14:02 < brownies> kanzure: ?
14:03 < nmz787> i don't follow, i need your help with a file parser mainly, and figuring out if there's a better way to background processes than django-celery
14:03 <@kanzure> brownies: i'm trying to describe why something like rvm and bundler is useful, except in the context of django
14:03 <@kanzure> django-celery is perfectly fine for spawning workers
14:03 < brownies> if he uses bundler, then... it's the same thing. same reasons.
14:03 < nmz787> :/
14:03 < nmz787> huh?
14:03 <@kanzure> brownies: he doesn't use bundler, this is a python project without any dependency management
14:03 <@kanzure> it's basically a blob of broken code on my system
14:04 < nmz787> right, it requires django, django-celery, and biopython
14:04 < nmz787> i think thats it
14:04 <@kanzure> brownies: maybe you know a way to convince him to actually use these tools
14:04 <@kanzure> brownies: because i seem to be failing
14:04 <@kanzure> yes but which version of those
14:04 < nmz787> should it always be 'the newest'
14:04 < nmz787> shouldn't it*
14:04 <@kanzure> i'd rather use the exact versions that you're using
14:05 <@kanzure> you don't want my system-wide version of biopython 'cause that could be anything
14:06 < nmz787> do you use debian?
14:07 < brownies> nmz787: you have to understand that the "app" you've made has to run on many different machines
14:07 < nmz787> sure
14:07 < brownies> even if it's *only* you *ever* working on it, you still need to account for dev vs. staging vs. production
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14:07 < nmz787> hrmm
14:07 < brownies> so, how do we maintain a uniform environment across machines? we do that by specifying "this app *requires* these packages, at this version, running on this python"
14:08 < brownies> nmz787: using different versions of packages in different places may break the app, so this is an attempt to ensure some degree of portability
14:08 < nmz787> sure
14:08 < nmz787> but it seems ugly
14:08 <@kanzure> and i don't want to debug this if 50% of my packages are wrong
14:08 < brownies> you are basically saying "this is what it was built and tested with; if you recreate that environment on your system, it should also work"
14:08 < nmz787> i'd rather the app be one file
14:08 < brownies> ...
14:08 < nmz787> sure
14:08 <@kanzure> what does that have to do with it?
14:08 <@kanzure> it's already like 50 files
14:08 < nmz787> right
14:09 < nmz787> i would love if it was 1 file
14:09 < nmz787> just like the old days
14:09 < brownies> i would love if i had a hot tub in my backyard, but... looking out there, i still don't see one.
14:09 < nmz787> well so what do i do ?
14:09 < nmz787> find the versions, then what
14:09 <@kanzure> curl -s https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | bash
14:09 < brownies> then you specify them, written down in a format that other people can understand
14:09 <@kanzure> mkvirtualenv enzyme-filter
14:09 <@kanzure> workon enzyme-filter
14:09 < brownies> other people have built tools to automatically understand such files in specific formats
14:09 <@kanzure> pip install thethingyouwant
14:09 < brownies> for ruby, people use bundler. for python, people use pip.
14:09 < brownies> pip + virtualenv.
14:10 <@kanzure> pip freeze > requirements.txt
14:10 < nmz787> kanzure: do i run those in the git repo dir?
14:10 <@kanzure> git add requirements.txt; git commit -m'yo dog, requirements'
14:10 <@kanzure> i suggest running the "pip freeze > requirements.txt" and git commands in the repo yes
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14:11 <@kanzure> you can also manually write requirements.txt in the format "django==5.5.5" on each line
14:11 <@kanzure> you can check which version you have with uh.. um.
14:12 <@kanzure> ah, with pip freeze | grep django
14:12 <@kanzure> well, actually, it's Django
14:13 <@kanzure> for instance, my system version of django is apparently 1.2.3
14:13 <@kanzure> so i'd write "Django==1.2.3"
14:13 < nmz787> well, I should upgrade Django then to the latest
14:13 < nmz787> before doing this
14:13 < nmz787> right?
14:14 <@kanzure> no
14:14 <@kanzure> because it might not work on latest django
14:14 < brownies> no... and hopefully you see *why* you shouldn't
14:14 < nmz787> but latest django is prob more secure
14:14 <@kanzure> latest django probably doesn't work with your code
14:14 < nmz787> so upgrade, take care of (possibly) broken stuff
14:14 <@kanzure> and even if it does, you have zero unit tests, so you can't be sure that it works
14:15 < nmz787> add to virtualenv burrito thing
14:15 < nmz787> i didnt unit test this anyway
14:15 <@kanzure> no don't upgrade django
14:15 <@kanzure> whateveryoudo don't do that.
14:15 < nmz787> ok
14:16  * brownies facepalms
14:16 < brownies> newer version != better
14:18 < nmz787> You asked me to pull without telling me which branch you
14:18 < nmz787> want to merge with, and 'branch.master.merge' in
14:18 < nmz787> your configuration file does not tell me, either. Please
14:18 < nmz787> specify which branch you want to use on the command line and
14:18 < nmz787> try again (e.g. 'git pull <repository> <refspec>').
14:18 < nmz787> See git-pull(1) for details.
14:18 < nmz787> so git pull didnt work
14:18 < brownies> eh? what did you run?
14:18 < nmz787> git pull
14:18 < brownies> why did you git pull?
14:18 <@kanzure> i committed things and pushed to the server
14:19 <@kanzure> and i think nmz787 also committed things
14:19 < nmz787> to prepare to commit and push req.ytxt
14:19 <@kanzure> anyway, i think a merge is probably okay
14:19 < nmz787> wait, no
14:19 <@kanzure> git pull origin master
14:19 < nmz787> why should it merge?
14:19 <@kanzure> because there are two different HEADs right now
14:19 < nmz787> why?
14:19 <@kanzure> there's mine (on the server) and yours
14:19 < nmz787> how did that happen?
14:19 <@kanzure> i committed in git
14:19 < brownies> just... git pull origin master
14:19 <@kanzure> and then pushed to the server
14:19 < brownies> you guys should learn about branches -_-
14:20 <@kanzure> well, i thought my changes should be on master
14:20 < nmz787> wtf is that?
14:20 < nmz787> why isn't this easier?
14:20 <@kanzure> this is very easy
14:20 <@kanzure> "git pull origin master"
14:20 < nmz787> no its not
14:20 < nmz787> why did we ever get off the same branch or master or head
14:20 < nmz787> etc
14:21 <@kanzure> you are still on master
14:21 < nmz787> it didnt seem to know that
14:21 <@kanzure> type git status and it will tell you that you're on master
14:21 <@kanzure> "git pull" was warning you that there were upstream changes
14:21 <@kanzure> sometimes you don't want an automerge to happen
14:21 <@kanzure> this is not one of those times
14:22 < nmz787> upstream changes??
14:22 < nmz787> you deleted files
14:22 <@kanzure> yeah. and then i pushed my commits to the server ("upstream").
14:22 < nmz787> so why didn't pull work? because I already said commit on req.txt?
14:22 <@kanzure> so, let's imagine the server didn't exist for a moment
14:22 <@kanzure> no
14:22 <@kanzure> pull didn't work because it was warning you that there were changes on the remote git repository
14:22 < nmz787> that's WHY i was pulling
14:23 < nmz787> because I knew there were changed
14:23 < nmz787> changes
14:23 <@kanzure> it was also telling you that to complete that operation you should type "git pull origin master"
14:23 < brownies> git pull didn't work because it wasn't specific enough
14:23 < brownies> never type "git pull" and nothing else
14:23 <@kanzure> well.. i do "git pull" all the time. it's really an alias for two other operations.
14:24 <@kanzure> "git pull" runs "git fetch" and then "git merge"
14:24 <@kanzure> "git fetch" updates your local repo's knowledge of some remote branch, plus pulls in those commits, without touching your branches
14:24 < brownies> once you have multiple remotes and multple branches, it becomes a pretty stupid idea
14:24 < nmz787> emote: skipping bad filename enzymeFilter/media/jszip/jszip/docs/ZIP spec.txt
14:24 <@kanzure> nmz787: that's ikiwiki printing out a statement, you can ignore that
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14:24 <@kanzure> ikiwiki generates a private wiki based on the files, but in this case we don't care
14:25 <@kanzure> and ikiwiki- for some unholy reason- hates filenames with spaces
14:25 < nmz787> ok
14:25 < nmz787> so I added the pip freeze>requirements.txt
14:26 <@kanzure> looking..
14:26 <@kanzure> ok looks good
14:27 <@kanzure> so now i'm running: mkvirtualenv enzyme-filter; workon enzyme-filter; pip install -r requirements.txt
14:27 <@kanzure> Downloading/unpacking BeautifulSoup==3.1.0.1 (from -r requirements.txt (line 1))
14:27 <@kanzure> Could not find a version that satisfies the requirement BeautifulSoup==3.1.0.1 (from -r requirements.txt (line 1)) (from versions: )
14:27 <@kanzure> um, which version of python is this?
14:28 < nmz787> sounded like that should be in req.txt!
14:28 < nmz787> i dunno
14:28 < nmz787> 2.X
14:28 <@kanzure> hmm
14:28 <@kanzure> python --version
14:28 < nmz787> 2.6.6
14:28 < nmz787> i dont think that should matter
14:28 <@kanzure> really? i'm using 2.6.6 too
14:28 <@kanzure> so um, how come it can't get that version of BeautifulSoup?
14:29 <@kanzure> are you even using BeautifulSoup in this project
14:29 < nmz787> just change beautiful soup to ver 3.2.0
14:29 < nmz787> yeah, i was
14:30 <@kanzure> but why does requirements.txt say 3.1.0.1
14:30 <@kanzure> maybe you installed it manually from them?
14:30 <@kanzure> ok anyway, i'm trying 3.2
14:30 < nmz787> because i just told you to change it
14:31 < nmz787> yeah i dont think it will matter
14:31 < nmz787> 3.2 is what my ubuntu has
14:31 < nmz787> so you should be able to dl that
14:31 <@kanzure> btw: i'm not on ubuntu (i'm on debian), which is more evidence of why pip is a good idea for isolating the web app from which system it's running on
14:32 < nmz787> yeah i know you're on deb
14:32 < nmz787> which is weird, because the jbei machine is deb, which is where i did pip freeze
14:33 < nmz787> well i don't think its using beautifulsoup
14:33 < nmz787> i grepped the entire dir, and its only in req.txt
14:33 <@kanzure> Could not find any downloads that satisfy the requirement iotop==0.4 (from -r requirements.txt (line 11))
14:33 < nmz787> dunno what that is
14:33 < nmz787> i only did what you told me!
14:34 < nmz787> any deps will be at the top of views.py
14:35 <@kanzure> still installing things.
14:35 < nmz787> i doubt you really need anything in req.txt
14:36 <@kanzure> biopython isn't listed
14:36 < nmz787> yeah
14:36 <@kanzure> which means that biopython isn't installed on that system
14:36 < nmz787> it is 1.54
14:36 < nmz787> yeah it is
14:36 < nmz787> i just imported it into python
14:36 < nmz787> on that sys
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14:37 <@kanzure> sure.. but pip looks at your installed libraries, and "pip freeze" dumps the full list. so somehow biopython is not installed. anyway, i'm adding it to requirements.txt
14:37 <@kanzure> and 1.54 seems to exist, so it's installing now.
14:38 < brownies> btw... sad news from the monkey front http://www.nytimes.com/2012/08/30/science/low-calorie-diet-doesnt-prolong-life-study-of-monkeys-finds.html?_r=1
14:38 <@kanzure> Could not find any downloads that satisfy the requirement reportbug==4.12.6 (from -r requirements.txt (line 18))
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14:39 <@kanzure> biopython fails to install with: error: option --single-version-externally-managed not recognized
14:40 < nmz787> python-biopython shows up as installed in dpkg
14:40 < nmz787> pip must be broken
14:40 < nmz787> just do apt-get install python-biopython
14:40 < nmz787> i don't think req.txt is helping at all
14:40 < nmz787> no one uses reportbug
14:41 <@kanzure> you had to do "pip freeze" because you didn't have a pip file from before; most people just write their requirements file as they go along
14:41 <@kanzure> so naturally "pip freeze" included a bunch of things that were installed system-wide
14:41 < nmz787> right
14:41 < nmz787> which is what /you/ said to do
14:41 <@kanzure> yep
14:42 < nmz787> i told you before that, django, biopython, and django-celery
14:42 < nmz787> if you have a vanilla debian install, if my shit is broken it deserves to be
14:42 < nmz787> it deserves to be fixed to be compatible with latest
14:42 < nmz787> IMO
14:42  * nmz787 shrugs
14:43 <@kanzure> before fixing things you have to make sure it works with the latest versions
14:43 <@kanzure> i mean, with the versions that you previously had working
14:43 <@kanzure> my debian is far from vanilla- it's customized like crazy, so trusting it is a terrible idea, and the project isn't far enough along to justify a custom vm
14:43 <@kanzure> jrayhawk would suggest a chroot but, again, that would be a few gigs for this :P
14:44 < brownies> pip is not exactly a stellar piece of software
14:44 <@kanzure> no
14:45  * kanzure is still installing things
14:45 < nmz787> geex
14:45 < nmz787> what are you installing?
14:46 <@kanzure> python-dev, for numpy
14:46 <@kanzure> because numpy has to compile things when it installs via an egg
14:46 < nmz787> why don't you just apt-get all that?
14:46 < chris_99> does anyone know about biotic interactions with yeast cells?
14:46 <@kanzure> nmz787: i already have numpy installed, but not in my virtualenv
14:46 < nmz787> chris_99: i am about to have a biotic reaction with some yeast
14:46 < nmz787> when i drink this beetr
14:46 < nmz787> beer
14:47 < chris_99> hehe
14:47 < nmz787> kanzure: and why doesnt that pass through?
14:47 <@kanzure> because that's not how virtualenvs work
14:47 <@kanzure> virtualenvs separate your code from my system installation
14:51 < nmz787> right, but.... umm
14:51 < nmz787> don't you already have numpy?
14:51 <@kanzure> i do have numpy. i don't have numpy in enzyme-filter's virtualenv.
14:52 <@kanzure> i think i have at least six versions of numpy on my system haha
14:52 <@kanzure> okay, so i've pushed a branch (since you seem to hate when i put things into master..)
14:52 <@kanzure> git fetch origin requirements
14:52 <@kanzure> git checkout origin/requirements
14:52 <@kanzure> then "git log" to see what i did
14:53 <@kanzure> to get back to master you would type "git checkout master" or "git branch -a" to see a list.
14:53 <@kanzure> oh oops i meant "git checkout remotes/origin/requirements"
14:53 < nmz787> what?
14:53 < nmz787> no, i hate branches!
14:53 < nmz787> :D
14:54 < nmz787> ugh
14:55 <@kanzure> so anyway, i think this should be in master, so you can pull master now with my changes
14:55 < brownies> this is kinda funny
14:55 <@kanzure> brownies: ?
14:55 < brownies> largely because i don't have to suffer through it, and i can just watch the action =P
14:56 <@kanzure> well, now the app can presumably work wherever, including on my system
14:56 <@kanzure> nmz787: so you wanted help with something in particular on this right? or just getting it installable?
14:56 < nmz787> hmm, ok
14:56 < nmz787> well its installed and running now, so the former
14:57 < nmz787> enzymeFilter/views.py is where 95% of stuff happens
14:57 <@kanzure> (enzyme-filter)kanzure@pikachu:~/local/enzyme-filter$ python manage.py runserver 0.0.0.0:4030
14:57 < nmz787> the rest is HTML templates and javascript and CSS crap
14:57 <@kanzure> Error: No module named djangoApps.enzymeFilter
14:57 <@kanzure> the heck is djangoApps ??
14:57 < nmz787> oh, the folder that is now enzyme-filter
14:58 <@kanzure> waait why is stuff like blastGene() in views.py
14:58 < nmz787> i like single file programs
14:59 <@kanzure> ok this is why it's slow
14:59 < nmz787> y?
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14:59 <@kanzure> BLAST should not be in your views file
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14:59 < nmz787> huh?
14:59 <@kanzure> it should be a separate task that the web app spawns
14:59 < nmz787> why not
14:59 <@kanzure> or it should be in your controller
14:59 <@kanzure> because views are supposed to be about rendering silly little templates
14:59 < nmz787> MVC blah blah, tl;dr that class
14:59 <@kanzure> oh god.
14:59 < nmz787> :D
14:59 <@kanzure> i give up
15:00 < nmz787> well that just calls BLAST anyway
15:00 < nmz787> and only if you ask it to
15:00 < nmz787> its not what is slow
15:00 <@kanzure> yes it is.. BLAST is blocking
15:00 < nmz787> no
15:00 <@kanzure> so that means your http request waits until it is done
15:00 < nmz787> BLAST doesnt get called
15:01 < nmz787> i'm pretty sure that is forked by biopython to the C version of NCBI tools
15:01 < nmz787> but even when I used that, it didn't make things slow
15:02 < nmz787> i could never figure out how to get celery and the rabbitmq server setup as daemons either
15:02 < nmz787> which kinda makes me not like celery
15:02 < nmz787> but i could just be dumb
15:03 <@kanzure> i think on ubuntu you just type "start celeryd" and make sure it's in your /etc/init/ folder
15:03 <@kanzure> something like that
15:04 < nmz787> so the stuff i need help with is the process*** at the bottom
15:04 < nmz787> they aren't using the ORM efficiently i think
15:04 <@kanzure> processFAA?
15:04 < nmz787> or rather, I shouldn't be using the ORM, because what I think I really want is raw SQL bulk inserts
15:05 < nmz787> FAA, FNA, and XLS
15:05 <@kanzure> first thing i suggest is moving the import statements out of the function..
15:05 <@kanzure> so you're importing data from these files?
15:05 < nmz787> well that's not the problem
15:05 < nmz787> yes
15:07 < nmz787> upload receives the files, then when all 3 are present they get processed
15:07 < brownies> o.O
15:07 <@kanzure> why are you uploading files? why not just run a script on files on the server
15:08 < nmz787> first there are some .py files in the root dir of the project that need run, to set up all the different ontology links (i.e. how to map one to the other)
15:08 < nmz787> because JGI didnt hire me
15:08 < nmz787> JBEI did
15:08 < nmz787> and JGI has the server
15:10 <@kanzure> oh they didn't let you on the server?
15:11 < nmz787> well, no, they don't want me messing with pip and virtualenv on their servers
15:13 <@kanzure> they sound lame
15:14 < nmz787> psh
15:14 < nmz787> they sequence DNA, not do synBio
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15:16 <@kanzure> nmz787: so, you think that the sql inserts are slow, or parsing the file?
15:16 <@kanzure> if the file is a few hundred megs, i think you should do a stream parser or something
15:16 <@kanzure> where you load a line at a time (or w/e small fragment makes sense)
15:19 <@kanzure> brownies: btw.. what do you think? http://diyhpl.us/wiki/diybio/faq/books/ try the sambrook one
15:22 < nmz787> the ORM stuff
15:22 <@kanzure> have you profiled it?
15:22 < nmz787> i can read the file and for loop through each line very fast
15:23 <@kanzure> you can add statements to get datetime and then check datetime again and print the difference between statements
15:23 < nmz787> not since last year, i don't remember
15:23 < nmz787> but i am sure its the ORM
15:23 <@kanzure> ok. i see. yeah, so some of the ORM statements might be querying all objects for some reason, or it might be the transaction committing that is sucking up time
15:26 < nmz787> i wrote it like i thought django wanted me to... as soon as I added something to the ORM, I retrieved it from there (even though it may have still been in a local var)
15:27 <@kanzure> oh, no, you don't need to do that
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15:27 < nmz787> basically I have that geneObject
15:28 < nmz787> which is getting built from the file data
15:29 < nmz787> if that geneObject was just some list or something that got built... then the whole thing inserted in one SQL call... i think that would fix things
15:29 < nmz787> rather than geneObject being an ORM object... with everytime I touch it, it calling the db
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15:35 < brownies> kanzure: much improved. i'll pick one up, thanks.
15:39 < nmz787> kanzure: do you have any recommendations on where to start, or things i should do to break this down
15:39 < nmz787> so i can start fixing it, properly
15:40 < nmz787> kanzure: FYI, my mentor, Patrik, originally just wanted scripts to run on his own box
15:40 < nmz787> but also foresaw that others would find utility in it
15:40 < nmz787> so I said 'O I know some Django!!!'
15:41 < nmz787> and got swept into CSS and javascript uploaders
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15:51 < skorket> evening all
15:52 < nmz787> hi
15:55 <@kanzure> nmz787: i suggest starting with unit tests, i guess.
15:56 < nmz787> what does that mean in this case?
15:56 < nmz787> generally i've just been uploading files and watching where it breaks
15:56 <@kanzure> well, this way you can make sure that code still works
15:56 < nmz787> or adding in printlines to things i know are wonky
15:57 <@kanzure> let's say that you have a function that does a multi-step calculation based on input
15:57 <@kanzure> you would write a unit test to see if the function still works with previous inputs and if those inputs still cause it to return the right answer
15:57 <@kanzure> https://docs.djangoproject.com/en/dev/topics/testing/
15:57 <@kanzure> in your case there's a file enzymeFilter/tests.py
15:57 <@kanzure> which is all lonely :(
15:58 <@kanzure> i think you run it with "python manage.py test"
15:59 < nmz787> that file is practically empty
15:59 <@kanzure> yep.. you gotta write tests to confirm that your stuff works / still works with new updates
15:59 <@kanzure> *new changes
16:00 < chris_99> couple of interesting courses starting soon - https://www.coursera.org/category/biology
16:00 <@kanzure> i think this is a good place to start because you can have a re-usable way to determine which parts are breaking
16:00 < nmz787> hmm
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16:08 < brownies> don't get too bogged down into TDD/BDD dogma
16:08 < brownies> just think of it as automating the tedious tasks you're doing right now to test your app
16:09 < nmz787> TDD/BDD?
16:10 < nmz787> well right now i open the webpage, upload a file, and wait for it to break, then fix/screw with... and repeat
16:10 < nmz787> i'll have to read that testing doc
16:11 < nmz787> new zealand is sposed to be pretty sweet
16:11 < nmz787> whoops
16:12 <@kanzure> yeah you shouldn't have to manually do any of that
16:12 <@kanzure> i'd be far too lazy to do that more than uh, once
16:13 < nmz787> oh
16:13 < nmz787> i'm the otherway, too lazy to learn the (right?) way
16:13 < nmz787> its not really too much though, click a few things, wait for breakage
16:14 <@kanzure> you're using "python manage.py runserver" right?
16:14 < nmz787> figuring out how to call a function in django from outside sounds PITA
16:14 < nmz787> yeah
16:15 <@kanzure> you just import your project and then call it
16:16 <@kanzure> https://docs.djangoproject.com/en/dev/topics/testing/#django.test.client.Client.post
16:16 <@kanzure> from myapp.models import Animal, etc.
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16:48 <@kanzure> so what is the "methods in molecular biology" series from springer?
16:48 <@kanzure> is this a journal, or is it more like updated textbook editions?
16:49 <@kanzure> "Methods in Molecular Biology is a book series from publisher Humana Press that presents biomedical and life science research methods and protocols. The book series was introduced by series editor Dr. John Walker [disambiguation needed] in 1983 and provides step-by-step instructions for carrying out experiments in a research lab.[1]"
16:49 <@kanzure> "As of April 2011, 867 volumes had been published in the series. The protocols are also available online at Springer Protocols."
16:50 < nmz787> its mainly protocols i think
16:50 < nmz787> like once a technique gets pretty good
16:50 <@kanzure> there's 126 books in the 2012 series
16:50 <@kanzure> http://www.springerlink.com/content/1064-3745/copyright/2012/
16:51 <@kanzure> 933 volumes
16:51 < nmz787> they compile a ton of original/influential/top-game papers, along with a good review tying it all together in the beginning
16:51 -!- hifrog [~swamp@p5B16D6F4.dip.t-dialin.net] has quit [Quit: Love Everything! Resistance is Futile.]
16:51 <@kanzure> so, "volume 2" of a book from this series will probably contain different protocols?
16:51 < nmz787> did you see that ACS Synthetic Biology comment i made early today?
16:51 < nmz787> they dont make it in paper format
16:51 <@kanzure> huh.
16:52 < nmz787> so i can't really even be too much of a fanboy
16:52 < nmz787> i woulda got the backissues
16:52 < nmz787> :)
16:53 -!- danielcc [62471046@gateway/web/freenode/ip.98.71.16.70] has joined ##hplusroadmap
16:53 <@kanzure> danielcc: hi
16:53 -!- nmz787 [~nathan@ool-45792f2b.dyn.optonline.net] has quit [Quit: Leaving.]
16:53 <@kanzure> wait don't leave
16:53 -!- nmz787 [~Nathan@ool-45792f2b.dyn.optonline.net] has joined ##hplusroadmap
16:53 <@kanzure> ok there you are
16:54 <@kanzure> danielcc: so you were saying you think you can get a 20 um spot size?
16:55 < danielcc> Brian: someone has offered me a 100W lazer for the project, though I tried just scratching borosilicate glass and think I may have gotten into the ballpark of the 20um goal
16:55 < danielcc> I will probably go this weekend and take a peak with an afm
16:56 < nmz787> oh its a 10.6 micron IR?
16:56 < nmz787> CO2?
16:57 < danielcc> I just got off the phone with a sr bioengineer and dear friend and he brought up a point that the glass may be to jagged if mechanically scratched(I guess we will see after the afm pictures are back) but I was curious if anyone knew of a chemical process to smooth things out
16:57 < danielcc> I was thinking something like a sulfuric acid and h2o2 bath
16:57 < danielcc> but I am but a humble EE
16:57 < nmz787> HF
16:58 < nmz787> but its nasty
16:58 < danielcc> I dont want to deal in hf if i dont have too...
16:58 < danielcc> I've seen my fair share of it in the SiC business for a lifetime
16:59 <@kanzure> glass is just an ideal material, but we will probably be prototyping with pdms too
16:59 < danielcc> my main question is does anyone here know of any modifications to the experiment before I go hit up the afm so I am not wasting microscope time?
17:00 <@kanzure> so you just drew a line with a 100W laser?
17:00 <@kanzure> nmz787 has a test image that he used before that tried out a number of patterns
17:00 <@kanzure> some svg file somewhere?
17:01 <@kanzure> nmz787: where is microfluidic-chip-test-1.svg ?
17:02 < danielcc> no I scored the glass with a very finely etched tungsten carbide tip
17:02 <@kanzure> wait, no that wasn't the file
17:04 <@kanzure> http://diyhpl.us/~bryan/papers2/diybio/mccorkle_tomkins-tinch_microchannels.svg
17:04 <@kanzure> but this was for playing with a laser
17:07 < danielcc> I am assuming also the accuracy is decent enough with this bit...
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17:07 < danielcc> sorry for the delay but someone just gave me a ring
17:07 < nmz787> well are you using CO2 laser?
17:08 <@kanzure> no he's using a tungsten carbide tip
17:08 < eudoxia> hey, strangewarp, you unfollowed Dale just before shit matched coordinates with the fan, now he's arguing with Max More
17:08 < nmz787> ok
17:08 < nmz787> oh
17:08 < nmz787> is the afm free?
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17:10 <@kanzure> nmz787: so he's wondering if he should do anything else to the sample before sending it off to afm
17:12 < danielcc> The AFM is in the lab I used to work at
17:13 < danielcc> the guys offered to let me come in and run it for old time sake assuming this project was not for profit
17:13 < danielcc> I however do not want to over extend my welcome, if you know what I mean
17:16 < nmz787> I think glass may crack if not cooled...
17:16 < nmz787> there is that kickstarter
17:16 < nmz787> http://www.kickstarter.com/projects/fsl/affordable-20x12-laser-cutter-engraver-assembled-i
17:16 -!- eudoxia [~eudoxia@r186-54-251-164.dialup.adsl.anteldata.net.uy] has quit [Ping timeout: 252 seconds]
17:17 < nmz787> place an array of TEC peltiers under there
17:17 < nmz787> the floor drops out
17:17 < nmz787> they are USA company
17:17 < nmz787> other products are chinese lasers upgraded with their electronics
17:20 < danielcc> I'm just wanting to think simplicity... A fella from work showed me this: http://www.instructables.com/id/Pocket-laser-engraver/step2/Rip-apart-the-DVD-Roms/
17:20 < nmz787> yeah blu-ray or IR is the only way to go really
17:20 < nmz787> excimer is what you want tho, and they're dam expensive
17:20 < nmz787> DRIE might do it
17:21 < danielcc> apparently the heads should be set to roughly what we need, but I was wanting to shoot kinda high with the borosilicate glass
17:21 < nmz787> http://en.wikipedia.org/wiki/Deep_reactive-ion_etching#Applications
17:21 < nmz787> g2g
17:21 < nmz787> would like to talk again later
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17:25 < danielcc> I feel certain that this deep etching is not going to be achievable in most home labs... though I do have a deep vacuum system laying around if anyone in the SC region wants to help put together a setup
17:25 < danielcc> I have actually used this method for making some microcantilevers
17:31 -!- tashoutang [~tata@pc131090206.ntunhs.edu.tw] has joined ##hplusroadmap
17:32 < tashoutang> morning
17:34 <@kanzure> hi.
17:38 < tashoutang> hi,@K
17:38 <@kanzure> tashoutang: press k then press tab
17:38 < tashoutang> kanzure
17:38 < tashoutang> my msn is michaeltashoutang@hotmail.com
17:38 -!- soylentbomb [~k@d149-67-118-140.col.wideopenwest.com] has quit [Quit: Leaving]
17:38 <@kanzure> my client does not notify me when someone says "K", but it does notify me for "kanzure"
17:39 < tashoutang> oK
17:39 < tashoutang> my skype is tashoutang-essan
17:39 <@kanzure> my contact details are on here: http://heybryan.org/
17:45 < tashoutang> OK
17:45 < tashoutang> :)
17:46 -!- nmz787 [~Nathan@ool-45792f2b.dyn.optonline.net] has joined ##hplusroadmap
17:57 <@kanzure> brownies: https://github.com/soundcloud/large-hadron-migrator
17:57 <@kanzure> "The basic idea is to perform the migration online while the system is live, without locking the table. In contrast to OAK and the facebook tool, we only use a copy table and triggers."
17:58 < brownies> kanzure: interesting! thanks
17:58 <@kanzure> so it looks like it just copies a giant million-row table to a temporary table and slowly migrates things over?
17:59 < brownies> although the fact that they assume the presence of an :id column is... stupid.
17:59 <@kanzure> how does this work in production when some of your users are migrated and others aren't?
17:59 <@kanzure> say your migration takes two hours..
17:59 < brownies> not sure, tbh, what they're doing.
17:59 <@kanzure> i guess you would write your code to check whether or not the migration is completed??
17:59 <@kanzure> e.g. in controller methods
18:00 < brownies> no, that would make it stupid and useless
18:00 < brownies> also, this already makes it mostly useless... "Lhm currently only works with MySQL databases"
18:00 <@kanzure> "TableMigrator does essentially the same thing, but more intelligently. First, we create a new table like the original one, and then apply one or more ALTER TABLE statements to the unused, empty table. Second we copy all rows from the original table into the new one. All this time, reads and writes are going to the original table, so the two tables are not consistent"
18:00 <@kanzure> "Finally, we acquire a write lock on the original table before copying over all new/changed rows, and swapping in the new table."
18:00 <@kanzure> https://github.com/freels/table_migrator (twitter's similar thing)
18:01 <@kanzure> "The solution to find updated or new rows is to use a column like updated_at (if a row is mutable) or created_at (if it is immutable) to determine which rows have been modified since the copy started. These rows are copied over to the new table using REPLACE"
18:01 < brownies> yeah, this all basically the obvious solution.
18:01 -!- danielcc [62471046@gateway/web/freenode/ip.98.71.16.70] has quit [Ping timeout: 245 seconds]
18:02 <@kanzure> "The default method (:multi_pass => true) copies over changed rows in a non-blocking manner multiple times until we can be reasonably sure that the final sweep will take very little time. The last sweep is done within the write lock, and then the tables are swapped. The length of time taken in the write lock is extremely short, hence the claim zero-downtime migration."
18:02 <@kanzure> yep ok
18:02 <@kanzure> i thought it would be something more interesting than that
18:03 < brownies> eh, what else can you do?
18:03 < brownies> i like that... classic untrained-engineer idiocy
18:03 <@kanzure> i don't know, something that would deserve the name 'large hadron' :)
18:03 < brownies> "the downtime is small, so we called it zero."
18:03 <@kanzure> haha
18:03 < brownies> morons.
18:03 <@kanzure> lim downtime_t with a subscript => 0
18:04 <@kanzure> hahah.
18:04 <@kanzure> "This method will not propagate normal DELETESs to the new table if they happen during/after the copy. In order to avoid this, use paranoid deletion, and update the column you are using to find changes appropriately."
18:04 <@kanzure> you should paranoid deletion anyway, but that's amusing
18:04 < brownies> haha
18:05 < brownies> i'm implementing paranoid deletion later today, from scratch
18:05 < brownies> because (surprise!) the author of the gem is an idiot
18:05 <@kanzure> oh, why?
18:05 <@kanzure> oh hm
18:05 <@kanzure> which gem were you using?
18:05 < brownies> if you use paranoid deletion, you can't use :default_scope
18:05 <@kanzure> i've tried a few, but i think i used rails3_acts_as_paranoid most recently
18:05 < brownies> let me take a look
18:05 < brownies> i surveyed the choices a while back, and decided they were all idiots
18:05 <@kanzure> sounds fun
18:06 <@kanzure> you know, out of all the times i've implemented paranoid delete, i don't recall ever making something that would periodically go through and actually delete really really old stuff
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18:07 < delinquentme> afternoon all!
18:07 < brownies> oh, hmmm
18:07 < brownies> kanzure: the README doesn't make mention of this :default_scope issue ...
18:07 < brownies> kanzure: which means, either it's fixed, or the author is an asshole.
18:07 <@kanzure> do a pull request :P
18:08 <@kanzure> with the README updated, not the solution (unless you have that too)
18:09 < brownies> bleh ... and he doesn't seem to manage his pull requests competently
18:09 <@kanzure> that's lame
18:09 <@kanzure> someone should make a script that looks at your gems' repositories on github and rates how likely they are to be idiots
18:09 <@kanzure> "Your rails app is made up of 43% idiocy, congratulations!"
18:10 <@kanzure> this is easy to determine: do they have lots of open issues, pull requests? do they pull their pull requests, or do they re-commit the changes?
18:10 <@kanzure> do they mix tabs and spaces?
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18:21 < brownies> hehe
18:21 < brownies> yeah, that would be useful.
18:21 < brownies> the non-idiots could proudly badge their READMEs
18:21 < brownies> "i'm only 10% idiot, according to idiotrubyists.com!"
18:22 -!- yashgaroth [~f@cpe-66-27-117-179.san.res.rr.com] has joined ##hplusroadmap
18:29 < yashgaroth> kanzure: methods in molecular biology is good, definitely worth the space
18:30 -!- tashoutang [~tata@pc131090206.ntunhs.edu.tw] has quit [Ping timeout: 268 seconds]
18:37 <@kanzure> yashgaroth: ok i'll grab 'em all
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19:06 < nmz787> ahh this is gold: http://www.youtube.com/playlist?list=PLD0444BD542B4D7D9&feature=plcp
19:07 < nmz787> About Walter + Eliza Hall Institute Movies from The Walter and Eliza Hall Institute of Medical Research
19:07 <@kanzure> yashgaroth: some of these books seem to be highly esoteric though
19:08 < yashgaroth> oh, totally
19:08 < foucist> you rails guys should be in my ridiculously awesome #offrails channel
19:08 -!- minimoose [~minimoose@pool-173-75-216-239.phlapa.fios.verizon.net] has quit [Quit: minimoose]
19:08 <@kanzure> "siRNA Techniques for Gene Silencing in Transgenic Wombats - Methods in Molecular Biology - 8th edition"
19:08 < yashgaroth> but when you gotta know about cyclooxygenases, you better hope you have vol. 644 handy
19:10 <@kanzure> cyclowhats?
19:10 <@kanzure> blaargh chrome removed --vertical-tabs https://code.google.com/p/chromium/issues/detail?id=99332#c25
19:10 < yashgaroth> hey man you've got the book now
19:11 <@kanzure> not quite yet
19:11 < nmz787> COX right yashgaroth?
19:11 < yashgaroth> yep, and one day when I'm stuck in limbo I can read up on it
19:11 <@kanzure> didn't you just experience a three month limbo?
19:12 < nmz787> he prob got to vol 643
19:12 <@kanzure> what a slacker
19:12 < nmz787> thats why he is ready for 644
19:12 < yashgaroth> not quite limbo enough to read up on COX
19:12 < nmz787> gene jokes
19:12 < nmz787> oh gosh
19:12 < yashgaroth> remembering how shitty work is, is giving me more motivation than unemployment ever did
19:12 < nmz787> genetic slurs
19:12 < yashgaroth> truncated cox
19:13 < nmz787> "heard your COX wasn't doing too well, nerd!"
19:13 < yashgaroth> hey girl I heard you're an expert in cox assays
19:13 < nmz787> lol
19:13 < nmz787> that's a good one
19:15 < brownies> chrome used to have vertical tabs?
19:15 < brownies> wild
19:16 -!- jk4930 is now known as transgenicWombat
19:19 < nmz787> "Disclaimer - Due to Chrome limitations, extensions cannot restore history from closed tabs"
19:20 <@kanzure> dafuq
19:20 <@kanzure> brownies: my religion is carefully constructed around the existence of https://addons.mozilla.org/en-US/firefox/addon/tree-style-tab/
19:22 <@kanzure> although opera does that better
19:23 < brownies> heh yea i used to use that pretty heavily
19:23 < brownies> nowadays i just stash everything in pinboard
19:24 < nmz787> can you reduce the visibility of firefox to that of chrome?
19:24 < nmz787> kanzure: does it retain your tab history?
19:25 <@kanzure> firefox has other tab history things
19:26 < nmz787> so it doesnt do it
19:26 < nmz787> i mean clicking back
19:26 < nmz787> after restoring a tab
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19:32 < nmz787> so toomanytabs doesn't actually get rid of the tabs visually?
19:32 < nmz787> nor does tree-style-tab?
19:36 < nmz787> this looks like what i want https://chrome.google.com/webstore/detail/bbcnbpafconjjigibnhbfmmgdbbkcjfi
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19:42 < nmz787> oh, bad reviews
19:43 < nmz787> i could just have like 10 different chromium installs
19:46 < foucist> chrome is fucking shit.. i really need to stop using it as my main browser
19:46 < brownies> what alternative is there, though?
19:47 < foucist> i use Sessions Buddy extension in chrome
19:47 < foucist> brownies: firefox or safari
19:47 < brownies> eh, i try out safari every now and then, but it feels slower
19:47 < brownies> and Firefox still leaks memory everywhere
19:48 < foucist> have you tried ff this summer?
19:48 < foucist> apparently they were fixing that big time
19:48 < foucist> i haven't tried it yet
19:48 < foucist> i definitely need a more memory efficient browser than chrome
19:48 < foucist> or i need to know which version of chrome is the most memory efficient and fix it at that
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19:51 < brownies> i heard something about that, but i haven't tried FF in a while
19:51 < foucist> brownies: i have my swap disabled for speed reasons, but if i go over 4gigs ram it crashes my computer..  chrome is painful since it tends to use up all my memory
19:51 < foucist> of course, i tend to have loads of tabs open
19:53 < brownies> =/
19:53 < brownies> yeah, i got in the habit of closing tabs, and instead pinboarding things that i wanted to read later
19:54 < nmz787> how do i add a sub comment to stackoverflow?
19:54 < nmz787> http://stackoverflow.com/questions/9981267/google-chrome-back-and-forward-history?answertab=oldest#tab-top
19:55 < foucist> brownies: i don't actually read anything later even if i bookmark or use readitlater/etc bookmarklets heh
19:56 < nmz787> yeah that's why i want to save my tabs, not bookmark them
19:56 < nmz787> ;)
19:56 < nmz787> the difference is, uh, retaining tab history
19:56 -!- ivan`_ is now known as ivan`
19:56 < nmz787> and the concept of loading/unloading... if i click a bookmark, i dont want to have to click around to delete it too
19:58 < foucist> i don't like bookmarks at all, i want a more of seamless logging interfce..  log all the sites and pages i went to, then when i "google" something, search my local cache first
19:58 < foucist> based off my history (not just links but actual content perhaps)
19:58 < nmz787> hmm, that would annoy me i.e slow me finding new stuff i think
19:59 < nmz787> maybe not
19:59 < brownies> foucist: yeah, neither do i, but it's a nice lie to tell myself so i don't drown in tabs
19:59 < brownies> foucist: try out historious ... might be what you're looking for
20:00 < foucist> cool
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20:40 < brownies> kanzure: looks like DelayedJob might be another one that's full of random unpredictable fail =/
20:43 <@kanzure> i don't think i'm smart enough to understand noscript
20:43 <@kanzure> how do i make it inform me of things (like xss attacks it spots) without disabling javascript everywherE?
20:43 <@kanzure> *everywhere?
20:49 < delinquentme> i just dont understand http://www.gizmag.com/walking-paper-robot-elastic-bands/23877/
20:49 < delinquentme> dude (painstakingly) makes a robot entirely out of paper and rubberbands
20:50 < nmz787> kanzure said not to follow your links
20:50 < nmz787> but i will this time
20:53 < skorket> nmz787, hows the laser cutter coming?
20:54 <@kanzure> 'gizmag' sounds like spam to me
20:55 < nmz787> gonna order a diode and power supply in the next few days
20:55 < tashoutang> http://www.panoramas.dk/mars/greeley-haven.html
20:56 < tashoutang> the view on Mars
20:56 < nmz787> looking into modelling the whole system as well, using goptical or something like it/better
20:56 < skorket> you have the steppers, drivers and hardware?
20:56 < nmz787> maybe this http://code.google.com/p/pyoptools/
20:56 < tashoutang> they can put the blue green algae there....
20:58 <@kanzure> firebug feels a little forced in comparison to chrome inspector
21:00 < nmz787> skorket: no not yet, going to wait til i get the laser and optics sorted out, I still need to try and find some CAD models for fenn, if I can find them, or CAD drawings of a few of the cutter components... so his model can be complete
21:00 < skorket> why do you need to simulate the optics?
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21:00 < nmz787> just want to
21:01 < nmz787> it will be good to learn, as I will prob need to do something similar when I try to do single-molecule fluorescence detection
21:01 < skorket> ah, I see, yeah, cool
21:01 < nmz787> i feel its stuff like that which separates good engineering/design from just screwing around
21:02 < nmz787> I trust things with nice spec sheets more than claims of 'it works great'.... but yeah mainly because I also am totally new to optics
21:02 < skorket> What diode are you getting?
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21:04 < nmz787> like most diagrams show rays eminating from a focus, but what if my rays eminate from somewhere else... then I need the simulator
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21:05 < skorket> No, I feel the same ways about some tools.  Even if my project is simple, I like getting my feet wet with the EDA packages that are available
21:22 <@kanzure> hmm http://code.google.com/p/pyoptools/
21:23 <@kanzure> so it's just a raytracer?
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21:55 <@kanzure> matplotlib guy died http://mail.scipy.org/pipermail/ipython-dev/2012-August/010135.html
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22:24 <@kanzure> oh geeze "那些自称“生物黑客”，并把该领域称之为“DIY生物学(DIYBio)”的狂热人士，开始进行他们自己的“合成生物学”试验项目"
22:25 <@kanzure> hahah genspace translates to "绅士空间" apparently? "gentleman space"
22:25 <@kanzure> "绅士" is gentleman i think
22:28 <@kanzure> "亿万富豪企业家文特尔" well that's one way to describe craig venter.. but i think this is wrong
22:30 < tashoutang> kanzure where did you see that?
22:31 < tashoutang> so they are very well informed!!!
22:35 <@kanzure> venter is not a billionaire
22:35 <@kanzure> to my knowledge.
22:35 <@kanzure> i think his networth is south of $500M
23:02 <@kanzure> 2 hour python/requests scraping presentation from pycon 2012 http://youtube.com/watch?v=52wxGESwQSA
23:02 <@kanzure> but he's really super slow
23:04 <@kanzure> "Interestingly: I'm actually a guy on the team that sends back that different HTML from Google. ;) See: 55:19"
23:05 <@kanzure> oh nevermind, that's just for user agents
23:12 <@kanzure> http://www.learningjquery.com/2009/04/better-stronger-safer-jquerify-bookmarklet/
23:17 <@kanzure> so that video in the last 40 minutes shows using twisted/gevent/promises to process scraped content. i don't see why he didn't just stick with celery?
23:18 <@kanzure> oh neat, python-requests supports async http requests
--- Log closed Thu Aug 30 00:00:11 2012