| --- Log opened Wed Aug 29 00:00:10 2012 | ||
| foucist | delinquentme: 11:19 < nmz787> delinquentme: I would use SCP | 00:09 |
|---|---|---|
| delinquentme | that was the last activity?? | 00:13 |
| foucist | delinquentme: right after you asked how to send a 2gb file | 00:13 |
| delinquentme | Ohhh | 00:14 |
| 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 | 00:16 |
| foucist | funny how ftp clients already solved the problem a long time ago | 00:17 |
| foucist | but i havne't used ftp in YEARS | 00:17 |
| foucist | well, probably not since i used windows | 00:18 |
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| delinquentme | NIGHT! | 01:07 |
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| archels | http://www.urbandictionary.com/define.php?term=Hacker%20Spaces | 01:54 |
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| Utopiah | looks accurate | 02:00 |
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| 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 | 04:49 | |
| 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 | 05:04 |
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| 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? | 05:46 |
| chris_99 | don't you need read permissions | 05:48 |
| nmz787 | derr | 05:50 |
| nmz787 | yes | 05:50 |
| nmz787 | thx | 05:50 |
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| OldCoder | minimoose, Good nick | 06:33 |
| minimoose | tx, OldCoder | 06:41 |
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| nmz787 | anyone here know SVN? | 08:19 |
| bkero | for a certain definition of know | 08:29 |
| bkero | nmz787: chmod g+x djangoApps | 08:30 |
| bkero | s-s-s-sticky bit | 08:30 |
| nmz787 | bkero: that was already done | 08:30 |
| nmz787 | svn status says the dir is locked tho | 08:31 |
| * bkero doesn't deal with svn locks | 08:31 | |
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| @kanzure | death to svn | 09:08 |
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| @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)." | 09:25 |
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| nmz787 | soo ACS Synthetic Biology is now offered in print | 10:18 |
| nmz787 | that's stupid | 10:18 |
| 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 | 10:19 |
| nmz787 | so 25 bucks a year for some ACS journals isn't too bad | 10:20 |
| nmz787 | but i really wanted print | 10:20 |
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| @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 | 10:25 |
| @kanzure | the at-home version exhausts your resources of food and drink | 10:28 |
| nmz787 | any opinions on http://phabricator.org | 10:29 |
| @kanzure | i'd look at redmine first probably | 10:29 |
| @kanzure | i'm not too hawt on running php | 10:30 |
| @kanzure | a lot of people just use github or unfuddle or something | 10:30 |
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| chris_99 | if i'm going to get a book on microbiology | 10:44 |
| chris_99 | what would you guys recommend | 10:44 |
| chris_99 | *molecular biology | 10:45 |
| nmz787 | why doesnt this work find / -name svn2|grep -v 'denied' | 10:48 |
| nmz787 | mol bio of the gene | 10:49 |
| nmz787 | mol bio of the cell is supposed to be good too | 10:49 |
| @kanzure | nmz787: do you mean "find ./" | 10:50 |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Ping timeout: 268 seconds] | 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. | 10:51 |
| 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 | 10:52 |
| 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 | 10:53 |
| @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 | 10:54 |
| 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 | 10:55 |
| nmz787 | with a space | 10:56 |
| nmz787 | not dash | 10:56 |
| nmz787 | is streaking really microbiology though? | 10:57 |
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| jrayhawk | '2|' is not a valid stream redirection | 11:00 |
| 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? | 11:01 |
| 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 | 11:02 |
| @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" | 11:03 |
| 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 | 11:04 |
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| @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) | 11:10 |
| jrayhawk | You may need to relogin in order to get the new groups | 11:12 |
| @kanzure | doh | 11:14 |
| @kanzure | nmz787: the only commit message in there is "Convert svn:ignore properties to .gitignore." | 11:15 |
| 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 | 11:16 |
| 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 | 11:17 |
| jrayhawk | 'enzmye' | 11:18 |
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| @kanzure | oh fooey | 11:26 |
| @kanzure | nmz787: ok i made a terrible typo | 11:26 |
| nmz787 | oh | 11:26 |
| @kanzure | nmz787: ok now "git push -f" will work | 11:27 |
| @kanzure | what did you do to convert it? | 11:27 |
| chris_99 | it's £185 for 100ug of GFP, isn't that rather expensive?! | 11:29 |
| 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 | 11:31 |
| 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 | 11:32 |
| 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] | 11:33 |
| 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 | 11:34 |
| 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 | 11:35 |
| @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? | 11:36 |
| jrayhawk | i suspect it's the wrong path or permissions are still wrong or something and git-svn doesn't give sufficient error messages | 11:37 |
| 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 | 11:38 |
| nmz787 | molecular cloning a lab manual... by sambrook and russel | 11:39 |
| nmz787 | i guess maniatis was on older editions | 11:39 |
| 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" | 11:40 |
| @kanzure | right | 11:41 |
| @kanzure | ok thanks | 11:41 |
| nmz787 | yeah i think the git svn is silently failing | 11:44 |
| @kanzure | does "svn log" work? | 11:44 |
| nmz787 | ok looks like removing the -A authors-transform.txt --stdlayout is working | 11:46 |
| nmz787 | i actually see files being downloaded | 11:46 |
| @kanzure | did you make authors-transform.txt? | 11:47 |
| @kanzure | or did you neglect that part :P | 11:47 |
| nmz787 | yes | 11:48 |
| nmz787 | i made it | 11:48 |
| @kanzure | hrrm | 11:48 |
| @kanzure | well ok | 11:48 |
| 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>" | 11:49 |
| nmz787 | well i'm not using it at all now | 11:53 |
| 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 | 12:00 |
| @kanzure | that looks like a valid SHA1 to me.. | 12:03 |
| nmz787 | rf -Rfing and trying again | 12:07 |
| gnusha | diyhpluswiki.git: 641e37c links to actual books | 12:09 |
| 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 | 12:10 |
| 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 | 12:11 |
| @kanzure | as far as i can tell there's no actually-useful free molecular biology book out there on the interwebs | 12:12 |
| nmz787 | the ones i like are free outside US copyright law | 12:13 |
| nmz787 | you should add mol bio of the gene | 12:14 |
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| @kanzure | ok grabbing | 12:18 |
| gnusha | diyhpluswiki.git: 095952d add a link to Molecular Biology of the Gene | 12:23 |
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| @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 | 12:31 |
| nmz787 | so now | 12:32 |
| nmz787 | shit, just boiled a pot of water dry | 12:33 |
| nmz787 | ok kanzure the repo should be all pushed | 12:36 |
| nmz787 | hmm, beer or coffee | 12:38 |
| @kanzure | sambrooks is pretty awesome, why haven't i read this yet? | 12:40 |
| nmz787 | dunno | 12:45 |
| 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 | 12:46 |
| nmz787 | i doubt most other students used it much | 12:47 |
| nmz787 | kanzure: did you ever make an equipment auction app? | 12:48 |
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| @kanzure | nope not yet | 12:48 |
| nmz787 | i wonder if there is cheap stuff within an hour of NYC | 12:48 |
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| @kanzure | i want to find a book like sambrooks except for motion control automation things | 12:50 |
| @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 | 12:51 |
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| @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 | 13:15 |
| @kanzure | http://pastebin.com/raw.php?i=AdJg9gwv | 13:16 |
| nmz787 | no | 13:16 |
| nmz787 | can you complain? | 13:17 |
| nmz787 | submit bug? | 13:17 |
| @kanzure | not sure where to submit this bug | 13:18 |
| @kanzure | i guess i should complain to aran dunkley | 13:19 |
| @kanzure | "Multibyte characters not working" | 13:20 |
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| nmz787 | kanzure: when do you have time to look at that enzymeFilter code? | 13:39 |
| nmz787 | with me | 13:39 |
| @kanzure | i can look at it in a few minutes (it's downloading but i'm on a slow connection) | 13:41 |
| nmz787 | cool | 13:42 |
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| @kanzure | nmz787: so what are all these multi-megabyte files in the main directory? | 13:47 |
| @kanzure | like CAZyall.faa | 13:47 |
| @kanzure | whog | 13:48 |
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| @kanzure | KEGG_KO_list | 13:48 |
| @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 | 13:49 |
| 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 | 13:50 |
| 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 | 13:51 |
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| nmz787 | brb, lemme switch to linux pidgin in VM | 13:52 |
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| @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 | 13:57 |
| @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 | 13:58 |
| 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 | 13:59 |
| @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. | 14:00 |
| 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? | 14:01 |
| @kanzure | because then you don't need me in the future | 14:02 |
| @kanzure | brownies: help me :( | 14:02 |
| brownies | kanzure: ? | 14:02 |
| 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 | 14:03 |
| 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 | 14:04 |
| @kanzure | you don't want my system-wide version of biopython 'cause that could be anything | 14:05 |
| nmz787 | do you use debian? | 14:06 |
| 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 | 14:07 |
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| 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" | 14:07 |
| 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 | 14:08 |
| 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. | 14:09 |
| @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 | 14:10 |
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| @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. | 14:11 |
| @kanzure | ah, with pip freeze | grep django | 14:12 |
| @kanzure | well, actually, it's Django | 14:12 |
| @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? | 14:13 |
| @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 | 14:14 |
| 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 | 14:15 |
| * brownies facepalms | 14:16 | |
| brownies | newer version != better | 14:16 |
| 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 | 14:18 |
| @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 -_- | 14:19 |
| @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 | 14:20 |
| @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 | 14:21 |
| 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 | 14:22 |
| 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. | 14:23 |
| @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 | 14:24 |
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| @kanzure | ikiwiki generates a private wiki based on the files, but in this case we don't care | 14:24 |
| @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 | 14:25 |
| @kanzure | looking.. | 14:26 |
| @kanzure | ok looks good | 14:26 |
| @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? | 14:27 |
| 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? | 14:28 |
| @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 | 14:29 |
| @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 | 14:30 |
| 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 | 14:31 |
| 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 | 14:32 |
| 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! | 14:33 |
| nmz787 | any deps will be at the top of views.py | 14:34 |
| @kanzure | still installing things. | 14:35 |
| nmz787 | i doubt you really need anything in req.txt | 14:35 |
| @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 | 14:36 |
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| @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. | 14:37 |
| 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)) | 14:38 |
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| @kanzure | biopython fails to install with: error: option --single-version-externally-managed not recognized | 14:39 |
| 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 | 14:40 |
| @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 | 14:41 |
| 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 | 14:42 | |
| @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 | 14:43 |
| brownies | pip is not exactly a stellar piece of software | 14:44 |
| @kanzure | no | 14:44 |
| * kanzure is still installing things | 14:45 | |
| nmz787 | geex | 14:45 |
| nmz787 | what are you installing? | 14:45 |
| @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 | 14:46 |
| 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 | 14:47 |
| 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. | 14:51 |
| @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 | 14:52 |
| @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 | 14:53 |
| nmz787 | ugh | 14:54 |
| @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 | 14:55 |
| @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 | 14:56 |
| 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 | 14:57 |
| @kanzure | waait why is stuff like blastGene() in views.py | 14:58 |
| nmz787 | i like single file programs | 14:58 |
| @kanzure | ok this is why it's slow | 14:59 |
| nmz787 | y? | 14:59 |
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| @kanzure | BLAST should not be in your views file | 14:59 |
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| 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 | 14:59 |
| 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 | 15:00 |
| 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 | 15:01 |
| 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 | 15:02 |
| @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 | 15:03 |
| 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 | 15:04 |
| 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 | 15:05 |
| 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 | 15:07 |
| 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 | 15:08 |
| @kanzure | oh they didn't let you on the server? | 15:10 |
| nmz787 | well, no, they don't want me messing with pip and virtualenv on their servers | 15:11 |
| @kanzure | they sound lame | 15:13 |
| nmz787 | psh | 15:14 |
| nmz787 | they sequence DNA, not do synBio | 15:14 |
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| @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) | 15:16 |
| @kanzure | brownies: btw.. what do you think? http://diyhpl.us/wiki/diybio/faq/books/ try the sambrook one | 15:19 |
| 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 | 15:22 |
| @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 | 15:23 |
| 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) | 15:26 |
| @kanzure | oh, no, you don't need to do that | 15:27 |
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| nmz787 | basically I have that geneObject | 15:27 |
| nmz787 | which is getting built from the file data | 15:28 |
| 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 | 15:29 |
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| brownies | kanzure: much improved. i'll pick one up, thanks. | 15:35 |
| 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 | 15:39 |
| 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!!!' | 15:40 |
| nmz787 | and got swept into CSS and javascript uploaders | 15:41 |
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| skorket | evening all | 15:51 |
| nmz787 | hi | 15:52 |
| @kanzure | nmz787: i suggest starting with unit tests, i guess. | 15:55 |
| 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 | 15:56 |
| @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 :( | 15:57 |
| @kanzure | i think you run it with "python manage.py test" | 15:58 |
| 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 | 15:59 |
| 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 | 16:00 |
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| 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 | 16:08 |
| nmz787 | TDD/BDD? | 16:09 |
| 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 | 16:10 |
| nmz787 | new zealand is sposed to be pretty sweet | 16:11 |
| nmz787 | whoops | 16:11 |
| @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 | 16:12 |
| 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 | 16:13 |
| @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 | 16:14 |
| @kanzure | you just import your project and then call it | 16:15 |
| @kanzure | https://docs.djangoproject.com/en/dev/topics/testing/#django.test.client.Client.post | 16:16 |
| @kanzure | from myapp.models import Animal, etc. | 16:16 |
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| @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? | 16:48 |
| @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." | 16:49 |
| 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/ | 16:50 |
| @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 |
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| @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. | 16:51 |
| nmz787 | so i can't really even be too much of a fanboy | 16:52 |
| nmz787 | i woulda got the backissues | 16:52 |
| nmz787 | :) | 16:52 |
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| @kanzure | danielcc: hi | 16:53 |
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| @kanzure | wait don't leave | 16:53 |
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| @kanzure | ok there you are | 16:53 |
| @kanzure | danielcc: so you were saying you think you can get a 20 um spot size? | 16:54 |
| 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 | 16:55 |
| nmz787 | oh its a 10.6 micron IR? | 16:56 |
| nmz787 | CO2? | 16:56 |
| 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 | 16:57 |
| 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 | 16:58 |
| @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? | 16:59 |
| @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? | 17:00 |
| @kanzure | nmz787: where is microfluidic-chip-test-1.svg ? | 17:01 |
| danielcc | no I scored the glass with a very finely etched tungsten carbide tip | 17:02 |
| @kanzure | wait, no that wasn't the file | 17:02 |
| @kanzure | http://diyhpl.us/~bryan/papers2/diybio/mccorkle_tomkins-tinch_microchannels.svg | 17:04 |
| @kanzure | but this was for playing with a laser | 17:04 |
| danielcc | I am assuming also the accuracy is decent enough with this bit... | 17:07 |
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| danielcc | sorry for the delay but someone just gave me a ring | 17:07 |
| nmz787 | well are you using CO2 laser? | 17:07 |
| @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? | 17:08 |
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| @kanzure | nmz787: so he's wondering if he should do anything else to the sample before sending it off to afm | 17:10 |
| danielcc | The AFM is in the lab I used to work at | 17:12 |
| 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 | 17:13 |
| 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 |
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| 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 | 17:17 |
| 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 | 17:20 |
| 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 | 17:21 |
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| 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 | 17:25 |
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| tashoutang | morning | 17:32 |
| @kanzure | hi. | 17:34 |
| 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 |
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| @kanzure | my client does not notify me when someone says "K", but it does notify me for "kanzure" | 17:38 |
| tashoutang | oK | 17:39 |
| tashoutang | my skype is tashoutang-essan | 17:39 |
| @kanzure | my contact details are on here: http://heybryan.org/ | 17:39 |
| tashoutang | OK | 17:45 |
| tashoutang | :) | 17:45 |
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| @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." | 17:57 |
| 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? | 17:58 |
| 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 | 17:59 |
| 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) | 18:00 |
| @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 |
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| @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 | 18:02 |
| 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 | 18:03 |
| @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 | 18:04 |
| 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 | 18:05 |
| @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 | 18:06 |
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| 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 | 18:07 |
| @kanzure | with the README updated, not the solution (unless you have that too) | 18:08 |
| 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!" | 18:09 |
| @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? | 18:10 |
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| 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!" | 18:21 |
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| yashgaroth | kanzure: methods in molecular biology is good, definitely worth the space | 18:29 |
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| @kanzure | yashgaroth: ok i'll grab 'em all | 18:37 |
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| nmz787 | ahh this is gold: http://www.youtube.com/playlist?list=PLD0444BD542B4D7D9&feature=plcp | 19:06 |
| 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 | 19:07 |
| yashgaroth | oh, totally | 19:08 |
| foucist | you rails guys should be in my ridiculously awesome #offrails channel | 19:08 |
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| @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 | 19:08 |
| @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 | 19:10 |
| @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? | 19:11 |
| 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 | 19:12 |
| 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 | 19:13 |
| brownies | chrome used to have vertical tabs? | 19:15 |
| brownies | wild | 19:15 |
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| nmz787 | "Disclaimer - Due to Chrome limitations, extensions cannot restore history from closed tabs" | 19:19 |
| @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/ | 19:20 |
| @kanzure | although opera does that better | 19:22 |
| brownies | heh yea i used to use that pretty heavily | 19:23 |
| brownies | nowadays i just stash everything in pinboard | 19:23 |
| nmz787 | can you reduce the visibility of firefox to that of chrome? | 19:24 |
| nmz787 | kanzure: does it retain your tab history? | 19:24 |
| @kanzure | firefox has other tab history things | 19:25 |
| nmz787 | so it doesnt do it | 19:26 |
| nmz787 | i mean clicking back | 19:26 |
| nmz787 | after restoring a tab | 19:26 |
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| nmz787 | so toomanytabs doesn't actually get rid of the tabs visually? | 19:32 |
| nmz787 | nor does tree-style-tab? | 19:32 |
| nmz787 | this looks like what i want https://chrome.google.com/webstore/detail/bbcnbpafconjjigibnhbfmmgdbbkcjfi | 19:36 |
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| nmz787 | oh, bad reviews | 19:42 |
| nmz787 | i could just have like 10 different chromium installs | 19:43 |
| foucist | chrome is fucking shit.. i really need to stop using it as my main browser | 19:46 |
| brownies | what alternative is there, though? | 19:46 |
| 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 | 19:47 |
| 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 | 19:48 |
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| 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 | 19:51 |
| brownies | =/ | 19:53 |
| brownies | yeah, i got in the habit of closing tabs, and instead pinboarding things that i wanted to read later | 19:53 |
| 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 | 19:54 |
| foucist | brownies: i don't actually read anything later even if i bookmark or use readitlater/etc bookmarklets heh | 19:55 |
| 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 |
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| nmz787 | and the concept of loading/unloading... if i click a bookmark, i dont want to have to click around to delete it too | 19:56 |
| 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 | 19:58 |
| 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 | 19:59 |
| foucist | cool | 20:00 |
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| brownies | kanzure: looks like DelayedJob might be another one that's full of random unpredictable fail =/ | 20:40 |
| @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? | 20:43 |
| 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 | 20:49 |
| nmz787 | kanzure said not to follow your links | 20:50 |
| nmz787 | but i will this time | 20:50 |
| skorket | nmz787, hows the laser cutter coming? | 20:53 |
| @kanzure | 'gizmag' sounds like spam to me | 20:54 |
| nmz787 | gonna order a diode and power supply in the next few days | 20:55 |
| tashoutang | http://www.panoramas.dk/mars/greeley-haven.html | 20:55 |
| 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.... | 20:56 |
| @kanzure | firebug feels a little forced in comparison to chrome inspector | 20:58 |
| 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? | 21:00 |
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| nmz787 | just want to | 21:00 |
| 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 | 21:01 |
| 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? | 21:02 |
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| nmz787 | like most diagrams show rays eminating from a focus, but what if my rays eminate from somewhere else... then I need the simulator | 21:04 |
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| 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 | 21:05 |
| @kanzure | hmm http://code.google.com/p/pyoptools/ | 21:22 |
| @kanzure | so it's just a raytracer? | 21:23 |
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| @kanzure | matplotlib guy died http://mail.scipy.org/pipermail/ipython-dev/2012-August/010135.html | 21:55 |
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| @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" | 22:24 |
| @kanzure | hahah genspace translates to "绅士空间" apparently? "gentleman space" | 22:25 |
| @kanzure | "绅士" is gentleman i think | 22:25 |
| @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 | 22:28 |
| tashoutang | kanzure where did you see that? | 22:30 |
| tashoutang | so they are very well informed!!! | 22:31 |
| @kanzure | venter is not a billionaire | 22:35 |
| @kanzure | to my knowledge. | 22:35 |
| @kanzure | i think his networth is south of $500M | 22:35 |
| @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 | 23:02 |
| @kanzure | "Interestingly: I'm actually a guy on the team that sends back that different HTML from Google. ;) See: 55:19" | 23:04 |
| @kanzure | oh nevermind, that's just for user agents | 23:05 |
| @kanzure | http://www.learningjquery.com/2009/04/better-stronger-safer-jquerify-bookmarklet/ | 23:12 |
| @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? | 23:17 |
| @kanzure | oh neat, python-requests supports async http requests | 23:18 |
| --- Log closed Thu Aug 30 00:00:11 2012 | ||
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