2013-02-05.log

--- Log opened Tue Feb 05 00:00:51 2013
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gnushahttps://secure.diyhpl.us/cgit/paperbot/commit/?id=715b73db Joe Rayhawk: Add phenny and translation-server as submodules.01:13
gnushapaperbot: reload papers01:13
paperbotgnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-24 02:03:09)01:13
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@kanzurejrayhawk: thank you01:14
@kanzurehttps://github.com/kanzure/pdfparanoia01:14
eleitlMorning.01:14
eleitlHow would you structure a Nerdnite talk about cryonics? The leitmotif is Futurama.01:15
eleitlwe need a way to keep the idiots entertained, while providing enough meat for the technical types01:15
@kanzurejrayhawk: actually it should be the paperbot branch of git://github.com/kanzure/translation-server.git but i forget how to specify a branch or change a submodule uri01:15
jrayhawkAh, okay01:16
eleitlFry memes seem like a good hangup01:19
eleitlPlus, Akbar'n'Jeff cryonics hut.01:19
@kanzuretoo much reddit01:19
eleitlRemember, we've got a bunch of idiots to entertain, too.01:19
eleitlWe have to be 'hip' (ack, ptui).01:20
eleitlI think we should also mention destructive brain scan.01:21
eleitlVitrification, of course.01:22
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eleitlEmphasize need to moar research.01:22
gnushahttps://secure.diyhpl.us/cgit/paperbot/commit/?id=24fcf417 Joe Rayhawk: translation server submodule: switch over to kanzure's github and the paperbot branch specifically01:22
gnushapaperbot: reload papers01:22
paperbotgnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-24 02:03:09)01:22
@kanzurehooray01:22
@kanzurethe illusion of progress!01:22
jrayhawkthat's the spirit!01:22
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eleitlso, I get no advice01:27
* eleitl <-- sad panda01:27
@kanzureeleitl: we're not exactly a media company01:27
@kanzurewhen i make presentations, i think about what i would want to see if i was in the audience and bored out of my mind01:28
@kanzureusually this means the most detail i can possibly muster01:28
@kanzuremost presentations seem to assume i'm a moron01:28
eleitlaudience is bimodal01:28
eleitlso we have two narratives at the same time01:28
eleitlone to make technical people perk up, other to engage people, reddit/imgur-style.01:29
eleitlit's a tool of recruitment, but in an entertaining way01:29
eleitlremember, I'm a 46 year old guy with no clue how young people work01:29
jrayhawki suspect attempting to appear hip and with it will backfire01:30
eleitldo normal nerds watch Futurama?01:31
eleitlaudience is Nerd Nite, but in Germany01:31
eleitlwe'01:31
@kanzureeh just copy ccc and you'll be good to go01:31
eleitlwe're trying to address these 5 people out of 500 who have clue01:32
eleitlI've never seen a CCC event01:32
eleitlnor Futurama, for that matter01:32
jrayhawkThe problem with culture is that it's highly highly contextual, and attempting to emulate it by copying superficial elements of it will only make you stand out like a sore thumb.01:32
eleitlyes01:32
eleitlis the reddit/imgur culture relevant to german geeks?01:33
eleitlif yes, I can connect01:33
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jrayhawkOr, rather, attempting to integrate with members of a culture by using superficial elements from that culture runs very strong risk of underestimating the depth of context and meaning of those elements to a degree insulting to those members.01:38
eleitldude01:38
eleitldo german nerds do futurama?01:38
eleitlthat's all I need to know01:38
jrayhawkNo idea!01:38
eleitlsomebody fetch me a german nerd01:39
jrayhawkkanzure why are there a bunch of external binary build products in /home/bryan/code/paperbot/translation-server01:40
@kanzureexternal=?01:40
jrayhawkor, rather, in /home/bryan/code/paperbot/translation-server/build01:40
jrayhawkthings like libnss shared objects01:40
jrayhawkwhich really seem like they should be, you know, shared objects01:40
jrayhawkin /usr/lib01:41
@kanzurei see, yeah i don't know about those01:41
@kanzurei assume build.sh pooped them out01:41
@kanzureby the way, gecko is huge and ridiculous01:42
jrayhawkhttp://gnusha.org/~jrayhawk/irc/paperbotbuild.txt pooping looking unlikely01:43
jrayhawkand yes, the mozilla project has always been an utter pig to build01:44
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eleitlit seems mozilla is committing suicide01:45
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@kanzurejrayhawk: xulrunner-sdk was a symlink01:47
@kanzureto /home/bryan/local/gecko-sdk/xulrunner-sdk01:47
jrayhawkuuugh01:47
@kanzurebecause translation-server's readme told me to and i wasn't thinking straight01:48
@kanzurefeel free to move gecko-sdk to wherever, but afaik there's no package for that.01:48
jrayhawkuh... xulrunner-dev perhaps?01:48
@kanzureworth a shot, i think there were packaging problems but i don't remember.01:50
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jrayhawkthis build system is an atrocity01:57
eleitlfirefox?01:57
jrayhawkNo, translation-server.git01:57
@kanzure"In devops, there only one build system, it is be call Perl."01:59
@kanzureeleitl: context is https://twitter.com/DEVOPS_BORAT02:00
jrayhawki guess i will go to sleep and decide on how much of this lunacy i really want to tackle02:02
@kanzurejrayhawk: what's currently broken?02:02
@kanzurexulrunner-dev doesn't work out of the box with this?02:03
jrayhawki should not have to copy around shared libraries ever02:03
jrayhawkif [ -e "$XULRUNNERSDKDIR/bin/xpcshell.exe" ]; then02:05
jrayhawkah, windows users. suddenly all is clear.02:05
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@kanzurewindows support was added to build.sh >12 months after it was written02:07
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@kanzureaip and ieee are working02:53
@kanzurehttps://github.com/kanzure/pdfparanoia02:53
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@kanzurepaperbot: http://intl.pnas.org/content/early/2013/01/30/1215501110/suppl/DCSupplemental03:06
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/fbd7212c4676d5076a49af19adf81d79.txt03:06
@kanzurepaperbot: http://intl.pnas.org/content/early/2013/01/30/1215501110.abstract03:06
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/S-nitrosylated%20SHP-2%20contributes%20to%20NMDA%20receptor-mediated%20excitotoxicity%20in%20acute%20ischemic%20stroke.pdf03:06
archelseleitl: re that "two worms, same brains" thing, they obviously do not have "identical brain cells" as NewScientist writes03:10
archelspaperbot: http://www.sciencedirect.com/science/article/pii/S009286741201500003:11
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/System-wide%20Rewiring%20Underlies%20Behavioral%20Differences%20in%20Predatory%20and%20Bacterial-Feeding%20Nematodes.pdf03:11
archelsthe reconstruction is beautiful http://turingbirds.com/temp/P.%20pacificus.%20reconstruction%20(Bumbarger%20et%20al.%20Neuron%202013).jpg03:15
eleitlobviously03:17
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eleitlthat's a pretty worm04:14
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strages_workhttp://prospect.rsc.org/blogs/cw/2013/02/04/quantum-chemistry-takes-on-virtual-reality/ neat application of haptic feedback08:51
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ephialtes480paperbot: http://www.mitpressjournals.org/doi/abs/10.1162/001152605462201509:16
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/490ea454a4b2969c003cd07d32167ffa.txt09:16
ephialtes480http://www.mitpressjournals.org/doi/pdf/10.1162/001152605462201509:17
ephialtes480paperbot: http://www.mitpressjournals.org/doi/pdf/10.1162/001152605462201509:17
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/5e74b13008997b5a78da2ad81fd07317.pdf09:17
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ephialtes480brilliant...09:27
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nmz787so supposedly unlocking phones is now seen as copyright infringement?10:58
nmz787if skipping a chapter in a book isn't illegal, why should skipping the network check code be illegal?10:59
ThomasEgimoney..11:05
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@kanzureneat, i'm a cypherpunk now https://twitter.com/_cypherpunks_/status/29886186244185702412:04
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nmz787nice12:13
@kanzure@maradydd wrote "@_cypherpunks_ oh hey I know that guy. He does good work."12:14
@kanzurehooray meredith likes my work12:14
ielowow12:15
ielotried to get relationship advice from people on irc12:15
ieloworst idea ever12:16
Mariuoh, kanzure .. did you see the Cyberpunk 2077 trailer on YouTube ?12:18
@kanzureno12:20
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nmz787kanzure: well she's saying you do good work, that doesn't mean she likes it :P12:28
@kanzureaww12:28
@kanzuredreams = crushed12:28
Mariu:p12:30
nmz787paperbot: http://www.sciencedirect.com/science/article/pii/S156757691000209212:37
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Dietary%20garlic%20%28.txt12:37
nmz787paperbot: http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=272179&_user=1694017&_pii=S1567576910002092&_check=y&_origin=article&_zone=toolbar&_coverDate=2010--31&view=c&originContentFamily=serial&wchp=dGLzVlS-zSkWb&pid=1-s2.0-S1567576910002092-main.pdf&_valck=1&md5=b2c94ff1536366d67cc4366cfaeae97f&ie=/sdarticle.pdf12:38
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/8e4c3fe9a8336d045c001672ca34d8b1.txt12:38
@kanzurehmm12:38
nmz787paperbot: http://www.sciencedirect.com/science?_ob=MiamiImageURL&_cid=272179&_user=1694017&_pii=S1567576910002092&_check=y&_origin=article&_zone=toolbar&_coverDate=2010--31&view=c&originContentFamily=serial&wchp=dGLzVlS-zSkWb&pid=1-s2.0-S1567576910002092-main.pdf12:38
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/dc952baf17a7f692376d750bdecc83a2.txt12:38
@kanzureno access?12:39
nmz787o12:39
nmz787no12:39
nmz787lemme try my other schools12:39
nmz787i really need to get a printer so i can send in my CMU reg papers12:39
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nmz787so chandni's laptop randomly turned off last night12:49
nmz787i think it's something with the batter, since it works with the wall attached12:49
nmz787jrayhawk: this might interest you http://nathanmccorkle.com/pdf/Dietary%20garlic%20(Allium%20sativum)%20lectins,%20ASA%20I%20and%20ASA%20II,%20are%20highly%20stable%20and%20immunogenic.pdf12:50
nmz787jrayhawk: tell me if it is, I can't tell if the immunigenisis is bad or not12:50
jrayhawkhot damn12:50
jrayhawkoh, yes, figure 1 looks to be the important one12:53
jrayhawk"highly stable" does not appear to mean "cooking stable"12:54
jrayhawkthis appears to be consistent with my experience; unboiled garlic fucks me up a bit.12:55
nmz787jrayhawk: so what would the immunogens do if the immune system didn't mess with them?12:57
nmz787jrayhawk: i guess what I'm really wondering is, if the shit is potent and fucks up cells (and that's why the body sets off in response to it) then would you wanna dose with raw garlic if you were sick?12:58
nmz787like stomach infection12:58
@kanzurehttp://blog.okfn.org/2013/02/05/we-need-an-open-database-of-clinical-trials/12:59
@kanzurehttp://www.alltrials.net/13:00
nmz787"s. It is of interest to note13:01
nmz787here that a garlic protein with sequence similarity to the lectin ASA II13:01
nmz787has been shown to possess both hemagglutination and cysteinyl13:01
nmz787protease activity"13:01
nmz787agglutination: 1. The act or process of agglutinating; adhesion of distinct parts.13:04
nmz787"Since stability of proteins in the GI tract could be another13:04
nmz787important parameter for immunogenic response, we have looked13:04
nmz787into the stability of garlic lectins ASA I and ASA II in SGF. Garlic lectins13:04
nmz787are resistant to peptic digestion in vitro as determined by SDS-PAGE13:04
nmz787and hemagglutination assay"13:04
nmz787". ASA I was found to retain 80100% activity13:06
nmz787at all pH values tested. On the other hand, ASA II retains 100% activity13:06
nmz787at pH 6 and 8, 40% at pH 10 and 12, and 25% at pH 2 and 4. The13:06
nmz787hemagglutination activity of both ASA I and ASA II was retained at13:06
nmz78760 C for 30 min, but was completely lost at 100 C incubation"13:06
nmz787a friend says his grandfather ate a clove or two of raw garlic along with nuts and grapefruit for breakfast every morning13:09
Mariuate ?13:12
Mariuwhat changed ?13:12
EnLilaSkohttp://www.kickstarter.com/projects/461687407/kickstarter-open-source-death-star13:16
chris_99lol13:17
ThomasEgii'd so laught if they get the money together13:18
ThomasEgisitting on 20mio to buy chicken wire13:18
chris_99hehe13:18
chris_99i'm glad it's open source, should someone wish to duplicate their efforts13:19
@kanzuresudo apt-get install death-star13:19
EnLilaSko:D13:19
@kanzureERR: The death star is not fully operational.13:19
MariuLOL13:19
@kanzurealderaan shot first, etc.13:19
ThomasEgiunmet dependencies13:19
ThomasEgican't get iron13:19
ThomasEgiyou may want to update your source lists13:20
@kanzurehttp://nerdapproved.com/wp-content/uploads/2011/09/alderaan-shot-first.gif13:20
Mariulol13:22
Mariu=]13:22
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ephialtes480brilliant kickstarter project.13:28
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nmz787https://petitions.whitehouse.gov/petition/secure-resources-and-funding-and-begin-construction-death-star-2016/wlfKzFkN13:36
@kanzurefuck the death star, let's do a dyson swarm or something13:38
jrayhawknmz787: there's likely to be some variance in response due to differences in genetics, adaptive immunity, gut flora, and intestinal permeability. Garlic is really complicated chemically and it's entirely reasonable to postulate that it has effects on the gut biome both directly and through immunomodulation based on its prevalence and success in traditional medical practices (see also: garlic enema).13:38
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jrayhawklectins have a wide variety of effects; you'd have to study the particular lectin. Some of them are fairly innocuous.13:43
nmz787huh13:44
nmz787garlic enema eh13:44
jrayhawkNot something I've ever done, but they do have some clinical trials.13:44
nmz787i've heard of using coffe13:45
nmz787and doing fecal transfer13:45
ArmilusDajjalcoldpress coffee13:45
ArmilusDajjalnot regular coffee13:45
ArmilusDajjalthe tannic acid will give you the shite13:45
nmz787ahh13:46
nmz787kanzure: I can't seem to track down the authors current info for this http://diyhpl.us/~bryan/papers2/paperbot/SU-8%20thick%20photoresist%20processing%20as%20a%20functional%20material%20for%20MEMS%20applications.pdf13:46
nmz787kanzure: the email given is bad now13:47
nmz787kanzure: and I want to contact them13:47
@kanzurehmm. this one will require some advanced sleuthing.13:50
@kanzurenmz787: try looking for patents by these guys. they seem to not have any papers after 2002 but maybe there's patents.13:54
nmz787kanzure: do you know anyone looking for a remote scientific programmer?13:59
nmz787i need some income to funnel into projects now that I have lab space... i don't need much $ since the lab is really relaxed with when they will want me to pay (if I start making money or getting in their way)14:00
@kanzurei dunno if enthought does remote14:00
nmz787(which is far off, and if i'm making money, well geez that's the point of me experimenting)14:00
@kanzurebut enthought would be enriching for you i think14:01
@kanzureor anyone in here i guess14:01
@kanzurei regularly get blasted by recruiters but never for explicitly scientific things.14:02
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juri_if its remote free software, keep me in mind, please. ;)14:05
nmz787juri_: what kind of projects would you be interested in working on?14:06
nmz787by free do you mean you'd work for free?14:06
juri_nmz: no. ;)14:07
@kanzurejuri_: i've been meaning to tell you this for a while, but you should be aware that if your goal is to optimize for cash income that your requirement of gpl-licensed software work is not necessarily beneficial towards that goal.14:07
juri_I'm a Free Software developer.14:07
juri_right now, i've specialied in OpenEMR, virtualization technologies (author of createvm), i'm wicked with file conversions (big into XSLT/SED), and quite a 3d printer geek.14:08
nmz787kanzure: know this person https://twitter.com/skry14:08
@kanzureeww xslt14:08
nmz787kanzure: ?14:08
nmz787exSlut14:09
juri_kanzure: tell me something i don't know. i used to make GOOD money as a software developer. then i developed morals. ;)14:09
@kanzurenmz787: no i don't seem to know this person14:09
juri_at one point, i was the youngest MCSE in the nation.14:10
juri_this was a while ago. ;)14:11
juri_everything i've written since i was ~20 was licensed under the GPL, and 95% of that made it online.14:13
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@kanzureOn Tue, Feb 5, 2013 at 3:47 PM, Peter Murray-Rust <pm286@cam.ac.uk> wrote:14:14
@kanzure> I use Apache FOP.  We should be able to:14:14
@kanzure> * read PDF into SVG14:14
@kanzure> * remove the rubbish14:14
@kanzurei can't seem to find how to use apache fop to write a pdf14:14
@kanzure> * write the primitives back into PDF. We might get font problems so you may14:15
@kanzurehttp://xmlgraphics.apache.org/fop/dev/#doc14:15
@kanzureit looks like this is possibly xslt related? http://xmlgraphics.apache.org/fop/fo/size.fo14:15
juri_looks like fun. ;)14:16
@kanzurewell pete is suggesting this as an alternative to my https://github.com/kanzure/pdfparanoia14:16
@kanzureso i'm trying to figure out how to actually make it work14:17
juri_xslt + sed is fun. i can certainly see that applying to a pdf stream.14:17
* juri_ takes a peek.14:18
@kanzurejuri_: can you look at pdfparanoia and see if you can duplicate the results in xslt?14:18
@kanzureor erm, i mean, possibly using something less evil14:18
@kanzurehere's the gist of how it works:14:18
@kanzurehttps://github.com/kanzure/pdfparanoia/blob/master/tests/test_aip.py14:18
@kanzurehttps://github.com/kanzure/pdfparanoia/blob/master/pdfparanoia/plugins/aip.py14:18
@kanzurebasically i use pdfminer to find /FlateDecode streams in a pdf file that contain suspicious text14:19
@kanzurethen i use manually delete the offending obj/endobj lines from the lines of the pdf file,14:19
@kanzurehttps://github.com/kanzure/pdfparanoia/blob/master/pdfparanoia/eraser.py14:19
juri_i'll take a look.14:20
juri_i've got three customers asking for time, plus i'm sick.. but being sick gives me some leway. ;P14:20
ephialtes480kanzure does that account for majority of ways watermarking is done? Are there significant exceptions?14:21
@kanzureephialtes480: it currently works for IEEE and AIP but others need to be added14:21
juri_... less evil than xslt? sacrelige. ;)14:22
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juri_well, i can certainly do the job in less lines than you have here.14:27
@kanzuretell me more14:27
juri_but for your purposes, i don't think that would be as maintainable.14:27
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@kanzurejuri_: well, what is the idea?14:30
juri_the approac i would use is to tokenize the stream as lines you're interested in, and lines you're not. you're doing object removal.14:31
juri_so, use sed to encode all lines in <boringline>"sometesthere"</boringline>, except the ones that match your interesting regex (object definitions).14:31
@kanzurethe text is encoded in some format inside the pdf, so sed can't pull that out with a regex unless something preprocesses it first14:32
juri_slap a header and footer on it, and you have an xml document. now, do a xslt transform that just responds to all the blocks you're interested by looking through your filter rules, and spit the rest out verbatim.14:32
juri_hmm. i'm tempted to just do a hex encode of the lines, for sed to handle.14:33
nmz787juri_: if you did that, please comment how to do it for other arbitraty sed commands, so if i have a pdf with a different search requirement, i can reuse your code easily14:35
juri_really, step 1 for me is always 'convert to a dumb xml format'.14:35
@kanzureonce you convert to a dumb xml format, how do you get it back to pdf?14:35
juri_that's the xml transform.14:36
juri_it just does writes of all the data back.14:36
@kanzureis there an existing xml transform that works to convert xml to pdf?14:36
juri_I've done this a ton with X12 formatted data. anything that has a concept of 'lines', basically.14:36
juri_xml is not a 'real' format that way.14:36
juri_your concept is sheared.14:36
@kanzurepdfquery uses pdfminer to dump a pdf into xml via lxml, and lxml then dumps to an xml format that currently can't be converted back to pdf.14:36
juri_interesting.14:37
@kanzureadobe has a pdfxml format, but it is nothing like the xml that lxml dumps for pdfquery.14:37
ephialtes480kanzure - let us say I wanted to add support for another kind of watermark - looking at the raw text of an example PDF, I see a suspect FlateDecode at the top which may be the watermark:14:37
ephialtes480<</Type/XObject/Resources<</ProcSet [/PDF /Text /ImageB /ImageC /ImageI]/Font<</F1 2 0 R>>>>/Subtype/Form/BBox[0 0 414 648]/Matrix [1 0 0 1 0 0]/Length 126/FormType 1/Filter/FlateDecode>>stream14:37
juri_yea, xml is not a format, think of it more as a linewise encoding.14:37
ephialtes480followed by some binary code14:37
ephialtes480and "endstream" end object etc.14:37
ephialtes480deleting this manually produces a garbled PDF, what is the catch here? reproducing some stream code of same length?14:37
juri_right. thats a line. and the next line not matching any regex, would get encoding with 'boringdata'.14:37
juri_the act of using XSLT to transform your (now) xml file back into a pdf would also use a 'xslt library' of functions to remove the target data.14:39
juri_i usually just use sed to break data into sections, and pull out atributes i'm interested in handling in the xslt.14:39
@kanzureephialtes480: you picked the wrong one :)14:39
@kanzureephialtes480: you have to start with the line that begins with "<number> 0 obj<<" and then delete up to and including the following "endobj"14:40
@kanzureephialtes480: if your pdf comes out garbled, you deleted the wrong object14:40
juri_here, let me paste an example.14:40
@kanzureephialtes480: another hint is that most of these watermarks seem to be the same between each page, so the size of the FlateDecode object will be the same each time. so if you see an object that isn't repeated on each page, chances are it isn't the watermark.14:41
ephialtes480thx, trying now!14:41
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juri_http://pastebin.com/vsRMzNJC14:45
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@kanzureyou wrote all of those regular expressions just now?14:45
juri_oh goodnes no.14:48
juri_that's about two days of work.14:48
ephialtes480kanzure success...14:49
@kanzureephialtes480: now write it up into python14:49
juri_well, that, and: http://pastebin.com/izZgpNuf14:49
@kanzureephialtes480: aip.py and ieee.py both work very similarly, they search for specific text and then make a list of object ids that need to be removed14:49
ephialtes480k, added to the list of todos...forked for now, thanks will issue pull requests if I complete a functioning one...14:50
@kanzureephialtes480: it's really simple to write, if it takes you more than 10 minutes let me know14:51
juri_http://www.open-emr.org/wiki/index.php/X12_837p_Reference14:51
juri_that's a prser, ane un-parser for the file format i just posted.14:51
juri_so that i, a lazy human, can edit the file format (which is very non-human-editable) in a text editor.14:52
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juri_now, the reason i was showing that, is that the xslt there and the SED do the same job, just forward / reverse.14:52
juri_xml is a good intimediary for binary formats, that's why its so readily used to replace them.14:53
juri_you don't need to really adhere to any kind of written format or spec to make something that is very useful, and you can make decisions about transforming the data in XSLT.14:54
@kanzurexml is a /good/ intermediary for binary formats? hrm.14:54
@kanzurei haven't used xml like that before.14:55
juri_the XSLT can be very sequence-picky, and show all of the data, some of the data, or even generate just messages instead of the output of the file. its pure transform, and a functional language. the sed is strictly serialized.14:55
juri_xml is a great replacement for binary formats.. as long as you do not care about CPU time. ;)14:56
jrayhawkor storage efficiency14:57
juri_agreed.14:57
juri_but once something is in xml (and really, all of it, which it sounds like you're having problems with), transforms are relatively simple, if wordy.14:58
jrayhawkor robustness to syntax errors, or ability to do timely random access14:58
jrayhawkreally why are we using xml again14:58
juri_I'm the author of the "xml form generator', which takes an XML file as input in openemr, generates some 7 different PHP files, a SQL file, and other fluff, to add a form into the OpenEMR system. the forms are simple, and have resulted in a lot of interchange between medical practitioners. you can imagine, writing all of that PHP with xslt gets both complicated, and simple.14:59
jrayhawkaaaaa15:00
@kanzureyeah that's a dumb way to do that15:00
@kanzurehave you heard of ORMs15:00
juri_the real win in that case is you don't administrate 7*N_FORMS php pages hand written for security problems.15:00
@kanzuremost of the modern orm libraries do form generation for you, so you only have to maintain the core library and some minor templates for when you insist on differences in the form infrastructure.15:01
juri_i've written an xml-only interface. upstream is insuficiently comfortable with xml to accept it.15:01
juri_nothing about OpenEMR is modern.15:01
@kanzurewhat's funny is that i call it modern but i'm pretty sure perl has been doing that for >15 years15:01
juri_parts of openemr are that old.15:02
jrayhawki can see justifying what you've done under entirely practical New Jersey Style principles, but claiming it has quality architecture just makes you look like a lunatic15:03
juri_it has a higher quality archetecture than what was there.15:03
juri_i don't consider it 'good'.15:04
ephialtes480kanzure, could you post an example of one of the aip files (for comparison)15:04
@kanzureephialtes480: there is an example in the tests/samples/aip/ folder15:04
jrayhawk'14:53 < juri_> xml is a good intimediary for binary formats' was more the thing at issue15:04
ephialtes480ah15:04
juri_i mean, hell, i just removed all of the popups from the program.. and it will take a programatic act of a diety to remove frames from it.15:04
@kanzureephialtes480: the unit tests can be used to confirm that it is working15:05
jrayhawkhaha15:05
@kanzurejuri_: maybe you should take a page out of gnu's book and use lots of small programs and services instead of monolithic monolithicness15:05
juri_jrayhawk: i enjoy it, and find it a fun aproach. ;)15:05
@kanzurethen you could install parts of the system via a package manager15:05
juri_there's a movement to do that in openemr, but i fear it is going to fail.15:06
@kanzurehow many users does openemr have?15:06
juri_i was happy just to get 'disable' buttons for the features my customers don't need.15:06
juri_thousands of clinics, unfortunately.15:06
@kanzurethat's not much.15:06
juri_its a lot for the way the project is (not) run.15:07
juri_still, focusing on your problem, i guess the first question i have, is you say you have a PDF -> XML parser. do you know if all the data 'made' it to the xml format?15:08
@kanzurei'm not confident enough in pdfparanoia at the moment to run it on my entire pdf collection15:09
@kanzurethere might be false positives15:09
@kanzureand then suddenly entire sections of my documents might be missing15:09
nmz787kanzure: why are you talking about xml if you have it working in pdfminer (or whatever pdf paranoia is using)15:09
@kanzurenmz787: curiosity15:10
juri_well, if you knew all of the data made it into the xml format, I'd be willing to pull it back out to create a file, as well as help convert your transforms into xslt. I'm a xslt geek. I don't enjoy writing the equivilent of that sed script, written by someone else however. ;)15:14
juri_s/enjoy writing/enjoy fixing/15:14
ephialtes480kanzure you get "Redistribution subject to AIP license or copyright" from the binary stream data. is that getting decoded by pdfminer methods?15:15
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@kanzureephialtes480: yes that is decoded by pdfminer15:17
ephialtes480ok, we are looking at more than 10 minutes :) I am tracing back your method calls to pdfminer, and am reading up on pdfminer so I can first decode the stream data I need to identify. the PDF has a lot of FlateDecodes that are not connected to watermark15:18
@kanzureto be honest, the quickest way to do this might be copy-and-paste of the aip.py version15:19
@kanzurethen change the text it is looking for15:19
ephialtes480right, but need to find the text it is look for15:19
ephialtes480which is in binary15:19
ephialtes480or whatever, and need to decode with pdfminer, no?15:19
ephialtes480This key line: if "Authorized licensed use limited to: " in data:15:20
ephialtes480                        evil_ids.append(objid)15:20
ephialtes480you are getting that quote from somewhere, and it isn't readable by simply opening the file15:20
ephialtes480(it shows when opening the file regularly but there may be extra spaces, etc.)15:21
ephialtes480thanks for now! later...15:23
@kanzurei got the quote by looking at the watermark with my eyeballs15:24
@kanzureit's visible on the bottom of each page15:24
@kanzurethere are not extra spaces really15:24
@kanzurewatermarks like that are applied in a very consistent manner by a pdf server that is pasting those in each time you download a pdf15:25
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nmz787hah jimmy kimmel announced on national TV to his 10th grade history teacher (who told him he would never amount to anything if he kept screwing around) that he was just about to high-five the president15:39
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@kanzurealibaba was acquired by yahoo?16:12
nmz787when?16:12
nmz787yahoo was the first auction site right?16:12
@kanzurehttp://www.crunchbase.com/company/alibaba16:12
@kanzurelooks like there might be an upcoming alibaba ipo16:12
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nmz787hah it says 'Offices16:33
nmz787edit16:33
nmz787united states of america16:33
nmz7876/F Chuangye Mansion, East Software Park16:33
nmz787No.99 Huaxing Road16:33
nmz787Hangzhou, 310099, CHN16:33
nmz787Read more: http://www.crunchbase.com/company/alibaba#ixzz2K4gjmmLO'16:33
nmz787pretty sure hangzhou is not continental U.S.16:33
@kanzureman i hate things that inject shit into pastes16:33
nmz787this lab equipment isn't priced too much http://www.tedpella.com/histo_html/unicore.htm16:35
nmz787it's actually priced like normal people tools are16:35
nmz787reasonably16:35
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@kanzureso is FlateDecode referencing the deflate algorithm?17:57
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@kanzureyashgaroth: how much does a CRO cost to make.18:37
yashgarothuhhh18:37
yashgarothdepends on the line of work, though I can't speak to specifics there, whether you're including operating expenses18:38
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yashgarothlike for a generic protein company maybe 200k upfront for equipment, plus 40k/BS 80k/PhD per year, and space runs about 2-3k per month18:40
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@kanzure"Pfizer has decided to outsource pretty much everything except early discovery to two leading CROs—Icon (Hubbard’s former employer) and Parexel, Hubbard says."18:43
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yashgarothoh man I just found out quintiles is owned by bain capital18:43
klafkawow 80k/phd18:44
klafkathat sucks18:44
@kanzurewho is offering 80k/phd?18:44
yashgarothalso, GMP and clinical trial stuff is way more expensive than generic R&D CROs18:44
@kanzuresure18:44
@kanzurei'm not as interested in the clinical trial CROs18:44
yashgaroththat's an average starting salary for a PhD, maybe a bit lowball but someone will take it18:45
yashgarothplenty of PhDs out of work that are flooding out of grad school18:45
klafkain what fields?18:45
yashgarothbio18:45
klafka...18:45
yashgarothnot like UCSF grads or whatever, but if you want "a PhD" you can get one for that18:46
@kanzureand a phd dropout will be cheaper18:46
klafkasssh18:46
klafkawell18:46
* klafka is more and more glad he went back to computers18:46
@kanzureklafka: eh you have >6 months of industry experience, nobody remembers your phd work anymore.18:46
yashgarothsure, but you want a PhD on the "about us" page so people will go "oh okay they have a PhD it's okay to send them money"18:46
klafkaaah18:47
klafkahah that's actually true kanz18:47
klafkakanzure:18:47
@kanzureyashgaroth: i've been thinking about just dumping $20,000 into a company to do scienceexchange.com things18:47
yashgarothI do have in "in" with the CEO of assaydepot, in that he bought me a sandwich yesterday18:48
@kanzurekevin?18:48
yashgaroth*an18:48
yashgarothyep18:48
@kanzureso he seems to be selling assaydepot licenses to pharma companies for $250k/year18:49
yashgarothselling licenses in what sense?18:49
@kanzurean instance18:49
@kanzureerm.. i guess you wont know what an instance is either.18:49
@kanzurein the software world, you can license access to a service, or sell bytes, or do lots of other things.18:50
yashgarotha dungeon created for your party to raid? no18:50
nmz787kanzure: what do you mean dump $20k into18:50
@kanzurenmz787: i mean, i don't have a lot of interest in making transgenic mouse strains, but if it's good business why not18:50
yashgarothoh so they pay 250k and get a la carte services from anyone on assaydepot?18:50
@kanzureno18:50
@kanzurethey pay 250k and they get the assaydepot software for managing their own internal labs18:51
yashgarothohhhh18:51
@kanzurehttp://diyhpl.us/wiki/transcripts/startup-science-2012/kevin-lustig-assay-depot18:51
@kanzure"Secondly we built this company without VC funding. The last company I founded in 2001 I raised $170 million. It was a terrible idea. We were well-paid. But it came back to bite us in the ass. Good luck. What we've done is that we've gone out and raised money from friends and family. I got my mother to kick in some money."18:51
* klafka is going to play with pandas18:51
@kanzure"It puts pressure on you when your mother puts in money. We are profitable as of this year. It's only now that we're going to go out and actually raise VC money, but instead of giving up 70% of the company like in my first go, we're going to give up 10% or 20% this time to maintain control."18:51
@kanzure"Our solution has been to take the public web based lab, for use by anyone, that we have availabel for free of charge, and turn it into an enterprise solution for pharma companies. "18:51
@kanzure"So we have private web based labs for pfizer, johnson and others, and these companies are using this platform- 10,000 scientists within each company to coordinate all of their research activities."18:51
yashgarothoh like an internal lab management software18:51
@kanzure"$250,000/license for pharma companies and charge through in the nose for integrations"18:52
klafkayeah18:52
klafkagive them a solutions engineer!18:52
klafkaor solutions architect!18:52
@kanzuresounds like a buzzword klafka18:52
klafkawith high billable rates18:52
klafkaintegrations engineer18:52
klafkawhatever18:52
yashgarothsolutions hacker18:52
@kanzure(TM) (R)18:52
nmz787kanzure: their site has totally different prices advertised from what it says when you click on it18:52
nmz787mass spec $10, then i click and it says $10018:53
klafkaa technical person to implement your too complex software in their archaic systems18:53
klafkamass spec for 10 is too cheap18:53
klafkaor seems a bit too cheap18:53
@kanzurenmz787: assaydepot is like scienceexchange sorta, i think they have this public site just for people who don't have an assaydepot license18:53
yashgarothdepends on the mass spec method18:53
klafkafair enough18:53
yashgaroththat is still like at-cost though18:53
nmz787but literally it says $10 then18:53
nmz787$10018:54
klafkaman i hate when i'm too tired and i keep going back and forth between 3 things even though i know what i need to actually do18:54
nmz787https://www.scienceexchange.com/18:54
nmz787klafka: i do that when i'm not tired18:54
@kanzure"[CROs is a] very fragmented industry with the top 10 controlling 56.1% of the market in 2008[10] and down to 55% in 2009.[11][12] One estimate had the size of the market set to reach $24 billion in 2010[13] and set to grow at a rate of 8.5% through 2015.[14]"18:54
yashgaroth$100 is pretty standard for protein MS18:54
klafkayeah18:54
klafkai know we get drugs gc/ms analyzed for like 14018:54
nmz787kanzure: so you want to invest in scienceexcahnge, or pay $20k for some experiments you have in mind18:54
@kanzureno i don't want to invest in scienceexchange18:54
@kanzureno i don't want to pay for experiments18:54
@kanzureneither of those things are what i said :p18:55
nmz78718:47 <@kanzure> yashgaroth: i've been thinking about just dumping $20,000 into18:55
nmz787                 a company to do scienceexchange.com things18:55
@kanzureyes, a CRO-like entity18:55
nmz787sound like you wanna spend $20k on lab science18:55
@kanzurehuh?18:55
yashgarothlike, buy a genetic analyzer and sell sequencing services?18:55
nmz787CRO?18:56
@kanzureyashgaroth: probably not "genetic analysis" because that market is going down constantly.18:56
yashgarothor an HPLC and sell analysis18:56
klafkawhat is the cost to sequence a genome btw now?18:56
@kanzureyashgaroth: and, even if it was something economically stable, i wouldn't want to do it myself either (i have better things to be doing)18:56
klafkais it down to 100 bucks yet?18:56
klafka(sequence not assemble)18:56
klafkadid the rate of change of sequencing costs flatten out yet?18:56
yashgaroth$100 is higher than the cost of the hard drive they'd send it to you on18:57
klafkayeah18:57
@kanzuresequencing is not predicted to flatten any time soon18:57
klafkathat's why i said sequence not assemble18:57
klafka:P18:57
yashgarothyeah yeah18:57
yashgarothok so kanzure what did you mean then, if not our guesses?18:58
@kanzureyashgaroth: your guess was right (HPLC might be ok)18:59
yashgarothah okay then18:59
@kanzurei'm still trying to figure out if it's good business or not18:59
yashgarothif you're located in a big biotech hub city, and have a decent operator to run it, then you could make some money19:00
yashgarothoffering pickup for samples, high-quality analysis/expertise, and fast results, why would anyone spring for their own HPLC and operator19:00
@kanzurehow much are people making on that at the moment, though?19:02
@kanzurei don't even know how much demand there is for random hplc runs19:02
yashgarothno idea, I've never had to hire an HPLC; it's certainly an investment on your part though19:02
nmz787HPLC is usually run by a dude who takes care of other big machines too19:03
nmz787or helps grad students set up runs for them to process19:03
nmz787so he prob makes 40-55k19:03
yashgarothtrue, it's not that hard to run; I was mostly scaling down from some sort of mass spec business19:03
@kanzurei bet i could get an hplc on credit, heh19:03
@kanzurei'm also sure i could find someone to pay <$20/hour who would be reliable19:04
yashgarothanyway if I knew how to start a biotech services business I'd just do that19:04
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yashgarothehh maybe19:04
@kanzurewell i think that's what all the people who get fired from roche do19:05
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nmz787kanzure: too bad portland isn't a hub city or you'd have an operator :P19:05
yashgarotheveryone gets fired from roche, it's like a rite of passage19:05
klafkawhy is that?19:05
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yashgarothwhy is what19:05
klafkadoes everyone get fired from roche19:05
klafkaor so many people19:05
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yashgarothno, that's more accurate as 'laid off', and 'from genentech/pfizer/GSK'19:06
@kanzureright19:06
yashgarothroche is pretty good about not shedding people constantly19:06
yashgarothexcept from the companies they acquire19:06
klafkai have an old roommate whose been working at genentech for like 5 years19:07
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klafkasince he got out of college19:07
yashgarothI have several colleagues who are ex-bay area genentech19:07
@kanzure"the entrepreneur's guide to a biotech startup" http://www.evelexa.com/resources/EGBS4_Kolchinsky.pdf19:13
@kanzure"Promoting your instrument as having a smaller "footprint" (area it takes up on the floor or bench) can differentiate it from competing products."19:16
@kanzuregeeze19:16
@kanzure"A more attractive alternative may be the Razor Blade model; sell or lease the instrument cheaply but charge for disposables."19:17
@kanzureyep.. i think that's why ABI was suing customers for using alternative reagents.19:17
yashgarotheveryone does that shit19:17
klafkauhh19:17
klafkahow is that legal?19:17
klafkado you sign a contract19:17
@kanzurei dunno, go read the court documents19:18
klafkaotherwise?19:18
cpopellSome might.19:18
@kanzurei don't recall who won that lawsuit19:18
yashgarothwell, everyone does the 'charge out the ass for disposables/reagents', the suing is a bit much19:18
@kanzure"Typical medical device products may have gross margins from 55%-70%." aww yeah.19:21
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@kanzureequipment loans http://www.nature.com/bioent/building/infra/082004/full/bioent821.html19:35
@kanzureno crap? "Negotiating leases on many individual pieces of equipment is time-consuming and daunting and, furthermore, in the biotech industry there is little justification for having the flexibility to return leased equipment. "19:37
@kanzurefenn: this might be interesting background material for bayh-dole things, http://www.nature.com/bioent/view/102004/full/bioent832.html19:44
streetykanzure: just noticed you asked me about pdfminer, not really used it since putting that repository on github. I managed to alter someone elses code to do roughly what I wanted  but that was the limit of my understanding20:10
streetysorry I can't be more help20:10
@kanzurethanks anyway. pdfparanoia is working for now.20:11
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@kanzure"When Lin and a partner opened Explora’s doors, the company had two employees and occupied 1,500 square feet of space. Now, it employs 17 full-time workers and covers 33,000 square feet of office and lab space at three locations in the region."20:22
@kanzure"The work requires a small animal research lab, known as a vivarium, which can cost several hundred thousand dollars to set up and about $200,000 annually to staff, Lin said."20:22
@kanzureso 2 employees and 1500 sq ft is probably not going to be $200k/year20:22
yashgarothfor rent and salaries? maybe half20:23
@kanzurealso, 33,000 sq ft of rats is a lot of rats20:25
yashgarothI really don't want to think about the smell20:26
@kanzuremaybe they have engineered some bacteria to make rat poo smell like lady farts20:26
yashgarothwe can give it an air of wintergreen, that's about the state of the art20:27
@kanzuredid anyone commercialize that btw? the less stinky ecoli strain?20:36
@kanzureiirc they won some igem prizes and then went back to their soulless lab jobs20:37
yashgarothI don't know if they designed the wintergreen synthase or whatever it was20:38
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nmz787yay i installed gnu emacs for windows, and it solved my problem!21:22
nmz787kanzure: would you have any idea of how to merge drivers from other ROMs into something like this http://themikmik.com/showthread.php?12584-ROM-PrimOG-Preview-1-5-6-2-12-_-Patch-Sense-4-0a-ICS-4-0-321:25
@kanzurewell, drivers can be loaded into the android kernel so i think you can just distribute the .ko files or whatever?21:38
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