--- Log opened Fri Aug 16 00:00:57 2013
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04:05 < fenn> optically levitated fluorescing nanoscale diamond particle: http://www.rochester.edu/largepics/nanodiamond.jpg
04:06 < fenn> it's ~100nm
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06:22 < archels> paperbot: http://onlinelibrary.wiley.com/doi/10.1002/wcs.142/pdf
06:22 < paperbot> http://libgen.org/scimag1/10.1002/wcs.142.pdf
06:23 < archels> <3
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06:24 < archels> paperbot: http://journals.lww.com/jinvestigativemed/Citation/2005/01010/A_Finite_Element_Model_of_the_Dendritic_Tree_to.369.aspx
06:24 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/4d2dd1be515117ad531a5578f7d89def.txt
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07:17 < JayDugger> paperbot: https://www.sciencemag.org/content/early/2013/08/14/science.1240889.full?sid=460ae2fe-57e0-4c32-b414-0738bbe8e1a9
07:19 < paperbot> http://pdf.highwire.org/stamped/sci/early/2013/08/14/science.1240889.full.pdf
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08:00 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure pushed 2 commits to master [+0/-0/±2] http://git.io/H_idCQ
08:00 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure d3c2ea5 - fix url-parser entry in package.json
08:00 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure 6d4ca0f - version bump to: v0.0.5
08:00 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure tagged 6d4ca0f as v0.0.5 http://git.io/-Yrrvg
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08:06 <@kanzure> oh right. this isn't going to work in browsers because it requires remote http to work.
08:06 <@kanzure> oh right, zotero forces you to navigate to the page that you want to parse
08:07 <@kanzure> i could also imagine a situation where you just route an http request through an http proxy endpoint on the same server as whatever served you the pile of browserified javascript
08:07 <@kanzure> cheerio can't be browserified unless you edit its index.js file.. but otherwise it works.
08:14 < EnLilaSko> http://i.imgur.com/4wREm1C.jpg
08:14 < EnLilaSko> Woho
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08:52 < ParahSailin> why would you want to browserfy cheerio
08:52 < ParahSailin> browsers already have html parser
08:55 <@kanzure> yes, but the idea is to browserify papermonk
08:55 <@kanzure> i don't want to have two separate libraries (one for node, one for browsers). that seems like way more work.
08:57 < ParahSailin> if you want the same source code to work in both places, then just put in a switch that detects if its running in the browser, then use sizzle as its selector instead of cheerio
08:58 <@kanzure> for the outbound requests, i was thinking of writing a wrapper around request that would either (1) send an http request (if in node) or (2) send an XHR request to a proxy on the local server (if in a browser) and otherwise the api would look exactly the same. but there's a third possibility where you are already on the page that you want to parse (like in zotero) that i don't know how to incorporate yet.
08:58 <@kanzure> as for sizzle vs cheerio i don't really want two separate sets of functions for parsing the same thing
08:59 <@kanzure> if they are compatible then that sound scool
08:59 <@kanzure> *sounds cool
08:59 < ParahSailin> at i understand it, cheerio works on the pseudo-dom data structures generated by node-htmlparser
09:00 <@kanzure> i just mean i don't want to have to write 2 versions of parseTitle, https://github.com/kanzure/papermonk-downloader-plosone/blob/master/src/parse.js
09:00 <@kanzure> (this version works with cheerio)
09:01 < ParahSailin> so i guess you could translate actual dom to psuedo dom so that you can use cheerio with it
09:03 < ParahSailin> or, it looks like cheerio is probably 99% compatible with jquery methods, so have a switch to detect if its in a browser, then require jquery else require cheerio
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09:08 < ParahSailin> kanzure: cheerio's traversal methods literally act on this sort of data record https://gist.github.com/rcallahan/a65e56dcd8a643d2e9ef
09:17 <@kanzure> iirc sizzle was a better idea than jquery
09:20 <@kanzure> i think the way to check if we're in a browser is to see if window === undefined
09:20 < ParahSailin> sizzle is the core functionality of jquery that we care about for this, but im not sure if there is a sizzle equivalent that acts on the dom records generated by htmlparser2
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09:21 < ParahSailin> i suppose that would be pretty easy to do, to modify cheerio traversal functions to have same syntax as sizzle
09:22 <@kanzure> grr that sounds annoying though. isn't there something that just works for this function?
09:23 <@kanzure> i guess nobody has wanted to parse html in node and then have the same shit work in a browser?
09:23 < ParahSailin> doesnt node.js support native compiled modules?
09:23 <@kanzure> definitely
09:23 < ParahSailin> maybe we should just make a fast jsdom in native code for node.js
09:23 <@kanzure> unfortunately that requires recompiling node to link the event loop with the webkit event loop
09:24 <@kanzure> i know these things because of my time spent on phantomjs/webkit/node
09:24 < ParahSailin> why is a browser event loop involved in this at all?
09:24 <@kanzure> because the way that the dom works in webkit is that there are event loops
09:24 < ParahSailin> just implement DOM in cpp as a node module
09:24 <@kanzure> that's what webkit provides
09:24 < ParahSailin> implement all the methods that jsdom does in cpp
09:25 <@kanzure> eh, i think it's overkill anyway
09:25 < ParahSailin> jsdom is obv not complete dom implementation, but its enough for sizzle's traversal functions
09:25 <@kanzure> cheerio is very fast
09:26 < ParahSailin> the window === undefined check will be more than adequate
09:26 <@kanzure> yeah
09:27 < ParahSailin> $ = (window === undefined)? require('cheerio').load(innerhtml) : require("jquery")
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09:29 <@kanzure> actually, browserify scans all files for each require() statement
09:29 <@kanzure> so we'll have to figure out how to disable browserify for cheerio
09:29 < ParahSailin> epicycles and epicycles
09:29 <@kanzure> because this don't work: echo "require('cheerio');" > main.js; browserify main.js > bundle.js
09:33 < ParahSailin> so we're allowing code transformations to make code slightly different for the two environments?
09:33 <@kanzure> what do you mean code transformations?
09:33 < ParahSailin> browserify :: JS -> JS?
09:33 <@kanzure> browserify is just a bundler
09:33 <@kanzure> because require() doesn't work in a browser
09:34 <@kanzure> so browserify provides require() and then puts all of the modules together
09:34 <@kanzure> there's something called browserify-cdn that lets you stream modules from a remote host, but i dunno if i care about that
09:34 < ParahSailin> browserify changes require() to requirejs?
09:34 < ParahSailin> or something similar?
09:34 <@kanzure> yeah
09:35 < ParahSailin> is browserify the only code transformation we are allowing?
09:35 <@kanzure> what other transformation are you imagining?
09:35 < ParahSailin> i dunno, avoiding the window === undefined stuff would be nice
09:35 <@kanzure> btw i don't think the browserify output will be committed
09:35 <@kanzure> oh, i see
09:36 < ParahSailin> #ifndef browser require(jquery) #endif whatever
09:36 <@kanzure> well, that can be shoved into a third-party module if it makes you feel better?
09:36 < ParahSailin> well i dont really get to say anything since you're the one doing all this
09:37 <@kanzure> uh, what? bad ideas are always bad ideas, even if i'm the one saying the bad ideas.
09:37 < ParahSailin> it seems like the divergence between the browser and node will just be in that one place
09:38 <@kanzure> nope, also http requests
09:38 < ParahSailin> so just have two very small wrapper index.js files: one requiring cheerio, other requiring jquery
09:38 < ParahSailin> ah right
09:38 < ParahSailin> i thought browserify already handled that though
09:39 <@kanzure> unfortunately browserify's http module only allows http requests to the server that the bundle was served from
09:39 < ParahSailin> pass thr cheerio-containing index.js to browserify, apply the other directly to node interpreter
09:40 < ParahSailin> kanzure: yeah makes sense, js xss rules and all
09:40 <@kanzure> not quite, there can/should only be one index.js because that's what package.json points to
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09:41 < ParahSailin> ok be two different packages, one is papermonk-browser, the other is papermonk-prime
09:42 < ParahSailin> if that's "ugly", its because you're trying to do something intrinsically ugly
09:42 <@kanzure> there's a few ways around the xhr restrictions in a browser: (1) the server can have a proxy and you xhr to the proxy with your actual request, (2) you only run the downloaders on pages from publishers and the requests are just pass-through because you're already there, (3) something that injects an iframe into the page and then reads the response (but this gets annoying for POST/PUT/DELETE/whatever.. GET is simple)
09:43 <@kanzure> #2 is how zotero works
09:44 <@kanzure> because you only run the translators when you're currently on a page
09:45 <@kanzure> #1 would mean that you could only run papermonk in a browser when it's served from a particular server. but if you have to connect to a server to run papermonk requests through a proxy, why not just use papermonk on the server-side? so that's sorta irrelevant.
09:46 <@kanzure> i think #2 or #3 is necessary because my original plan was to make this something that can replace zotero's translators so that the zotero people will maintain my scrapers for me
09:48 < ParahSailin> is zotero a browser extension?
09:48 <@kanzure> yeah
09:49 <@kanzure> firefox-only
09:49 < ParahSailin> so then it would have its own sort of javascript jail that may or may not allow cross site requests
09:49 < ParahSailin> or is that a chrome only feature
09:50 <@kanzure> that's also present in firefox/gecko
09:50 <@kanzure> this is why the zotero translators only interact with the page/site that is currently loaded on the page
09:50 < ParahSailin> https://developer.mozilla.org/en-US/docs/Extension_Frequently_Asked_Questions#I_cannot_initiate_an_XMLHttpRequest_from_my_extension
09:50 <@kanzure> except.. through the zotero api.. which passes-through to the firefox extension api.
09:51 <@kanzure> oh hm
09:51 <@kanzure> i think those conditions are satisfied in zotero
09:53 <@kanzure> i'm trying to see if there's any zotero translator that uses an iframe or xhr or something
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10:00 <@kanzure> yeah i'm actually clueless here
10:02 <@kanzure> this one is interesting, https://github.com/zotero/zotero-connectors
10:02 <@kanzure> " The Zotero bookmarklet, part of https://github.com/zotero/zotero-connectors, runs Zotero translators in the browser. While it wasn't designed with modularity in mind, with some effort you could modify it to pass the item metadata to your JS instead of saving it to zotero.org."
10:02 <@kanzure> " translation-server (https://github.com/zotero/translation-server) is our current sever-side implementation of Zotero's translation architecture. It provides a simple API to extract metadata from a URL. zotero-node was our previous attempt at this; translation-server is somewhat more difficult to install, but faster, more compatible with translators, more stable, and actively maintained."
10:02 <@kanzure> "ProQuest PME (https://github.com/proquest/pme) is ProQuest's attempt to adapt about 20 of our translators (out of ~280 total) to work in their bookmarklet as part of RefWorks Flow (http://flow.proquest.com/). I've never tested it, but it exists."
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10:17 <@kanzure> this is some weird shit https://github.com/zotero/zotero-connectors/blob/master/build.sh
10:18 <@kanzure> ah.. Zotero.HTTP.doGet
10:19 <@kanzure> here's one that does an xhr-like operation (Zotero.HTTP.doGet)-- https://github.com/zotero/translators/blob/master/Stanford%20Encyclopedia%20of%20Philosophy.js
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10:25 <@kanzure> i've been waiting to tell zotero about what i'm up to because they have a /lot/ of activity and it's sorta rude to bring them a half-working proposal. this bookmarklet system seems curious.
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11:16 < KnightSirThom> !lastgame knightsirthom
11:16 < KnightSirThom> sorry wrong channel
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11:42 < archels> kanzure: do we know anyone in Zürich?
11:43 <@kanzure> eugen leitl might be nearby
11:43 <@kanzure> zakwilson
11:43 <@kanzure> there's a bunch of synthetic biology people at ETH
11:44 <@kanzure> wait, which zurich?
11:44 <@kanzure> oh i see it's in switzerland
11:45 <@kanzure> most of the hackteria people are supposed to be in switzerland
11:46 < archels> this event is from the University of Zurich, not ETH, but they are right next to each other
11:48 < archels> I'm not sure about the details of the relation between the two, but there are speakers from ETH coming, so it seems amiable
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11:54 < ParahSailin> i know some swiss people
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12:07 <@kanzure> oh man. shell script hell. https://github.com/zotero/provo this is how they test translators.
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12:12 <@kanzure> pfft the zotero people are suspicious
12:12 <@kanzure> 12:04 < simonster> the main disadvantages would be portability and performance
12:13 <@kanzure> performance should increase because papermonk doesn't have a dependency on firefox/gecko
12:13 <@kanzure> and portability.. eh. the zotero api is intricately linked to firefox, which has zero portability.
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15:04 < Reinhard> opensuse was a failure
15:04 < Reinhard> welp :/
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15:07 < n_bentha> http://www.extremetech.com/extreme/163997-carbyne-a-new-form-of-carbon-thats-stronger-than-graphene
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15:10 < ThomasEgi> reminds me of asbestos. sure that stuff isn't going to cause supercancer?
15:16 < poppingtonic> paperbot: http://www.jstor.org/stable/2384389
15:17 < n_bentha> that article is pretty bad (the one i posted earlier). this one is better: http://www.technologyreview.com/view/518301/new-form-of-carbon-is-stronger-than-graphene-and-diamond/
15:19 < paperbot> http://libgen.org/scimag/get.php?doi=10.2307%2F2384389
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16:18 < poppingtonic> http://boingboing.net/2013/08/16/an-urban-legend-documented.html
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17:36 <@kanzure> ParahSailin: unrelated, but here's a browserify bloat-finding tool https://github.com/hughsk/disc
17:51 <@kanzure> ParahSailin: so yeah, the zotero api allows unrestricted xhr. but the bookmarklets obviously have restricted xhr. so some translators are just flat out not included in the bookmarklets. according to simonster.
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18:13 <@kanzure> oh, my iframe + xhr idea is bad because of X-Frame-Options: SAMEORIGIN. i forgot.
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18:50 < juul> kanzure: what's your iframe + xhr idea?
18:50 <@kanzure> the one i mentioned above. nevermind though. it wouldn't work.
18:51 <@kanzure> there's no point in trying to hammer a browser into doing something that violates the security model of the web
18:51 <@kanzure> especially because i don't control publishers' servers
18:52 < juul> ok
18:52 < juul> i'm considering abusing the security model to sandbox user-written code
18:53 < juul> it's probably a bad idea
18:53 < juul> but i'm gonna do it anyway
18:53 <@kanzure> is ogden on drugs?
18:53 < juul> what?
18:53 <@kanzure> max. your homie, right?
18:54 < juul> no he's probably one of the sanest people i know
18:54 <@kanzure> i don't mean he's insane
18:54 <@kanzure> i mean he seems to push 50-100 commits/day reliably
18:54 < juul> haha, yeah
18:54 <@kanzure> not all of them great i guess
18:54 < juul> him and substack are a powerhouse
18:54 <@kanzure> substack is just a robot from the future trapped on earth
18:54 < juul> and he also finds time to come play at sudo room
18:55 < juul> yesterday ogden was 3d printing voxel graphics
18:55 <@kanzure> sometimes i spoof my commits to spread them out temporally but still..
18:55 <@kanzure> yeah, i saw some node modules about voxel/stl/3d printing things
18:55 < juul> yep
18:55 <@kanzure> and something about voxel hosting. shrug..
18:56 < juul> he did the in-browser minecraft world
18:56 < juul> not actual minecraft, but minecraft graphics
18:56 <@kanzure> i saw that because of the ardrone simulator that uses it
18:57 < juul> ah
18:57 <@kanzure> juul: i'm rewriting zotero to be a more modular and sane system. and less monolithic.
18:57 <@kanzure> juul: https://github.com/kanzure/papermonk
18:57 <@kanzure> juul: https://github.com/kanzure/papermonk-downloader-plosone
18:58 <@kanzure> at the moment i'm working on browserify compatibility. which is also why i was concerned about xhr+cors. but even zotero's bookmarklet system (where it dumps all of their 100s of translators into a giant bookmarklet) just drop/don't use translators that use remote http requests. so i guess i'm okay with a similar caveat.
18:59 < juul> oh niiice
19:00 <@kanzure> anyway this will soon replace paperbot
19:00 <@kanzure> and then i will have to start on rewriting pdfparanoia into javascript
19:00 <@kanzure> so that we can do streaming pdf watermark removal and streaming pdf pirating
19:00 < juul> oh, i assume there are good pdf libraries for js?
19:00 <@kanzure> probably not
19:00 < juul> ok
19:00 <@kanzure> python just has pdfminer, and it blows
19:01 < juul> fsf used to have pdf as one of their top priorities for free software
19:01 <@kanzure> i think juri_ worked on that or knows of it
19:01 <@kanzure> it was all xml xpath rewriting rules or something. it was really scary.
19:02 < juul> oh, yeah that sounds unfun
19:02 <@kanzure> i don't see any pdf parser modules on npmjs.org
19:02 < ParahSail1n> you really like javascript...
19:02 <@kanzure> to be honest, pdfparanoia just uses pdfminer for parsing, and then i manipulate pdfs manually and against the spec
19:02 <@kanzure> i don't like javascript at all, i fucking hate it
19:03 < ParahSail1n> to want to write a pdf parser in it
19:03 < juul> i guess there's this https://github.com/mozilla/pdf.js/
19:03 <@kanzure> that's a viewer
19:03 < juul> yeah, not ideal
19:03 <@kanzure> s/against the spec/by violating the spec
19:04 < juul> btw, a bit off topic, but some of my friends wrote Lua EventMachine
19:04 < juul> it's an interesting take on event-based network programming
19:04 < juul> no callbacks
19:05 < juul> or at least, no explicit callbacks
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19:06 < ParahSail1n> lua is awesome because, like js, there's only one numerical type
19:06 < juul> well, in node, there are libs to have multiple numeric types
19:06 < juul> heavily used in the 3D programming stuff
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19:42 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure tagged f5218f5 as v0.0.6 http://git.io/ND2lng
19:42 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure pushed 4 commits to master [+0/-0/±9] http://git.io/FRTLdg
19:42 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure 7f6e54a - replace request with hyperquest Also, use concat-stream to buffer the response body for parsing. Eventually, parsing will switch to some sort of stream-based html parser and metadata will be emitted as it's parsed or something.
19:42 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure 97d9e94 - also switch pdf downloading to hyperquest
19:42 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure 9bff2d7 - Merge branch 'use-hyperquest' into master Replace request with hyperquest.
19:42 < Not-002> [kanzure/papermonk-downloader-plosone] kanzure f5218f5 - version bump to: v0.0.6
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21:06 <@kanzure> juul: you wouldn't happen to know what to do with three different streams, would you? i have a request=hyperquest.get() and request.pipe(trumpeter) and output = through() and trumpeter.selectAll("title", function(title) { output.queue({title: title}); }) but what do i do about request.on("error") or giving "output" to the user as a stream to work with?
21:08 <@kanzure> the user has to be given something
21:08 <@kanzure> originally i was passing in a callback, and then passing a metadata dictionary into the callback (so callback(error, metadata)) but this doesn't make sense if i have streams and pipes available
21:15 < heath> hyperquest?
21:15 < heath> got it https://github.com/substack/hyperquest
21:17  * heath hasn't worked with streams as much as he would like
21:19 <@kanzure> heath: https://gist.github.com/kanzure/6255244
21:19 <@kanzure> heath: that's essentially what i'm trying to figur eout
21:20 < heath> pubsub
21:20 < heath> i imagine that's a way
21:21 < heath> https://github.com/mroderick/PubSubJS
21:21 < Noryokusha> welcome back heath
21:21 < Noryokusha> whered you go
21:23 < heath> it's the weekend, i'm trying to restrict my computer usage
21:27 < Noryokusha> do some pushups
21:27 < Noryokusha> ill compete with you
21:27 < Noryokusha> first to get 100 pushups wins
21:28 < heath> i probably already won this contest then :)
21:28  * heath walks away for awhile
21:31 < ParahSail1n> paperbot, http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060410#s5
21:32 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Non-Invasive%20Brain-to-Brain%20Interface%20%28BBI%29%3A%20Establishing%20Functional%20Links%20between%20Two%20Brains.pdf
21:32 <@kanzure> i don't think pubsub is the right answer
21:38 < heath> request within hyperquest is an instance of EventEmitter
21:38 < heath> you could attach an event listener for the error
21:38 <@kanzure> attach to what?
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21:40 < heath> you have it in your code, what's wrong with    //request.on("error", function(error){..});
21:40 <@kanzure> uh?
21:41 <@kanzure> because i don't want to handle the error, i want the user to
21:41 <@kanzure> even if i do write something there, i still need to tell the user
21:41 <@kanzure> see?
21:42 < heath> it's not clear to me how the user is using the system i guess
21:42 <@kanzure> downloader.download().pipe(pdfstream)
21:43 <@kanzure> or, really, it's more like a stream of metadata and pdf and other files
21:43 <@kanzure> and the user might save to that to the file system (i don't really care)
21:46 < Noryokusha> lol damn you heath
21:46 < Noryokusha> i can barely do 20
21:47 < heath> kanzure: maybe promises? this seems a bit much, but it would work
21:47 < heath> https://github.com/kriskowal/q
21:48 <@kanzure> no thanks, i think there's a way to do it with just streams or event emitters
21:48 <@kanzure> promises are a different beast
21:48 <@kanzure> promises are a way to organize callback spaghetti. i was trying to get away from using a callback.
21:48 <@kanzure> current version: https://github.com/kanzure/papermonk-downloader-plosone/blob/master/index.js#L24
21:48 <@kanzure> line 29 calls the callback
21:49 < heath> that's why i suggested it, the only other option i can think of is a callback for the download function
22:29 <@kanzure> neat, https://superevr.com/blog/2012/top-level-universal-xss/
22:29 <@kanzure> http://io./cgi-bin/whois?query=%3Ca%20href=%22%22%3E%3Cu%3EArbitrary%20HTML!%3C/u%3E%3C/a%3E%3C/h3%3E%3Cimg%20src=%22http://humananatura.files.wordpress.com/2011/08/hn-initials.jpg%22%3E%3Cscript%3Ealert('this%20will%20pop%20up%20in%20firefox!');%3C/script%3E%3Ch3%3E
22:48 <@kanzure> not bad https://www.runscope.com/ .. i think they bought http://requestb.in/ but that doesn't make sense because it was an open source project.
23:14 < rigel> so this whole couchdb thing
23:14 < rigel> that stores binary objects, no?
23:15 < rigel> all these streaming media servers use SQL
23:15 < rigel> and im wondering if thats still necessary
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23:28 < heath> rigel: that's mongo
23:28 < heath> couch is all json
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--- Log closed Sat Aug 17 00:00:58 2013