January 2015 - Pharo-users - lists.pharo.org

Re: [Pharo-users] Rule engine

by Evan Donahue

I would be curious to hear more about the various projects mentioned in this thread. I am working on a constraint logic system that has been used as a backend for a variety of inference systems in other languages. Thanks, Evan -- View this message in context: http://forum.world.st/Rule-engine-tp4801671p4802961.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

Jan. 31, 2015

Re: [Pharo-users] Seaside - How do I install Scriptaculous on a clean Seaside install (via Configuration Browser) on Pharo?

by Mircea S.

Well, I undertook a hands-on approach and finally figured it out. Mainly because I was following the Seaside book and the chapter on Scriptaculous. The packages needed for Scriptaculous to work are listed in the book here: http://book.seaside.st/book/web-20/scriptaculous/frameworks/installation Then you need to find a repository to get them from, after a little poking around here: http://www.smalltalkhub.com/mc/Seaside/ I chose the Seaside31 repository, which is what I apparently managed to install a few hours ago. http://www.smalltalkhub.com/mc/Seaside/Seaside31/main Then I had to Do-It a couple of times on (maybe there is a faster way to do this): Gofer new url:'http://www.smalltalkhub.com/mc/Seaside/Seaside31/main'; package: 'Javascript-Core'; load. Gofer new url:'http://www.smalltalkhub.com/mc/Seaside/Seaside31/main'; package: 'Prototype-Core'; load. Gofer new url:'http://www.smalltalkhub.com/mc/Seaside/Seaside31/main'; package: 'Scriptaculous-Core'; load. Gofer new url:'http://www.smalltalkhub.com/mc/Seaside/Seaside31/main'; package: 'Scriptaculous-Components'; load. Pe 31 ian. 2015, la 16:23, Johan Brichau <johan(a)inceptive.be> a scris: > Hi Mircea, > > Pharoâs Configuration browser loads the default group of the Metacello configuration, which unfortunately was set to âCoreâ for Seaside 3.1. > So, you will need to load additional groups programmatically: > > (ConfigurationOfSeaside3 project version: #stable) load: #(âScriptaculousâ âJSONâ) > > If you want to get the list of possible groups to load, inspect: > > (ConfigurationOfSeaside3 project version: #stable) groups > > This is something we fixed for Seaside 3.2, where the default will load everything to help newcomers. > We prefer not to change the existing 3.1 configuration versions to not break existing uses, but itâs fixed in the upcoming version. > > Btw, Scriptaculous is really outdated. You will prefer to use jQuery and jQuery-UI (or any other JS frameworkâ¦) > > cheers > Johan > >> On 31 Jan 2015, at 15:01, Mircea S. <mircea(a)unom.ro> wrote: >> >> I used the method described here to install Seaside3 on Pharo. All is well, but Scriptaculous doesn't come preinstalled. How do I get it? >> >> Seaside3 : >> >> 1: Go to the configuration manager >> >> 2: Select the Seaside 3 configuration. Click on Install. >> >> 3: Wait while it loads. Takes a couple of minutes on an i7 and a decent network link. >> >> 4: Open a Workspace and start a ZincServerAdaptor on the port you like (here 8080): ZnZincServerAdaptor startOn: 8080. (then CMD+d for Do It) >> >> 7: Access Seaside from your browser. >> >> 8: Install Scriptaculous, but how? > >

Jan. 31, 2015

Re: [Pharo-users] NumericalMethods and SciSmalltalk

by stepharo

Le 27/1/15 00:29, Werner Kassens a Ã©crit : > let me rephrase it <g> just that there are no misunderstandings, > NumericalMethods is independent of SciSmalltalk and does work in Pharo4 By SciTalk will include its own copy of NumericalMethods. Stef > werner > > > On 01/26/2015 10:22 PM, Ignacio Sniechowski wrote: >> That was my question. If in Pharo 4 the NumericalMethods package will be >> deprecated and instead SciSmalltalk will be de defacto package for >> stats. > >

Jan. 31, 2015

Re: [Pharo-users] Updated Pharo Days Schedule

by Ben Coman

Le 27/1/15 23:18, Ben Coman a Ã©crit : On Wed, Jan 28, 2015 at 2:09 AM, Sven Van Caekenberghe <sven(a)stfx.eu> wrote: > Hi Ben, > > I totally understand your question, but I known from experience that > things are always very hectic and connecting with off-site people is > usually quite hard. > cool. just giving it a bump ;). > > The main thing around your Delay work is to find someone knowledgeable > enough ;-) Or someone who wants to be knowledgable :). On Sat, Jan 31, 2015 at 5:30 PM, stepharo <stepharo(a)free.fr> wrote: > I will read it. > I have to fix one chapter of updated pharo > finish the mustache chapter and I will take time to at least have a > look precisely > > I appreciate that Stef. I know you have a heavy load. Actually (and I should have been more explicit) I was thinking this Delay stuff might be interesting knowledge to any robotics guys that might one day want to do soft-realtime control with Pharo (nudge-nudge). cheers -ben

Jan. 31, 2015

Re: [Pharo-users] how to debug zinc server errors from tests

by Ben Coman

On Sat, Jan 31, 2015 at 4:48 AM, Sven Van Caekenberghe <sven(a)stfx.eu> wrote: > > > On 30 Jan 2015, at 12:18, Ben Coman <btc(a)openInWorld.com> wrote: > > > > If there is a particular test you want to run outside of the test > framework, essentially you reproduce TestCase>>runCase in the Workspace. > > For example... > > MyClassTest new setUp testMyTest > > Actually the proper usage is > > MyTestCase run: #testSelector > > or > > MyTestCase debug: #testSelector > > Ahhh... Usually I do this when a test fails intermittently such that clicking on TestRunner's list of failed tests doesn't bring up a debugger. So my hack was to avoid the "on: self class failure , self class skip, self class warning, self class error do: [ ... ]" exception handling in #runCase:. #debug: is much better than my hack - thanks. cheers -ben

Jan. 31, 2015

Re: [Pharo-users] Seaside - How do I install Scriptaculous on a clean Seaside install (via Configuration Browser) on Pharo?

by Johan Brichau

Hi Mircea, Pharoâs Configuration browser loads the default group of the Metacello configuration, which unfortunately was set to âCoreâ for Seaside 3.1. So, you will need to load additional groups programmatically: (ConfigurationOfSeaside3 project version: #stable) load: #(âScriptaculousâ âJSONâ) If you want to get the list of possible groups to load, inspect: (ConfigurationOfSeaside3 project version: #stable) groups This is something we fixed for Seaside 3.2, where the default will load everything to help newcomers. We prefer not to change the existing 3.1 configuration versions to not break existing uses, but itâs fixed in the upcoming version. Btw, Scriptaculous is really outdated. You will prefer to use jQuery and jQuery-UI (or any other JS frameworkâ¦) cheers Johan > On 31 Jan 2015, at 15:01, Mircea S. <mircea(a)unom.ro> wrote: > > I used the method described here to install Seaside3 on Pharo. All is well, but Scriptaculous doesn't come preinstalled. How do I get it? > > Seaside3 : > > 1: Go to the configuration manager > > 2: Select the Seaside 3 configuration. Click on Install. > > 3: Wait while it loads. Takes a couple of minutes on an i7 and a decent network link. > > 4: Open a Workspace and start a ZincServerAdaptor on the port you like (here 8080): ZnZincServerAdaptor startOn: 8080. (then CMD+d for Do It) > > 7: Access Seaside from your browser. > > 8: Install Scriptaculous, but how?

Jan. 31, 2015

Seaside - How do I install Scriptaculous on a clean Seaside install (via Configuration Browser) on Pharo?

by Mircea S.

I used the method described here to install Seaside3 on Pharo. All is well, but Scriptaculous doesn't come preinstalled. How do I get it? Seaside3 : 1: Go to the configuration manager 2: Select the Seaside 3 configuration. Click on Install. 3: Wait while it loads. Takes a couple of minutes on an i7 and a decent network link. 4: Open a Workspace and start a ZincServerAdaptor on the port you like (here 8080): ZnZincServerAdaptor startOn: 8080. (then CMD+d for Do It) 7: Access Seaside from your browser. 8: Install Scriptaculous, but how?

Jan. 31, 2015

Re: [Pharo-users] Conditional CSV parsing

by stepharo

Sven I just added a section on your chapter :)

Jan. 31, 2015

Re: [Pharo-users] any imap + smtp client available?

by stepharo

I'm. Create a repo on smalltalkHub and try. Let me know if you need some help. Did you check in PharoExtras/Coral (we are reviving it slowly) because I imagine that there is also a readline command and terminal. Le 26/1/15 17:08, Martin BÃ¤hr a Ã©crit : > Excerpts from David T. Lewis's message of 2015-01-26 16:57:10 +0100: >>>>>>> due to compute power constraints, i am running "pharo" as my only >>>>>>> application via xinit, having to constantly switch between "pharo" >>>>>>> and console (for mutt) is becoming painful. :) >>>>>> another approach to that problem (which i am interested in) is to have >>>>>> a terminal within pharo. >>>> Are you aware of CommandShell (http://wiki.squeak.org/squeak/1914)? >>> thank you for pointing me to documentation. this will help for some of my >>> commandline work. it won't help to run mutt, sup (the mail client i use) >>> or tmux though. for those a full terminal emulator is needed. >> FYI, Ian Piumarta implemented telnet with full terminal (VT102) emulation. >> It uses a pty interface and thus supports mutt and text editors directly >> in the image. >> http://squeakvm.org/unix/goodies.html#html/goodies.m4.2.0 >> It works very well and does exactly what you want, but it was written more >> than 10 years ago and I cannot say what would be required to make it work >> on Pharo. > Ohhhhh! must . have . this . now ! > > thank you so much for this find! > > is anyone more familiar with pharo willing to work with me on this to see if we > can get it to work? > > greetings, martin. >

Jan. 31, 2015

Re: [Pharo-users] Conditional CSV parsing

by stepharo

hernan if you need some help you can also find a smart student and ask ESUG to sponsor him during a summertalk. Stef Le 26/1/15 21:03, HernÃ¡n Morales Durand a Ã©crit : > > > 2015-01-26 9:01 GMT-03:00 Sven Van Caekenberghe <sven(a)stfx.eu > <mailto:sven@stfx.eu>>: > > HernÃ¡n, > > > On 26 Jan 2015, at 08:00, HernÃ¡n Morales Durand > <hernan.morales(a)gmail.com <mailto:hernan.morales@gmail.com>> wrote: > > > > It is possible :) > > I work with DNA sequences, there could be millions of common > SNPs in a genome. > > Still weird for CSV. How many record are there then ? > > > We genotyped few individuals (24 records) but now we have a genotyping > platform (GeneTitan) with array plates allowing up to 96 samples, > which is up to 2.6 million of markers. The first run I completed > generated CSVs of 1 million of records (see attach). Sadly the > high-level analysis of this data (annotation, clustering, > discrimination) now is performed with R with packages like SNPolisher. > > And this is microarray analysis, NGS platforms produce larger volumes > of data in a shorter period of time (several genomes in a day). See > http://www.slideshare.net/allenday/renaissance-in-medicine-strata-nosql-and… > for the 2014-2020 predictions. > > Feel free to contact me if you want to experiment with metrics. > > I assume they all have the same number of fields ? > > > Yes, never seen CSV file with variable number of fields (in this domain) > > Anyway, could you point me to the specification of the format you > want to read ? > > > Actually I have no rush for this, I want to avoid awk, sed and shell > scripts in the next run. I would like to avoid Python but spreads like > a virus. > > I will be working mostly with CSV's from Axiom annotation files [1] > and genotyping results. Other file formats I use are genotype file > formats for programs like PLINK [2] (PED files, column 7 onwards) and > HaploView. Is worst than you might think, because you have to > transpose the output generated by genotyping platforms (millions of > records), and then filter & cut them by chromosome because those Java > programs cannot deal with all chromosomes at the same time. > > And to the older the that you used to use ? > > > http://www.smalltalkhub.com/#!/~hernan/CSV > <http://www.smalltalkhub.com/#%21/%7Ehernan/CSV> > > Cheers, > HernÃ¡n > > > [1] http://www.affymetrix.com/support/technical/annotationfilesmain.affx > [2] http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped > <http://pngu.mgh.harvard.edu/%7Epurcell/plink/data.shtml#ped> > > > Thx, > > Sven > > > Cheers, > > > > HernÃ¡n > > > > > > 2015-01-26 3:33 GMT-03:00 Sven Van Caekenberghe <sven(a)stfx.eu > <mailto:sven@stfx.eu>>: > > > > > On 26 Jan 2015, at 06:32, HernÃ¡n Morales Durand > <hernan.morales(a)gmail.com <mailto:hernan.morales@gmail.com>> wrote: > > > > > > > > > > > > 2015-01-23 18:00 GMT-03:00 Sven Van Caekenberghe <sven(a)stfx.eu > <mailto:sven@stfx.eu>>: > > > > > > > On 23 Jan 2015, at 20:53, HernÃ¡n Morales Durand > <hernan.morales(a)gmail.com <mailto:hernan.morales@gmail.com>> wrote: > > > > > > > > Hi Sven, > > > > > > > > 2015-01-23 16:06 GMT-03:00 Sven Van Caekenberghe > <sven(a)stfx.eu <mailto:sven@stfx.eu>>: > > > > Hi HernÃ¡n, > > > > > > > > > On 23 Jan 2015, at 19:50, HernÃ¡n Morales Durand > <hernan.morales(a)gmail.com <mailto:hernan.morales@gmail.com>> wrote: > > > > > > > > > > I used to use a CSV parser from Squeak where I could > attach conditional iterations: > > > > > > > > > > csvParser rowsSkipFirst: 2 do: [: row | " some action > ignoring first 2 fields on each row " ]. > > > > > csvParser rowsSkipLast: 2 do: [: row | " some action > ignoring last 2 fields on each row " ]. > > > > > > > > With NeoCSVParser you can describe how each field is read > and converted, using the same mechanism you can ignore fields. > Have a look at the senders of #addIgnoredField from the unit tests. > > > > > > > > > > > > I am trying to understand the implementation, I see you > included #addIgnoredFields: for consecutive fields in > Neo-CSV-Core-SvenVanCaekenberghe.21 > > > > A question about usage then, adding ignored field(s) > requires adding field types on all other remaining fields? > > > > > > Yes, like this: > > > > > > testReadWithIgnoredField > > > | input | > > > input := (String crlf join: #( '1,2,a,3' '1,2,b,3' > '1,2,c,3' '')). > > > self > > > assert: ((NeoCSVReader on: input readStream) > > > addIntegerField; > > > addIntegerField; > > > addIgnoredField; > > > addIntegerField; > > > upToEnd) > > > equals: { > > > #(1 2 3). > > > #(1 2 3). > > > #(1 2 3).} > > > > > > > > > > > > May be you like to know if you make a pass to NeoCSV, for some > data sets I have 1 million of columns, it would be nice an > addFieldsInterval: or such. > > > > 1 million columns ? How is that possible, useful ? > > > > The reader is like a builder. You could try to do this yourself > by writing a little loop or two. > > > > But still, 1 million ? > > > > > Thank you. > > > > > > HernÃ¡n > > > > > > > > > > > >

Jan. 31, 2015