- Pharo-users - lists.pharo.org

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 Btw, Scriptaculous is really outdated.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

Re: [Pharo-users] Rule engine

by stepharo

I know that Herve Verjus and Marc-Philippe Huget wrote and publish a forward and backward chainer. Now I would be interested in a system that can also use objects for facts. So Udo told me that he is doing a rete. Now if I remember correctly kris gybels had a rete . Stef Le 26/1/15 09:50, HernÃ¡n Morales Durand a Ã©crit : > Hello, > > If anyone is working in a rule engine we could merge efforts because I > have implemented one (or something like that) for a project. > Cheers, > > HernÃ¡n >

Jan. 31, 2015

Re: [Pharo-users] Updated Pharo Days Schedule

by Ignacio Sniechowski

Great news. Thanks!! Best, Nacho *Lic. Ignacio Sniechowski, MBA* *Prosavic SRL* *Tel: (011) 4542-6714* On Sat, Jan 31, 2015 at 6:20 AM, stepharo <stepharo(a)free.fr> wrote: > All the presentations were recorded on a cheap video camera and we will > upload them. > Martin should have them. > > Stef > > Le 27/1/15 18:19, Andy Burnett a Ã©crit : > >> Any chance that the presentations will be video recorded? I can't attend >> but I would love to watch. >> >> Cheers >> Andy >> >> >> >> >> > >

Jan. 31, 2015

Re: [Pharo-users] New book for Pharo :)

by stepharo

> I second that: you never fail to impress. Excellent work, Steph !!! Thanks but you know this is just one step after the other. Stef > > > On 29-01-2015 14:55, blake wrote: >> You never fail to impress, Steph. Excellent work. >> >> On Wed, Jan 28, 2015 at 9:21 AM, stepharo <stepharo(a)free.fr >> <mailto:stepharo@free.fr>> wrote: >> >> Didier Besset offered his great book "Object-Oriented >> Implementation of Numerical Methods >> An Introduction with Smalltalk and Java" to the community. >> > (...) > -- > The information contained in this message is confidential and intended > to the recipients specified in the headers. If you received this > message by error, notify the sender immediately. The unauthorized use, > disclosure, copy or alteration of this message are strictly forbidden > and subjected to civil and criminal sanctions. > > == > > This email may be signed using PGP key *ID: 1455478743A83CC3*

Jan. 31, 2015

Re: [Pharo-users] New book for Pharo :)

by stepharo

Excellent I guess that serge is back from PharoDays and he will give you access to Sci Stef Le 29/1/15 08:51, HernÃ¡n Morales Durand a Ã©crit : > We could probably start with > RBClassRegexRefactoring new > renameClasses; > replace: '^Dhb(.*)$' with: 'NM$1' ignoreCase: false; > execute. > or whatever prefix you prefer :) > > I wrote some DHB extensions for easier building of matrices, > if anyone give me access to the SciSmalltalk repository I could push > them for review. > > HernÃ¡n > > > > > > 2015-01-29 4:05 GMT-03:00 stepharo <stepharo(a)free.fr > <mailto:stepharo@free.fr>>: > > So hernan > how do we make progress? > > >

Jan. 31, 2015

Re: [Pharo-users] Problem due to deprecation of class Url in Pharo 3 and Moose 5.0

by PBKResearch

Hello All Just a follow-up to this query posted three weeks ago. I was e-mailed a week ago by Monty telling me about an alternative approach to my problem: "Hi Peter. I'm writing you because of your post on the Pharo users list two weeks ago on problems with Todd Blanchard's HTML/CSS parser and ZnUrl. I'm a maintainer of PharoExtras/XMLParser on SmalltalkHub, and you may not know, but there's an optional HTML parsing add-on in the repo, ConfigurationOfXMLParserHTML. This loads two other parsers, SAXHTMLHandler (SAX) and XMLHTMLParser (DOM, probably the one you want), that convert malformed HTML to well-formed XML. [remainder clipped]" I was a bit unsure about this, partly because I am not very familiar with XML, partly because it seemed perverse to change the representation just to analyse the DOM. However, now I have looked into it more it seems very sensible; the manipulation of the XML version of the DOM is much easier. So I have decided to discontinue using the Blanchard parser and switch to XMLHTMLParser, which has the additional advantage of being actively maintained. The moral is that it is always worth posting questions here. There are many people watching, and there is the chance of a bit of lateral thinking. Posted here also because my attempts to e-mail Monty directly have failed, so thanks again Monty. Peter Kenny From: PBKResearch [mailto:peter@pbkresearch.co.uk] Sent: 10 January 2015 10:41 To: 'pharo-users(a)lists.pharo.org' Subject: Problem due to deprecation of class Url in Pharo 3 and Moose 5.0 Hello I have run into a problem in moving some existing work from earlier versions of Pharo/Moose. I have found a work around, but I wonder if there is a tidier way of handling it. I make frequent use of Todd Blanchard's HTML parser and validator, HTMCSS (http://smalltalkhub.com/#!/~ToddBlanchard/HTMCSSValidatingParser) which was originally written for Squeak but has performed without trouble on earlier versions of Pharo. When I try to use it on Moose 5.0, I get frequent warning messages about Url being deprecated. I have made the problem go away by commenting out the deprecation warning in Url class>>new, but I wonder what should be done on a more permanent basis. [clipped] Thanks in advance for any help or suggestions. Peter Kenny

Jan. 31, 2015