February 2013 - Pharo-users

Re: [Pharo-users] Does a Stepper Widget exist for Pharo?

by Sean P. DeNigris

For an idea, take a look at DateModel, which is similar, but with a calendar icon instead of the stepper arrows. "DateModel new openWithSpec" -- View this message in context: http://forum.world.st/Does-a-Stepper-Widget-exist-for-Pharo-tp4671822p46718… Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

Feb. 24, 2013

Re: [Pharo-users] Does a Stepper Widget exist for Pharo?

by stephane ducasse

Note that I know but this would be a nice addition. S. On Feb 24, 2013, at 6:53 PM, MartinW <wm(a)fastmail.fm> wrote: > I am looking for a Stepper Widget - 2 buttons placed directly above each > other, that will increase/decrease a numerical value. Does something like > this exist for Pharo? > > If not, how would i start to build one? There are so many different Button > classes in the image :) > > See attached image of a Stepper: > <http://forum.world.st/file/n4671822/Stepper.png> > > > > -- > View this message in context: http://forum.world.st/Does-a-Stepper-Widget-exist-for-Pharo-tp4671822.html > Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >

Feb. 24, 2013

Does a Stepper Widget exist for Pharo?

by MartinW

I am looking for a Stepper Widget - 2 buttons placed directly above each other, that will increase/decrease a numerical value. Does something like this exist for Pharo? If not, how would i start to build one? There are so many different Button classes in the image :) See attached image of a Stepper: <http://forum.world.st/file/n4671822/Stepper.png> -- View this message in context: http://forum.world.st/Does-a-Stepper-Widget-exist-for-Pharo-tp4671822.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

Feb. 24, 2013

[JOB][Research] Postdoc position: IDEs

by Marcus Denker

Infrastructure for new generation IDEs ===================================== About Inria and the job ----------------------- Inria, with its academic, institutional and industrial partners, is commited to major research and innovation projects in the field of computational sciences. The institute disseminates across France thanks to its eight research centres. The Inria Lille - Nord Europe research centre, inaugurated in 2008, employs 357 people, including 250 scientists, in its seventeen research teams. Recognised for its significant contribution to the social and economic development of the Nord - Pas-de-Calais region, the Inria Lille - Nord Europe research centre promotes a policy of close cooperation with major businesses and small enterprises. By encouraging synergies between researchers and industrial partners, Inria contributes to the transfer of skills and expertise in computational technologies and provides access to top-level European and international research in order to support innovation and businesses, particularly in the region of Lille. Whether designing innovative software for business or logistics, modelling living cells or fusion plasma, or developing medical simulators or interfaces to facilitate human-computer interaction, our research opens up new possibilities that can revolutionise common practice and contribute to a better understanding of the natural phenomena which surround us. The goal of the RMoD research team at Inria Lille is to support re-modularization of object-oriented applications. This objective is tackled from two complementary perspectives: reengineering and modularity constructs for programming languages. For more information on RMOD, see http://rmod.lille.inria.fr Mission ------- The objectives will be to reconsider and develop a new infrastructure to build new and modern IDEs. The goal of this postdoc is to help the RMOD team rethinking the infrastructure of Pharo from the point of view of its user interface and interaction foundation as well as code navigation. The following topics will be analysed and rethought : - Alternate models of event handling - Decomposing responsibilities of event handler and dispatchers. - Alternative ways to navigate code - Queries to access code elements - Smart handling of coding contexts - Management of window plague - Support for contextual refactorings and automated code transformation. Skills and profile ------------------ - English - Pharo: http://www.pharo.org - User interface design, Vector graphics - IDE design and user interactions Benefits --------- - Possibility of French courses - Help for housing - Participation for transportation - Scientific Resident card and help for husband/wife visa Additional information ----------------------- - Duration : 16 months - Salary: 2 620,84 â¬ gross/month - Monthly salary after taxes : around 2 138 â¬ (medical insurance included) - For the first selections, please apply before March 2013, 22nd. - Before applying, please contact the scientist advisor: stephane.ducasse(a)inria.fr - More information: http://rmod.lille.inria.fr/web/pier/blog/2013-02-22 Security and defense procedure ------------------------------ In the interests of protecting its scientific and technological assets, Inria is a restricted-access establishment. Consequently, it follows special regulations for welcoming any person who wishes to work with the institute. The final acceptance of each candidate thus depends on applying this security and defense procedure.

Feb. 24, 2013

Re: [Pharo-users] NB crash boom

by Sean P. DeNigris

Issue 7583: [ENH]: NB system example https://code.google.com/p/pharo/issues/detail?id=7583 -- View this message in context: http://forum.world.st/NB-crash-boom-tp4669980p4671786.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

Feb. 24, 2013

PhyloclassTalk (was: Re: [squeak-dev] [ANN] BioSqueak 0.4)

by HernÃ¡n Morales Durand

Hello Hannes, Sorry for the late response, I have been working intensively in an application using BioSmalltalk. Here is a post with some screenshots: http://biosmalltalk.blogspot.com.ar/2013/02/phyloclasstalk-preview.html as I've said, it is developed in Pharo but most subsystems work in Squeak too. I cross-post to the Pharo users list in case someone is interested. El 16/02/2013 16:00, H. Hirzel escribiÃ³: > Hello HernÃ¡n > > Thank you for your elaboration on the topic of BioSqueak. > > On 2/1/13, HernÃ¡n Morales Durand <hernan.morales(a)gmail.com> wrote: >> >> Hello Hannes, >> Thanks for the feedback! Some answers then between the lines: >> >> El 01/02/2013 11:35, H. Hirzel escribiÃ³: >>> Hello HernÃ¡n >>> >>> This is interesting. >>> http://biosmalltalk.blogspot.com/ >>> >>> I understand that you have constructed an internal domain specific >>> language (a DSL, a query language) for dealing with genetic data in >>> Smalltalk >>> >>> search := BioNCBIWWWBlastClient new nucleotide query: >>> 'CCCTCAAACAT...TTTGAGGAG'; >>> hitListSize: 150; >>> filterLowComplexity; >>> expectValue: 10; >>> wordSize: 11; >>> blastn; >>> blastPlainService; >>> alignmentViewFlatQueryAnchored; >>> formatTypeXML; >>> fetch. >>> search outputToFile: 'blast-query-result.xml' contents: search result. >>> >>> Is there a description of this DSL? >> >> Is not a DSL in the traditional sense, i.e., using ANTLR, Lex or Yacc, >> but a "DSL" which is embedded thus inheriting the syntax and execution >> semantics of Smalltalk. > > Yes, I understand, the regular thing in Smalltalk as every Smalltalk > domain model could be considered a DSL to a certain extent/ > > Lukas Renggli has a useful classification on DSLs in his PhD dissertation on > 'Dynamic Language Embedding'' > http://scg.unibe.ch/archive/phd/renggli-phd.pdf > Chapter 2 > > According to that you probably have an Internal DSL (chapter 2.1), right? > Yes, it would fit into the Internal DSL category. I didn't knew about that classification, thanks for sharing. > >> To clarify: I've not built a DSL specification for the QBlast API, >> although I'm willing to develop DSLs for bioinformatics APIs in a >> Smalltalk language workbench (anyone?). > > OK > >> Currently the messages for performing alignments at the NCBI are based >> in the API specification, >> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html . > > The unary >> sends are the result of a plan to reduce parametrization and to >> replicate or customize Blast settings through a UI. This is because >> geneticists experiment changing Blast parameters over time and I want my >> system not to be tied to textual parameters. >> > > >> > The data is kept in XML files and >> > all is read into the image to be queried. It seems that you don't have >> > a problem with the image size? >> >> Yes I had problems with image size and performance, a lot indeed. > >> Actually working with XML DOM with alignments of 5000 or more hits >> Squeak (and Pharo of course) started to show slowliness. So I cannot >> keep all XML nodes in memory. To overcome this problem I've tried the >> SAX (push) parser and the XMLPullParser (which is a StAX parser). Then >> my idea was to reduce the tree by specifying only the XML nodes which >> I'm interested for. After reducing the nodes, I wrote custom XML tree >> classes with a specific API to query blast XML results, taken form the >> DTD specification. AFAIK this is known as a XML digester, which is >> somewhat "evolved" in Java >> (http://commons.apache.org/digester/xmlrules.html) > > I understand that you took > http://www.squeaksource.com/XMLSupport/ > (the XML support repo for Pharo, for Squeak XML support is in > the trunk image) > and modified it. > >> I have built a >> dynamic query builder in Morphic for querying the XML providing the >> possibility of persist and update the filters. Unfortunately for Squeak >> users I'm using the Polymorph API, which I think is not available in >> Squeak. > > A screen shot would be appreciated... :-) > Ok, the blog post includes some screenshots. >> We worked using the XML push/pull parsers for reading genomes and they >> worked acceptably. But it is impossible to keep nodes for 3 GBytes of >> XML at least for now in Squeak/Pharo. > > According to my experience keeping XML structures in the image is > inefficient in terms of memory usage. More efficient ways are needed > and XML is then only for reading/writing to external files. > Exactly, XML is not good at all for big data. >> More and critical problems arise when trying to work with microarray >> data (big data) in Smalltalk which is not document-oriented. I had to >> switch to "solutions" like SQL, or HDF5 using Pytables with >> well-designed scheme for our input. The advantages are that supports >> indexing and reading data in blocks, besides tools like Vitables or >> HDFView to navigate the data. Until someone provides some bits in this >> field, there is little opportunity for using Smalltalk. > > But what I understand is that people keep DNA data in memory for speed > reasons and use C++ or Perl programs to deal with it. > It really depends of the type of analysis, I've seen most starter bioinformaticians prefer Python over Perl because of the nicer syntax and more complete library support. I don't know big data projects using C++ with raw DNA data. Compression with indexing, and specialized file formats are used these days, splitting data in clusters where needed. I would love to see some Smalltalkers working on dataspaces too. See these presentations: http://www.slideshare.net/mndoci/presentations >>> I would welcome a short writeup with a general introduction to what >>> you are doing in http://biosmalltalk.blogspot.com/. > > >> >> We have submitted a paper recently and we are waiting for the review >> results. On the other side we are preparing another paper for a >> phylogenetics decision support system which includes text-mining and a >> rule engine. I will try to write an entry in the next week with >> screenshots. > > Any news on this? > No news so far, still in the reviewing process. Best regards, HernÃ¡n > Kind regards > Hannes > > >> Best regards, >> >> HernÃ¡n >> >>> Kind regards >>> >>> Hannes Hirzel >>> >>> On 2/1/13, HernÃ¡n Morales Durand <hernan.morales(a)gmail.com> wrote: >>>> Hi, >>>> >>>> Few days ago I created a port of BioSmalltalk for Squeak too. >>>> BioSmalltalk is a library for doing Bioinformatics with Smalltalk. This >>>> port is labelled "BioSqueak" and I expect to release a version for >>>> Windows sometime soon. You can find it in: >>>> >>>> http://code.google.com/p/biosmalltalk/downloads/list >>>> >>>> I'm very interested in feedback. >>>> Thanks for reading. >>>> >>>> HernÃ¡n >>>> >>>> -- >>>> HernÃ¡n Morales >>>> Institute of Veterinary Genetics (IGEVET) >>>> http://igevet.fcv.unlp.edu.ar >>>> National Scientific and Technical Research Council (CONICET). >>>> La Plata (1900), Buenos Aires, Argentina. >>>> Telephone: +54 (0221) 421-1799. >>>> Internal: 422 >>>> Fax: 425-7980 or 421-1799. >>>> >>>> >>> >>> >> >> >> > >

Feb. 23, 2013

Re: [Pharo-users] MongoTalk "ns name too long" error

by Sabine KnÃ¶fel

Hi Norbert ah, ok...that works! Thank you! Sabine |theCollection theString| theCollection := self database addCollection: 'persons'. theString := '{ "personnelNumber" : "002", "bankAccountNumber" : "45215460", "lastName" : "Tester", "plz" : "79214", "nextTripNumber" : 1, "displayBubbleTip" : "some", "fax" : "+49-762-34834-99", "isEmployer" : false, "street" : "Haslacher Strasse 2", "blz" : "68050101", "tableOfAccounts" : "SKR03", "place" : "Freiburg", "bankName" : "Comdirekt Bank", "subtractPaymentInKind" : true, "email" : "sabde.ddfel(a)gmail.com", "creationTimestamp" : "23.02.2013-10:39-143192709", "phone" : "+49-762-34834", "mobile" : "+49-151-38374637", "firstName" : "Susi" }'. theCollection add: (Dictionary new at: '002' put: theString; yourself). -- View this message in context: http://forum.world.st/MongoTalk-ns-name-too-long-error-tp4671488p4671642.ht… Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

Feb. 23, 2013

Re: [Pharo-users] MongoTalk "ns name too long" error

by Norbert Hartl

Sabine, addCollection: is used to add a collection to a database. You need add your entry _to_ a collection. So (self database addCollection: 'mycollection') add: {â¦} should work. Norbert Am 22.02.2013 um 15:39 schrieb Sabine KnÃ¶fel <sabine.knoefel(a)gmail.com>: > Hi, > > I try to add the following instance to my MongoDB: > > self database addCollection: '{ > "personnelNumber" : "002", > "bankAccountNumber" : "45215460", > "lastName" : "Tester", > "plz" : "79214", > "nextTripNumber" : 1, > "displayBubbleTip" : "some", > "fax" : "+49-762-34834-99", > "isEmployer" : false, > "street" : "Haslacher Strasse 2", > "blz" : "68050101", > "tableOfAccounts" : "SKR03", > "place" : "Freiburg", > "bankName" : "Comdirekt Bank", > "subtractPaymentInKind" : true, > "email" : "sabine.knfffel(a)fmail.com", > "creationTimestamp" : "22.02.2013-15:08-72889452", > "phone" : "+49-762-34834", > "mobile" : "+49-151-38374637", > "firstName" : "Theo" > }' > > I get this error back from the database: > a Dictionary('code'->10080 'errmsg'->'exception: ns name too long, max size > is 128' 'ok'->0.0 ) > > It seems that MongoDB is trying to add an index (with a field "ns") which is > a composition of all my fields: > > { > "v": NumberInt(1), > "key": { > "_id": NumberInt(1) > }, > "ns": "RKA24B.{\r\t \t\"personnelNumber\" : > \"002\",\r\t\"bankAccountNumber\" : \"45215460\",\r\t \r........this is > longer than 128 sings and causes the error..........}", > "name": "_id_" > } > > Writing above instance to the database DIRECTLY from shell (or with > RockMongo) works fine. > What is wrong within Mongotalk? (the testcases work fine because the test > objects are small enough) how can I write my instance to the database, how > can I avoid that MongoTalk tries to create the index thing? > > Adding a line with id > "_id": "512fff76e79dc751e180c000001", > does not work either. > > Sabine > > > > -- > View this message in context: http://forum.world.st/MongoTalk-ns-name-too-long-error-tp4671488.html > Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >

Feb. 22, 2013

MongoTalk "ns name too long" error

by Sabine KnÃ¶fel

Hi, I try to add the following instance to my MongoDB: self database addCollection: '{ "personnelNumber" : "002", "bankAccountNumber" : "45215460", "lastName" : "Tester", "plz" : "79214", "nextTripNumber" : 1, "displayBubbleTip" : "some", "fax" : "+49-762-34834-99", "isEmployer" : false, "street" : "Haslacher Strasse 2", "blz" : "68050101", "tableOfAccounts" : "SKR03", "place" : "Freiburg", "bankName" : "Comdirekt Bank", "subtractPaymentInKind" : true, "email" : "sabine.knfffel(a)fmail.com", "creationTimestamp" : "22.02.2013-15:08-72889452", "phone" : "+49-762-34834", "mobile" : "+49-151-38374637", "firstName" : "Theo" }' I get this error back from the database: a Dictionary('code'->10080 'errmsg'->'exception: ns name too long, max size is 128' 'ok'->0.0 ) It seems that MongoDB is trying to add an index (with a field "ns") which is a composition of all my fields: { "v": NumberInt(1), "key": { "_id": NumberInt(1) }, "ns": "RKA24B.{\r\t \t\"personnelNumber\" : \"002\",\r\t\"bankAccountNumber\" : \"45215460\",\r\t \r........this is longer than 128 sings and causes the error..........}", "name": "_id_" } Writing above instance to the database DIRECTLY from shell (or with RockMongo) works fine. What is wrong within Mongotalk? (the testcases work fine because the test objects are small enough) how can I write my instance to the database, how can I avoid that MongoTalk tries to create the index thing? Adding a line with id "_id": "512fff76e79dc751e180c000001", does not work either. Sabine -- View this message in context: http://forum.world.st/MongoTalk-ns-name-too-long-error-tp4671488.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

Feb. 22, 2013

Re: [Pharo-users] Programmatically generating classes and methods

by Tudor Girba

+1 Doru On Sun, Feb 17, 2013 at 7:30 PM, Sven Van Caekenberghe <sven(a)stfx.eu> wrote: > > On 17 Feb 2013, at 18:48, Mariano Martinez Peck <marianopeck(a)gmail.com> > wrote: > > > On Sun, Feb 17, 2013 at 12:38 PM, Sven Van Caekenberghe <sven(a)stfx.eu> > wrote: > > Sun, Sean, Ben, > > > > Thanks for the answers, I think I know the direction now, time to start > experimenting. > > > > > > Hi Sven. > > > > If I were you, I would take a look to FuelMetalevel tests. There we > create classes, traits, methods, etc programmatically and for tests. It is > quite hard to do things silently...and you may let lots of stuff in middle > state even after having run the tests. So I recommend to take a look to our > tests. To do that: > > > > 1) get the package FuelMetalevel and FuelMetalevelTests from ' > http://ss3.gemstone.com/ss/Fuel' > > > > 2) Check methods of class FLClassSerializationTest, FLSerializationTest > protocol 'class-factory' and finally, ClassFactoryForTestCase (be sure to > be in Pharo 2.0) > > Hey Mariano, great pointer - Thanks. > > The Fuel codebase is really impressive ! > > Sven > > > Best, > > > > Sven > > > > On 17 Feb 2013, at 14:14, "Sean P. DeNigris" <sean(a)clipperadams.com> > wrote: > > > > > Sven Van Caekenberghe-2 wrote > > >> Can someone point me to the right/official way to programmatically add > > >> classes and methods in Pharo 2.0 ? > > > > > > I may be misunderstanding you, but the new class template in Nautilus > is the > > > method, and I always use #compile:classified: for methods. > > > > > > HTH, > > > Sean > > > > > > > > > -- > > > View this message in context: > http://forum.world.st/Programmatically-generating-classes-and-methods-tp467… > > > Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. > > > > -- > > Sven Van Caekenberghe > > http://stfx.eu > > Smalltalk is the Red Pill > > > > -- > > Mariano > > http://marianopeck.wordpress.com > > > -- www.tudorgirba.com "Every thing has its own flow"

Feb. 22, 2013