February 2013 - Pharo-users

NB crash boom
by DeNigris Sean Feb. 24, 2013

Feb. 24, 2013

Why is this simple experiment crashing the vm? It seemed like such a small change from the getenv example that I was sure it would succeed. Mac 10.8.2 with lastest nbcog vm... run: str "self run: 'open http://www.google.com'." <primitive: #primitiveNativeCall module: #NativeBoostPlugin error: errorCode > ^ self nbCall: #( int system (String str) ) module: NativeBoost CLibrary Thanks, Sean

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PhyloclassTalk (was: Re: [squeak-dev] [ANN] BioSqueak 0.4)
by HernÃ¡n Morales Durand Feb. 23, 2013

Feb. 23, 2013

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. >>>> >>>> >>> >>> >> >> >> > >

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MongoTalk "ns name too long" error
by Sabine KnÃ¶fel Feb. 23, 2013

Feb. 23, 2013

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.

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Programmatically generating classes and methods
by Sven Van Caekenberghe Feb. 22, 2013

Feb. 22, 2013

Hi, Can someone point me to the right/official way to programmatically add classes and methods in Pharo 2.0 ? I can find some methods on Class and I guess the Compiler can be used as well, but it is all pretty confusing. I want the proper notifications and other mechanisms to be triggered. Thx, Sven -- Sven Van Caekenberghe http://stfx.eu Smalltalk is the Red Pill

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Looking for MongoTalk documentation/tutorial/blog/intro...
by Sabine KnÃ¶fel Feb. 22, 2013

Feb. 22, 2013

Hi, installing and running MongoDB with MongoTalk was quite easy and I want to look deeper in it. Is there a documentation/tutorial/blog/intro/anything available for MongoTalk? Sabine -- View this message in context: http://forum.world.st/Looking-for-MongoTalk-documentation-tutorial-blog-int… Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

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Large cursor support: how to?
by Torsten Bergmann Feb. 21, 2013

Feb. 21, 2013

The class "Cursor" has class variables containing the forms for the different cursors. You can change them with Cursor classPool at: #MoveCursor put: cursor. In general you can set it to any form like this: |form cursor| form := (Form extent: 23@23 depth: 32 fromArray: #( 0 0 0 0 0 0 0 ... 0 0) "the array representing the form" offset: 0@0). cursor := Cursor extent: 23@23 depth: 32. cursor offset: -12 @ -12. cursor bits: form bits. Cursor classPool at: #MoveCursor put: cursor. "the cursor you may want to change" cursor beCursor If in Pharo 2.0 just open Tools -> Configuration Browser. There you will find a configuration for "Vista Cursor" which should give you an example. Have fun T.

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Large cursor support: how to?
by phil＠highoctane.be Feb. 21, 2013

Feb. 21, 2013

Hello, I am using pretty large cursors on Windows and OSX since my eyesight isn't that great. When using Pharo on OSX, the cursor is superb when in OSX apps, but in Pharo, the cursor is that ugly magnified 16x16 kind of form. I had a look in there and all cursors appear to be that kind of size. How would you go in changing that cursor support to support larger cursor forms? One thing which is great in Pharo is the ability to change all fonts at will, and set things up for a pretty neat visually accessible environment (large fonts take their toll on performance and memory but that's another story). So, can someone give me some pointers? TIA Phil

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ESUG at Google Open Source Blog
by Carla F. Griggio Feb. 20, 2013

Feb. 20, 2013

Hello everybody! Last Friday the Google Open Source Blog published a post about ESUG's GSOC 2012. Have a look! http://google-opensource.blogspot.fr/2013/02/some-small-talk-with-esug.html Congratulations once again to everybody that participated :) Cheers! Carla

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Slices and monticello - add to package... or add package to ... ? + procedure
by phil＠highoctane.be Feb. 19, 2013

Feb. 19, 2013

I was educating myself on slices. Maybe I'll be able to contribute a bit properly one of these days. Reading from http://code.google.com/p/pharo/wiki/HowToContribute. Creating a slice in my own package-cache is all fine. Now, to add it to the PharoInbox, I watched the screencast: http://www.pharocasts.com/2010/03/how-to-contribute-to-pharo.html There is this thing were we need to go to the PharoInbox repo in the right pane on monticello. The right click and select the Add to package.. option and then select the slice. All right, I can understand but this feels like unnatural to be on a repository and ask to "Add to package..." where what I want to do is to add the package to the repository. I understand that this is required to have the repository associated with the package so that I can save the package to one of its associated repositories. Maybe "Associate with package..." may be more helpful. Also the procedure on HowToContribute is not right anymore. As the UI changed. There is my version: # How to make a slice Slice: Your modification affect more than one package: you have to create a SLICE package in your package cache A SLICE is just a package with dependents ones, so you have to indicate the dependent packages. ## Procedure Open the Monticello browser. You should see one or more packages marked as modified (they have an asterisk before their name). Select your package-cache repository on the right hand pane. Create the new SLICE (click on the ''+SLICE'' button) and follow the instructions. ### Old way _Mark all_ the modified packages (the ones with asterisks before their names) required by your SLICE package. To do this, right click on the SLICE package in the left pane and select ''add required package'', then select the package from the next menu. Repeat for all modified packages. (Yeah, boring) ### New way (Pharo 2.0 at least) Put the issue tracker number in the Issue Number box and hit "Grab" to get the title of the issue. The (un)select in the list of "Dirty Packages to be included in the slice" ### Back to regular programming... Select your package-cache repository, this will enable the save button. Save the SLICE package (click on the ''Save'' button). An mcz package will be saved in your cache for the SLICE package and all the modified packages. (Name: something along the lines of SLICE-Issue-XXXX-YYYY-ZZZZ-Comment-Initials.1) You will be prompted for a log message (for each one of them ?), type a useful comment for the first package, (copy it and paste it on the others - sure?). Make sure to give the number of the issue your SLICE addresses in the comment. Publish the package to PharoInbox repository. # Hwo to publish to the PharoInbox repository Open monticello. Select the PharoInbox repository on the right pane. Right click the repository and select "Add to package..." (this will associate the package to the repository). You'll be presented with a list of possible packages. Pick up your slice. Then, go back to Monticello Browser with a list of packages on the left and a list of repositories on the right. Select on your slice on the left. Select the PharoInbox repository on the right. Click the Save button on the top bar. That's it, slice now in PharoInbox. Phil

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Pharo By Example 2 Book - Assembled Files in PDF form.
by phil＠highoctane.be Feb. 19, 2013

Feb. 19, 2013

Hi all, I struggled with the fact that the PBE2 book was in tex format and not all chapters were together in a single PDF. So, I ran the scripts in order to get a version with all the parts put together. This should be made into a Jenkins job I think so that we can have the PBE2 and other books in PDF form for easier dissemination. Here is the current assembly: https://www.dropbox.com/s/t8pesgxsovy61k5/PBE2-Assembled-20130213.pdf 412 pages of Pharo explanations. How lovely! Enjoy, Phil

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