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  • Idiomatic ruby for temporary variables within a method

    - by Andrew Grimm
    Within a method, I am using i and j as temporary variables while calculating other variables. What is an idiomatic way of getting rid of i and j once they are no longer needed? Should I use blocks for this purpose? i = positions.first while nucleotide_at_position(i-1) == nucleotide_at_position(i) raise "Assumption violated" if i == 1 i -= 1 end first_nucleotide_position = i j = positions.last while nucleotide_at_position(j+1) == nucleotide_at_position(j) raise "Assumption violated" if j == sequence.length j += 1 end last_nucleotide_position = j Background: I'd like to get rid of i and j once they are no longer needed so that they aren't used by any other code in the method. Gives my code less opportunity to be wrong. I don't know the name of the concept - is it "encapsulation"? The closest concepts I can think of are (warning: links to TV Tropes - do not visit while working) Chekhov'sGun or YouHaveOutlivedYourUsefulness. Another alternative would be to put the code into their own methods, but that may detract from readability.

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  • Calling another ruby script from a ruby script

    - by Andrew Grimm
    In ruby, is it possible to specify to call another ruby script using the same ruby interpreter as the original script is being run by? For example, if a.rb runs b.rb a couple of times, is it possible to replace system("ruby", "b.rb", "foo", "bar") with something like run_ruby("b.rb", "foo", "bar") so that if you used ruby1.9.1 a.rb on the original, ruby1.9.1 would be used on b.rb, but if you just used ruby a.rb on the original, ruby would be used on b.rb? I'd prefer not to use shebangs, as I'd like it to be able to run on different computers, some of which don't have /usr/bin/env.

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  • Running another ruby script from a ruby script

    - by Andrew Grimm
    In ruby, is it possible to specify to call another ruby script using the same ruby interpreter as the original script is being run by? For example, if a.rb runs b.rb a couple of times, is it possible to replace system("ruby", "b.rb", "foo", "bar") with something like run_ruby("b.rb", "foo", "bar") so that if you used ruby1.9.1 a.rb on the original, ruby1.9.1 would be used on b.rb, but if you just used ruby a.rb on the original, ruby would be used on b.rb? I'd prefer not to use shebangs, as I'd like it to be able to run on different computers, some of which don't have /usr/bin/env. Edit: I didn't mean load or require and the like, but spawning new processes (so I can use multiple CPUs).

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  • Programmatically printing git revision and checking for uncommitted changes

    - by Andrew Grimm
    To ensure that my scientific analysis is reproducible, I'd like to programmatically check if there are any modifications to the code base that aren't checked in, and if not, print out what commit is being used. For example, if there are uncommitted changes, it should output Warning: uncommitted changes made. This output may not be reproducible. Else, produce Current commit: d27ec73cf2f1df89cbccd41494f579e066bad6fe Ideally, it should use "plumbing", not "porcelain".

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  • Can I ensure all tests contain an assertion in test/unit?

    - by Andrew Grimm
    With test/unit, and minitest, is it possible to fail any test that doesn't contain an assertion, or would monkey-patching be required (for example, checking if the assertion count increased after each test was executed)? Background: I shouldn't write unit tests without assertions - at a minimum, I should use assert_nothing_raised if I'm smoke testing to indicate that I'm smoke testing. Usually I write tests that fail first, but I'm writing some regression tests. Alternatively, I could supply an incorrect expected value to see if the test is comparing the expected and actual value.

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  • Is removing unused functionality a bad thing?

    - by Andrew Grimm
    Is it possible for YAGNI to apply in the past tense? You created some functionality, it was used a little bit a while ago, but you aren't using it any more, and you don't want to maintain it, so you'd rather delete it. Is getting rid of unused or rarely-used functionality neccessarily a bad thing? Background: I use source control, so if I need the functionality again, I can get it. I'm the only user of my software (I'm a bioinformatician analyzing a data set). One scenario where I came across this was that I was using inheritance, with a parent class, and two child classes. One was handling files generated by 454 sequencing (next-generation sequencing), and the other was handling files generated by Sanger sequencing (previous-generation sequencing). I was actively maintaining the latter, but not the former. Maybe my mistake was using inheritance rather than composition, but that's a slightly different story.

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  • How should I avoid memoization causing bugs in Ruby?

    - by Andrew Grimm
    Is there a consensus on how to avoid memoization causing bugs due to mutable state? In this example, a cached result had its state mutated, and therefore gave the wrong result the second time it was called. class Greeter def initialize @greeting_cache = {} end def expensive_greeting_calculation(formality) case formality when :casual then "Hi" when :formal then "Hello" end end def greeting(formality) unless @greeting_cache.has_key?(formality) @greeting_cache[formality] = expensive_greeting_calculation(formality) end @greeting_cache[formality] end end def memoization_mutator greeter = Greeter.new first_person = "Bob" # Mildly contrived in this case, # but you could encounter this in more complex scenarios puts(greeter.greeting(:casual) << " " << first_person) # => Hi Bob second_person = "Sue" puts(greeter.greeting(:casual) << " " << second_person) # => Hi Bob Sue end memoization_mutator Approaches I can see to avoid this are: greeting could return a dup or clone of @greeting_cache[formality] greeting could freeze the result of @greeting_cache[formality]. That'd cause an exception to be raised when memoization_mutator appends strings to it. Check all code that uses the result of greeting to ensure none of it does any mutating of the string. Is there a consensus on the best approach? Is the only disadvantage of doing (1) or (2) decreased performance? (I also suspect freezing an object may not work fully if it has references to other objects) Side note: this problem doesn't affect the main application of memoization: as Fixnums are immutable, calculating Fibonacci sequences doesn't have problems with mutable state. :)

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  • How did Perl gain a reputation for being a write-only language?

    - by Andrew Grimm
    How did Perl gain a reputation (deserved, undeserved, or used to be deserved, no longer so) of being a "write only language"? Was it The syntax of the language Specific features that were available in the language Specific features not being available in the language (or at least old versions of it) The kind of tasks Perl was being used for The kind of people who use Perl (people who aren't full-time programmers) Criticism from people committed to another language Something else? Background: I'd like to know if some aspects that gave Perl the reputation of being write-only also apply to other languages (specifically ruby). Disclaimer: I recognise that Perl doesn't force people to do write-only code (can any language?), and that you can write bad code in any language.

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  • Align col in a bootstrap collapsable menu

    - by Grimm
    I got my hands on bootstrap recently and I'm still discovering it. I made collapsable menu from a tutorial online but now that I want to had an image on each entry of my menu that I wasn't expecting. I want my image to be always aligned to the text in the menu but it still getting on top of it. I tried to remove row and col tag and forget about the responsiveness of my menu but it still doesn't work... Here is the source code of my menu: <div id="menu" class="menu nav-collapse collapse width"> <div class="collapse-inner"> <div class="navbar navbar-inverse"> <div class="menu_titlenav nav-tabs nav-stacked"> <h3>Menu</h3> </div> </div> <div class="row well menu_entry"> <div class="span2 search_ico_ina"></div> <div class="span9 search_ent_ina">Recherche</div> </div> <div class="row well menu_entry" > <div class="span2 pro_ico_ina"></div> <div class="span9 pro_ent_ina">Espace PRO</div> </div> <div class="row well menu_entry"> <div class="span2 account_ico_ina"></div> <div class="span9 account_ent_ina">Mon Compte</div> </div> </div> </div> and the entire source: http://jsfiddle.net/Grimtork/JLFMW/

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  • Logging a certain event only once in ruby

    - by Andrew Grimm
    Are there any logging frameworks in ruby that allow you to log a specific event type only once? logger = IdealLogger.new logger.log(:happy_path, "We reached the happy path") # => logs this message logger.log(:happy_path, "We reached the happy path yet again") # => Doesn't log this logger.log(:sad_path, "We've encountered a sad path!") # => logs this message Also, is there a term for the concept of logging a certain event type only once?

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  • How do you remove functionality from a program in ruby?

    - by Andrew Grimm
    You have some code you want to remove associated with an obsolete piece of functionality from a ruby project. How do ensure that you get rid of all of the code? Some guidelines that usually help in refactoring ruby apply, but there are added challenges because having code that isn't being called by anything won't break any unit tests.

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  • Is it possible to store only a checksum of a large file in git?

    - by Andrew Grimm
    I'm a bioinformatician currently extracting normal-sized sequences from genomic files. Some genomic files are large enough that I don't want to put them into the main git repository, whereas I'm putting the extracted sequences into git. Is it possible to tell git "Here's a large file - don't store the whole file, just take its checksum, and let me know if that file is missing or modified." If that's not possible, I guess I'll have to either git-ignore the large files, or, as suggested in this question, store them in a submodule.

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  • Determining whether one array contains the contents of another array in ruby

    - by Andrew Grimm
    In ruby, how do I test that one array not only has the elements of another array, but contain them in that particular order? correct_combination = [1, 2, 3, 4, 5] [1, 5, 8, 2, 3, 4, 5].function_name(correct_combination) # => false [8, 10, 1, 2, 3, 4, 5, 9].function_name(correct_combination) # => true I tried using include, but that is used to test whether [1,2,3].include?(2) is true or not.

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  • VBA/SQL recordsets

    - by intruesiive
    The project I'm asking about is for sending an email to teachers asking what books they're using for the classes they're teaching next semester, so that the books can be ordered. I have a query that compares the course number of this upcoming semester's classes to the course numbers of historical textbook orders, pulling out only those classes that are being taught this semester. That's where I get lost. I have a table that contains the following: -Professor -Course Number -Year -Book -Title The data looks like this: professor year course number title smith 13 1111 Pride and Prejudice smith 13 1111 The Fountainhead smith 13 1222 The Alchemist smith 12 1111 Pride and Prejudice smith 11 1222 Infinite Jest smith 10 1333 The Bible smith 13 1333 The Bible smith 12 1222 The Alchemist smith 10 1111 Moby Dick johnson 12 1222 The Tipping Point johnson 11 1333 Anna Kerenina johnson 10 1333 Everything is Illuminated johnson 12 1222 The Savage Detectives johnson 11 1333 In Search of Lost Time johnson 10 1333 Great Expectations johnson 9 1222 Proust on the Shore Here's what I need the code to do "on paper": Group the records by professor. Determine every unique course number in that group, and group records by course number. For each unique course number, determine the highest year associated. Then spit out every record with that professor+course number+year combination. With the sample data, the results would be: professor year course number title smith 13 1111 Pride and Prejudice smith 13 1111 The Fountainhead smith 13 1222 The Alchemist smith 13 1333 The Bible johnson 12 1222 The Tipping Point johnson 11 1333 Anna Kerenina johnson 12 1222 The Savage Detectives johnson 11 1333 In Search of Lost Time I'm thinking I should make a record set for each teacher, and within that, another record set for each course number. Within the course number record set, I need the system to determine what the highest year number is - maybe store that in a variable? Then pull out every associated record so that if the teacher ordered 3 books the last time they taught that class (whether it was in 2013 or 2012 and so on) all three books display. I'm not sure I'm thinking of record sets in the right way, though. My SQL so far is basic and clearly doesn't work: SELECT [All].Professor, [All].Course, Max([All].Year) FROM [All] GROUP BY [All].Professor, [All].Course; Thanks for your help.

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  • Microsoft Claims Success Versus Autorun Malware

    Microsoft recently used a post on the Threat Research and Response Blog section of its Malware Protection Center to describe how it is winning the battle against autorun malware. Although there is certainly no shortage of malware in the virtual world Microsoft has plenty of statistics to back its claims and it has displayed them with pride.... DNS Configured Correctly? Test Your Internal DNS With Our Free DNS Advisor Tool From Infoblox.

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  • Databases and Beer

    - by Johnm
    It is a bit of a no-brainer: Include the word "beer" in a subject line of an e-mail or blog post title and you can be certain that it will be read. While there are times this practice might be a ploy to increase readership, it is not the case for this blog post. There is inspiration that can be drawn from other industries to which we, as database professionals, can apply in our industry. In this post I will highlight one of my favorite participants of the brewing industry. The Boston Beer Company started in the 1970s in Boston, Massachusetts. Others may be more familiar with this company through their Samuel Adams Boston Lager and other various seasonal beers. I am continually inspired by their commitment to mastery of the brewing process to which they evangelize frequently in their commercials. They also are continually in pursuit of pushing the boundaries of beer as we know it while working within traditional constraints. A recent example of this is their collaboration with Weihenstephan Brewery of Munich, Germany to produce the soon to be released Infinium beer. This beer, while brewed as an ale, is touted as something closer to something like Champaign - all while complying with the Reinheitsgebot. The Reinheitsgebot is also known as the "German Beer Purity Law" which was originated in 1516. This law states that beer is to consist of water, barley, hops and yeast. That's it. Quite a limiting constraint indeed. and yet, The Boston Beer Company pushed forward. Much like the process of brewing, the discipline of database design and architecture is one that is continually in process and driven by the pursuit of mastery. While we do not have purity laws to constrain us, we have many other types: best practices, company policies, government regulations, security and budgets. Through our fellow comrades, we discuss the challenges and constraints in which we operate. We boil down the principles and theories that define our profession. We reassemble these into something that is complementary to the business needs that we must fulfill. As a result, it is not uncommon to see something amazingly innovative in a small business who is pushing the boundaries of their database well beyond its intended state. It is equally common to see innovation in the use of features available in the more advanced features of databases that are found in large businesses. The tag line for The Boston Beer Company is: "Take Pride In Your Beer.", I would like to offer an alternative and say "Take Pride In Your Database." So, As you pour your next Boston Lager into a frosted glass, consider those who spend their lives mastering the craft of brewing and strive to interject their spirit into everything that you do as a database professional. Cheers!

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