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  • Bioperl, equivalent of IO::ScalarArray for array of Seq objects?

    - by Ryan Thompson
    In perl, we have IO::ScalarArray for treating the elements of an array like the lines of a file. In BioPerl, we have Bio::SeqIO, which can produce a filehandle that reads and writes Bio::Seq objects instead of strings representing lines of text. I would like to do a combination of the two: I would like to obtain a handle that reads successive Bio::Seq objects from an array of such objects. Is there any way to do this? Would it be trivial for me to implement a module that does this? My reason for wanting this is that I would like to be able to write a subroutine that accepts either a Bio::SeqIO handle or an array of Bio::Seq objects, and I'd like to avoid writing separate loops based on what kind of input I get. Perhaps the following would be better than writing my own IO module? sub process_sequences { my $input = $_[0]; # read either from array of Bio::Seq or from Bio::SeqIO my $nextseq; if (ref $input eq 'ARRAY') { my $pos = 0 $nextseq = sub { return $input->[$pos++] if $pos < @$input}; } } else { $nextseq = sub { $input->getline(); } } while (my $seq = $nextseq->()) { do_cool_stuff_with($seq) } }

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  • Code Access Security and Sharepoint WebParts

    - by Gordon Carpenter-Thompson
    I've got a vague handle on how Code Access Security works in Sharepoint. I have developed a custom webpart and setup a CAS policy in my Manifest <CodeAccessSecurity> <PolicyItem> <PermissionSet class="NamedPermissionSet" version="1" Description="Permission set for Okana"> <IPermission class="Microsoft.SharePoint.Security.SharePointPermission, Microsoft.SharePoint.Security, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" version="1" ObjectModel="True" Impersonate="True" /> <IPermission class="SecurityPermission" version="1" Flags="Assertion, Execution, ControlThread, ControlPrincipal, RemotingConfiguration" /> <IPermission class="AspNetHostingPermission" version="1" Level="Medium" /> <IPermission class="DnsPermission" version="1" Unrestricted="true" /> <IPermission class="EventLogPermission" version="1" Unrestricted="true"> <Machine name="localhost" access="Administer" /> </IPermission> <IPermission class="EnvironmentPermission" version="1" Unrestricted="true" /> <IPermission class="System.Configuration.ConfigurationPermission, System.Configuration, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" version="1" Unrestricted="true"/> <IPermission class="System.Net.WebPermission, System, Version=1.0.5000.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" version="1" Unrestricted="true" /> <IPermission class="System.Net.WebPermission, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" Unrestricted="true" /> <IPermission class="System.Security.Permissions.FileIOPermission, mscorlib, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" version="1" Unrestricted="true" PathDiscovery="*AllFiles*" /> <IPermission class="IsolatedStorageFilePermission" version="1" Allowed="AssemblyIsolationByUser" UserQuota="9223372036854775807" /> <IPermission class="PrintingPermission" version="1" Level="DefaultPrinting" /> <IPermission class="PerformanceCounterPermission" version="1"> <Machine name="localhost"> <Category name="Enterprise Library Caching Counters" access="Write"/> <Category name="Enterprise Library Cryptography Counters" access="Write"/> <Category name="Enterprise Library Data Counters" access="Write"/> <Category name="Enterprise Library Exception Handling Counters" access="Write"/> <Category name="Enterprise Library Logging Counters" access="Write"/> <Category name="Enterprise Library Security Counters" access="Write"/> </Machine> </IPermission> <IPermission class="ReflectionPermission" version="1" Unrestricted="true"/> <IPermission class="SecurityPermission" version="1" Flags="SerializationFormatter, UnmanagedCode, Infrastructure, Assertion, Execution, ControlThread, ControlPrincipal, RemotingConfiguration, ControlAppDomain,ControlDomainPolicy" /> <IPermission class="SharePointPermission" version="1" ObjectModel="True" /> <IPermission class="SmtpPermission" version="1" Access="Connect" /> <IPermission class="SqlClientPermission" version="1" Unrestricted="true"/> <IPermission class="WebPartPermission" version="1" Connections="True" /> <IPermission class="WebPermission" version="1"> <ConnectAccess> <URI uri="$OriginHost$"/> </ConnectAccess> </IPermission> </PermissionSet> <Assemblies> .... </Assemblies> This is correctly converted into a wss_custom_wss_minimaltrust.config when it is deployed onto the Sharepoint server and mostly works. To get the WebPart working fully, however I find that I need to modify the wss_custom_wss_minimaltrust.config by hand after deployment and set Unrestricted="true" on the permissions set <PermissionSet class="NamedPermissionSet" version="1" Description="Permission set for MyApp" Name="mywebparts.wsp-86d8cae1-7db2-4057-8c17-dc551adb17a2-1"> to <PermissionSet class="NamedPermissionSet" version="1" Description="Permission set for MyApp" Name="mywebparts.wsp-86d8cae1-7db2-4057-8c17-dc551adb17a2-1" Unrestricted="true"> It's all because I'm loading a User Control from the webpart. I don't believe there is a way to enable that using CAS but am willing to be proven wrong. Is there a way to set something in the manifest so I don't need to make this fix by hand? Thanks

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  • How can I save BioPerl sequence nested features in genbank or embl format?

    - by Ryan Thompson
    In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence. However, when I use BioPerl to write a sequence object to a file in genbank or embl format, only the top-level features are written to the file, not the sub-features nested within the top-level features. How can I store my subfeatures in sequence files? Should I just convert all my subfeatures into top-level features, and then reconstruct the tree structure next time I read in the sequence?

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  • NoSql Crash Course/Tutorial

    - by Chris Thompson
    Hi all, I've seen NoSQL pop up quite a bit on SO and I have a solid understanding of why you would use it (from here, Wikipedia, etc). This could be due to the lack of concrete and uniform definition of what it is (more of a paradigm than concrete implementation), but I'm struggling to wrap my head around how I would go about designing a system that would use it or how I would implement it in my system. I'm really stuck in a relational-db mindset thinking of things in terms of tables and joins... At any rate, does anybody know of a crash course/tutorial on a system that would use it (kind of a "hello world" for a NoSQL-based system) or a tutorial that takes an existing "Hello World" app based on SQL and converts it to NoSQL (not necessarily in code, but just a high-level explanation). I see this having one solid answer, but if you guys feel like it should be community wiki, I'll be happy to change it. Thanks! Chris

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  • Showing renames in hg status?

    - by Ryan Thompson
    I know that Mercurial can track renames of files, but how do I get it to show me renames instead of adds/removes when I do hg status? For instance, instead of: A bin/extract-csv-column.pl A bin/find-mirna-binding.pl A bin/xls2csv-separate-sheets.pl A lib/Text/CSV/Euclid.pm R src/extract-csv-column.pl R src/find-mirna-binding.pl R src/modules/Text/CSV/Euclid.pm R src/xls2csv-separate-sheets.pl I want some indication that four files have been moved. I think I read somewhere that the output is like this to preserve backward-compatibility with something-or-other, but I'm not worried about that.

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  • Access to Perl's empty angle "<>" operator from an actual filehandle?

    - by Ryan Thompson
    I like to use the nifty perl feature where reading from the empty angle operator <> magically gives your program UNIX filter semantics, but I'd like to be able to access this feature through an actual filehandle (or IO::Handle object, or similar), so that I can do things like pass it into subroutines and such. Is there any way to do this? This question is particularly hard to google, because searching for "angle operator" and "filehandle" just tells me how to read from filehandles using the angle operator.

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  • Nasty redirect loop in WordPress (trailing slash, no trailing slash, and so on)

    - by Brett W. Thompson
    Hi, I read a ton of pages and tried lots of solutions but none have worked yet! My problem is that: test.asifa.net/asifa-wp Redirects to: test.asifa.net/asifa-wp/ Which redirects to the first page. What's a little bizarre is asifa-wp produces: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <title>301 Moved Permanently</title> </head><body> <h1>Moved Permanently</h1> <p>The document has moved <a href="http://test.asifa.net/asifa-wp/">here</a>.</p> </body></html> Whereas asifa-wp/ produces an empty page but the following headers (curl -v output): * About to connect() to test.asifa.net port 80 (#0) * Trying 69.163.203.138... connected * Connected to test.asifa.net (69.163.203.138) port 80 (#0) > GET /asifa-wp/ HTTP/1.1 > User-Agent: curl/7.18.2 (i386-redhat-linux-gnu) libcurl/7.18.2 NSS/3.12.0.3 zlib/1.2.3 libidn/0.6.14 libssh2/0.18 > Host: test.asifa.net > Accept: */* > < HTTP/1.1 301 Moved Permanently < Date: Sun, 13 Jun 2010 05:40:12 GMT < Server: Apache < X-Powered-By: PHP/5.2.13 < X-Pingback: http://test.asifa.net/asifa-wp/xmlrpc.php < Set-Cookie: _icl_current_language=en; expires=Mon, 14-Jun-2010 05:40:12 GMT; path=/asifa-wp/ < Location: http://test.asifa.net/asifa-wp < Vary: Accept-Encoding < Content-Length: 0 < Content-Type: text/html; charset=UTF-8 .htaccess looks like: # BEGIN WordPress <IfModule mod_rewrite.c> RewriteEngine On RewriteBase /asifa-wp/ RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteRule . /asifa-wp/index.php [L] </IfModule> # END WordPress Any help at all would be tremendously appreciated!!!

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  • Integration (math) in C++

    - by Chris Thompson
    Hi all, I'm looking for a library to find the integral of a given set of random data (rather than a function) in C++ (or C, but preferably C++). There is another question asking about integration in C but the answers discuss more how to integrate a function (I think...). I understand that this can be done simply by calculating the area under the line segment between each pair of points from start to finish, but I'd rather not reinvent the wheel if this has already been done. I apologize in advance if this is a duplicate; I searched pretty extensively to no avail. My math isn't as strong as I'd like it so it's entirely possible I'm using the wrong terminology. Thanks in advance for any help! Chris

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  • How to read from a method that returns a filehandle in perl?

    - by Ryan Thompson
    I have an object with a method that returns a filehandle, and I want to read from that handle. The following doesn't work, because the right angle bracket of the method call is interpreted as the closing angle bracket of the input reader: my $input = <$object->get_handle()>; That gets parsed as: my $input = ( < $object- > ) get_handle() >; which is obviously a syntax error. Is there any way I can perform a method call within an angle operator, or do I need to break it into two steps like this? my $handle = $object->get_handle(); my $input = <$handle>;

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  • WCF competitive consumer pattern

    - by Simon Thompson
    Is it possible to create a WCF service (web service) that only accepts a single connection at any one time with all other calls either queued or rejected. Need to implement the competitive consumer pattern where there are a number of clients which could deal with task at hand but when a client askes for more work a task must go to only one of them. Usual done as part of an enterprise service bus but can not find one that I'm happy to start using so looking to get this behaviour through a WCF service. Any ideas people ?

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  • SWI-Prolog Semantic Web Library and Python Interface

    - by John Peter Thompson Garcés
    I want to write a Python web application that queries RDF triples using Prolog. I found pyswip for interfacing Python with SWI-Prolog, and I am currently looking into SWI-Prolog's RDF capabilities. I am wondering if anyone has tried this before--and if anyone has: what did your setup look like? How do you get pyswip to work with the SWI-Prolog semantic web library? Or is there another Python-Prolog interface that makes this easier?

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  • When opening a file in perl, how can I automatically use STDIN/OUT if the file name is "-"?

    - by Ryan Thompson
    I have a perl program that takes input and output file arguments, and I'd like to support the convention of using "-" to specify standard input/output. The problem is that I can't just open the file name, because open(my $input, '<', '-') opens a file called -, not standard input. So I have to do something like this: my $input_fh; if ($input_filename eq '-') { # Special case: get the stdin handle $input_fh = *STDIN{IO}; } else { # Standard case: open the file open($input_fh, '<', $input_filename); } And similarly for the output file. Is there any way to do this without testing for the special case myself? I know I could hack the ARGV filehandle to do this for input, but that won't work for output.

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  • How to hide the console of batch scripts without losing std err/out streams

    - by cooper.thompson
    My question is similar to Running a CMD or BAT in silent mode, but with one additional constraint. If you use WshScript.Run in vbscript, you lose access to the standard in/error/out streams of the process. WshScript.Exec gives you access to the standard streams, but you can't hide your windows. How can you have your cake (hide the windows) and eat it too (have direct access to the console streams)? I'm currently thinking about a C++ executable which creates a new Windows Station and Desktop, (see MSDN) and runs a specified script within that new Desktop (I'm not yet an expert on Window Stations and Desktops, so this idea may be retarded). This idea is based loosely on Condor's USE_VISIBLE_DESKTOP feature, which, if disabled, runs Condor jobs in a non-visible Desktop. I haven't quite figured out if this requires elevated priveledge. The tradeoff of this approach is that your script can disappear into limbo if it blocks on user input. Does anyone have any additional ideas? Or feedback on the approach outlined above? Edit: Also, the purpose of our script is to set up the user environment, so running as another user, or as a system scheduled task isn't really an option (unless there are clever tricks I don't know about).

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  • How can I split my conkeror-rc config over multiple files?

    - by Ryan Thompson
    Short version: can you help me fill in this code? var conkeror_settings_dir = ".conkeror.mozdev.org/settings"; function load_all_js_files_in_dir (dir) { var full_path = get_home_directory().appendRelativePath(dir); // YOUR CODE HERE } load_all_js_files_in_dir(conkeror_settings_dir); Background I'm trying out Conkeror for web browsing. It's an emacs-like browser running on Mozilla's rendering engine, using javascript as configuration language (filling the role that elisp plays for emacs). In my emacs config, I have split my customizations into a series of files, where each file is a single unit of related options (for example, all my perl-related settings might be in perl-settings.el. All these settings files are loaded automatically by a function in my .emacs that simply loads every elisp file under my "settings" directory. I am looking to structure my Conkeror config in the same way, with my main conkeror-rc file basically being a stub that loads all the js files under a certain directory relative to my home directory. Unfortunately, I am much less literate in javascript than I am in elisp, so I don't even know how to "source" a file.

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  • Memory leak when declaring NSString from ABRecordCopyValue

    - by Ben Thompson
    I am using the following line of code... NSString *clientFirstName = (NSString *)ABRecordCopyValue(person, kABPersonFirstNameProperty); The 'analyse' feature on Xcode is saying that this giving rise to a potential memory leak. I am not releasing clientFirstName at all as I have neither alloc or retain'd it. However, I am conscious that ABRecordCopyValue may not be returning an object as say a command like [NSMutableArray arrayWithArray:someArray] would which might mean I am indeed creating a new object that I control and must release. Keen to hear thoughts...

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  • Is there a way to split a widescreen monitor in to two or more virtual monitors?

    - by Mike Thompson
    Like most developers I have grown to love dual monitors. I won't go into all the reasons for their goodness; just take it as a given. However, they are not perfect. You can never seem to line them up "just right". You always end up with the monitors at slight funny angles. And of course the bezel always gets in the way. And this is with identical monitors. The problem is much worse with different monitors -- VMWare's multi monitor feature won't even work with monitors of differnt resolutions. When you use multiple monnitors, one of them becomes your primary monitor of focus. Your focus may flip from one monitor to the other, but at any point in time you are usually focusing on only one monitor. There are exceptions to this (WinDiff, Excel), but this is generally the case. I suggest that having a single large monitor with all the benefits of multiple smaller monitors would be a better solution. Wide screen monitors are fantastic, but it is hard to use all the space efficiently. If you are writing code you are generally working on the left-hand side of the window. If you maximize an editor on a wide-screen monitor the right-hand side of the window will be a sea of white. Programs like WinSplit Revolution will help to organise your windows, but this is really just addressing the symptom, not the problem. Even with WinSplit Revolution, when you maximise a window it will take up the whole screen. You can't lock a window into a specific section of the screen. This is where virtual monitors comes in. What would be really nice is a video driver that sits on top of the existing driver, but allows a single monitor to be virtualised into multiple monitors. Control Panel would see your single physical monitor as two or more virtual monitors. The software could even support a virtual bezel to emphasise what is happening, or you could opt for seamless mode. Programs like WinSplit Revolution and UltraMon would still work. This virtual video driver would allow you to slice & dice your physical monitor into as many virtual monitors as you want. Does anybody know if such software exists? If not, are there any budding Windows display driver guru's out there willing to take up the challenge? I am not after the myriad of virtual desktop/window manager programs that are available. I get frustrated with these programs. They seem good at first but they usually have some strange behaviour and don't work well with other programs (such as WinSplit Revolution). I want the real thing!

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  • How to use R's ellipsis feature when writing your own function?

    - by Ryan Thompson
    The R language has a nifty feature for defining functions that can take a variable number of arguments. For example, the function data.frame takes any number of arguments, and each argument becomes the data for a column in the resulting data table. Example usage: > data.frame(letters=c("a", "b", "c"), numbers=c(1,2,3), notes=c("do", "re", "mi")) letters numbers notes 1 a 1 do 2 b 2 re 3 c 3 mi The function's signature includes an ellipsis, like this: function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, stringsAsFactors = default.stringsAsFactors()) { [FUNCTION DEFINITION HERE] } I would like to write a function that does something similar, taking multiple values and consolidating them into a single return value (as well as doing some other processing). In order to do this, I need to figure out how to "unpack" the ... from the function's arguments within the function. I don't know how to do this. The relevant line in the function definition of data.frame is object <- as.list(substitute(list(...)))[-1L], which I can't make any sense of. So how can I convert the ellipsis from the function's signature into, for example, a list? To be more specific, how can I write get_list_from_ellipsis in the code below? my_ellipsis_function(...) { input_list <- get.list.from.ellipsis(...) output_list <- lapply(X=input_list, FUN=do_something_interesting) return(output_list) } my_ellipsis_function(a=1:10,b=11:20,c=21:30)

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  • How can I manually interpolate string escapes in a Perl string?

    - by Ryan Thompson
    In perl suppose I have a string like 'hello\tworld\n', and what I want is: 'hello world ' That is, "hello", then a literal tab character, then "world", then a literal newline. Or equivalently, "hello\tworld\n" (note the double quotes). In other words, is there a function for taking a string with escape sequences and returning an equivalent string with all the escape sequences interpolated?

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  • Can I customize the indentation of ternary operators in emacs' cperl-mode?

    - by Ryan Thompson
    In emacs cperl-mode, ternary operators are not treated specially. If you break them over multiple lines, cperl-mode simply indents each line the same way it indents any continued statement, like this: $result = ($foo == $bar) ? 'result1' : ($foo == $baz) ? 'result2' : ($foo == $qux) ? 'result3' : ($foo == $quux) ? 'result4' : fail_result; This is not very readable. Is there some way that I can convince cperl-mode indent like this? $result = ($foo == $bar) ? 'result1' : ($foo == $baz) ? 'result2' : ($foo == $qux) ? 'result3' : ($foo == $quux) ? 'result4' : fail_result; By the way, code example from this question.

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  • More efficient way to find & tar millions of files

    - by Stu Thompson
    I've got a job running on my server at the command line prompt for a two days now: find data/ -name filepattern-*2009* -exec tar uf 2008.tar {} ; It is taking forever, and then some. Yes, there are millions of files in the target directory. But just running... find data/ -name filepattern-*2009* -print > filesOfInterest.txt ...takes only two hours or so. At the rate my job is running, it won't be finished for a couple of weeks.. That seems unreasonable. Is there a more efficient to do this? Maybe with a more complicated bash script? A secondary questions is "why is my current approach so slow?"

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  • What database table structure should I use for versions, codebases, deployables?

    - by Zac Thompson
    I'm having doubts about my table structure, and I wonder if there is a better approach. I've got a little database for version control repositories (e.g. SVN), the packages (e.g. Linux RPMs) built therefrom, and the versions (e.g. 1.2.3-4) thereof. A given repository might produce no packages, or several, but if there are more than one for a given repository then a particular version for that repository will indicate a single "tag" of the codebase. A particular version "string" might be used to tag a version of the source code in more than one repository, but there may be no relationship between "1.0" for two different repos. So if packages P and Q both come from repo R, then P 1.0 and Q 1.0 are both built from the 1.0 tag of repo R. But if package X comes from repo Y, then X 1.0 has no relationship to P 1.0. In my (simplified) model, I have the following tables (the x_id columns are auto-incrementing surrogate keys; you can pretend I'm using a different primary key if you wish, it's not really important): repository - repository_id - repository_name (unique) ... version - version_id - version_string (unique for a particular repository) - repository_id ... package - package_id - package_name (unique) - repository_id ... This makes it easy for me to see, for example, what are valid versions of a given package: I can join with the version table using the repository_id. However, suppose I would like to add some information to this database, e.g., to indicate which package versions have been approved for release. I certainly need a new table: package_version - version_id - package_id - package_version_released ... Again, the nature of the keys that I use are not really important to my problem, and you can imagine that the data column is "promotion_level" or something if that helps. My doubts arise when I realize that there's really a very close relationship between the version_id and the package_id in my new table ... they must share the same repository_id. Only a small subset of package/version combinations are valid. So I should have some kind of constraint on those columns, enforcing that ... ... I don't know, it just feels off, somehow. Like I'm including somehow more information than I really need? I don't know how to explain my hesitance here. I can't figure out which (if any) normal form I'm violating, but I also can't find an example of a schema with this sort of structure ... not being a DBA by profession I'm not sure where to look. So I'm asking: am I just being overly sensitive?

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  • Showing renames in hg log?

    - by Ryan Thompson
    I know that Mercurial can track renames of files, but how do I get it to show me renames instead of adds/removes when I do hg log? For instance, instead of: A bin/extract-csv-column.pl A bin/find-mirna-binding.pl A bin/xls2csv-separate-sheets.pl A lib/Text/CSV/Euclid.pm R src/extract-csv-column.pl R src/find-mirna-binding.pl R src/modules/Text/CSV/Euclid.pm R src/xls2csv-separate-sheets.pl I want some indication that four files have been moved. I think I read somewhere that the output is like this to preserve backward-compatibility with something-or-other, but I'm not worried about that.

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