latexrakutexbibtex

Extracting from .bib file with Raku (previously aka Perl 6)

I have this .bib file for reference management while writing my thesis in LaTeX:

@article{garg2017patch,
  title={Patch testing in patients with suspected cosmetic dermatitis: A retrospective study},
  author={Garg, Taru and Agarwal, Soumya and Chander, Ram and Singh, Aashim and Yadav, Pravesh},
  journal={Journal of Cosmetic Dermatology},
  year={2017},
  publisher={Wiley Online Library}
}

@article{hauso2008neuroendocrine,
  title={Neuroendocrine tumor epidemiology},
  author={Hauso, Oyvind and Gustafsson, Bjorn I and Kidd, Mark and Waldum, Helge L and Drozdov, Ignat and Chan, Anthony KC and Modlin, Irvin M},
  journal={Cancer},
  volume={113},
  number={10},
  pages={2655--2664},
  year={2008},
  publisher={Wiley Online Library}
}

@article{siperstein1997laparoscopic,
  title={Laparoscopic thermal ablation of hepatic neuroendocrine tumor metastases},
  author={Siperstein, Allan E and Rogers, Stanley J and Hansen, Paul D and Gitomirsky, Alexis},
  journal={Surgery},
  volume={122},
  number={6},
  pages={1147--1155},
  year={1997},
  publisher={Elsevier}
}

If anyone wants to know what bib file is, you can find it detailed here.

I'd like to parse this with Perl 6 to extract the key along with the title like this:

garg2017patch: Patch testing in patients with suspected cosmetic dermatitis: A retrospective study

hauso2008neuroendocrine: Neuroendocrine tumor epidemiology

siperstein1997laparoscopic: Laparoscopic thermal ablation of hepatic neuroendocrine tumor metastases

Can you please help me to do this, maybe in two ways:

  1. Using basic Perl 6
  2. Using a Perl 6 Grammar
Solution

  • TL;DR

    A one-liner in a shell

    I'll start with terse code that's perfect for some scenarios[1], and which someone might write if they're familiar with shell and Raku basics and in a hurry:

    > raku -e 'for slurp() ~~ m:g / "@article\{" (<-[,]>+) \, \s+
"title=\{" (<-[}]>+) \} / -> $/ { put "$0: $1\n" }' < derm.bib

    This produces precisely the output you specified:

    garg2017patch: Patch testing in patients with suspected cosmetic dermatitis: A retrospective study

hauso2008neuroendocrine: Neuroendocrine tumor epidemiology

siperstein1997laparoscopic: Laparoscopic thermal ablation of hepatic neuroendocrine tumor metastases

    Same single statement, but in a script

    Skipping shell escapes and adding:

    ► use tio.run to run the code below

    for slurp()                        # "slurp" (read all of) stdin and then

~~ m :global                       # match it "globally" (all matches) against

/ '@article{' (<-[,]>+) ',' \s+    # a "nextgen regex" that uses (`(...)`) to
  'title={' (<-[}]>+) '}'  /       # capture the article id and title and then

-> $/ { put "$0: $1\n" }           # for each article, print "article id: title".

    Don't worry if the above still seems like pure gobbledygook. Later sections explain the above while also introducing code that's more general, clean, and readable.[2]

    Four statements instead of one

    my \input = slurp;

my \pattern = rule { '@article{' ( <-[,]>+ ) ','
                       'title={' ( <-[}]>+ ) }

my \articles = input .match: pattern, :global;

for articles -> $/ { put "$0: $1\n" }

    my declares a lexical variable. Raku supports sigils at the start of variable names. But it also allows devs to "slash them out" as I have done.

    my \pattern ...

    my \pattern = rule { '@article{' ( <-[,]>+ ) ','
                       'title={' ( <-[}]>+ ) }

    I've switched the pattern syntax from / ... / in the original one-liner to rule { ... }. I did this to:

    Raku regexes/rules can be (often are) used with "adverbs". These are convenient shortcuts that modify how patterns are applied.

    I've already used an adverb in the earlier versions of this code. The "global" adverb (specified using :global or its shorthand alias :g) directs the matching engine to consume all of the input, generating a list of as many matches as it contains, instead of returning just the first match.

    While there are shorthand aliases for adverbs, some are used so repeatedly that it's a lot tidier to bundle them up into distinct rule declarators. That's why I've used rule. It bundles up two adverbs appropriate for matching many data formats like .bib files:

    Ratcheting (:r / :ratchet) tells the compiler that when an "atom" (a sub-pattern in a rule that is treated as one unit) has matched, there can be no going back on that. If an atom further on in the pattern in the same rule fails, then the whole rule immediately fails.

    This eliminates any risk of the "pathological backtracking" discussed earlier.

    Significant space handling (:s / :sigspace) tells the compiler that an atom followed by literal spacing that is in the pattern indicates that a "token" boundary pattern, aka ws should be appended to the atom.

    Thus this adverb deals with tokenizing. Did you spot that I'd dropped the \s+ from the pattern compared to the original one in the one-liner? That's because :sigspace, which use of rule implies, takes care of that automatically:

    say 'x@y x    @  y' ~~ m:g:s /x\@y/;   # (｢x@y｣)               <-- only one match
say 'x@y x    @  y' ~~ m:g   /x \@ y/; # (｢x@y｣)               <-- only one match
say 'x@y x    @  y' ~~ m:g:s /x \@ y/; # (｢x@y｣ ｢x    @  y｣)   <-- two matches

    You might wonder why I've reverted to using / ... / to show these two examples. Turns out that while you can use rule { ... } with the .match method (described in the next section), you can't use rule with m. No problem; I just used :s instead to get the desired effect. (I didn't bother to use :r for ratcheting because it makes no difference for this pattern/input.)

    To round out this dive into the difference between classic regexes (which can also be written regex { ... }) and rule rules, let me mention the other main option: token. The token declarator implies the :ratchet adverb, but not the :sigspace one. So it also eliminates the pathological backtracking risk of a regex (or / ... /) but, just like a regex, and unlike a rule, a token ignores whitespace used by a dev in writing out the rule's pattern.

    my \articles = input .match: pattern, :global

    This line uses the method form (.match) of the m routine used in the one-liner solution.

    The result of a match when :global is used is a list of Match objects rather than just one. In this case we'll get three, corresponding to the three articles in the input file.

    for articles -> $/ { put "$0: $1\n" }

    This for statement successively binds a Match object corresponding to each of the three articles in your sample file to the symbol $/ inside the code block ({ ... }).

    Per Raku doc on $/, "$/ is the match variable, so it usually contains objects of type Match.". It also provides some other conveniences; we take advantage of one of these conveniences related to numbered captures:

    Interlude

    This would be a good time to take a break. Maybe just a cuppa, or return here another day.

    The last part of this answer builds up and thoroughly explains a grammar-based approach. Reading it may provide further insight into the solutions above and will show how to extend Raku's parsing to more complex scenarios.

    But first...

    A "boring" practical approach

    I want to parse this with Raku. Can anyone help?

    Raku may make writing parsers less tedious than with other tools. But less tedious is still tedious. And Raku parsing is currently slow.

    In most cases, the practical answer when you want to parse well known formats and/or really big files is to find and use an existing parser. This might mean not using Raku at all, or using an existing Raku module, or using an existing non-Raku parser in Raku.

    A suggested starting point is to search for the file format on modules.raku.org or raku.land. Look for a publicly shared parsing module already specifically packaged for Raku for the given file format. Then do some simple testing to see if you have a good solution.

    At the time of writing there are no matches for 'bib'.

    Even if you don't know C, there's almost certainly a 'bib' parsing C library already available that you can use. And it's likely to be the fastest solution. It's typically surprisingly easy to use an external library in your own Raku code, even if it's written in another programming language.

    Using C libs is done using a feature called NativeCall. The doc I just linked may well be too much or too little, but please feel free to visit the freenode IRC channel #raku and ask for help. (Or post an SO question.) We're friendly folk. :)

    If a C lib isn't right for a particular use case, then you can probably still use packages written in some other language such as Perl, Python, Ruby, Lua, etc. via their respective Inline::* language adapters.

    The steps are:

    (At least, that's the theory. Again, if you need help, please pop on the IRC channel or post an SO question.)

    The Perl adapter is the most mature so I'll use that as an example. Let's say you use Perl's Text::BibTex packages and now wish to use Raku with that package. First, setup it up as it's supposed to be per its README. Then, in Raku, write something like:

    use Text::BibTeX::BibFormat:from<Perl5>;
...
@blocks = $entry.format;

    Explanation of these two lines:

    A Raku grammar / parser

    OK. Enough "boring" practical advice. Let's now try have some fun creating a grammar based Raku parser good enough for the example from your question.

    ► use glot.io to run the code below

    unit grammar bib;

rule TOP { <article>* }

rule article { '@article{' $<id>=<-[,]>+ ','
                  <kv-pairs>
               '}'
}

rule kv-pairs { <kv-pair>* % ',' }
        
rule kv-pair { $<key>=\w* '={' ~ '}' $<value>=<-[}]>* }

    With this grammar in place, we can now write something like:

    die "Use CommaIDE?" unless bib .parsefile: 'derm.bib';

for $<article> -> $/ { put "$<id>: $<kv-pairs><kv-pair>[0]<value>\n" }

    to generate exactly the same output as the previous solutions.

    When a match or parse fails, by default Raku just returns Nil, which is, well, rather terse feedback.

    There are several nice debugging options to figure out what's going on with a regex or grammar, but the best option by far is to use CommaIDE's Grammar-Live-View.

    If you haven't already installed and used Comma, you're missing one of the best parts of using Raku. The features built in to the free version of Comma ("Community Edition") include outstanding grammar development / tracing / debugging tools.

    Explanation of the 'bib' grammar

    unit grammar bib;

    The unit declarator is used at the start of a source file to tell Raku that the rest of the file declares a named package of code of a particular type.

    The grammar keyword specifies a grammar. A grammar is like a class, but contains named "rules" -- not just named methods, but also named regexs, tokens, and rules. A grammar also inherits a bunch of general purpose rules from a base grammar.

    rule TOP {

    Unless you specify otherwise, parsing methods (.parse and .parsefile) that are called on a grammar start by calling the grammar's rule named TOP (declared with a rule, token, regex, or method declarator).

    As a, er, rule of thumb, if you don't know if you should be using a rule, regex, token, or method for some bit of parsing, use a token. (Unlike regex patterns, tokens don't risk pathological backtracking.)

    But I've used a rule. Like token patterns, rules also avoid the pathological backtracking risk. But, in addition rules interpret some whitespace in the pattern to be significant, in a natural manner. (See this SO answer for precise details.)

    rules are typically appropriate towards the top of the parse tree. (Tokens are typically appropriate towards the leaves.)

    rule TOP { <article>* }

    The space at the end of the rule (between the * and pattern closing }) means the grammar will match any amount of whitespace at the end of the input.

    <article> invokes another named rule in this grammar.

    Because it looks like one should allow for any number of articles per bib file, I added a * (zero or more quantifier) at the end of <article>*.

    rule article { '@article{' $<id>=<-[,]>+ ','
                  <kv-pairs>
               '}'
}

    If you compare this article pattern with the ones I wrote for the earlier Raku rules based solutions, you'll see various changes:

    Rule in original one-liner Rule in this grammar
    Kept pattern as simple as possible. Introduced <kv-pairs> and closing }
    No attempt to echo layout of your input. Visually echoes your input.

    <[...]> is the Raku syntax for a character class, like[...] in traditional regex syntax. It's more powerful, but for now all you need to know is that the - in <-[,]> indicates negation, i.e. the same as the ^ in the [^,] syntax of ye olde regex. So <-[,]>+ attempts a match of one or more characters, none of which are ,.

    $<id>=<-[,]>+ tells Raku to attempt to match the quantified "atom" on the right of the = (i.e. the <-[,]>+ bit) and store the results at the key <id> within the current match object. The latter will be hung from a branch of the parse tree; we'll get to precisely where later.

    rule kv-pairs { <kv-pair>* % ',' }

    This pattern illustrates one of several convenient Raku regex features. It declares you want to match zero or more kv-pairs separated by commas.

    (In more detail, the % regex infix operator requires that matches of the quantified atom on its left are separated by the atom on its right.)

    rule kv-pair { $<key>=\w* '={' ~ '}' $<value>=<-[}]>* }

    The new bit here is '={' ~ '}'. This is another convenient regex feature. The regex Tilde operator parses a delimited structure (in this case one with a ={ opener and } closer) with the bit between the delimiters matching the quantified regex atom on the right of the closer. This confers several benefits but the main one is that error messages can be clearer.

    I could have used the ~ approach in the /.../ regex in the one-liner, and vice-versa. But I wanted this grammar solution to continue the progression toward illustrating "better practice" idioms.

    Constructing / deconstructing the parse tree

    for $<article> { put "$<id>: $<kv-pairs><kv-pair>[0]<value>\n" }`

    $<article>, $<id> etc. refer to named match objects that are stored somewhere in the "parse tree". But how did they get there? And exactly where is "there"?

    Returning to the top of the grammar:

    rule TOP {

    If a .parse is successful, a single 'TOP' level match object is returned. (After a parse is complete the variable $/ is also bound to that top match object.) During parsing a tree will have been formed by hanging other match objects off this top match object, and then others hung off those, and so on.

    Addition of match objects to a parse tree is done by adding either a single generated match object, or a list of them, to either a Positional (numbered) or Associative (named) capture of a "parent" match object. This process is explained below.

    rule TOP { <article>* }

    <article> invokes a match of the rule named article. An invocation of the rule <article> has two effects:

    1. Raku tries to match the rule.

    2. If it matches, Raku captures that match by generating a corresponding match object and adding it to the parse tree under the key <article> of the parent match object. (In this case the parent is the top match object.)

    If the successfully matched pattern had been specified as just <article>, rather than as <article>*, then only one match would have been attempted, and only one value, a single match object, would have been generated and added under the key <article>.

    But the pattern was <article>*, not merely <article>. So Raku attempts to match the article rule as many times as it can. If it matches at all, then a list of one or more match objects is stored as the value of the <article> key. (See my answer to "How do I access the captures within a match?" for a more detailed explanation.)

    $<article> is short for $/<article>. It refers to the value stored under the <article> key of the current match object (which is stored in $/). In this case that value is a list of 3 match objects corresponding to the 3 articles in the input.

    rule article { '@article{' $<id>=<-[,]>+ ','

    Just as the top match object has several match objects hung off of it (the three captures of article matches that are stored under the top match object's <article> key), so too do each of those three article match objects have their own "child" match objects hanging off of them.

    To see how that works, let's consider just the first of the three article match objects, the one corresponding to the text that starts "@article{garg2017patch,...". The article rule matches this article. As it's doing that matching, the $<id>=<-[,]>+ part tells Raku to store the match object corresponding to the id part of the article ("garg2017patch") under that article match object's <id> key.

    Hopefully this is enough (quite possibly way too much!) and I can at last exhaustively (exhaustingly?) explain the last line of code, which, once again, was:

    for $<article> -> $/ { put "$<id>: $<kv-pairs><kv-pair>[0]<value>\n" }`

    At the level of the for, the variable $/ refers to the top of the parse tree generated by the parse that just completed. Thus $<article>, which is shorthand for $/<article>, refers to the list of three article match objects.

    The for then iterates over that list, binding $/ within the lexical scope of the -> $/ { ... } block to each of those 3 article match objects in turn.

    The $<id> bit is shorthand for $/<id>, which inside the block refers to the <id> key within the article match object that $/ has been bound to. In other words, $<id> inside the block is equivalent to $<article><id> outside the block.

    The $<kv-pairs><kv-pair>[0]<value> follows the same scheme, albeit with more levels and a positional child (the [0]) in the midst of all the key (named/ associative) children.

    (Note that there was no need for the article pattern to include a $<kv-pairs>=<kv-pairs> because Raku just presumes a pattern of the form <foo> should store its results under the key <foo>. If you wish to disable that, write a pattern with a non-alpha character as the first symbol. For example, use <.foo> if you want to have exactly the same matching effect as <foo> but just not store the matched input in the parse tree.)

    Phew!

    When the automatically generated parse tree isn't what you want

    As if all the above were not enough, I need to mention one more thing.

    The parse tree strongly reflects the tree structure of the grammar's rules calling one another from the top rule down to leaf rules. But the resulting structure is sometimes inconvenient.

    Often one still wants a tree, but a simpler one, or perhaps some non-tree data structure.

    The primary mechanism for generating exactly what you want from a parse, when the automatic results aren't suitable, is make. (This can be used in code blocks inside rules or factored out into Action classes that are separate from grammars.)

    In turn, the primary use case for make is to generate a sparse tree of nodes hanging off the parse tree, such as an AST.

    Footnotes

    [1] Basic Raku is good for exploratory programming, spikes, one-offs, PoCs and other scenarios where the emphasis is on quickly producing working code that can be refactored later if need be.

    [2] Raku's regexes/rules scale up to arbitrary parsing, as introduced in the latter half of this answer. This contrasts with past generations of regex which could not.[3]

    [3] That said, ZA̡͊͠͝LGΌ ISͮ̂҉̯͈͕̹̘̱ TO͇̹̺ͅƝ̴ȳ̳ TH̘Ë͖́̉ ͠P̯͍̭O̚​N̐Y̡ remains a great and relevant read. Not because Raku rules can't parse (X)HTML. In principle they can. But for a task as monumental as correctly handling full arbitrary in-the-wild XHTML I would strongly recommend you use an existing parser written expressly for that purpose. And this applies generally for existing formats; it's best not to reinvent the wheel. But the good news with Raku rules is that if you need to write a full parser, not just a bunch of regexes, you can do so, and it need not involve going insane!