import: cran: Parse DESCRIPTION instead of HTML.
* guix/import/cran.scm (description->alist, listify, beautify-description, description->package): New procedures. (table-datum, downloads->url, nodes->text, cran-sxml->sexp): Remove proceduces. (latest-release): Use parsed DESCRIPTION instead of SXML. * tests/cran.scm: Rewrite to match importer.
This commit is contained in:
Ricardo Wurmus
parent
b6a222757b
commit
0f6b9e9828
@ -20,26 +20,26 @@
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(define-module (guix import cran)
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#:use-module (ice-9 match)
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#:use-module (ice-9 regex)
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#:use-module ((ice-9 rdelim) #:select (read-string))
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#:use-module (srfi srfi-1)
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#:use-module (srfi srfi-26)
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#:use-module (sxml simple)
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#:use-module (sxml match)
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#:use-module (sxml xpath)
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#:use-module (guix http-client)
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#:use-module (guix hash)
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#:use-module (guix store)
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#:use-module (guix base32)
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#:use-module ((guix download) #:select (download-to-store))
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#:use-module (guix import utils)
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#:use-module ((guix build-system r) #:select (cran-uri))
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#:use-module (guix upstream)
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#:use-module (guix packages)
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#:use-module (gnu packages)
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#:export (cran->guix-package
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%cran-updater))
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;;; Commentary:
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;;;
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;;; Generate a package declaration template for the latest version of an R
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;;; package on CRAN, using the HTML description downloaded from
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;;; package on CRAN, using the DESCRIPTION file downloaded from
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;;; cran.r-project.org.
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;;;
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;;; Code:
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@ -67,6 +67,31 @@
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((lst ...) `(list ,@(map string->license lst)))
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(_ #f)))
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(define (description->alist description)
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"Convert a DESCRIPTION string into an alist."
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(let ((lines (string-split description #\newline))
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(parse (lambda (line acc)
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(if (string-null? line) acc
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;; Keys usually start with a capital letter and end with
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;; ":". There are some exceptions, unfortunately (such
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;; as "biocViews"). There are no blanks in a key.
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(if (string-match "^[A-Za-z][^ :]+:( |\n|$)" line)
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;; New key/value pair
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(let* ((pos (string-index line #\:))
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(key (string-take line pos))
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(value (string-drop line (+ 1 pos))))
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(cons (cons key
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(string-trim-both value))
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acc))
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;; This is a continuation of the previous pair
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(match-let ((((key . value) . rest) acc))
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(cons (cons key (string-join
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(list value
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(string-trim-both line))))
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rest)))))))
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(fold parse '() lines)))
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(define (format-inputs names)
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"Generate a sorted list of package inputs from a list of package NAMES."
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(map (lambda (name)
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@ -82,125 +107,94 @@ package definition."
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((package-inputs ...)
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`((,type (,'quasiquote ,(format-inputs package-inputs)))))))
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(define (table-datum tree label)
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"Extract the datum node following a LABEL in the sxml table TREE. Only the
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first cell of a table row is considered a label cell."
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((node-pos 1)
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((sxpath `(xhtml:tr
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(xhtml:td 1) ; only first cell can contain label
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(equal? ,label)
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,(node-parent tree) ; go up to label cell
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,(node-parent tree) ; go up to matching row
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(xhtml:td 2))) ; select second cell
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tree)))
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(define %cran-url "http://cran.r-project.org/web/packages/")
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(define (cran-fetch name)
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"Return an sxml representation of the CRAN page for the R package NAME,
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or #f on failure. NAME is case-sensitive."
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"Return an alist of the contents of the DESCRIPTION file for the R package
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NAME, or #f on failure. NAME is case-sensitive."
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;; This API always returns the latest release of the module.
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(let ((cran-url (string-append %cran-url name "/")))
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(false-if-exception
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(xml->sxml (http-fetch cran-url)
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#:trim-whitespace? #t
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#:namespaces '((xhtml . "http://www.w3.org/1999/xhtml"))
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#:default-entity-handler
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(lambda (port name)
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(case name
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((nbsp) " ")
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((ge) ">=")
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((gt) ">")
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((lt) "<")
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(else
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(format (current-warning-port)
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"~a:~a:~a: undefined entitity: ~a\n"
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cran-url (port-line port) (port-column port)
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name)
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(symbol->string name))))))))
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(let ((url (string-append %cran-url name "/DESCRIPTION")))
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(description->alist (read-string (http-fetch url)))))
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(define (downloads->url downloads)
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"Extract from DOWNLOADS, the downloads item of the CRAN sxml tree, the
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download URL."
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(string-append "mirror://cran/"
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;; Remove double dots, because we want an
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;; absolute path.
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(regexp-substitute/global
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#f "\\.\\./"
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(string-join ((sxpath '((xhtml:a 1) @ href *text*))
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(table-datum downloads " Package source: ")))
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'pre 'post)))
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(define (listify meta field)
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"Look up FIELD in the alist META. If FIELD contains a comma-separated
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string, turn it into a list and strip off parenthetic expressions. Return the
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empty list when the FIELD cannot be found."
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(let ((value (assoc-ref meta field)))
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(if (not value)
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'()
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;; Strip off parentheses
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(let ((items (string-split (regexp-substitute/global
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#f "( *\\([^\\)]+\\)) *"
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value 'pre 'post)
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#\,)))
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;; When there is whitespace inside of items it is probably because
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;; this was not an actual list to begin with.
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(remove (cut string-any char-set:whitespace <>)
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(map string-trim-both items))))))
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(define (nodes->text nodeset)
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"Return the concatenation of the text nodes among NODESET."
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(string-join ((sxpath '(// *text*)) nodeset) " "))
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(define (beautify-description description)
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"Improve the package DESCRIPTION by turning a beginning sentence fragment
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into a proper sentence and by using two spaces between sentences."
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(let ((cleaned (if (string-prefix? "A " description)
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(string-append "This package provides a"
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(substring description 1))
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description)))
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;; Use double spacing between sentences
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(regexp-substitute/global #f "\\. \\b"
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cleaned 'pre ". " 'post)))
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(define (cran-sxml->sexp sxml)
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"Return the `package' s-expression for a CRAN package from the SXML
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representation of the package page."
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(define (description->package meta)
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"Return the `package' s-expression for a CRAN package from the alist META,
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which was derived from the R package's DESCRIPTION file."
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(define (guix-name name)
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(if (string-prefix? "r-" name)
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(string-downcase name)
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(string-append "r-" (string-downcase name))))
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(sxml-match-let*
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(((*TOP* (xhtml:html
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,head
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(xhtml:body
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(xhtml:h2 ,name-and-synopsis)
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(xhtml:p ,description)
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,summary
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(xhtml:h4 "Downloads:") ,downloads
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. ,rest)))
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sxml))
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(let* ((name (match:prefix (string-match ": " name-and-synopsis)))
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(synopsis (match:suffix (string-match ": " name-and-synopsis)))
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(version (nodes->text (table-datum summary "Version:")))
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(license ((compose string->license nodes->text)
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(table-datum summary "License:")))
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(home-page (nodes->text ((sxpath '((xhtml:a 1)))
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(table-datum summary "URL:"))))
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(source-url (downloads->url downloads))
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(tarball (with-store store (download-to-store store source-url)))
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(sysdepends (map match:substring
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(list-matches
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"[^ ]+"
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;; Strip off comma and parenthetical
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;; expressions.
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(regexp-substitute/global
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#f "(,|\\([^\\)]+\\))"
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(nodes->text (table-datum summary
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"SystemRequirements:"))
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'pre 'post))))
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(imports (map guix-name
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((sxpath '(// xhtml:a *text*))
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(table-datum summary "Imports:")))))
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`(package
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(name ,(guix-name name))
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(version ,version)
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(source (origin
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(method url-fetch)
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(uri (cran-uri ,name version))
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(sha256
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(base32
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,(bytevector->nix-base32-string (file-sha256 tarball))))))
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(build-system r-build-system)
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,@(maybe-inputs sysdepends)
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,@(maybe-inputs imports 'propagated-inputs)
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(home-page ,(if (string-null? home-page)
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(string-append %cran-url name)
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home-page))
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(synopsis ,synopsis)
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;; Use double spacing
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(description ,(regexp-substitute/global #f "\\. \\b" description
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'pre ". " 'post))
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(license ,license)))))
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(let* ((name (assoc-ref meta "Package"))
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(synopsis (assoc-ref meta "Title"))
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(version (assoc-ref meta "Version"))
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(license (string->license (assoc-ref meta "License")))
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;; Some packages have multiple home pages. Some have none.
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(home-page (match (listify meta "URL")
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((url rest ...) url)
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(_ (string-append %cran-url name))))
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(source-url (match (cran-uri name version)
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((url rest ...) url)
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(_ #f)))
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(tarball (with-store store (download-to-store store source-url)))
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(sysdepends (map string-downcase (listify meta "SystemRequirements")))
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(propagate (map guix-name (lset-union equal?
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(listify meta "Imports")
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(listify meta "LinkingTo")
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(delete "R"
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(listify meta "Depends"))))))
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`(package
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(name ,(guix-name name))
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(version ,version)
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(source (origin
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(method url-fetch)
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(uri (cran-uri ,name version))
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(sha256
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(base32
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,(bytevector->nix-base32-string (file-sha256 tarball))))))
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(properties ,`(,'quasiquote ((,'upstream-name . ,name))))
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(build-system r-build-system)
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,@(maybe-inputs sysdepends)
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,@(maybe-inputs propagate 'propagated-inputs)
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(home-page ,(if (string-null? home-page)
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(string-append %cran-url name)
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home-page))
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(synopsis ,synopsis)
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(description ,(beautify-description (assoc-ref meta "Description")))
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(license ,license))))
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(define (cran->guix-package package-name)
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"Fetch the metadata for PACKAGE-NAME from cran.r-project.org, and return the
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`package' s-expression corresponding to that package, or #f on failure."
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(let ((module-meta (cran-fetch package-name)))
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(and=> module-meta cran-sxml->sexp)))
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(and=> module-meta description->package)))
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;;;
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@ -209,32 +203,33 @@ representation of the package page."
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(define (latest-release package)
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"Return an <upstream-source> for the latest release of PACKAGE."
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(define name
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(if (string-prefix? "r-" package)
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(string-drop package 2)
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package))
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(define sxml
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(cran-fetch name))
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(define (package->cran-name package)
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(match (package-source package)
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((? origin? origin)
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(match (origin-uri origin)
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((url rest ...)
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(let ((end (string-rindex url #\_))
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(start (string-rindex url #\/)))
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;; The URL ends on
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;; (string-append "/" name "_" version ".tar.gz")
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(substring url start end)))
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(_ #f)))
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(_ #f)))
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(and sxml
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(sxml-match-let*
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(((*TOP* (xhtml:html
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,head
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(xhtml:body
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(xhtml:h2 ,name-and-synopsis)
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(xhtml:p ,description)
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,summary
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(xhtml:h4 "Downloads:") ,downloads
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. ,rest)))
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sxml))
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(let ((version (nodes->text (table-datum summary "Version:")))
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(url (downloads->url downloads)))
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;; CRAN does not provide signatures.
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(upstream-source
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(package package)
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(version version)
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(urls (list url)))))))
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(define cran-name
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(package->cran-name (specification->package package)))
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(define meta
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(cran-fetch cran-name))
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(and meta
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(let ((version (assoc-ref meta "Version")))
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;; CRAN does not provide signatures.
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(upstream-source
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(package package)
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(version version)
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(urls (cran-uri cran-name version))))))
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(define (cran-package? package)
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"Return true if PACKAGE is an R package from CRAN."
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189
tests/cran.scm
189
tests/cran.scm
@ -19,120 +19,84 @@
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(define-module (test-cran)
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#:use-module (guix import cran)
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#:use-module (guix tests)
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#:use-module (srfi srfi-1)
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#:use-module (srfi srfi-64)
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#:use-module (srfi srfi-26)
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#:use-module (ice-9 match))
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(define sxml
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'(*TOP* (xhtml:html
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(xhtml:head
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(xhtml:title "CRAN - Package my-example-sxml"))
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(xhtml:body
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(xhtml:h2 "my-example-sxml: Short description")
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(xhtml:p "Long description")
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(xhtml:table
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(@ (summary "Package my-example-sxml summary"))
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(xhtml:tr
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(xhtml:td "Version:")
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(xhtml:td "1.2.3"))
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(xhtml:tr
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(xhtml:td "Depends:")
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(xhtml:td "R (>= 3.1.0)"))
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(xhtml:tr
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(xhtml:td "SystemRequirements:")
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(xhtml:td "cairo (>= 1.2 http://www.cairographics.org/)"))
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(xhtml:tr
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(xhtml:td "Imports:")
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(xhtml:td
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(xhtml:a (@ (href "../scales/index.html"))
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"scales")
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" (>= 0.2.3), "
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(xhtml:a (@ (href "../proto/index.html"))
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"proto")
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", "
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(xhtml:a (@ (href "../Rcpp/index.html")) "Rcpp")
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" (>= 0.11.0)"))
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(xhtml:tr
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(xhtml:td "Suggests:")
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(xhtml:td
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(xhtml:a (@ (href "../some/index.html"))
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"some")
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", "
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(xhtml:a (@ (href "../suggestions/index.html"))
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"suggestions")))
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(xhtml:tr
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(xhtml:td "License:")
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(xhtml:td
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(xhtml:a (@ (href "../../licenses/MIT")) "MIT")))
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(xhtml:tr
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(xhtml:td "URL:")
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(xhtml:td
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(xhtml:a (@ (href "http://gnu.org/s/my-example-sxml"))
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"http://gnu.org/s/my-example-sxml")
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", "
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(xhtml:a (@ (href "http://alternative/home/page"))
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"http://alternative/home/page"))))
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(xhtml:h4 "Downloads:")
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(xhtml:table
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(@ (summary "Package my-example-sxml downloads"))
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(xhtml:tr
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(xhtml:td " Reference manual: ")
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(xhtml:td
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(xhtml:a (@ (href "my-example-sxml.pdf"))
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" my-example-sxml.pdf ")))
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(xhtml:tr
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(xhtml:td " Package source: ")
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(xhtml:td
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(xhtml:a
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(@ (href "../../../src/contrib/my-example-sxml_1.2.3.tar.gz"))
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" my-example-sxml_1.2.3.tar.gz "))))
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(xhtml:h4 "Reverse dependencies:")
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(xhtml:table
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(@ (summary "Package my-example-sxml reverse dependencies"))
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(xhtml:tr
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(xhtml:td "Reverse depends:")
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(xhtml:td "Too many."))
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(xhtml:tr
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(xhtml:td "Reverse imports:")
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(xhtml:td "Likewise."))
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(xhtml:tr
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(xhtml:td "Reverse suggests:")
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(xhtml:td "Uncountable.")))))))
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(define description "
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Package: My-Example
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Type: Package
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Title: Example package
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Version: 1.2.3
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Date: 2015-12-10
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Author: Ricardo Wurmus
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Maintainer: Guix Schmeeks <guix@gnu.org>
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URL: http://gnu.org/s/my-example
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Description: This is a long description
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spanning multiple lines: and it could confuse the parser that
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there is a colon : on the lines.
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And: this line continues the description.
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biocViews: 0
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SystemRequirements: Cairo (>= 0)
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Depends: A C++11 compiler. Version 4.6.* of g++ (as
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currently in Rtools) is insufficient; versions 4.8.*, 4.9.* or
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later will be fine.
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License: GPL (>= 3)
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Imports: Rcpp (>= 0.11.5), proto, Scales
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LinkingTo: Rcpp, BH
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NeedsCompilation: yes
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Repository: CRAN
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Date/Publication: 2015-07-14 14:15:16
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")
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(define simple-table
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'(xhtml:table
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(xhtml:tr
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(xhtml:td "Numbers")
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(xhtml:td "123"))
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(xhtml:tr
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(@ (class "whatever"))
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(xhtml:td (@ (class "unimportant")) "Letters")
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(xhtml:td "abc"))
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(xhtml:tr
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(xhtml:td "Letters")
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(xhtml:td "xyz"))
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(xhtml:tr
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(xhtml:td "Single"))
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(xhtml:tr
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(xhtml:td "not a value")
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(xhtml:td "not a label")
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(xhtml:td "also not a label"))))
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(define description-alist
|
||||
((@@ (guix import cran) description->alist) description))
|
||||
|
||||
(define simple-alist
|
||||
'(("Key" . "Value")
|
||||
("SimpleList" . "R, Rcpp, something, whatever")
|
||||
("BadList" . "This is not a real list, you know?")
|
||||
("List" . "R (>= 2.2), BH (for no reason), GenomicRanges")))
|
||||
|
||||
(test-begin "cran")
|
||||
|
||||
(test-equal "table-datum: return list of first table cell matching label"
|
||||
'((xhtml:td "abc"))
|
||||
((@@ (guix import cran) table-datum) simple-table "Letters"))
|
||||
(test-assert "description->alist: contains all valid keys"
|
||||
(let ((keys '("Package" "Type" "Title" "Version" "Date"
|
||||
"Author" "Maintainer" "URL" "Description"
|
||||
"SystemRequirements" "Depends" "License"
|
||||
"Imports" "biocViews" "LinkingTo"
|
||||
"NeedsCompilation" "Repository"
|
||||
"Date/Publication")))
|
||||
(lset= string=? keys (map car description-alist))))
|
||||
|
||||
(test-equal "table-datum: return empty list if no match"
|
||||
(test-equal "listify: return empty list if key cannot be found"
|
||||
'()
|
||||
((@@ (guix import cran) table-datum) simple-table "Astronauts"))
|
||||
((@@ (guix import cran) listify) simple-alist "Letters"))
|
||||
|
||||
(test-equal "table-datum: only consider the first cell as a label cell"
|
||||
(test-equal "listify: split comma-separated value into elements"
|
||||
'("R" "Rcpp" "something" "whatever")
|
||||
((@@ (guix import cran) listify) simple-alist "SimpleList"))
|
||||
|
||||
(test-equal "listify: strip off parentheses"
|
||||
'("R" "BH" "GenomicRanges")
|
||||
((@@ (guix import cran) listify) simple-alist "List"))
|
||||
|
||||
(test-equal "listify: ignore values that are no lists"
|
||||
'()
|
||||
((@@ (guix import cran) table-datum) simple-table "not a label"))
|
||||
((@@ (guix import cran) listify) simple-alist "BadList"))
|
||||
|
||||
(test-equal "beautify-description: use double spacing"
|
||||
"This is a package. It is great. Trust me Mr. Hendrix."
|
||||
((@@ (guix import cran) beautify-description)
|
||||
"This is a package. It is great. Trust me Mr. Hendrix."))
|
||||
|
||||
(test-assert "cran-sxml->sexp"
|
||||
(test-equal "beautify-description: transform fragment into sentence"
|
||||
"This package provides a function to establish world peace"
|
||||
((@@ (guix import cran) beautify-description)
|
||||
"A function to establish world peace"))
|
||||
|
||||
(test-assert "description->package"
|
||||
;; Replace network resources with sample data.
|
||||
(mock ((guix build download) url-fetch
|
||||
(lambda* (url file-name #:key (mirrors '()))
|
||||
@ -140,32 +104,37 @@
|
||||
(lambda ()
|
||||
(display
|
||||
(match url
|
||||
("mirror://cran/src/contrib/my-example-sxml_1.2.3.tar.gz"
|
||||
("mirror://cran/src/contrib/My-Example_1.2.3.tar.gz"
|
||||
"source")
|
||||
(_ (error "Unexpected URL: " url))))))))
|
||||
(match ((@@ (guix import cran) cran-sxml->sexp) sxml)
|
||||
(match ((@@ (guix import cran) description->package) description-alist)
|
||||
(('package
|
||||
('name "r-my-example-sxml")
|
||||
('name "r-my-example")
|
||||
('version "1.2.3")
|
||||
('source ('origin
|
||||
('method 'url-fetch)
|
||||
('uri ('cran-uri "my-example-sxml" 'version))
|
||||
('uri ('cran-uri "My-Example" 'version))
|
||||
('sha256
|
||||
('base32
|
||||
(? string? hash)))))
|
||||
('properties ('quasiquote (('upstream-name . "My-Example"))))
|
||||
('build-system 'r-build-system)
|
||||
('inputs
|
||||
('quasiquote
|
||||
(("cairo" ('unquote 'cairo)))))
|
||||
('propagated-inputs
|
||||
('quasiquote
|
||||
(("r-proto" ('unquote 'r-proto))
|
||||
(("r-bh" ('unquote 'r-bh))
|
||||
("r-proto" ('unquote 'r-proto))
|
||||
("r-rcpp" ('unquote 'r-rcpp))
|
||||
("r-scales" ('unquote 'r-scales)))))
|
||||
('home-page "http://gnu.org/s/my-example-sxml")
|
||||
('synopsis "Short description")
|
||||
('description "Long description")
|
||||
('license 'x11)))
|
||||
('home-page "http://gnu.org/s/my-example")
|
||||
('synopsis "Example package")
|
||||
('description
|
||||
"This is a long description spanning multiple lines: \
|
||||
and it could confuse the parser that there is a colon : on the \
|
||||
lines. And: this line continues the description.")
|
||||
('license 'gpl3+)))
|
||||
(x
|
||||
(begin
|
||||
(format #t "~s\n" x)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user