(define-module (gn packages bnw)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages maths)
#:use-module (gnu packages python)
#:use-module (gnu packages statistics)
#:use-module (gn packages javascript)
#:use-module (gn packages web))
(define-public bnw
(let ((commit "73ba58868451b5fc6611e1feaa9b63f17b6cd19d")
(revision "5"))
(package
(name "bnw")
(version (git-version "genenet8_initial_1.3" revision commit)) ; Oct 11, 2021
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ziejd2/BNW")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"150aq4cg3yxhgv8vw6mxkq94ib1v0s94c2cibd5fpw92vgf24y9n"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file "var_lib_genenet_bnw/localscore/libRmath.so")
(delete-file-recursively "bnw-env")
(delete-file "var_lib_genenet_bnw/k-best/src/get_kbest_nets")
(delete-file "var_lib_genenet_bnw/k-best/src/get_kbest_parents")
(for-each delete-file (find-files "." "\\.dll$"))
(for-each delete-file (find-files "." "\\.o$"))
(for-each
(lambda (file)
(delete-file (string-append "sourcecodes/scripts/" file)))
;; accordion.js, create_table.js and table.css are original files.
'(;"FileSaver.min.js" ; sha256 mismatch
;"canvas-toBlob.js" ; sha256 mismatch
;"cytoscape-dagre.min.js" ; sha256 mismatch
;"cytoscape-panzoom.js" ; sha256 mismatch
;"cytoscape.js-panzoom.css" ; sha256 mismatch
;"cytoscape.min.js"
;"d3-selection-multi.v1.js"
;"d3.v4.min.js" ; some work needs to be done on our package
;"dagre.js" ; sha256 mismatch
;"font-awesome.css" ; sha256 mismatch
;"fontawesome-webfont.eot" ; sha256 mismatch
;"fontawesome-webfont.svg" ; sha256 mismatch
;"fontawesome-webfont.ttf" ; sha256 mismatch
;"fontawesome-webfont.woff" ; sha256 mismatch
;"jquery.min.js" ; sha256 mismatch
;"lodash.js" ; sha256 mismatch
))
#t))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'patch-source
(lambda _
;; sourcecodes/matrix.php hardcodes $dir=/tmp/bnw
(substitute* "sourcecodes/matrix.php"
(("/tmp/bnw") "/var/lib/genenet/bnw/"))
#t))
(add-after 'patch-source-shebangs 'patch-more-shebangs
(lambda* (#:key inputs #:allow-other-keys)
(let ((graphviz (assoc-ref inputs "graphviz"))
(octave (assoc-ref inputs "octave"))
(python (assoc-ref inputs "python"))
(rmath (assoc-ref inputs "rmath")))
(for-each (lambda (file)
(patch-shebang file
(list (string-append octave "/bin"))))
(find-files "sourcecodes/run_scripts" "^run"))
(substitute* (find-files "sourcecodes" "(^run|py$)")
(("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3")
(which "python3"))
(("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python")
(which "python3")))
(substitute*
(append (find-files "sourcecodes" ".php")
(find-files "sourcecodes/run_scripts"))
(("/usr/bin/dot") (string-append graphviz "/bin/dot")))
(substitute* "var_lib_genenet_bnw/build.sh"
(("./localscore/libRmath.so")
(string-append rmath "/lib/libRmath.so")))
#t)))
(add-after 'patch-source-shebangs 'replace-javascript
(lambda* (#:key inputs #:allow-other-keys)
(let ((jquery (assoc-ref inputs "jquery"))
(awesome (assoc-ref inputs "awesome"))
(cyto (assoc-ref inputs "cytoscape"))
(cs-dagre (assoc-ref inputs "cyto-dagre"))
(d3js-4 (assoc-ref inputs "d3js-4"))
(d3js-multi (assoc-ref inputs "d3js-multi"))
(dagre (assoc-ref inputs "dagre"))
(lodash (assoc-ref inputs "lodash"))
(canvas-toblob (assoc-ref inputs "canvas-toblob"))
(filesaver (assoc-ref inputs "filesaver"))
(panzoom (assoc-ref inputs "panzoom"))
(js-path "/share/genenetwork2/javascript/"))
(substitute* "sourcecodes/layout_cyto.php"
(("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js")
"./scripts/cytoscape.min.js")
(("https://cdn.jsdelivr.net/npm/cytoscape-dagre@2.2.2/cytoscape-dagre.min.js")
"./scripts/cytoscape-dagre.min.js")
(("https://unpkg.com/dagre@0.7.4/dist/dagre.js")
"./scripts/dagre.js")
(("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css")
"./scripts/cytoscape.js-panzoom.css")
(("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js")
"./scripts/cytoscape-panzoom.js")
(("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css")
"./scripts/font-awesome.css")
(("https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js")
"./scripts/jquery.min.js")
(("https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js")
"./scripts/lodash.js"))
(substitute* "sourcecodes/layout_svg_no.php"
(("http://d3js.org/d3.v4.min.js")
"./scripts/d3.v4.min.js")
(("http://d3js.org/d3-selection-multi.v1.js")
"./scripts/d3-selection-multi.v1.js")
(("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js")
"./scripts/canvas-toBlob.js")
(("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js")
"./scripts/FileSaver.min.js"))
;; Against Google's ToS to make available offline:
;; https://developers.google.com/chart/interactive/faq?csw=1#offline
;(substitute* '("sourcecodes/network_layout_evd.php"
; "sourcecodes/network_layout_evd_2.php"
; "sourcecodes/network_layout_inv.php"
; "sourcecodes/network_layout_inv_2.php")
; (("https://www.google.com/jsapi") "https://www.gstatic.com/charts/loader.js"))
)
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(copy-recursively "." out))
#t))
(add-after 'install 'install-javascript-libraries
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(scripts (string-append out "/sourcecodes/scripts/"))
(fonts (string-append out "/sourcecodes/fonts/"))
(jquery (assoc-ref inputs "jquery"))
(awesome (assoc-ref inputs "awesome"))
(cyto (assoc-ref inputs "cytoscape"))
(cs-dagre (assoc-ref inputs "cyto-dagre"))
(d3js-4 (assoc-ref inputs "d3js-4"))
(d3js-multi (assoc-ref inputs "d3js-multi"))
(dagre (assoc-ref inputs "dagre"))
(lodash (assoc-ref inputs "lodash"))
(canvas-toblob (assoc-ref inputs "canvas-toblob"))
(filesaver (assoc-ref inputs "filesaver"))
(panzoom (assoc-ref inputs "panzoom"))
(js-path "/share/genenetwork/javascript/")
(js-path2 "/share/genenetwork2/javascript/"))
(unless (file-exists? (string-append scripts "cytoscape.min.js"))
(symlink (string-append cyto js-path2 "cytoscape/cytoscape.min.js")
(string-append scripts "cytoscape.min.js")))
(unless (file-exists? (string-append scripts "cytoscape-dagre.min.js"))
(symlink (string-append cs-dagre "/share/javascript/cytoscape-dagre.min.js")
(string-append scripts "cytoscape-dagre.min.js")))
(unless (file-exists? (string-append scripts "dagre.js"))
(symlink (string-append dagre js-path2 "dagre/dagre.js")
(string-append scripts "dagre.js")))
(unless (file-exists? (string-append scripts "cytoscape.js-panzoom.css"))
(symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape.js-panzoom.css")
(string-append scripts "cytoscape.js-panzoom.css")))
(unless (file-exists? (string-append scripts "cytoscape-panzoom.js"))
(symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape-panzoom.js")
(string-append scripts "cytoscape-panzoom.js")))
(unless (file-exists? (string-append scripts "font-awesome.css"))
(symlink (string-append awesome "/share/web/font-awesomecss/font-awesome.css")
(string-append scripts "font-awesome.css"))
;; font-awesome.css depends on the other font-awesome files,
;; by default in the ../fonts/ folder. Because we remove the
;; bundled (and minimally modified) version we have to make
;; some adjustments, namely moving the font files.
(mkdir-p fonts)
(for-each
(lambda (font)
(symlink (string-append awesome "/share/web/font-awesomefonts"
"/fontawesome-webfont." font)
(string-append fonts "fontawesome-webfont." font)))
'("eot" "woff" "woff2" "ttf" "svg")))
(unless (file-exists? (string-append scripts "jquery.min.js"))
(symlink (string-append jquery "/share/web/jquery/jquery.min.js")
(string-append scripts "jquery.min.js")))
(unless (file-exists? (string-append scripts "lodash.js"))
(symlink (string-append lodash js-path2 "lodash/lodash.js")
(string-append scripts "lodash.js")))
(unless (file-exists? (string-append scripts "d3.v4.min.js"))
(symlink (string-append d3js-4 js-path "d3js/d3.min.js")
(string-append scripts "d3.v4.min.js")))
(unless (file-exists? (string-append scripts "d3-selection-multi.v1.js"))
(symlink (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js")
(string-append scripts "d3-selection-multi.v1.js")))
(unless (file-exists? (string-append scripts "canvas-toBlob.js"))
(symlink (string-append canvas-toblob js-path "canvas-toblob/canvas-toBlob.js")
(string-append scripts "canvas-toBlob.js")))
(unless (file-exists? (string-append scripts "FileSaver.min.js"))
(symlink (string-append filesaver js-path2 "filesaver/FileSaver.min.js")
(string-append scripts "FileSaver.min.js")))
#t)))
(add-after 'install 'make-files-executable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each
(lambda (file)
(chmod file #o555))
(append (find-files out "\\.(sh|py)$")
(find-files
(string-append out "/sourcecodes/run_scripts/") "^run")))
#t)))
(add-after 'make-files-executable 'wrap-executables
(lambda* (#:key outputs #:allow-other-keys)
(for-each
(lambda (script)
(wrap-program script
`("PATH" prefix (,(dirname (which "cp"))))
`("PYTHONPATH" prefix (,(getenv "PYTHONPATH")))))
(find-files (string-append (assoc-ref outputs "out")
"/sourcecodes/run_scripts") "^run"))
(for-each
(lambda (script)
(wrap-program script
`("PATH" prefix (,(dirname (which "cut"))))))
(append
(find-files (string-append (assoc-ref outputs "out")
"/sourcecodes") "\\.sh$")
(find-files (string-append (assoc-ref outputs "out")
"/var_lib_genenet_bnw") "\\.sh$")))
#t))
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "var_lib_genenet_bnw"
(invoke "sh" "build.sh")))))))
(inputs
`(("graphviz" ,graphviz)
("octave" ,octave-cli)
("python" ,python)
("python-plotly" ,python-plotly)
("rmath" ,rmath-standalone)
;; the javascript libraries:
("awesome" ,web-font-awesome)
("canvas-toblob" ,javascript-canvas-toblob)
("cyto-dagre" ,javascript-cytoscape-dagre)
("cytoscape" ,javascript-cytoscape)
("d3js-4" ,javascript-d3js-4)
("d3js-multi" ,javascript-d3js-multi)
("dagre" ,javascript-dagre)
("filesaver" ,javascript-filesaver)
("jquery" ,web-jquery)
("lodash" ,javascript-lodash)
("panzoom" ,javascript-cytoscape-panzoom)))
(native-inputs
;; get_best_knets isn't buildable with anything newer than gcc-5.
`(("gcc" ,(@ (gnu packages commencement) gcc-toolchain-5))))
(home-page "http://compbio.uthsc.edu/BNW/")
(synopsis "Bayesian Network Webserver")
(description
"This contains the code for the @dfn{Bayesian Network Webserver} (BNW).")
(license (list license:gpl2
license:gpl2+
license:lgpl2.1+)))))
