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authorEfraim Flashner2020-09-09 03:18:20 -0500
committerEfraim Flashner2020-09-09 03:18:20 -0500
commit36241fc8645ad4069974a8f3a5889029681eb85a (patch)
tree47bf0976dbb77662faf551fe89f292dbabb1f970 /gn/packages
parentd59a0232dbc699caf991f00b96038ccd62005927 (diff)
downloadguix-bioinformatics-36241fc8645ad4069974a8f3a5889029681eb85a.tar.gz
ratspub: Update to 0.4.2
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/javascript.scm55
-rw-r--r--gn/packages/ratspub.scm63
2 files changed, 87 insertions, 31 deletions
diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm
index 1325a29..ab56bcf 100644
--- a/gn/packages/javascript.scm
+++ b/gn/packages/javascript.scm
@@ -270,6 +270,37 @@ positioned on or around Cytoscape elements. It is useful for tooltips and
overlays, for example.")
(license license:expat)))
+(define-public js-cytoscape-svg-vendor-0.3.1
+ (package
+ (name "js-cytoscape-svg-vendor")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://unpkg.com/cytoscape-svg@" version
+ "/cytoscape-svg.js"))
+ (sha256
+ (base32
+ "0ic0m91a4a4517c6f8nwf649yyq6xma57rxp8cyk4261qhk70494"))))
+ (build-system trivial-build-system)
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let* ((out (assoc-ref %outputs "out"))
+ (dest (string-append out "//share/javascript")))
+ (mkdir-p dest)
+ (copy-file (assoc-ref %build-inputs "source")
+ (string-append dest "/cytoscape-svg.js"))
+ #t))))
+ (home-page "https://kinimesi.github.io/cytoscape-svg")
+ (synopsis "Cytoscape.js extension to export the current graph view as an SVG")
+ (description
+ "A Cytoscape.js extension to export the current graph view as an SVG.")
+ (license license:gpl3)
+ (properties `((hidden? . #t)))))
+
(define-public javascript-qtip2
(package
(name "javascript-qtip2")
@@ -1594,6 +1625,30 @@ widgets, and themes built on top of the jQuery JavaScript Library.")
Popper will automatically put the tooltip in the right place near the button.")
(license license:expat)))
+(define-public js-popper-1.12.9
+ (package
+ (name "js-popper")
+ (version "1.12.9")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/popperjs/popper-core")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0j7gfb7agvvzxv09vq8yr5h04pls5a8md2qw62qyn20112p0hdzs"))))
+ (build-system minify-build-system)
+ (arguments
+ `(#:javascript-files '("dist/umd/popper.js")))
+ (home-page "https://popper.js.org/")
+ (synopsis "Tooltip and popover positioning engine")
+ (description
+ "Given an element, such as a button, and a tooltip element describing it,
+Popper will automatically put the tooltip in the right place near the button.")
+ (license license:expat)))
+
(define-public javascript-zxcvbn-async
(package
(name "javascript-zxcvbn-async")
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index d385ebf..9f32a6f 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -20,23 +20,22 @@
(define-public ratspub
(package
(name "ratspub")
- (version "0.4.1")
+ (version "0.4.2")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/chen42/ratspub")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
+ ;; Keep the service running on port 4200.
+ (modules '((guix build utils)))
+ (snippet
+ '(begin (substitute* "server.py"
+ (("4201") "4200"))
+ #t))
(sha256
(base32
- "1daf0qd0lyvfp9ab1qvhj37xvrrzkwvsfnickls5i9lbpgisizm4"))
- ;(modules '((guix build utils)))
- ;(snippet
- ; '(begin (substitute* "server.py"
- ; ;; Keep the service running on port 4200
- ; (("4200") "4201"))
- ; #t))
- ))
+ "1b3ddr4wzs7cz826dfl618rqrnfbvihd4fwhjlsj7n92r6n4bpjl"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no test suite
@@ -44,6 +43,11 @@
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
+ (add-after 'unpack 'patch-datadir
+ (lambda _
+ (substitute* "server.py"
+ (("^datadir.*") "datadir = \"/export/ratspub/\"\n"))
+ #t))
(add-after 'unpack 'patch-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@@ -52,21 +56,15 @@
"templates/tableview.html"
"templates/tableview0.html"
"templates/userarchive.html")
- ;(("https.*FileSaver.js.*>") "/static/FileSaver.js\">") ; Something about our copy is different
- ;(("https.*cytoscape-svg.js.*>") "/static/cytoscape-svg.js\">") ; TODO
- (("https.*cytoscape.min.js.*>") "/static/cytoscape.min.js\">"))
+ (("https.*FileSaver.js.*\\\">") "/static/FileSaver.js\">")
+ (("https.*cytoscape-svg.js.*\\\">") "/static/cytoscape-svg.js\">")
+ (("https.*cytoscape.min.js.*\\\">") "/static/cytoscape.min.js\">"))
(substitute* "templates/layout.html"
- (("https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css.*")
- "/static/bootstrap.min.css\">\n")
- (("https://.*.bootstrapcdn.com/bootstrap/4.*/js/bootstrap.min.js.*")
- "/static/bootstrap.min.js\"></script>\n")
- (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css")
- "/static/font-awesome.min.css")
- (("https://code.jquery.com/jquery-3.2.1.slim.min.js.*")
- "/static/jquery.slim.min.js\"></script>\n")
- ;(("https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js.*")
- ; "/static/popper.min.js\"></script>\n")
- )
+ (("https.*bootstrap.min.css.*\\\">") "/static/bootstrap.min.css\">")
+ (("https.*4.*bootstrap.min.js.*\\\">") "/static/bootstrap.min.js\">")
+ (("https.*4.7.0/css/font-awesome.min.css") "/static/font-awesome.min.css")
+ (("https.*jquery-3.2.1.slim.min.js.*\\\">") "/static/jquery.slim.min.js\">")
+ (("https.*1.12.9/umd/popper.min.js.*\\\">") "/static/popper.min.js\">"))
(substitute* "ratspub.py"
(("hostname") (string-append inetutils "/bin/hostname"))))
#t))
@@ -81,10 +79,10 @@
(awesome (assoc-ref inputs "font-awesome"))
(bootstrap (assoc-ref inputs "bootstrap"))
(cytoscape (assoc-ref inputs "cytoscape"))
+ (cytoscape-svg (assoc-ref inputs "cytoscape-svg"))
(jquery (assoc-ref inputs "jquery"))
(js-filesaver (assoc-ref inputs "js-filesaver"))
- ;(js-popper (assoc-ref inputs "js-popper"))
- )
+ (js-popper (assoc-ref inputs "js-popper")))
(symlink (string-append awesome
"/share/web/font-awesomecss/font-awesome.min.css")
(string-append out "/static/font-awesome.min.css"))
@@ -97,16 +95,18 @@
(symlink (string-append cytoscape
"/share/genenetwork2/javascript/cytoscape/cytoscape.min.js")
(string-append out "/static/cytoscape.min.js"))
+ (symlink (string-append cytoscape-svg
+ "/share/javascript/cytoscape-svg.js")
+ (string-append out "/static/cytoscape-svg.js"))
(symlink (string-append jquery
"/share/web/jquery/jquery.slim.min.js")
(string-append out "/static/jquery.slim.min.js"))
(symlink (string-append js-filesaver
"/share/javascript/FileSaver.js")
(string-append out "/static/FileSaver.js"))
- ;(symlink (string-append js-popper
- ; "/share/web/popper/popper.min.js")
- ; (string-append out "/static/popper.min.js"))
- )
+ (symlink (string-append js-popper
+ "/share/javascript/popper.min.js")
+ (string-append out "/static/popper.min.js")))
#t))
(add-after 'install 'wrap-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
@@ -130,11 +130,12 @@
(native-inputs
`(("bootstrap" ,web-bootstrap)
("cytoscape" ,javascript-cytoscape)
+ ;("cytoscape-svg" ,js-cytoscape-svg-0.3.1) ; TODO
+ ("cytoscape-svg" ,js-cytoscape-svg-vendor-0.3.1)
("font-awesome" ,web-font-awesome)
("jquery" ,web-jquery)
("js-filesaver" ,js-filesaver-1.3.2)
- ;("js-popper" ,js-popper) ; empty output
- ))
+ ("js-popper" ,js-popper-1.12.9)))
(home-page "http://rats.pub/")
(synopsis "Relationship with Addiction Through Searches of PubMed")
(description