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(define-module (gn packages ratspub)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system python)
#:use-module (gnu packages admin)
#:use-module (gnu packages bioinformatics)
#:use-module (gn packages javascript)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gn packages web))
(define-public ratspub
(package
(name "ratspub")
(version "0.3.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/chen42/ratspub.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1ii3721mqd3dbpjkhqi7yqjd9bqcf0g19kdbb8265pmbfjjsg164"))
(modules '((guix build utils)))
(snippet
'(begin (substitute* "server.py"
;; Keep the service running on port 4200
(("4201") "4200")
;; Backport to python-keras-2.2.4
(("learning_rate") "lr") )
#t))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(add-after 'unpack 'patch-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(inetutils (assoc-ref inputs "inetutils")))
(substitute* '("templates/cytoscape.html"
"templates/tableview.html"
"templates/tableview0.html"
"templates/userarchive.html")
(("script src=.*")
"script src=\"/static/cytoscape.min.js\"></script>\n"))
(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")
)
(substitute* "ratspub.py"
(("hostname") (string-append inetutils "/bin/hostname"))))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(copy-recursively "." out))
#t))
(add-after 'install 'install-javascript
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(awesome (assoc-ref inputs "font-awesome"))
(bootstrap (assoc-ref inputs "bootstrap"))
(cytoscape (assoc-ref inputs "cytoscape"))
(jquery (assoc-ref inputs "jquery"))
;(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"))
(symlink (string-append bootstrap
"/share/web/bootstrap/css/bootstrap.min.css")
(string-append out "/static/bootstrap.min.css"))
(symlink (string-append bootstrap
"/share/web/bootstrap/js/bootstrap.min.js")
(string-append out "/static/bootstrap.min.js"))
(symlink (string-append cytoscape
"/share/genenetwork2/javascript/cytoscape/cytoscape.min.js")
(string-append out "/static/cytoscape.min.js"))
(symlink (string-append jquery
"/share/web/jquery/jquery.slim.min.js")
(string-append out "/static/jquery.slim.min.js"))
;(symlink (string-append js-popper
; "/share/web/popper/popper.min.js")
; (string-append out "/static/popper.min.js"))
)
#t))
(add-after 'install 'wrap-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/server.py")
`("PATH" ":" prefix (,(dirname (which "edirect.pl"))
,(dirname (which "dirname"))
,(dirname (which "grep"))
,(dirname (which "sed"))))
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("edirect" ,edirect)
("inetutils" ,inetutils)
("python-bcrypt" ,python-bcrypt)
("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
("python-keras" ,python-keras-for-ratspub)
("python-nltk" ,python-nltk)
("tensorflow" ,tensorflow)))
(native-inputs
`(("bootstrap" ,web-bootstrap)
("cytoscape" ,javascript-cytoscape)
("font-awesome" ,web-font-awesome)
("jquery" ,web-jquery)
;("js-popper" ,js-popper) ; empty output
))
(home-page "http://rats.pub/")
(synopsis "Relationship with Addiction Through Searches of PubMed")
(description
"RatsPub searches PubMed to find sentences that contain the query terms
(i.e., gene symbols) and drug addiction-related keywords. These gene-keyword
relationships are presented as an interactive graph that can efficiently answer
the question \"What do we know about these genes and addiction?\". Data from
@acronym{EBI GWAS, European Bioinformatics Institute Genome-Wide Association
Studies} catalog are also included in the search to better answer this
question.")
(license license:expat)))
;; We want a copy of python-keras with the AUC optimizer backported.
;; We skip the tests because we "test in production".
;; That's a lie. The test suite just takes a long time to run.
(define-public python-keras-for-ratspub
(hidden-package
(package
(inherit python-keras)
(source
(origin
(inherit (package-source python-keras))
(patches (search-patches "keras-auc-optimizer.patch"))))
(arguments
(substitute-keyword-arguments (package-arguments python-keras)
((#:phases phases)
`(modify-phases ,phases
(delete 'check))))))))
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