diff options
Diffstat (limited to 'gn/packages/ratspub.scm')
| -rw-r--r-- | gn/packages/ratspub.scm | 213 |
1 files changed, 187 insertions, 26 deletions
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm index 29e1313..b664799 100644 --- a/gn/packages/ratspub.scm +++ b/gn/packages/ratspub.scm @@ -1,11 +1,16 @@ (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 (gn packages bioinformatics) + #:use-module (gnu packages bioinformatics) #:use-module (gn packages javascript) + #:use-module (gnu packages machine-learning) + #:use-module (gnu packages python) + #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gn packages web)) @@ -13,19 +18,27 @@ (define-public ratspub (package (name "ratspub") - (version "0.1") + (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 - "0cm9g38fxpa52458mdmhzhghj5c7b8l3k1b764zs9hdrki5s7wi7")))) + (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 + `(#:tests? #f ; no test suite #:phases (modify-phases %standard-phases (delete 'configure) @@ -34,12 +47,24 @@ (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) (inetutils (assoc-ref inputs "inetutils"))) - (substitute* "templates/cytoscape.html" + (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/.*") - "/static/bootstrap.min.css\">\n")) + (("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)) @@ -51,31 +76,58 @@ (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")) - (bootstrap (assoc-ref inputs "bootstrap"))) + (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 bootstrap - "/share/web/bootstrap/css/bootstrap.min.css") - (string-append out "/static/bootstrap.min.css"))) + (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")))) - `("PYTHONPATH" ":" prefix (,path)))) + `("PATH" ":" prefix (,(dirname (which "edirect.pl")) + ,(dirname (which "dirname")) + ,(dirname (which "grep")) + ,(dirname (which "sed")))) + `("PYTHONPATH" ":" prefix (,path)))) #t))))) (inputs - `(("edirect" ,edirect-gn) + `(("edirect" ,edirect) ("inetutils" ,inetutils) - ("python-flask" ,python-flask) - ("python-nltk" ,python-nltk))) + ("python-bcrypt" ,python-bcrypt) + ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) + ("python-keras" ,python-keras-for-ratspub) + ("python-nltk" ,python-nltk) + ("tensorflow" ,tensorflow))) (native-inputs - `(("cytoscape" ,javascript-cytoscape) - ("bootstrap" ,web-bootstrap))) + `(("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 @@ -86,4 +138,113 @@ 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 #f))) + (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)))))))) + +(define-public hrdp-project + (package + (name "hrdp-project") + (version "0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noderboarder/hrdp-project") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ag7jm43p35yh0cqcn53wg4iw7sgfypw10mxq5klxvhgj3r6cf7i")))) + (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 _ + (substitute* "./app/templates/layout.html" + (("https://.*.bootstrapcdn.com/bootstrap/4.*/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://code.jquery.com/jquery-3.*.slim.min.js.*") + "/static/jquery.slim.min.js\"></script>\n") + ;(("https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js.*") + ; "/static/popper.min.js\"></script>\n") + ) + #t)) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (python (assoc-ref inputs "python"))) + (delete-file "main.py") + (with-output-to-file "main.py" + (lambda () + (format #t "#!~a/bin/python +from app import create_app + +app = create_app() + +if __name__ == '__main__': + app.run(debug=True, port=4222)~%" + python))) + (chmod "main.py" #o555) + (copy-recursively "." out)) + #t)) + (add-after 'install 'install-javascript + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (bootstrap (assoc-ref inputs "bootstrap")) + (jquery (assoc-ref inputs "jquery")) + ;(js-popper (assoc-ref inputs "js-popper")) + ) + (symlink (string-append bootstrap + "/share/web/bootstrap/css/bootstrap.min.css") + (string-append out "/app/static/bootstrap.min.css")) + (symlink (string-append bootstrap + "/share/web/bootstrap/js/bootstrap.min.js") + (string-append out "/app/static/bootstrap.min.js")) + (symlink (string-append jquery + "/share/web/jquery/jquery.slim.min.js") + (string-append out "/app/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 "/main.py") + `("PYTHONPATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("python" ,python) + ("python-flask-sqlalchemy" ,python-flask-sqlalchemy))) + (native-inputs + `(("bootstrap" ,web-bootstrap) + ("jquery" ,web-jquery) + ;("js-popper" ,js-popper) ; empty output + )) + (home-page "https://github.com/noderboarder/hrdp-project") + (synopsis "") + (description "") + (license license:expat))) |