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authorEfraim Flashner2020-03-15 04:33:59 -0500
committerEfraim Flashner2020-03-15 04:33:59 -0500
commitec9a0ae00428f944717ff5e4d97da52a500647ce (patch)
tree92d0176ea39b88f1e87578f2431abc725c9e8e3c
parentda457bd06f88fddcd7bfa510e7aac6358ffd028d (diff)
downloadguix-bioinformatics-wip-ratspub.tar.gz
WIP: update ratspub to 0.2-1.1b516eewip-ratspub
As a package it is ready, but it tries to write to files in it's directory, which is in the store, meaning the service will need to be rewritten.
-rw-r--r--gn/packages/javascript.scm24
-rw-r--r--gn/packages/ratspub.scm182
2 files changed, 133 insertions, 73 deletions
diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm
index 79a8060..e6d1d7e 100644
--- a/gn/packages/javascript.scm
+++ b/gn/packages/javascript.scm
@@ -1121,3 +1121,27 @@ widgets, and themes built on top of the jQuery JavaScript Library.")
(name "js-jquery-ui")
(arguments `(#:javascript-files '("ui/jquery-ui.js")))
(build-system minify-build-system)))
+
+(define-public js-poppler
+ (package
+ (name "js-poppler")
+ (version "2.0.6")
+ (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
+ "0lzy981p9nja2l3xa2zvals6q31v3bzpxxa85yn9pm7wkj3vglf2"))))
+ (build-system minify-build-system)
+ (arguments
+ `(#:javascript-files '("src/poppler.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)))
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 290b9e2..3394592 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -6,87 +6,123 @@
#:use-module (gnu packages admin)
#:use-module (gn packages bioinformatics)
#:use-module (gn packages javascript)
+ #:use-module (gnu packages time)
+ #: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 "0.1")
- (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"))))
- (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"
- (("script src=.*")
- "script src=\"/static/cytoscape.min.js\"></script>\n"))
- (substitute* "templates/layout.html"
- (("https://stackpath.bootstrapcdn.com/bootstrap/.*")
- "/static/bootstrap.min.css\">\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"))
- (cytoscape (assoc-ref inputs "cytoscape"))
- (bootstrap (assoc-ref inputs "bootstrap")))
- (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")))
- #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-gn)
- ("inetutils" ,inetutils)
- ("python-flask" ,python-flask)
- ("python-nltk" ,python-nltk)))
- (native-inputs
- `(("cytoscape" ,javascript-cytoscape)
- ("bootstrap" ,web-bootstrap)))
- (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
+ (let ((commit "1b516ee692248f4cd75570d9750b14f78554b41f")
+ (revision "1"))
+ (package
+ (name "ratspub")
+ (version (git-version "0.2" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/chen42/ratspub.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "16zr89993h1idkazradivm9yjgl695wdr34d2qbwj4nmaxfrg8dy"))))
+ (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/poppler.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-poppler (assoc-ref inputs "js-poppler")))
+ (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-poppler
+ "/share/web/poppler/poppler.min.js")
+ (string-append out "/static/poppler.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-gn)
+ ("inetutils" ,inetutils)
+ ("python-bcrypt" ,python-bcrypt)
+ ("python-flask" ,python-flask)
+ ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+ ("python-nltk" ,python-nltk)
+ ("python-pytz" ,python-pytz)))
+ (native-inputs
+ `(("bootstrap" ,web-bootstrap)
+ ("cytoscape" ,javascript-cytoscape)
+ ("font-awesome" ,web-font-awesome)
+ ("jquery" ,web-jquery)
+ ("js-poppler" ,js-poppler)))
+ (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 #f)))
+ (license #f))))