gn: genecup testing

2 files changed, 270 insertions, 1 deletions

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 85c73c7..1c00139 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -11,6 +11,7 @@
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gn packages javascript)
@@ -139,7 +140,7 @@
        ("jquery" ,web-jquery)
        ("js-filesaver" ,js-filesaver-1.3.2)
        ("js-popper" ,js-popper-1.12.9)))
-    (home-page "http://rats.pub/")
+    (home-page "https://rats.pub/")
     (synopsis "Relationship with Addiction Through Searches of PubMed")
     (description
      "RatsPub is a tool to efficiently and comprehensively answer the question
@@ -266,3 +267,142 @@ if __name__ == '__main__':
     (synopsis "")
     (description "")
     (license license:expat)))
+
+(define-public genecup
+  (package
+    (name "genecup")
+    (version "1.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/hakangunturkun/GeneCup")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              ;; Change the port for running the service.
+              (modules '((guix build utils)))
+              (snippet
+               '(begin (substitute* "server.py"
+                         (("4200") "4204"))
+                       #t))
+              (sha256
+               (base32 "0ddgqjiacr0f33x0f9s10v3rqr3mmr92jwniprk22a167ncvfgx3"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f  ; no test suite
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (add-after 'unpack 'make-files-writable
+           (lambda _
+             (for-each make-file-writable (find-files "."))))
+         (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"))
+                   (inetutils (assoc-ref inputs "inetutils")))
+               (substitute* '("templates/cytoscape.html"
+                              "templates/tableview.html"
+                              "templates/tableview0.html"
+                              "templates/userarchive.html")
+                 (("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.*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))
+         (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"))
+                   (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")))
+               (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 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/javascript/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)
+       ("python-pandas" ,python-pandas)
+       ("python-regex" ,python-regex)
+       ("tensorflow" ,tensorflow)))
+    (native-inputs
+     `(("bootstrap" ,web-bootstrap)
+       ("cytoscape" ,javascript-cytoscape-3.17)
+       ;("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-1.12.9)))
+    (home-page "http://genecut.org")
+    (synopsis "Using PubMed to find out how a gene contributes to addiction")
+    (description "GeneCup automatically extracts information from PubMed and
+@url{https://www.ebi.ac.uk/gwas/, @acronym{NHGRI-EBI GWAS, European
+Bioinformatics Institute Genome-Wide Association Studies}} catalog on the
+relationship of any gene with a custom list of keywords hierarchically organized
+into an ontology.  The users create an ontology by identifying categories of
+concepts and a list of keywords for each concept.")
+    (license license:expat)))
+
+(define-public genecup-with-tensorflow-native
+  (package
+    (inherit
+      (tensowflow-native-instead-of-tensorflow genecup))
+    (name "genecup-with-tensorflow-native")))
diff --git a/gn/services/genecup-container.scm b/gn/services/genecup-container.scm
new file mode 100644
index 0000000..eae3f9c
--- /dev/null
+++ b/gn/services/genecup-container.scm
@@ -0,0 +1,129 @@
+(define-module (gn services genecup-container))
+
+(use-modules (gnu)
+             (gn packages ratspub)
+             (guix download)
+             (guix modules)
+             (guix packages)
+             (guix records)
+             (ice-9 match))
+(use-service-modules shepherd)
+(use-package-modules certs compression)
+
+(define-record-type* <genecup-configuration>
+  genecup-configuration
+  make-genecup-configuration
+  genecup-configuration?
+  (package  genecup-configuration-package   ; package
+            (default genecup)))
+
+(define %punkt.zip
+  (origin
+    (method url-fetch)
+    (uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip")
+    (sha256
+     (base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s"))))
+
+(define genecup-activation
+  (match-lambda
+    (($ <genecup-configuration> package)
+     #~(begin
+         (let ((nltk_data "/var/cache/nltk_data/tokenizers")
+               (data_dir "/export/ratspub"))
+           (unless (file-exists? "/export2/PubMed")
+             (mkdir-p "/export2/PubMed"))
+           (unless (file-exists? nltk_data)
+             (begin
+               ;; The correct way would be to use python-nltk to download the data
+               ;; python3 -m nltk.downloader -d /var/cache/nltk_data punkt
+               (mkdir-p nltk_data)
+               (chdir nltk_data)
+               (invoke #$(file-append unzip "/bin/unzip") "-q" #$%punkt.zip)))
+           (unless (file-exists? (string-append data_dir "/userspub.sqlite"))
+             (begin
+               (install-file #$(file-append package "/userspub.sqlite") data_dir)
+               (chmod (string-append data_dir "/userspub.sqlite") #o554))))))))
+
+(define genecup-shepherd-service
+  (match-lambda
+    (($ <genecup-configuration> package)
+     (with-imported-modules (source-module-closure
+                              '((gnu build shepherd)
+                                (gnu system file-systems)))
+       (list (shepherd-service
+               (provision '(genecup))
+               (requirement '(networking))
+               (modules '((gnu build shepherd)
+                          (gnu system file-systems)))
+               (start #~(make-forkexec-constructor/container
+                          (list #$(file-append package "/server.py"))
+                          ;; Needs to run from the directory it is located in.
+                          #:directory #$package
+                          #:log-file "/var/log/genecup.log"
+                          ;; We don't need to set TMPDIR because we're inside a container.
+                          #:environment-variables
+                          '("EDIRECT_PUBMED_MASTER=/export2/PubMed"
+                            "NLTK_DATA=/var/cache/nltk_data"
+                            "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt")
+                          #:mappings (list (file-system-mapping
+                                             (source "/export2/PubMed")
+                                             (target source)
+                                             (writable? #t))
+                                           (file-system-mapping
+                                             (source "/export/ratspub")
+                                             (target source)
+                                             (writable? #t))
+                                           (file-system-mapping
+                                             (source "/var/cache/nltk_data")
+                                             (target source))
+                                           (file-system-mapping
+                                             (source "/etc/ssl/certs")
+                                             (target source)))))
+               (stop  #~(make-kill-destructor))))))))
+
+(define genecup-service-type
+  (service-type
+    (name 'genecup)
+    (extensions
+      (list
+        (service-extension shepherd-root-service-type
+                           genecup-shepherd-service)
+        (service-extension activation-service-type
+                           genecup-activation)
+        ;; Make sure we get all the dependencies of RatsPub.
+        (service-extension profile-service-type
+                           (compose list genecup-configuration-package))))
+    (default-value (genecup-configuration))
+    (description
+     "Run a GeneCup Webserver.")))
+
+(operating-system
+  (host-name "genecup")
+  (timezone "Etc/UTC")
+  (locale "en_US.utf8")
+
+  (bootloader (bootloader-configuration
+               (bootloader grub-bootloader)
+               (target "does-not-matter")))
+  (file-systems (list (file-system
+                        (device "does-not-matter")
+                        (mount-point "/")
+                        (type "does-not-matter"))))
+  ;; TODO: A more minimal kernel for use in a docker image
+  ;; (kernel linux-libre-vm)
+  ;; No firmware for VMs.
+  (firmware '())
+  (packages (cons nss-certs %base-packages)) ;(list nss-certs))
+
+  (services (list (service genecup-service-type
+                           (genecup-configuration
+                             ;; genecup for docker, genecup-with-tensorflow-native for architecture specific speed optimizations.
+                             ;(package genecup))))))
+                             (package genecup-with-tensorflow-native))))))
+
+;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/genecup-container.scm --network --share=/export2/PubMed=/export2/PubMed --share=/export/ratspub=/export/ratspub
+;; For docker it isn't necessary to list the shared folders at build time.
+;; guix system docker-image -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/genecup-container.scm --network
+;; Docker instructions:
+;; docker load --input genecup-docker-image.tar.gz
+;; docker run -d --privileged --net=host --name genecup --volume /path/to/PubMed:/export2/PubMed guix