ratspub: remove definitions as they are replaced by genecup

1 files changed, 0 insertions, 129 deletions

diff --git a/gn/services/ratspub-container.scm b/gn/services/ratspub-container.scm
deleted file mode 100644
index 1bf9fc6..0000000
--- a/gn/services/ratspub-container.scm
+++ /dev/null
@@ -1,129 +0,0 @@
-(define-module (gn services ratspub-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* <ratspub-configuration>
-  ratspub-configuration
-  make-ratspub-configuration
-  ratspub-configuration?
-  (package  ratspub-configuration-package   ; package
-            (default ratspub)))
-
-(define %punkt.zip
-  (origin
-    (method url-fetch)
-    (uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip")
-    (sha256
-     (base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s"))))
-
-(define ratspub-activation
-  (match-lambda
-    (($ <ratspub-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 #$(file-append package "/userspub.sqlite") data_dir)
-               (chmod (string-append data_dir "/userspub.sqlite") #o554))))))))
-
-(define ratspub-shepherd-service
-  (match-lambda
-    (($ <ratspub-configuration> package)
-     (with-imported-modules (source-module-closure
-                              '((gnu build shepherd)
-                                (gnu system file-systems)))
-       (list (shepherd-service
-               (provision '(ratspub))
-               (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/ratspub.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 ratspub-service-type
-  (service-type
-    (name 'ratspub)
-    (extensions
-      (list
-        (service-extension shepherd-root-service-type
-                           ratspub-shepherd-service)
-        (service-extension activation-service-type
-                           ratspub-activation)
-        ;; Make sure we get all the dependencies of RatsPub.
-        (service-extension profile-service-type
-                           (compose list ratspub-configuration-package))))
-    (default-value (ratspub-configuration))
-    (description
-     "Run a RatsPub Webserver.")))
-
-(operating-system
-  (host-name "ratspub")
-  (timezone "Etc/UTC")
-  (locale "en_US.utf8")
-
-  (bootloader (bootloader-configuration
-               (bootloader grub-bootloader)
-               (targets '("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 (list nss-certs))
-
-  (services (list (service ratspub-service-type
-                           (ratspub-configuration
-                             ;; ratspub for docker, ratspub-with-tensorflow-native for architecture specific speed optimizations.
-                             ;(package ratspub))))))
-                             (package ratspub-with-tensorflow-native))))))
-
-;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/ratspub-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/ratspub-container.scm --network
-;; Docker instructions:
-;; docker load --input ratspub-docker-image.tar.gz
-;; docker run -d --privileged --net=host --name ratspub --volume /path/to/PubMed:/export2/PubMed guix