diff options
| -rw-r--r-- | guix.scm | 96 |
1 files changed, 84 insertions, 12 deletions
diff --git a/guix.scm b/guix.scm index 6605e9e..fc6ebbc 100644 --- a/guix.scm +++ b/guix.scm @@ -19,6 +19,7 @@ (define-module (guix) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix build-system pyproject) + #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (guix download) #:use-module (guix gexp) @@ -45,13 +46,81 @@ (define %source-dir (dirname (current-filename))) -(define nltk-punkt +(define nltk-punkt-source (origin (method url-fetch) (uri "https://raw.githubusercontent.com/nltk/nltk_data/gh-pages/packages/tokenizers/punkt.zip") (sha256 (base32 "1v306rjpjfcqd8mh276lfz8s1d22zgj8n0lfzh5nbbxfjj4hghsi")))) +(define-public nltk-punkt + (package + (name "nltk-punkt") + (version "1.0") + (source nltk-punkt-source) + (build-system gnu-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (delete 'check) + (replace 'unpack + (lambda* (#:key source #:allow-other-keys) + (invoke "unzip" source))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (string-append (assoc-ref outputs "out") + "/share/nltk_data/tokenizers/punkt"))) + (mkdir-p out) + (copy-recursively "punkt" out))))))) + (native-inputs (list unzip)) + (home-page "https://www.nltk.org/nltk_data/") + (synopsis "NLTK Punkt sentence tokenizer models") + (description "Pre-trained models for the Punkt sentence boundary +detection tokenizer, used by NLTK's sent_tokenize function.") + (license license:asl2.0))) + +(define minipubmed-source + (origin + (method url-fetch) + (uri "https://git.genenetwork.org/genecup/plain/minipubmed.tgz") + (sha256 + (base32 "116k7plhn7xkbv170035si7xhbfqb1ff15rxqwimjrwm8rb1bbcc")))) + +(define-public minipubmed + (package + (name "minipubmed") + (version "1.0") + (source minipubmed-source) + (build-system gnu-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (delete 'check) + (replace 'unpack + (lambda* (#:key source #:allow-other-keys) + (invoke "tar" "xzf" source))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (string-append (assoc-ref outputs "out") + "/share/minipubmed"))) + ;; Generate test.xml from pmid.list + (with-directory-excursion "minipubmed" + (system "cat pmid.list | fetch-pubmed -path PubMed/Archive/ > test.xml")) + (mkdir-p out) + (copy-recursively "minipubmed" out))))))) + (inputs (list edirect)) + (home-page "https://genecup.org") + (synopsis "Mini PubMed archive for GeneCup testing") + (description "A small collection of 2473 PubMed abstracts for testing +GeneCup with four gene symbols (gria1, crhr1, drd2, and penk).") + (license license:expat))) + (define-public python-google-genai (package (name "python-google-genai") @@ -119,15 +188,19 @@ access to Gemini models.") (("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\">"))))) - (add-after 'unpack 'install-punkt + (add-after 'unpack 'setup-minipubmed (lambda* (#:key inputs #:allow-other-keys) - (mkdir-p "nlp/tokenizers") - (invoke "unzip" #$(this-package-native-input "nltk-punkt") - "-d" "nlp/tokenizers"))) - (add-after 'unpack 'extract-pubmed-archive - (lambda _ - (invoke "gzip" "-d" "minipubmed.tgz") - (invoke "tar" "xvf" "minipubmed.tar"))) + (delete-file "minipubmed.tgz") + (let ((pubmed (string-append (assoc-ref inputs "minipubmed") + "/share/minipubmed")) + (punkt (string-append (assoc-ref inputs "nltk-punkt") + "/share/nltk_data/tokenizers/punkt"))) + ;; Patch default pubmed path to store location + (substitute* "more_functions.py" + (("\\./minipubmed") pubmed)) + ;; Copy punkt tokenizer data + (mkdir-p "nlp/tokenizers") + (copy-recursively punkt "nlp/tokenizers/punkt")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -194,6 +267,7 @@ access to Gemini models.") `(("edirect" ,edirect) ("inetutils" ,inetutils) ("gzip" ,gzip) + ("minipubmed" ,minipubmed) ("tar" ,tar) ;; JavaScript assets symlinked into static/ ("bootstrap" ,web-bootstrap) @@ -202,10 +276,8 @@ access to Gemini models.") ("font-awesome" ,web-font-awesome) ("jquery" ,web-jquery) ("js-filesaver" ,js-filesaver-1.3.2) + ("nltk-punkt" ,nltk-punkt) ("js-popper" ,js-popper-1.12.9))) - (native-inputs - `(("nltk-punkt" ,nltk-punkt) - ("unzip" ,unzip))) (home-page "http://genecup.org") (synopsis "GeneCup: gene-addiction relationship search using PubMed") (description "GeneCup automatically extracts information from PubMed and |