diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 77 |
1 files changed, 58 insertions, 19 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index a555a59..7116156 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -49,6 +49,7 @@ #:use-module (gnu packages version-control) #:use-module (gnu packages web) #:use-module (gnu packages xml) + #:use-module (gnu packages serialization) #:use-module (gn packages bioinformatics) #:use-module (gn packages crates-io) #:use-module (gn packages gemma) @@ -115,7 +116,7 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "0d902ec267d96b87648669a7a43b699c8a22a3de") + (let ((commit "b13447ff27581b2018e374e1d672dd680f06f177") (revision "5")) (package (name "genenetwork3") @@ -129,7 +130,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "159f6h2jcc6ydb8xwnjaqksbp52ycjwnf10bcy6fd2zvh1g8bjad")))) + "0xpcrsigk1fprhbz53rdyxchxvbjkcy2dmi0b3w9sg701q6bjlkg")))) (inputs (list python-click)) (native-inputs @@ -191,8 +192,39 @@ (description "GeneNetwork3 API for data science and machine learning.") (license license:agpl3+)))) + +(define-public temporary-python-flask-session + ;; This is a stop-gap to get the applications building with the guix channel + ;; set to 61428cc. + ;; Remove this as soon as the applications are building with mainline + ;; python-flask-session. + (package + (name "temporary-python-flask-session") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "flask_session" version)) + (sha256 + (base32 + "1zs20zpq6gxz9gsccbd2jrrbbcfvh0x9z9741gkr8dhh07mlbq10")))) + (build-system pyproject-build-system) + (arguments + '(#:tests? #f)) ; Tests require the various storage backends to be present + (inputs + (list python-flit-core)) + (propagated-inputs + (list python-cachelib python-flask python-msgspec)) + (home-page "https://github.com/fengsp/flask-session") + (synopsis "Adds server-side session support to your Flask application") + (description + "Flask-Session is an extension for Flask that adds support for +Server-side sessions, with a variety of different backends for session +storage.") + (license license:bsd-3))) + (define-public genenetwork2 - (let ((commit "314c6d597a96ac903071fcb6e50df3d9e88935e9") + (let ((commit "ffc39ef4b9d850375888161d0f38f797ce37e785") (revision "4")) (package (name "genenetwork2") @@ -205,7 +237,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "143a1b9jr5f0c184j06szrg6ly7kd2fn547pmb97iya658zai7gq")))) + "0b7dzbg5zzpm9p98047n36wwc25gfwr7hb2ns8l4z586p06m1yph")))) (native-inputs (list graphviz)) (propagated-inputs @@ -267,6 +299,8 @@ javascript-uikit javascript-underscore-string javascript-zxcvbn + javascript-xterm + javascript-xterm-style js-jstat js-md5 js-parsley @@ -284,7 +318,8 @@ python-cssselect python-flask python-flask-debugtoolbar - python-flask-session + ;;python-flask-session + temporary-python-flask-session python-htmlgen python-ijson python-jinja2 @@ -294,7 +329,6 @@ python-mysqlclient python-numpy python-pandas - python-pillow python-pylint python-pymonad python-pytest @@ -306,9 +340,9 @@ python-scipy python-setuptools python-simplejson - python-sqlalchemy python-wrapper python-xlsxwriter + python-pillow-9 r r-ctl r-qtl @@ -316,8 +350,6 @@ redis rust-qtlreaper which - ; javascript-xterm -- disabled until we know what to do with it, not working on production - ; javascript-xterm-style ; javascript-xterm-addon-fit )) (inputs @@ -436,8 +468,8 @@ )))))) (define-public gn-uploader - (let ((commit "848bd536ce8d34f0b1ddada7b170f56f6465b317") - (version "0.1.0")) + (let ((commit "a675d462d2771f9e6c497c2385c985c2a6bb8806") + (version "0.1.1")) (package (name "gn-uploader") (version (string-append version "-" (string-take commit 8))) @@ -447,10 +479,11 @@ (uri (git-reference (url "https://git.genenetwork.org/gn-uploader") (commit commit))) + (file-name (git-file-name name version)) (hash (content-hash (base32 - "1qlimmbb820q1w76iv3bid5vv29rwrdd0xk3jskqg66v9yirqqyi"))))) + "0wa5ww43jimwgw9wvz5rmpxhva0fvbd5cqaf6m6d2d57v4klapsi"))))) (build-system python-build-system) (arguments (list @@ -476,10 +509,14 @@ python-pymonad python-jsonpickle python-mysqlclient - python-flask-session - javascript-jquery - javascript-bootstrap - javascript-datatables + ;;python-flask-session + temporary-python-flask-session + web-bootstrap-5 + javascript-jquery-1 + javascript-datatables-bootstrap5 + javascript-datatables-select + javascript-datatables-buttons-3 + javascript-datatables-scroller-2 node-resumablejs)) (synopsis "GeneNetwork Quality Control Application") (description @@ -490,7 +527,7 @@ (license license:agpl3+)))) (define-public gn-auth - (let ((commit "e345a04030249c99237a7f4e1e80e29918e99c7c") + (let ((commit "8ff5d551633177d5ff07544348b2e04c4de5654e") (revision "01")) (package (name "gn-auth") @@ -504,7 +541,7 @@ (hash (content-hash (base32 - "17srcxk5zwnsx97jqmg1csarmjsny8z8k7q435kq19p472f27yv7"))))) + "1pjcbrvmqipbni65ffq808gxzh2ywdwi28pm3gfqwq1z1jf627sx"))))) (build-system python-build-system) (arguments (list @@ -568,8 +605,10 @@ (invoke "pytest" "-k" "unit_test"))))))) (native-inputs (list python-mypy + python-wheel python-pylint - python-pytest)) + python-pytest + python-setuptools)) (propagated-inputs (list python-authlib python-pymonad |