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authorArun Isaac2023-08-31 12:37:30 +0100
committerArun Isaac2023-08-31 12:37:30 +0100
commit9a653d2d9aa566f6273bd2ceb3be7ac533fb372c (patch)
tree400854af85e391eac053a1dd8b0ee10f560a7694
parent2398844e27a3f80884ed2a008a30a9e6295e9133 (diff)
downloadguix-bioinformatics-9a653d2d9aa566f6273bd2ceb3be7ac533fb372c.tar.gz
Move gn-auth to (gn packages genenetwork).
-rw-r--r--gn/packages/genenetwork.scm102
-rw-r--r--gn/packages/gn-auth.scm69
2 files changed, 74 insertions, 97 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 36d3ae6..6e5bbce 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -463,47 +463,93 @@
(description "Genenetwork installation sumo.")
(license license:agpl3+))))
+(define-public gn-auth
+ (package
+ (name "gn-auth")
+ (version "1.0.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/genenetwork/gn-auth.git")
+ (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd")))
+ (hash
+ (content-hash
+ (base32
+ "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l")))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-k" "unit_test")))))))
+ (native-inputs
+ (list python-mypy
+ python-pytest
+ python-pylint
+ python-hypothesis
+ python-pytest-mock
+ python-mypy-extensions))
+ (propagated-inputs
+ (list gunicorn
+ python-flask
+ python-redis
+ python-authlib
+ python-pymonad
+ yoyo-migrations
+ python-bcrypt ;; remove after removing all references
+ python-mysqlclient
+ python-argon2-cffi
+ python-email-validator))
+ (home-page "https://github.com/genenetwork/gn-auth")
+ (synopsis "Authentication and Authorisation server for GeneNetwork services")
+ (description "Authentication and Authorisation server for GeneNetwork services.")
+ (license license:agpl3+)))
+
;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
(define-public genenetwork2-files-small
(let ((pfff "xx"))
(package
- (name "genenetwork2-files-small")
- (version "1.0")
- (source
- (origin
- (method url-fetch)
- (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4")
- (file-name (string-append name "-" pfff))
- (sha256
- (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj"))))
- (build-system trivial-build-system)
- (native-inputs `(("lz4" ,lz4)
- ("tar" ,tar)
- ("source" ,source)))
+ (name "genenetwork2-files-small")
+ (version "1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4")
+ (file-name (string-append name "-" pfff))
+ (sha256
+ (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj"))))
+ (build-system trivial-build-system)
+ (native-inputs `(("lz4" ,lz4)
+ ("tar" ,tar)
+ ("source" ,source)))
- (arguments
- `(#:modules ((guix build utils))
- #:builder
- (let* ((out (assoc-ref %outputs "out"))
- (name "gn2_data_s")
- (tarfn (string-append name ".tar"))
- (targetdir (string-append out "/share/genenetwork2/")))
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (let* ((out (assoc-ref %outputs "out"))
+ (name "gn2_data_s")
+ (tarfn (string-append name ".tar"))
+ (targetdir (string-append out "/share/genenetwork2/")))
(begin
(use-modules (guix build utils))
(let ((source (assoc-ref %build-inputs "source"))
(lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4"))
(tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")))
(and
- (zero? (system* lz4unpack source "-d" tarfn))
- (zero? (system* tar "xf" tarfn))
- (mkdir-p targetdir)
- (copy-recursively name targetdir)))))))
- (home-page "http://genenetwork.org/")
- (synopsis "Small file archive to run on genenetwork")
- (description "Genenetwork genotype and mapping files.")
- (license license:agpl3+))))
+ (zero? (system* lz4unpack source "-d" tarfn))
+ (zero? (system* tar "xf" tarfn))
+ (mkdir-p targetdir)
+ (copy-recursively name targetdir)))))))
+ (home-page "http://genenetwork.org/")
+ (synopsis "Small file archive to run on genenetwork")
+ (description "Genenetwork genotype and mapping files.")
+ (license license:agpl3+))))
(define-public genenetwork2-database-small
(let ((md5 "93e745e9c"))
diff --git a/gn/packages/gn-auth.scm b/gn/packages/gn-auth.scm
deleted file mode 100644
index a87b22c..0000000
--- a/gn/packages/gn-auth.scm
+++ /dev/null
@@ -1,69 +0,0 @@
-(define-module (gn packages gn-auth)
- #:use-module (guix)
- #:use-module (guix gexp)
- #:use-module (guix packages)
- #:use-module (guix download)
- #:use-module (guix git-download)
- #:use-module (guix build-system python)
- #:use-module ((guix licenses) #:prefix license:)
-
- ;; Packages from guix
- #:use-module (gnu packages check)
-
- #:use-module (gnu packages django)
-
- #:use-module (gnu packages python-web)
- #:use-module (gnu packages python-xyz)
- #:use-module (gnu packages python-check)
- #:use-module (gnu packages python-crypto)
-
- #:use-module (gnu packages databases)
-
- ;; Packages from guix-bioinformatics
- #:use-module (gn packages python-web))
-
-(define-public gn-auth
- (package
- (name "gn-auth")
- (version "1.0.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/genenetwork/gn-auth.git")
- (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd")))
- (hash
- (content-hash
- (base32
- "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l")))))
- (build-system python-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-k" "unit_test")))))))
- (native-inputs
- (list python-mypy
- python-pytest
- python-pylint
- python-hypothesis
- python-pytest-mock
- python-mypy-extensions))
- (propagated-inputs
- (list gunicorn
- python-flask
- python-redis
- python-authlib
- python-pymonad
- yoyo-migrations
- python-bcrypt ;; remove after removing all references
- python-mysqlclient
- python-argon2-cffi
- python-email-validator))
- (home-page "https://github.com/genenetwork/gn-auth")
- (synopsis "Authentication and Authorisation server for GeneNetwork services")
- (description "Authentication and Authorisation server for GeneNetwork services.")
- (license license:agpl3+)))