From 9a653d2d9aa566f6273bd2ceb3be7ac533fb372c Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 31 Aug 2023 12:37:30 +0100 Subject: Move gn-auth to (gn packages genenetwork). --- gn/packages/genenetwork.scm | 102 ++++++++++++++++++++++++++++++++------------ 1 file changed, 74 insertions(+), 28 deletions(-) (limited to 'gn/packages/genenetwork.scm') 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")) -- cgit v1.2.3 From aaa6e53e7b623105d05e67e95186aba5b4671010 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 13:05:11 +0300 Subject: Pin python to python@3.8.5 * gn/packages/genenetwork.scm: (genenetwork3, genenetwork2): Using python@3.8.5 Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 6e5bbce..7d8cb43 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -135,7 +135,7 @@ python-pytest-mock)) (propagated-inputs (list gemma-wrapper - python-wrapper + `("python" (specification->package "python@3.8.5")) csvdiff gn-rust-correlation python-bcrypt ;; Replace use of bcrypt with argon below @@ -218,7 +218,7 @@ ("gn-rust-correlation" ,gn-rust-correlation) ("glibc-utf8-locales" ,glibc-utf8-locales) ("nginx" ,nginx) - ("python" ,python-wrapper) + ("python" ,(specification->package "python@3.8.5")) ("python-pillow" ,python-pillow) ("python-coverage" ,python-coverage) ("python-configparser" ,python-configparser) ;; maintenance/scripts -- cgit v1.2.3 From 6f4a72968e473a52ac1a58971e7150823e96ba16 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 19:18:24 +0300 Subject: Revert "Pin python to python@3.8.5" This reverts commit aaa6e53e7b623105d05e67e95186aba5b4671010. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 7d8cb43..6e5bbce 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -135,7 +135,7 @@ python-pytest-mock)) (propagated-inputs (list gemma-wrapper - `("python" (specification->package "python@3.8.5")) + python-wrapper csvdiff gn-rust-correlation python-bcrypt ;; Replace use of bcrypt with argon below @@ -218,7 +218,7 @@ ("gn-rust-correlation" ,gn-rust-correlation) ("glibc-utf8-locales" ,glibc-utf8-locales) ("nginx" ,nginx) - ("python" ,(specification->package "python@3.8.5")) + ("python" ,python-wrapper) ("python-pillow" ,python-pillow) ("python-coverage" ,python-coverage) ("python-configparser" ,python-configparser) ;; maintenance/scripts -- cgit v1.2.3 From 543a0d0afd5205c839c79c27d57b4b43c9742387 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 5 Sep 2023 14:15:28 +0300 Subject: Adjust how native/propagated inputs are defined for GN3 Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 83 +++++++++++++++++++++++---------------------- 1 file changed, 42 insertions(+), 41 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 6e5bbce..c7dba3b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -127,48 +127,49 @@ (inputs (list python-click)) (native-inputs - (list python-hypothesis - python-mypy - python-mypy-extensions - python-pylint - python-pytest - python-pytest-mock)) + `(("python-hypothesis" ,python-hypothesis) + ("python-mypy" ,python-mypy) + ("python-mypy-extensions" ,python-mypy-extensions) + ("python-pylint" ,python-pylint) + ("python-pytest" ,python-pytest) + ("python-pytest-mock" ,python-pytest-mock))) (propagated-inputs - (list gemma-wrapper - python-wrapper - csvdiff - gn-rust-correlation - python-bcrypt ;; Replace use of bcrypt with argon below - python-argon2-cffi - python-flask - python-flask-cors - ;; Not working in Python > 3.8 - ;; python-ipfshttpclient - python-lmdb - python-mysqlclient - python-numpy - python-pandas - ;; python-pingouin << build failing - python-pingouin-without-tests - python-plotly - python-scikit-learn - python-pymonad - python-redis - python-requests - python-scipy - python-authlib - python-sparqlwrapper - python-email-validator - python-xapian-bindings - r-optparse - r-qtl - r-rjson - r-stringi - r-wgcna - r-ctl - rust-qtlreaper - diffutils - yoyo-migrations)) + `(("gemma-wrapper" ,gemma-wrapper) + ("python-wrapper" ,python-wrapper) + ("csvdiff" ,csvdiff) + ("gn-rust-correlation" ,gn-rust-correlation) + ;; Replace use of bcrypt with argon below + ("python-bcrypt" ,python-bcrypt) + ("python-argon2-cffi" ,python-argon2-cffi) + ("python-flask" ,python-flask) + ("python-flask-cors" ,python-flask-cors) + ;; Not working in Python > 3.8 + ;; python-ipfshttpclient + ("python-lmdb" ,python-lmdb) + ("python-mysqlclient" ,python-mysqlclient) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ;; python-pingouin << build failing + ("python-pingouin-without-tests" ,python-pingouin-without-tests) + ("python-plotly" ,python-plotly) + ("python-scikit-learn" ,python-scikit-learn) + ("python-pymonad" ,python-pymonad) + ("python-redis" ,python-redis) + ("python-requests" ,python-requests) + ("python-scipy" ,python-scipy) + ("python-authlib" ,python-authlib) + ("python-sparqlwrapper" ,python-sparqlwrapper) + ("python-email-validator" ,python-email-validator) + ("python-xapian-bindings" ,python-xapian-bindings) + ("r-optparse" ,r-optparse) + ("r-qtl" ,r-qtl) + ("r-rjson" ,r-rjson) + ("r-stringi" ,r-stringi) + ("r-wgcna" ,r-wgcna) + ("r-ctl" ,r-ctl) + ("rust-qtlreaper" ,rust-qtlreaper) + ("diffutils" ,diffutils) + ("yoyo-migrations" ,yoyo-migrations))) (build-system python-build-system) (arguments (list #:phases -- cgit v1.2.3 From ebd0a22dd7388379a530b4171e4bd47602d07ebc Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 5 Sep 2023 14:24:48 +0300 Subject: gn: genenetwork: Update mypy and yoyo * gn/packages/genenetwork.scm: Import (guix packages). (genenetwork3): Use yoyo-migrations v8.2.0 and python-mypy v0.981. Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index c7dba3b..b2c6611 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -14,6 +14,7 @@ #:use-module (guix scripts graph) #:use-module (guix store) #:use-module (guix gexp) + #:use-module (guix packages) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioconductor) @@ -128,7 +129,7 @@ (list python-click)) (native-inputs `(("python-hypothesis" ,python-hypothesis) - ("python-mypy" ,python-mypy) + ("python-mypy" ,python-mypy-0.981) ("python-mypy-extensions" ,python-mypy-extensions) ("python-pylint" ,python-pylint) ("python-pytest" ,python-pytest) @@ -169,7 +170,7 @@ ("r-ctl" ,r-ctl) ("rust-qtlreaper" ,rust-qtlreaper) ("diffutils" ,diffutils) - ("yoyo-migrations" ,yoyo-migrations))) + ("yoyo-migrations" ,yoyo-migrations-8.2.0))) (build-system python-build-system) (arguments (list #:phases -- cgit v1.2.3 From 2a1cbd69761a2a32e1df525307b1aabc9b0fcb8e Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 6 Sep 2023 13:10:20 +0300 Subject: gn: gn-auth: Update yoyo and mypy Update yoyo and mypy to allow the use of Python-3.10 --- gn/packages/genenetwork.scm | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b2c6611..ab8f8bd 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -489,23 +489,23 @@ (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs - (list python-mypy - python-pytest - python-pylint - python-hypothesis - python-pytest-mock - python-mypy-extensions)) + `(("python-mypy" ,python-mypy-0.981) + ("python-pytest" ,python-pytest) + ("python-pylint" ,python-pylint) + ("python-hypothesis" ,python-hypothesis) + ("python-pytest-mock" ,python-pytest-mock) + ("python-mypy-extensions" ,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)) + `(("gunicorn" ,gunicorn) + ("python-flask" ,python-flask) + ("python-redis" ,python-redis) + ("python-authlib" ,python-authlib) + ("python-pymonad" ,python-pymonad) + ("yoyo-migrations" ,yoyo-migrations-8.2.0) + ("python-bcrypt" ,python-bcrypt) ;; remove after removing all references + ("python-mysqlclient" ,python-mysqlclient) + ("python-argon2-cffi" ,python-argon2-cffi) + ("python-email-validator" ,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.") -- cgit v1.2.3 From bfd4ccbbe6ad79ff9a02ca6c8656914f1fc4c414 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Wed, 20 Sep 2023 10:40:41 +0300 Subject: gn: genenetwork2: Add htmx. * gn/packages/genenetwork.scm (genenetwork2) [propagated-inputs]: Add htmx. --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ab8f8bd..5cd663e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -287,6 +287,7 @@ ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) ("javascript-shapiro-wilk" ,javascript-shapiro-wilk) ("javascript-underscore-string" ,javascript-underscore-string) + ("javascript-htmx" ,javascript-htmx) ("javascript-qtip2" ,javascript-qtip2) ("javascript-d3js" ,javascript-d3js) ("javascript-nvd3" ,javascript-nvd3) -- cgit v1.2.3 From 5676b7bb6c6d80a9364c61260aa7aaa2b4baf21e Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 25 Sep 2023 13:33:32 +0300 Subject: Delete python-mypy-0.981. * gn/packages/python.scm (python-mypy-0.981): Delete it. * gn/packages/genenetwork.scm (genenetwork3)[native-inputs]: Replace python-mypy-0.981 with upstream's python-mypy. Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 2 +- gn/packages/python.scm | 25 +------------------------ 2 files changed, 2 insertions(+), 25 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5cd663e..4ce207d 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -129,7 +129,7 @@ (list python-click)) (native-inputs `(("python-hypothesis" ,python-hypothesis) - ("python-mypy" ,python-mypy-0.981) + ("python-mypy" ,python-mypy) ("python-mypy-extensions" ,python-mypy-extensions) ("python-pylint" ,python-pylint) ("python-pytest" ,python-pytest) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index d728ef3..020a6a9 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1899,27 +1899,4 @@ concepts.") (base32 "1al030ix0w63hr4s3mqry6s0mlqdj8p242pdqks06br7c25nx3yj")))) (propagated-inputs (modify-inputs (package-propagated-inputs yoyo-migrations) - (append python-importlib-metadata))))) - -(define-public python-mypy-0.981 - (package - (inherit python-mypy) - (name "python-mypy") - (version "0.981") - (source - (origin - ;; Because of https://github.com/python/mypy/issues/9584, the - ;; mypyc/analysis directory is missing in the PyPI archive, leading to - ;; test failures. - (method git-fetch) - (uri (git-reference - (url "https://github.com/python/mypy") - (commit (string-append "v" version)) - ;; Fetch git submodules otherwise typeshed is not fetched. - ;; Typeshed is a collection of Python sources type annotation - ;; (data) files. - (recursive? #t))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0awigl51an7466yk236f9vsbqpz2jzd6dsg9v5a4cia37vz4li0a")))))) + (append python-importlib-metadata))))) -- cgit v1.2.3 From de23151c31cd078d40d715e63daf2529d8e35a12 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 12:43:03 +0300 Subject: gn-auth: Update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4ce207d..4768ca8 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd"))) + (commit "a8ebba8266618ec53fe485ee84d09d0cdff898a1"))) (hash (content-hash (base32 - "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l"))))) + "0ksdzkrb9z9br9mca9dxprfp57wj7ffd9gqnbsxg2gq0yj1ri9af"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 9e8f9d8e65290d8fdee9b15cb1afddf1a4f01466 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 12:54:32 +0300 Subject: gn-auth: Update commit and hash * Update the commit hash and the hash of the files after updating the guix-bioinformatics channel configurations for the gn-auth channel. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4768ca8..40c8857 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "a8ebba8266618ec53fe485ee84d09d0cdff898a1"))) + (commit "51534a303c22f919ec5b237f7bcc948e66978fdc"))) (hash (content-hash (base32 - "0ksdzkrb9z9br9mca9dxprfp57wj7ffd9gqnbsxg2gq0yj1ri9af"))))) + "0gp1lyx3r227s078hab079dckc8iambvnq1yd84qr03yi4ch8q19"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 9be94892e0a2446f104a72f680a926020ad8578c Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 13:04:22 +0300 Subject: gn-auth: Use upstream python-mypy --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 40c8857..d2b59c5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "51534a303c22f919ec5b237f7bcc948e66978fdc"))) + (commit "f4b9e51192a8dea3399ca83226a47a518b3ea5c5"))) (hash (content-hash (base32 - "0gp1lyx3r227s078hab079dckc8iambvnq1yd84qr03yi4ch8q19"))))) + "054i9va4850dcfiwzz79r4w4h2cinh3d6l1l4jc8s4sy7bjb50zp"))))) (build-system python-build-system) (arguments (list @@ -490,7 +490,7 @@ (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs - `(("python-mypy" ,python-mypy-0.981) + `(("python-mypy" ,python-mypy) ("python-pytest" ,python-pytest) ("python-pylint" ,python-pylint) ("python-hypothesis" ,python-hypothesis) -- cgit v1.2.3 From 761a61bd77d1a4ade316bebe30aee1a136071025 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 13:42:13 +0300 Subject: gn-auth: Use newer setup.py Use updated setup.py to try and fix issues with the `sanity-check` phase. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d2b59c5..69d2e23 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "f4b9e51192a8dea3399ca83226a47a518b3ea5c5"))) + (commit "971c15423bbc3c090c28eca7a50caf90a5ad5411"))) (hash (content-hash (base32 - "054i9va4850dcfiwzz79r4w4h2cinh3d6l1l4jc8s4sy7bjb50zp"))))) + "07lkbdjhqr0qfw8v4rzqw1phyi63qxknzyyavsqmimrvx8wkq4nd"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 31bc467225bab461ba758e2e31299eb47c8e5c44 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 14:33:27 +0300 Subject: gn-auth: List packages to install List all packages to install to hopefully fix failure in `sanity-check` phase. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 69d2e23..42296c0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "971c15423bbc3c090c28eca7a50caf90a5ad5411"))) + (commit "9961237078834c342e5bf7d7d6ffd7f27be09c67"))) (hash (content-hash (base32 - "07lkbdjhqr0qfw8v4rzqw1phyi63qxknzyyavsqmimrvx8wkq4nd"))))) + "1nmwcwa897gv4dmn16swk7g9lsnl7jnzlb6qbsg38pgiwhyh6mrk"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From c094f4635a6bcdeed697875ea991f91b670e675e Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 17:49:28 +0300 Subject: gn-auth: Fix missing import --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 42296c0..eaab3cd 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "9961237078834c342e5bf7d7d6ffd7f27be09c67"))) + (commit "acd1a3d29900cff70ccc82dbe8ad1dc4b4c0fe8e"))) (hash (content-hash (base32 - "1nmwcwa897gv4dmn16swk7g9lsnl7jnzlb6qbsg38pgiwhyh6mrk"))))) + "19c0qshj511w4rhfbj5d9gvcscnbsjhk6xnr10ajjvr61w42qmq4"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 51931f0b587749d31825cee74d0ff76c5aedf6eb Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 6 Oct 2023 12:54:57 +0300 Subject: genenetwork3: Add python-pyld to propagated-inputs. * gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add python-ld. Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index eaab3cd..ac26fd0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -153,6 +153,7 @@ ;; python-pingouin << build failing ("python-pingouin-without-tests" ,python-pingouin-without-tests) ("python-plotly" ,python-plotly) + ("python-pyld" ,python-pyld) ("python-scikit-learn" ,python-scikit-learn) ("python-pymonad" ,python-pymonad) ("python-redis" ,python-redis) -- cgit v1.2.3 From d55876c9480b058541c586e5cf29064ae5e0dfef Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 27 Oct 2023 09:45:27 +0300 Subject: Update dependencies: genenetwork3 and gn-auth * genenetwork3: Remove `yoyo-migrations` as a dependency * gn-auth: Use the upstream `yoyo-migrations` * Remove temporary local definition for yoyo-migrations. --- gn/packages/genenetwork.scm | 5 ++--- gn/packages/python.scm | 20 -------------------- 2 files changed, 2 insertions(+), 23 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ac26fd0..4fb8908 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -170,8 +170,7 @@ ("r-wgcna" ,r-wgcna) ("r-ctl" ,r-ctl) ("rust-qtlreaper" ,rust-qtlreaper) - ("diffutils" ,diffutils) - ("yoyo-migrations" ,yoyo-migrations-8.2.0))) + ("diffutils" ,diffutils))) (build-system python-build-system) (arguments (list #:phases @@ -503,7 +502,7 @@ ("python-redis" ,python-redis) ("python-authlib" ,python-authlib) ("python-pymonad" ,python-pymonad) - ("yoyo-migrations" ,yoyo-migrations-8.2.0) + ("yoyo-migrations" ,yoyo-migrations) ("python-bcrypt" ,python-bcrypt) ;; remove after removing all references ("python-mysqlclient" ,python-mysqlclient) ("python-argon2-cffi" ,python-argon2-cffi) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index c23d894..db2f4c9 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1836,23 +1836,3 @@ complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.") (license license:bsd-3))) - -(define-public yoyo-migrations-8.2.0 - (package - (inherit yoyo-migrations) - (name "yoyo-migrations") - (version "8.2.0") - (source - (origin - ;; We use the upstream repository, as the tests are not included in the - ;; PyPI releases. - (method hg-fetch) - (uri (hg-reference - (url "https://hg.sr.ht/~olly/yoyo") - (changeset (string-append "v" version "-release")))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 "1al030ix0w63hr4s3mqry6s0mlqdj8p242pdqks06br7c25nx3yj")))) - (propagated-inputs - (modify-inputs (package-propagated-inputs yoyo-migrations) - (append python-importlib-metadata))))) -- cgit v1.2.3 From 4914e019ce278bdf0eed3fb708e2f6bdd5b3d4ad Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Dec 2023 16:45:05 +0300 Subject: gn-auth: Remove bcrypt dependency --- gn/packages/genenetwork.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4fb8908..3e90ecb 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -503,7 +503,6 @@ ("python-authlib" ,python-authlib) ("python-pymonad" ,python-pymonad) ("yoyo-migrations" ,yoyo-migrations) - ("python-bcrypt" ,python-bcrypt) ;; remove after removing all references ("python-mysqlclient" ,python-mysqlclient) ("python-argon2-cffi" ,python-argon2-cffi) ("python-email-validator" ,python-email-validator))) -- cgit v1.2.3 From 62acd7e5e33e018ec3af2fcff556c55e73f308f5 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Dec 2023 16:45:29 +0300 Subject: gn-auth: add flask-cors dependency. --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 3e90ecb..4cf4612 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -503,6 +503,7 @@ ("python-authlib" ,python-authlib) ("python-pymonad" ,python-pymonad) ("yoyo-migrations" ,yoyo-migrations) + ("python-flask-cors" ,python-flask-cors) ("python-mysqlclient" ,python-mysqlclient) ("python-argon2-cffi" ,python-argon2-cffi) ("python-email-validator" ,python-email-validator))) -- cgit v1.2.3 From 7a4bf91e019fe084f92a90535cbfffb7c119b9a7 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 29 Dec 2023 19:06:01 +0000 Subject: gn: genenetwork3: Update to 0.1.0-4.093163e. --- gn/packages/genenetwork.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4cf4612..ff87f99 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -111,10 +111,11 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "f52247c15f3694f3dd5fd0fd79c3e15376137e07")) + (let ((commit "093163ebd511700078f998fa754e786435a81d1b") + (revision "4")) (package (name "genenetwork3") - (version (git-version "0.1.0" "3" commit)) + (version (git-version "0.1.0" revision commit)) (source (origin (method git-fetch) @@ -124,7 +125,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0ac0dr8dny65x4xvm8gw6ap3g8g0j933ipy9116idcws31rk2adk")))) + "06vfrfw1p60scrnxwfd2daxr8hdd6bjd27pdppwxs7k65nvync4s")))) (inputs (list python-click)) (native-inputs @@ -688,3 +689,5 @@ ; (directory-union ; "genenetwork2" ; (list genenetwork2 genenetwork-graph dag-svg-file))) + +genenetwork3 -- cgit v1.2.3 From 9d8990a85f1c321397bef6e879845479e5c4a403 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 2 Jan 2024 10:53:46 +0300 Subject: gnqc-py: New package --- gn/packages/genenetwork.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ff87f99..139b46c 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -467,6 +467,48 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public gnqc-py + (package + (name "gnqc-py") + (version "0.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/fredmanglis/gnqc_py.git") + (commit "c81a3d948b3bc0db20a530fa1aa428b35b5d6145"))) + (hash + (content-hash + (base32 + "1101pql7zpijn36i9phcakfx1r5dcvdf6ix0v4ndjzmzx3d0xyi2"))))) + (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 + `(("python-mypy" ,python-mypy + "python-pylint" ,python-pylint + "python-pytest" ,python-pytest + "python-hypothesis" ,python-hypothesis))) + (propagated-inputs + `(("gunicorn" ,gunicorn + "python-redis" ,python-redis + "python-flask" ,python-flask + "python-pyyaml" ,python-pyyaml + "python-jsonpickle" ,python-jsonpickle + "python-mysqlclient" ,python-mysqlclient))) + (synopsis "GeneNetwork Quality Control Application") + (description + "GeneNetwork qc is a quality control application for the data files that + eventually are used to add to the data in the GeneNetwork project.") + (home-page "https://gitlab.com/fredmanglis/gnqc_py") + (license license:agpl3+))) + (define-public gn-auth (package (name "gn-auth") -- cgit v1.2.3 From 72b54fdd4aa582fee3e4e6d1bf3f46c9f44764c8 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 30 Dec 2023 09:23:07 +0000 Subject: gn: genenetwork2: Substitute new path to default_settings.py. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 139b46c..0dafb3c 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -341,7 +341,7 @@ (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) ) - (substitute* '("etc/default_settings.py") + (substitute* '("gn2/default_settings.py") ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) -- cgit v1.2.3 From bc88ac43051bcb5d5fdf7975c47d805601200be8 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 13:55:52 +0000 Subject: gn: genenetwork2: Update to 3.11-3.ff67963. * gn/packages/genenetwork.scm (genenetwork2): Update to 3.11-3.ff67963. --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 0dafb3c..8b1216b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,10 +186,10 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "bfe557dc1e537dc78a82a30817ecf2ca3004d978")) + (let ((commit "ff679636d3ee9ae2388fab3fe5d091ef2f00a8e3")) (package (name "genenetwork2") - (version (git-version "3.11" "2" commit)) + (version (git-version "3.11" "3" commit)) (source (origin (method git-fetch) (uri (git-reference @@ -198,7 +198,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "1bn0j0fpk4hcicgfird62x5wq2n6lj4rs1ggw69dcxyf4qdxbk5d")))) + "0ap7q7v42c5sg4kjy76zdn6h6w5a3f534i5644rya5a1akmss7hg")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 8c75815e1ba02dcad7500e56b2dfe0987105b3db Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 13:56:35 +0000 Subject: Remove genenetwork3 return. This was introduced accidentally in 7a4bf91e019fe084f92a90535cbfffb7c119b9a7. * gn/packages/genenetwork.scm: Remove genenetwork3 return. --- gn/packages/genenetwork.scm | 2 -- 1 file changed, 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 8b1216b..890d7e5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -731,5 +731,3 @@ ; (directory-union ; "genenetwork2" ; (list genenetwork2 genenetwork-graph dag-svg-file))) - -genenetwork3 -- cgit v1.2.3 From 05dd63817302e890a16a33fc3b5f88fa07a8184d Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 16:55:32 +0000 Subject: gn: genenetwork2: Use G-expressions. * gn/packages/genenetwork.scm (genenetwork2): Use G-expressions. --- gn/packages/genenetwork.scm | 387 +++++++++++++++----------------------------- 1 file changed, 126 insertions(+), 261 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 890d7e5..6be016e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -202,270 +202,135 @@ (native-inputs (list graphviz)) (propagated-inputs - `(("genenetwork3" ,genenetwork3) - ("parallel" ,parallel) ;; GNU parallel - ("coreutils" ,coreutils) - ("git" ,git) - ("which" ,which) - ("grep" ,grep) - ("r" ,r) - ("r-ctl" ,r-ctl) - ("r-qtl" ,r-qtl) - ("r-wgcna" ,r-wgcna) - ("redis" ,redis) - ("mariadb" ,mariadb) - ("gemma" ,gemma-gn2) - ("gemma-wrapper" ,gemma-wrapper) - ("plink-ng-gn" ,plink-ng-gn) - ("rust-qtlreaper" ,rust-qtlreaper) - ("gn-rust-correlation" ,gn-rust-correlation) - ("glibc-utf8-locales" ,glibc-utf8-locales) - ("nginx" ,nginx) - ("python" ,python-wrapper) - ("python-pillow" ,python-pillow) - ("python-coverage" ,python-coverage) - ("python-configparser" ,python-configparser) ;; maintenance/scripts - ("python-flask" ,python-flask) - ("gunicorn" ,gunicorn) - ("python-autopep8" ,python-autopep8) - ("python-cssselect" ,python-cssselect) - ("python-flask-debugtoolbar" ,python-flask-debugtoolbar) - ("python-htmlgen" ,python-htmlgen) - ("python-ijson" ,python-ijson) - ("python-jinja2" ,python-jinja2) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-setuptools" ,python-setuptools) - ("python-scipy" ,python-scipy) - ("python-lxml" ,python-lxml) - ("python-mysqlclient" ,python-mysqlclient) - ("python-mypy" ,python-mypy) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pylint" ,python-pylint) - ("python-pymonad" ,python-pymonad) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-simplejson" ,python-simplejson) - ("python-markdown" ,python-markdown) - ("python-rdflib" ,python-rdflib) - ("python-authlib" ,python-authlib) - ("python-flask-session" ,python-flask-session) - ;; TODO: Get rid of Python R bindings - ("python-rpy2" ,python-rpy2) - ("python-beautifulsoup4" ,python-beautifulsoup4) - ;; Disable for now. Build fails on Penguin2 - ;; ("python-flask-socketio" ,python-flask-socketio) - ("python-xlsxwriter" ,python-xlsxwriter) - ;; All the external js dependencies - ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) - ("javascript-cytoscape" ,javascript-cytoscape) - ("javascript-panzoom" ,javascript-cytoscape-panzoom) - ("javascript-qtip" ,javascript-cytoscape-qtip) - ("javascript-chroma" ,javascript-chroma) - ("javascript-d3-tip" ,javascript-d3-tip) - ("javascript-jscolor" ,javascript-jscolor) - ("javascript-colorbox" ,javascript-colorbox) - ("javascript-jszip" ,javascript-jszip) - ("js-jstat" ,js-jstat) - ("js-md5" ,js-md5) - ("js-parsley" ,js-parsley) - ("javascript-plotly" ,javascript-plotly) - ("javascript-typeahead" ,javascript-typeahead) - ("js-underscore" ,js-underscore) - ("js-smart-time-ago" ,js-smart-time-ago) - ("javascript-nouislider" ,javascript-nouislider) - ("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser) - ("javascript-ckeditor" ,javascript-ckeditor) - ("javascript-datatables" ,javascript-datatables) - ("javascript-datatables-scroller" ,javascript-datatables-scroller) - ("javascript-datatables-buttons" ,javascript-datatables-buttons) - ("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap) - ("javascript-datatables-plugins" ,javascript-datatables-plugins) - ("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder) - ("javascript-datatables-col-resize" ,javascript-datatables-col-resize) - ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) - ("javascript-shapiro-wilk" ,javascript-shapiro-wilk) - ("javascript-underscore-string" ,javascript-underscore-string) - ("javascript-htmx" ,javascript-htmx) - ("javascript-qtip2" ,javascript-qtip2) - ("javascript-d3js" ,javascript-d3js) - ("javascript-nvd3" ,javascript-nvd3) - ("javascript-bootstrap" ,javascript-bootstrap) - ("javascript-jquery" ,javascript-jquery) - ("javascript-zxcvbn" ,javascript-zxcvbn) - ("javascript-jquery-ui" ,javascript-jquery-ui) - ("javascript-jquery-cookie" ,javascript-jquery-cookie) - ("javascript-xterm" ,javascript-xterm) - ("javascript-xterm-style" ,javascript-xterm-style) - ("javascript-xterm-addon-fit",javascript-xterm-addon-fit) - ("javascript-font-awesome" ,javascript-font-awesome))) + (list genenetwork3 + parallel + coreutils + git + which + grep + r + r-ctl + r-qtl + r-wgcna + redis + mariadb + gemma + gemma-wrapper + plink-ng-gn + rust-qtlreaper + gn-rust-correlation + glibc-utf8-locales + nginx + python-wrapper + python-pillow + python-coverage + python-configparser + python-flask + gunicorn + python-autopep8 + python-cssselect + python-flask-debugtoolbar + python-htmlgen + python-ijson + python-jinja2 + python-pytest + python-pytest-mock + python-sqlalchemy + python-setuptools + python-scipy + python-lxml + python-mysqlclient + python-mypy + python-numpy + python-pandas + python-pylint + python-pymonad + python-redis + python-requests + python-simplejson + python-markdown + python-rdflib + python-authlib + python-flask-session + python-rpy2 + python-beautifulsoup4 + python-xlsxwriter + javascript-twitter-post-fetcher + javascript-cytoscape + javascript-cytoscape-panzoom + javascript-cytoscape-qtip + javascript-chroma + javascript-d3-tip + javascript-jscolor + javascript-colorbox + javascript-jszip + js-jstat + js-md5 + js-parsley + javascript-plotly + javascript-typeahead + js-underscore + js-smart-time-ago + javascript-nouislider + javascript-purescript-genome-browser + javascript-ckeditor + javascript-datatables + javascript-datatables-scroller + javascript-datatables-buttons + javascript-datatables-buttons-bootstrap + javascript-datatables-plugins + javascript-datatables-col-reorder + javascript-datatables-col-resize + javascript-datatables-buttons-styles + javascript-shapiro-wilk + javascript-underscore-string + javascript-htmx + javascript-qtip2 + javascript-d3js + javascript-nvd3 + javascript-bootstrap + javascript-jquery + javascript-zxcvbn + javascript-jquery-ui + javascript-jquery-cookie + javascript-xterm + javascript-xterm-style + javascript-xterm-addon-fit + javascript-font-awesome)) (inputs - `(("javascript-colorbox" ,(package-source javascript-colorbox)))) + (list javascript-colorbox)) (build-system python-build-system) (arguments - `(#:tests? #f ; no 'setup.py test' - #:phases - (modify-phases %standard-phases - (delete 'reset-gzip-timestamps) - (add-after 'unpack 'fix-paths-scripts - (lambda _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python3") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which"))) - #t)) - ; (add-after 'unpack 'patch-javascript - ; (lambda* (#:key inputs #:allow-other-keys) - ; (let ((colorbox (assoc-ref inputs "javascript-colorbox")) - ; (gn2 "/share/genenetwork2/javascript/")) - ; (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") - ; (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") - ; #t))) - (add-before 'install 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ( - ; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) - ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) - (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) - ) - - (substitute* '("gn2/default_settings.py") - ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) - (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) - (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) - ) - ))) - ; (add-after 'install 'generate-graph - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (call-with-output-file - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages" - ; "/wqflask/dependency-graph.html") - ; (lambda (port) - ; (format - ; port "~a" - ; ,(call-with-output-string - ; (lambda (p) - ; (with-output-to-port p - ; (lambda () - ; (run-with-store - ; (open-connection) - ; (export-graph - ; (list this-package) - ; p - ; #:node-type %package-node-type - ; #:backend %d3js-backend))))))))))) - ;(add-after 'install 'generate-dag-svg-file - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (let* ((output-dir - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages/wqflask/")) - ; (dot-file - ; (string-append - ; output-dir - ; "dependency-graph.dot")) - ; (svg-file - ; (string-append - ; output-dir - ; "dependency-graph.svg"))) - ; (begin - ; (call-with-output-file - ; dot-file - ; (lambda (port) - ; (format - ; port "~a" - ; ,(call-with-output-string - ; (lambda (p) - ; (with-output-to-port p - ; (lambda () - ; (run-with-store - ; (open-connection) - ; (export-graph - ; (list this-package) - ; p - ; #:node-type %package-node-type - ; #:backend %graphviz-backend))))))))) - ; (invoke "dot" "-Tsvg" "-o" svg-file dot-file))))) - - ;; TODO: Use this to replace the two previous phases. - ;(add-after 'install 'install-generated-files - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (let ((output-dir - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages/wqflask/"))) - ; (install-file (string-append %dag-svg-file "/dependency-graph.dot") output-dir) - ; (install-file (string-append %dag-svg-file "/dependency-graph.svg") output-dir) - ; (install-file (string-append %genenetwork-graph "/dependency-graph.html") output-dir) - ; #t))) - - #! - (add-after 'install 'generate-dependency-file - (lambda* (#:key inputs outputs #:allow-other-keys) - (call-with-output-file - (string-append - (assoc-ref outputs "out") - "/lib/python" - (python-version (assoc-ref inputs "python")) - "/site-packages" - "/wqflask/DEPENDENCIES.md" - ) - (lambda (port) - (format - port " -#### System Inputs (generated from ~a package defined in ~a) -|Name | Description | -|-----|-------------| -~a -" - ,(package-name this-package) - (string-append - "[genenetwork.scm]" - "(http://git.genenetwork.org/" - "guix-bioinformatics/guix-bioinformatics" - "/src/branch/master/gn/packages/" - "genenetwork.scm)") - ,(apply - string-append - (map - (lambda (input) - (let* ((pkg (cadr input)) - (name (package-name pkg)) - (version (package-version pkg)) - (home-page (package-home-page pkg)) - (description (package-synopsis pkg))) - (string-append - "| **[" name "](" home-page ")** v" - version"| " - description " |\n"))) - (package-propagated-inputs this-package)))))))) - !# - ))) - (home-page "http://genenetwork.org/") - (synopsis "Full genenetwork services") - (description "Genenetwork installation sumo.") - (license license:agpl3+)))) + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + (delete 'reset-gzip-timestamps) + (add-after 'unpack 'fix-paths-scripts + (lambda _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python3") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which"))))) + (add-before 'install 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) + (substitute* '("gn2/default_settings.py") + (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))))))))) + (home-page "http://genenetwork.org/") + (synopsis "Full genenetwork services") + (description "Genenetwork installation sumo.") + (license license:agpl3+)))) (define-public gnqc-py (package -- cgit v1.2.3 From 7a4299e73635f0b68f548105f05cfdd6ecb234bd Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 16:57:24 +0000 Subject: gn: genenetwork2: Install bundled fonts. * gn/packages/genenetwork.scm (genenetwork2)[arguments]: Add install-bundled-fonts and fix-font-paths phases. --- gn/packages/genenetwork.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 6be016e..d499d8a 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -305,6 +305,19 @@ #:phases #~(modify-phases %standard-phases (delete 'reset-gzip-timestamps) + (add-after 'install 'install-bundled-fonts + (lambda _ + ;; Install bundled fonts. + (for-each (lambda (font-file) + (install-file font-file (string-append #$output "/share/fonts/"))) + (find-files "gn2/wqflask/static/fonts" + "\\.ttf$")))) + (add-after 'unpack 'fix-font-paths + (lambda _ + ;; Set absolute store paths to installed bundled fonts. + (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" + (("\\./gn2/wqflask/static/fonts") + (string-append #$output "/gn2/wqflask/static/fonts"))))) (add-after 'unpack 'fix-paths-scripts (lambda _ (substitute* "bin/genenetwork2" -- cgit v1.2.3 From 22cb97904b4efed9f51b5699f0a25648c7e995f6 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 17:15:39 +0000 Subject: gn: genenetwork2: Fix path to installed bundled fonts. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d499d8a..f6c45b4 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -317,7 +317,7 @@ ;; Set absolute store paths to installed bundled fonts. (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" (("\\./gn2/wqflask/static/fonts") - (string-append #$output "/gn2/wqflask/static/fonts"))))) + (string-append #$output "/share/fonts"))))) (add-after 'unpack 'fix-paths-scripts (lambda _ (substitute* "bin/genenetwork2" -- cgit v1.2.3 From 4ba4df365b6c5764c90e3ff939648f11110e04e5 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 3 Jan 2024 00:30:21 +0000 Subject: gn: genenetwork3: Update to 0.1.0-5.6bb4a5f. * gn/packages/genenetwork.scm (genenetwork3): Update to 0.1.0-5.6bb4a5f. --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index f6c45b4..ec0426b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -111,8 +111,8 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "093163ebd511700078f998fa754e786435a81d1b") - (revision "4")) + (let ((commit "6bb4a5f05c1a2c96b7da1780ae4a1d70c7cc4afb") + (revision "5")) (package (name "genenetwork3") (version (git-version "0.1.0" revision commit)) @@ -125,7 +125,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "06vfrfw1p60scrnxwfd2daxr8hdd6bjd27pdppwxs7k65nvync4s")))) + "13nvi2gwwb0shra0d9rsfhppa9ky4bhgh1zgb34790ax0g9lwa97")))) (inputs (list python-click)) (native-inputs -- cgit v1.2.3 From 250f5bb11be7596d77cb8993afb3cc7e741530d3 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 3 Jan 2024 00:33:25 +0000 Subject: gn: genenetwork2: Update to 3.11-4.c1d377e. * gn/packages/genenetwork.scm (genenetwork2): Update to 3.11-4.c1d377e. --- gn/packages/genenetwork.scm | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ec0426b..1ad63c0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,10 +186,11 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "ff679636d3ee9ae2388fab3fe5d091ef2f00a8e3")) + (let ((commit "c1d377ec86b902f76e47fc4506a9ff260d788082") + (revision "4")) (package (name "genenetwork2") - (version (git-version "3.11" "3" commit)) + (version (git-version "3.11" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -198,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "0ap7q7v42c5sg4kjy76zdn6h6w5a3f534i5644rya5a1akmss7hg")))) + "03l01nr0pg52pdnc6sajnsvylw61j68x6zz6mi5ygkimbj4093sa")))) (native-inputs (list graphviz)) (propagated-inputs @@ -305,19 +306,17 @@ #:phases #~(modify-phases %standard-phases (delete 'reset-gzip-timestamps) - (add-after 'install 'install-bundled-fonts - (lambda _ - ;; Install bundled fonts. - (for-each (lambda (font-file) - (install-file font-file (string-append #$output "/share/fonts/"))) - (find-files "gn2/wqflask/static/fonts" - "\\.ttf$")))) - (add-after 'unpack 'fix-font-paths - (lambda _ - ;; Set absolute store paths to installed bundled fonts. + (add-after 'unpack 'fix-paths-to-static-files + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Set absolute store paths to installed static files. (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" (("\\./gn2/wqflask/static/fonts") - (string-append #$output "/share/fonts"))))) + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/fonts"))) + (substitute* "gn2/wqflask/views.py" + (("\\./gn2/wqflask/static/gif/error") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/gif/error"))))) (add-after 'unpack 'fix-paths-scripts (lambda _ (substitute* "bin/genenetwork2" -- cgit v1.2.3 From 25cb9ad70155a08c088ff28bf54c06e12293105b Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 3 Jan 2024 14:56:04 +0300 Subject: gnqc-py: Fix syntax error. --- gn/packages/genenetwork.scm | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 1ad63c0..4e3dc21 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -368,17 +368,17 @@ (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs - `(("python-mypy" ,python-mypy - "python-pylint" ,python-pylint - "python-pytest" ,python-pytest - "python-hypothesis" ,python-hypothesis))) + `(("python-mypy" ,python-mypy) + ("python-pylint" ,python-pylint) + ("python-pytest" ,python-pytest) + ("python-hypothesis" ,python-hypothesis))) (propagated-inputs - `(("gunicorn" ,gunicorn - "python-redis" ,python-redis - "python-flask" ,python-flask - "python-pyyaml" ,python-pyyaml - "python-jsonpickle" ,python-jsonpickle - "python-mysqlclient" ,python-mysqlclient))) + `(("gunicorn" ,gunicorn) + ("python-redis" ,python-redis) + ("python-flask" ,python-flask) + ("python-pyyaml" ,python-pyyaml) + ("python-jsonpickle" ,python-jsonpickle) + ("python-mysqlclient" ,python-mysqlclient))) (synopsis "GeneNetwork Quality Control Application") (description "GeneNetwork qc is a quality control application for the data files that -- cgit v1.2.3 From e947a1e5c330595eee3a27185e042cf3b73689da Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Thu, 15 Feb 2024 13:59:30 +0300 Subject: gn: javascript: Add javascript-uikit. * gn/packages/javascript.scm: (javascript-uikit): New package. * gn/packages/javascript.scm: (genenetwork2) [propagated-inputs]:Add javascript-uikit. --- gn/packages/genenetwork.scm | 1 + gn/packages/javascript.scm | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 35 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4e3dc21..8d690f2 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -271,6 +271,7 @@ javascript-plotly javascript-typeahead js-underscore + javascript-uikit js-smart-time-ago javascript-nouislider javascript-purescript-genome-browser diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 81558fe..e24990b 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -2012,3 +2012,37 @@ vector graphics.") (description "Ace is a code editor written in JavaScript. ") (license license:expat))) + +(define-public javascript-uikit + (package + (name "javascript-uikit") + (version "3.7.4") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/uikit/uikit/releases/download/v" + version "/uikit" "-" version ".zip")) + (sha256 + (base32 "1qhhz3iki1nbyffg6qa7x2937708hjr9gf6mkn4v4cdl9j0mgyv0")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (unzip (string-append (assoc-ref %build-inputs "unzip") + "/bin/unzip")) + (targetdir (string-append out "/share/genenetwork2/javascript/uikit")) + (source (assoc-ref %build-inputs "source"))) + (invoke unzip source) + (copy-recursively "." targetdir))))) + (native-inputs + `(("source" ,source) + ("unzip" ,unzip))) + (home-page "https://getuikit.com/") + (synopsis "UIkit is a lightweight and modular front-end framework +for developing fast and powerful web interfaces.") + (description "UIkit is a lightweight and modular front-end framework +for developing fast and powerful web interfaces.") + (license license:bsd-3))) -- cgit v1.2.3 From 336799a9ea0d495693336283961f8853cf1cb614 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 26 Feb 2024 11:44:42 +0000 Subject: gn: gn-auth: Use list-style inputs. * gn/packages/genenetwork.scm (gn-auth)[native-inputs, propagated-inputs]: List them directly instead of using an association list. --- gn/packages/genenetwork.scm | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 8d690f2..a316464 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -411,23 +411,23 @@ (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs - `(("python-mypy" ,python-mypy) - ("python-pytest" ,python-pytest) - ("python-pylint" ,python-pylint) - ("python-hypothesis" ,python-hypothesis) - ("python-pytest-mock" ,python-pytest-mock) - ("python-mypy-extensions" ,python-mypy-extensions))) + (list python-hypothesis + python-mypy + python-mypy-extensions + python-pylint + python-pytest + python-pytest-mock)) (propagated-inputs - `(("gunicorn" ,gunicorn) - ("python-flask" ,python-flask) - ("python-redis" ,python-redis) - ("python-authlib" ,python-authlib) - ("python-pymonad" ,python-pymonad) - ("yoyo-migrations" ,yoyo-migrations) - ("python-flask-cors" ,python-flask-cors) - ("python-mysqlclient" ,python-mysqlclient) - ("python-argon2-cffi" ,python-argon2-cffi) - ("python-email-validator" ,python-email-validator))) + (list gunicorn + python-argon2-cffi + python-authlib + python-email-validator + python-flask + python-flask-cors + python-mysqlclient + python-pymonad + python-redis + yoyo-migrations)) (home-page "https://github.com/genenetwork/gn-auth") (synopsis "Authentication and Authorisation server for GeneNetwork services") (description "Authentication and Authorisation server for GeneNetwork services.") -- cgit v1.2.3 From 08df252121f5167966e4e8a3c8e34dddedf7bc57 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 26 Feb 2024 11:45:28 +0000 Subject: gn: gn-auth: Update to commit 10ec3b1. * gn/packages/genenetwork.scm (gn-auth): Update to commit 10ec3b1. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index a316464..99423f7 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -396,11 +396,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "acd1a3d29900cff70ccc82dbe8ad1dc4b4c0fe8e"))) + (commit "10ec3b1f851897c2cce89356b4404c18f9f11a2f"))) (hash (content-hash (base32 - "19c0qshj511w4rhfbj5d9gvcscnbsjhk6xnr10ajjvr61w42qmq4"))))) + "1p7mcimg1fhdxjmhi6p6snpq73h5h8h6ya2lx9c9kr8r3zn67pb5"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 5fa3e2bcaafb498ec3bca51f72545f5a16b5a527 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 1 Mar 2024 11:15:13 +0000 Subject: gn: gn-auth: Update to commit 8a20071. * gn/packages/genenetwork.scm (gn-auth): Update to commit 8a20071. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 99423f7..1084a63 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -396,11 +396,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "10ec3b1f851897c2cce89356b4404c18f9f11a2f"))) + (commit "8a20071dc8009b5b9439d10e17a2a57883b7b363"))) (hash (content-hash (base32 - "1p7mcimg1fhdxjmhi6p6snpq73h5h8h6ya2lx9c9kr8r3zn67pb5"))))) + "1p8vcdpj9wlkfaxzmg3b6372zad9m2byrz7rzg6fdl26v95wd4qm"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 60a524a955455b2f36fd82e95926f50220608ab0 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Sat, 2 Mar 2024 16:20:48 +0300 Subject: gn-auth: Update the commit and hash. --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 1084a63..7030515 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -390,17 +390,17 @@ (define-public gn-auth (package (name "gn-auth") - (version "1.0.0") + (version "1.0.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "8a20071dc8009b5b9439d10e17a2a57883b7b363"))) + (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) (hash (content-hash (base32 - "1p8vcdpj9wlkfaxzmg3b6372zad9m2byrz7rzg6fdl26v95wd4qm"))))) + "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 2c3dc85ef14c1d9c1f8e69daf9bcda0dadb308ff Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 3 Mar 2024 07:05:40 -0600 Subject: gn: xterm: comment out xterm.js package because of suspect sources - the hash value changed. Also needs fixing of the code that uses it in gn2. * gn/packages/genenetwork.scm (xterm.js): Comment out packages --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 7030515..b7e3f6f 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -295,9 +295,9 @@ javascript-zxcvbn javascript-jquery-ui javascript-jquery-cookie - javascript-xterm - javascript-xterm-style - javascript-xterm-addon-fit + ; javascript-xterm -- disabled until we know what to do with it, not working on production + ; javascript-xterm-style + ; javascript-xterm-addon-fit javascript-font-awesome)) (inputs (list javascript-colorbox)) -- cgit v1.2.3 From b27452660632d72e1b066acff9072f4a5b645c3e Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 4 Mar 2024 08:11:10 +0300 Subject: genenetwork2: Update commit and hash to build with missing templates --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b7e3f6f..ad27cb0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "c1d377ec86b902f76e47fc4506a9ff260d788082") + (let ((commit "a0b8e0a2d0c35542a47f906192d08d39bff290ff") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "03l01nr0pg52pdnc6sajnsvylw61j68x6zz6mi5ygkimbj4093sa")))) + "0awspvn2fyllr5dkyskf62zxr38m2dhn8jiyzh8rq036mmd4ixya")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 2356005a27de00613f9ae29dde021953cd05fc1f Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Mar 2024 06:52:10 +0300 Subject: genenetwork2: Update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ad27cb0..9d545fb 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "a0b8e0a2d0c35542a47f906192d08d39bff290ff") + (let ((commit "084ce21fb1d8263e9d8f50ed1fe74799af10fb52") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "0awspvn2fyllr5dkyskf62zxr38m2dhn8jiyzh8rq036mmd4ixya")))) + "02x47kilmi8a00vd1bbcvzsgxnhyxjx4wva64b1jv2ijjgypbbgk")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 768d3b78aeeb12e84edd3b7e64270bf946df1c55 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Mar 2024 07:08:07 +0300 Subject: genenetwork2: Fix commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 9d545fb..ad27cb0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "084ce21fb1d8263e9d8f50ed1fe74799af10fb52") + (let ((commit "a0b8e0a2d0c35542a47f906192d08d39bff290ff") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "02x47kilmi8a00vd1bbcvzsgxnhyxjx4wva64b1jv2ijjgypbbgk")))) + "0awspvn2fyllr5dkyskf62zxr38m2dhn8jiyzh8rq036mmd4ixya")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From c6a011042bc7dec4476d4b66d035930416d3561a Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Mar 2024 07:50:34 +0300 Subject: genenetwork2: update commit and hash to fetch configs from app --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ad27cb0..dda9bf8 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "a0b8e0a2d0c35542a47f906192d08d39bff290ff") + (let ((commit "9983b4273622dc5fd8b7d43d10d935f07e3c9eb6") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "0awspvn2fyllr5dkyskf62zxr38m2dhn8jiyzh8rq036mmd4ixya")))) + "1ihjx5a1k8nsd88i85simv09k393jcrijy024ds5pb48k5hc9sff")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 645cfb51a968e58b286e8af7a6fa3fefa6b512a8 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 6 Mar 2024 06:00:17 +0300 Subject: genenetwork2: update commit and hash Removes use of configs from `gn2.utility.tools` module since they are not up to date. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index dda9bf8..5298490 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "9983b4273622dc5fd8b7d43d10d935f07e3c9eb6") + (let ((commit "1e81c74ee8752ad2913b4e610ba7575638755385") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "1ihjx5a1k8nsd88i85simv09k393jcrijy024ds5pb48k5hc9sff")))) + "18g4dd3h737slqmp1ql2jqqzmzql3mx3b4xy72d7qwhwwhc7hcgv")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 3414d825a9799f30d92e5188378cb7ad69db0eb0 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 8 Mar 2024 02:55:29 +0300 Subject: gn-uploader: Update package definition --- gn/packages/genenetwork.scm | 85 +++++++++++++++++++++++---------------------- 1 file changed, 44 insertions(+), 41 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5298490..dae4b54 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -345,47 +345,50 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) -(define-public gnqc-py - (package - (name "gnqc-py") - (version "0.0.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.com/fredmanglis/gnqc_py.git") - (commit "c81a3d948b3bc0db20a530fa1aa428b35b5d6145"))) - (hash - (content-hash - (base32 - "1101pql7zpijn36i9phcakfx1r5dcvdf6ix0v4ndjzmzx3d0xyi2"))))) - (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 - `(("python-mypy" ,python-mypy) - ("python-pylint" ,python-pylint) - ("python-pytest" ,python-pytest) - ("python-hypothesis" ,python-hypothesis))) - (propagated-inputs - `(("gunicorn" ,gunicorn) - ("python-redis" ,python-redis) - ("python-flask" ,python-flask) - ("python-pyyaml" ,python-pyyaml) - ("python-jsonpickle" ,python-jsonpickle) - ("python-mysqlclient" ,python-mysqlclient))) - (synopsis "GeneNetwork Quality Control Application") - (description - "GeneNetwork qc is a quality control application for the data files that - eventually are used to add to the data in the GeneNetwork project.") - (home-page "https://gitlab.com/fredmanglis/gnqc_py") - (license license:agpl3+))) +(define-public gn-uploader + (let ((commit "6ced7085193affa636f229e72dc19175a3a06cfe") + (version "0.0.1")) + (package + (name "gn-uploader") + (version (string-append version (string-take commit 8))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) + (hash + (content-hash + (base32 + "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) + (native-inputs + `(("python-mypy" ,python-mypy) + ("python-pylint" ,python-pylint) + ("python-pytest" ,python-pytest) + ("python-hypothesis" ,python-hypothesis))) + (propagated-inputs + `(("gunicorn" ,gunicorn) + ("python-redis" ,python-redis) + ("python-flask" ,python-flask) + ("python-pyyaml" ,python-pyyaml) + ("python-jsonpickle" ,python-jsonpickle) + ("python-mysqlclient" ,python-mysqlclient))) + (synopsis "GeneNetwork Quality Control Application") + (description + "gn-uploader is a service allowing upload of new data into GeneNetwork, + that does quality control for the data files that is being uploaded to ensure + it fulfils all conditions before it can be accepted.") + (home-page "https://git.genenetwork.org/gn-uploader") + (license license:agpl3+)))) (define-public gn-auth (package -- cgit v1.2.3 From 869598d39a532c6acc83bb0b9d21baaa79476973 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 8 Mar 2024 10:10:08 +0300 Subject: gn-uploader: Use more modern list-style inputs. Fix version number. --- gn/packages/genenetwork.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index dae4b54..98d92ac 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -350,7 +350,7 @@ (version "0.0.1")) (package (name "gn-uploader") - (version (string-append version (string-take commit 8))) + (version (string-append version "-" (string-take commit 8))) (source (origin (method git-fetch) @@ -371,17 +371,17 @@ (when tests? (invoke "pytest" "-m" "unit_test"))))))) (native-inputs - `(("python-mypy" ,python-mypy) - ("python-pylint" ,python-pylint) - ("python-pytest" ,python-pytest) - ("python-hypothesis" ,python-hypothesis))) + (list python-mypy + python-pylint + python-pytest + python-hypothesis)) (propagated-inputs - `(("gunicorn" ,gunicorn) - ("python-redis" ,python-redis) - ("python-flask" ,python-flask) - ("python-pyyaml" ,python-pyyaml) - ("python-jsonpickle" ,python-jsonpickle) - ("python-mysqlclient" ,python-mysqlclient))) + (list gunicorn + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, -- cgit v1.2.3 From 36b5aadb6017cbadbddf3fa7b270c9cb4797fc24 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 11 Mar 2024 17:08:21 -0500 Subject: gn: Add genenetwork2-production variant * gn/packages/genenetwork.scm (genenetwork-stable): New variable. --- gn/packages/genenetwork.scm | 89 ++++++++++++++++++++++++++------------------- 1 file changed, 51 insertions(+), 38 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 98d92ac..38b66b2 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -5,6 +5,7 @@ #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix download) + #:use-module (guix git) #:use-module (guix git-download) #:use-module (guix build-system cargo) #:use-module (guix build-system gnu) @@ -345,50 +346,62 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public genenetwork2-stable + (let ((commit "2c122f99098cf84d4b67953f2a3ef05dab762c9c") + (revision "1")) + (package + (inherit genenetwork2) + (name "genenetwork2-stable") + (version (string-append "stable-" (git-version "3.11" revision commit))) + (source + (git-checkout + (url "https://github.com/genenetwork/genenetwork2") + (branch "prod")))))) + (define-public gn-uploader (let ((commit "6ced7085193affa636f229e72dc19175a3a06cfe") (version "0.0.1")) (package - (name "gn-uploader") - (version (string-append version "-" (string-take commit 8))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.genenetwork.org/gn-uploader") - (commit commit))) - (hash - (content-hash - (base32 - "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-m" "unit_test"))))))) - (native-inputs - (list python-mypy - python-pylint - python-pytest - python-hypothesis)) - (propagated-inputs - (list gunicorn - python-redis - python-flask - python-pyyaml - python-jsonpickle - python-mysqlclient)) - (synopsis "GeneNetwork Quality Control Application") - (description - "gn-uploader is a service allowing upload of new data into GeneNetwork, + (name "gn-uploader") + (version (string-append version "-" (string-take commit 8))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) + (hash + (content-hash + (base32 + "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) + (native-inputs + (list python-mypy + python-pylint + python-pytest + python-hypothesis)) + (propagated-inputs + (list gunicorn + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) + (synopsis "GeneNetwork Quality Control Application") + (description + "gn-uploader is a service allowing upload of new data into GeneNetwork, that does quality control for the data files that is being uploaded to ensure it fulfils all conditions before it can be accepted.") - (home-page "https://git.genenetwork.org/gn-uploader") - (license license:agpl3+)))) + (home-page "https://git.genenetwork.org/gn-uploader") + (license license:agpl3+)))) (define-public gn-auth (package -- cgit v1.2.3 From 6585db1b6af0ed66feb4425121ff3885e6381a98 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 13 Mar 2024 04:59:29 +0300 Subject: genenetwork2: Update commit and hash - get commit with bugfixes. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 38b66b2..9a15bc0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -187,7 +187,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "1e81c74ee8752ad2913b4e610ba7575638755385") + (let ((commit "b9e04ad79e0039edba25d58f8bc03e4d2a17583b") (revision "4")) (package (name "genenetwork2") @@ -200,7 +200,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "18g4dd3h737slqmp1ql2jqqzmzql3mx3b4xy72d7qwhwwhc7hcgv")))) + "1ri56g5hl2n0q7cz15sbvjmrr5pmsrp274frkvvcgr9ddxjlzd9p")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From e03c9118ed42d69fbadad23ff41ad7922e84f701 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 13 Mar 2024 05:14:25 +0300 Subject: gn-uploader: Update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 9a15bc0..477bbd8 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -359,7 +359,7 @@ (branch "prod")))))) (define-public gn-uploader - (let ((commit "6ced7085193affa636f229e72dc19175a3a06cfe") + (let ((commit "13bc6684cc2f90b1fdac306a2ce9a8849911b43f") (version "0.0.1")) (package (name "gn-uploader") @@ -373,7 +373,7 @@ (hash (content-hash (base32 - "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) + "1ckbp9hy1yi779iism7hw2bgc8bmw7fkjnyx6xalv4zh6cz4zzn0"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 03c9a8bb9716b48bd853b3be54be4cbd50bcc615 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 19 Mar 2024 05:32:50 +0300 Subject: gn-uploader: update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 477bbd8..f72d066 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -359,7 +359,7 @@ (branch "prod")))))) (define-public gn-uploader - (let ((commit "13bc6684cc2f90b1fdac306a2ce9a8849911b43f") + (let ((commit "38227b8e482ea10f8bb111a1a90f22f8f019e2ab") (version "0.0.1")) (package (name "gn-uploader") @@ -373,7 +373,7 @@ (hash (content-hash (base32 - "1ckbp9hy1yi779iism7hw2bgc8bmw7fkjnyx6xalv4zh6cz4zzn0"))))) + "0vbys9icgwxx2i82mq5yk0lp9869zr0mnjfcdnna647g8cyxzyzq"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From df839ea519decf3693437f5556fa44bc5a994a9c Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Mon, 18 Mar 2024 18:20:06 +0300 Subject: Add javascript-linkify, javascript-linkify-html to genenetwork. * gn/packages/genenetwork.scm (genenetwork2) [propagated-inputs]: Add javacript-linkify and javascript-linkify-html. Acked-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index f72d066..a28075e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -296,6 +296,8 @@ javascript-zxcvbn javascript-jquery-ui javascript-jquery-cookie + javascript-linkify + javascript-linkify-html ; javascript-xterm -- disabled until we know what to do with it, not working on production ; javascript-xterm-style ; javascript-xterm-addon-fit -- cgit v1.2.3 From 2fdbf2445e5293ba9a12b154c58774e73dfeabe5 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 19 Mar 2024 15:20:36 +0300 Subject: gn-uploader: update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index a28075e..ffcd449 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -361,7 +361,7 @@ (branch "prod")))))) (define-public gn-uploader - (let ((commit "38227b8e482ea10f8bb111a1a90f22f8f019e2ab") + (let ((commit "a4ed5d821921e43b73ecaf2ef802fab2b74d0b63") (version "0.0.1")) (package (name "gn-uploader") @@ -375,7 +375,7 @@ (hash (content-hash (base32 - "0vbys9icgwxx2i82mq5yk0lp9869zr0mnjfcdnna647g8cyxzyzq"))))) + "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 27970a971d821fc598eb5050f76585e83fefe2c0 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Tue, 19 Mar 2024 14:36:52 +0300 Subject: gn: genenetwork3: Add python-biopython. * gn/packages/genenetwork.scm (genenetwork3) [propated-inputs]: Add python-biopython. Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ffcd449..b26c53e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -165,6 +165,7 @@ ("python-sparqlwrapper" ,python-sparqlwrapper) ("python-email-validator" ,python-email-validator) ("python-xapian-bindings" ,python-xapian-bindings) + ("python-biopython" ,python-biopython) ("r-optparse" ,r-optparse) ("r-qtl" ,r-qtl) ("r-rjson" ,r-rjson) -- cgit v1.2.3 From f95867933281683eab207b806550f8b637447608 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 24 Mar 2024 09:01:32 +0100 Subject: genenetwork-stable: fix URL problem R/qtl api --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b26c53e..91063b9 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -350,7 +350,7 @@ (license license:agpl3+)))) (define-public genenetwork2-stable - (let ((commit "2c122f99098cf84d4b67953f2a3ef05dab762c9c") + (let ((commit "42b37bba21530aab104bd2fbbddb27ce7cd7de7c") (revision "1")) (package (inherit genenetwork2) -- cgit v1.2.3 From 184ef672921b525dd542e44eff5f17a77952394a Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 11:37:46 +0200 Subject: gn: genenetwork3: reformat package list AND fix tabs2spaces * gn/packages/genenetwork.scm (genenetwork3) --- gn/packages/genenetwork.scm | 144 +++++++++++++++++++++----------------------- 1 file changed, 70 insertions(+), 74 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 91063b9..ce99066 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -130,50 +130,46 @@ (inputs (list python-click)) (native-inputs - `(("python-hypothesis" ,python-hypothesis) - ("python-mypy" ,python-mypy) - ("python-mypy-extensions" ,python-mypy-extensions) - ("python-pylint" ,python-pylint) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock))) + (list python-hypothesis + python-mypy + python-mypy-extensions + python-pylint + python-pytest + python-pytest-mock)) (propagated-inputs - `(("gemma-wrapper" ,gemma-wrapper) - ("python-wrapper" ,python-wrapper) - ("csvdiff" ,csvdiff) - ("gn-rust-correlation" ,gn-rust-correlation) - ;; Replace use of bcrypt with argon below - ("python-bcrypt" ,python-bcrypt) - ("python-argon2-cffi" ,python-argon2-cffi) - ("python-flask" ,python-flask) - ("python-flask-cors" ,python-flask-cors) - ;; Not working in Python > 3.8 - ;; python-ipfshttpclient - ("python-lmdb" ,python-lmdb) - ("python-mysqlclient" ,python-mysqlclient) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ;; python-pingouin << build failing - ("python-pingouin-without-tests" ,python-pingouin-without-tests) - ("python-plotly" ,python-plotly) - ("python-pyld" ,python-pyld) - ("python-scikit-learn" ,python-scikit-learn) - ("python-pymonad" ,python-pymonad) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-scipy" ,python-scipy) - ("python-authlib" ,python-authlib) - ("python-sparqlwrapper" ,python-sparqlwrapper) - ("python-email-validator" ,python-email-validator) - ("python-xapian-bindings" ,python-xapian-bindings) - ("python-biopython" ,python-biopython) - ("r-optparse" ,r-optparse) - ("r-qtl" ,r-qtl) - ("r-rjson" ,r-rjson) - ("r-stringi" ,r-stringi) - ("r-wgcna" ,r-wgcna) - ("r-ctl" ,r-ctl) - ("rust-qtlreaper" ,rust-qtlreaper) - ("diffutils" ,diffutils))) + (list gemma-wrapper + python-wrapper + csvdiff + gn-rust-correlation + python-bcrypt ;; Replace use of bcrypt with argon below + python-argon2-cffi + python-flask + python-flask-cors + python-lmdb + python-mysqlclient + python-numpy + python-pandas + python-pingouin-without-tests + python-plotly + python-pyld + python-scikit-learn + python-pymonad + python-redis + python-requests + python-scipy + python-authlib + python-sparqlwrapper + python-email-validator + python-xapian-bindings + python-biopython + r-optparse + r-qtl + r-rjson + r-stringi + r-wgcna + r-ctl + rust-qtlreaper + diffutils)) (build-system python-build-system) (arguments (list #:phases @@ -273,7 +269,7 @@ javascript-plotly javascript-typeahead js-underscore - javascript-uikit + javascript-uikit js-smart-time-ago javascript-nouislider javascript-purescript-genome-browser @@ -288,7 +284,7 @@ javascript-datatables-buttons-styles javascript-shapiro-wilk javascript-underscore-string - javascript-htmx + javascript-htmx javascript-qtip2 javascript-d3js javascript-nvd3 @@ -297,8 +293,8 @@ javascript-zxcvbn javascript-jquery-ui javascript-jquery-cookie - javascript-linkify - javascript-linkify-html + javascript-linkify + javascript-linkify-html ; javascript-xterm -- disabled until we know what to do with it, not working on production ; javascript-xterm-style ; javascript-xterm-addon-fit @@ -363,7 +359,7 @@ (define-public gn-uploader (let ((commit "a4ed5d821921e43b73ecaf2ef802fab2b74d0b63") - (version "0.0.1")) + (version "0.0.1")) (package (name "gn-uploader") (version (string-append version "-" (string-take commit 8))) @@ -371,33 +367,33 @@ (origin (method git-fetch) (uri (git-reference - (url "https://git.genenetwork.org/gn-uploader") - (commit commit))) + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) (hash - (content-hash - (base32 - "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) + (content-hash + (base32 + "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-m" "unit_test"))))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) (native-inputs (list python-mypy - python-pylint - python-pytest - python-hypothesis)) + python-pylint + python-pytest + python-hypothesis)) (propagated-inputs (list gunicorn - python-redis - python-flask - python-pyyaml - python-jsonpickle - python-mysqlclient)) + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, @@ -414,21 +410,21 @@ (origin (method git-fetch) (uri (git-reference - (url "https://github.com/genenetwork/gn-auth.git") - (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) + (url "https://github.com/genenetwork/gn-auth.git") + (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) (hash - (content-hash - (base32 - "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) + (content-hash + (base32 + "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) (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"))))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) (native-inputs (list python-hypothesis python-mypy -- cgit v1.2.3 From 4a8d467bcf0024960f3b88842be32a64f610c022 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 11:42:19 +0200 Subject: gn: genenetwork3: sorted package names and added R to propagated inputs to make Rscript available on the path * gn/packages/genenetwork.scm (genenetwork3) [propagated-inputs]: Add r. --- gn/packages/genenetwork.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ce99066..e439fdd 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -140,9 +140,13 @@ (list gemma-wrapper python-wrapper csvdiff + diffutils gn-rust-correlation - python-bcrypt ;; Replace use of bcrypt with argon below + python-authlib python-argon2-cffi + python-bcrypt ;; Replace use of bcrypt with argon + python-biopython + python-email-validator python-flask python-flask-cors python-lmdb @@ -152,24 +156,21 @@ python-pingouin-without-tests python-plotly python-pyld - python-scikit-learn python-pymonad python-redis python-requests + python-scikit-learn python-scipy - python-authlib python-sparqlwrapper - python-email-validator python-xapian-bindings - python-biopython + r + r-ctl r-optparse r-qtl r-rjson r-stringi r-wgcna - r-ctl - rust-qtlreaper - diffutils)) + rust-qtlreaper)) (build-system python-build-system) (arguments (list #:phases -- cgit v1.2.3 From e200b1c3ea52776bbc701f9912d0fcbc86b79a2e Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 14:32:10 +0200 Subject: gn: Add genenetwork3-production variant * gn/packages/genenetwork.scm (genenetwork3-stable): New variable. --- gn/packages/genenetwork.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index e439fdd..d89852d 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -346,6 +346,18 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public genenetwork3-stable + (let ((commit "25d3f3d7a13a9d94b561b1d824ba0b428a3fc006") + (revision "1")) + (package + (inherit genenetwork3) + (name "genenetwork3-stable") + (version (string-append "stable-" (git-version "3.11" revision commit))) + (source + (git-checkout + (url "https://github.com/genenetwork/genenetwork3") + (branch "prod")))))) + (define-public genenetwork2-stable (let ((commit "42b37bba21530aab104bd2fbbddb27ce7cd7de7c") (revision "1")) -- cgit v1.2.3 From 10f9f0f19a0bb8c354ee68f0479edf606e3a2dd1 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 15:17:17 +0200 Subject: gn: genenetwork3: sorted package names and moved python-test and python-test-mock into propagated inputs * gn/packages/genenetwork.scm (genenetwork3) [propagated-inputs]: add testing --- gn/packages/genenetwork.scm | 161 ++++++++++++++++++++++---------------------- 1 file changed, 81 insertions(+), 80 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d89852d..d05d9f5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -133,17 +133,14 @@ (list python-hypothesis python-mypy python-mypy-extensions - python-pylint - python-pytest - python-pytest-mock)) + python-pylint)) (propagated-inputs - (list gemma-wrapper - python-wrapper - csvdiff + (list csvdiff diffutils + gemma-wrapper gn-rust-correlation - python-authlib python-argon2-cffi + python-authlib python-bcrypt ;; Replace use of bcrypt with argon python-biopython python-email-validator @@ -157,11 +154,14 @@ python-plotly python-pyld python-pymonad + python-pytest + python-pytest-mock python-redis python-requests python-scikit-learn python-scipy python-sparqlwrapper + python-wrapper python-xapian-bindings r r-ctl @@ -203,103 +203,104 @@ (list graphviz)) (propagated-inputs (list genenetwork3 - parallel coreutils - git - which - grep - r - r-ctl - r-qtl - r-wgcna - redis - mariadb gemma gemma-wrapper - plink-ng-gn - rust-qtlreaper - gn-rust-correlation + git glibc-utf8-locales - nginx - python-wrapper - python-pillow - python-coverage - python-configparser - python-flask + gn-rust-correlation + grep gunicorn + javascript-bootstrap + javascript-chroma + javascript-ckeditor + javascript-colorbox + javascript-cytoscape + javascript-cytoscape-panzoom + javascript-cytoscape-qtip + javascript-d3-tip + javascript-d3js + javascript-datatables + javascript-datatables-buttons + javascript-datatables-buttons-bootstrap + javascript-datatables-buttons-styles + javascript-datatables-col-reorder + javascript-datatables-col-resize + javascript-datatables-plugins + javascript-datatables-scroller + javascript-font-awesome + javascript-htmx + javascript-jquery + javascript-jquery-cookie + javascript-jquery-ui + javascript-jscolor + javascript-jszip + javascript-linkify + javascript-linkify-html + javascript-nouislider + javascript-nvd3 + javascript-plotly + javascript-purescript-genome-browser + javascript-qtip2 + javascript-shapiro-wilk + javascript-twitter-post-fetcher + javascript-typeahead + javascript-uikit + javascript-underscore-string + javascript-zxcvbn + js-jstat + js-md5 + js-parsley + js-smart-time-ago + js-underscore + mariadb + nginx + parallel + plink-ng-gn + python-authlib python-autopep8 + python-beautifulsoup4 + python-configparser + python-coverage python-cssselect + python-flask python-flask-debugtoolbar + python-flask-session python-htmlgen python-ijson python-jinja2 - python-pytest - python-pytest-mock - python-sqlalchemy - python-setuptools - python-scipy python-lxml - python-mysqlclient + python-markdown python-mypy + python-mysqlclient python-numpy python-pandas + python-pillow python-pylint python-pymonad + python-pytest + python-pytest-mock + python-rdflib python-redis python-requests - python-simplejson - python-markdown - python-rdflib - python-authlib - python-flask-session python-rpy2 - python-beautifulsoup4 + python-scipy + python-setuptools + python-simplejson + python-sqlalchemy + python-wrapper python-xlsxwriter - javascript-twitter-post-fetcher - javascript-cytoscape - javascript-cytoscape-panzoom - javascript-cytoscape-qtip - javascript-chroma - javascript-d3-tip - javascript-jscolor - javascript-colorbox - javascript-jszip - js-jstat - js-md5 - js-parsley - javascript-plotly - javascript-typeahead - js-underscore - javascript-uikit - js-smart-time-ago - javascript-nouislider - javascript-purescript-genome-browser - javascript-ckeditor - javascript-datatables - javascript-datatables-scroller - javascript-datatables-buttons - javascript-datatables-buttons-bootstrap - javascript-datatables-plugins - javascript-datatables-col-reorder - javascript-datatables-col-resize - javascript-datatables-buttons-styles - javascript-shapiro-wilk - javascript-underscore-string - javascript-htmx - javascript-qtip2 - javascript-d3js - javascript-nvd3 - javascript-bootstrap - javascript-jquery - javascript-zxcvbn - javascript-jquery-ui - javascript-jquery-cookie - javascript-linkify - javascript-linkify-html + r + r-ctl + r-qtl + r-wgcna + 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 - javascript-font-awesome)) + )) (inputs (list javascript-colorbox)) (build-system python-build-system) -- cgit v1.2.3 From 467279ce30a02b9cbb6ddfca48ef15f117a6d85f Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 15:21:57 +0200 Subject: gn: genenetwork3-stable: disable testing for now * gn/packages/genenetwork.scm (genenetwork3-stable) disable testing --- gn/packages/genenetwork.scm | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d05d9f5..3e8a2ed 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -354,6 +354,9 @@ (inherit genenetwork3) (name "genenetwork3-stable") (version (string-append "stable-" (git-version "3.11" revision commit))) + (arguments + (list + #:tests? #f)) ; temporary disable on production setup (source (git-checkout (url "https://github.com/genenetwork/genenetwork3") -- cgit v1.2.3 From 3d3bdd5c74c41385f4c7fa00d12e25e44a04b4aa Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 2 Apr 2024 10:13:46 +0300 Subject: gn-uploader: update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 3e8a2ed..efb0ea8 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -375,7 +375,7 @@ (branch "prod")))))) (define-public gn-uploader - (let ((commit "a4ed5d821921e43b73ecaf2ef802fab2b74d0b63") + (let ((commit "60fde66e02dba842b20fa126ff3b2ed9ec2638e6") (version "0.0.1")) (package (name "gn-uploader") @@ -389,7 +389,7 @@ (hash (content-hash (base32 - "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) + "1q04viyf7d0q30k3424hrzsh9wxhhgs7hywlhzl3m68jki4zq1i7"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 404a97f8973cf1199e147b7117ac562580a70634 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 2 Apr 2024 09:30:18 +0200 Subject: genenetwork3-stable: Update commit and hash. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index efb0ea8..2d7fab5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "25d3f3d7a13a9d94b561b1d824ba0b428a3fc006") + (let ((commit "b04458b6ff745c9d0d1101527bec6eeafd911d05") (revision "1")) (package (inherit genenetwork3) -- cgit v1.2.3 From 4bce9fa4e3ebc3036ec94207b392d0c5b5d869d1 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 2 Apr 2024 16:32:16 +0200 Subject: genenetwork3-stable: Update commit and hash. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2d7fab5..2053e78 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "b04458b6ff745c9d0d1101527bec6eeafd911d05") + (let ((commit "c094d2db352a39cc001b21ad4195fc32de24c863") (revision "1")) (package (inherit genenetwork3) -- cgit v1.2.3 From 5871a33c424510c9fad10a240d355dfb31b027e7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 04:08:07 -0500 Subject: genenetwork3-stable: patch path to R script --- gn/packages/genenetwork.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2053e78..a0c8a57 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "c094d2db352a39cc001b21ad4195fc32de24c863") + (let ((commit "8414f1d74f6b09205d3cfd09240c787323474626") (revision "1")) (package (inherit genenetwork3) @@ -356,7 +356,13 @@ (version (string-append "stable-" (git-version "3.11" revision commit))) (arguments (list - #:tests? #f)) ; temporary disable on production setup + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'update-paths + (lambda _ + (substitute* "gn3/api/rqtl.py" + (("scripts/rqtl_wrapper.R)" + (string-append #$output "/scripts/rqtl_wrapper.R")))))))) (source (git-checkout (url "https://github.com/genenetwork/genenetwork3") -- cgit v1.2.3 From 75ff5fe367f6de7d1bb7ad4c3fb29ed97d32bd10 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 04:47:55 -0500 Subject: genenetwork3-stable: patch path to R script - missing bracket --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index a0c8a57..20e91be 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -353,7 +353,7 @@ (package (inherit genenetwork3) (name "genenetwork3-stable") - (version (string-append "stable-" (git-version "3.11" revision commit))) + (version (string-append (git-version "3.11" revision commit))) (arguments (list #:phases @@ -361,7 +361,7 @@ (add-before 'build 'update-paths (lambda _ (substitute* "gn3/api/rqtl.py" - (("scripts/rqtl_wrapper.R)" + (("scripts/rqtl_wrapper.R)") (string-append #$output "/scripts/rqtl_wrapper.R")))))))) (source (git-checkout -- cgit v1.2.3 From fe1e3e87f25c34267c25e1cca1b6063660fb9236 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 04:57:09 -0500 Subject: genenetwork3-stable: copy R script into destination --- gn/packages/genenetwork.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 20e91be..af0fea3 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -356,13 +356,21 @@ (version (string-append (git-version "3.11" revision commit))) (arguments (list + #:tests? #f #:phases #~(modify-phases %standard-phases (add-before 'build 'update-paths (lambda _ (substitute* "gn3/api/rqtl.py" (("scripts/rqtl_wrapper.R)") - (string-append #$output "/scripts/rqtl_wrapper.R")))))))) + (string-append #$output "/scripts/rqtl_wrapper.R"))))) + (add-before 'install 'install-scripts + (lambda _ + (begin + (mkdir (string-append #$output "scripts")) + (install-file "scripts/rqtl_wrapper.R" + (string-append #$output "/scripts")))))))) + (source (git-checkout (url "https://github.com/genenetwork/genenetwork3") -- cgit v1.2.3 From 31e8932290d54ac8710fb3a496fa083ad640d39c Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 05:08:35 -0500 Subject: genenetwork3-stable: copy other R scripts into destination --- gn/packages/genenetwork.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index af0fea3..5bd4c71 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -368,8 +368,13 @@ (lambda _ (begin (mkdir (string-append #$output "scripts")) - (install-file "scripts/rqtl_wrapper.R" - (string-append #$output "/scripts")))))))) + (for-each (lambda (fn) + (install-file fn + (string-append #$output "/scripts"))) + '("scripts/rqtl_wrapper.R" + "scripts/ctl_analysis.R" + "scripts/wgcna_analysis.R" + )))))))) (source (git-checkout -- cgit v1.2.3 From 65cb368fe12bd2604d6f36d5d50404ac58d08673 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 05:11:41 -0500 Subject: genenetwork3-stable: modify files using R scripts --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5bd4c71..4ceac43 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -362,8 +362,8 @@ (add-before 'build 'update-paths (lambda _ (substitute* "gn3/api/rqtl.py" - (("scripts/rqtl_wrapper.R)") - (string-append #$output "/scripts/rqtl_wrapper.R"))))) + (("scripts/") + (string-append #$output "/scripts/"))))) (add-before 'install 'install-scripts (lambda _ (begin -- cgit v1.2.3 From 6303fe046b944a380704eb02144cca777fee689b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 06:14:59 -0500 Subject: genenetwork3-stable: modify files that use R scripts --- gn/packages/genenetwork.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4ceac43..c404c53 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "8414f1d74f6b09205d3cfd09240c787323474626") + (let ((commit "d8203aaa523895fd8b1ff6cc124f2e8a53932a07") (revision "1")) (package (inherit genenetwork3) @@ -361,9 +361,14 @@ #~(modify-phases %standard-phases (add-before 'build 'update-paths (lambda _ - (substitute* "gn3/api/rqtl.py" + (for-each (lambda (fn) + (substitute* (string-append "gn3/" fn) (("scripts/") - (string-append #$output "/scripts/"))))) + (string-append #$output "/scripts/")))) + '("api/rqtl.py" + "computations/wgcna.py" + "computations/ctl.py" + "api/general.py")))) (add-before 'install 'install-scripts (lambda _ (begin -- cgit v1.2.3 From 9dd4e53a93f7c3a9aa970b6e2a787e4122461c13 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 06:43:34 -0500 Subject: genenetwork3-stable: update hash --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index c404c53..f7337c4 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "d8203aaa523895fd8b1ff6cc124f2e8a53932a07") + (let ((commit "e5569c3bb1c0d59ff7142273c5f51fe19f06cfe8") (revision "1")) (package (inherit genenetwork3) -- cgit v1.2.3 From 1a6522f3a5a7d0990e50fe5dd91f286f62e083e7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 4 Apr 2024 05:49:19 -0500 Subject: javascript-d3panels: add variable and add to genenetwork2 --- gn/packages/genenetwork.scm | 23 +++++++++++++++++++---- gn/packages/javascript.scm | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 55 insertions(+), 4 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index f7337c4..e3ec17f 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -220,6 +220,7 @@ javascript-cytoscape-qtip javascript-d3-tip javascript-d3js + javascript-d3panels javascript-datatables javascript-datatables-buttons javascript-datatables-buttons-bootstrap @@ -373,7 +374,7 @@ (lambda _ (begin (mkdir (string-append #$output "scripts")) - (for-each (lambda (fn) + (for-each (lambda (fn) (install-file fn (string-append #$output "/scripts"))) '("scripts/rqtl_wrapper.R" @@ -387,16 +388,30 @@ (branch "prod")))))) (define-public genenetwork2-stable - (let ((commit "42b37bba21530aab104bd2fbbddb27ce7cd7de7c") + (let ((commit "fd3de3dd7e0fac465bde193bd78085bd3434e885") (revision "1")) (package (inherit genenetwork2) (name "genenetwork2-stable") - (version (string-append "stable-" (git-version "3.11" revision commit))) + (version (string-append "stable-" (git-version "3.12" revision commit))) (source (git-checkout (url "https://github.com/genenetwork/genenetwork2") - (branch "prod")))))) + (branch "prod"))) + (arguments + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'update-font-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + (for-each (lambda (fn) + (substitute* (string-append "gn2/" fn) + (("\\./gn2/wqflask/static/fonts/") + (string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts/")))) + '("utility/Plot.py" + "wqflask/marker_regression/display_mapping_results.py")))) + )))))) (define-public gn-uploader (let ((commit "60fde66e02dba842b20fa126ff3b2ed9ec2638e6") diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 2d1668b..f92ada9 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -433,6 +433,7 @@ tables with minimal effort.") (description "Scroller is a virtual rendering plug-in for DataTables which allows large datasets to be drawn on screen very quickly. Virtual rendering means is that only the visible portion of the table is drawn, while the scrolling container gives the visual impression that the whole table is visible, allowing excellent browser performance.") (license license:expat))) + (define-public javascript-xterm (package (name "javascript-xterm") @@ -805,6 +806,41 @@ without tying yourself to a proprietary framework, combining powerful visualization components and a data-driven approach to DOM manipulation.") (license license:bsd-3))) +(define-public javascript-d3panels + (package + (name "javascript-d3panels") + (version "1.8.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kbroman/d3panels.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1pmv24x4k0iy2mbibwwk8f85c6mljyqj2qwn03sq3pg93r16a0b5")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir (string-append out "/share/genenetwork2/javascript/d3panels")) + (source (assoc-ref %build-inputs "source"))) + (install-file (string-append source "/d3panels.js") targetdir) + (install-file (string-append source "/d3panels.min.js") targetdir) + (install-file (string-append source "/d3panels.css") targetdir) + (install-file (string-append source "/d3panels.min.css") targetdir) + (install-file (string-append source "/README.md") targetdir) + (install-file (string-append source "/NEWS.md") targetdir) + (install-file (string-append source "/LICENSE.md") targetdir) + )))) + (home-page "https://kbroman.org/d3panels") + (synopsis "d3panels for QTL mapping") + (description "This is a set of D3-based graphic panels, to be combined into larger multi-panel charts. They were developed for the R/qtlcharts package.") + (license license:expat))) + (define-public javascript-jquery (package (inherit web-jquery) -- cgit v1.2.3 From 914ae94d48bd8a7619102263eb654a764877dbc6 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 4 Apr 2024 11:14:18 -0500 Subject: Add recent javascript-d3 library --- gn/packages/genenetwork.scm | 3 ++- gn/packages/javascript.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index e3ec17f..21de18a 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -219,7 +219,8 @@ javascript-cytoscape-panzoom javascript-cytoscape-qtip javascript-d3-tip - javascript-d3js + javascript-d3js ;; very old + javascript-d3js-7 javascript-d3panels javascript-datatables javascript-datatables-buttons diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index f92ada9..d8c9af9 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -894,6 +894,46 @@ visualization components and a data-driven approach to DOM manipulation.") (install-file "d3.min.js" targetdir) (install-file "LICENSE" (string-append out "/share/doc/d3js-" ,version)))))))) +(define-public javascript-d3js-7 + (package + (name "javascript-d3js-7") + (version "7.9.0") + (source + (origin + (method url-fetch) + ;; note that D3 no longer provides a prebuilt JS file - except through CDS + (uri (string-append "https://files.genenetwork.org/software/d3.v" version ".min.js.gz")) + (sha256 + (base32 "0k7g40zb65s12z1zchvimj5xibkrqff5sylbrhcwmwpcplpigid7")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (module-name "d3js-7") + (gzip (string-append (assoc-ref %build-inputs "gzip") + "/bin/gzip")) + (targetdir (string-append out "/share/genenetwork2/javascript/" module-name)) + (jsname (string-append "d3.v" "7.9.0" ".min.js")) + (gzname (string-append jsname ".gz")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file (pk source) (pk (string-append targetdir "/" gzname))) + (invoke gzip "-fd" (string-append targetdir "/" gzname)))))) + (native-inputs + `(("source" ,source) + ("gzip" ,gzip))) + (home-page "https://d3js.org/") + (synopsis "JavaScript library for visualizing data") + (description "D3.js is a JavaScript library for manipulating documents based +on data. D3 helps you bring data to life using HTML, SVG, and CSS. D3's +emphasis on web standards gives you the full capabilities of modern browsers +without tying yourself to a proprietary framework, combining powerful +visualization components and a data-driven approach to DOM manipulation.") + (license license:bsd-3))) + (define-public javascript-d3js-multi (package (name "javascript-d3js-multi") -- cgit v1.2.3 From 3aa257007eeb4169ab4c3357bd7d5b3bb80a89f8 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 5 Apr 2024 02:26:10 -0500 Subject: genenetwork2-stable: update hash --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 21de18a..ac9072a 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -389,7 +389,7 @@ (branch "prod")))))) (define-public genenetwork2-stable - (let ((commit "fd3de3dd7e0fac465bde193bd78085bd3434e885") + (let ((commit "95e634ca90d52922812b93df162686b348288651") (revision "1")) (package (inherit genenetwork2) -- cgit v1.2.3 From 7f9908d03acd6d2c44733188122313036dc63b64 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Thu, 9 May 2024 18:34:00 +0300 Subject: Fix path to error GIFs. Co-authored-by: Alexander --- gn/packages/genenetwork.scm | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ac9072a..eab8a07 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -319,6 +319,10 @@ (string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts"))) (substitute* "gn2/wqflask/views.py" + (("\\./gn2/wqflask/static/gif/error") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/gif/error"))) + (substitute* "gn2/wqflask/app_errors.py" (("\\./gn2/wqflask/static/gif/error") (string-append (site-packages inputs outputs) "/gn2/wqflask/static/gif/error"))))) -- cgit v1.2.3 From e09f102357ffe615d1043167c9e2bed3e2b6b418 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 12 Jun 2024 13:04:19 -0500 Subject: gn-uploader: Fix indentation. --- gn/packages/genenetwork.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index eab8a07..5801cb5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -445,16 +445,16 @@ (invoke "pytest" "-m" "unit_test"))))))) (native-inputs (list python-mypy - python-pylint - python-pytest - python-hypothesis)) + python-pylint + python-pytest + python-hypothesis)) (propagated-inputs (list gunicorn - python-redis - python-flask - python-pyyaml - python-jsonpickle - python-mysqlclient)) + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, -- cgit v1.2.3 From 9f5097a76eb87abb16006c0d9e6080c2231fdb3d Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 13 Jun 2024 09:09:47 -0500 Subject: gn-uploader: javascript-bootstrap: New dependency Bundle javascript-bootstrap with gn-uploader for styling. --- gn/packages/genenetwork.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5801cb5..39bad71 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -454,7 +454,8 @@ python-flask python-pyyaml python-jsonpickle - python-mysqlclient)) + python-mysqlclient + javascript-bootstrap)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, -- cgit v1.2.3 From 22a779d83b39158459055b22a6d75e770054784c Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 14 Jun 2024 10:44:38 -0500 Subject: gn-uploader: (javascript-jquery): New dependency JQuery is needed to get the bootstrap plugins working correctly. --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 39bad71..10619da 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -455,6 +455,7 @@ python-pyyaml python-jsonpickle python-mysqlclient + javascript-jquery javascript-bootstrap)) (synopsis "GeneNetwork Quality Control Application") (description -- cgit v1.2.3