Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics

3 files changed, 88 insertions, 18 deletions

diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 5a01dbf..245af84 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -4,6 +4,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages node)
@@ -22,7 +23,7 @@
   #:use-module (srfi srfi-1))
 
 (define-public cwltool ; guix: needs work
-  (let ((commit "e12d36b6efbc5d4a6ff7b4fbfd7387bff8f72727"))
+  (let ((commit "15539fba76993f951af9eba913bea6d677c74005"))
   (package
     (name "cwltool")
     (version "1.0.20181012180214")
@@ -35,12 +36,12 @@
         ;       ".tar.gz"))
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/genenetwork/cwltool.git")
+               (url "https://github.com/genenetwork/cwltool.git") ;; my repo for Python 3.7
                (commit commit)))
-         (file-name (git-file-name name version))
+         (file-name (git-file-name name (string-append version "-" (string-take commit 7))))
         (sha256
           (base32
-            "1zhba1hfizrw3bxfmhpjds92pj79hyyv5k7sglw24z52kg1in67p"))))
+            "1qwfa82car7477sy0cb5bj4964w7zq7dcw2bdcls6c2i9qdp0586"))))
     (build-system python-build-system)
     (propagated-inputs ; a lot of these are used for testing
      `(("git" ,git)
@@ -66,7 +67,6 @@
        ("python-schema-salad" ,python-schema-salad)
        ("python-html5lib" ,python-html5lib)
        ("python-rdflib-jsonld" ,python-rdflib-jsonld)
-       ("python-typing-extensions" ,python-typing-extensions)
        ("python-scandir" ,python-scandir)
        ("python-psutil" ,python-psutil)
        ))
@@ -88,17 +88,56 @@
       "Common workflow language reference implementation")
     (license license:asl2.0))))
 
+(define-public python-cachecontrol
+  (package
+    (name "python-cachecontrol")
+    (version "0.11.7")
+    (source
+     (origin
+       (method url-fetch)
+       ;; Pypi does not have tests.
+       (uri (string-append
+             "https://github.com/ionrock/cachecontrol/archive/v"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1yfhwihx1b1xjsx0r19va2m0r2s91im03x4d7pwzp87368f2lkkp"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ;; Recent version breaks on cherrypy
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-redis" ,python-redis)
+       ("python-webtest" ,python-webtest)
+       ("python-mock" ,python-mock)))
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-lockfile" ,python-lockfile)))
+    (home-page "https://github.com/ionrock/cachecontrol")
+    (synopsis "The httplib2 caching algorithms for use with requests")
+    (description "CacheControl is a port of the caching algorithms in
+@code{httplib2} for use with @code{requests} session objects.")
+    (license license:asl2.0)))
+
+
 (define-public python-schema-salad
+  (let ((commit "eb85c3d49b99b7643e8a12248e2dc05504910c1e"))
   (package
     (name "python-schema-salad")
     (version "3.0.20181129082112")
     (source
       (origin
-        (method url-fetch)
-        (uri (pypi-uri "schema-salad" version))
-        (sha256
-          (base32
-            "1xg70v82q053vz1sg8sc99alnkrm2kk05w6698vgmngl1767sk97"))))
+        ; (method url-fetch)
+        ; (uri (pypi-uri "schema-salad" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/genenetwork/schema_salad.git") ;; my repo for Python3.7
+             (commit commit)))
+       (file-name (git-file-name name (string-append version "-" (string-take commit 7))))
+       (sha256
+        (base32
+         "174f224zzjr0nbjlq3ypciyfijnibasysrgjswvx8yhan2dizlhr"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f)) ;; CWL includes no tests.
     (inputs
@@ -119,7 +158,7 @@
       "Schema Annotations for Linked Avro Data (SALAD)")
     (description
       "Schema Annotations for Linked Avro Data (SALAD)")
-    (license license:asl2.0)))
+    (license license:asl2.0))))
 
 ; (define-public python2-schema-salad
 ;  (package-with-python2 python-schema-salad))
diff --git a/gn/packages/edash.scm b/gn/packages/edash.scm
index 6324d3a..8d23a08 100644
--- a/gn/packages/edash.scm
+++ b/gn/packages/edash.scm
@@ -5,14 +5,17 @@
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system python)
   #:use-module (gnu packages web)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages time)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages check)
   #:use-module (gn packages web)
+  #:use-module (gnu packages sqlite)
   #:use-module (gn packages python))
 
 (define-public python-s3transfer-0.1.13
@@ -442,6 +445,30 @@ with the Specification.")
     "Connexion - API first applications with OpenAPI/Swagger and Flask")
   (license license:asl2.0)))
 
+(define-public python-flask-cors
+  (package
+    (name "python-flask-cors")
+    (version "3.0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "Flask-Cors" version))
+       (sha256
+        (base32
+         "1v6gq4vjgyxi8q8lxawpdfhq01adb4bznnabp08ks5nzbwibz43y"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-flask" ,python-flask)
+       ("python-six" ,python-six)
+       ("python-nose" ,python-nose)))
+    (home-page
+     "https://github.com/corydolphin/flask-cors")
+    (synopsis
+     "A Flask extension adding a decorator for CORS support")
+    (description
+     "A Flask extension adding a decorator for CORS support")
+    (license license:expat)))
+
 (define-public edash
   (let ((md5 "93e745e9c"))
     (package
@@ -460,6 +487,7 @@ with the Specification.")
     ;;(inputs `(("sassc" ,sassc)))
     (propagated-inputs
      `(("python" ,python)
+       ("glibc-locales" ,glibc-locales)
        ("gunicorn" ,gunicorn)
        ("python-wrapper" ,python-wrapper)
        ("python-elasticsearch" ,python-elasticsearch)
@@ -467,7 +495,7 @@ with the Specification.")
        ("python-jinja2" ,python-jinja2)
        ("python-markdown" ,python-markdown)
        ("python-misaka" ,python-misaka)
-       ("python-pygit2" ,python-pygit2)
+       ;; ("python-pygit2" ,python-pygit2)
        ("web-bootstrap" ,web-bootstrap)
        ;;("sassc" ,sassc)
        ("python-boto3" ,python-boto3)
@@ -480,8 +508,11 @@ with the Specification.")
        ("python-flask-mail" ,python-flask-mail)
        ("python-flask-wtf" ,python-flask-wtf)
        ("sqlite" ,sqlite)
-       ("python-ipython" ,python-ipython)
-       ))
+       ;; ("python-ipython" ,python-ipython)
+       ("python-swagger-ui-bundle" ,python-swagger-ui-bundle)
+       ("python-connexion" ,python-connexion)
+       ("python-schedule" ,python-schedule)
+       ("python-flask-cors" ,python-flask-cors)))
     (arguments
      `(#:modules ((guix build utils))
        #:builder
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 75f7cab..651a635 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -37,6 +37,7 @@
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
+  #:use-module (gnu packages python-xyz)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -379,7 +380,7 @@ functions.")
 (define-public python-setuptools
   (package
     (name "python-setuptools")
-    (version "40.6.2")
+    (version "40.6.0")
     (source
      (origin
       (method url-fetch)
@@ -753,9 +754,8 @@ the older versions.")
         (base32
           "04h8brrbbx151dfa2cvvlnxgmb5wa00mhd2z7nd20s8kyibfkq1p"))))
   (build-system python-build-system)
-  (propagated-inputs
-    `(("python-version" ,python-version)
-      ("python-typing" ,python-typing)))
+  (inputs
+    `(("python-version" ,python-version)))
   (home-page "http://www.mypy-lang.org/")
   (synopsis
     "Experimental type system extensions for programs checked with the mypy typechecker.")