From f129c4fc90fd70b6a468537bda8c497f2bee2277 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 21 Nov 2020 04:33:15 -0600
Subject: cwltools: updated

---
 gn/packages/cwl.scm    | 66 ++++++++++++++++++++++++++++++++++++++------------
 gn/packages/python.scm | 10 ++++----
 2 files changed, 55 insertions(+), 21 deletions(-)

(limited to 'gn/packages')

diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 3e0576c..9871ed9 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -2,29 +2,61 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gn packages python)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages node)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages time)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages xml))
 
-(define-public cwltool
+(define-public python-pydot ;; can be updated in GNU Guix - this is a copy
   (package
-    (name "cwltool")
-    (version "3.0.20200710214758")
+    (name "python-pydot")
+    (version "1.4.1")
     (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "cwltool" version))
-        (sha256
-         (base32
-          "1qbqkhinkhzg98jf24d5gnafsw23kng76rbi2hfvzl18bdsp1zz5"))))
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pydot" version))
+       (sha256
+        (base32
+         "00az4cbf8bv447lkk9xi6pjm7gcc7ia33y4pm71fwfwis56rv76l"))))
+    (build-system python-build-system)
+    (native-inputs
+     ;; For tests.
+     `(("python-chardet" ,python-chardet)))
+    (propagated-inputs
+     `(("python-pyparsing" ,python-pyparsing)))
+    (home-page "https://github.com/erocarrera/pydot")
+    (synopsis "Python interface to Graphviz's DOT language")
+    (description
+     "Pydot provides an interface to create, handle, modify and process
+graphs in Graphviz's DOT language, written in pure Python.")
+    (license license:expat)))
+
+
+(define-public cwltool
+  (let ((commit "78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf")
+        (revision "1"))
+    (package
+    (name "cwltool")
+    (version "3.0.20201117141248")
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/common-workflow-language/cwltool.git")
+                     (commit commit)))
+               (file-name (git-file-name name version))
+               (sha256
+                (base32
+                 "1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -38,9 +70,7 @@
            (lambda _
              ;; Tries to connect to the internet.
              (delete-file "tests/test_udocker.py")
-             (substitute* "tests/test_http_input.py"
-               (("https://raw.githubusercontent.com/common-workflow-language/cwltool/main")
-                "."))
+             (delete-file "tests/test_http_input.py")
              (substitute* "tests/test_load_tool.py"
                (("def test_load_graph_fragment_from_packed")
                 "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_load_graph_fragment_from_packed"))
@@ -53,10 +83,13 @@
                 "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false"))
              #t)))))
     (propagated-inputs
-     `(("python-bagit" ,python-bagit)
+     `(("git" ,git)
+       ("python-argcomplete" ,python-argcomplete)
+       ("python-bagit" ,python-bagit)
        ("python-coloredlogs" ,python-coloredlogs)
        ("python-mypy-extensions" ,python-mypy-extensions)
        ("python-prov" ,python-prov)
+       ("python-pydot" ,python-pydot)
        ("python-psutil" ,python-psutil)
        ("python-rdflib" ,python-rdflib)
        ("python-requests" ,python-requests)
@@ -85,7 +118,7 @@
     (synopsis "Common workflow language reference implementation")
     (description
      "Common workflow language reference implementation.")
-    (license license:asl2.0)))
+    (license license:asl2.0))))
 
 (define-public cwl-runner
   (package
@@ -105,5 +138,6 @@
      "https://github.com/common-workflow-language/common-workflow-language")
     (synopsis "Common workflow language reference implementation")
     (description
-     "Common workflow language reference implementation.")
-    (license license:asl2.0)))
+     "Common workflow language alternate entry point to allow cwl-runner 
+script as an implementation-agnostic script interpreter.") 
+     (license license:asl2.0)))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 00194e1..a9c2770 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1100,14 +1100,14 @@ server.")
 (define-public python-schema-salad
   (package
     (name "python-schema-salad")
-    (version "7.0.20200612160654")
+    (version "7.0.20200811075006")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "schema-salad" version))
         (sha256
          (base32
-          "15ma3lb6fkfc6sj75hnmmg0jj8q3pc5yrlyx15lpdd4dcp2jc39s"))))
+          "0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-cachecontrol" ,python-cachecontrol-0.11)
@@ -1116,8 +1116,8 @@ server.")
        ("python-rdflib" ,python-rdflib)
        ("python-rdflib-jsonld" ,python-rdflib-jsonld)
        ("python-requests" ,python-requests)
-       ;; This needs to be fixed before upstreaming
-       ("python-ruamel.yaml" ,python38-ruaml.yaml-0.15.76)
+       ;; This needs to be fixed before upstreaming - fixed?
+       ("python-ruamel.yaml" ,python-ruamel.yaml)
        ("python-setuptools" ,python-setuptools)
        ("python-typing-extensions" ,python-typing-extensions)))
     (native-inputs
@@ -1528,7 +1528,7 @@ handles recursion and lists.")
     (description "This package provides a SPARQL Slurper for rdflib.")
     (license license:asl2.0)))
 
-(define-public python38-ruaml.yaml-0.15.76
+(define-public python38-ruaml.yaml-0.15.76 ;; no longer in use 
   (package
     (inherit python-ruamel.yaml)
     (name "python-ruamel.yaml")
-- 
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