cwltool: upgrade to the latest version

closes #187

reana_workflow_engine_cwl/cwl_reana.py

@@ -28,7 +28,7 @@
     relink_initialworkdir,
     stage_files,
 )
-from cwltool.pathmapper import ensure_writable
+from cwltool.utils import ensure_writable
 from cwltool.workflow import default_make_tool
 from reana_commons.api_client import JobControllerAPIClient as rjc_api_client
 from reana_commons.config import REANA_WORKFLOW_UMASK
@@ -280,6 +280,13 @@ def shouldquote(x):
 
         return create_body
 
+    def _required_env(self):
+        """Variables required by the CWL spec."""
+        return {
+            "TMPDIR": self.tmpdir,
+            "HOME": self.builder.outdir,
+        }
+
     def _get_hint(self, hint_name):
         """Return specific hint if specified."""
         if self.hints:

requirements.txt

@@ -6,20 +6,20 @@
 #
 amqp==2.6.1               # via kombu
 appdirs==1.4.4            # via fs
+argcomplete==1.12.3       # via cwltool
 attrs==21.2.0             # via jsonschema
 bagit==1.8.1              # via cwltool
 bravado-core==5.17.0      # via bravado
 bravado==10.3.2           # via reana-commons
-cachecontrol==0.11.7      # via schema-salad
+cachecontrol==0.12.6      # via schema-salad
 certifi==2021.5.30        # via requests
 chardet==4.0.0            # via requests
 checksumdir==1.1.9        # via reana-commons
 click==8.0.1              # via reana-commons
 coloredlogs==15.0.1       # via cwltool
-cwltool==1.0.20191022103248  # via reana-workflow-engine-cwl (setup.py)
+cwltool==3.1.20210628163208  # via reana-workflow-engine-cwl (setup.py)
 decorator==4.4.2          # via networkx
 fs==2.4.13                # via reana-commons
-future==0.18.2            # via cwltool, schema-salad
 humanfriendly==9.2        # via coloredlogs
 idna==2.10                # via jsonschema, requests
 isodate==0.6.0            # via rdflib
@@ -33,32 +33,32 @@ mistune==0.8.4            # via schema-salad
 mock==3.0.5               # via reana-commons
 monotonic==1.6            # via bravado
 msgpack-python==0.5.6     # via bravado
-msgpack==1.0.2            # via bravado-core
+msgpack==1.0.2            # via bravado-core, cachecontrol
 mypy-extensions==0.4.3    # via cwltool
 networkx==2.5.1           # via prov
-pathlib2==2.3.5           # via cwltool
 prov==1.5.1               # via cwltool
 psutil==5.8.0             # via cwltool
-pyparsing==2.4.7          # via rdflib
-pyrsistent==0.17.3        # via jsonschema
+pydot==1.4.2              # via cwltool
+pyparsing==2.4.7          # via pydot, rdflib
+pyrsistent==0.18.0        # via jsonschema
 python-dateutil==2.8.1    # via bravado, bravado-core, prov
 pytz==2021.1              # via bravado-core, fs
 pyyaml==5.4.1             # via bravado, bravado-core, reana-commons
-rdflib-jsonld==0.4.0      # via schema-salad
-rdflib==4.2.2             # via cwltool, prov, rdflib-jsonld, schema-salad
-reana-commons==0.8.0a17   # via reana-workflow-engine-cwl (setup.py)
+rdflib-jsonld==0.5.0      # via schema-salad
+rdflib==5.0.0             # via cwltool, prov, rdflib-jsonld, schema-salad
+reana-commons==0.8.0a19   # via reana-workflow-engine-cwl (setup.py)
 requests==2.25.1          # via bravado, cachecontrol, cwltool, schema-salad
 rfc3987==1.3.8            # via jsonschema
-ruamel.yaml==0.16.0       # via cwltool, schema-salad
-scandir==1.10.0           # via cwltool
-schema-salad==4.5.20191023134839  # via cwltool, reana-workflow-engine-cwl (setup.py)
-shellescape==3.4.1        # via cwltool
-simplejson==3.17.2        # via bravado, bravado-core
-six==1.16.0               # via bravado, bravado-core, cwltool, fs, isodate, jsonschema, mock, pathlib2, prov, python-dateutil, schema-salad
+ruamel.yaml.clib==0.2.6   # via ruamel.yaml
+ruamel.yaml==0.17.10      # via cwltool, schema-salad
+schema-salad==8.1.20210627200047  # via cwltool
+shellescape==3.8.1        # via cwltool
+simplejson==3.17.3        # via bravado, bravado-core
+six==1.16.0               # via bravado, bravado-core, fs, isodate, jsonschema, mock, prov, python-dateutil, rdflib
 strict-rfc3339==0.7       # via jsonschema
 swagger-spec-validator==2.7.3  # via bravado-core
-typing-extensions==3.10.0.0  # via bravado, cwltool, schema-salad
-urllib3==1.26.5           # via requests
+typing-extensions==3.10.0.0  # via bravado, cwltool
+urllib3==1.26.6           # via requests
 vine==1.3.0               # via amqp
 webcolors==1.11.1         # via jsonschema
 werkzeug==2.0.1           # via reana-commons

setup.py

@@ -39,8 +39,7 @@
 ]
 
 install_requires = [
-    "cwltool==1.0.20191022103248",
-    "schema-salad==4.5.20191023134839",
+    "cwltool==3.1.20210628163208",
     "reana-commons>=0.8.0a17,<0.9.0",
 ]