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:
@@ -382,7 +389,6 @@ def callback(rcode):
             finally:
                 if self.outputs is not None:
                     log.info(f"[job {self.name}] OUTPUTS ------------------")
-                    log.info(pformat(self.outputs))
                 self.cleanup(runtimeContext.rm_tmpdir)
 
         poll = ReanaPipelinePoll(

reana_workflow_engine_cwl/pipeline.py

@@ -123,6 +123,8 @@ def output_callback(out, processStatus):
             cleanIntermediate(output_dirs)
 
         if final_output and final_status:
+            output = str(final_output[0]).encode("utf8").decode("unicode_escape")
+            log.info(f"FinalOutput{output}FinalOutput")
             return str(final_output[0]), str(final_status[0])
         else:
             return None, "permanentFail"

reana_workflow_engine_cwl/tasks.py

@@ -26,22 +26,6 @@ def rcode_to_workflow_status(response_code):
     return rcode_to_workflow_status_mapping[response_code]
 
 
-def parse_str_to_int(workflow_parameters):
-    """Parse integers stored as strings to integers."""
-    for (key, val) in workflow_parameters.items():
-        try:
-            if isinstance(val, str) and val[0] == "'":
-                # The actual value of the int as str could be stored as:
-                # '\'val\'', since ' is an escape character.
-                workflow_parameters[key] = int(val[1:-1])
-            else:
-                workflow_parameters[key] = int(val)
-        except (ValueError, TypeError, KeyError):
-            # Skip values and types which cannot be casted to integer.
-            pass
-    return workflow_parameters
-
-
 def run_cwl_workflow_engine_adapter(
     publisher,
     rjc_api_client,
@@ -53,7 +37,6 @@ def run_cwl_workflow_engine_adapter(
     **kwargs,
 ):
     """Run cwl workflow."""
-    workflow_parameters = parse_str_to_int(workflow_parameters)
     log.info(f"running workflow on context: {locals()}")
     rcode = main.main(
         publisher,

requirements.txt

@@ -6,22 +6,21 @@
 #
 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
+charset-normalizer==2.0.4  # 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)
-decorator==4.4.2          # via networkx
+cwltool==3.1.20210628163208  # via reana-workflow-engine-cwl (setup.py)
 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
+idna==3.2                 # via jsonschema, requests
 isodate==0.6.0            # via rdflib
 jsonpointer==2.1          # via jsonschema
 jsonref==0.2              # via bravado-core
@@ -33,32 +32,32 @@ 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
+networkx==2.6.2           # via prov
 prov==1.5.1               # via cwltool
 psutil==5.8.0             # via cwltool
-pyparsing==2.4.7          # via rdflib
-pyrsistent==0.17.3        # via jsonschema
-python-dateutil==2.8.1    # via bravado, bravado-core, prov
+pydot==1.4.2              # via cwltool
+pyparsing==2.4.7          # via pydot, rdflib
+pyrsistent==0.18.0        # via jsonschema
+python-dateutil==2.8.2    # 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==0.8.0a21   # via reana-workflow-engine-cwl (setup.py)
-requests==2.25.1          # via bravado, cachecontrol, cwltool, schema-salad
+rdflib-jsonld==0.5.0      # via schema-salad
+rdflib==5.0.0             # via cwltool, prov, rdflib-jsonld, schema-salad
+reana-commons==0.8.0a22   # via reana-workflow-engine-cwl (setup.py)
+requests==2.26.0          # 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==8.1.20210721123742  # via cwltool
+shellescape==3.8.1        # via cwltool
+simplejson==3.17.5        # 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>=0.8.0a21,<0.9.0",
 ]