Merge branch '21815-trigrams-exclude-ids'

[arvados.git] / sdk / cwl / arvados_cwl / runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index f6aab4b93f05110c6ed29d60bdb1c061921e013a..c80a4b3f2f3d6210e1da0bbaf069f84c0a42bfa8 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -2,11 +2,6 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
 #
 # SPDX-License-Identifier: Apache-2.0
 

-from future import standard_library
-standard_library.install_aliases()
-from future.utils import  viewvalues, viewitems
-from past.builtins import basestring
-

 import os
 import sys
 import re
 import os
 import sys
 import re


@@ -36,16 +31,8 @@ from typing import (
     Union,
     cast,
 )
     Union,
     cast,
 )

-from cwltool.utils import (
-    CWLObjectType,
-    CWLOutputAtomType,
-    CWLOutputType,
-)

 
 

-if os.name == "posix" and sys.version_info[0] < 3:
-    import subprocess32 as subprocess
-else:
-    import subprocess
+import subprocess

 
 from schema_salad.sourceline import SourceLine, cmap
 
 
 from schema_salad.sourceline import SourceLine, cmap
 


@@ -75,6 +62,7 @@ from . import done
 from . context import ArvRuntimeContext
 from .perf import Perf
 
 from . context import ArvRuntimeContext
 from .perf import Perf
 

+basestring = (bytes, str)

 logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
 
 logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
 


@@ -106,7 +94,7 @@ def find_defaults(d, op):
         if "default" in d:
             op(d)
         else:
         if "default" in d:
             op(d)
         else:

-            for i in viewvalues(d):
+            for i in d.values():

                 find_defaults(i, op)
 
 def make_builder(joborder, hints, requirements, runtimeContext, metadata):
                 find_defaults(i, op)
 
 def make_builder(joborder, hints, requirements, runtimeContext, metadata):


@@ -570,7 +558,7 @@ def packed_workflow(arvrunner, tool, merged_map, runtimeContext, git_info):
                   rewrite_out=rewrites,
                   loader=tool.doc_loader)
 
                   rewrite_out=rewrites,
                   loader=tool.doc_loader)
 

-    rewrite_to_orig = {v: k for k,v in viewitems(rewrites)}
+    rewrite_to_orig = {v: k for k,v in rewrites.items()}

 
     def visit(v, cur_id):
         if isinstance(v, dict):
 
     def visit(v, cur_id):
         if isinstance(v, dict):


@@ -828,7 +816,8 @@ class Runner(Process):
                  priority=None, secret_store=None,
                  collection_cache_size=256,
                  collection_cache_is_default=True,
                  priority=None, secret_store=None,
                  collection_cache_size=256,
                  collection_cache_is_default=True,

-                 git_info=None):
+                 git_info=None,
+                 reuse_runner=False):

 
         self.loadingContext = loadingContext.copy()
 
 
         self.loadingContext = loadingContext.copy()
 


@@ -861,6 +850,7 @@ class Runner(Process):
         self.enable_dev = self.loadingContext.enable_dev
         self.git_info = git_info
         self.fast_parser = self.loadingContext.fast_parser
         self.enable_dev = self.loadingContext.enable_dev
         self.git_info = git_info
         self.fast_parser = self.loadingContext.fast_parser

+        self.reuse_runner = reuse_runner

 
         self.submit_runner_cores = 1
         self.submit_runner_ram = 1024  # defaut 1 GiB
 
         self.submit_runner_cores = 1
         self.submit_runner_ram = 1024  # defaut 1 GiB


@@ -934,7 +924,7 @@ class Runner(Process):
             if "cwl.output.json" in outc:
                 with outc.open("cwl.output.json", "rb") as f:
                     if f.size() > 0:
             if "cwl.output.json" in outc:
                 with outc.open("cwl.output.json", "rb") as f:
                     if f.size() > 0:

-                        outputs = json.loads(f.read().decode())
+                        outputs = json.loads(str(f.read(), 'utf-8'))

             def keepify(fileobj):
                 path = fileobj["location"]
                 if not path.startswith("keep:"):
             def keepify(fileobj):
                 path = fileobj["location"]
                 if not path.startswith("keep:"):