Windoc modify

[kapilkd13]

modifying installation instructions on windows and adding a solution to a problem that user may encounter

[mr-c]

Is this a bug with Python, Virtualenv, or us? Do you have any external references for this?

[kapilkd13]

It appears to be a problem with python itself. I encountered this problem when working on py3 for windows and related issue is here http://bugs.python.org/issue20614

[mr-c]

Okay. I find these instructions confusing. Isn't SYSTEMROOT already set? Is this the responsibility of the user to check and fix, or a developer looking to (re)use the code?

[kapilkd13]

On my system SYSTEMROOT was not set by default (also checked on one other Windows system). Actually this problem is not related to cwltool, but since our test_examples unit test https://github.com/common-workflow-language/cwltool/blob/master/tests/test_examples.py#L123 creates a python cmdline instruction as job and this error occured during unit testing, I decided to add this information.
A better wording can be used, what do you suggest. 😄

[mr-c]

Line wrap at 80 columns please. Also, I do not see any workflow calling python at the given link

[kapilkd13]

If we run test_examples.test_partial_scatter, a python command line instruction is generated as below. Here I got this error.

Resolved 'E:\GitHub\gsoc\cwltool\tests\..\tests\wf\scatterfail.cwl' to 'file:///E:/GitHub/gsoc/cwltool/tests/wf/scatterfail.cwl'
[workflow scatterfail.cwl] start
[step step1] start
[workflow step1] start
[step sstep1] start
[jobee sstep1] c:\users\kapilk~1\appdata\local\temp\tmpxnohco$ python \
    -c \
    'from __future__ import print_function
import sys
print(sys.argv[1])
if sys.argv[1] == "2":
  exit(1)
else:
  f = open("foo"+sys.argv[1]+".txt", "wb")
  content = sys.argv[1]+"\n"
  f.write(content.encode('"'"'utf-8'"'"'))
if sys.argv[1] == "5":
  exit(1)
' \
    1
1
after
[jolb sstep1] completed success
[step sstep1] completed success
[step sstep2] start
[jobee sstep2] c:\users\kapilk~1\appdata\local\temp\tmp0rjlug$ cat \
    /C/users/kapilk~1/appdata/local/temp/tmpnzk_wf/stgae130961-a089-4793-b067-019a7abdd6b3/foo1.txt
cat: /C/users/kapilk~1/appdata/local/temp/tmpnzk_wf/stgae130961-a089-4793-b067-019a7abdd6b3/foo1.txt: No such file or directory
after
[joboo sstep2] completed permanentFail
[step sstep2] completed permanentFail
[workflow step1] completed permanentFail
[step step1] start
[workflow step1_2] start
[step sstep1_2] start
[jobee sstep1_2] c:\users\kapilk~1\appdata\local\temp\tmp32cq41$ python \
    -c \
    'from __future__ import print_function
import sys
print(sys.argv[1])
if sys.argv[1] == "2":
  exit(1)
else:
  f = open("foo"+sys.argv[1]+".txt", "wb")
  content = sys.argv[1]+"\n"
  f.write(content.encode('"'"'utf-8'"'"'))
if sys.argv[1] == "5":
  exit(1)
' \
    2
2
[job sstep1_2] Job error:
E:GitHub\gsoc\cwltool\tests\wf\echo.cwl:20:3: Error collecting output for parameter 'out':
E:GitHub\gsoc\cwltool	ests\wf\echo.cwl:23:7:   Did not find output file with glob pattern: '['foo2.txt']'
[joboo sstep1_2] completed permanentFail
[step sstep1_2] Output is missing expected field file:///E:/GitHub/gsoc/cwltool/tests/wf/scatterfail.cwl#step1/subtool/sstep1/out
[step sstep1_2] completed permanentFail
[workflow step1_2] completed permanentFail
[step step1] start
[workflow step1_3] start
[step sstep1_3] start
[jobee sstep1_3] c:\users\kapilk~1\appdata\local\temp\tmpdwpn_3$ python \
    -c \
    'from __future__ import print_function
import sys
print(sys.argv[1])
if sys.argv[1] == "2":
  exit(1)
else:
  f = open("foo"+sys.argv[1]+".txt", "wb")
  content = sys.argv[1]+"\n"
  f.write(content.encode('"'"'utf-8'"'"'))
if sys.argv[1] == "5":
  exit(1)
' \
    3
3
after
[jolb sstep1_3] completed success
[step sstep1_3] completed success
[step sstep2_3] start
[jobee sstep2_2] c:\users\kapilk~1\appdata\local\temp\tmpzly48y$ cat \
    /C/users/kapilk~1/appdata/local/temp/tmpswvggv/stg906b6972-c95c-4bf0-9029-0f877f8bfe8e/foo3.txt
cat: /C/users/kapilk~1/appdata/local/temp/tmpswvggv/stg906b6972-c95c-4bf0-9029-0f877f8bfe8e/foo3.txt: No such file or directory
after
[joboo sstep2_2] completed permanentFail
[step sstep2_3] completed permanentFail
[workflow step1_3] completed permanentFail
[step step1] completed permanentFail
[workflow scatterfail.cwl] completed permanentFail


========================== 1 passed in 10.48 seconds ==========================

Process finished with exit code 0

Sorry about the line wrap. I will fix it.

[mr-c]

So that's a bug with cwltool under windows -- we should find a way to fix that without user intervention.

[mr-c]

as per d8d9b66 this commit will be removed/reverted

[kapilkd13]

@mr-c I think we can merge this PR

[mr-c]

@kapilkd13 Thanks!