cached cannot handle URLs as input files

[jjkoehorst]

Expected Behavior

The files should download

Actual Behavior

It cannot find the file but it will not download it

Workflow Code

See the traceback for the input yaml file

Full Traceback

cwltool --debug --tmpdir $PWD/TEMP --cachedir CACHE fastqc.yaml

INFO /usr/local/bin/cwltool 3.1.20230624081518
INFO Resolved 'fastqc.yaml' to 'file:///Volumes/Git/m-unlock/cwl/tests/quality/fastqc.yaml'
DEBUG Parsed job order from command line: {
    "id": "fastqc.yaml",
    "fastq": [
        {
            "class": "File",
            "location": "http://download.systemsbiology.nl/unlock/cwl/test_data/amplicon/forward.fastq.gz"
        },
        {
            "class": "File",
            "location": "http://download.systemsbiology.nl/unlock/cwl/test_data/amplicon/reverse.fastq.gz"
        }
    ],
    "nanopore_reads": null,
    "threads": 1
}
ERROR Got workflow error
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/cwltool/executors.py", line 217, in run_jobs
    for job in jobiter:
  File "/usr/local/lib/python3.9/site-packages/cwltool/command_line_tool.py", line 836, in job
    visit_class([cachebuilder.files, cachebuilder.bindings], ("File"), _checksum)
  File "/usr/local/lib/python3.9/site-packages/cwltool/utils.py", line 220, in visit_class
    visit_class(d, cls, op)
  File "/usr/local/lib/python3.9/site-packages/cwltool/utils.py", line 220, in visit_class
    visit_class(d, cls, op)
  File "/usr/local/lib/python3.9/site-packages/cwltool/utils.py", line 215, in visit_class
    op(rec)
  File "/usr/local/lib/python3.9/site-packages/cwltool/process.py", line 1345, in compute_checksums
    with fs_access.open(location, "rb") as f:
  File "/usr/local/lib/python3.9/site-packages/cwltool/stdfsaccess.py", line 38, in open
    return open(self._abs(fn), mode)
FileNotFoundError: [Errno 2] No such file or directory: 'http://download.systemsbiology.nl/unlock/cwl/test_data/amplicon/forward.fastq.gz'
ERROR Workflow error:
[Errno 2] No such file or directory: 'http://download.systemsbiology.nl/unlock/cwl/test_data/amplicon/forward.fastq.gz'
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/cwltool/executors.py", line 217, in run_jobs
    for job in jobiter:
  File "/usr/local/lib/python3.9/site-packages/cwltool/command_line_tool.py", line 836, in job
    visit_class([cachebuilder.files, cachebuilder.bindings], ("File"), _checksum)
  File "/usr/local/lib/python3.9/site-packages/cwltool/utils.py", line 220, in visit_class
    visit_class(d, cls, op)
  File "/usr/local/lib/python3.9/site-packages/cwltool/utils.py", line 220, in visit_class
    visit_class(d, cls, op)
  File "/usr/local/lib/python3.9/site-packages/cwltool/utils.py", line 215, in visit_class
    op(rec)
  File "/usr/local/lib/python3.9/site-packages/cwltool/process.py", line 1345, in compute_checksums
    with fs_access.open(location, "rb") as f:
  File "/usr/local/lib/python3.9/site-packages/cwltool/stdfsaccess.py", line 38, in open
    return open(self._abs(fn), mode)
FileNotFoundError: [Errno 2] No such file or directory: 'http://download.systemsbiology.nl/unlock/cwl/test_data/amplicon/forward.fastq.gz'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/cwltool/main.py", line 1298, in main
    (out, status) = real_executor(
  File "/usr/local/lib/python3.9/site-packages/cwltool/executors.py", line 61, in __call__
    return self.execute(process, job_order_object, runtime_context, logger)
  File "/usr/local/lib/python3.9/site-packages/cwltool/executors.py", line 144, in execute
    self.run_jobs(process, job_order_object, logger, runtime_context)
  File "/usr/local/lib/python3.9/site-packages/cwltool/executors.py", line 251, in run_jobs
    raise WorkflowException(str(err)) from err
cwltool.errors.WorkflowException: [Errno 2] No such file or directory: 'http://download.systemsbiology.nl/unlock/cwl/test_data/amplicon/forward.fastq.gz'

Your Environment

• cwltool version: 3.1.20230624081518
  Check using cwltool --version

[jjkoehorst]

Duplicate of #1842 and #1828 I think