Avoid relink if not having permissions

[bogdang989]

Fixes #1042

[codecov]

Codecov Report

Merging #1045 into master will decrease coverage by 13.2%.
The diff coverage is 100%.

@@             Coverage Diff             @@
##           master    #1045       +/-   ##
===========================================
- Coverage   79.05%   65.85%   -13.21%     
===========================================
  Files          30       30               
  Lines        6030     6030               
  Branches     1496     1496               
===========================================
- Hits         4767     3971      -796     
- Misses        883     1679      +796     
  Partials      380      380

Impacted Files	Coverage Δ
cwltool/job.py	60.39% <100%> (-7.01%)	⬇️
cwltool/singularity.py	24.83% <0%> (-55.56%)	⬇️
cwltool/provenance.py	28.26% <0%> (-52.18%)	⬇️
cwltool/update.py	37.73% <0%> (-30.19%)	⬇️
cwltool/executors.py	63.4% <0%> (-15.47%)	⬇️
cwltool/mutation.py	70% <0%> (-15%)	⬇️
cwltool/docker.py	40.78% <0%> (-14.04%)	⬇️
cwltool/load_tool.py	71.28% <0%> (-12.88%)	⬇️
cwltool/argparser.py	76.3% <0%> (-9.48%)	⬇️
cwltool/factory.py	85.36% <0%> (-7.32%)	⬇️
... and 9 more

---

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[codecov]

Codecov Report

Merging #1045 into master will increase coverage by 5.69%.
The diff coverage is 66.66%.

@@            Coverage Diff             @@
##           master    #1045      +/-   ##
==========================================
+ Coverage   73.33%   79.03%   +5.69%     
==========================================
  Files          34       30       -4     
  Lines        6855     6033     -822     
  Branches     1743     1496     -247     
==========================================
- Hits         5027     4768     -259     
+ Misses       1296      885     -411     
+ Partials      532      380     -152

Impacted Files	Coverage Δ
cwltool/job.py	67.17% <66.66%> (+3.41%)	⬆️
cwltool/resolver.py	43.47% <0%> (-33.58%)	⬇️
cwltool/update.py	67.92% <0%> (-18.25%)	⬇️
cwltool/pack.py	83.75% <0%> (-0.11%)	⬇️
cwltool/context.py	97.29% <0%> (-0.05%)	⬇️
cwltool/__main__.py
cwltool/flatten.py
cwltool/main.py
cwltool/utils.py
cwltool/provenance.py	80.44% <0%> (+0.06%)	⬆️
... and 16 more

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[mr-c]

We need to fix the source of these root owned files, not ignore them and clutter the user's storage system.

$ cwltool stage_array_in_dir.cwl --infiles README.rst --infiles CODE_OF_CONDUCT.md 
/home/michael/cwltool/env3/bin/cwltool 1.0.20181221153915
Resolved 'stage_array_in_dir.cwl' to 'file:///home/michael/cwltool/stage_array_in_dir.cwl'
[job stage_array_in_dir.cwl] /tmp/4zbs2e73$ docker \
    run \
    -i \
    --volume=/tmp/4zbs2e73:/AYRcZJ:rw \
    --volume=/tmp/gar1cr_9:/tmp:rw \
    --volume=/home/michael/cwltool/README.rst:/AYRcZJ/staged/README.rst:ro \
    --volume=/home/michael/cwltool/CODE_OF_CONDUCT.md:/AYRcZJ/staged/CODE_OF_CONDUCT.md:ro \
    --workdir=/AYRcZJ \
    --read-only=true \
    --user=1000:1000 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/AYRcZJ \
    --cidfile=/tmp/f9ahyhbr/20190422184929-544639.cid \
    debian:stretch-slim \
    ls \
    staged
CODE_OF_CONDUCT.md
README.rst
[job stage_array_in_dir.cwl] Max memory used: 0MiB
Exception while running job
Traceback (most recent call last):
  File "/home/michael/cwltool/cwltool/job.py", line 333, in _execute
    inplace_update=self.inplace_update)
  File "/home/michael/cwltool/cwltool/job.py", line 148, in relink_initialworkdir
    os.remove(host_outdir_tgt)
PermissionError: [Errno 13] Permission denied: '/tmp/4zbs2e73/staged/README.rst'
[job stage_array_in_dir.cwl] completed permanentFail
{}
Final process status is permanentFail
(env3) michael@debian:~/cwltool$ ls -la /tmp/4zbs2e73/staged/
total 8
drwxr-xr-x 2 root    root    4096 Apr 22 18:49 .
drwx------ 3 michael michael 4096 Apr 22 18:49 ..
-rwxr-xr-x 1 root    root       0 Apr 22 18:49 CODE_OF_CONDUCT.md
-rwxr-xr-x 1 root    root       0 Apr 22 18:49 README.rst

[alexiswl]

We need to fix the source of these root owned files, not ignore them and clutter the user's storage system.

I don't think the source of the files are necessarily the issues, but the way that they're mounted on docker.

I have a quite complicated tool where I mount files through a listing and also use a complex js to set the input value for a schema

The docker command becomes as follows:

docker \
    run \
    -i \
    --mount=type=bind,source=/tmp/6if0my13,target=/SdfLVG \
    --mount=type=bind,source=/tmp/5prz__i8,target=/tmp \
    --mount=type=bind,source=/tmp/tmp.IylnrvsNFw/outputs/analysis_outputs/AlignCollapseFusionCaller/0pt2pctDragonMixv2_DNA_rep1,target=/SdfLVG/var/lib/cwl/stgf373ef55-5da0-4f9d-98bc-80b9b425ec15/0pt2pctDragonMixv2_DNA_rep1,readonly \
    --mount=type=bind,source=/tmp/tmp.IylnrvsNFw/outputs/analysis_outputs/StitchedRealigned/0pt2pctDragonMixv2_DNA_rep1,target=/SdfLVG/var/lib/cwl/stgbb136a5c-43aa-4dfd-877e-d41dc9141857/0pt2pctDragonMixv2_DNA_rep1,readonly \
    --mount=type=bind,source=/tmp/tmp.IylnrvsNFw/outputs/analysis_outputs/MergedAnnotation/0pt2pctDragonMixv2_DNA_rep1,target=/SdfLVG/var/lib/cwl/stg1780b2a0-cf8f-4350-95ee-be7c835e6eb1/0pt2pctDragonMixv2_DNA_rep1,readonly \
    --mount=type=bind,source=/tmp/s9py_pdm/0pt2pctDragonMixv2_DNA_rep1_Failed_Exon_coverage_QC.txt,target=/SdfLVG/var/lib/cwl/stg80f1ea23-73fd-4d1d-8739-3db9c101435f/0pt2pctDragonMixv2_DNA_rep1_Failed_Exon_coverage_QC.txt,readonly \
    --mount=type=bind,source=/tmp/jwzg252o/0pt2pctDragonMixv2_DNA_rep1.AlignCollapseFusionCaller_metrics.json.gz,target=/SdfLVG/var/lib/cwl/stgd48ad50b-7b59-4e5b-96b4-3d27825cd6d7/0pt2pctDragonMixv2_DNA_rep1.AlignCollapseFusionCaller_metrics.json.gz,readonly \
    --mount=type=bind,source=/tmp/sr5gxf0v/0pt2pctDragonMixv2_DNA_rep1.tar.gz,target=/SdfLVG/var/lib/cwl/stg2dfd35aa-f1f9-44de-bdd1-5b29c4f6dff7/0pt2pctDragonMixv2_DNA_rep1.tar.gz,readonly \
    --mount=type=bind,source=/tmp/gsq7uj8a/0pt2pctDragonMixv2_DNA_rep1.tar.gz,target=/SdfLVG/var/lib/cwl/stgabc1fa11-b3b1-46b2-ab64-baab8eadfde7/0pt2pctDragonMixv2_DNA_rep1.tar.gz,readonly \
    --mount=type=bind,source=/tmp/ufymeqhv/0pt2pctDragonMixv2_DNA_rep1.tar.gz,target=/SdfLVG/var/lib/cwl/stgc608e7c4-8447-481a-85cc-a0e7234b0570/0pt2pctDragonMixv2_DNA_rep1.tar.gz,readonly \
    --workdir=/SdfLVG \
    --read-only=true \
    --net=none \
    --user=1000:1000 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/SdfLVG \
    --cidfile=/tmp/igt9ibcg/20210810170514-913731.cid \
    umccr/alpine-pandas:1.2.2 \
    python \
    create-output-dir.py \
    '--custom-output-dir-entry={"copy_method":"copy_method","dir":"/SdfLVG/var/lib/cwl/stgf373ef55-5da0-4f9d-98bc-80b9b425ec15/0pt2pctDragonMixv2_DNA_rep1","files_list_str":["0pt2pctDragonMixv2_DNA_rep1.bam","0pt2pctDragonMixv2_DNA_rep1.bam.bai","0pt2pctDragonMixv2_DNA_rep1.bam.md5sum","evidence.0pt2pctDragonMixv2_DNA_rep1.bam","evidence.0pt2pctDragonMixv2_DNA_rep1.bam.bai"]}' \
    --output-directory-name \
    0pt2pctDragonMixv2_DNA_rep1 \
    '--custom-output-dir-entry={"copy_method":"copy_method","dir":"/SdfLVG/var/lib/cwl/stgbb136a5c-43aa-4dfd-877e-d41dc9141857/0pt2pctDragonMixv2_DNA_rep1","files_list_str":["0pt2pctDragonMixv2_DNA_rep1.stitched.bam","0pt2pctDragonMixv2_DNA_rep1.stitched.bam.bai"]}' \
    '--custom-output-dir-entry={"copy_method":"copy_method","dir":"/SdfLVG/var/lib/cwl/stg1780b2a0-cf8f-4350-95ee-be7c835e6eb1/0pt2pctDragonMixv2_DNA_rep1","files_list_str":["0pt2pctDragonMixv2_DNA_rep1_MergedSmallVariantsAnnotated.json.gz","0pt2pctDragonMixv2_DNA_rep1_MergedSmallVariantsAnnotated.json.gz.jsi"]}' \
    '--custom-output-dir-entry={"copy_method":"copy_method","file_list":["/SdfLVG/var/lib/cwl/stg80f1ea23-73fd-4d1d-8739-3db9c101435f/0pt2pctDragonMixv2_DNA_rep1_Failed_Exon_coverage_QC.txt","/SdfLVG/var/lib/cwl/stgd48ad50b-7b59-4e5b-96b4-3d27825cd6d7/0pt2pctDragonMixv2_DNA_rep1.AlignCollapseFusionCaller_metrics.json.gz"]}' \
    '--custom-output-dir-entry={"copy_method":"copy_method","tarball":"/SdfLVG/var/lib/cwl/stg2dfd35aa-f1f9-44de-bdd1-5b29c4f6dff7/0pt2pctDragonMixv2_DNA_rep1.tar.gz"}' \
    '--custom-output-dir-entry={"copy_method":"copy_method","tarball":"/SdfLVG/var/lib/cwl/stgabc1fa11-b3b1-46b2-ab64-baab8eadfde7/0pt2pctDragonMixv2_DNA_rep1.tar.gz"}' \
    '--custom-output-dir-entry={"copy_method":"copy_method","tarball":"/SdfLVG/var/lib/cwl/stgc608e7c4-8447-481a-85cc-a0e7234b0570/0pt2pctDragonMixv2_DNA_rep1.tar.gz"}'

Looking at the 3rd mount argument:

$ ls -lsrthd /tmp/tmp.IylnrvsNFw/outputs/analysis_outputs/AlignCollapseFusionCaller/0pt2pctDragonMixv2_DNA_rep1
4.0K drwxr-xr-x 5 alexiswl alexiswl 4.0K Aug  3 10:38 /tmp/tmp.IylnrvsNFw/outputs/analysis_outputs/AlignCollapseFusionCaller/0pt2pctDragonMixv2_DNA_rep1

Looks fine to me,

However the output directory (even if its not used)

$ ls -lsrthd /tmp/6if0my13/var/lib/cwl/stgf373ef55-5da0-4f9d-98bc-80b9b425ec15/0pt2pctDragonMixv2_DNA_rep1
4.0K drwxr-xr-x 2 root root 4.0K Aug 10 17:05 /tmp/6if0my13/var/lib/cwl/stgf373ef55-5da0-4f9d-98bc-80b9b425ec15/0pt2pctDragonMixv2_DNA_rep1

I'm running docker version 20.10.7 on a WSL2 backend?

This causes the following error:

ERROR Exception while running job
Traceback (most recent call last):
  File "/home/alexiswl/anaconda3/envs/cwl-ica/lib/python3.8/site-packages/cwltool/job.py", line 404, in _execute
    relink_initialworkdir(
  File "/home/alexiswl/anaconda3/envs/cwl-ica/lib/python3.8/site-packages/cwltool/job.py", line 157, in relink_initialworkdir
    shutil.rmtree(host_outdir_tgt)
  File "/home/alexiswl/anaconda3/envs/cwl-ica/lib/python3.8/shutil.py", line 722, in rmtree
    onerror(os.rmdir, path, sys.exc_info())
  File "/home/alexiswl/anaconda3/envs/cwl-ica/lib/python3.8/shutil.py", line 720, in rmtree
    os.rmdir(path)
PermissionError: [Errno 13] Permission denied: '/tmp/6if0my13/var/lib/cwl/stgf373ef55-5da0-4f9d-98bc-80b9b425ec15/0pt2pctDragonMixv2_DNA_rep1'
WARNING [job create_output_directory] completed permanentFail
DEBUG [job create_output_directory] outputs {}
ERROR [step create_output_directory] Output is missing expected field file:///c/Users/awluc/OneDrive/GitHub/UMCCR/cwl-ica/workflows/tso500-ctdna-post-processing-pipeline/1.0.0/tso500-ctdna-post-processing-pipeline__1.0.0.cwl#tso500-ctdna-post-processing-pipeline--1.0.0/create_output_directory/output_directory
DEBUG [step create_output_directory] produced output {}
WARNING [step create_output_directory] completed permanentFail
INFO [workflow ] completed permanentFail
DEBUG [workflow ] outputs {
    "post_processing_output_directory": null
}
DEBUG [job create_output_directory] Removing input staging directory /tmp/0j14kt6s
DEBUG [job create_output_directory] Removing temporary directory /tmp/5prz__i8
{
    "post_processing_output_directory": null
}
WARNING Final process status is permanentFail