croo fails on atac-seq-pipeline output

[ro-joshi]

OS/Platform and dependencies

• OS or Platform: SCG cluster
• Conda version: conda 4.7.12
• Caper version 0.5.1
• Croo version 0.2.0

Describe the bug After successfully running the atac-seq-pipeline, croo metadata.json (also croo metadata.json --out-def-json ~/repos/atac-seq-pipeline/atac.croo.json) fails with:

[CaperURI] symlinking from local to local, src: /N/projects/curtis/rohan/processed-TCGA-ATAC/atac/278c3788-f103-4cf1-8f13-c96f669cbc42/call-jsd/execution/glob-fc36854b6867c1581ab159b09dd7e2f4/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.jsd_plot.png
[CaperURI] symlinking skipped, target: /N/projects/curtis/rohan/processed-TCGA-ATAC/atac/278c3788-f103-4cf1-8f13-c96f669cbc42/qc/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.jsd_plot.png
Traceback (most recent call last):
  File "/N/users/rojoshi/anaconda3/envs/encode-atac-seq-pipeline/bin/croo", line 13, in <module>
    main()
  File "/N/users/rojoshi/anaconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 240, in main
    co.organize_output()
  File "/N/users/rojoshi/anaconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 112, in organize_output
    target_url = CaperURI(target_uri).get_url()
  File "/N/users/rojoshi/anaconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/caper/caper_uri.py", line 285, in get_url
    return self.get_file(uri_type=URI_URL, no_copy=True)
  File "/N/users/rojoshi/anaconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/caper/caper_uri.py", line 290, in get_file
    return self.copy(target_uri_type=uri_type, no_copy=no_copy)
  File "/N/users/rojoshi/anaconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/caper/caper_uri.py", line 324, in copy
    path = self.__get_url()
  File "/N/users/rojoshi/anaconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/caper/caper_uri.py", line 668, in __get_url
    path=self._uri))
NotImplementedError: Cannot find a mapping from path to URL in MAPPING_PATH_TO_URL for path /N/projects/curtis/rohan/processed-TCGA-ATAC/atac/278c3788-f103-4cf1-8f13-c96f669cbc42/qc/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.jsd_plot.png

[leepc12]

Just fixed and uploaded to PyPI. It will take several minutes for the pip repo to be updated.

$ pip install croo==0.2.1

[ro-joshi]

Thanks