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con / opfvta-reexecution

Container-based Replication of https://doi.org/10.1038/s41398-022-01812-5
Apache License 2.0
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OCI Image failing #68

Closed TheChymera closed 7 months ago

TheChymera commented 7 months ago

Any idea why this could be happening?

[deco]~/docsrc/opfvta-reexecution ❱ make analysis-oci OCI_BINARY=podman
Makefile:126: warning: overriding recipe for target 'article-upload'
Makefile:122: warning: ignoring old recipe for target 'article-upload'
podman run \
    -it \
    --rm \
    -v /home/chymera/docsrc/opfvta-reexecution:/opt \
    -v /home/chymera/docsrc/opfvta-reexecution/inputs/opfvta_bidsdata:/usr/share/opfvta_bidsdata \
    -v /home/chymera/docsrc/opfvta-reexecution/inputs/mouse-brain-templates/mouse-brain-templates:/usr/share/mouse_brain_atlases \
    -v /home/chymera/docsrc/opfvta-reexecution/scratch:/root/.scratch \
    -v /home/chymera/docsrc/opfvta-reexecution/code/empty:/opfvta/ \
    --workdir /opt/code \
    docker.io/centerforopenneuroscience/opfvta:2.0.0-alpha \
    ./produce-analysis.sh podman
Trying to pull docker.io/centerforopenneuroscience/opfvta:2.0.0-alpha...
Getting image source signatures
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Writing manifest to image destination
/opt/code/opfvta /opt/code
rubber --clean article.tex
removing tree pythontex-files-article
removing tree pythontex-files-article
rm _minted-article -rf
rubber --clean pitch.tex
removing tree pythontex-files-pitch
removing tree pythontex-files-pitch
rm _minted-pitch -rf
rubber --clean review.tex
removing tree pythontex-files-review
rm _minted-review -rf
pushd prepare && ./run.sh
/opt/code/opfvta/prepare /opt/code/opfvta
!!! Repository 'gentoo' has sync-uri attribute, but is missing sync-type attribute
Failed to import duecredit due to No module named 'duecredit'
/usr/lib/python3.10/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
/usr/lib/python3.10/site-packages/bids/layout/bids_layout.py:116: UserWarning: 'dataset_description.json' file is missing from project root. You may want to set the root path to a valid BIDS project.
  warnings.warn("'dataset_description.json' file is missing from "
Traceback (most recent call last):
  File "/opt/code/opfvta/prepare/preprocess.py", line 17, in <module>
    generic(bids_base,
  File "/usr/lib/python3.10/site-packages/samri/pipelines/preprocess.py", line 392, in generic
    bids_base, out_base, out_dir, template, registration_mask, data_selection, functional_scan_types, structural_scan_types, subjects_sessions, func_ind, struct_ind = common_select(
  File "/usr/lib/python3.10/site-packages/samri/pipelines/preprocess.py", line 734, in common_select
    data_selection = bids_data_selection(bids_base, structural_match, functional_match, subjects, sessions)
  File "/usr/lib/python3.10/site-packages/samri/pipelines/utils.py", line 240, in bids_data_selection
    df = df[~df.path.str.contains(base + ".*/\.")]
  File "/usr/lib/python3.10/site-packages/pandas/core/generic.py", line 5902, in __getattr__
    return object.__getattribute__(self, name)
  File "/usr/lib/python3.10/site-packages/pandas/core/accessor.py", line 182, in __get__
    accessor_obj = self._accessor(obj)
  File "/usr/lib/python3.10/site-packages/pandas/core/strings/accessor.py", line 181, in __init__
    self._inferred_dtype = self._validate(data)
  File "/usr/lib/python3.10/site-packages/pandas/core/strings/accessor.py", line 235, in _validate
    raise AttributeError("Can only use .str accessor with string values!")
AttributeError: Can only use .str accessor with string values!. Did you mean: 'std'?
make: *** [Makefile:55: data] Error 1
make: *** [Makefile:76: analysis-oci] Error 2
yarikoptic commented 7 months ago
in a repo I found on laptop - it didn't fail ```shell removing tree pythontex-files-review rm _minted-review -rf pushd prepare && ./run.sh /opt/code/opfvta/prepare /opt/code/opfvta !!! Repository 'gentoo' has sync-uri attribute, but is missing sync-type attribute Failed to import duecredit due to No module named 'duecredit' /usr/lib/python3.10/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8 warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:283: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:296: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) /usr/lib/python3.10/site-packages/samri/pipelines/utils.py:335: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. res_df = res_df.append(_df) path modality subject session ... acq run type scan_type 1917 /root/.scratch/opfvta/bids/sub-6257/ses-ofM/fu... cbv 6257 ofM ... EPI 0 func 1915 /root/.scratch/opfvta/bids/sub-6257/ses-ofM/an... T2w 6257 ofM ... TurboRARE NaN anat 1923 /root/.scratch/opfvta/bids/sub-6259/ses-ofM/fu... cbv 6259 ofM ... EPI 0 func 1928 /root/.scratch/opfvta/bids/sub-6259/ses-ofMr1/... cbv 6259 ofMr1 ... EPI 1 func 1931 /root/.scratch/opfvta/bids/sub-6259/ses-ofMr1/... cbv 6259 ofMr1 ... EPI 0 func ... ... ... ... ... ... ... ... ... ... 2220 /root/.scratch/opfvta/bids/sub-6654/ses-ofMr1/... T2w 6654 ofMr1 ... TurboRARE NaN anat 2228 /root/.scratch/opfvta/bids/sub-6655/ses-ofM/fu... cbv 6655 ofM ... EPI 0 func 2233 /root/.scratch/opfvta/bids/sub-6655/ses-ofMr1/... cbv 6655 ofMr1 ... EPI 0 func 2226 /root/.scratch/opfvta/bids/sub-6655/ses-ofM/an... T2w 6655 ofM ... TurboRARE NaN anat ```

and it lacked 

/usr/lib/python3.10/site-packages/bids/layout/bids_layout.py:116: UserWarning: 'dataset_description.json' file is missing from project root. You may want to set the root path to a valid BIDS project.
  warnings.warn("'dataset_description.json' file is missing from "

so possible I have some dataset_description.json you don't have... but I see only ./inputs/opfvta_bidsdata/dataset_description.json and I have it and I guess you do too? if not -- did you install subdatasets? (we discovered that gettting that data gets only atlas, not bids data)...

TheChymera commented 7 months ago

This seems to be triggered by failing to download the data. Pretty cryptic error message.