[Debian-med-packaging] Bug#974178: python3-biom-format: debci tests fail: Object of type bytes is not JSON serializable

Sat Nov 21 13:11:47 GMT 2020

Hi,

On Wed, 11 Nov 2020 11:56:10 +0800 Drew Parsons <dparsons at debian.org> wrote:
> Package: python3-biom-format
> Version: 2.1.9-2
> Severity: normal
>
> debci tests for python3-biom-format are show test error triggered by
> python3-h5py 3.1.0-1exp1 from experimental.
>
> The odd thing is that the error trace does not directly refer to h5py,
> it's a json problem:
>
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/biom/assets/exercise_api.py",
line 95, in <module>
> out.write(table.to_json('rc-testing'))
> File "/usr/lib/python3/dist-packages/biom/table.py", line 4720, in to_json
> dumps(samp[1]), dumps(samp[2])))
> File "/usr/lib/python3.8/json/__init__.py", line 231, in dumps
> return _default_encoder.encode(obj)
> File "/usr/lib/python3.8/json/encoder.py", line 199, in encode
> chunks = self.iterencode(o, _one_shot=True)
> File "/usr/lib/python3.8/json/encoder.py", line 257, in iterencode
> return _iterencode(o, 0)
> File "/usr/lib/python3.8/json/encoder.py", line 179, in default
> raise TypeError(f'Object of type {o.__class__.__name__} '
> TypeError: Object of type bytes is not JSON serializable
>

Thanks for this bug report!

Just uploaded a new upstream revision for python-biom-format, the
autopkgtests seem fine locally now:

autopkgtest [13:08:06]: test run-unit-test: [-----------------------

System information
==================
         Platform:    linux
   Python version:    3.9.0+ (default, Oct 19 2020, 09:51:18)  [GCC 10.2.0]
Python executable:    /usr/bin/python3

Dependency versions
===================
click version:    7.1.2
NumPy version:    1.19.4
SciPy version:    1.5.3
 h5py version:    3.1.0

biom-format package information
===============================
biom-format version:    2.1.10

The input file is a valid BIOM-formatted file.

The input file is a valid BIOM-formatted file.
+ table=examples/min_sparse_otu_table_hdf5.biom
+ obsmd=examples/obs_md.txt
+ [ ! -f examples/min_sparse_otu_table_hdf5.biom ]
+ biom show-install-info

System information
==================
         Platform:    linux
   Python version:    3.9.0+ (default, Oct 19 2020, 09:51:18)  [GCC 10.2.0]
Python executable:    /usr/bin/python3

Dependency versions
===================
click version:    7.1.2
NumPy version:    1.19.4
SciPy version:    1.5.3
 h5py version:    3.1.0

biom-format package information
===============================
biom-format version:    2.1.10

+ biom validate-table -i examples/min_sparse_otu_table_hdf5.biom

The input file is a valid BIOM-formatted file.
+ biom add-metadata -i examples/min_sparse_otu_table_hdf5.biom -o
test_add_metadata.biom --observation-metadata-fp examples/obs_md.txt
--sc-separated taxonomy
+ biom convert -i examples/min_sparse_otu_table_hdf5.biom -o
test_json.biom --to-json
+ biom convert -i examples/min_sparse_otu_table_hdf5.biom -o
test_tsv.txt --to-tsv
+ biom validate-table -i test_json.biom

The input file is a valid BIOM-formatted file.
+ biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5
+ biom validate-table -i test_hdf5.biom

The input file is a valid BIOM-formatted file.
+ biom convert -i test_json.biom -o test_tsv.txt --to-tsv
+ biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type
OTU table
+ biom validate-table -i test_hdf5.biom

The input file is a valid BIOM-formatted file.
+ biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type
OTU table
+ biom validate-table -i test_json.biom

The input file is a valid BIOM-formatted file.
+ biom head -i examples/min_sparse_otu_table_hdf5.biom
# Constructed from biom file
#OTU ID    Sample1    Sample2    Sample3    Sample4    Sample5
GG_OTU_1    0.0    0.0    1.0    0.0    0.0
GG_OTU_2    5.0    1.0    0.0    2.0    3.0
GG_OTU_3    0.0    0.0    1.0    4.0    0.0
GG_OTU_4    2.0    1.0    1.0    0.0    0.0
GG_OTU_5    0.0    1.0    1.0    0.0    0.0
+ biom table-ids -i examples/min_sparse_otu_table_hdf5.biom
Sample1
Sample2
Sample3
Sample4
Sample5
Sample6
+ biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o
test_norm.biom -p
+ cat
+ biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o
test_subset.biom -a observation -s ids.txt
/usr/lib/python3/dist-packages/biom/table.py:4077: FutureWarning: arrays
to stack must be passed as a "sequence" type such as list or tuple.
Support for non-sequence iterables such as generators is deprecated as
of NumPy 1.16 and will raise an error in the future.
  data = np.hstack(h5_data[start:end]
/usr/lib/python3/dist-packages/biom/table.py:4079: FutureWarning: arrays
to stack must be passed as a "sequence" type such as list or tuple.
Support for non-sequence iterables such as generators is deprecated as
of NumPy 1.16 and will raise an error in the future.
  indices = np.hstack(h5_indices[start:end]
+ biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom
Num samples: 6
Num observations: 5
Total count: 27
Table density (fraction of non-zero values): 0.500

Counts/sample summary:
 Min: 3.000
 Max: 7.000
 Median: 4.000
 Mean: 4.500
 Std. dev.: 1.500
 Sample Metadata Categories: None provided
 Observation Metadata Categories: None provided

Counts/sample detail:
Sample2: 3.000
Sample5: 3.000
Sample3: 4.000
Sample6: 4.000
Sample4: 6.000
Sample1: 7.000
+ cat
+ biom from-uc -i uctest -o test_uc.biom
+ echo If this message was shown, then all commands executed without failure
If this message was shown, then all commands executed without failure
autopkgtest [13:08:27]: test run-unit-test: -----------------------]
autopkgtest [13:08:27]: test run-unit-test:  - - - - - - - - - - results
- - - - - - - - - -
run-unit-test        PASS
autopkgtest [13:08:27]: test autodep8-python3: preparing testbed

But lets wait for debci results

Regards,
Nilesh