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hotfix to ensure sample-names are always strings #49

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merged 8 commits into from
Apr 19, 2023
Merged

hotfix to ensure sample-names are always strings #49

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56b13c7
hotfix to ensure sample-names are always strings
charles-cowart Apr 12, 2023
29781c4
Testing updates to code-coverage
charles-cowart Apr 12, 2023
486832d
Fix test_klp test
charles-cowart Apr 13, 2023
b7123b0
test
charles-cowart Apr 13, 2023
9f21702
test
charles-cowart Apr 13, 2023
44bef64
remove assertion
charles-cowart Apr 17, 2023
c85dc7f
Remove CI debugging stmt. Issue was w/Qiita.
charles-cowart Apr 18, 2023
3625127
regression-test added.
charles-cowart Apr 19, 2023
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4 changes: 2 additions & 2 deletions .github/workflows/qiita-plugin-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ jobs:
conda config --add channels conda-forge
conda create -q --yes -n qiita python=3.9 libgfortran numpy nginx cython redis
conda activate qiita
pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click
pip install sphinx sphinx-bootstrap-theme nose-timer Click

- name: Qiita install
shell: bash -l {0}
Expand Down Expand Up @@ -137,7 +137,7 @@ jobs:

nosetests --with-doctest --with-coverage -v --cover-package=qp_klp

- uses: codecov/codecov-action@v1
- uses: codecov/codecov-action@v3
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: codecov.yml
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10 changes: 8 additions & 2 deletions qp_klp/process_amplicon_job.py
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Expand Up @@ -306,9 +306,15 @@ def process_amplicon(mapping_file_path, qclient, run_identifier, out_dir,
for study_id in gpf_job.prep_file_paths:
for prep_file_path in gpf_job.prep_file_paths[study_id]:
metadata = pd.read_csv(prep_file_path,
dtype=str,
delimiter='\t',
index_col='sample_name').to_dict(
'index')
index_col='sample_name')
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index_col does not interact as expected with dtype. This will still incur a type conversion. Converting it to str after the fact is lossy. Please set remove, and set an explicit index with set_index after parse

>>> df = pd.read_csv('clinical_metadata_formatted.tsv', sep='\t', dtype=str, index_col='sample-id')
>>> df.index[:5]
Float64Index([10317.000106498, 10317.000107092, 10317.000106499,
              10317.000107093, 10317.000106684],
             dtype='float64', name='sample-id')

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@wasade I can see it - it didn't happen in the case that spawned this hot fix but in general if the index column gets interpreted as a numeric directly instead of getting casted to string first with the other columns before then being converted when it becomes the index, you would get potential data loss.

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I think we're in agreement. Please do not allow the index column to be cast to numeric.


# force sample_names (index) to be of type string.
metadata.index = metadata.index.map(str)
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# convert to standard dictionary.
metadata = metadata.to_dict('index')

# determine data_type based on target_gene column.
target_gene = metadata[list(metadata.keys())[0]]['target_gene']
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9 changes: 6 additions & 3 deletions qp_klp/process_metagenomics_job.py
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Expand Up @@ -287,13 +287,16 @@ def process_metagenomics(sample_sheet_path, lane_number, qclient,
for study_id in gpf_job.prep_file_paths:
for prep_file_path in gpf_job.prep_file_paths[study_id]:
metadata = pd.read_csv(prep_file_path,
dtype=str,
delimiter='\t',
index_col='sample_name').to_dict(
'index')
index_col='sample_name')
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# force sample_names (index) to be of type string.
metadata.index = metadata.index.map(str)
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# determine data_type based on sample-sheet
# value will be from the Assay field
data = {'prep_info': dumps(metadata),
data = {'prep_info': dumps(metadata.to_dict('index')),
'study': study_id,
'data_type': assay_type}

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2 changes: 1 addition & 1 deletion qp_klp/tests/test_klp.py
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Expand Up @@ -129,7 +129,7 @@ def setUp(self):
"Date,2/26/20,,,,,,,,,\n",
"Workflow,GenerateFASTQ,,,,,,,,,\n",
"Application,FASTQ Only,,,,,,,,,\n",
"Assay,Metagenomics,,,,,,,,,\n",
"Assay,Metagenomic,,,,,,,,,\n",
"Description,,,,,,,,,,\n",
"Chemistry,Default,,,,,,,,,\n",
",,,,,,,,,,\n",
Expand Down