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Reformat example data away from frictionless #110

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Nov 12, 2024
Merged

Reformat example data away from frictionless #110

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32cbb20
Reformat test data & update author
ebolyen Nov 8, 2024
37e1dc9
remove frictionless
ebolyen Nov 8, 2024
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1 change: 0 additions & 1 deletion environment-files/2024.10-q2-fmt-environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,4 +7,3 @@ dependencies:
- pip
- pip:
- q2-fmt@git+https://github.com/qiime2/q2-fmt.git@dev
- frictionless
1 change: 0 additions & 1 deletion environment-files/development-q2-fmt-environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,4 +7,3 @@ dependencies:
- pip
- pip:
- q2-fmt@git+https://github.com/qiime2/q2-fmt.git@dev
- frictionless
1 change: 0 additions & 1 deletion environment-files/q2-fmt-qiime2-amplicon-2024.10.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,4 +7,3 @@ dependencies:
- pip
- pip:
- q2-fmt@git+https://github.com/qiime2/q2-fmt.git@dev
- frictionless
6 changes: 1 addition & 5 deletions q2_fmt/_examples.py
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Expand Up @@ -66,13 +66,9 @@ def peds_md_factory():


def peds_dist_factory():
import pandas as pd
df = transform(_get_data_from_tests('peds_dist'),
from_type=TabularDataResourceDirFmt,
to_type=pd.DataFrame)
return qiime2.Artifact.import_data(
"Dist1D[Ordered, Matched] % Properties('peds')",
df
_get_data_from_tests('peds_dist.table.jsonl')
)


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51 changes: 26 additions & 25 deletions q2_fmt/tests/data/peds_dist/data.ndjson → q2_fmt/tests/data/peds_dist.table.jsonl
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@@ -1,25 +1,26 @@
{"id":"76575c97","measure":0.2868217054,"transfered_donor_features":37,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":1.0}
{"id":"efb2f65b","measure":0.6434108527,"transfered_donor_features":83,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":2.0}
{"id":"45d2f050","measure":0.4728682171,"transfered_donor_features":61,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":3.0}
{"id":"ed726564","measure":0.5426356589,"transfered_donor_features":70,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":4.0}
{"id":"c9e65e6b","measure":0.5968992248,"transfered_donor_features":77,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":5.0}
{"id":"32882f3f","measure":0.2325581395,"transfered_donor_features":30,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":1.0}
{"id":"702ac37a","measure":0.480620155,"transfered_donor_features":62,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":2.0}
{"id":"ec83471f","measure":0.3953488372,"transfered_donor_features":51,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":3.0}
{"id":"e9b009ec","measure":0.511627907,"transfered_donor_features":66,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":4.0}
{"id":"cd005b96","measure":0.519379845,"transfered_donor_features":67,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":5.0}
{"id":"2769cc8e","measure":0.4226190476,"transfered_donor_features":71,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":1.0}
{"id":"a04549ba","measure":0.7202380952,"transfered_donor_features":121,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":2.0}
{"id":"ea845f9c","measure":0.6845238095,"transfered_donor_features":115,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":3.0}
{"id":"d1c602df","measure":0.7083333333,"transfered_donor_features":119,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":4.0}
{"id":"743793ec","measure":0.7321428571,"transfered_donor_features":123,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":5.0}
{"id":"8ea7fa9e","measure":0.4341085271,"transfered_donor_features":56,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":1.0}
{"id":"d1a7bf51","measure":0.6356589147,"transfered_donor_features":82,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":2.0}
{"id":"df976735","measure":0.4263565891,"transfered_donor_features":55,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":3.0}
{"id":"2028a351","measure":0.5581395349,"transfered_donor_features":72,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":4.0}
{"id":"a628cc67","measure":0.5968992248,"transfered_donor_features":77,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":5.0}
{"id":"f88f3e2c","measure":0.4418604651,"transfered_donor_features":57,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":1.0}
{"id":"3597719a","measure":0.3643410853,"transfered_donor_features":47,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":2.0}
{"id":"baafb929","measure":0.5348837209,"transfered_donor_features":69,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":3.0}
{"id":"dd9369b1","measure":0.503875969,"transfered_donor_features":65,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":4.0}
{"id":"e868515c","measure":0.5658914729,"transfered_donor_features":73,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":5.0}
{"doctype":{"name":"table.jsonl","format":"application/x-json-lines","version":"1.0"},"direction":"row","style":"key:value","fields":[{"name":"id","type":"string","missing":false,"title":"Sample ID","description":"Sample IDs","extra":{"name":"id"}},{"name":"measure","type":"number","missing":false,"title":"Sample PEDS","description":"Proportional Engraftment of Donor Strains","extra":{"name":"measure"}},{"name":"transfered_donor_features","type":"integer","missing":false,"title":"Transfered Reference Features","description":"...","extra":{"name":"transfered_donor_features"}},{"name":"total_donor_features","type":"integer","missing":false,"title":"Total Reference Features","description":"...","extra":{"name":"total_donor_features"}},{"name":"donor","type":"string","missing":false,"title":"Donor","description":"Donor","extra":{"name":"donor"}},{"name":"subject","type":"string","missing":false,"title":"SubjectID","description":"Subject IDs linking samples across time","extra":{"name":"subject"}},{"name":"group","type":"integer","missing":false,"title":"time_point","description":"Time","extra":{"name":"group"}}],"index":[],"title":"","description":"","extra":{}}
{"id":"76575c97","measure":0.2868217054,"transfered_donor_features":37,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":1}
{"id":"efb2f65b","measure":0.6434108527,"transfered_donor_features":83,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":2}
{"id":"45d2f050","measure":0.4728682171,"transfered_donor_features":61,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":3}
{"id":"ed726564","measure":0.5426356589,"transfered_donor_features":70,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":4}
{"id":"c9e65e6b","measure":0.5968992248,"transfered_donor_features":77,"total_donor_features":129,"donor":"a74441b7","subject":"s1","group":5}
{"id":"32882f3f","measure":0.2325581395,"transfered_donor_features":30,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":1}
{"id":"702ac37a","measure":0.480620155,"transfered_donor_features":62,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":2}
{"id":"ec83471f","measure":0.3953488372,"transfered_donor_features":51,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":3}
{"id":"e9b009ec","measure":0.511627907,"transfered_donor_features":66,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":4}
{"id":"cd005b96","measure":0.519379845,"transfered_donor_features":67,"total_donor_features":129,"donor":"a74441b7","subject":"s2","group":5}
{"id":"2769cc8e","measure":0.4226190476,"transfered_donor_features":71,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":1}
{"id":"a04549ba","measure":0.7202380952,"transfered_donor_features":121,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":2}
{"id":"ea845f9c","measure":0.6845238095,"transfered_donor_features":115,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":3}
{"id":"d1c602df","measure":0.7083333333,"transfered_donor_features":119,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":4}
{"id":"743793ec","measure":0.7321428571,"transfered_donor_features":123,"total_donor_features":168,"donor":"cfd4c979","subject":"s3","group":5}
{"id":"8ea7fa9e","measure":0.4341085271,"transfered_donor_features":56,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":1}
{"id":"d1a7bf51","measure":0.6356589147,"transfered_donor_features":82,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":2}
{"id":"df976735","measure":0.4263565891,"transfered_donor_features":55,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":3}
{"id":"2028a351","measure":0.5581395349,"transfered_donor_features":72,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":4}
{"id":"a628cc67","measure":0.5968992248,"transfered_donor_features":77,"total_donor_features":129,"donor":"a74441b7","subject":"s4","group":5}
{"id":"f88f3e2c","measure":0.4418604651,"transfered_donor_features":57,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":1}
{"id":"3597719a","measure":0.3643410853,"transfered_donor_features":47,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":2}
{"id":"baafb929","measure":0.5348837209,"transfered_donor_features":69,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":3}
{"id":"dd9369b1","measure":0.503875969,"transfered_donor_features":65,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":4}
{"id":"e868515c","measure":0.5658914729,"transfered_donor_features":73,"total_donor_features":129,"donor":"a74441b7","subject":"s5","group":5}
51 changes: 0 additions & 51 deletions q2_fmt/tests/data/peds_dist/dataresource.json
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6 changes: 3 additions & 3 deletions setup.py
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Expand Up @@ -18,11 +18,11 @@
'q2_fmt': [
'assets/*',
'citations.bib'],
'q2_fmt.tests': ['data/*', 'data/peds_dist/*'],
'q2_fmt.tests': ['data/*'],

},
author='Liz Gehret',
author_email='elizabeth.gehret@nau.edu',
author='Chloe Herman',
author_email='crh423@nau.edu',
description='QIIME 2 Plugin used for FMT analyses.',
license='BSD-3-Clause',
url='https://github.com/qiime2/q2-fmt',
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