✨ Add Sample Concept #683
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✨ Add Sample Concept #683
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kf_lib_data_ingest/target_api_plugins/kids_first_dataservice.py
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| @@ -429,6 +429,79 @@ def submit(cls, host, body): | |||
| return submit(host, cls, body) | |||
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| class Sample: | |||
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Maybe we should add a class docstring that explains BIOSPECIMEN_GROUP was a previously existing concept that has been used in ingest packages and that's why some fields (external_id) in the Biospecimen and/or Sample class first extract from SAMPLE and then secondarily extract from BIOSPECIMEN_GROUP
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Tests might be failing bc you also have to add |
kf_lib_data_ingest/target_api_plugins/kids_first_dataservice.py
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do you mean in all_targets? it's there :) |
znatty22
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🚨 Don't mess up formmatting 🚨 Don't mess up formmatting point to sample when building sample key concept 🐛 Add submit function to sample
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🚧 Working on documentation for samples and biospecimens 📝 Document samples and specimens 🔥 Remove test text 🚨 Enable black linting 📝 re-word docs for better clarity Co-authored-by: Natasha Singh <[email protected]> Update docs/source/design/concepts/samples_and_specimens.rst Co-authored-by: Natasha Singh <[email protected]> Update docs/source/design/concepts/samples_and_specimens.rst Co-authored-by: Natasha Singh <[email protected]> Update docs/source/design/concepts/samples_and_specimens.rst Co-authored-by: Natasha Singh <[email protected]> Update docs/source/design/concepts/samples_and_specimens.rst Co-authored-by: Natasha Singh <[email protected]> Update docs/source/design/concepts/samples_and_specimens.rst Co-authored-by: Natasha Singh <[email protected]> Update docs/source/design/concepts/index.rst Co-authored-by: Natasha Singh <[email protected]> 🚨 Keep docs under 80 character line length 🚨 Documentation line length
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## Release 1.21.0 ### Summary - Emojis: ✨ x2, ? x2 - Categories: Additions x2, Other Changes x2 ### New features and changes - [#686](#686) - ✨ D3B-586 sample relationship - [7cb601c](7cb601c) by [chris-s-friedman](https://github.com/chris-s-friedman) - [#683](#683) - ✨ Add Sample Concept - [026ed61](026ed61) by [chris-s-friedman](https://github.com/chris-s-friedman) - [#684](#684) - 🔧 add ucsf center - [469d097](469d097) by [HuangXiaoyan0106](https://github.com/HuangXiaoyan0106) - [#680](#680) - 📝 add Variantyx sequencer - [8ccf9ec](8ccf9ec) by [HuangXiaoyan0106](https://github.com/HuangXiaoyan0106)
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Add Concept for Sample
This PR adds the concept for Sample. The approach for adding sample is to give it many of the same entities of biospecimen that make sense, such as shipping information, volume, etc and then make sample a parent to biospecimen, to indicate the relationship between biospecimen and sample. In the kf target api config, biospecimen and sample may be used interchangeable with preference given towards the sample entry.
Documentation for concepts is also added to the documentation site.