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python3 -m venv .venv source .venv/bin/activate python3 -m pip install schematicpy |
Setup Python Environment
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pyenv install 3.10.11
pyenv virtualenv 3.10.11 schematic_3_10_11
pyenv activate schematic_3_10_11
pyenv -m pip install schematic_3_10_11
pip install schematicpy |
Edit Configuration
The following parameters need to be set in the config.yml:
https://github.com/Sage-Bionetworks/schematic/blob/develop/config.yml
Initalize
schematic init -c ~/GitHub/schematic/config.yml
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Command Line Reference
https://sage-schematic.readthedocs.io/en/develop/cli_reference.html
Need to run commands from ~/schematic
Data Model
Summary
A data model defines attributes (i.e. data elements) describing metadata associated with any given dataset type. The data model also describes relationships between these attributes.
Documentation
/wiki/spaces/SCHEM/pages/2473623559
Build a Data Model
The data model is defined in a table, then stored (i.e. serialized) in a JSON-LD schema.
The JSON-LD schema follows the Schema.org way of specifying attributes
/wiki/spaces/SCHEM/pages/2453176326/2967568387
https://linkml.io/linkml/intro/tutorial.html
https://docs.google.com/spreadsheets/d/1vDdcqt3Lgehyq1iCnlF1H9JZi63pLj-u/edit#gid=1939820452
https://portal.includedcc.org/dashboard
https://linkml.io/schemasheets/#examples
https://docs.google.com/spreadsheets/d/1w6zDfz3_yrCjjrqfpXBGNmd0LZL4B03gr1KfzJtk5Cs/edit#gid=674286209
https://docs.google.com/presentation/d/129pSx58qDm7Y1OQmSSHKDq6tsoD3pW_gDRNXiX2rd0w/edit#slide=id.g4d21a8c2ba_0_11
/wiki/spaces/SCHEM/pages/24584192172453176326
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Install Schematic
Schematic will run on Python 3.10. We must control the Python Environment. PyEnv is one option., https://fathomtech.io/blog/python-environments-with-pyenv-and-vitualenv/
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pyenv install 3.10.11 pyenv virtualenv 3.10.11 schematic_3_10_11 pyenv activate schematic_3_10_11 pyenv -m pip install schematic_3_10_11 pip install schematicpy |
Data model visualizer?
Build a Data Model
/wiki/spaces/SCHEM/pages/2473623559
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`schematic model --config config.hyml submit --manifest_path manifest.csv --datset_id synId -- manifest_record_type table
JSON for Linking Data JSON-LD
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RegEx - extract individual and specimen ID from filenames
Data Model
Lref gdrive file url https://docs.google.com/document/d/1nZGLRKW5LXpY-LBrtrgs4MyO-fb0kDDeouEOvW36xo0/edit#heading=h.o7ihd22lafi
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