Schematic + Data Curator App Workflow Notes

Repository

https://github.com/Sage-Bionetworks/schematic

Install

Schematic will run on Python 3.10. We must control the Pytheon Environment. PyEnv is one option., https://fathomtech.io/blog/python-environments-with-pyenv-and-vitualenv/

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

Create a data model formatted as a CSV

Where is the reference to how data model needs to be formatted?

Convert data model from CSV to JSONLD

schematic schema convert input.csv output.jsonld

schematic CLI reference -- schema convert CSV > JSONLD

AD Data Models https://github.com/adknowledgeportal/data-models
DCA app development version https://dca-dev.app.sagebionetworks.org/
Abby's request for testing

https://sagebionetworks.slack.com/archives/C02A2FBN3G8/p1682116574295509
model-ad.data.model.jsonld https://github.com/adknowledgeportal/test-data-model/blob/main/model-ad/model-ad.data.model.jsonld

AD Portal DCA https://sagebio.shinyapps.io/adknowledgeportal-data-curator/
AD Portal DCA Test Project - Main https://www.synapse.org/#!Synapse:syn33582398/wiki/619343
github – data_curator https://github.com/adknowledgeportal/data_curator
github – test-data-model https://github.com/adknowledgeportal/test-data-model

Annotate study folder with contentType = 'dataset' https://www.synapse.org/#!Synapse:syn36759435/tables/
Add CSV + JSONLD to github – test-data-model https://github.com/adknowledgeportal/test-data-model
data_curator - https://github.com/adknowledgeportal/data_curator/blob/18dc00723f2e95a98525ff695401ac67e7785475/schematic_config.yml#L31
Data Model Validation Rules /wiki/spaces/SCHEM/pages/2645262364
RegEx - extract individual and specimen ID from filenames