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Add Not Applicable as a valid value
Update format and content of auto-generate Dataset View JSON schema
Template for Synapse project schema that relates DUO codes to access restrictions
Remove maxItems from JSON schema
Adjust File Longitudinal Event Type description to better describe intent of attribute
Added Data Catalog attributes, descriptions, and model definition. Descriptions contain notes on equivalent annotations in other MC2 data model components
Add Grant End Date as attribute and include in Grant View model
* Added 3D ATAC-PALM assay to assay.csv --------- Co-authored-by: mc2center-bot[bot] <[email protected]> Co-authored-by: Orion Banks <[email protected]>
* Update institution_name.csv Added Institutions for grantView annotation * Update institution_alias.csv
update valid values, collate CSVs, generate JSON-LD (schematic 24.12.1)
Add mapping of assay annotations to portal icon tags for the CCKP
This reverts commit 691193c.
To help prepare resource content tags for the CCKP, this file relates valid values for assay with high level categorical labels. This is intended to be used as input during portal sync operations.
Indicate duoCodes annotation is required to satisfy if statement and trigger ARs
Add duoCodes requirement to template if statement
* remove redundant "Download Template" link (fix for #186) * add back in link mapping to landing page (fix for #187) * remove unnecessary tracked files from main * create doc pages for valid values during pre-build * create docs navigation during on_files * remove nav links from docs config * add PyYAML to pip install * stop tracking valid value doc pages * rename filanem from `template.csv` to `reference.csv` * add comments and helper functions for easier future maintenance * fix bug with rendering backslashes * lint * update config.nav * add logic checking for doc pages for robustness * rename ambiguous variable
Curation + CRDC mapping updates
Limit template generation to only those used in GitHub docs Don't need to save JSON schemas - they are invalid and if they are needed, they can be built later Remove -r flag from rm, to make sure we don't delete folders on accident Save links generated by schematic manifest get -s to txt file
Ignore release_output.txt - we can change this if we decide to integrate google sheet links into our docs later
schematic 24.12.1
Add Imaging Level 2 attributes to GeoMx Imaging
Add Sequencing Level 1 attributes to GeoMx Level 1
Add Sequencing Level 2 attributes to GeoMx Level 2
Add Sequencing Level 3 attributes to GeoMx Level 3
schematic 24.12.1
Remove list of valid values from DSP Dataset File Formats and adjust description.
Remove mapping for DSP Dataset File Formats
Fix description of outputs
schematic 24.12.1
* standardize format of model docs * remove unnecessary bolding from headers * remove extra whitespace from table markdown
V10.0.0 release prep
* Create qc_attribute_mapping.csv * Move qc_attribute_mapping.csv into qc_model folder
* Fix column names and add definitions NGS reads-type columns were missing descriptions because Reads wasn't capitalized Added attribute definitions for GeoMx Tags and GeoMx Tissue Stain (columns already in template) * Create GC_v6.0.4_MC2_10.0.0_map_5-9-25.csv From updated mappings (will be continuously updated): https://docs.google.com/spreadsheets/d/1LLpSIFAh12YdKnGfzXMxGpoKCaEH90nDx-QvncaIJlk/edit?usp=sharing * Added CODEX to assay values * Move AR-related content to Governance AR-related content has been moved to governanceDUO repo and will no longer be maintained here * Update sequencingLevel1 attributes Add NGS Library Source Material and NGS Library Source Molecule attributes * Delete librarySource.csv * Create librarySourceMaterial.csv * Create librarySourceMolecule.csv * Add new valid value mappings Add valid values mappings for NGS Library Source Material and NGS Library Source Molecule attributes, from sequencingLevel1/librarySourceMolecule.csv and sequencingLevel1/librarySelection.csv, respectively * Add attributes to sequencingLevel1 NGS Library Source Molecule and NGS Library Source Material * Add attributes to sequencingLevel2 NGS Library Source Molecule and NGS Library Source Material * Add attributes to geomcLevel1 NGS Library Source Material, NGS Library Source Molecule * Add attributes to geomxLevel2 NGS Library Source Material, NGS Library Source Molecule * Add DCC as a file format * Delete mc2.DatasetView_TEMPLATE.schema.json Template is superseded by v10.0.0 JSON; v10.0.0 is valid Synapse JSON. JSON schema is not currently used in our curation workflow - v10.0.0 schema is being maintained as an example of valid JSON schema, since there were some changes that needed to be made previously to create useable JSON schemas from schematic auto-generated outputs * Update qc_attribute_mapping.csv * Add additional source attributes to GC mapping * Add Study Number of Samples * Update GC_v6.0.4_MC2_11.0.0_map_6-24-25.csv * Make model CSV * Convert CSV to JSON-LD schematic 25.4.1 * Update mc2_qc.model.csv * Build qc JSON-LD schematic 25.4.1 --------- Co-authored-by: aditya-nath-sage <[email protected]>
aditigopalan
requested review from
Bankso,
aclayton555 and
vpchung
as code owners
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