deriva-ml 1.13.2__py3-none-any.whl → 1.13.3__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- deriva_ml/database_model.py +5 -11
- deriva_ml/dataset.py +279 -295
- deriva_ml/dataset_aux_classes.py +10 -10
- deriva_ml/demo_catalog.py +90 -67
- deriva_ml/deriva_definitions.py +43 -4
- deriva_ml/deriva_ml_base.py +24 -29
- deriva_ml/deriva_model.py +17 -5
- deriva_ml/execution.py +23 -3
- deriva_ml/history.py +2 -0
- deriva_ml/schema_setup/annotations.py +341 -126
- deriva_ml/schema_setup/create_schema.py +33 -65
- deriva_ml/schema_setup/policy.json +7 -3
- deriva_ml/upload.py +3 -3
- {deriva_ml-1.13.2.dist-info → deriva_ml-1.13.3.dist-info}/METADATA +2 -2
- deriva_ml-1.13.3.dist-info/RECORD +31 -0
- {deriva_ml-1.13.2.dist-info → deriva_ml-1.13.3.dist-info}/WHEEL +1 -1
- deriva_ml-1.13.2.dist-info/RECORD +0 -31
- {deriva_ml-1.13.2.dist-info → deriva_ml-1.13.3.dist-info}/entry_points.txt +0 -0
- {deriva_ml-1.13.2.dist-info → deriva_ml-1.13.3.dist-info}/licenses/LICENSE +0 -0
- {deriva_ml-1.13.2.dist-info → deriva_ml-1.13.3.dist-info}/top_level.txt +0 -0
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import argparse
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import sys
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from deriva.core.ermrest_model import Model, Table
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from deriva.core.utils.core_utils import tag as deriva_tags
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from ..deriva_model import DerivaModel
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from ..upload import bulk_upload_configuration
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def
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def catalog_annotation(model: DerivaModel) -> None:
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"""Set the annotations for a catalog.
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This routine will dynamically walk the domain schema and create menu bar for the catalog based on the current
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configuration. A side effect is that the annotation attribute of the catalog will be updated and the result
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pushed to the catalog.
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Args:
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model: A deriva model to the current catalog.
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"""
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catalog_id = model.catalog.catalog_id
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ml_schema = model.ml_schema
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catalog_annotation = {
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deriva_tags.display: {"name_style": {"underline_space": True}},
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deriva_tags.chaise_config: {
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"headTitle": "Catalog ML",
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"navbarBrandText": "ML Data Browser",
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"systemColumnsDisplayEntry": ["RID"],
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"systemColumnsDisplayCompact": ["RID"],
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"defaultTable": {"table": "Dataset", "schema": "deriva-ml"},
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"deleteRecord": True,
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"showFaceting": True,
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"shareCiteAcls": True,
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"exportConfigsSubmenu": {"acls": {"show": ["*"], "enable": ["*"]}},
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"resolverImplicitCatalog": False,
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"navbarMenu": {
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"newTab": False,
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"children": [
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{
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"name": "User Info",
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"children": [
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{
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"url": f"/chaise/recordset/#{catalog_id}/public:ERMrest_Client",
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"name": "Users",
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},
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{
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"url": f"/chaise/recordset/#{catalog_id}/public:ERMrest_Group",
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"name": "Groups",
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},
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{
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"url": f"/chaise/recordset/#{catalog_id}/public:ERMrest_RID_Lease",
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"name": "ERMrest RID Lease",
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},
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],
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},
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{ # All the primary tables in deriva-ml schema.
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"name": "Deriva-ML",
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"children": [
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{
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"url": f"/chaise/recordset/#{catalog_id}/{ml_schema}:Workflow",
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"name": "Workflow",
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},
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{
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"url": f"/chaise/recordset/#{catalog_id}/{ml_schema}:Execution",
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"name": "Execution",
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},
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{
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"url": f"/chaise/recordset/#{catalog_id}/{ml_schema}:Execution_Metadata",
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"name": "Execution Metadata",
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},
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{
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"url": f"/chaise/recordset/#{catalog_id}/{ml_schema}:Execution_Asset",
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"name": "Execution Asset",
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},
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{
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"url": f"/chaise/recordset/#{catalog_id}/{ml_schema}:Dataset",
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"name": "Dataset",
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},
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{
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"url": f"/chaise/recordset/#{catalog_id}/{ml_schema}:Dataset_Version",
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"name": "Dataset Version",
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},
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],
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},
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{ # All the primary tables in deriva-ml schema.
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"name": "WWW",
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"children": [
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{
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"url": f"/chaise/recordset/#{catalog_id}/WWW:Page",
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"name": "Page",
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},
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{
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"url": f"/chaise/recordset/#{catalog_id}/WWW:File",
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"name": "File",
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},
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],
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},
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{
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"name": model.domain_schema,
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"children": [
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{
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"name": tname,
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"url": f"/chaise/recordset/#{catalog_id}/{model.domain_schema}:{tname}",
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}
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for tname in model.schemas[model.domain_schema].tables
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# Don't include controlled vocabularies, association tables, or feature tables.
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if not (
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model.is_vocabulary(tname)
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or model.is_association(tname, pure=False, max_arity=3)
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)
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],
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},
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{ # Vocabulary menu which will list all the controlled vocabularies in deriva-ml and domain.
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"name": "Vocabulary",
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"children": [
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{"name": f"{ml_schema} Vocabularies", "header": True}
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]
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+ [
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{
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"url": f"/chaise/recordset/#{catalog_id}/{ml_schema}:{tname}",
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"name": tname,
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}
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for tname in model.schemas[model.ml_schema].tables
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if model.is_vocabulary(tname)
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]
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+ [
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{
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"name": f"{model.domain_schema} Vocabularies",
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"header": True,
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}
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]
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+ [
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{
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"url": f"/chaise/recordset/#{catalog_id}/{model.domain_schema}:{tname}",
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"name": tname,
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}
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for tname in model.schemas[model.domain_schema].tables
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if model.is_vocabulary(tname)
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],
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},
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{ # List of all of the asset tables in deriva-ml and domain schemas.
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"name": "Assets",
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"children": [
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{
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"url": f"/chaise/recordset/#{catalog_id}/{ml_schema}:{tname}",
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"name": tname,
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}
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for tname in model.schemas[model.ml_schema].tables
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if model.is_asset(tname)
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]
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+ [
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{
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"url": f"/chaise/recordset/#{catalog_id}/{model.domain_schema}:{tname}",
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"name": tname,
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}
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for tname in model.schemas[model.domain_schema].tables
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if model.is_asset(tname)
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],
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},
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{
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"url": "/chaise/recordset/#0/ermrest:registry@sort(RID)",
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"name": "Catalog Registry",
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},
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{
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"name": "Documentation",
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"children": [
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{
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"url": "https://github.com/informatics-isi-edu/deriva-ml/blob/main/docs/ml_workflow_instruction.md",
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"name": "ML Notebook Instruction",
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},
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{
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"url": "https://informatics-isi-edu.github.io/deriva-ml/",
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"name": "Deriva-ML Documentation",
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},
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],
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},
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],
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},
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},
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deriva_tags.bulk_upload: bulk_upload_configuration(model=model),
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}
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model.annotations.update(catalog_annotation)
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model.apply()
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def asset_annotation(asset_table: Table):
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schema = asset_table.schema.name
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asset_name = asset_table.name
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model = DerivaModel(asset_table.schema.model)
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def fkey_column(column):
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"""Map the column name to a FK if a constraint exists on the column"""
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return next(
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(
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(fk.name[0].name, fk.name[1])
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for fk in asset_table.foreign_keys
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if asset_table.columns[column] in fk.column_map
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),
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column,
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)
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annotations = {
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deriva_tags.table_display: {
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"row_name": {"row_markdown_pattern": "{{{Filename}}}"}
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},
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deriva_tags.visible_columns: {
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"*": [
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"RID",
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"RCT",
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"RMT",
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[schema, f"{asset_name}_RCB_fkey"],
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[schema, f"{asset_name}_RMB_fkey"],
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"URL",
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"Filename",
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"Description",
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"Length",
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"MD5",
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{
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"source": [
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{
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"inbound": [
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schema,
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f"{asset_name}_Asset_Type_{asset_name}_fkey",
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]
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},
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{
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"outbound": [
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schema,
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f"{asset_name}_Asset_Type_Asset_Type_fkey",
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]
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},
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"RID",
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],
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"markdown_name": "Asset Types",
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},
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]
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+ [fkey_column(c) for c in model.asset_metadata(asset_table)],
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},
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}
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asset_table.annotations.update(annotations)
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model.apply()
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def generate_annotation(model: Model, schema: str) -> dict:
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catalog_id = model.catalog.catalog_id
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schema = model.ml_schema
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workflow_annotation = {
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deriva_tags.visible_columns: {
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"*": [
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"RID",
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[schema, "Workflow_RCB_fkey"],
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[schema, "Workflow_RMB_fkey"],
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"Name",
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"Description",
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{
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"*": [
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"RID",
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[schema, "Execution_RCB_fkey"],
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[schema, "Execution_RMB_fkey"],
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"RCT",
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"Description",
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{"source": [{"outbound": [schema, "Execution_Workflow_fkey"]}, "RID"]},
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},
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}
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deriva_tags.table_display: {
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"row_name": {"row_markdown_pattern": "{{{Filename}}}"}
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},
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dataset_annotation = {
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deriva_tags.visible_columns: {
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"
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"*": [
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"RID",
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"URL",
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"Description",
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"
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[schema, "
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# },
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# "markdown_name": "ROC Plot"
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# }
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[schema, "Dataset_RCB_fkey"],
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[schema, "Dataset_RMB_fkey"],
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{
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"source": [
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{"outbound": ["deriva-ml", "Dataset_Version_fkey"]},
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"Version",
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],
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"markdown_name": "Dataset Version",
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},
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],
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"detailed": [
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"RID",
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"RCT",
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"RMT",
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"RCB",
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"RMB",
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# {
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# "display": {
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# "template_engine": "handlebars",
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# "markdown_pattern": "{{#if (eq _Execution_Asset_Type \"2-5QME\")}} ::: iframe []("
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# "https://dev.eye-ai.org/~vivi/deriva-webapps/plot/?config=test-line"
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# "-plot&Execution_Asset_RID={{{RID}}}){style=\"min-width:1000px; "
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# "min-height:700px; height:70vh;\" class=\"chaise-autofill\"} \\n::: {"
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# "{/if}}"
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# },
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# "markdown_name": "ROC Plot"
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# },
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125
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"URL",
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"Filename",
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342
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"Description",
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128
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-
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129
|
-
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130
|
-
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{
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"source": [
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{"inbound": ["deriva-ml", "Dataset_Dataset_Type_Dataset_fkey"]},
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{
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347
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"outbound": [
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"deriva-ml",
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"Dataset_Dataset_Type_Dataset_Type_fkey",
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]
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},
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"RID",
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353
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+
],
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"markdown_name": "Dataset Types",
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},
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{
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"source": [
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{"outbound": ["deriva-ml", "Dataset_Version_fkey"]},
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"Version",
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],
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361
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"markdown_name": "Dataset Version",
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},
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363
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[schema, "Dataset_RCB_fkey"],
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364
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[schema, "Dataset_RMB_fkey"],
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365
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],
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132
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133
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135
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deriva_tags.table_display: {
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"row_name": {"row_markdown_pattern": "{{{Filename}}}"}
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}
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}
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140
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-
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dataset_annotation = {
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|
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# Setup Facet on types
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143
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# Make types in visible columns
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144
|
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# Have all connected values be visible FK.
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145
|
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}
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146
|
-
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schema_annotation = {
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148
|
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"name_style": {"underline_space": True},
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149
|
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}
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150
|
-
|
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151
|
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catalog_annotation = {
|
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152
|
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deriva_tags.display: {"name_style": {"underline_space": True}},
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153
|
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deriva_tags.chaise_config: {
|
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154
|
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"headTitle": "Catalog ML",
|
|
155
|
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"navbarBrandText": "ML Data Browser",
|
|
156
|
-
"systemColumnsDisplayEntry": ["RID"],
|
|
157
|
-
"systemColumnsDisplayCompact": ["RID"],
|
|
158
|
-
"navbarMenu": {
|
|
159
|
-
"newTab": False,
|
|
160
|
-
"children": [
|
|
366
|
+
"filter": {
|
|
367
|
+
"and": [
|
|
368
|
+
{"source": "RID"},
|
|
369
|
+
{"source": "Description"},
|
|
161
370
|
{
|
|
162
|
-
"
|
|
163
|
-
"children": [
|
|
371
|
+
"source": [
|
|
164
372
|
{
|
|
165
|
-
"
|
|
166
|
-
|
|
373
|
+
"inbound": [
|
|
374
|
+
"deriva-ml",
|
|
375
|
+
"Dataset_Dataset_Type_Dataset_fkey",
|
|
376
|
+
]
|
|
167
377
|
},
|
|
168
378
|
{
|
|
169
|
-
"
|
|
170
|
-
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
"url": f"/chaise/recordset/#{catalog_id}/public:ERMrest_RID_Lease",
|
|
174
|
-
"name": "ERMrest RID Lease",
|
|
379
|
+
"outbound": [
|
|
380
|
+
"deriva-ml",
|
|
381
|
+
"Dataset_Dataset_Type_Dataset_Type_fkey",
|
|
382
|
+
]
|
|
175
383
|
},
|
|
384
|
+
"RID",
|
|
176
385
|
],
|
|
386
|
+
"markdown_name": "Dataset Types",
|
|
177
387
|
},
|
|
178
388
|
{
|
|
179
|
-
"
|
|
180
|
-
"
|
|
181
|
-
{
|
|
182
|
-
"url": f"/chaise/recordset/#{catalog_id}/{schema}:Workflow",
|
|
183
|
-
"name": "Workflow",
|
|
184
|
-
},
|
|
185
|
-
{
|
|
186
|
-
"url": f"/chaise/recordset/#{catalog_id}/{schema}:Workflow_Type",
|
|
187
|
-
"name": "Workflow Type",
|
|
188
|
-
},
|
|
189
|
-
{
|
|
190
|
-
"url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution",
|
|
191
|
-
"name": "Execution",
|
|
192
|
-
},
|
|
193
|
-
{
|
|
194
|
-
"url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution_Metadata",
|
|
195
|
-
"name": "Execution Metadata",
|
|
196
|
-
},
|
|
197
|
-
{
|
|
198
|
-
"url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution_Metadata_Type",
|
|
199
|
-
"name": "Execution Metadata Type",
|
|
200
|
-
},
|
|
201
|
-
{
|
|
202
|
-
"url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution_Asset",
|
|
203
|
-
"name": "Execution Asset",
|
|
204
|
-
},
|
|
205
|
-
{
|
|
206
|
-
"url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution_Asset_Type",
|
|
207
|
-
"name": "Execution Asset Type",
|
|
208
|
-
},
|
|
209
|
-
{
|
|
210
|
-
"url": f"/chaise/recordset/#{catalog_id}/{schema}:Dataset",
|
|
211
|
-
"name": "Dataset",
|
|
212
|
-
},
|
|
213
|
-
],
|
|
389
|
+
"source": [{"outbound": [schema, "Dataset_RCB_fkey"]}, "RID"],
|
|
390
|
+
"markdown_name": "Created By",
|
|
214
391
|
},
|
|
215
|
-
|
|
392
|
+
{
|
|
393
|
+
"source": [{"outbound": [schema, "Dataset_RMB_fkey"]}, "RID"],
|
|
394
|
+
"markdown_name": "Modified By",
|
|
395
|
+
},
|
|
396
|
+
]
|
|
216
397
|
},
|
|
217
|
-
|
|
218
|
-
|
|
219
|
-
|
|
220
|
-
|
|
221
|
-
|
|
222
|
-
|
|
398
|
+
}
|
|
399
|
+
}
|
|
400
|
+
|
|
401
|
+
schema_annotation = {
|
|
402
|
+
"name_style": {"underline_space": True},
|
|
403
|
+
}
|
|
404
|
+
|
|
405
|
+
dataset_version_annotation = {
|
|
406
|
+
deriva_tags.visible_columns: {
|
|
407
|
+
"*": [
|
|
408
|
+
"RID",
|
|
409
|
+
"RCT",
|
|
410
|
+
"RMT",
|
|
411
|
+
[schema, "Dataset_Version_RCB_fkey"],
|
|
412
|
+
[schema, "Dataset_Version_RMB_fkey"],
|
|
413
|
+
{
|
|
414
|
+
"source": [
|
|
415
|
+
{"outbound": [schema, "Dataset_Version_Dataset_fkey"]},
|
|
416
|
+
"RID",
|
|
417
|
+
]
|
|
418
|
+
},
|
|
419
|
+
"Description",
|
|
420
|
+
{
|
|
421
|
+
"display": {
|
|
422
|
+
"template_engine": "handlebars",
|
|
423
|
+
"markdown_pattern": "[{{{Version}}}](https://{{{$location.host}}}/id/{{{$catalog.id}}}/{{{Dataset}}}@{{{Snapshot}}})",
|
|
424
|
+
},
|
|
425
|
+
"markdown_name": "Version",
|
|
426
|
+
},
|
|
427
|
+
"Minid",
|
|
428
|
+
{
|
|
429
|
+
"source": [
|
|
430
|
+
{"outbound": [schema, "Dataset_Version_Execution_fkey"]},
|
|
431
|
+
"RID",
|
|
432
|
+
]
|
|
433
|
+
},
|
|
434
|
+
]
|
|
435
|
+
},
|
|
436
|
+
deriva_tags.visible_foreign_keys: {"*": []},
|
|
437
|
+
deriva_tags.table_display: {
|
|
438
|
+
"row_name": {
|
|
439
|
+
"row_markdown_pattern": "{{{$fkey_deriva-ml_Dataset_Version_Dataset_fkey.RID}}}:{{{Version}}}"
|
|
440
|
+
}
|
|
223
441
|
},
|
|
224
|
-
deriva_tags.bulk_upload: bulk_upload_configuration(model=DerivaModel(model)),
|
|
225
442
|
}
|
|
226
443
|
|
|
227
444
|
return {
|
|
228
445
|
"workflow_annotation": workflow_annotation,
|
|
229
446
|
"dataset_annotation": dataset_annotation,
|
|
230
447
|
"execution_annotation": execution_annotation,
|
|
231
|
-
"execution_asset_annotation": execution_asset_annotation,
|
|
232
|
-
"execution_metadata_annotation": execution_metadata_annotation,
|
|
233
448
|
"schema_annotation": schema_annotation,
|
|
234
|
-
"
|
|
449
|
+
"dataset_version_annotation": dataset_version_annotation,
|
|
235
450
|
}
|
|
236
451
|
|
|
237
452
|
|
|
@@ -240,7 +455,7 @@ def main():
|
|
|
240
455
|
parser.add_argument("--catalog_id", type=str, required=True)
|
|
241
456
|
parser.add_argument("--schema_name", type=str, required=True)
|
|
242
457
|
args = parser.parse_args()
|
|
243
|
-
generate_annotation(args.catalog_id)
|
|
458
|
+
generate_annotation(args.catalog_id, args.schema_name)
|
|
244
459
|
|
|
245
460
|
|
|
246
461
|
if __name__ == "__main__":
|