deriva-ml 1.8.10__py3-none-any.whl → 1.9.0__py3-none-any.whl

deriva_ml/execution.py

@@ -54,7 +54,9 @@ except ImportError:  # Graceful fallback if IceCream isn't installed.
 try:
     from jupyter_server.serverapp import list_running_servers
 except ImportError:
-    list_running_servers = lambda: []
+
+    def list_running_servers():
+        return []
 
 
 class Execution:
@@ -155,7 +157,6 @@ class Execution:
         self._initialize_execution(reload)
 
     def _save_runtime_environment(self):
-
         runtime_env_path = ExecMetadataVocab.runtime_env.value
         runtime_env_dir = self.execution_metadata_path(runtime_env_path)
         with NamedTemporaryFile(
@@ -253,17 +254,9 @@ class Execution:
 
     def _create_notebook_checkpoint(self):
         """Trigger a checkpoint creation using Jupyter's API."""
-        notebook_name = self._ml_object._notebook
-
-        # Look for the server running this notebook.
-        root = Path("").absolute().parent.as_posix()
-        servers = list(list_running_servers())
-        # Jupyterhub seems to handle root_dir differently then server case.
-        server = (
-            servers
-            if len(servers) == 1
-            else [s for s in servers if s["root_dir"] == root]
-        )[0]
+
+        server, session = self._ml_object._get_notebook_session()
+        notebook_name = session["notebook"]["path"]
         notebook_url = f"{server['url']}api/contents/{notebook_name}"
 
         # Get notebook content
@@ -275,7 +268,7 @@ class Execution:
             # Execution metadata cannot be in a directory, so map path into filename.
             checkpoint_path = (
                 self.execution_metadata_path(ExecMetadataVocab.runtime_env.value)
-                / f"{notebook_name.as_posix().replace('/','_')}.checkpoint"
+                / f"{notebook_name.replace('/', '_')}.checkpoint"
             )
             with open(checkpoint_path, "w", encoding="utf-8") as f:
                 json.dump(notebook_content, f)
@@ -295,7 +288,7 @@ class Execution:
         minutes, seconds = divmod(remainder, 60)
         duration = f"{round(hours, 0)}H {round(minutes, 0)}min {round(seconds, 4)}sec"
 
-        if self._ml_object._notebook:
+        if self._ml_object._is_notebook:
             self._create_notebook_checkpoint()
 
         self.update_status(Status.completed, "Algorithm execution ended.")
@@ -367,7 +360,7 @@ class Execution:
             if m := is_feature_asset_dir(p):
                 try:
                     self.update_status(
-                        Status.running, f'Uploading feature {m["feature_name"]}...'
+                        Status.running, f"Uploading feature {m['feature_name']}..."
                     )
                     feature_assets[m["target_table"], m["feature_name"]] = (
                         self._ml_object.upload_assets(p)

deriva_ml/execution_configuration.py

@@ -1,12 +1,12 @@
 from __future__ import annotations
 
 import json
-from typing import Optional, Any
+from typing import Optional
 
 from pydantic import (
     BaseModel,
     conlist,
-    ConfigDict, field_validator,
+    ConfigDict,
 )
 from pathlib import Path
 
@@ -36,7 +36,6 @@ class Workflow(BaseModel):
     checksum: Optional[str]
 
 
-
 class ExecutionConfiguration(BaseModel):
     """Define the parameters that are used to configure a specific execution.
 
@@ -69,23 +68,21 @@ class ExecutionConfiguration(BaseModel):
             config = json.load(fd)
         return ExecutionConfiguration.model_validate(config)
 
-    def download_execution_configuration(
-        self, configuration_rid: RID
-    ) -> ExecutionConfiguration:
-        """Create an ExecutionConfiguration object from a catalog RID that points to a JSON representation of that
-        configuration in hatrac
-
-        Args:
-            configuration_rid: RID that should be to an asset table that refers to an execution configuration
-
-        Returns:
-            A ExecutionConfiguration object for configured by the parameters in the configuration file.
-        """
-        AssertionError("Not Implemented")
-        return ExecutionConfiguration.load_configuration(configuration_rid)
-
-        # configuration = self.retrieve_rid(configuration_rid)
-        # with NamedTemporaryFile("w+", delete=False, suffix=".json") as dest_file:
-        #    hs = HatracStore("https", self.host_name, self.credential)
-        #    hs.get_obj(path=configuration["URL"], destfilename=dest_file.name)
-        #    return ExecutionConfiguration.load_configuration(Path(dest_file.name))
+    # def download_execution_configuration(
+    #     self, configuration_rid: RID
+    # ) -> ExecutionConfiguration:
+    #     """Create an ExecutionConfiguration object from a catalog RID that points to a JSON representation of that
+    #     configuration in hatrac
+    #
+    #     Args:
+    #         configuration_rid: RID that should be to an asset table that refers to an execution configuration
+    #
+    #     Returns:
+    #         A ExecutionConfiguration object for configured by the parameters in the configuration file.
+    #     """
+    #     AssertionError("Not Implemented")
+    #     configuration = self.retrieve_rid(configuration_rid)
+    #     with NamedTemporaryFile("w+", delete=False, suffix=".json") as dest_file:
+    #         hs = HatracStore("https", self.host_name, self.credential)
+    #         hs.get_obj(path=configuration["URL"], destfilename=dest_file.name)
+    #         return ExecutionConfiguration.load_configuration(Path(dest_file.name))

deriva_ml/schema_setup/annotations.py

@@ -240,7 +240,7 @@ def main():
     parser.add_argument("--catalog_id", type=str, required=True)
     parser.add_argument("--schema_name", type=str, required=True)
     args = parser.parse_args()
-    generate_annotation(args.catalog_id, args.schema_name)
+    generate_annotation(args.catalog_id)
 
 
 if __name__ == "__main__":

deriva_ml/schema_setup/create_schema.py

@@ -1,5 +1,6 @@
 import argparse
 import sys
+from typing import Optional
 
 from deriva.core import DerivaServer, get_credential
 from deriva.core.ermrest_model import Model
@@ -32,7 +33,7 @@ def define_table_workflow(workflow_annotation: dict):
     )
 
 
-def define_table_dataset(dataset_annotation: dict = None):
+def define_table_dataset(dataset_annotation: Optional[dict] = None):
     return Table.define(
         tname="Dataset",
         column_defs=[
@@ -154,7 +155,7 @@ def create_www_schema(model: Model):
 
 
 def create_ml_schema(
-    model: Model, schema_name: str = "deriva-ml", project_name: str = None
+    model: Model, schema_name: str = "deriva-ml", project_name: Optional[str] = None
 ):
     if model.schemas.get(schema_name):
         model.schemas[schema_name].drop(cascade=True)

deriva_ml/upload.py

@@ -483,7 +483,7 @@ def upload_directory(
 
 @validate_call(config=ConfigDict(arbitrary_types_allowed=True))
 def upload_asset(
-    model: DerivaModel, file: Path | str, table: Table | str, **kwargs: Any
+    model: DerivaModel, file: Path | str, table: Table, **kwargs: Any
 ) -> dict:
     """Upload the specified file into Hatrac and update the associated asset table.
 

{deriva_ml-1.8.10.dist-info → deriva_ml-1.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.8.10
+Version: 1.9.0
 Summary: Utilities to simplify use of Dervia and Pandas to create reproducable ML pipelines
 Author-email: ISRD <isrd-dev@isi.edu>
 Requires-Python: >=3.10

deriva_ml-1.9.0.dist-info/RECORD

@@ -0,0 +1,27 @@
+deriva_ml/__init__.py,sha256=r1Z9N5vtZkAET7emqhpAx2bf_xJUp5wHOc4_DIplsG8,1082
+deriva_ml/database_model.py,sha256=HaJoxKSogc-xLGaZfEviqRAWO9wUy52h7yK8by6FKxM,14838
+deriva_ml/dataset.py,sha256=XIXyTej55WduvEOGitG5SJIfPYrQu36cXjCoCNHNMwQ,60746
+deriva_ml/dataset_aux_classes.py,sha256=YxjQnu2kS9kK_f8bGqhmgE6ty9GNeitCxfvReT9vaM0,6537
+deriva_ml/dataset_bag.py,sha256=aOJxFA9t5apjE5BNBrk8Pi9R1Cp8AWnnaL-10P8ELrQ,11515
+deriva_ml/demo_catalog.py,sha256=zQAHWSvrVPxMg-vyRUqoC0Jj5RhfGjkBwXW3mBksLhA,10986
+deriva_ml/deriva_definitions.py,sha256=jNiInYA2Cb1GE4OOT1CofxBygdLDSOmNsw5Wl6NbZQE,8943
+deriva_ml/deriva_ml_base.py,sha256=B0_0R0tgx4o30VM-QSSKIGy2BN5kOBcYKuYGvmPkwMg,46953
+deriva_ml/deriva_model.py,sha256=B4gwr3-92IQU-mEZlusgNEnRyulD96esWGS67q9MzHk,12024
+deriva_ml/execution.py,sha256=on8hAtuZr9qFiyxuk_vDCmnRJ9Cv4kFOgHK4HY4CmV8,29585
+deriva_ml/execution_configuration.py,sha256=vsdL31J09dz7CQDd2rYXIjyBPwNlgAWvrTqsXNWi82g,3357
+deriva_ml/execution_environment.py,sha256=bCRKrCELDbGQDo7_FKfw7e8iMzVjSRZK3baKkqH5-_0,3264
+deriva_ml/feature.py,sha256=7e8WYPCfJSrGxJh9oUTduYSnB5ekybRhXa_0HIigS_w,5459
+deriva_ml/history.py,sha256=qTDLDs8Ow_6r7mDO0gZm0Fg81SWKOAgtCU5pzZoDRgM,2828
+deriva_ml/test_functions.py,sha256=-eqLHjjCQCLBNAr1ofbZekNiCOfMISSACRxT_YHER8I,4396
+deriva_ml/upload.py,sha256=P35ViZzlNNbsXVbnTyq-G781nGHbX4md1tiCp3c_KKI,22264
+deriva_ml/schema_setup/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+deriva_ml/schema_setup/annotations.py,sha256=v0gTpmWYxRqsQ-bcnQzsr8WowGv2pi9pZUsO3WWnu1U,9528
+deriva_ml/schema_setup/create_schema.py,sha256=BRdYeWW5I8HxuATkB1hkKuIw4n-JQu620xod7EQoVSE,10674
+deriva_ml/schema_setup/policy.json,sha256=77sf0Imy6CAQV0_VwwbA56_KROJ05WXsvT-Wjtkk538,1633
+deriva_ml/schema_setup/table_comments_utils.py,sha256=-2_ubEpoH7ViLVb-ZfW9wZbQ26DTKNgjkCABMzGu4i4,2140
+deriva_ml-1.9.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.9.0.dist-info/METADATA,sha256=REDBcboXpGhYbG7bVaICPhZP81cDLoSiCdiY7PX8GrQ,669
+deriva_ml-1.9.0.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
+deriva_ml-1.9.0.dist-info/entry_points.txt,sha256=ZiOvrYj022x544TQwi018ujeHRRDahNmwJnzn5ThacM,242
+deriva_ml-1.9.0.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.9.0.dist-info/RECORD,,

deriva_ml/build/lib/schema_setup/alter_annotation.py

@@ -1,36 +0,0 @@
-import sys
-import argparse
-from deriva.core import DerivaServer, get_credential, ErmrestCatalog
-from deriva.core.ermrest_model import builtin_types, Schema, Table, Column, ForeignKey
-from annotation_temp import generate_annotation
-
-
-def alter_table_annotation(catalog, schema_name: str, table_name: str, annotation: dict):
-    model_root = catalog.getCatalogModel()
-    table = model_root.dataset_table(schema_name, table_name)
-    table.alter(annotations=annotation)
-
-
-def alter_schema_annotation(catalog, schema_name: str, annotation: dict):
-    model_root = catalog.getCatalogModel()
-    schema = model_root.schemas[schema_name]
-    schema.alter(annotations=annotation)
-
-def main():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--hostname', type=str, required=True)
-    parser.add_argument('--schema_name', type=str, required=True)
-    parser.add_argument('--catalog_id', type=str, required=True)
-    args = parser.parse_args()
-    credentials = get_credential(args.hostname)
-    catalog = ErmrestCatalog('https', args.hostname, args.catalog_id, credentials)
-
-    annotations = generate_annotation(args.schema_name, args.catalog_id)
-    alter_table_annotation(catalog, args.schema_name, 'Workflow', annotations["workflow_annotation"])
-    alter_table_annotation(catalog, args.schema_name, 'Execution', annotations["execution_annotation"])
-    alter_table_annotation(catalog, args.schema_name, 'Execution_Metadata', annotations["execution_metadata_annotation"])
-    alter_table_annotation(catalog, args.schema_name, 'Execution_Assets', annotations["execution_assets_annotation"])
-    alter_schema_annotation(catalog, args.schema_name, annotations["schema_annotation"])
-
-if __name__ == "__main__":
-    sys.exit(main())

deriva_ml/build/lib/schema_setup/annotation_temp.py

@@ -1,255 +0,0 @@
-import argparse
-import sys
-
-
-def generate_annotation(catalog_id: str, schema: str) -> dict:
-    workflow_annotation = {
-        "tag:isrd.isi.edu,2016:visible-columns": {
-            "*": [
-                "RID",
-                "Name",
-                "Description",
-                {
-                    "display": {"markdown_pattern": "[{{{URL}}}]({{{URL}}})"},
-                    "markdown_name": "URL"
-                },
-                "Checksum",
-                "Version",
-                {
-                    "source": [
-                        {
-                            "outbound": [
-                                schema,
-                                "Workflow_Workflow_Type_fkey"
-                            ]
-                        },
-                        "RID"
-                    ]
-                }
-            ]
-        }
-    }
-
-    execution_annotation = {
-        "tag:isrd.isi.edu,2016:visible-columns": {
-            "*": [
-                "RID",
-                [
-                    schema,
-                    "Execution_RCB_fkey"
-                ],
-                "RCT",
-                "Description",
-                {"source": [
-                    {"outbound": [
-                        "eye-ai",
-                        "Execution_Workflow_fkey"
-                    ]
-                    },
-                    "RID"
-                ]
-                },
-                "Duration",
-                "Status",
-                "Status_Detail"
-            ]
-        },
-        "tag:isrd.isi.edu,2016:visible-foreign-keys": {
-            "detailed": [
-                {
-                    "source": [
-                        {
-                            "inbound": [
-                                schema,
-                                "Dataset_Execution_Execution_fkey"
-                            ]
-                        },
-                        {
-                            "outbound": [
-                                schema,
-                                "Dataset_Execution_Dataset_fkey"
-                            ]
-                        },
-                        "RID"
-                    ],
-                    "markdown_name": "Dataset"
-                },
-                {
-                    "source": [
-                        {
-                            "inbound": [
-                                schema,
-                                "Execution_Assets_Execution_Execution_fkey"
-                            ]
-                        },
-                        {
-                            "outbound": [
-                                schema,
-                                "Execution_Assets_Execution_Execution_Assets_fkey"
-                            ]
-                        },
-                        "RID"
-                    ],
-                    "markdown_name": "Execution Assets"
-                },
-                {
-                    "source": [
-                        {
-                            "inbound": [
-                                schema,
-                                "Execution_Metadata_Execution_fkey"
-                            ]
-                        },
-                        "RID"
-                    ],
-                    "markdown_name": "Execution Metadata"
-                }
-            ]
-        }
-    }
-
-    execution_assets_annotation = {
-        "tag:isrd.isi.edu,2016:table-display": {
-            "row_name": {
-                "row_markdown_pattern": "{{{Filename}}}"
-            }
-        },
-        "tag:isrd.isi.edu,2016:visible-columns": {
-            "compact": [
-                "RID",
-                "URL",
-                "Description",
-                "Length",
-                [
-                    schema,
-                    "Execution_Assets_Execution_Asset_Type_fkey"
-                ],
-                # {
-                #     "display": {
-                #         "template_engine": "handlebars",
-                #         "markdown_pattern": "{{#if (eq  _Execution_Asset_Type \"2-5QME\")}}\n ::: iframe []("
-                #                             "https://dev.eye-ai.org/~vivi/deriva-webapps/plot/?config=test-line"
-                #                             "-plot&Execution_Assets_RID={{{RID}}}){class=chaise-autofill "
-                #                             "style=\"min-width: 500px; min-height: 300px;\"} \\n:::\n {{/if}}"
-                #     },
-                #     "markdown_name": "ROC Plot"
-                # }
-            ],
-            "detailed": [
-                "RID",
-                "RCT",
-                "RMT",
-                "RCB",
-                "RMB",
-                # {
-                #     "display": {
-                #         "template_engine": "handlebars",
-                #         "markdown_pattern": "{{#if (eq _Execution_Asset_Type \"2-5QME\")}} ::: iframe []("
-                #                             "https://dev.eye-ai.org/~vivi/deriva-webapps/plot/?config=test-line"
-                #                             "-plot&Execution_Assets_RID={{{RID}}}){style=\"min-width:1000px; "
-                #                             "min-height:700px; height:70vh;\" class=\"chaise-autofill\"} \\n::: {"
-                #                             "{/if}}"
-                #     },
-                #     "markdown_name": "ROC Plot"
-                # },
-                "URL",
-                "Filename",
-                "Description",
-                "Length",
-                "MD5",
-                [
-                    schema,
-                    "Execution_Assets_Execution_Asset_Type_fkey"
-                ]
-            ]
-        }
-    }
-
-    execution_metadata_annotation = {
-        "tag:isrd.isi.edu,2016:table-display": {
-            "row_name": {
-                "row_markdown_pattern": "{{{Filename}}}"
-            }
-        }
-    }
-
-    schema_annotation = {
-        "headTitle": "Catalog ML",
-        "navbarMenu": {
-            "newTab": False,
-            "children": [
-                {
-                    "name": "User Info",
-                    "children": [
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/public:ERMrest_Client",
-                            "name": "Users"
-                        },
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/public:ERMrest_Group",
-                            "name": "Groups"
-                        },
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/public:ERMrest_RID_Lease",
-                            "name": "ERMrest RID Lease"
-                        }
-                    ]
-                },
-                {
-                    "name": "FaceBase-ML",
-                    "children": [
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/{schema}:Workflow",
-                            "name": "Workflow"
-                        },
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/{schema}:Workflow_Type",
-                            "name": "Workflow Type"
-                        },
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution",
-                            "name": "Execution"
-                        },
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution_Metadata",
-                            "name": "Execution Metadata"
-                        },
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution_Metadata_Type",
-                            "name": "Execution Metadata Type"
-                        },
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution_Assets",
-                            "name": "Execution Assets"
-                        },
-                        {
-                            "url": f"/chaise/recordset/#{catalog_id}/{schema}:Execution_Asset_Type",
-                            "name": "Execution Asset Type"
-                        }
-                    ]
-                }
-            ]
-        },
-        "navbarBrandText": "ML Data Browser",
-        "systemColumnsDisplayEntry": ["RID"],
-        "systemColumnsDisplayCompact": ["RID"]
-    }
-
-    return {"workflow_annotation": workflow_annotation,
-            "execution_annotation": execution_annotation,
-            "execution_assets_annotation": execution_assets_annotation,
-            "execution_metadata_annotation": execution_metadata_annotation,
-            "schema_annotation": schema_annotation
-            }
-
-
-def main():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--catalog_id', type=str, required=True)
-    parser.add_argument('--schema_name', type=str, required=True)
-    args = parser.parse_args()
-    return generate_annotation(args.catalog_id, args.schema_name)
-
-
-if __name__ == "__main__":
-    sys.exit(main())

deriva_ml/build/lib/schema_setup/create_schema.py

@@ -1,165 +0,0 @@
-import sys
-
-from deriva.core import DerivaServer, get_credential
-from deriva.core.ermrest_model import builtin_types, Schema, Table, Column, ForeignKey
-from deriva.chisel import Model, Schema, Table, Column, ForeignKey
-from deriva_ml.schema_setup.annotation_temp import generate_annotation
-import argparse
-
-
-def create_schema_if_not_exist(model, schema_name, schema_comment=None):
-    if schema_name not in model.schemas:
-        schema = model.create_schema(Schema.define(schema_name, schema_comment))
-        return schema
-    else:
-        schema = model.schemas[schema_name]
-        return schema
-
-
-def create_table_if_not_exist(schema, table_name, create_spec):
-    if table_name not in schema.tables:
-        table = schema.create_table(create_spec)
-        return table
-    else:
-        table = schema.tables[table_name]
-        return table
-
-
-def define_table_workflow(workflow_annotation: dict):
-    table_def = Table.define(
-        'Workflow',
-        column_defs=[
-            Column.define('Name', builtin_types.text),
-            Column.define('Description', builtin_types.markdown),
-            Column.define('URL', builtin_types.ermrest_uri),
-            Column.define('Checksum', builtin_types.text),
-            Column.define('Version', builtin_types.text)
-        ],
-        fkey_defs=[
-            ForeignKey.define(
-                ['RCB'],
-                'public', 'ERMrest_Client',
-                ['ID']
-            )
-        ],
-        annotations=workflow_annotation
-    )
-    return table_def
-
-
-def define_table_execution(execution_annotation: dict):
-    table_def = Table.define(
-        'Execution',
-        column_defs=[
-            Column.define('Description', builtin_types.markdown),
-            Column.define('Duration', builtin_types.text),
-            Column.define('Status', builtin_types.text),
-            Column.define('Status_Detail', builtin_types.text)
-        ],
-        fkey_defs=[
-            ForeignKey.define(
-                ['RCB'],
-                'public', 'ERMrest_Client',
-                ['ID']
-            )
-        ],
-        annotations=execution_annotation
-    )
-    return table_def
-
-
-def define_asset_execution_metadata(schema: str, execution_metadata_annotation: dict):
-    table_def = Table.define_asset(
-        sname=schema,
-        tname='Execution_Metadata',
-        hatrac_template='/hatrac/metadata/{{MD5}}.{{Filename}}',
-        fkey_defs=[
-            ForeignKey.define(
-                ['RCB'],
-                'public', 'ERMrest_Client',
-                ['ID']
-            )
-        ],
-        annotations=execution_metadata_annotation
-    )
-    return table_def
-
-
-def define_asset_execution_assets(schema: str, execution_assets_annotation: dict):
-    table_def = Table.define_asset(
-        sname=schema,
-        tname='Execution_Assets',
-        hatrac_template='/hatrac/execution_assets/{{MD5}}.{{Filename}}',
-        fkey_defs=[
-            ForeignKey.define(
-                ['RCB'],
-                'public', 'ERMrest_Client',
-                ['ID']
-            )
-        ],
-        annotations=execution_assets_annotation
-    )
-    return table_def
-
-
-def setup_ml_workflow(model, schema_name, catalog_id):
-    curie_template = catalog_id+':{RID}'
-    schema = create_schema_if_not_exist(model, schema_name)
-    # get annotations
-    annotations = generate_annotation(catalog_id, schema_name)
-    # Workflow
-    workflow_table = create_table_if_not_exist(schema, 'Workflow',
-                                               define_table_workflow(annotations["workflow_annotation"]))
-    table_def_workflow_type_vocab = Table.define_vocabulary(
-        tname='Workflow_Type', curie_template=curie_template
-    )
-    workflow_type_table = schema.create_table(table_def_workflow_type_vocab)
-    workflow_table.add_reference(workflow_type_table)
-
-    # Execution
-    execution_table = create_table_if_not_exist(schema, 'Execution',
-                                                define_table_execution(annotations["execution_annotation"]))
-    execution_table.add_reference(workflow_table)
-    # dataset_table = create_table_if_not_exist(schema, 'Dataset', define_table_dataset(schema))
-    # association_dataset_execution = schema.create_association(dataset_table, execution_table)
-
-    # Execution Metadata
-    execution_metadata_table = create_table_if_not_exist(schema, 'Execution_Metadata',
-                                                         define_asset_execution_metadata(schema,
-                                                                                         annotations["execution_metadata_annotation"]))
-    execution_metadata_table.add_reference(execution_table)
-    table_def_metadata_type_vocab = Table.define_vocabulary(tname='Execution_Metadata_Type',
-                                                            curie_template=curie_template)
-    metadata_type_table = schema.create_table(table_def_metadata_type_vocab)
-    execution_metadata_table.add_reference(metadata_type_table)
-
-    # Execution Asset
-    execution_assets_table = create_table_if_not_exist(schema, 'Execution_Assets',
-                                                       define_asset_execution_assets(schema,
-                                                                                     annotations["execution_assets_annotation"]))
-    association_execution_execution_asset = schema.create_association(execution_assets_table, execution_table)
-
-    table_def_execution_product_type_vocab = Table.define_vocabulary(
-        tname='Execution_Asset_Type', curie_template=curie_template
-    )
-    execution_asset_type_table = schema.create_table(table_def_execution_product_type_vocab)
-    execution_assets_table.add_reference(execution_asset_type_table)
-    # image_table = create_table_if_not_exist(schema, 'Image', define_asset_image(schema))
-    # association_image_execution_asset = schema.create_association(execution_assets_table, image_table)
-
-
-def main():
-    scheme = 'https'
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--hostname', type=str, required=True)
-    parser.add_argument('--schema_name', type=str, required=True)
-    parser.add_argument('--catalog_id', type=str, required=True)
-    args = parser.parse_args()
-    credentials = get_credential(args.hostname)
-    server = DerivaServer(scheme, args.hostname, credentials)
-    model = Model.from_catalog(server.connect_ermrest(args.catalog_id))
-    setup_ml_workflow(model, args.schema_name, args.catalog_id)
-
-
-if __name__ == "__main__":
-    sys.exit(main())