oak-ai -> ontogpt

.cruft.json

@@ -4,9 +4,9 @@
   "checkout": null,
   "context": {
     "cookiecutter": {
-      "project_name": "oak-ai",
-      "__project_slug": "oak_ai",
-      "project_description": "OAK AI",
+      "project_name": "ontogpt",
+      "__project_slug": "ontogpt",
+      "project_description": "ontogpt",
       "min_python_version": "3.9",
       "file_name": "OAK for Artifical Intelligence",
       "greeting_recipient": "World",

LICENSE

@@ -1,5 +1,5 @@
 
-Copyright (c) 2022, Harshad Hegde
+Copyright (c) 2022, Caufield, J. H., Hegde, H., Harris, N. L., Joachimiak, M. P., Moxon, S. A., Reese, J. T. & Mungall, C. J.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -12,7 +12,7 @@ modification, are permitted provided that the following conditions are met:
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 
-* Neither the name of pytest-oak-ai nor the names of its
+* Neither the name of ontogpt nor the names of its
   contributors may be used to endorse or promote products derived from
   this software without specific prior written permission.
 

src/ontogpt/__init__.py

@@ -1,4 +1,4 @@
-"""oak-ai package."""
+"""ontogpt package."""
 from importlib import metadata
 
 try:

src/ontogpt/cli.py

@@ -1,4 +1,4 @@
-"""Command line interface for oak-ai."""
+"""Command line interface for ontogpt."""
 import codecs
 import logging
 import pickle
@@ -152,7 +152,7 @@ def write_extraction(
 )
 @click.version_option(__version__)
 def main(verbose: int, quiet: bool, cache_db: str, skip_annotator):
-    """CLI for oak-ai.
+    """CLI for ontogpt.
 
     :param verbose: Verbosity while running.
     :param quiet: Boolean to be quiet or verbose.

src/ontogpt/templates/ibd.py

@@ -1,204 +1,221 @@
-"""IBD template."""
 from __future__ import annotations
-
+from datetime import datetime, date
 from enum import Enum
-from typing import Any, List, Optional
-
-from pydantic import BaseModel as BaseModel
-from pydantic import Field
+from typing import List, Dict, Optional, Any, Union, Literal
+from pydantic import BaseModel as BaseModel, Field
+from linkml_runtime.linkml_model import Decimal
 
 metamodel_version = "None"
 version = "None"
 
-
 class WeakRefShimBaseModel(BaseModel):
-    __slots__ = "__weakref__"
-
-
-class ConfiguredBaseModel(
-    WeakRefShimBaseModel,
-    validate_assignment=True,
-    validate_all=True,
-    underscore_attrs_are_private=True,
-    extra="forbid",
-    arbitrary_types_allowed=True,
-):
-    pass
+   __slots__ = '__weakref__'
+
+class ConfiguredBaseModel(WeakRefShimBaseModel,
+                validate_assignment = True, 
+                validate_all = True, 
+                underscore_attrs_are_private = True, 
+                extra = 'forbid', 
+                arbitrary_types_allowed = True):
+    pass                    
 
 
 class GeneLocationEnum(str, Enum):
+
+
     dummy = "dummy"
-
+    
 
 class GOCellComponentType(str, Enum):
+
+
     dummy = "dummy"
-
+    
 
 class CellType(str, Enum):
+
+
     dummy = "dummy"
+
 
+class NullDataOptions(str, Enum):
+
+    UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION"
+    NOT_APPLICABLE = "NOT_APPLICABLE"
+    NOT_MENTIONED = "NOT_MENTIONED"
+
+
 
 class IBDAnnotations(ConfiguredBaseModel):
-    genes: Optional[List[str]] = Field(
-        default_factory=list, description="""semicolon-separated list of genes"""
-    )
-    organisms: Optional[List[str]] = Field(
-        default_factory=list, description="""semicolon-separated list of organism taxons"""
-    )
+
+    genes: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of genes""")
+    organisms: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of organism taxons""")
     gene_organisms: Optional[List[GeneOrganismRelationship]] = Field(default_factory=list)
-    activities: Optional[List[str]] = Field(
-        default_factory=list, description="""semicolon-separated list of molecular activities"""
-    )
-    gene_functions: Optional[List[GeneMolecularActivityRelationship]] = Field(
-        default_factory=list,
-        description="""semicolon-separated list of gene to molecular activity relationships""",
-    )
-    cellular_processes: Optional[List[str]] = Field(
-        default_factory=list, description="""semicolon-separated list of cellular processes"""
-    )
-    pathways: Optional[List[str]] = Field(
-        default_factory=list, description="""semicolon-separated list of pathways"""
-    )
-    gene_gene_interactions: Optional[List[GeneGeneInteraction]] = Field(
-        default_factory=list,
-        description="""semicolon-separated list of gene to gene interactions""",
-    )
-    gene_localizations: Optional[List[GeneSubcellularLocalizationRelationship]] = Field(
-        default_factory=list,
-        description="""semicolon-separated list of genes plus their location in the cell;\
-            for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"""",
-    )
+    activities: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of molecular activities""")
+    gene_functions: Optional[List[GeneMolecularActivityRelationship]] = Field(default_factory=list, description="""semicolon-separated list of gene to molecular activity relationships""")
+    cellular_processes: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of cellular processes""")
+    pathways: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of pathways""")
+    gene_gene_interactions: Optional[List[GeneGeneInteraction]] = Field(default_factory=list, description="""semicolon-separated list of gene to gene interactions""")
+    gene_localizations: Optional[List[GeneSubcellularLocalizationRelationship]] = Field(default_factory=list, description="""semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"""")
+
 
 
 class ExtractionResult(ConfiguredBaseModel):
-    """A result of extracting knowledge on text."""
-
+    """
+    A result of extracting knowledge on text
+    """
     input_id: Optional[str] = Field(None)
     input_title: Optional[str] = Field(None)
     input_text: Optional[str] = Field(None)
     raw_completion_output: Optional[str] = Field(None)
     prompt: Optional[str] = Field(None)
-    extracted_object: Optional[Any] = Field(
-        None, description="""The complex objects extracted from the text"""
-    )
-    named_entities: Optional[List[Any]] = Field(
-        default_factory=list, description="""Named entities extracted from the text"""
-    )
+    extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""")
+    named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""")
+
 
 
 class NamedEntity(ConfiguredBaseModel):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class Gene(NamedEntity):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class Pathway(NamedEntity):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class CellularProcess(NamedEntity):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class MolecularActivity(NamedEntity):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class GeneLocation(NamedEntity):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class Organism(NamedEntity):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class Molecule(NamedEntity):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class CompoundExpression(ConfiguredBaseModel):
-    pass
+
+    None
+
 
 
 class GeneOrganismRelationship(CompoundExpression):
+
     gene: Optional[str] = Field(None)
     organism: Optional[str] = Field(None)
+
 
 
 class GeneMolecularActivityRelationship(CompoundExpression):
+
     gene: Optional[str] = Field(None)
     molecular_activity: Optional[str] = Field(None)
+
 
 
 class GeneMolecularActivityRelationship2(CompoundExpression):
+
     gene: Optional[str] = Field(None)
     molecular_activity: Optional[str] = Field(None)
     target: Optional[str] = Field(None)
+
 
 
 class GeneSubcellularLocalizationRelationship(CompoundExpression):
+
     gene: Optional[str] = Field(None)
     location: Optional[str] = Field(None)
+
 
 
 class GeneGeneInteraction(CompoundExpression):
+
     gene1: Optional[str] = Field(None)
     gene2: Optional[str] = Field(None)
+
 
 
 class Triple(CompoundExpression):
-    """Abstract parent for Relation Extraction tasks."""
-
+    """
+    Abstract parent for Relation Extraction tasks
+    """
     subject: Optional[str] = Field(None)
     predicate: Optional[str] = Field(None)
     object: Optional[str] = Field(None)
-    qualifier: Optional[str] = Field(
-        None, description="""A qualifier for the statements, e.g. \"NOT\" for negation"""
-    )
-    subject_qualifier: Optional[str] = Field(
-        None,
-        description="""An optional qualifier or modifier for the subject of the statement,\
-            e.g. \"high dose\" or \"intravenously administered\"""",
-    )
-    object_qualifier: Optional[str] = Field(
-        None,
-        description="""An optional qualifier or modifier for the object of the statement,\
-            e.g. \"severe\" or \"with additional complications\"""",
-    )
+    qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""")
+    subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""")
+    object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""")
+
 
 
 class TextWithTriples(ConfiguredBaseModel):
+
     publication: Optional[Publication] = Field(None)
     triples: Optional[List[Triple]] = Field(default_factory=list)
+
 
 
 class RelationshipType(NamedEntity):
+
     id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
 
 
 class Publication(ConfiguredBaseModel):
+
     id: Optional[str] = Field(None, description="""The publication identifier""")
     title: Optional[str] = Field(None, description="""The title of the publication""")
     abstract: Optional[str] = Field(None, description="""The abstract of the publication""")
     combined_text: Optional[str] = Field(None)
     full_text: Optional[str] = Field(None, description="""The full text of the publication""")
+
 
 
 class AnnotatorResult(ConfiguredBaseModel):
+
     subject_text: Optional[str] = Field(None)
     object_id: Optional[str] = Field(None)
     object_text: Optional[str] = Field(None)
+
+
 
 
 # Update forward refs
@@ -224,3 +241,4 @@ class AnnotatorResult(ConfiguredBaseModel):
 RelationshipType.update_forward_refs()
 Publication.update_forward_refs()
 AnnotatorResult.update_forward_refs()
+

tests/__init__.py

@@ -1,4 +1,4 @@
-"""Tests for oak-ai."""
+"""Tests for ontogpt."""
 import logging
 import os
 from pathlib import Path