From b25082a468ee6d0af83b844079457f214f3b4e5f Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 24 Sep 2024 12:32:59 -0400 Subject: [PATCH 1/8] Pin to linkml 1.8.3 to avoid pydantic weirdness --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d2bd920c2..594ecef14 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ fastapi = {version = ">=0.88.0", optional = true} gilda = ">=1.0.0" inflect = ">=6.0.2" inflection = ">=0.5.1" -linkml = "^1.8.0" +linkml = "^1.8.3" linkml-owl = "^0.3.0" myst-parser = {version = ">=0.18.1", extras = ["docs"], optional = true} oaklib = ">=0.5.28" From ea2ad35ad4efd9be9f8bf10aca9c9bc9a26ece90 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 24 Sep 2024 12:37:19 -0400 Subject: [PATCH 2/8] Bump to v1.0.5 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 594ecef14..8f94f3814 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "ontogpt" -version = "1.0.4" +version = "1.0.5" description = "OntoGPT" authors = ["Chris Mungall ", "J. 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src/ontogpt/engines/spires_engine.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/ontogpt/engines/spires_engine.py b/src/ontogpt/engines/spires_engine.py index 855382d76..6cdcdc63a 100644 --- a/src/ontogpt/engines/spires_engine.py +++ b/src/ontogpt/engines/spires_engine.py @@ -504,19 +504,21 @@ def _parse_response_to_dict( # First split the text into sections, denoted by presence of multiple newlines # Each section may still have multiple fields, but we don't know how # they will be formatted - sections = results.replace("*","").split("\n\n") + sections = results.replace("*", "").split("\n\n") ann = {} for section in sections: lines = section.splitlines() continued_line = "" for line in lines: - line = line.replace("*","").strip() + line = line.replace("*", "").strip() # The line may be split into multiple lines, # and we can only tell if there's a delimiter at the end of this one # (though it may just be a misplaced delimiter) # TODO: this could be a different delimiter, globally defined if line.endswith(";"): - logging.info(f"This line ends in a delimiter, assuming continuation: {line}") + logging.info( + f"This line ends in a delimiter, assuming continuation: {line}" + ) continued_line = line continue # If there's nothing after the colon, From 499d055d232092d229f07403526d8454a8db6768 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 24 Sep 2024 12:40:31 -0400 Subject: [PATCH 5/8] Linting knowledge engine --- src/ontogpt/engines/knowledge_engine.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/ontogpt/engines/knowledge_engine.py b/src/ontogpt/engines/knowledge_engine.py index 3e701b0d9..40ae76801 100644 --- a/src/ontogpt/engines/knowledge_engine.py +++ b/src/ontogpt/engines/knowledge_engine.py @@ -51,11 +51,13 @@ def chunk_text_by_sentence(text: str, window_size=3) -> Iterator[str]: left_index = max(0, right_index - window_size) yield ". ".join(sentences[left_index:right_index]) + def chunk_text_by_char(text: str, window_size=1000) -> Iterator[str]: """Chunk text into windows of characters.""" for i in range(0, len(text), window_size): yield text[i : i + window_size] + @dataclass class KnowledgeEngine(ABC): """ From 955dd8763013d47bf99534f5bc8b092156949c08 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 24 Sep 2024 12:40:54 -0400 Subject: [PATCH 6/8] Linting topic classifier engine --- src/ontogpt/engines/topic_classifier_engine.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontogpt/engines/topic_classifier_engine.py b/src/ontogpt/engines/topic_classifier_engine.py index ef7fcc1c9..21f73d1e1 100644 --- a/src/ontogpt/engines/topic_classifier_engine.py +++ b/src/ontogpt/engines/topic_classifier_engine.py @@ -8,6 +8,7 @@ logger = logging.getLogger(__name__) + @dataclass class TopicClassifierEngine(KnowledgeEngine): """Engine for classifying input text based on its topic.""" From 4a1a731687d32582a5bfeaf9a463bc7ba258ede6 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 24 Sep 2024 12:45:46 -0400 Subject: [PATCH 7/8] Add docstrings to engines --- .../engines/embedding_similarity_engine.py | 22 ++++++++++++++-- src/ontogpt/engines/mapping_engine.py | 26 ++++++++++++++++++- src/ontogpt/engines/reasoner_engine.py | 22 +++++++++++++++- src/ontogpt/engines/synonym_engine.py | 14 +++++++++- .../engines/topic_classifier_engine.py | 15 ++++++++++- 5 files changed, 93 insertions(+), 6 deletions(-) diff --git a/src/ontogpt/engines/embedding_similarity_engine.py b/src/ontogpt/engines/embedding_similarity_engine.py index 09ca5a8e1..07955b606 100644 --- a/src/ontogpt/engines/embedding_similarity_engine.py +++ b/src/ontogpt/engines/embedding_similarity_engine.py @@ -1,4 +1,22 @@ -"""Similarity engine.""" +""" +Embedding similarity engine. + +This module provides functionality for calculating the similarity between entities +using embeddings and cosine similarity. It includes classes and methods for +searching for similar entities and retrieving textual representations of entities. + +Classes: + EmbeddingSimilarity: A dataclass representing the similarity between two entities. + SimilarityEngine: A class for calculating similarity between entities. + +Methods: + SimilarityEngine.similarity(entity1: str, entity2: str) -> EmbeddingSimilarity: + Get similarity between two entities. + SimilarityEngine.search(entity1: str, entities: List[str]) -> Iterable[EmbeddingSimilarity]: + Search for similar entities. + SimilarityEngine.entity_text(entity: str) -> str: + Get text representation for an entity. +""" import logging from dataclasses import dataclass @@ -25,7 +43,7 @@ class EmbeddingSimilarity: @dataclass class SimilarityEngine(KnowledgeEngine): - """Engine for generating synonyms.""" + """Engine for finding embedding similarity.""" adapter: BasicOntologyInterface = None autolabel: bool = True diff --git a/src/ontogpt/engines/mapping_engine.py b/src/ontogpt/engines/mapping_engine.py index c704e2dab..0a25db297 100644 --- a/src/ontogpt/engines/mapping_engine.py +++ b/src/ontogpt/engines/mapping_engine.py @@ -1,4 +1,28 @@ -"""Synonym engine.""" +""" +Mapping engine. + +This module provides the `MappingEngine` class, which is responsible for generating and resolving mappings between concepts in different ontologies. It utilizes various classes and enums to represent mapping tasks, categorized mappings, and confidence levels. + +Classes: + MappingPredicate: Enum representing different types of mapping predicates. + Confidence: Enum representing different levels of confidence. + CategorizedMapping: Model representing a categorized mapping with various attributes. + MappingTask: Model representing a mapping task with various attributes. + MappingTaskCollection: Model representing a collection of mapping tasks. + Relationship: Model representing a relationship between concepts. + Concept: Model representing a concept with various attributes. + MappingEngine: Engine class for generating and resolving mappings. + +Functions: + categorize_mapping: Categorizes a mapping between a subject and an object using a template. + _parse: Parses the payload from the categorization process into a `CategorizedMapping`. + categorize_mappings: Categorizes multiple mappings between subjects and object sources. + run_tasks: Runs a collection of mapping tasks and categorizes the results. + generate_tasks: Generates mapping tasks from a collection or specified subjects and object sources. + from_sssom: Generates tasks from an SSSOM file. + categorize_sssom_mapping: Categorizes a single SSSOM mapping. + _concept: Retrieves a concept from an ontology adapter. +""" import logging from copy import deepcopy diff --git a/src/ontogpt/engines/reasoner_engine.py b/src/ontogpt/engines/reasoner_engine.py index 1b2925fa3..c2d38bc1b 100644 --- a/src/ontogpt/engines/reasoner_engine.py +++ b/src/ontogpt/engines/reasoner_engine.py @@ -1,4 +1,24 @@ -"""Reasoner engine.""" +""" +Reasoner engine. + +This module provides the implementation of the ReasonerEngine class, which is used to perform reasoning tasks using a Language Model (LLM). The engine takes an ontology and a query task as input, translates it into an LLM prompt, and performs reasoning over the ontology. + +Classes: + ReasonerResult: Represents the result of a reason query. + ReasonerResultSet: Represents a set of reasoner results. + ReasonerEngine: Engine for performing reasoning using an LLM. + +Functions: + flatten_list(lst): Flattens a nested list into a single list. + reason(task, template_path=None, strict=False, evaluate=None): Performs reasoning over axioms and query entailments. + reason_multiple(task_collection, **kwargs): Performs reasoning over multiple tasks. + _parse_single_answer(payload, task): Parses a single answer from the payload. + evaluate(result, task): Evaluates the result against the task. + +Usage: + The ReasonerEngine can be used to perform reasoning tasks such as finding superclasses of a given class. + It can also provide explanations for the reasoning process. +""" import logging import re diff --git a/src/ontogpt/engines/synonym_engine.py b/src/ontogpt/engines/synonym_engine.py index 49dda3cec..e2d21a57f 100644 --- a/src/ontogpt/engines/synonym_engine.py +++ b/src/ontogpt/engines/synonym_engine.py @@ -1,4 +1,16 @@ -"""Synonym engine.""" +""" +Synonym engine. + +This module defines the SynonymEngine class, which is responsible for generating synonyms for given named entities within a specified domain. + +Classes: + SynonymEngine: Inherits from KnowledgeEngine and provides a method to retrieve synonyms. + +Methods: + synonyms(named_entity: str, domain: str) -> List[str]: + Retrieves synonyms for the given named entity within the specified domain. +""" + from dataclasses import dataclass from typing import List diff --git a/src/ontogpt/engines/topic_classifier_engine.py b/src/ontogpt/engines/topic_classifier_engine.py index 21f73d1e1..ca38e7bda 100644 --- a/src/ontogpt/engines/topic_classifier_engine.py +++ b/src/ontogpt/engines/topic_classifier_engine.py @@ -1,4 +1,17 @@ -"""Topic classifier engine.""" +""" +Topic classifier engine. + +This module contains the `TopicClassifierEngine` class, which inherits from `KnowledgeEngine`. +The engine is designed to classify input text based on a given topic. + +Classes: + TopicClassifierEngine: Engine for classifying input text based on its topic. + +Methods: + binary_classify(topic: str, text: str) -> bool: + Given a topic description, indicate whether it applies to the input text. + Returns True if the text matches the topic, otherwise returns False. +""" import logging From 8c4fab8a149f9f1a59305d25413c77b3f4f88bcf Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 24 Sep 2024 12:53:37 -0400 Subject: [PATCH 8/8] Further Linting --- src/ontogpt/clients/llm_client.py | 1 + src/ontogpt/engines/embedding_similarity_engine.py | 2 +- src/ontogpt/engines/mapping_engine.py | 12 +++++++++--- src/ontogpt/engines/reasoner_engine.py | 13 ++++++++++--- src/ontogpt/engines/synonym_engine.py | 10 +++++++--- src/ontogpt/evaluation/maxo/eval_maxo.py | 4 +++- src/ontogpt/utils/clinical_cases.py | 2 +- src/ontogpt/webapp/main.py | 4 +--- 8 files changed, 33 insertions(+), 15 deletions(-) diff --git a/src/ontogpt/clients/llm_client.py b/src/ontogpt/clients/llm_client.py index 6768e934d..38a4896af 100644 --- a/src/ontogpt/clients/llm_client.py +++ b/src/ontogpt/clients/llm_client.py @@ -20,6 +20,7 @@ # Necessary to avoid repeated debug messages litellm.suppress_debug_info = True + @dataclass class LLMClient: diff --git a/src/ontogpt/engines/embedding_similarity_engine.py b/src/ontogpt/engines/embedding_similarity_engine.py index 07955b606..1b8e6cd4b 100644 --- a/src/ontogpt/engines/embedding_similarity_engine.py +++ b/src/ontogpt/engines/embedding_similarity_engine.py @@ -2,7 +2,7 @@ Embedding similarity engine. This module provides functionality for calculating the similarity between entities -using embeddings and cosine similarity. It includes classes and methods for +using embeddings and cosine similarity. It includes classes and methods for searching for similar entities and retrieving textual representations of entities. Classes: diff --git a/src/ontogpt/engines/mapping_engine.py b/src/ontogpt/engines/mapping_engine.py index 0a25db297..9e8cd7448 100644 --- a/src/ontogpt/engines/mapping_engine.py +++ b/src/ontogpt/engines/mapping_engine.py @@ -1,7 +1,11 @@ """ Mapping engine. -This module provides the `MappingEngine` class, which is responsible for generating and resolving mappings between concepts in different ontologies. It utilizes various classes and enums to represent mapping tasks, categorized mappings, and confidence levels. +This module provides the `MappingEngine` class, +which is responsible for generating and resolving +mappings between concepts in different ontologies. +It utilizes various classes and enums to represent +mapping tasks, categorized mappings, and confidence levels. Classes: MappingPredicate: Enum representing different types of mapping predicates. @@ -14,11 +18,13 @@ MappingEngine: Engine class for generating and resolving mappings. Functions: - categorize_mapping: Categorizes a mapping between a subject and an object using a template. + categorize_mapping: Categorizes a mapping between a subject + and an object using a template. _parse: Parses the payload from the categorization process into a `CategorizedMapping`. categorize_mappings: Categorizes multiple mappings between subjects and object sources. run_tasks: Runs a collection of mapping tasks and categorizes the results. - generate_tasks: Generates mapping tasks from a collection or specified subjects and object sources. + generate_tasks: Generates mapping tasks from a collection or + specified subjects and object sources. from_sssom: Generates tasks from an SSSOM file. categorize_sssom_mapping: Categorizes a single SSSOM mapping. _concept: Retrieves a concept from an ontology adapter. diff --git a/src/ontogpt/engines/reasoner_engine.py b/src/ontogpt/engines/reasoner_engine.py index c2d38bc1b..57b44180e 100644 --- a/src/ontogpt/engines/reasoner_engine.py +++ b/src/ontogpt/engines/reasoner_engine.py @@ -1,7 +1,12 @@ """ Reasoner engine. -This module provides the implementation of the ReasonerEngine class, which is used to perform reasoning tasks using a Language Model (LLM). The engine takes an ontology and a query task as input, translates it into an LLM prompt, and performs reasoning over the ontology. +This module provides the implementation of the +ReasonerEngine class, which is used to perform +reasoning tasks using a Language Model (LLM). +The engine takes an ontology and a query task as input, +translates it into an LLM prompt, and performs +reasoning over the ontology. Classes: ReasonerResult: Represents the result of a reason query. @@ -10,13 +15,15 @@ Functions: flatten_list(lst): Flattens a nested list into a single list. - reason(task, template_path=None, strict=False, evaluate=None): Performs reasoning over axioms and query entailments. + reason(task, template_path=None, strict=False, evaluate=None): Performs + reasoning over axioms and query entailments. reason_multiple(task_collection, **kwargs): Performs reasoning over multiple tasks. _parse_single_answer(payload, task): Parses a single answer from the payload. evaluate(result, task): Evaluates the result against the task. Usage: - The ReasonerEngine can be used to perform reasoning tasks such as finding superclasses of a given class. + The ReasonerEngine can be used to perform reasoning tasks + such as finding superclasses of a given class. It can also provide explanations for the reasoning process. """ diff --git a/src/ontogpt/engines/synonym_engine.py b/src/ontogpt/engines/synonym_engine.py index e2d21a57f..74b7c0654 100644 --- a/src/ontogpt/engines/synonym_engine.py +++ b/src/ontogpt/engines/synonym_engine.py @@ -1,14 +1,18 @@ """ Synonym engine. -This module defines the SynonymEngine class, which is responsible for generating synonyms for given named entities within a specified domain. +This module defines the SynonymEngine class, +which is responsible for generating synonyms +for given named entities within a specified domain. Classes: - SynonymEngine: Inherits from KnowledgeEngine and provides a method to retrieve synonyms. + SynonymEngine: Inherits from KnowledgeEngine and + provides a method to retrieve synonyms. Methods: synonyms(named_entity: str, domain: str) -> List[str]: - Retrieves synonyms for the given named entity within the specified domain. + Retrieves synonyms for the given named entity + within the specified domain. """ from dataclasses import dataclass diff --git a/src/ontogpt/evaluation/maxo/eval_maxo.py b/src/ontogpt/evaluation/maxo/eval_maxo.py index bce44500d..bf52118b8 100644 --- a/src/ontogpt/evaluation/maxo/eval_maxo.py +++ b/src/ontogpt/evaluation/maxo/eval_maxo.py @@ -244,7 +244,9 @@ def eval(self) -> EvaluationObjectSetRE: if extraction.extracted_object is not None: # Process all multi-object triples to 1 to 1 triples # so they may be more directly compared - for extracted_triple in extraction.extracted_object.action_annotation_relationships: + for ( + extracted_triple + ) in extraction.extracted_object.action_annotation_relationships: new_triple = extracted_triple for object in extracted_triple.object: new_triple.object = [object] diff --git a/src/ontogpt/utils/clinical_cases.py b/src/ontogpt/utils/clinical_cases.py index 6c8cf704d..2aaffea57 100644 --- a/src/ontogpt/utils/clinical_cases.py +++ b/src/ontogpt/utils/clinical_cases.py @@ -30,4 +30,4 @@ def get_kanjee_prompt() -> str: " the diagnoses. Again, the goal is to be as specific as possible with each of the " "diagnoses. Do you have any questions, Dr. GPT-4?\n\nHere is the case:" ) - return prompt \ No newline at end of file + return prompt diff --git a/src/ontogpt/webapp/main.py b/src/ontogpt/webapp/main.py index 6ae7007de..b7f906306 100644 --- a/src/ontogpt/webapp/main.py +++ b/src/ontogpt/webapp/main.py @@ -55,9 +55,7 @@ class Query(BaseModel): def get_engine(datamodel: str, llm_model: str): if datamodel not in engines: template_details = get_template_details(template=datamodel) - engines[datamodel] = SPIRESEngine( - model=llm_model, template_details=template_details - ) + engines[datamodel] = SPIRESEngine(model=llm_model, template_details=template_details) return engines[datamodel]