diff --git a/poetry.lock b/poetry.lock index 58f60ffdd..9aca96e0b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,13 +1,13 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "adeft" -version = "0.11.2" +version = "0.12.3" description = "Acromine based Disambiguation of Entities From Text" optional = false -python-versions = "*" +python-versions = ">=3.7" files = [ - {file = "adeft-0.11.2.tar.gz", hash = "sha256:bf9b239d7989217b7d673eaf46ac2e8c1bfc97a0aac9a75cc2231e07438fc0a5"}, + {file = "adeft-0.12.3.tar.gz", hash = "sha256:3106eb30e5a655caf67db8433b265afa3f292e99bcdf76a720d0c180d2d4b8bb"}, ] [package.dependencies] @@ -15,7 +15,7 @@ appdirs = "*" boto3 = "*" flask = "*" nltk = "*" -scikit-learn = ">=0.20.0" +scikit-learn = ">=1.0" [package.extras] test = ["pytest", "pytest-cov"] @@ -218,19 +218,16 @@ files = [ ] [[package]] -name = "ansiwrap" -version = "0.8.4" -description = "textwrap, but savvy to ANSI colors and styles" +name = "ansicolors" +version = "1.1.8" +description = "ANSI colors for Python" optional = false python-versions = "*" files = [ - {file = "ansiwrap-0.8.4-py2.py3-none-any.whl", hash = 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"fastapi", "uvicorn"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.9.7 || >3.9.7,<4.0" -content-hash = "57f3d82ad605cf9ec344c0597abfccf790c9a8be99c21b302e14a5a4dee04afa" +content-hash = "6810458081d5d7de66103247b9e2fe6ba9621ed1da63b379f1497d1bdfd6aa30" diff --git a/pyproject.toml b/pyproject.toml index 03059d027..ac9e648ba 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -69,7 +69,8 @@ docs = [ web = [ "fastapi", "uvicorn", - "Jinja2" + "Jinja2", + "python-multipart" ] recipes = [ "recipe-scrapers" diff --git a/src/ontogpt/webapp/html/form.html b/src/ontogpt/webapp/html/form.html index fafa0541f..1b94152e5 100644 --- a/src/ontogpt/webapp/html/form.html +++ b/src/ontogpt/webapp/html/form.html @@ -3,10 +3,42 @@ OntoGPT SPIRES: Enter text +
+

Information Extraction with SPIRES

Select Schema:
-->
-
- + This process currently uses GPT-4-Turbo through the OpenAI API. +
+
+ Please be patient, can take up to 10s
diff --git a/src/ontogpt/webapp/html/results.html b/src/ontogpt/webapp/html/results.html index 92f4b0dd9..eff739eeb 100644 --- a/src/ontogpt/webapp/html/results.html +++ b/src/ontogpt/webapp/html/results.html @@ -1,11 +1,29 @@ - - SPIRES: Results + + SPIRES: Results + -
+
Try another!
diff --git a/src/ontogpt/webapp/main.py b/src/ontogpt/webapp/main.py index ac099ff9d..a9faec281 100644 --- a/src/ontogpt/webapp/main.py +++ b/src/ontogpt/webapp/main.py @@ -1,4 +1,5 @@ """Webapp main function.""" + from io import StringIO from pathlib import Path from typing import Dict @@ -9,7 +10,6 @@ from starlette.staticfiles import StaticFiles from starlette.templating import Jinja2Templates -from ontogpt.engines.knowledge_engine import DATAMODELS from ontogpt.engines.spires_engine import SPIRESEngine from ontogpt.io.html_exporter import HTMLExporter from ontogpt.io.template_loader import get_template_details @@ -18,6 +18,29 @@ static_dir = this_path / "static" html_dir = this_path / "html" +DATAMODELS = [ + "biological_process.BiologicalProcess", + "biotic_interaction.BioticInteraction", + "cell_type.CellTypeDocument", + "condition", + "ctd.ChemicalToDiseaseDocument", + "data_sheets_schema", + "diagnostic_procedure.DiagnosticProceduretoPhenotypeAssociation", + "dietitian_notes", + "drug.DrugMechanism", + "emapa_simple", + "environmental_sample.Study", + "figure", + "go_simple", + "gocam.GoCamAnnotations", + "mendelian_disease.MendelianDisease", + "maxo", + "mondo_simple", + "phenotype.Trait", + "reaction.Reaction", + "recipe.Recipe", + "treatment.DiseaseTreatmentSummary", +] class Query(BaseModel): text: str @@ -37,7 +60,9 @@ class Query(BaseModel): def get_engine(datamodel: str): if datamodel not in engines: template_details = get_template_details(template=datamodel) - engines[datamodel] = SPIRESEngine(template_details=template_details) + engines[datamodel] = SPIRESEngine( + model="gpt-4-turbo", template_details=template_details, model_source="openai" + ) return engines[datamodel]