diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index e522cdc..b66e511 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -52,6 +52,32 @@ jobs: steps: - uses: actions/checkout@v3 +<<<<<<< HEAD + - name: Install MacOS extra tools and add extra setup + if: ${{ matrix.os == 'macos' }} + run: | + sudo mkdir -p /tmp + sudo chmod 777 /tmp + + brew install gnu-sed + echo 'export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"' >> ~/.bashrc + echo 'export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"' >> ~/.bash_profile + + - name: Prepare conda environment (windows) + if: ${{ matrix.os == 'windows' }} + run: | + $env:Path += ";C:\Program Files\Git\usr\bin" + sed -i s/python\ 3\.8/python\ ${{ matrix.python_version }}/ conda/dev.yaml + cat conda/dev.yaml + + - name: Prepare conda environment + if: ${{ matrix.os != 'windows' }} + run: | + sed -i s/python\ 3\.8/python\ ${{ matrix.python_version }}/ conda/dev.yaml + cat conda/dev.yaml + +======= +>>>>>>> upstream/main - uses: conda-incubator/setup-miniconda@v3 with: miniconda-version: "latest" diff --git a/.idea/.gitignore b/.idea/.gitignore new file mode 100644 index 0000000..26d3352 --- /dev/null +++ b/.idea/.gitignore @@ -0,0 +1,3 @@ +# Default ignored files +/shelf/ +/workspace.xml diff --git a/.idea/anamnesis.ai.iml b/.idea/anamnesis.ai.iml new file mode 100644 index 0000000..788e50d --- /dev/null +++ b/.idea/anamnesis.ai.iml @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml new file mode 100644 index 0000000..105ce2d --- /dev/null +++ b/.idea/inspectionProfiles/profiles_settings.xml @@ -0,0 +1,6 @@ + + + + \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml new file mode 100644 index 0000000..81d6200 --- /dev/null +++ b/.idea/misc.xml @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml new file mode 100644 index 0000000..f7bf212 --- /dev/null +++ b/.idea/modules.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 0000000..35eb1dd --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/conda/dev.yaml b/conda/dev.yaml index 03feea2..2d8bc59 100644 --- a/conda/dev.yaml +++ b/conda/dev.yaml @@ -3,11 +3,20 @@ channels: - nodefaults - conda-forge dependencies: +<<<<<<< HEAD + - python 3.8 +======= - python +>>>>>>> upstream/main - pip - poetry - nodejs # used by semantic-release - shellcheck - pip: +<<<<<<< HEAD + # distlib issue + - paginate +======= # distlib issues - paginate +>>>>>>> upstream/main diff --git a/poetry.lock b/poetry.lock index 27d63d4..fc76c86 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,6 +1,119 @@ # This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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"3b422848c1915ace059145c6ffa34db2cff1171151912b69163049e5e0f98bf6" +>>>>>>> upstream/main diff --git a/pyproject.toml b/pyproject.toml index 94dbc82..40bc742 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,8 +14,13 @@ exclude = [ [tool.poetry.dependencies] python = ">=3.8.1,<4" +<<<<<<< HEAD +langchain = "^0.1.12" +openai = "^1.14.1" +======= sqlmodel = ">=0.0.16" fhir-resources = ">=7.1.0" +>>>>>>> upstream/main [tool.poetry.group.dev.dependencies] diff --git a/src/anamnesisai/anamnesisai.py b/src/anamnesisai/anamnesisai.py index 0c7fed1..4110a44 100644 --- a/src/anamnesisai/anamnesisai.py +++ b/src/anamnesisai/anamnesisai.py @@ -1 +1,64 @@ -"""Anamnesis.ai.""" +# from dotenv import load_dotenv +# load_dotenv() +import json +import os + +from langchain import OpenAI +from langchain.embeddings import HuggingFaceEmbeddings +from langchain.prompts import ( + SemanticSimilarityExampleSelector, +) +from langchain.prompts.prompt import PromptTemplate +from langchain.utilities import SQLDatabase +from langchain.vectorstores import Chroma +from langchain_experimental.sql import SQLDatabaseChain + +with open("resource_templates.json", "r") as f: + resource_templates = json.load(f) + + +def db_chain(): + db_user = "root" + db_password = "root" + db_host = "localhost" + db_name = "Fhir" + + db = SQLDatabase.from_uri( + f"mysql+pymysql://{db_user}:{db_password}@{db_host}/{db_name}", + sample_rows_in_table_info=3, + ) + llm = OpenAI(openai_api_key=os.environ["API_KEY"], temperature=0.7) + + embeddings = HuggingFaceEmbeddings( + model_name="sentence-transformers/all-MiniLM-L6-v2" + ) + to_vectorize = [" ".join(example.values()) for example in database] + vectorstore = Chroma.from_texts( + to_vectorize, embeddings, metadatas=database + ) # need to create a database file to share the format of sql database + example_selector = SemanticSimilarityExampleSelector( + vectorstore=vectorstore, + k=2, + ) + fhir_prompt = """You are a FHIR Resource generating expert. Given a converstion between doctor and patient, first create a syntactically correct FHIR resource in JSON Format as specified by the user then look at the results and return the FHIR resource to the input conversation. + Never create random values for values that are not present in the conversation. You must only the columns that are needed to answer the question. Wrap each column name in backticks (`) to denote them as delimited identifiers. + Generate the following FHIR resources based on the conversation and exam: + Patient: Capture the patient's demographics and medical history details. + Practitioner: Identify the doctor involved in the encounter. + Encounter: Describe the patient-doctor interaction, including the reason for the visit. + Observation: Record the patient's reported symptoms and the physical exam findings. + + Use clear and concise language for each resource. Maintain patient confidentiality and adhere to HIPAA regulations. Strive for accuracy and consistency in your FHIR structures. + resource_template = resource_templates["resource"] + No pre-amble. + """ + + example_prompt = PromptTemplate( + input_variables=["Conversation"], + template="\nConversation: {Conversation}\nFhir: {Resource}\nResource Template: {ResourceTemplate}", + ) + + chain = SQLDatabaseChain.from_llm( + llm, db, verbose=True, prompt=few_shot_prompt + ) + return chain diff --git a/src/anamnesisai/templates/allergy.json b/src/anamnesisai/templates/allergy.json new file mode 100644 index 0000000..84343a9 --- /dev/null +++ b/src/anamnesisai/templates/allergy.json @@ -0,0 +1,12 @@ +{ + "AllergyIntolerance": { + "resourceType": "AllergyIntolerance", + "id": "", + "patient": { + "reference": "Patient/" + }, + "substance": { + "coding": [] + } + } +} diff --git a/src/anamnesisai/templates/careplan.json b/src/anamnesisai/templates/careplan.json new file mode 100644 index 0000000..6071e87 --- /dev/null +++ b/src/anamnesisai/templates/careplan.json @@ -0,0 +1,4 @@ +{ + "resourceType": "CarePlan", + "id": "" +} diff --git a/src/anamnesisai/templates/condition.json b/src/anamnesisai/templates/condition.json new file mode 100644 index 0000000..06d88ae --- /dev/null +++ b/src/anamnesisai/templates/condition.json @@ -0,0 +1,4 @@ +{ + "resourceType": "Condition", + "id": "" +} diff --git a/src/anamnesisai/templates/diagnostic_report.json b/src/anamnesisai/templates/diagnostic_report.json new file mode 100644 index 0000000..dc94468 --- /dev/null +++ b/src/anamnesisai/templates/diagnostic_report.json @@ -0,0 +1,4 @@ +{ + "resourceType": "DiagnosticReport", + "id": "" +} diff --git a/src/anamnesisai/templates/encounter.json b/src/anamnesisai/templates/encounter.json new file mode 100644 index 0000000..d70447e --- /dev/null +++ b/src/anamnesisai/templates/encounter.json @@ -0,0 +1,35 @@ +{ + "resourceType": "Encounter", + "id": "", + "status": "finished", + "subject": { + "reference": "Patient/" + }, + "participant": [ + { + "type": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/encounter-participant-type", + "code": "TPA" + } + ] + } + ], + "actor": { + "reference": "Practitioner/" + } + } + ], + "reasonCode": [ + { + "coding": [ + { + "system": "", + "code": "" + } + ] + } + ] +} diff --git a/src/anamnesisai/templates/medication_request.json b/src/anamnesisai/templates/medication_request.json new file mode 100644 index 0000000..3801772 --- /dev/null +++ b/src/anamnesisai/templates/medication_request.json @@ -0,0 +1,4 @@ +{ + "resourceType": "MedicationRequest", + "id": "" +} diff --git a/src/anamnesisai/templates/observation.json b/src/anamnesisai/templates/observation.json new file mode 100644 index 0000000..4ddd3aa --- /dev/null +++ b/src/anamnesisai/templates/observation.json @@ -0,0 +1,25 @@ +{ + "resourceType": "Observation", + "id": "", + "status": "final", + "subject": { + "reference": "Patient/" + }, + "category": { + "coding": [ + { + "system": "", + "code": "" + } + ] + }, + "code": { + "coding": [ + { + "system": "", + "code": "" + } + ] + }, + "value": "" +} diff --git a/src/anamnesisai/templates/patients.json b/src/anamnesisai/templates/patients.json new file mode 100644 index 0000000..41fb940 --- /dev/null +++ b/src/anamnesisai/templates/patients.json @@ -0,0 +1,37 @@ +{ + "resourceType": "Patient", + "id": "", + "active": true, + "name": [ + { + "use": "official", + "text": "" + } + ], + "telecom": [ + { + "system": "phone", + "value": "" + }, + { + "system": "email", + "value": "" + } + ], + "birthDate": "", + "gender": "", + "maritalStatus": { + "coding": [ + { + "system": "", + "code": "" + } + ] + }, + "address": [ + { + "use": "home", + "text": "" + } + ] +} diff --git a/src/anamnesisai/templates/practitioner.json b/src/anamnesisai/templates/practitioner.json new file mode 100644 index 0000000..54b4347 --- /dev/null +++ b/src/anamnesisai/templates/practitioner.json @@ -0,0 +1,17 @@ +{ + "resourceType": "Practitioner", + "id": "", + "active": true, + "name": [ + { + "use": "official", + "text": "" + } + ], + "telecom": [ + { + "system": "phone", + "value": "" + } + ] +} diff --git a/src/anamnesisai/templates/procedure.json b/src/anamnesisai/templates/procedure.json new file mode 100644 index 0000000..f2ba960 --- /dev/null +++ b/src/anamnesisai/templates/procedure.json @@ -0,0 +1,4 @@ +{ + "resourceType": "Procedure", + "id": "" +}