feat: Fhir template (#13)

.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"

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

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]

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

src/anamnesisai/templates/allergy.json

@@ -0,0 +1,12 @@
+{
+  "AllergyIntolerance": {
+    "resourceType": "AllergyIntolerance",
+    "id": "<AllergyIntolerance ID>",
+    "patient": {
+      "reference": "Patient/<Patient ID>"
+    },
+    "substance": {
+      "coding": []
+    }
+  }
+}

src/anamnesisai/templates/careplan.json

@@ -0,0 +1,4 @@
+{
+  "resourceType": "CarePlan",
+  "id": "<Placeholder: diisi setelah care plan tersedia>"
+}

src/anamnesisai/templates/condition.json

@@ -0,0 +1,4 @@
+{
+  "resourceType": "Condition",
+  "id": "<Placeholder: diisi setelah diagnosis tersedia>"
+}

src/anamnesisai/templates/diagnostic_report.json

@@ -0,0 +1,4 @@
+{
+  "resourceType": "DiagnosticReport",
+  "id": "<Placeholder: diisi setelah hasil pemeriksaan tersedia>"
+}

src/anamnesisai/templates/encounter.json

@@ -0,0 +1,35 @@
+{
+  "resourceType": "Encounter",
+  "id": "<Encounter ID>",
+  "status": "finished",
+  "subject": {
+    "reference": "Patient/<Patient ID>"
+  },
+  "participant": [
+    {
+      "type": [
+        {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/encounter-participant-type",
+              "code": "TPA"
+            }
+          ]
+        }
+      ],
+      "actor": {
+        "reference": "Practitioner/<Practitioner ID>"
+      }
+    }
+  ],
+  "reasonCode": [
+    {
+      "coding": [
+        {
+          "system": "<Reason Code System>",
+          "code": "<Reason Code>"
+        }
+      ]
+    }
+  ]
+}

src/anamnesisai/templates/medication_request.json

@@ -0,0 +1,4 @@
+{
+  "resourceType": "MedicationRequest",
+  "id": "<Placeholder: diisi setelah prescription details tersedia>"
+}

src/anamnesisai/templates/observation.json

@@ -0,0 +1,25 @@
+{
+  "resourceType": "Observation",
+  "id": "<Observation ID>",
+  "status": "final",
+  "subject": {
+    "reference": "Patient/<Patient ID>"
+  },
+  "category": {
+    "coding": [
+      {
+        "system": "<Observation Category Coding System>",
+        "code": "<Observation Category Code>"
+      }
+    ]
+  },
+  "code": {
+    "coding": [
+      {
+        "system": "<Observation Code System>",
+        "code": "<Observation Code>"
+      }
+    ]
+  },
+  "value": "<Observation Value>"
+}

src/anamnesisai/templates/patients.json

@@ -0,0 +1,37 @@
+{
+  "resourceType": "Patient",
+  "id": "<Patient ID>",
+  "active": true,
+  "name": [
+    {
+      "use": "official",
+      "text": "<Patient Full Name>"
+    }
+  ],
+  "telecom": [
+    {
+      "system": "phone",
+      "value": "<Patient Phone Number>"
+    },
+    {
+      "system": "email",
+      "value": "<Patient Email Address>"
+    }
+  ],
+  "birthDate": "<Patient Date of Birth>",
+  "gender": "<Patient Gender>",
+  "maritalStatus": {
+    "coding": [
+      {
+        "system": "<Marital Status Coding System>",
+        "code": "<Marital Status Code>"
+      }
+    ]
+  },
+  "address": [
+    {
+      "use": "home",
+      "text": "<Patient Address>"
+    }
+  ]
+}

src/anamnesisai/templates/practitioner.json

@@ -0,0 +1,17 @@
+{
+  "resourceType": "Practitioner",
+  "id": "<Practitioner ID>",
+  "active": true,
+  "name": [
+    {
+      "use": "official",
+      "text": "<Practitioner Full Name>"
+    }
+  ],
+  "telecom": [
+    {
+      "system": "phone",
+      "value": "<Practitioner Phone Number>"
+    }
+  ]
+}

src/anamnesisai/templates/procedure.json

@@ -0,0 +1,4 @@
+{
+  "resourceType": "Procedure",
+  "id": "<Placeholder: diisi setelah procedures tersedia>"
+}