From 065932aa991bd5febb9bf05877470873e4006116 Mon Sep 17 00:00:00 2001 From: Ivar Flakstad <69173633+ivarflakstad@users.noreply.github.com> Date: Tue, 12 Mar 2024 08:40:17 +0100 Subject: [PATCH 1/6] Dockerize search app --- .gitignore | 2 +- .python-version | 1 + Dockerfile | 20 + README.md | 11 +- .../clinical_trial_sql_query_engine.py | 15 +- docker-compose.yml | 6 +- docker/Dockerfile.local | 21 - poetry.lock | 4936 ++++++++++++++++- pyproject.toml | 15 +- requirements/base.txt | 11 - requirements/development.txt | 1 - scripts/docker-entrypoint.sh | 3 - 12 files changed, 4982 insertions(+), 60 deletions(-) create mode 100644 .python-version create mode 100644 Dockerfile delete mode 100644 docker/Dockerfile.local delete mode 100644 requirements/base.txt delete mode 100644 requirements/development.txt delete mode 100755 scripts/docker-entrypoint.sh diff --git a/.gitignore b/.gitignore index 212554c9..3392b055 100644 --- a/.gitignore +++ b/.gitignore @@ -158,4 +158,4 @@ cython_debug/ # be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore # and can be added to the global gitignore or merged into this file. For a more nuclear # option (not recommended) you can uncomment the following to ignore the entire idea folder. -#.idea/ \ No newline at end of file +.idea/ diff --git a/.python-version b/.python-version new file mode 100644 index 00000000..2c073331 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 00000000..7e400ec0 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,20 @@ +# pull official base image +FROM python:3.11-slim + +# install system dependencies +RUN apt-get update && apt-get -y install libpq-dev gcc + + +# install python dependencies +COPY ./pyproject.toml / +COPY ./poetry.lock / +RUN pip install poetry uvicorn +RUN poetry config virtualenvs.create false +RUN poetry install --compile + +COPY ./app /app +COPY .env /.env + +EXPOSE 8000 + +CMD ["uvicorn", "app.main:app", "--host=0.0.0.0", "--port", "80"] diff --git a/README.md b/README.md index bed303c0..a897cdcb 100644 --- a/README.md +++ b/README.md @@ -82,15 +82,16 @@ The project might have multiple branches: `master`, `development`, etc. which ca ``` -### Tools Required - -- A text editor or an IDE (VsCode is Preferred) - ### Installation All installation steps go here. -- Install `poetry` for the dependencies. - `poetry install` +- Make sure `pyenv` is installed. +- Create a new virtual environment `python -m venv .venv` +- Activate the env `source .venv/bin/activate` +- Install poetry and uvicorn `pip install poetry uvicorn` +- Install dependencies `poetry install` +- Now you can run the project with `uvicorn ` - Set up Embedding Server from [TEI](https://github.com/huggingface/text-embeddings-inference/tree/main) diff --git a/app/rag/retrieval/clinical_trials/clinical_trial_sql_query_engine.py b/app/rag/retrieval/clinical_trials/clinical_trial_sql_query_engine.py index b2fdfa6c..b769dd4b 100644 --- a/app/rag/retrieval/clinical_trials/clinical_trial_sql_query_engine.py +++ b/app/rag/retrieval/clinical_trials/clinical_trial_sql_query_engine.py @@ -19,15 +19,12 @@ from typing import List from sqlalchemy import create_engine from pyvis.network import Network -import phoenix as px from app.config import OPENAPI_KEY, CLINICAL_TRIALS_TABLE_INFO_DIR, POSTGRES_ENGINE, EMBEDDING_MODEL_API, EMBEDDING_MODEL_NAME from app.services.search_utility import setup_logger logger = setup_logger('ClinicalTrialText2SQLEngine') -#px.launch_app(port=6060) - class TableInfo(BaseModel): """ Information regarding a structured table. @@ -47,7 +44,7 @@ class ClinicalTrialText2SQLEngine: """ def __init__(self, config): self.config = config - + self.llm = OpenAI(model="gpt-3.5-turbo", api_key=str(OPENAPI_KEY)) self.engine = create_engine(str(POSTGRES_ENGINE)) @@ -56,8 +53,8 @@ def __init__(self, config): self.sql_database = SQLDatabase(self.engine) self.table_node_mapping = SQLTableNodeMapping(self.sql_database) self.sql_retriever = SQLRetriever(self.sql_database) - - self.table_schema_objs = [SQLTableSchema(table_name=t.table_name, context_str=t.table_summary) for t in self.get_all_table_info()] + + self.table_schema_objs = [SQLTableSchema(table_name=t.table_name, context_str=t.table_summary) for t in self.get_all_table_info()] self.embed_model = TextEmbeddingsInference(base_url=EMBEDDING_MODEL_API, model_name=EMBEDDING_MODEL_NAME) self.obj_index = ObjectIndex.from_objects(objects=self.table_schema_objs, object_mapping=self.table_node_mapping, index_cls=VectorStoreIndex, embed_model=self.embed_model) @@ -85,7 +82,7 @@ def _get_table_info_with_index(self, idx: int) -> str: raise ValueError( f"More than one file matching index: {list(results_gen)}" ) - + def get_all_table_info(self): file_counts = len(os.listdir(CLINICAL_TRIALS_TABLE_INFO_DIR)) table_infos = [] @@ -122,7 +119,7 @@ def parse_response_to_sql(self, response: ChatResponse) -> str: response = response[:sql_result_start] logger.debug(f"ClinicalTrialText2SQLEngine.parse_response_to_sql sql: {response}") return response.strip().strip("```").strip() - + def get_response_synthesis_prompt(self, query_str, sql_query, context_str) -> PromptTemplate: response_synthesis_prompt_str = ( "Given an input question, synthesize a response from the query results.\n" @@ -179,7 +176,7 @@ def call_text2sql(self, search_text:str): except Exception as ex: logger.exception("ClinicalTrialText2SQLEngine.call_text2sql Exception -", exc_info = ex, stack_info=True) raise ex - + return { "result" : str(response) } diff --git a/docker-compose.yml b/docker-compose.yml index ac9dfa8c..09002b30 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,14 +1,10 @@ version: '3.8' services: - web: build: context: . - dockerfile: docker/Dockerfile.local - command: ./scripts/docker-entrypoint.sh - volumes: - - ./app:/usr/src/app + dockerfile: Dockerfile ports: - 8000:8000 depends_on: diff --git a/docker/Dockerfile.local b/docker/Dockerfile.local deleted file mode 100644 index af166350..00000000 --- a/docker/Dockerfile.local +++ /dev/null @@ -1,21 +0,0 @@ -# pull 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(>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "81b2fa642d7f2d1219cf80112ace12d689d053d81be7f7addb98144d56fc0fb2" +content-hash = "adff3ef924c9b8303f9fdb36249067cb83877de0c9628b2bba8c1c1b335a524a" diff --git a/pyproject.toml b/pyproject.toml index 0bfbd1f7..397d42bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [tool.poetry] -name = "search" +name = "app" version = "0.1.0" description = "A healthcare search engine" authors = ["raahul"] @@ -7,7 +7,18 @@ readme = "README.md" [tool.poetry.dependencies] python = "^3.11" - +fastapi = "^0.109.0" +fastapi-doc-http-response = "^0.0.3" +fastapi-redis-cache = "^0.2.5" +fastapi-versioning = "^0.10.0" +llama-index = "^0.10.18" +phoenix = "^0.9.1" +pyvis = "^0.3.2" +requests = "^2.31.0" +sqlalchemy = "^2.0.15" +authx = "1.0.1b1" +itsdangerous = "^2.1.2" +llama-index-embeddings-text-embeddings-inference = "^0.1.2" [build-system] requires = ["poetry-core"] diff --git a/requirements/base.txt b/requirements/base.txt deleted file mode 100644 index dbe0bdd8..00000000 --- a/requirements/base.txt +++ /dev/null @@ -1,11 +0,0 @@ -authx==0.9.1 -fastapi==0.110.0 -fastapi_doc_http_response==0.0.3 -fastapi_redis_cache==0.2.5 -fastapi_versioning==0.10.0 -llama_index==0.10.17 -phoenix==0.9.1 -pyvis==0.3.2 -Requests==2.31.0 -SQLAlchemy==1.4.39 -starlette==0.37.2 diff --git a/requirements/development.txt b/requirements/development.txt deleted file mode 100644 index a3e81b8d..00000000 --- a/requirements/development.txt +++ /dev/null @@ -1 +0,0 @@ --r base.txt diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh deleted file mode 100755 index fbf18d71..00000000 --- a/scripts/docker-entrypoint.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -alembic upgrade head -python server.py From daa8c2f60ff40c1ed593147754ed84e642db3b1b Mon Sep 17 00:00:00 2001 From: Ivar Flakstad <69173633+ivarflakstad@users.noreply.github.com> Date: Tue, 12 Mar 2024 08:45:40 +0100 Subject: [PATCH 2/6] Fix tests ci --- .github/workflows/tests.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index dd836f35..0e16a95a 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -10,7 +10,7 @@ jobs: strategy: max-parallel: 4 matrix: - python-version: ["3.10", "3.11"] + python-version: "3.11" services: postgres: @@ -26,17 +26,17 @@ jobs: steps: - uses: actions/checkout@v2 - - name: Setup Python ${{ matrix.python-version }} + - name: Setup Python uses: actions/setup-python@v2 with: - python-version: ${{ matrix.python-version }} - cache: 'pip' - cache-dependency-path: '**/requirements/development.txt' + python-version: "3.11" + cache: 'poetry' + cache-dependency-path: 'poetry.lock' - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install -r app/requirements/development.txt + python -m pip install poetry + poetry install - name: Run tests env: From 476f71e454c8c2b7b40107d02f4dfa3a0906e9e9 Mon Sep 17 00:00:00 2001 From: Ivar Flakstad <69173633+ivarflakstad@users.noreply.github.com> Date: Tue, 12 Mar 2024 09:08:18 +0100 Subject: [PATCH 3/6] Remove matrix setup for CI --- .github/workflows/tests.yaml | 20 ++++++-------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index 0e16a95a..1984440a 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -7,10 +7,6 @@ on: jobs: tests: runs-on: ubuntu-latest - strategy: - max-parallel: 4 - matrix: - python-version: "3.11" services: postgres: @@ -24,19 +20,15 @@ jobs: options: --health-cmd pg_isready --health-interval 5s --health-timeout 5s --health-retries 5 steps: - - uses: actions/checkout@v2 - - - name: Setup Python - uses: actions/setup-python@v2 + - uses: actions/checkout@v4 + - name: Install poetry + run: pipx install poetry + - uses: actions/setup-python@v5 with: - python-version: "3.11" cache: 'poetry' - cache-dependency-path: 'poetry.lock' - name: Install dependencies - run: | - python -m pip install poetry - poetry install + run: poetry install - name: Run tests env: @@ -45,4 +37,4 @@ jobs: DB_USER: postgres DB_PASS: postgres DB_BASE: db_test - run: cd app && pytest . + run: cd app && poetry run pytest From 6d1550d187c7156a8303ad1f7cf61e8d9bf6cf69 Mon Sep 17 00:00:00 2001 From: Ivar Flakstad <69173633+ivarflakstad@users.noreply.github.com> Date: Tue, 12 Mar 2024 10:02:38 +0100 Subject: [PATCH 4/6] Move pytest dependency to poetry dev group --- README.md | 2 +- poetry.lock | 48 +++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 3 +++ 3 files changed, 51 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a897cdcb..b1dcfc86 100644 --- a/README.md +++ b/README.md @@ -91,7 +91,7 @@ All installation steps go here. - Activate the env `source .venv/bin/activate` - Install poetry and uvicorn `pip install poetry uvicorn` - Install dependencies `poetry install` -- Now you can run the project with `uvicorn ` +- Now you can run the project with `uvicorn app.main:app --reload` - Set up Embedding Server from [TEI](https://github.com/huggingface/text-embeddings-inference/tree/main) diff --git a/poetry.lock b/poetry.lock index 6750c7dd..9136dee0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1377,6 +1377,17 @@ files = [ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["jaraco.collections", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"] +[[package]] +name = "iniconfig" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" +optional = false +python-versions = ">=3.7" +files = [ + {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, + {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, +] + [[package]] name = "ipython" version = "8.22.2" @@ -2945,6 +2956,21 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa typing = ["typing-extensions"] xmp = ["defusedxml"] +[[package]] +name = "pluggy" +version = "1.4.0" +description = "plugin and hook calling mechanisms for python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"}, + {file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"}, +] + +[package.extras] +dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] + [[package]] name = "posthog" version = "3.5.0" @@ -3382,6 +3408,26 @@ files = [ {file = "pyreadline3-3.4.1.tar.gz", hash = "sha256:6f3d1f7b8a31ba32b73917cefc1f28cc660562f39aea8646d30bd6eff21f7bae"}, ] +[[package]] +name = "pytest" +version = "8.1.1" +description = "pytest: simple powerful testing with Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "pytest-8.1.1-py3-none-any.whl", hash = "sha256:2a8386cfc11fa9d2c50ee7b2a57e7d898ef90470a7a34c4b949ff59662bb78b7"}, + {file = "pytest-8.1.1.tar.gz", hash = "sha256:ac978141a75948948817d360297b7aae0fcb9d6ff6bc9ec6d514b85d5a65c044"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "sys_platform == \"win32\""} +iniconfig = "*" +packaging = "*" +pluggy = ">=1.4,<2.0" + +[package.extras] +testing = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] + [[package]] name = "python-dateutil" version = "2.9.0.post0" @@ -4936,4 +4982,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "adff3ef924c9b8303f9fdb36249067cb83877de0c9628b2bba8c1c1b335a524a" +content-hash = "31f72ae06483834cc1ee4833903297e05c498a3b96accd0d8372c6eecc84b6cc" diff --git a/pyproject.toml b/pyproject.toml index 397d42bf..3b329604 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,9 @@ authx = "1.0.1b1" itsdangerous = "^2.1.2" llama-index-embeddings-text-embeddings-inference = "^0.1.2" +[tool.poetry.group.dev.dependencies] +pytest = "^8.1.1" + [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" From 4e7561767d3859e29a0baddf15d3cd06d884143a Mon Sep 17 00:00:00 2001 From: Ivar Flakstad <69173633+ivarflakstad@users.noreply.github.com> Date: Tue, 12 Mar 2024 10:03:40 +0100 Subject: [PATCH 5/6] Running CI on push alone is enough --- .github/workflows/tests.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index 1984440a..21c26328 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -2,7 +2,6 @@ name: Tests on: push: - pull_request: jobs: tests: From 25fbcf88a4a640ce5b1135e04492ba5cca6bb031 Mon Sep 17 00:00:00 2001 From: Ivar Flakstad <69173633+ivarflakstad@users.noreply.github.com> Date: Tue, 12 Mar 2024 10:06:08 +0100 Subject: [PATCH 6/6] Add test stub so CI passes --- app/tests/test_stub.py | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 app/tests/test_stub.py diff --git a/app/tests/test_stub.py b/app/tests/test_stub.py new file mode 100644 index 00000000..201975fc --- /dev/null +++ b/app/tests/test_stub.py @@ -0,0 +1,2 @@ +def test_placeholder(): + pass