make streaming work end to end

app.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 import gradio as gr
 from dotenv import load_dotenv
+
 from medirag.cache.local import SemanticCaching
 from medirag.index.local import DailyMedIndexer
 from medirag.rag.qa import RAG, DailyMedRetrieve
@@ -43,14 +44,25 @@ async def ask_med_question(query, enable_stream):
         if enable_stream:
             # Stream response using RAGWorkflow
             result = await rag_workflow.run(query=query)
-            accumulated_response = ""
-
-            async for chunk in result.async_response_gen():
-                accumulated_response += chunk
-                yield accumulated_response  # Accumulate and yield the updated response
 
-            # Save the accumulated response to the cache after streaming is complete
-            sm.save(query, accumulated_response)
+            # Handle streaming response
+            if hasattr(result, 'async_response_gen'):
+                accumulated_response = ""
+
+                async for chunk in result.async_response_gen():
+                    accumulated_response += chunk
+                    yield accumulated_response  # Accumulate and yield the updated response
+
+                # Save the accumulated response to the cache after streaming is complete
+                sm.save(query, accumulated_response)
+            elif isinstance(result, str):
+                # Handle non-streaming string response
+                yield result
+                sm.save(query, result)
+            else:
+                # Handle unexpected response types
+                print("Unexpected response type:", result)
+                yield "An unexpected error occurred."
         else:
             # Use RAG without streaming
             response = rag(query).answer

poetry.lock

@@ -476,66 +476,29 @@ development = ["black", "flake8", "mypy", "pytest", "types-colorama"]
 
 [[package]]
 name = "contourpy"
-version = "1.2.1"
+version = "1.3.0"
 description = "Python library for calculating contours of 2D quadrilateral grids"
 optional = false
 python-versions = ">=3.9"
 files = [
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-    {file = "contourpy-1.2.1.tar.gz", hash = "sha256:4d8908b3bee1c889e547867ca4cdc54e5ab6be6d3e078556814a22457f49423c"},
+    {file = "contourpy-1.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:880ea32e5c774634f9fcd46504bf9f080a41ad855f4fef54f5380f5133d343c7"},
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+    {file = "contourpy-1.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:69375194457ad0fad3a839b9e29aa0b0ed53bb54db1bfb6c3ae43d111c31ce41"},
+    {file = "contourpy-1.3.0-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:7a52040312b1a858b5e31ef28c2e865376a386c60c0e248370bbea2d3f3b760d"},
 ]
 
 [package.dependencies]
-numpy = ">=1.20"
+numpy = ">=1.23"
 
 [package.extras]
 bokeh = ["bokeh", "selenium"]
 docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
-mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.8.0)", "types-Pillow"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.11.1)", "types-Pillow"]
 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
-test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
+test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
@@ -1288,13 +1251,13 @@ trio = ["trio (>=0.22.0,<0.26.0)"]
 
 [[package]]
 name = "httpx"
-version = "0.27.0"
+version = "0.27.2"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpx-0.27.0-py3-none-any.whl", hash = "sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5"},
-    {file = "httpx-0.27.0.tar.gz", hash = "sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5"},
+    {file = "httpx-0.27.2-py3-none-any.whl", hash = "sha256:7bb2708e112d8fdd7829cd4243970f0c223274051cb35ee80c03301ee29a3df0"},
+    {file = "httpx-0.27.2.tar.gz", hash = "sha256:f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2"},
 ]
 
 [package.dependencies]
@@ -1309,6 +1272,7 @@ brotli = ["brotli", "brotlicffi"]
 cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "huggingface-hub"
@@ -1776,13 +1740,13 @@ langchain-core = ">=0.2.10,<0.3.0"
 
 [[package]]
 name = "langsmith"
-version = "0.1.104"
+version = "0.1.105"
 description = "Client library to connect to the LangSmith LLM Tracing and Evaluation Platform."
 optional = false
 python-versions = "<4.0,>=3.8.1"
 files = [
-    {file = "langsmith-0.1.104-py3-none-any.whl", hash = "sha256:049cd312952a0db9f5edeed3b9a8616e66ef86e5490c835c8bb054569203b0d0"},
-    {file = "langsmith-0.1.104.tar.gz", hash = "sha256:7892dfe452d143fba573d7eb28dbff3202d2f2daacab8c7276ffe4a850179d4d"},
+    {file = "langsmith-0.1.105-py3-none-any.whl", hash = "sha256:a0098d0bc60ee79792109b0c1fef8252e21fd2dc424f4d902b8d9eb75160438b"},
+    {file = "langsmith-0.1.105.tar.gz", hash = "sha256:a8717ef90f3f740c202aa6878da89d4581ff28998336b48b831a92b855c460c3"},
 ]
 
 [package.dependencies]
@@ -2300,19 +2264,19 @@ files = [
 
 [[package]]
 name = "minijinja"
-version = "2.0.1"
+version = "2.2.0"
 description = "An experimental Python binding of the Rust MiniJinja template engine."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "minijinja-2.0.1-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ade637bf4826258811a785ccc4e5d41cd2bdf4ec317b1ed3daa4dbbdd020f37d"},
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-    {file = "minijinja-2.0.1.tar.gz", hash = "sha256:e774beffebfb8a1ad17e638ef70917cf5e94593f79acb8a8fff7d983169f3a4e"},
+    {file = "minijinja-2.2.0-cp38-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl", hash = "sha256:e4154fcf72e81be01c2733b770e6cb3e584851cb2fa73c58e347b04967d3d7c0"},
+    {file = "minijinja-2.2.0-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4b05e0070c08b550fa9a09ff9c051f47424674332dd56cc54b997dd602887907"},
+    {file = "minijinja-2.2.0-cp38-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:360ea4a93fdf1fe327f3e70eed20ecb29f324ca28fae177de0605dcc29869300"},
+    {file = "minijinja-2.2.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c9cad5ccb021ef25b6a271158f4d6636474edb08cd1dd49355aac6b68a48aebb"},
+    {file = "minijinja-2.2.0-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:7a85c67c519b413fc4892854782927e1244a24cbbb3a3cb0ac5e57d9fdb1868c"},
+    {file = "minijinja-2.2.0-cp38-abi3-win32.whl", hash = "sha256:e431a2467dd6e1bcb7c511e9fbad012b02c6e5453acdd9fbd4c4af0d34a3d1c5"},
+    {file = "minijinja-2.2.0-cp38-abi3-win_amd64.whl", hash = "sha256:d4df7e4a09be4249c8243207fa89e6f4d22b853c2b565a99f48e478a30713822"},
+    {file = "minijinja-2.2.0.tar.gz", hash = "sha256:4411052c7a60f8d56468cc6d17d45d72be3d5e89e9578a04f8336cc56601523c"},
 ]
 
 [[package]]
@@ -3464,6 +3428,24 @@ tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 [package.extras]
 dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
+[[package]]
+name = "pytest-asyncio"
+version = "0.24.0"
+description = "Pytest support for asyncio"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytest_asyncio-0.24.0-py3-none-any.whl", hash = "sha256:a811296ed596b69bf0b6f3dc40f83bcaf341b155a269052d82efa2b25ac7037b"},
+    {file = "pytest_asyncio-0.24.0.tar.gz", hash = "sha256:d081d828e576d85f875399194281e92bf8a68d60d72d1a2faf2feddb6c46b276"},
+]
+
+[package.dependencies]
+pytest = ">=8.2,<9"
+
+[package.extras]
+docs = ["sphinx (>=5.3)", "sphinx-rtd-theme (>=1.0)"]
+testing = ["coverage (>=6.2)", "hypothesis (>=5.7.1)"]
+
 [[package]]
 name = "pytest-cov"
 version = "5.0.0"
@@ -3741,13 +3723,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "rich"
-version = "13.7.1"
+version = "13.8.0"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "rich-13.7.1-py3-none-any.whl", hash = "sha256:4edbae314f59eb482f54e9e30bf00d33350aaa94f4bfcd4e9e3110e64d0d7222"},
-    {file = "rich-13.7.1.tar.gz", hash = "sha256:9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432"},
+    {file = "rich-13.8.0-py3-none-any.whl", hash = "sha256:2e85306a063b9492dffc86278197a60cbece75bcb766022f3436f567cae11bdc"},
+    {file = "rich-13.8.0.tar.gz", hash = "sha256:a5ac1f1cd448ade0d59cc3356f7db7a7ccda2c8cbae9c7a90c28ff463d3e91f4"},
 ]
 
 [package.dependencies]
@@ -5278,4 +5260,4 @@ multidict = ">=4.0"
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<3.13"
-content-hash = "949dc820fb098705fd25967197d2815fe03f9d67126756bfad76dfc43fe0f843"
+content-hash = "45accb38e74b5646d74896c8545504072d577c8a87b71d379753672353e613be"

pyproject.toml

@@ -38,6 +38,7 @@ pytest-cov = "^5.0.0"
 types-requests = "^2.32.0.20240712"
 mypy = "^1.11.1"
 pytest-mock = "^3.14.0"
+pytest-asyncio = "^0.24.0"
 
 
 [tool.ruff]

tests/rag/test_wf.py

@@ -0,0 +1,34 @@
+import pytest
+from dotenv import load_dotenv
+
+from medirag.index.local import DailyMedIndexer
+from medirag.rag.wf import RAGWorkflow
+
+load_dotenv()  # take environment variables from .env.
+
+
+@pytest.mark.asyncio
+async def test_wf_with_example(data_dir):
+    # Example usage:
+    index_path = data_dir.joinpath("daily_bio_bert_indexed")
+    # Ensure the path is correct and the directory exists
+    assert index_path.exists(), f"Directory not found: {index_path}"
+
+    # Initialize the indexer and load the index
+    indexer = DailyMedIndexer(persist_dir=index_path)
+    indexer.load_index()
+
+    top_k = 3  # Adjust the number of documents to retrieve
+    top_n = 3  # Adjust the number of top-ranked documents to select
+
+    # Pass the indexer to the workflow
+    workflow = RAGWorkflow(indexer=indexer, timeout=60, top_k=top_k, top_n=top_n)
+    query = "What information do you have about Clopidogrel?"
+
+    result = await workflow.run(query=query)
+    accumulated_response = ""
+    if hasattr(result, 'async_response_gen'):
+        async for chunk in result.async_response_gen():
+            accumulated_response += chunk
+
+    assert len(accumulated_response) > 0