Sphinxbio nls/add plate chain template (#12502)

Co-authored-by: Nicholas Larus-Stone <7347808+nlarusstone@users.noreply.github.com>
Co-authored-by: Eugene Yurtsev <eyurtsev@gmail.com>

templates/neo4j-generation/neo4j_generation/utils.py

@@ -1,11 +1,7 @@
 from typing import List, Optional
 
-from langchain.graphs.graph_document import (
+from langchain.graphs.graph_document import Node as BaseNode
-    Node as BaseNode,
+from langchain.graphs.graph_document import Relationship as BaseRelationship
-)
-from langchain.graphs.graph_document import (
-    Relationship as BaseRelationship,
-)
 from langchain.pydantic_v1 import BaseModel, Field
 
 

templates/plate-chain/LICENSE

@@ -0,0 +1,13 @@
+Copyright 2023 SphinxBio, Inc.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

templates/plate-chain/README.md

@@ -0,0 +1 @@
+# plate-chain

templates/plate-chain/examples/byonoy_absolute_example.csv

@@ -0,0 +1,34 @@
+,1,2,3,4,5,6,7,8,9,10,11,12
+A,0.065,0.063,0.061,0.070,0.061,0.060,0.065,0.064,0.063,0.063,0.059,0.073
+B,0.188,0.164,0.213,0.219,0.161,0.176,0.184,0.172,0.176,0.164,0.181,0.173
+C,0.207,0.190,0.218,0.190,0.211,0.182,0.215,0.211,0.187,0.184,0.208,0.171
+D,0.076,0.081,0.093,0.071,0.081,0.075,0.106,0.071,0.073,0.084,0.076,0.081
+E,0.076,0.069,0.082,0.099,0.094,0.072,0.086,0.064,0.070,0.067,0.068,0.074
+F,0.080,0.067,0.077,0.067,0.068,0.066,0.069,0.074,0.068,0.078,0.065,0.066
+G,0.061,0.076,0.063,0.069,0.083,0.074,0.071,0.067,0.066,0.067,0.067,0.068
+H,0.080,0.090,0.074,0.066,0.074,0.075,0.076,0.079,0.071,0.066,0.063,0.069
+
+
+
+,1,2,3,4,5,6,7,8,9,10,11,12
+A,Sample 1,Sample 2,Sample 3,Sample 4,Sample 5,Sample 6,Sample 7,Sample 8,Sample 9,Sample 10,Sample 11,Sample 12
+B,Sample 13,Sample 14,Sample 15,Sample 16,Sample 17,Sample 18,Sample 19,Sample 20,Sample 21,Sample 22,Sample 23,Sample 24
+C,Sample 25,Sample 26,Sample 27,Sample 28,Sample 29,Sample 30,Sample 31,Sample 32,Sample 33,Sample 34,Sample 35,Sample 36
+D,Sample 37,Sample 38,Sample 39,Sample 40,Sample 41,Sample 42,Sample 43,Sample 44,Sample 45,Sample 46,Sample 47,Sample 48
+E,Sample 49,Sample 50,Sample 51,Sample 52,Sample 53,Sample 54,Sample 55,Sample 56,Sample 57,Sample 58,Sample 59,Sample 60
+F,Sample 61,Sample 62,Sample 63,Sample 64,Sample 65,Sample 66,Sample 67,Sample 68,Sample 69,Sample 70,Sample 71,Sample 72
+G,Sample 73,Sample 74,Sample 75,Sample 76,Sample 77,Sample 78,Sample 79,Sample 80,Sample 81,Sample 82,Sample 83,Sample 84
+H,Sample 85,Sample 86,Sample 87,Sample 88,Sample 89,Sample 90,Sample 91,Sample 92,Sample 93,Sample 94,Sample 95,Sample 96
+
+
+
+Sample Wavelength (nm),540
+Reference Wavelength (nm),-1
+
+
+
+Smart Validation,Pass,
+Plate Well Assignment,Pass,Measured values of assigned wells indicate correct plate layout.
+Plate Orientation,,
+Replicates,,
+Standards,,

templates/plate-chain/plate_chain/__init__.py

@@ -0,0 +1,2 @@
+
+__ALL__ = ["chain"]

templates/plate-chain/plate_chain/chain.py

@@ -0,0 +1,91 @@
+import base64
+import json
+
+from langchain.chat_models import ChatOpenAI
+from langchain.prompts import ChatPromptTemplate, SystemMessagePromptTemplate
+from langchain.pydantic_v1 import Field
+from langchain.schema.output_parser import StrOutputParser
+from langserve import CustomUserType
+
+from .prompts import (
+    AI_REPONSE_DICT,
+    FULL_PROMPT,
+    USER_EXAMPLE_DICT,
+    create_prompt,
+)
+from .utils import parse_llm_output
+
+llm = ChatOpenAI(temperature=0, model="gpt-4")
+
+prompt = ChatPromptTemplate.from_messages(
+    [
+        SystemMessagePromptTemplate.from_template(FULL_PROMPT),
+        ("human", "{user_example}"),
+        ("ai", "{ai_response}"),
+        ("human", "{input}"),
+    ],
+)
+
+
+# ATTENTION: Inherit from CustomUserType instead of BaseModel otherwise
+# the server will decode it into a dict instead of a pydantic model.
+class FileProcessingRequest(CustomUserType):
+    """Request including a base64 encoded file."""
+
+    # The extra field is used to specify a widget for the playground UI.
+    file: str = Field(..., extra={"widget": {"type": "base64file"}})
+    num_plates: int = None
+    num_rows: int = 8
+    num_cols: int = 12
+
+
+def _load_file(request: FileProcessingRequest):
+    return base64.b64decode(request.file.encode("utf-8")).decode('utf-8')
+
+
+def _load_prompt(request: FileProcessingRequest):
+    return create_prompt(
+            num_plates=request.num_plates,
+            num_rows=request.num_rows,
+            num_cols=request.num_cols,
+        )
+
+def _get_col_range_str(request: FileProcessingRequest):
+    if request.num_cols:
+        return f"from 1 to {request.num_cols}"
+    else:
+        return ""
+
+
+def _get_json_format(request: FileProcessingRequest):
+    return json.dumps(
+        [
+            {
+                "row_start": 12,
+                "row_end": 12 + request.num_rows - 1,
+                "col_start": 1,
+                "col_end": 1 + request.num_cols - 1,
+                "contents": "Entity ID",
+            }
+        ]
+    )
+
+chain = (
+    {
+        # Should add validation to ensure numeric indices
+        "input": _load_file,
+        "hint": _load_prompt,
+        "col_range_str": _get_col_range_str,
+        "json_format": _get_json_format,
+        "user_example": lambda x: USER_EXAMPLE_DICT[
+            x.num_rows * x.num_cols
+        ],
+        "ai_response": lambda x: AI_REPONSE_DICT[
+            x.num_rows * x.num_cols
+        ],
+    }
+    | prompt
+    | llm
+    | StrOutputParser()
+    | parse_llm_output
+).with_types(input_type=FileProcessingRequest)

templates/plate-chain/plate_chain/utils.py

@@ -0,0 +1,31 @@
+import json
+
+from pydantic import BaseModel, Field, conint
+
+
+class LLMPlateResponse(BaseModel):
+    row_start: conint(ge=0) = Field(
+        ..., description="The starting row of the plate (0-indexed)"
+    )
+    row_end: conint(ge=0) = Field(
+        ..., description="The ending row of the plate (0-indexed)"
+    )
+    col_start: conint(ge=0) = Field(
+        ..., description="The starting column of the plate (0-indexed)"
+    )
+    col_end: conint(ge=0) = Field(
+        ..., description="The ending column of the plate (0-indexed)"
+    )
+    contents: str
+
+
+def parse_llm_output(result: str):
+    """
+    Based on the prompt we expect the result to be a string that looks like:
+
+    '[{"row_start": 12, "row_end": 19, "col_start": 1, \
+    "col_end": 12, "contents": "Entity ID"}]'
+
+    We'll load that JSON and turn it into a Pydantic model
+    """
+    return [LLMPlateResponse(**plate_r) for plate_r in json.loads(result)]

templates/plate-chain/pyproject.toml

@@ -0,0 +1,25 @@
+[tool.poetry]
+name = "plate_chain"
+version = "0.0.1"
+description = ""
+authors = []
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.9,<4.0"
+langchain = ">=0.0.313, <0.1"
+openai = "^0.28.1"
+langserve = "^0.0.19"
+
+[tool.poetry.group.dev.dependencies]
+langchain-cli = ">=0.0.4"
+fastapi = "^0.104.0"
+sse-starlette = "^1.6.5"
+
+[tool.langserve]
+export_module = "plate_chain.__init__"
+export_attr = "chain"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"