Spaces:
GIZ
/
Running on CPU Upgrade

SDSN-demo / utils /semantic_search.py
prashant
session state error fix
2918b13
raw
history blame
18.2 kB
from haystack.nodes import TransformersQueryClassifier
from haystack.nodes import EmbeddingRetriever, FARMReader
from haystack.nodes.base import BaseComponent
from haystack.document_stores import InMemoryDocumentStore
from markdown import markdown
from annotated_text import annotation
from haystack.schema import Document
from typing import List, Text
from typing_extensions import Literal
from utils.preprocessing import processingpipeline
from utils.streamlitcheck import check_streamlit
from haystack.pipelines import Pipeline
import logging
try:
from termcolor import colored
except:
pass
try:
import streamlit as st
except ImportError:
logging.info("Streamlit not installed")
@st.cache(allow_output_mutation=True)
def loadQueryClassifier():
"""
retuns the haystack query classifier model
model = shahrukhx01/bert-mini-finetune-question-detection
"""
query_classifier = TransformersQueryClassifier(model_name_or_path=
"shahrukhx01/bert-mini-finetune-question-detection")
return query_classifier
class QueryCheck(BaseComponent):
"""
Uses Query Classifier from Haystack, process the query based on query type
1. https://docs.haystack.deepset.ai/docs/query_classifier
"""
outgoing_edges = 1
def run(self, query):
"""
mandatory method to use the cusotm node. Determines the query type, if
if the query is of type keyword/statement will modify it to make it more
useful for sentence transoformers.
"""
query_classifier = loadQueryClassifier()
result = query_classifier.run(query=query)
if result[1] == "output_1":
output = {"query":query,
"query_type": 'question/statement'}
else:
output = {"query": "find all issues related to {}".format(query),
"query_type": 'statements/keyword'}
return output, "output_1"
def run_batch(self, query):
pass
@st.cache(allow_output_mutation=True)
def runSemanticPreprocessingPipeline(file_path, file_name,
split_by: Literal["sentence", "word"] = 'sentence',
split_respect_sentence_boundary = False,
split_length:int = 2, split_overlap = 0,
removePunc = False)->List[Document]:
"""
creates the pipeline and runs the preprocessing pipeline,
the params for pipeline are fetched from paramconfig
Params
------------
file_name: filename, in case of streamlit application use
st.session_state['filename']
file_path: filepath, in case of streamlit application use
st.session_state['filepath']
removePunc: to remove all Punctuation including ',' and '.' or not
split_by: document splitting strategy either as word or sentence
split_length: when synthetically creating the paragrpahs from document,
it defines the length of paragraph.
split_respect_sentence_boundary: Used when using 'word' strategy for
splititng of text.
Return
--------------
List[Document]: When preprocessing pipeline is run, the output dictionary
has four objects. For the Haysatck implementation of semantic search we,
need to use the List of Haystack Document, which can be fetched by
key = 'documents' on output.
"""
semantic_processing_pipeline = processingpipeline()
output_semantic_pre = semantic_processing_pipeline.run(file_paths = file_path,
params= {"FileConverter": {"file_path": file_path, \
"file_name": file_name},
"UdfPreProcessor": {"removePunc": removePunc, \
"split_by": split_by, \
"split_length":split_length,\
"split_overlap": split_overlap,
"split_respect_sentence_boundary":split_respect_sentence_boundary}})
return output_semantic_pre
@st.cache(hash_funcs={"builtins.SwigPyObject": lambda _: None},allow_output_mutation=True)
def loadRetriever(embedding_model:Text = None, embedding_model_format:Text = None,
embedding_layer:int = None, retriever_top_k:int = 10,
document_store:InMemoryDocumentStore = None):
"""
Returns the Retriever model based on params provided.
1. https://docs.haystack.deepset.ai/docs/retriever#embedding-retrieval-recommended
2. https://www.sbert.net/examples/applications/semantic-search/README.html
3. https://github.com/deepset-ai/haystack/blob/main/haystack/nodes/retriever/dense.py
Params
---------
embedding_model: Name of the model to be used for embedding. Check the links
provided in documentation
embedding_model_format: check the github link of Haystack provided in documentation
embedding_layer: check the github link of Haystack provided in documentation
retriever_top_k: Number of Top results to be returned by retriever
document_store: InMemoryDocumentStore, write haystack Document list to DocumentStore
and pass the same to function call. Can be done using createDocumentStore from utils.
Return
-------
retriever: emebedding model
"""
logging.info("loading retriever")
if document_store is None:
logging.warning("Retriever initialization requires the DocumentStore")
return
retriever = EmbeddingRetriever(
embedding_model=embedding_model,top_k = retriever_top_k,
document_store = document_store,
emb_extraction_layer=embedding_layer, scale_score =True,
model_format=embedding_model_format, use_gpu = True)
if check_streamlit:
st.session_state['retriever'] = retriever
return retriever
@st.cache(hash_funcs={"builtins.SwigPyObject": lambda _: None},allow_output_mutation=True)
def createDocumentStore(documents:List[Document], similarity:str = 'cosine'):
"""
Creates the InMemory Document Store frm haystack list of Documents.
It is mandatory component for Retriever to work in Haystack frame work.
Params
-------
documents: List of haystack document. If using the preprocessing pipeline,
can be fetched key = 'documents; on output of preprocessing pipeline.
similarity: scoring function, can be either 'cosine' or 'dot_product'
Return
-------
document_store: InMemory Document Store object type.
"""
document_store = InMemoryDocumentStore(similarity = similarity)
document_store.write_documents(documents)
# if check_streamlit:
# if 'retriever' in st.session_state:
# retriever = st.session_state['retriever']
# document_store.update_embeddings(retriever)
return document_store
@st.cache(hash_funcs={"builtins.SwigPyObject": lambda _: None},allow_output_mutation=True)
def semanticSearchPipeline(documents:List[Document], embedding_model:Text = None,
embedding_model_format:Text = None,
embedding_layer:int = None, retriever_top_k:int = 10,
reader_model:str = None, reader_top_k:int = 10):
"""
creates the semantic search pipeline and document Store object from the
list of haystack documents. Retriever and Reader model are read from
paramconfig. The top_k for the Reader and Retirever are kept same, so that
all the results returned by Retriever are used, however the context is
extracted by Reader for each retrieved result. The querycheck is added as
node to process the query.
1. https://docs.haystack.deepset.ai/docs/retriever#embedding-retrieval-recommended
2. https://www.sbert.net/examples/applications/semantic-search/README.html
3. https://github.com/deepset-ai/haystack/blob/main/haystack/nodes/retriever/dense.py
4. https://docs.haystack.deepset.ai/docs/reader
Params
----------
documents: list of Haystack Documents, returned by preprocessig pipeline.
embedding_model: Name of the model to be used for embedding. Check the links
provided in documentation
embedding_model_format: check the github link of Haystack provided in documentation
embedding_layer: check the github link of Haystack provided in documentation
retriever_top_k: Number of Top results to be returned by retriever
reader_model: Name of the model to be used for Reader node in hasyatck
Pipeline. Check the links provided in documentation
reader_top_k: Reader will use retrieved results to further find better matches.
As purpose here is to use reader to extract context, the value is
same as retriever_top_k.
Return
---------
semanticsearch_pipeline: Haystack Pipeline object, with all the necessary
nodes [QueryCheck, Retriever, Reader]
document_store: As retriever can work only with Haystack Document Store, the
list of document returned by preprocessing pipeline.
"""
document_store = createDocumentStore(documents)
if check_streamlit:
if 'retriever' in st.session_state:
# if st.session_state['retriever']:
retriever = st.session_state['retriever']
else:
if embedding_model:
retriever = loadRetriever(embedding_model = embedding_model,
embedding_model_format=embedding_model_format,
embedding_layer=embedding_layer,
retriever_top_k= retriever_top_k,
document_store = document_store)
st.session_state['retriever'] = retriever
else:
logging.warning("no streamlit enviornment found, neither embedding model \
provided")
return
elif embedding_model:
retriever = loadRetriever(embedding_model = embedding_model,
embedding_model_format=embedding_model_format,
embedding_layer=embedding_layer,
retriever_top_k= retriever_top_k,
document_store = document_store)
document_store.update_embeddings(retriever)
retriever.document_store = document_store
querycheck = QueryCheck()
if check_streamlit:
if 'reader' in st.session_state:
reader = st.session_state['reader']
else:
if reader_model:
reader = FARMReader(model_name_or_path=reader_model,
top_k = reader_top_k, use_gpu=True)
st.session_state['reader'] = reader
semanticsearch_pipeline = Pipeline()
semanticsearch_pipeline.add_node(component = querycheck, name = "QueryCheck",
inputs = ["Query"])
semanticsearch_pipeline.add_node(component = retriever, name = "EmbeddingRetriever",
inputs = ["QueryCheck.output_1"])
semanticsearch_pipeline.add_node(component = reader, name = "FARMReader",
inputs= ["EmbeddingRetriever"])
return semanticsearch_pipeline, document_store
def semanticsearchAnnotator(matches: List[List[int]], document):
"""
Annotates the text in the document defined by list of [start index, end index]
Example: "How are you today", if document type is text, matches = [[0,3]]
will give answer = "How", however in case we used the spacy matcher then the
matches = [[0,3]] will give answer = "How are you". However if spacy is used
to find "How" then the matches = [[0,1]] for the string defined above.
"""
start = 0
annotated_text = ""
for match in matches:
start_idx = match[0]
end_idx = match[1]
if check_streamlit():
annotated_text = (annotated_text + document[start:start_idx]
+ str(annotation(body=document[start_idx:end_idx],
label="Context", background="#964448", color='#ffffff')))
else:
annotated_text = (annotated_text + document[start:start_idx]
+ colored(document[start_idx:end_idx],
"green", attrs = ['bold']))
start = end_idx
annotated_text = annotated_text + document[end_idx:]
if check_streamlit():
st.write(
markdown(annotated_text),
unsafe_allow_html=True,
)
else:
print(annotated_text)
def semantic_search(query:Text,documents:List[Document],embedding_model:Text,
embedding_model_format:Text,
embedding_layer:int, reader_model:str,
retriever_top_k:int = 10, reader_top_k:int = 10):
"""
Performs the Semantic search on the List of haystack documents which is
returned by preprocessing Pipeline.
Params
-------
query: Keywords that need to be searche in documents.
documents: List fo Haystack documents returned by preprocessing pipeline.
"""
semanticsearch_pipeline, doc_store = semanticSearchPipeline(documents,
embedding_model= embedding_model,
embedding_layer= embedding_layer,
embedding_model_format= embedding_model_format,
reader_model= reader_model, retriever_top_k= retriever_top_k,
reader_top_k= reader_top_k)
results = semanticsearch_pipeline.run(query = query)
if check_streamlit:
st.markdown("##### Top few semantic search results #####")
else:
print("Top few semantic search results")
for i,answer in enumerate(results['answers']):
temp = answer.to_dict()
start_idx = temp['offsets_in_document'][0]['start']
end_idx = temp['offsets_in_document'][0]['end']
match = [[start_idx,end_idx]]
doc = doc_store.get_document_by_id(temp['document_id']).content
st.write("Result {}".format(i+1))
semanticsearchAnnotator(match, doc)
# if 'document_store' in st.session_state:
# document_store = st.session_state['document_store']
# temp = document_store.get_all_documents()
# if st.session_state['filename'] != temp[0].meta['name']:
# document_store = InMemoryDocumentStore()
# document_store.write_documents(documents)
# if 'retriever' in st.session_state:
# retriever = st.session_state['retriever']
# document_store.update_embeddings(retriever)
# # querycheck =
# # embedding_model = config.get('semantic_search','RETRIEVER')
# # embedding_model_format = config.get('semantic_search','RETRIEVER_FORMAT')
# # embedding_layer = int(config.get('semantic_search','RETRIEVER_EMB_LAYER'))
# # retriever_top_k = int(config.get('semantic_search','RETRIEVER_TOP_K'))
# # retriever = EmbeddingRetriever(
# # document_store=document_store,
# # embedding_model=embedding_model,top_k = retriever_top_k,
# # emb_extraction_layer=embedding_layer, scale_score =True,
# # model_format=embedding_model_format, use_gpu = True)
# # document_store.update_embeddings(retriever)
# else:
# embedding_model = config.get('semantic_search','RETRIEVER')
# embedding_model_format = config.get('semantic_search','RETRIEVER_FORMAT')
# retriever = EmbeddingRetriever(
# document_store=document_store,
# embedding_model=embedding_model,top_k = retriever_top_k,
# emb_extraction_layer=embedding_layer, scale_score =True,
# model_format=embedding_model_format, use_gpu = True)
# else:
# document_store = InMemoryDocumentStore()
# document_store.write_documents(documents)
# embedding_model = config.get('semantic_search','RETRIEVER')
# embedding_model_format = config.get('semantic_search','RETRIEVER_FORMAT')
# embedding_layer = int(config.get('semantic_search','RETRIEVER_EMB_LAYER'))
# retriever_top_k = int(config.get('semantic_search','RETRIEVER_TOP_K'))
# retriever = EmbeddingRetriever(
# document_store=document_store,
# embedding_model=embedding_model,top_k = retriever_top_k,
# emb_extraction_layer=embedding_layer, scale_score =True,
# model_format=embedding_model_format, use_gpu = True)
# st.session_state['retriever'] = retriever
# document_store.update_embeddings(retriever)
# st.session_state['document_store'] = document_store
# querycheck = QueryCheck()
# st.session_state['querycheck'] = querycheck
# reader_model = config.get('semantic_search','READER')
# reader_top_k = retriever_top_k
# reader = FARMReader(model_name_or_path=reader_model,
# top_k = reader_top_k, use_gpu=True)
# st.session_state['reader'] = reader
# querycheck = QueryCheck()
# reader_model = config.get('semantic_search','READER')
# reader_top_k = retriever_top_k
# reader = FARMReader(model_name_or_path=reader_model,
# top_k = reader_top_k, use_gpu=True)
# semanticsearch_pipeline = Pipeline()
# semanticsearch_pipeline.add_node(component = querycheck, name = "QueryCheck",
# inputs = ["Query"])
# semanticsearch_pipeline.add_node(component = retriever, name = "EmbeddingRetriever",
# inputs = ["QueryCheck.output_1"])
# semanticsearch_pipeline.add_node(component = reader, name = "FARMReader",
# inputs= ["EmbeddingRetriever"])
# return semanticsearch_pipeline, document_store