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Runtime error
Abhilash V J
commited on
Commit
Β·
bd5eb62
1
Parent(s):
458615d
Added file uplaod option
Browse files- .gitattributes +34 -34
- .ipynb_checkpoints/Test DB-checkpoint.ipynb +6 -0
- .streamlit/secrets.toml +1 -0
- README.md +13 -13
- Test DB.ipynb +60 -0
- app.py +241 -172
- pinecorn.haystack-pipeline.yml.yml +55 -0
- requirements.txt +6 -6
.gitattributes
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saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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.ipynb_checkpoints/Test DB-checkpoint.ipynb
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{
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"cells": [],
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"metadata": {},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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.streamlit/secrets.toml
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pinecone_apikey = "6a76246e-2b5f-46f5-aab8-9cf43d6c94fb"
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README.md
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---
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title: Haystack QA
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emoji: π
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colorFrom: yellow
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colorTo: green
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sdk: streamlit
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sdk_version: 1.15.2
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app_file: app.py
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pinned: false
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license: apache-2.0
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---
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Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
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---
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title: Haystack QA
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emoji: π
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colorFrom: yellow
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colorTo: green
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sdk: streamlit
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sdk_version: 1.15.2
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app_file: app.py
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pinned: false
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license: apache-2.0
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---
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Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
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Test DB.ipynb
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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "5736235d",
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"metadata": {},
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"outputs": [],
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"source": [
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"from haystack.document_stores import PineconeDocumentStore"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "c4925511",
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"metadata": {},
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"outputs": [],
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"source": [
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"document_store = PineconeDocumentStore(\n",
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" api_key= \"6a76246e-2b5f-46f5-aab8-9cf43d6c94fb\",\n",
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" index='qa_demo',\n",
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" similarity=\"cosine\",\n",
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" embedding_dim=768\n",
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" )"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "c884286a",
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"metadata": {},
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"outputs": [],
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"source": [
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"document_store.get"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.10"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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app.py
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import os
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import sys
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import logging
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from pathlib import Path
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from json import JSONDecodeError
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import pandas as pd
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import streamlit as st
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from annotated_text import annotation
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from markdown import markdown
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import json
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from haystack import Document
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import pandas as pd
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from haystack.document_stores import PineconeDocumentStore
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from haystack.nodes import EmbeddingRetriever, FARMReader
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from haystack.pipelines import ExtractiveQAPipeline
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document_store
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#
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"""
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import os
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import sys
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import logging
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from pathlib import Path
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from json import JSONDecodeError
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import pandas as pd
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import streamlit as st
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from annotated_text import annotation
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from markdown import markdown
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import json
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from haystack import Document
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import pandas as pd
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from haystack.document_stores import PineconeDocumentStore
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from haystack.nodes import EmbeddingRetriever, FARMReader
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from haystack.pipelines import ExtractiveQAPipeline
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import shutil
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import uuid
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from pathlib import Path
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from haystack.pipelines import Pipeline
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from haystack.nodes import TextConverter, PreProcessor, FileTypeClassifier, PDFToTextConverter, DocxToTextConverter
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preprocessor = PreProcessor(
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clean_empty_lines=True,
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clean_whitespace=True,
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clean_header_footer=False,
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split_by="word",
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split_length=100,
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split_respect_sentence_boundary=True
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)
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file_type_classifier = FileTypeClassifier()
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text_converter = TextConverter()
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pdf_converter = PDFToTextConverter()
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docx_converter = DocxToTextConverter()
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FILE_UPLOAD_PATH= "./data/uploads/"
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os.makedirs(FILE_UPLOAD_PATH, exist_ok=True)
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# @st.cache
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def create_doc_store():
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document_store = PineconeDocumentStore(
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api_key= st.secrets["pinecone_apikey"],
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index='qa_demo',
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similarity="cosine",
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embedding_dim=768
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)
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return document_store
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# @st.cache
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# def create_pipe(document_store):
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# retriever = EmbeddingRetriever(
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# document_store=document_store,
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# embedding_model="sentence-transformers/multi-qa-mpnet-base-dot-v1",
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# model_format="sentence_transformers",
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# )
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# reader = FARMReader(model_name_or_path="deepset/roberta-base-squad2", use_gpu=False)
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# pipe = ExtractiveQAPipeline(reader, retriever)
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# return pipe
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def query(pipe, question, top_k_reader, top_k_retriever):
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res = pipe.run(
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query=question, params={"Retriever": {"top_k": top_k_retriever}, "Reader": {"top_k": top_k_reader}}
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)
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answer_df = []
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# for r in res['answers']:
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# ans_dict = res['answers'][0].meta
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# ans_dict["answer"] = r.context
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# answer_df.append(ans_dict)
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# result = pd.DataFrame(answer_df)
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# result.columns = ["Source","Title","Year","Link","Answer"]
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# result[["Answer","Link","Source","Title","Year"]]
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return res
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|
74 |
+
document_store = create_doc_store()
|
75 |
+
# pipe = create_pipe(document_store)
|
76 |
+
retriever = EmbeddingRetriever(
|
77 |
+
document_store=document_store,
|
78 |
+
embedding_model="sentence-transformers/multi-qa-mpnet-base-dot-v1",
|
79 |
+
model_format="sentence_transformers",
|
80 |
+
)
|
81 |
+
reader = FARMReader(model_name_or_path="deepset/roberta-base-squad2", use_gpu=False)
|
82 |
+
pipe = ExtractiveQAPipeline(reader, retriever)
|
83 |
+
|
84 |
+
indexing_pipeline_with_classification = Pipeline()
|
85 |
+
indexing_pipeline_with_classification.add_node(
|
86 |
+
component=file_type_classifier, name="FileTypeClassifier", inputs=["File"]
|
87 |
+
)
|
88 |
+
indexing_pipeline_with_classification.add_node(
|
89 |
+
component=text_converter, name="TextConverter", inputs=["FileTypeClassifier.output_1"]
|
90 |
+
)
|
91 |
+
indexing_pipeline_with_classification.add_node(
|
92 |
+
component=pdf_converter, name="PdfConverter", inputs=["FileTypeClassifier.output_2"]
|
93 |
+
)
|
94 |
+
indexing_pipeline_with_classification.add_node(
|
95 |
+
component=docx_converter, name="DocxConverter", inputs=["FileTypeClassifier.output_4"]
|
96 |
+
)
|
97 |
+
indexing_pipeline_with_classification.add_node(
|
98 |
+
component=preprocessor,
|
99 |
+
name="Preprocessor",
|
100 |
+
inputs=["TextConverter", "PdfConverter", "DocxConverter"],
|
101 |
+
)
|
102 |
+
indexing_pipeline_with_classification.add_node(
|
103 |
+
component=document_store, name="DocumentStore", inputs=["Preprocessor"]
|
104 |
+
)
|
105 |
+
|
106 |
+
def set_state_if_absent(key, value):
|
107 |
+
if key not in st.session_state:
|
108 |
+
st.session_state[key] = value
|
109 |
+
|
110 |
+
# Adjust to a question that you would like users to see in the search bar when they load the UI:
|
111 |
+
DEFAULT_QUESTION_AT_STARTUP = os.getenv("DEFAULT_QUESTION_AT_STARTUP", "My blog post discusses remote work. Give me statistics.")
|
112 |
+
DEFAULT_ANSWER_AT_STARTUP = os.getenv("DEFAULT_ANSWER_AT_STARTUP", "7% more remote workers have been at their current organization for 5 years or fewer")
|
113 |
+
|
114 |
+
# Sliders
|
115 |
+
DEFAULT_DOCS_FROM_RETRIEVER = int(os.getenv("DEFAULT_DOCS_FROM_RETRIEVER", "3"))
|
116 |
+
DEFAULT_NUMBER_OF_ANSWERS = int(os.getenv("DEFAULT_NUMBER_OF_ANSWERS", "3"))
|
117 |
+
|
118 |
+
|
119 |
+
st.set_page_config(page_title="Haystack Demo", page_icon="https://haystack.deepset.ai/img/HaystackIcon.png")
|
120 |
+
|
121 |
+
# Persistent state
|
122 |
+
set_state_if_absent("question", DEFAULT_QUESTION_AT_STARTUP)
|
123 |
+
set_state_if_absent("answer", DEFAULT_ANSWER_AT_STARTUP)
|
124 |
+
set_state_if_absent("results", None)
|
125 |
+
|
126 |
+
|
127 |
+
# Small callback to reset the interface in case the text of the question changes
|
128 |
+
def reset_results(*args):
|
129 |
+
st.session_state.answer = None
|
130 |
+
st.session_state.results = None
|
131 |
+
st.session_state.raw_json = None
|
132 |
+
|
133 |
+
# Title
|
134 |
+
st.write("# Haystack Search Demo")
|
135 |
+
st.markdown(
|
136 |
+
"""
|
137 |
+
This demo takes its data from two sample data csv with statistics on various topics. \n
|
138 |
+
Ask any question on this topic and see if Haystack can find the correct answer to your query! \n
|
139 |
+
*Note: do not use keywords, but full-fledged questions.* The demo is not optimized to deal with keyword queries and might misunderstand you.
|
140 |
+
""",
|
141 |
+
unsafe_allow_html=True,
|
142 |
+
)
|
143 |
+
|
144 |
+
# Sidebar
|
145 |
+
st.sidebar.header("Options")
|
146 |
+
st.sidebar.write("## File Upload:")
|
147 |
+
data_files = st.sidebar.file_uploader(
|
148 |
+
"upload", type=["pdf", "txt", "docx"], accept_multiple_files=True, label_visibility="hidden"
|
149 |
+
)
|
150 |
+
ALL_FILES = []
|
151 |
+
for data_file in data_files:
|
152 |
+
# Upload file
|
153 |
+
if data_file:
|
154 |
+
file_path = Path(FILE_UPLOAD_PATH) / f"{uuid.uuid4().hex}_{data_file.name}"
|
155 |
+
with file_path.open("wb") as buffer:
|
156 |
+
shutil.copyfileobj(data_file.file, buffer)
|
157 |
+
ALL_FILES.append(file_path)
|
158 |
+
st.sidebar.write(str(data_file.name) + " β
")
|
159 |
+
indexing_pipeline_with_classification.run(file_paths=ALL_FILES)
|
160 |
+
|
161 |
+
if len(ALL_FILES) > 0:
|
162 |
+
document_store.update_embeddings(retriever, update_existing_embeddings=False)
|
163 |
+
|
164 |
+
top_k_reader = st.sidebar.slider(
|
165 |
+
"Max. number of answers",
|
166 |
+
min_value=1,
|
167 |
+
max_value=10,
|
168 |
+
value=DEFAULT_NUMBER_OF_ANSWERS,
|
169 |
+
step=1,
|
170 |
+
on_change=reset_results,
|
171 |
+
)
|
172 |
+
top_k_retriever = st.sidebar.slider(
|
173 |
+
"Max. number of documents from retriever",
|
174 |
+
min_value=1,
|
175 |
+
max_value=10,
|
176 |
+
value=DEFAULT_DOCS_FROM_RETRIEVER,
|
177 |
+
step=1,
|
178 |
+
on_change=reset_results,
|
179 |
+
)
|
180 |
+
# data_files = st.file_uploader(
|
181 |
+
# "upload", type=["csv"], accept_multiple_files=True, label_visibility="hidden"
|
182 |
+
# )
|
183 |
+
# for data_file in data_files:
|
184 |
+
# # Upload file
|
185 |
+
# if data_file:
|
186 |
+
# raw_json = upload_doc(data_file)
|
187 |
+
|
188 |
+
question = st.text_input(
|
189 |
+
value=st.session_state.question,
|
190 |
+
max_chars=100,
|
191 |
+
on_change=reset_results,
|
192 |
+
label="question",
|
193 |
+
label_visibility="hidden",
|
194 |
+
)
|
195 |
+
col1, col2 = st.columns(2)
|
196 |
+
col1.markdown("<style>.stButton button {width:100%;}</style>", unsafe_allow_html=True)
|
197 |
+
col2.markdown("<style>.stButton button {width:100%;}</style>", unsafe_allow_html=True)
|
198 |
+
|
199 |
+
# Run button
|
200 |
+
run_pressed = col1.button("Run")
|
201 |
+
if run_pressed:
|
202 |
+
|
203 |
+
run_query = (
|
204 |
+
run_pressed or question != st.session_state.question
|
205 |
+
)
|
206 |
+
# Get results for query
|
207 |
+
if run_query and question:
|
208 |
+
reset_results()
|
209 |
+
st.session_state.question = question
|
210 |
+
|
211 |
+
with st.spinner(
|
212 |
+
"π§ Performing neural search on documents... \n "
|
213 |
+
):
|
214 |
+
try:
|
215 |
+
st.session_state.results = query(
|
216 |
+
pipe, question, top_k_reader=top_k_reader, top_k_retriever=top_k_retriever
|
217 |
+
)
|
218 |
+
except JSONDecodeError as je:
|
219 |
+
st.error("π An error occurred reading the results. Is the document store working?")
|
220 |
+
except Exception as e:
|
221 |
+
logging.exception(e)
|
222 |
+
if "The server is busy processing requests" in str(e) or "503" in str(e):
|
223 |
+
st.error("π§βπΎ All our workers are busy! Try again later.")
|
224 |
+
else:
|
225 |
+
st.error(f"π An error occurred during the request. {str(e)}")
|
226 |
+
|
227 |
+
|
228 |
+
if st.session_state.results:
|
229 |
+
|
230 |
+
st.write("## Results:")
|
231 |
+
|
232 |
+
for count, result in enumerate(st.session_state.results['answers']):
|
233 |
+
answer, context = result.answer, result.context
|
234 |
+
start_idx = context.find(answer)
|
235 |
+
end_idx = start_idx + len(answer)
|
236 |
+
source = f"[{result.meta['Title']}]({result.meta['link']})"
|
237 |
+
# Hack due to this bug: https://github.com/streamlit/streamlit/issues/3190
|
238 |
+
st.write(
|
239 |
+
markdown(f'**Source:** {source} \n {context[:start_idx] } {str(annotation(answer, "ANSWER", "#8ef"))} {context[end_idx:]} \n '),
|
240 |
+
unsafe_allow_html=True,
|
241 |
+
)
|
pinecorn.haystack-pipeline.yml.yml
ADDED
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# To allow your IDE to autocomplete and validate your YAML pipelines, name them as <name of your choice>.haystack-pipeline.yml
|
2 |
+
|
3 |
+
version: ignore
|
4 |
+
|
5 |
+
components: # define all the building-blocks for Pipeline
|
6 |
+
- name: DocumentStore
|
7 |
+
type: ElasticsearchDocumentStore
|
8 |
+
params:
|
9 |
+
index=: qa_demo
|
10 |
+
similarity: cosine
|
11 |
+
embedding_dim: 768
|
12 |
+
- name: Retriever
|
13 |
+
type: BM25Retriever
|
14 |
+
params:
|
15 |
+
document_store: DocumentStore # params can reference other components defined in the YAML
|
16 |
+
top_k: 5
|
17 |
+
- name: Reader # custom-name for the component; helpful for visualization & debugging
|
18 |
+
type: FARMReader # Haystack Class name for the component
|
19 |
+
params:
|
20 |
+
model_name_or_path: deepset/roberta-base-squad2
|
21 |
+
context_window_size: 500
|
22 |
+
return_no_answer: true
|
23 |
+
- name: TextFileConverter
|
24 |
+
type: TextConverter
|
25 |
+
- name: PDFFileConverter
|
26 |
+
type: PDFToTextConverter
|
27 |
+
- name: Preprocessor
|
28 |
+
type: PreProcessor
|
29 |
+
params:
|
30 |
+
split_by: word
|
31 |
+
split_length: 1000
|
32 |
+
- name: FileTypeClassifier
|
33 |
+
type: FileTypeClassifier
|
34 |
+
|
35 |
+
pipelines:
|
36 |
+
- name: query # a sample extractive-qa Pipeline
|
37 |
+
nodes:
|
38 |
+
- name: Retriever
|
39 |
+
inputs: [Query]
|
40 |
+
- name: Reader
|
41 |
+
inputs: [Retriever]
|
42 |
+
- name: indexing
|
43 |
+
nodes:
|
44 |
+
- name: FileTypeClassifier
|
45 |
+
inputs: [File]
|
46 |
+
- name: TextFileConverter
|
47 |
+
inputs: [FileTypeClassifier.output_1]
|
48 |
+
- name: PDFFileConverter
|
49 |
+
inputs: [FileTypeClassifier.output_2]
|
50 |
+
- name: Preprocessor
|
51 |
+
inputs: [PDFFileConverter, TextFileConverter]
|
52 |
+
- name: Retriever
|
53 |
+
inputs: [Preprocessor]
|
54 |
+
- name: DocumentStore
|
55 |
+
inputs: [Retriever]
|
requirements.txt
CHANGED
@@ -1,7 +1,7 @@
|
|
1 |
-
protobuf==3.19
|
2 |
-
streamlit==1.13
|
3 |
-
st-annotated-text
|
4 |
-
farm-haystack[pinecone]
|
5 |
-
pinecone-client
|
6 |
-
datasets
|
7 |
tensorboard
|
|
|
1 |
+
protobuf==3.19
|
2 |
+
streamlit==1.13
|
3 |
+
st-annotated-text
|
4 |
+
farm-haystack[pinecone]
|
5 |
+
pinecone-client
|
6 |
+
datasets
|
7 |
tensorboard
|