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Rspace doc loader (#11511)

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**Description:**

Add a document loader for the RSpace Electronic Lab Notebook
(www.researchspace.com), so that scientific documents and research notes
can be easily pulled into Langchain pipelines.

**Issue**

This is an new contribution, rather than an issue fix.

 **Dependencies:** 
  
There are no new required dependencies.
In order to use the loader, clients will need to install rspace_client
SDK using `pip install rspace_client`

---------

Co-authored-by: richarda23 <richard.c.adams@infinityworks.com>
Co-authored-by: Bagatur <baskaryan@gmail.com>
This commit is contained in:
Richard Adams
2023-10-12 23:05:38 +01:00
committed by GitHub
parent 9d1867c77f
commit 35965df20d
5 changed files with 336 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

130
libs/langchain/langchain/document_loaders/rspace.py Normal file
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@@ -0,0 +1,130 @@
import os
from typing import Any, Dict, Iterator, List, Optional, Union
from langchain.docstore.document import Document
from langchain.document_loaders import PyPDFLoader
from langchain.document_loaders.base import BaseLoader
from langchain.utils import get_from_dict_or_env
class RSpaceLoader(BaseLoader):
"""
Loads content from RSpace notebooks, folders, documents or PDF Gallery files into
Langchain documents.
Maps RSpace document <-> Langchain Document in 1-1. PDFs are imported using PyPDF.
Requirements are rspace_client (`pip install rspace_client`) and PyPDF if importing
PDF docs (`pip install pypdf`).
"""
def __init__(
self, global_id: str, api_key: Optional[str] = None, url: Optional[str] = None
):
"""api_key: RSpace API key - can also be supplied as environment variable
'RSPACE_API_KEY'
url: str
The URL of your RSpace instance - can also be supplied as environment
variable 'RSPACE_URL'
global_id: str
The global ID of the resource to load,
e.g. 'SD12344' (a single document); 'GL12345'(A PDF file in the gallery);
'NB4567' (a notebook); 'FL12244' (a folder)
"""
args: Dict[str, Optional[str]] = {
"api_key": api_key,
"url": url,
"global_id": global_id,
}
verified_args: Dict[str, str] = RSpaceLoader.validate_environment(args)
self.api_key = verified_args["api_key"]
self.url = verified_args["url"]
self.global_id: str = verified_args["global_id"]
@classmethod
def validate_environment(cls, values: Dict) -> Dict:
"""Validate that API key and URL exists in environment."""
values["api_key"] = get_from_dict_or_env(values, "api_key", "RSPACE_API_KEY")
values["url"] = get_from_dict_or_env(values, "url", "RSPACE_URL")
if "global_id" not in values or values["global_id"] is None:
raise ValueError(
"No value supplied for global_id. Please supply an RSpace global ID"
)
return values
def _create_rspace_client(self) -> Any:
"""Create a RSpace client."""
try:
from rspace_client.eln import eln, field_content
except ImportError:
raise ImportError("You must run " "`pip install rspace_client`")
try:
eln = eln.ELNClient(self.url, self.api_key)
eln.get_status()
except Exception:
raise Exception(
f"Unable to initialise client - is url {self.url} or "
f"api key correct?"
)
return eln, field_content.FieldContent
def _get_doc(self, cli: Any, field_content: Any, d_id: Union[str, int]) -> Document:
content = ""
doc = cli.get_document(d_id)
content += f"<h2>{doc['name']}<h2/>"
for f in doc["fields"]:
content += f"{f['name']}\n"
fc = field_content(f["content"])
content += fc.get_text()
content += "\n"
return Document(
metadata={"source": f"rspace: {doc['name']}-{doc['globalId']}"},
page_content=content,
)
def _load_structured_doc(self) -> Iterator[Document]:
cli, field_content = self._create_rspace_client()
yield self._get_doc(cli, field_content, self.global_id)
def _load_folder_tree(self) -> Iterator[Document]:
cli, field_content = self._create_rspace_client()
if self.global_id:
docs_in_folder = cli.list_folder_tree(
folder_id=self.global_id[2:], typesToInclude=["document"]
)
doc_ids: List[int] = [d["id"] for d in docs_in_folder["records"]]
for doc_id in doc_ids:
yield self._get_doc(cli, field_content, doc_id)
def _load_pdf(self) -> Iterator[Document]:
cli, field_content = self._create_rspace_client()
file_info = cli.get_file_info(self.global_id)
_, ext = os.path.splitext(file_info["name"])
if ext.lower() == ".pdf":
outfile = f"{self.global_id}.pdf"
cli.download_file(self.global_id, outfile)
pdf_loader = PyPDFLoader(outfile)
for pdf in pdf_loader.lazy_load():
pdf.metadata["rspace_src"] = self.global_id
yield pdf
def lazy_load(self) -> Iterator[Document]:
if self.global_id and "GL" in self.global_id:
for d in self._load_pdf():
yield d
elif self.global_id and "SD" in self.global_id:
for d in self._load_structured_doc():
yield d
elif self.global_id and self.global_id[0:2] in ["FL", "NB"]:
for d in self._load_folder_tree():
yield d
else:
raise ValueError("Unknown global ID type")
def load(self) -> List[Document]:
return list(self.lazy_load())

44
libs/langchain/poetry.lock generated
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{file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
{file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
@@ -7660,6 +7684,7 @@ files = [
{file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
{file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
{file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
{file = "PyYAML-6.0.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5"},
{file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
{file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
{file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
@@ -8426,6 +8451,21 @@ files = [
[package.dependencies]
pyasn1 = ">=0.1.3"
[[package]]
name = "rspace-client"
version = "2.5.0"
description = "A client for calling RSpace ELN and Inventory APIs"
optional = true
python-versions = ">=3.7.11,<4.0.0"
files = [
{file = "rspace-client-2.5.0.tar.gz", hash = "sha256:101abc83d094051d2babcaa133fa1a47221b3d5953d72eef3c331ef7084071a1"},
{file = "rspace_client-2.5.0-py3-none-any.whl", hash = "sha256:b1072df88dfa8f068f3137584d20cf135493b0521a9809c2f6ddec6b378a9cc3"},
]
[package.dependencies]
beautifulsoup4 = ">=4.9.3,<5.0.0"
requests = ">=2.25.1,<3.0.0"
[[package]]
name = "ruff"
version = "0.0.249"
@@ -10843,7 +10883,7 @@ cli = ["typer"]
cohere = ["cohere"]
docarray = ["docarray"]
embeddings = ["sentence-transformers"]
extended-testing = ["aiosqlite", "amazon-textract-caller", "anthropic", "arxiv", "assemblyai", "atlassian-python-api", "beautifulsoup4", "bibtexparser", "cassio", "chardet", "dashvector", "esprima", "faiss-cpu", "feedparser", "geopandas", "gitpython", "gql", "html2text", "jinja2", "jq", "lxml", "markdownify", "motor", "mwparserfromhell", "mwxml", "newspaper3k", "numexpr", "openai", "openai", "openapi-schema-pydantic", "pandas", "pdfminer-six", "pgvector", "psychicapi", "py-trello", "pymupdf", "pypdf", "pypdfium2", "pyspark", "rank-bm25", "rapidfuzz", "rapidocr-onnxruntime", "requests-toolbelt", "scikit-learn", "sqlite-vss", "streamlit", "sympy", "telethon", "timescale-vector", "tqdm", "xata", "xmltodict"]
extended-testing = ["aiosqlite", "amazon-textract-caller", "anthropic", "arxiv", "assemblyai", "atlassian-python-api", "beautifulsoup4", "bibtexparser", "cassio", "chardet", "dashvector", "esprima", "faiss-cpu", "feedparser", "geopandas", "gitpython", "gql", "html2text", "jinja2", "jq", "lxml", "markdownify", "motor", "mwparserfromhell", "mwxml", "newspaper3k", "numexpr", "openai", "openai", "openapi-schema-pydantic", "pandas", "pdfminer-six", "pgvector", "psychicapi", "py-trello", "pymupdf", "pypdf", "pypdfium2", "pyspark", "rank-bm25", "rapidfuzz", "rapidocr-onnxruntime", "requests-toolbelt", "rspace_client", "scikit-learn", "sqlite-vss", "streamlit", "sympy", "telethon", "timescale-vector", "tqdm", "xata", "xmltodict"]
javascript = ["esprima"]
llms = ["clarifai", "cohere", "huggingface_hub", "manifest-ml", "nlpcloud", "openai", "openlm", "torch", "transformers"]
openai = ["openai", "tiktoken"]
@@ -10853,4 +10893,4 @@ text-helpers = ["chardet"]
[metadata]
lock-version = "2.0"
python-versions = ">=3.8.1,<4.0"
content-hash = "de11d7f6257615dd61f579d5137d5a6b9ee5433e0d9b3cac3feb8a759ad70393"
content-hash = "3a5bca34a60eaa9b66a4d1f9ec14de5e6a0e5ca1071a0a874499fe122cc0ee36"

2
libs/langchain/pyproject.toml
View File

@@ -138,6 +138,7 @@ timescale-vector = {version = "^0.0.1", optional = true}
typer = {version= "^0.9.0", optional = true}
anthropic = {version = "^0.3.11", optional = true}
aiosqlite = {version = "^0.19.0", optional = true}
rspace_client = {version = "^2.5.0", optional = true}
[tool.poetry.group.test.dependencies]
@@ -366,6 +367,7 @@ extended_testing = [
"motor",
"timescale-vector",
"anthropic",
"rspace_client",
]
[tool.ruff]

35
libs/langchain/tests/unit_tests/document_loaders/test_rspace_loader.py Normal file
View File

@@ -0,0 +1,35 @@
import unittest
from langchain.document_loaders.rspace import RSpaceLoader
class TestRSpaceLoader(unittest.TestCase):
url = "https://community.researchspace.com"
api_key = "myapikey"
global_id = "SD12345"
def test_valid_arguments(self) -> None:
loader = RSpaceLoader(
url=TestRSpaceLoader.url,
api_key=TestRSpaceLoader.api_key,
global_id=TestRSpaceLoader.global_id,
)
self.assertEqual(TestRSpaceLoader.url, loader.url) # add assertion here
self.assertEqual(TestRSpaceLoader.api_key, loader.api_key) # add assertion here
self.assertEqual(
TestRSpaceLoader.global_id, loader.global_id
) # add assertion here
def test_missing_apikey_raises_validation_error(self) -> None:
with self.assertRaises(ValueError) as cm:
RSpaceLoader(url=TestRSpaceLoader.url, global_id=TestRSpaceLoader.global_id)
e = cm.exception
self.assertRegex(str(e), r"Did not find api_key")
def test_missing_url_raises_validation_error(self) -> None:
with self.assertRaises(ValueError) as cm:
RSpaceLoader(
api_key=TestRSpaceLoader.api_key, global_id=TestRSpaceLoader.global_id
)
e = cm.exception
self.assertRegex(str(e), r"Did not find url")