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zotero topic modeling
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*.py[cod] | |
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*.so | |
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{file = "umap-learn-0.5.5.tar.gz", hash = "sha256:c54d607364413eade968b73ba07c8b3ea14412817f53cd07b6f720ac957293c4"}, | |
] | |
[[package]] | |
name = "urllib3" | |
version = "2.1.0" | |
requires_python = ">=3.8" | |
summary = "HTTP library with thread-safe connection pooling, file post, and more." | |
files = [ | |
{file = "urllib3-2.1.0-py3-none-any.whl", hash = "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3"}, | |
{file = "urllib3-2.1.0.tar.gz", hash = "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"}, | |
] |
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[project] | |
name = "" | |
version = "" | |
description = "" | |
authors = [ | |
{name = "Guilherme Pires", email = "[email protected]"}, | |
] | |
dependencies = [ | |
"pyzotero>=1.5.18", | |
"bertopic>=0.16.0", | |
"safetensors>=0.4.1", | |
"python-dotenv>=1.0.0", | |
] | |
requires-python = ">=3.10" | |
readme = "README.md" | |
license = {text = "MIT"} | |
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import os | |
import logging | |
import json | |
import argparse | |
from pyzotero import zotero | |
import numpy as np | |
from sklearn.feature_extraction.text import CountVectorizer | |
from sklearn.decomposition import LatentDirichletAllocation | |
from dotenv import load_dotenv | |
from tqdm import tqdm | |
logger = logging.getLogger(__name__) | |
def main(args): | |
library_id = args.library_id | |
api_key = args.api_key | |
bertopic_model = args.bertopic_model | |
library_type = "user" | |
zot = zotero.Zotero(library_id, library_type, api_key) | |
items = zot.everything(zot.items()) | |
if args.verbose: | |
items = tqdm(items) | |
logging.basicConfig(encoding='utf-8', level=logging.DEBUG) | |
logger.info("Extracting abstracts and titles from Zotero library") | |
abstracts = [item['data'].get('abstractNote', '') for item in items] | |
titles = [item['data'].get('title', '') for item in items] | |
to_model = [abstract + title for abstract, title in zip(abstracts, titles)] | |
if args.bertopic_model: | |
logger.info("Using BERTopic model") | |
from bertopic import BERTopic | |
topic_model = BERTopic.load(bertopic_model) | |
logger.info("Transforming abstracts into topics") | |
topics, _ = topic_model.transform(to_model) | |
if args.tag_items: | |
# Tag items with topics | |
for idx, item in enumerate(items): | |
if 'abstractNote' in item['data']: | |
topic = topics[idx] | |
if topic != -1: | |
tags = topic_model.get_topic(topic)[0] | |
zot.add_tags(item, [tag[0] for tag in tags]) | |
table = topic_model.get_topic_info() | |
tags = table.set_index("Topic").loc[topics].Representation.values | |
else: | |
logger.info("Using LDA model") | |
vectorizer = CountVectorizer(max_df=0.85, min_df=2, stop_words='english', lowercase=True) | |
X = vectorizer.fit_transform(to_model) | |
lda = LatentDirichletAllocation(n_components=100, random_state=0) | |
topics = lda.fit_transform(X).argmax(axis=1) | |
topic_words = np.array(vectorizer.get_feature_names_out()) | |
top_feature_idx = lda.components_.argsort(axis=1)[topics, -20:] | |
tags = topic_words[top_feature_idx].tolist() | |
if args.tag_items: | |
for i, item in enumerate(items): | |
if 'abstractNote' in item['data']: | |
topic = lda.transform(X[i]).argmax() | |
top_feature_idx = lda.components_[topic].argsort()[-20:] | |
tags = topic_words[top_feature_idx].tolist() | |
zot.add_tags(item, tags) | |
topics = dict(zip(titles, tags)) | |
print(json.dumps(topics, indent=4)) | |
if __name__ == "__main__": | |
load_dotenv() | |
parser = argparse.ArgumentParser() | |
parser.add_argument("--library-id", help="Zotero library ID", default=os.getenv("ZOTERO_LIBRARY_ID")) | |
parser.add_argument("--api-key", help="Zotero API key", default=os.getenv("ZOTERO_API_KEY")) | |
parser.add_argument("--bertopic-model", help="BERTopic model", default=None) | |
#parser.add_argument("--bertopic-model", help="BERTopic model", default="MaartenGr/BERTopic_Wikipedia") | |
parser.add_argument("--tag-items", help="Tag items with topics", action="store_true") | |
parser.add_argument("--verbose", help="Verbose logging", action="store_true") | |
args = parser.parse_args() | |
main(args) |
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