aurelian 0.3.2__py3-none-any.whl

aurelian/utils/search_utils.py

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+import re
+
+import requests
+from duckduckgo_search import DDGS
+from markdownify import markdownify
+
+from aurelian.utils.pubmed_utils import doi_to_pmid, extract_doi_from_url, get_pmcid_text, get_pmid_text
+
+MAX_LENGTH_TRUNCATE_CONTENT = 20000
+
+
+def web_search(query: str, max_results=10, **kwargs) -> str:
+    """Search the web using DuckDuckGo
+
+    Example:
+        >>> result = web_search("Winner of 2024 nobel prize in chemistry")
+        >>> assert "Baker" in result
+
+
+    Args:
+        query:
+        max_results:
+        **kwargs:
+
+    Returns:
+
+    """
+    ddgs = DDGS(**kwargs)
+    results = ddgs.text(query, max_results=max_results)
+    if len(results) == 0:
+        return "No results found! Try a less restrictive/shorter query."
+    postprocessed_results = [f"[{result['title']}]({result['href']})\n{result['body']}" for result in results]
+    return "## Search Results\n\n" + "\n\n".join(postprocessed_results)
+
+
+def retrieve_web_page(url: str) -> str:
+    """Retrieve the text of a web page.
+
+    Example:
+        >>> url = "https://en.wikipedia.org/wiki/COVID-19"
+        >>> text = retrieve_web_page(url)
+        >>> assert "COVID-19" in text
+
+    PMCs are redirected:
+
+        >>> url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC5048378/"
+        >>> text = retrieve_web_page(url)
+        >>> assert "integrated stress response (ISR)" in text
+
+    URLs with DOIs:
+
+        >>> url = "https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00889-8"
+        >>> text = retrieve_web_page(url)
+        >>> assert "photosynthesis" in text
+
+    Args:
+        url: URL of the web page
+
+    Returns:
+        str: The text of the web page
+
+    """
+    if url.startswith("https://pmc.ncbi.nlm.nih.gov/articles/PMC"):
+        url = url.strip("/")
+        pmc_id = url.split("/")[-1]
+        # print(f"REWIRING URL: Fetching PMC ID: {pmc_id}")
+        return get_pmcid_text(pmc_id)
+
+    doi = extract_doi_from_url(url)
+    if doi:
+        # print(f"REWIRING URL: Fetching DOI: {doi}")
+        pmid = doi_to_pmid(doi)
+        return get_pmid_text(pmid)
+
+    response = requests.get(url, timeout=20)
+    response.raise_for_status()  # Raise an exception for bad status codes
+
+    # Convert the HTML content to Markdown
+    markdown_content = markdownify(response.text).strip()
+
+    # Remove multiple line breaks
+    markdown_content = re.sub(r"\n{3,}", "\n\n", markdown_content)
+
+    return truncate_content(markdown_content, 10000)
+
+
+def truncate_content(content: str, max_length: int = MAX_LENGTH_TRUNCATE_CONTENT) -> str:
+    if len(content) <= max_length:
+        return content
+    else:
+        return (
+            content[: max_length // 2]
+            + f"\n..._This content has been truncated to stay below {max_length} characters_...\n"
+            + content[-max_length // 2 :]
+        )

aurelian-0.3.2.dist-info/LICENSE

@@ -0,0 +1,22 @@
+
+The MIT License (MIT)
+
+Copyright (c) 2025 Monarch Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

aurelian-0.3.2.dist-info/METADATA

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+Metadata-Version: 2.3
+Name: aurelian
+Version: 0.3.2
+Summary: aurelian
+License: MIT
+Author: Author 1
+Author-email: author@org.org
+Requires-Python: >=3.11,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Provides-Extra: bioservices
+Provides-Extra: chem
+Provides-Extra: gocam
+Provides-Extra: gradio
+Provides-Extra: linkml
+Provides-Extra: pdfminer
+Provides-Extra: rdkit
+Requires-Dist: bioservices (>=1.12.0) ; extra == "bioservices"
+Requires-Dist: bs4 (>=0.0.2)
+Requires-Dist: cairosvg (>=2.7.1,<3.0.0)
+Requires-Dist: click
+Requires-Dist: duckduckgo-search (>=7.3.2)
+Requires-Dist: gocam ; extra == "gocam"
+Requires-Dist: gradio (>=5.23.3,<6.0.0) ; extra == "gradio"
+Requires-Dist: importlib-metadata (>=8.2.0)
+Requires-Dist: linkml ; extra == "linkml"
+Requires-Dist: linkml-store[llm,mongodb] (>=0.2.4)
+Requires-Dist: logfire (>=3.5.3)
+Requires-Dist: markdownify (>=0.14.1)
+Requires-Dist: markitdown (>=0.0.1a4)
+Requires-Dist: mcp[cli] (>=1.3.0,<2.0.0)
+Requires-Dist: oaklib (>=0.6.19)
+Requires-Dist: pdfminer-six ; extra == "pdfminer"
+Requires-Dist: pydantic-ai (>=0.0.29)
+Requires-Dist: pypaperbot (>=1.4.1)
+Requires-Dist: pytest-asyncio (>=0.25.3,<0.26.0)
+Requires-Dist: rdkit ; extra == "rdkit" or extra == "chem"
+Requires-Dist: tabulate (>=0.9.0)
+Requires-Dist: undetected-chromedriver (>=3.5.5)
+Requires-Dist: wikipedia (>=1.4.0)
+Description-Content-Type: text/markdown
+
+
+# Aurelian: Agentic Universal Research Engine for Literature, Integration, Annotation, and Navigation
+
+| [Documentation](https://monarch-initiative.github.io/aurelian) |
+
+```
+aurelian --help
+```
+
+Most commands will start up a different AI agent.
+
+## Examples of use
+
+### TALISMAN
+
+gene set enrichment
+
+### Aria
+
+checking papers against checklists
+
+### GO-CAM agent
+
+This agent is for exploring, chatting with, and reviewing GO-CAMs
+
+Docs: [gocam_agent](https://monarch-initiative.github.io/aurelian/agents/gocam_agent/)
+
+It can be used to generate reviews according to guidelines for GO-CAMs:
+
+* [GO-CAM Reviews](https://cmungall.github.io/go-cam-reviews/)
+
+It can also generate SVGs, demonstrating innate knowledge of both the visual grammar of pathway diagrams and the semantics of the underlying biology.
+
+
+<img alt="img" src="https://cmungall.github.io/go-cam-reviews/figures/FIG-646ff70100005137-IL33_signaling_pathway__Human_.svg" />
+
+### GO-Ann agent
+
+This agent is for exploring, chatting with, and reviewing standard annotations
+
+
+Docs: [go_ann_agent](https://monarch-initiative.github.io/aurelian/agents/go_ann_agent/)
+
+Example review using TF guidelines:
+
+https://github.com/geneontology/go-annotation/issues/5743
+
+## Troubleshooting
+
+### Installing linkml-store
+
+Some agents require linkml-store pre-indexed. E.g. a mongodb with gocams for cam agent.
+Consult the [linkml-store documentation](https://linkml.io/linkml-store/) for more information.
+
+### Semantic search over ontologies
+
+If an agent requires ontology search it will use the semsql/OAK sqlite database.
+The first time querying it will use linkml-store to create an LLM index. Requires OAI key.
+This may be slow first iteration. Will be cached until your pystow cache regenerates.
+

aurelian-0.3.2.dist-info/RECORD

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aurelian-0.3.2.dist-info/WHEEL

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aurelian-0.3.2.dist-info/entry_points.txt

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