Feat: Redesign and refactor agent module (#9113)

### What problem does this PR solve? #9082 #6365 <u> **WARNING: it's not compatible with the older version of `Agent` module, which means that `Agent` from older versions can not work anymore.**</u> ### Type of change - [x] New Feature (non-breaking change which adds functionality)
2025-12-08 20:42:30 +08:00 · 2025-07-30 19:41:09 +08:00
parent 07e37560fc
commit d9fe279dde
124 changed files with 7744 additions and 18226 deletions
--- a/agent/tools/pubmed.py
+++ b/agent/tools/pubmed.py
@ -0,0 +1,105 @@
+#
+#  Copyright 2024 The InfiniFlow Authors. All Rights Reserved.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+import logging
+import os
+import time
+from abc import ABC
+from Bio import Entrez
+import re
+import xml.etree.ElementTree as ET
+from agent.tools.base import ToolParamBase, ToolMeta, ToolBase
+from api.utils.api_utils import timeout
+
+
+class PubMedParam(ToolParamBase):
+    """
+    Define the PubMed component parameters.
+    """
+
+    def __init__(self):
+        self.meta:ToolMeta = {
+            "name": "pubmed_search",
+            "description": """
+PubMed is an openly accessible, free database which includes primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. 
+In addition to MEDLINE, PubMed provides access to:
+ - older references from the print version of Index Medicus, back to 1951 and earlier
+ - references to some journals before they were indexed in Index Medicus and MEDLINE, for instance Science, BMJ, and Annals of Surgery
+ - very recent entries to records for an article before it is indexed with Medical Subject Headings (MeSH) and added to MEDLINE
+ - a collection of books available full-text and other subsets of NLM records[4]
+ - PMC citations
+ - NCBI Bookshelf
+            """,
+            "parameters": {
+                "query": {
+                    "type": "string",
+                    "description": "The search keywords to execute with PubMed. The keywords should be the most important words/terms(includes synonyms) from the original request.",
+                    "default": "{sys.query}",
+                    "required": True
+                }
+            }
+        }
+        super().__init__()
+        self.top_n = 12
+        self.email = "A.N.Other@example.com"
+
+    def check(self):
+        self.check_positive_integer(self.top_n, "Top N")
+
+    def get_input_form(self) -> dict[str, dict]:
+        return {
+            "query": {
+                "name": "Query",
+                "type": "line"
+            }
+        }
+
+class PubMed(ToolBase, ABC):
+    component_name = "PubMed"
+
+    @timeout(os.environ.get("COMPONENT_EXEC_TIMEOUT", 12))
+    def _invoke(self, **kwargs):
+        if not kwargs.get("query"):
+            self.set_output("formalized_content", "")
+            return ""
+
+        last_e = ""
+        for _ in range(self._param.max_retries+1):
+            try:
+                Entrez.email = self._param.email
+                pubmedids = Entrez.read(Entrez.esearch(db='pubmed', retmax=self._param.top_n, term=kwargs["query"]))['IdList']
+                pubmedcnt = ET.fromstring(re.sub(r'<(/?)b>|<(/?)i>', '', Entrez.efetch(db='pubmed', id=",".join(pubmedids),
+                                                                                       retmode="xml").read().decode("utf-8")))
+                self._retrieve_chunks(pubmedcnt.findall("PubmedArticle"),
+                                      get_title=lambda child: child.find("MedlineCitation").find("Article").find("ArticleTitle").text,
+                                      get_url=lambda child: "https://pubmed.ncbi.nlm.nih.gov/" + child.find("MedlineCitation").find("PMID").text,
+                                      get_content=lambda child: child.find("MedlineCitation") \
+                                                                    .find("Article") \
+                                                                    .find("Abstract") \
+                                                                    .find("AbstractText").text \
+                                                                    if child.find("MedlineCitation")\
+                                                                            .find("Article").find("Abstract")  \
+                                                                    else "No abstract available")
+                return self.output("formalized_content")
+            except Exception as e:
+                last_e = e
+                logging.exception(f"PubMed error: {e}")
+                time.sleep(self._param.delay_after_error)
+
+        if last_e:
+            self.set_output("_ERROR", str(last_e))
+            return f"PubMed error: {last_e}"
+
+        assert False, self.output()