scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py"
-)
+
+__FILE__ = "./src/scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -57,12 +56,8 @@ columns = {
     "nlm_id": Column(String, comment="the unique ID of NLM", default="."),
     "factor": Column(Float(3), comment="the IF of journal"),
     "jcr": Column(String, comment="the partition of JCR", default="."),
-    "journal": Column(
-        String, comment="the title of journal", primary_key=True
-    ),
-    "journal_abbr": Column(
-        String, comment="the abbreviation of journal", default="."
-    ),
+    "journal": Column(String, comment="the title of journal", primary_key=True),
+    "journal_abbr": Column(String, comment="the abbreviation of journal", default="."),
     "issn": Column(String, comment="the ISSN of journal", default="."),
     "eissn": Column(String, comment="the eISSN of journal", default="."),
 }
@@ -124,13 +119,10 @@ class ImpactFactorJCREngine:
         with suppress_output():
             for field in keys:
                 if "%" in value:
-                    result = self.query.filter(
-                        FactorData.__dict__[field].like(value)
-                    )
+                    result = self.query.filter(FactorData.__dict__[field].like(value))
                 else:
                     result = self.query.filter(
-                        func.lower(FactorData.__dict__[field])
-                        == func.lower(value)
+                        func.lower(FactorData.__dict__[field]) == func.lower(value)
                     )
 
                 if result.count():

scitex/scholar/impact_factor/jcr/build_database.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/scholar/impact_factor/jcr/build_database.py"
-)
+
+__FILE__ = "./src/scitex/scholar/impact_factor/jcr/build_database.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -50,6 +49,8 @@ BASE_DIR = Path(__file__).resolve().parent.parent.parent  # scholar/
 DATA_DIR = BASE_DIR / "data" / "impact_factor"
 
 """Functions & Classes"""
+
+
 def parse_jcr_excel(excel_path: Path) -> Iterator[Dict]:
     """
     Parse JCR Excel file and yield journal records.

scitex/scholar/integration/base.py

@@ -64,7 +64,8 @@ class BaseMapper(ABC):
             Year as int or None
         """
         import re
-        match = re.search(r'\b(19|20)\d{2}\b', date_str)
+
+        match = re.search(r"\b(19|20)\d{2}\b", date_str)
         if match:
             try:
                 return int(match.group(0))
@@ -111,7 +112,7 @@ class BaseImporter(ABC):
         collection_id: Optional[str] = None,
         collection_name: Optional[str] = None,
         limit: Optional[int] = None,
-        **kwargs
+        **kwargs,
     ) -> Papers:
         """Import items from a collection.
 
@@ -132,7 +133,7 @@ class BaseImporter(ABC):
         tags: List[str],
         match_all: bool = False,
         limit: Optional[int] = None,
-        **kwargs
+        **kwargs,
     ) -> Papers:
         """Import items with specific tags.
 
@@ -157,11 +158,7 @@ class BaseImporter(ABC):
         Returns:
             Papers collection
         """
-        return self.import_collection(
-            collection_id=None,
-            limit=limit,
-            **kwargs
-        )
+        return self.import_collection(collection_id=None, limit=limit, **kwargs)
 
     def import_to_library(
         self,
@@ -187,15 +184,12 @@ class BaseImporter(ABC):
         for i, paper in enumerate(paper_list, 1):
             try:
                 paper_id = self.library_manager.save_resolved_paper(
-                    paper_data=paper,
-                    project=self.project
+                    paper_data=paper, project=self.project
                 )
 
                 results[paper.metadata.basic.title or f"paper_{i}"] = paper_id
 
-                logger.info(
-                    f"[{i}/{len(paper_list)}] Saved: {paper_id}"
-                )
+                logger.info(f"[{i}/{len(paper_list)}] Saved: {paper_id}")
 
             except Exception as e:
                 logger.error(
@@ -247,7 +241,7 @@ class BaseExporter(ABC):
         self,
         papers: Union[Papers, List[Paper]],
         collection_name: Optional[str] = None,
-        **kwargs
+        **kwargs,
     ) -> Dict[str, str]:
         """Export Papers to reference manager.
 
@@ -278,9 +272,7 @@ class BaseExporter(ABC):
         output_path = Path(output_path)
         output_path.parent.mkdir(parents=True, exist_ok=True)
 
-        self.bibtex_handler.papers_to_bibtex(
-            papers, output_path=output_path
-        )
+        self.bibtex_handler.papers_to_bibtex(papers, output_path=output_path)
 
         logger.success(f"Exported BibTeX: {output_path}")
         return output_path

scitex/scholar/integration/mendeley/exporter.py

@@ -58,7 +58,7 @@ class MendeleyExporter(BaseExporter):
 
                 mendeley = Mendeley(
                     client_id=self.credentials["app_id"],
-                    client_secret=self.credentials["app_secret"]
+                    client_secret=self.credentials["app_secret"],
                 )
 
                 session = mendeley.start_client_credentials_flow().authenticate()
@@ -156,9 +156,7 @@ class MendeleyExporter(BaseExporter):
                 )
                 continue
 
-        logger.success(
-            f"Exported {len(results)}/{len(paper_list)} papers to Mendeley"
-        )
+        logger.success(f"Exported {len(results)}/{len(paper_list)} papers to Mendeley")
 
         return results
 

scitex/scholar/integration/mendeley/importer.py

@@ -62,7 +62,7 @@ class MendeleyImporter(BaseImporter):
 
                 mendeley = Mendeley(
                     client_id=self.credentials["app_id"],
-                    client_secret=self.credentials["app_secret"]
+                    client_secret=self.credentials["app_secret"],
                 )
 
                 if self.credentials.get("access_token"):
@@ -142,7 +142,7 @@ class MendeleyImporter(BaseImporter):
                             pdf_entry = {
                                 "url": file.file_url,
                                 "source": "mendeley",
-                                "mendeley_file_id": file.id
+                                "mendeley_file_id": file.id,
                             }
                             paper.metadata.url.pdfs.append(pdf_entry)
 
@@ -213,7 +213,7 @@ class MendeleyImporter(BaseImporter):
                             pdf_entry = {
                                 "url": file.file_url,
                                 "source": "mendeley",
-                                "mendeley_file_id": file.id
+                                "mendeley_file_id": file.id,
                             }
                             paper.metadata.url.pdfs.append(pdf_entry)
 

scitex/scholar/integration/mendeley/linker.py

@@ -48,7 +48,7 @@ class MendeleyLinker(BaseLinker):
             credentials=credentials,
             project=project,
             config=config,
-            sync_interval=sync_interval
+            sync_interval=sync_interval,
         )
 
     def _create_importer(self) -> MendeleyImporter:
@@ -58,7 +58,7 @@ class MendeleyLinker(BaseLinker):
             app_secret=self.credentials["app_secret"],
             access_token=self.credentials["access_token"],
             project=self.project,
-            config=self.config
+            config=self.config,
         )
 
     def _create_exporter(self) -> MendeleyExporter:
@@ -68,7 +68,7 @@ class MendeleyLinker(BaseLinker):
             app_secret=self.credentials["app_secret"],
             access_token=self.credentials["access_token"],
             project=self.project,
-            config=self.config
+            config=self.config,
         )
 
     def _create_mapper(self) -> MendeleyMapper:

scitex/scholar/integration/mendeley/mapper.py

@@ -141,7 +141,9 @@ class MendeleyMapper(BaseMapper):
         paper._mendeley_profile_id = item.get("profile_id", "")
         paper._mendeley_notes = item.get("notes", "")
 
-        logger.debug(f"Converted Mendeley document '{paper.metadata.basic.title}' to Paper")
+        logger.debug(
+            f"Converted Mendeley document '{paper.metadata.basic.title}' to Paper"
+        )
 
         return paper
 
@@ -160,10 +162,9 @@ class MendeleyMapper(BaseMapper):
             for author in paper.metadata.basic.authors:
                 parts = author.split(",")
                 if len(parts) == 2:
-                    authors.append({
-                        "first_name": parts[1].strip(),
-                        "last_name": parts[0].strip()
-                    })
+                    authors.append(
+                        {"first_name": parts[1].strip(), "last_name": parts[0].strip()}
+                    )
                 else:
                     authors.append({"last_name": author.strip()})
 
@@ -204,7 +205,9 @@ class MendeleyMapper(BaseMapper):
         if websites:
             mendeley_doc["websites"] = websites
 
-        logger.debug(f"Converted Paper '{paper.metadata.basic.title}' to Mendeley document")
+        logger.debug(
+            f"Converted Paper '{paper.metadata.basic.title}' to Mendeley document"
+        )
 
         return mendeley_doc
 

scitex/scholar/integration/zotero/__main__.py

@@ -27,7 +27,7 @@ def cmd_import(args):
         library_id=args.library_id or os.getenv("ZOTERO_LIBRARY_ID"),
         library_type=args.library_type,
         api_key=args.api_key or os.getenv("ZOTERO_API_KEY"),
-        project=args.project
+        project=args.project,
     )
 
     if args.collection:
@@ -35,7 +35,7 @@ def cmd_import(args):
             collection_name=args.collection,
             limit=args.limit,
             include_pdfs=args.include_pdfs,
-            include_annotations=args.include_annotations
+            include_annotations=args.include_annotations,
         )
     elif args.tags:
         tags = args.tags.split(",")
@@ -44,13 +44,13 @@ def cmd_import(args):
             match_all=args.match_all,
             limit=args.limit,
             include_pdfs=args.include_pdfs,
-            include_annotations=args.include_annotations
+            include_annotations=args.include_annotations,
         )
     else:
         papers = importer.import_all(
             limit=args.limit,
             include_pdfs=args.include_pdfs,
-            include_annotations=args.include_annotations
+            include_annotations=args.include_annotations,
         )
 
     if args.save_to_library:
@@ -67,7 +67,7 @@ def cmd_export(args):
         library_id=args.library_id or os.getenv("ZOTERO_LIBRARY_ID"),
         library_type=args.library_type,
         api_key=args.api_key or os.getenv("ZOTERO_API_KEY"),
-        project=args.project
+        project=args.project,
     )
 
     papers = Papers.from_project(args.project)
@@ -77,7 +77,7 @@ def cmd_export(args):
             papers,
             collection_name=args.collection,
             create_collection=args.create_collection,
-            update_existing=args.update_existing
+            update_existing=args.update_existing,
         )
         logger.success(f"Exported {len(results)} papers to Zotero")
 
@@ -97,14 +97,14 @@ def cmd_sync(args):
         library_type=args.library_type,
         api_key=args.api_key or os.getenv("ZOTERO_API_KEY"),
         project=args.project,
-        sync_interval=args.interval
+        sync_interval=args.interval,
     )
 
     if args.once:
         stats = linker.sync_once(
             bidirectional=args.bidirectional,
             auto_import=args.auto_import,
-            auto_export=args.auto_export
+            auto_export=args.auto_export,
         )
         logger.success(f"Sync stats: {stats}")
     else:
@@ -112,7 +112,7 @@ def cmd_sync(args):
         linker.start_sync(
             bidirectional=args.bidirectional,
             auto_import=args.auto_import,
-            auto_export=args.auto_export
+            auto_export=args.auto_export,
         )
 
 
@@ -122,23 +122,19 @@ def main():
         description="SciTeX Scholar - Zotero Integration CLI"
     )
     parser.add_argument(
-        "--library-id",
-        help="Zotero library ID (or set ZOTERO_LIBRARY_ID env var)"
+        "--library-id", help="Zotero library ID (or set ZOTERO_LIBRARY_ID env var)"
     )
     parser.add_argument(
         "--library-type",
         default="user",
         choices=["user", "group"],
-        help="Library type (default: user)"
+        help="Library type (default: user)",
     )
     parser.add_argument(
-        "--api-key",
-        help="Zotero API key (or set ZOTERO_API_KEY env var)"
+        "--api-key", help="Zotero API key (or set ZOTERO_API_KEY env var)"
     )
     parser.add_argument(
-        "--project",
-        default="default",
-        help="Scholar project name (default: default)"
+        "--project", default="default", help="Scholar project name (default: default)"
     )
 
     subparsers = parser.add_subparsers(dest="command", help="Command")
@@ -148,27 +144,23 @@ def main():
     import_parser.add_argument("--collection", help="Collection name")
     import_parser.add_argument("--tags", help="Comma-separated tags")
     import_parser.add_argument(
-        "--match-all",
-        action="store_true",
-        help="Require all tags (AND logic)"
+        "--match-all", action="store_true", help="Require all tags (AND logic)"
     )
     import_parser.add_argument("--limit", type=int, help="Maximum items to import")
     import_parser.add_argument(
         "--no-pdfs",
         dest="include_pdfs",
         action="store_false",
-        help="Skip PDF attachments"
+        help="Skip PDF attachments",
     )
     import_parser.add_argument(
         "--no-annotations",
         dest="include_annotations",
         action="store_false",
-        help="Skip PDF annotations"
+        help="Skip PDF annotations",
     )
     import_parser.add_argument(
-        "--save-to-library",
-        action="store_true",
-        help="Save to Scholar library"
+        "--save-to-library", action="store_true", help="Save to Scholar library"
     )
     import_parser.set_defaults(include_pdfs=True, include_annotations=True)
 
@@ -178,18 +170,16 @@ def main():
         "--format",
         default="zotero",
         choices=["zotero", "bibtex", "ris"],
-        help="Export format (default: zotero)"
+        help="Export format (default: zotero)",
     )
     export_parser.add_argument("--collection", help="Zotero collection name")
     export_parser.add_argument(
         "--create-collection",
         action="store_true",
-        help="Create collection if not exists"
+        help="Create collection if not exists",
     )
     export_parser.add_argument(
-        "--update-existing",
-        action="store_true",
-        help="Update existing items"
+        "--update-existing", action="store_true", help="Update existing items"
     )
     export_parser.add_argument("--output", help="Output file path (for bibtex/ris)")
 
@@ -199,28 +189,20 @@ def main():
         "--interval",
         type=int,
         default=60,
-        help="Sync interval in seconds (default: 60)"
+        help="Sync interval in seconds (default: 60)",
     )
+    sync_parser.add_argument("--once", action="store_true", help="Sync once and exit")
     sync_parser.add_argument(
-        "--once",
-        action="store_true",
-        help="Sync once and exit"
-    )
-    sync_parser.add_argument(
-        "--bidirectional",
-        action="store_true",
-        help="Sync both directions"
+        "--bidirectional", action="store_true", help="Sync both directions"
     )
     sync_parser.add_argument(
         "--auto-import",
         action="store_true",
         default=True,
-        help="Auto-import from Zotero"
+        help="Auto-import from Zotero",
     )
     sync_parser.add_argument(
-        "--auto-export",
-        action="store_true",
-        help="Auto-export to Zotero"
+        "--auto-export", action="store_true", help="Auto-export to Zotero"
     )
 
     args = parser.parse_args()
@@ -256,6 +238,7 @@ def main():
     except Exception as e:
         logger.error(f"Error: {e}")
         import traceback
+
         traceback.print_exc()
         sys.exit(1)
 

scitex/scholar/integration/zotero/exporter.py

@@ -66,12 +66,15 @@ class ZoteroExporter:
 
             try:
                 from pyzotero import zotero
+
                 self._zot = zotero.Zotero(
                     library_id=self.library_id,
                     library_type=self.library_type,
-                    api_key=self.api_key
+                    api_key=self.api_key,
+                )
+                logger.info(
+                    f"Connected to Zotero {self.library_type} library: {self.library_id}"
                 )
-                logger.info(f"Connected to Zotero {self.library_type} library: {self.library_id}")
             except ImportError:
                 raise ImportError(
                     "pyzotero not installed. Install with: pip install pyzotero"
@@ -125,7 +128,9 @@ class ZoteroExporter:
 
                 if existing_key:
                     # Update existing item
-                    logger.info(f"[{i}/{len(paper_list)}] Updating existing item: {existing_key}")
+                    logger.info(
+                        f"[{i}/{len(paper_list)}] Updating existing item: {existing_key}"
+                    )
                     zotero_item["version"] = self._get_item_version(zot, existing_key)
                     zot.update_item(zotero_item, existing_key)
                     item_key = existing_key
@@ -148,9 +153,7 @@ class ZoteroExporter:
 
                 results[paper.metadata.basic.title or f"paper_{i}"] = item_key
 
-                logger.success(
-                    f"[{i}/{len(paper_list)}] Exported: {item_key}"
-                )
+                logger.success(f"[{i}/{len(paper_list)}] Exported: {item_key}")
 
             except Exception as e:
                 logger.error(
@@ -158,9 +161,7 @@ class ZoteroExporter:
                 )
                 continue
 
-        logger.success(
-            f"Exported {len(results)}/{len(paper_list)} papers to Zotero"
-        )
+        logger.success(f"Exported {len(results)}/{len(paper_list)} papers to Zotero")
 
         return results
 
@@ -314,7 +315,7 @@ class ZoteroExporter:
         """
         # Search by DOI
         if paper.metadata.id.doi:
-            items = zot.items(q=f'doi:{paper.metadata.id.doi}')
+            items = zot.items(q=f"doi:{paper.metadata.id.doi}")
             if items:
                 logger.debug(f"Found existing item by DOI: {items[0]['key']}")
                 return items[0]["key"]
@@ -324,7 +325,10 @@ class ZoteroExporter:
             # Exact title search
             items = zot.items(q=paper.metadata.basic.title)
             for item in items:
-                if item["data"].get("title", "").lower() == paper.metadata.basic.title.lower():
+                if (
+                    item["data"].get("title", "").lower()
+                    == paper.metadata.basic.title.lower()
+                ):
                     logger.debug(f"Found existing item by title: {item['key']}")
                     return item["key"]
 

scitex/scholar/integration/zotero/importer.py

@@ -65,12 +65,15 @@ class ZoteroImporter:
 
             try:
                 from pyzotero import zotero
+
                 self._zot = zotero.Zotero(
                     library_id=self.library_id,
                     library_type=self.library_type,
-                    api_key=self.api_key
+                    api_key=self.api_key,
+                )
+                logger.info(
+                    f"Connected to Zotero {self.library_type} library: {self.library_id}"
                 )
-                logger.info(f"Connected to Zotero {self.library_type} library: {self.library_id}")
             except ImportError:
                 raise ImportError(
                     "pyzotero not installed. Install with: pip install pyzotero"
@@ -106,7 +109,9 @@ class ZoteroImporter:
             for coll in collections:
                 if coll["data"]["name"] == collection_name:
                     collection_id = coll["key"]
-                    logger.info(f"Found collection '{collection_name}': {collection_id}")
+                    logger.info(
+                        f"Found collection '{collection_name}': {collection_id}"
+                    )
                     break
 
             if not collection_id:
@@ -184,7 +189,7 @@ class ZoteroImporter:
         # Search by tags
         query_parts = []
         for tag in tags:
-            query_parts.append(f'tag:{tag}')
+            query_parts.append(f"tag:{tag}")
 
         operator = " && " if match_all else " || "
         query = operator.join(query_parts)
@@ -274,7 +279,7 @@ class ZoteroImporter:
                 pdf_entry = {
                     "url": attachment_url,
                     "source": "zotero",
-                    "zotero_key": attachment_key
+                    "zotero_key": attachment_key,
                 }
 
                 if pdf_entry not in paper.metadata.url.pdfs:
@@ -346,15 +351,12 @@ class ZoteroImporter:
             try:
                 # Save to library
                 paper_id = self.library_manager.save_resolved_paper(
-                    paper_data=paper,
-                    project=self.project
+                    paper_data=paper, project=self.project
                 )
 
                 results[paper.metadata.basic.title or f"paper_{i}"] = paper_id
 
-                logger.info(
-                    f"[{i}/{len(paper_list)}] Saved to library: {paper_id}"
-                )
+                logger.info(f"[{i}/{len(paper_list)}] Saved to library: {paper_id}")
 
             except Exception as e:
                 logger.error(

scitex/scholar/integration/zotero/linker.py

@@ -61,14 +61,14 @@ class ZoteroLinker:
             library_type=library_type,
             api_key=api_key,
             project=project,
-            config=config
+            config=config,
         )
         self.exporter = ZoteroExporter(
             library_id=library_id,
             library_type=library_type,
             api_key=api_key,
             project=project,
-            config=config
+            config=config,
         )
         self.mapper = ZoteroMapper(config=config)
         self.library_manager = LibraryManager(project=project, config=config)
@@ -158,12 +158,7 @@ class ZoteroLinker:
         Returns:
             Dict with sync statistics
         """
-        stats = {
-            "imported": 0,
-            "exported": 0,
-            "updated": 0,
-            "errors": 0
-        }
+        stats = {"imported": 0, "exported": 0, "updated": 0, "errors": 0}
 
         try:
             if auto_import:
@@ -223,12 +218,13 @@ class ZoteroLinker:
                     paper = self.mapper.zotero_to_paper(item)
 
                     # Determine if new or updated
-                    event_type = "added" if item_key not in self._synced_items else "updated"
+                    event_type = (
+                        "added" if item_key not in self._synced_items else "updated"
+                    )
 
                     # Save to library
                     paper_id = self.library_manager.save_resolved_paper(
-                        paper_data=paper,
-                        project=self.project
+                        paper_data=paper, project=self.project
                     )
 
                     # Track synced item
@@ -408,7 +404,7 @@ class ZoteroLinker:
             "last_sync_version": self._last_sync_version,
             "synced_items_count": len(self._synced_items),
             "sync_interval": self.sync_interval,
-            "callbacks_registered": len(self._callbacks)
+            "callbacks_registered": len(self._callbacks),
         }