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

scitex/scholar/metadata_engines/individual/ArXivEngine.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/scholar/engines/individual/ArXivEngine.py"
-)
+
+__FILE__ = "./src/scitex/scholar/engines/individual/ArXivEngine.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -75,18 +74,15 @@ class ArXivEngine(BaseDOIEngine):
     @retry(
         stop=stop_after_attempt(3),
         wait=wait_exponential(multiplier=1, min=2, max=10),
-        retry=retry_if_exception_type(
-            (requests.HTTPError, requests.ConnectionError)
-        ),
+        retry=retry_if_exception_type((requests.HTTPError, requests.ConnectionError)),
     )
     def _search_by_doi(self, doi: str, return_as: str) -> Optional[Dict]:
         """Search solely on doi"""
-        doi = doi.replace("https://doi.org/", "").replace(
-            "http://doi.org/", ""
-        )
+        doi = doi.replace("https://doi.org/", "").replace("http://doi.org/", "")
         # Extract arXiv ID - handle both "arXiv." and "arxiv." (case-insensitive)
         import re
-        match = re.search(r'arxiv\.(\d+\.\d+)', doi, re.IGNORECASE)
+
+        match = re.search(r"arxiv\.(\d+\.\d+)", doi, re.IGNORECASE)
         arxiv_id = match.group(1) if match else doi.split("arXiv.")[-1]
 
         params = {
@@ -102,9 +98,7 @@ class ArXivEngine(BaseDOIEngine):
                 "dict",
                 "json",
             ], "return_as must be either of 'dict' or 'json'"
-            response = self.session.get(
-                self.base_url, params=params, timeout=30
-            )
+            response = self.session.get(self.base_url, params=params, timeout=30)
             response.raise_for_status()
 
             feed = feedparser.parse(response.text)
@@ -162,18 +156,14 @@ class ArXivEngine(BaseDOIEngine):
     @retry(
         stop=stop_after_attempt(3),
         wait=wait_exponential(multiplier=1, min=2, max=10),
-        retry=retry_if_exception_type(
-            (requests.HTTPError, requests.ConnectionError)
-        ),
+        retry=retry_if_exception_type((requests.HTTPError, requests.ConnectionError)),
     )
     def _search_by_metadata(
         self,
         title: str,
         year: Optional[Union[int, str]] = None,
         authors: Optional[List[str]] = None,
-        max_results: Optional[
-            int
-        ] = 5,  # Increased from 1 to get more candidates
+        max_results: Optional[int] = 5,  # Increased from 1 to get more candidates
         return_as: Optional[str] = "dict",
     ) -> Optional[Dict]:
         """Search by metadata other than doi"""
@@ -201,9 +191,7 @@ class ArXivEngine(BaseDOIEngine):
                 "dict",
                 "json",
             ], "return_as must be either of 'dict' or 'json'"
-            response = self.session.get(
-                self.base_url, params=params, timeout=30
-            )
+            response = self.session.get(self.base_url, params=params, timeout=30)
             response.raise_for_status()
 
             feed = feedparser.parse(response.text)
@@ -230,17 +218,13 @@ class ArXivEngine(BaseDOIEngine):
     @retry(
         stop=stop_after_attempt(3),
         wait=wait_exponential(multiplier=1, min=2, max=10),
-        retry=retry_if_exception_type(
-            (requests.HTTPError, requests.ConnectionError)
-        ),
+        retry=retry_if_exception_type((requests.HTTPError, requests.ConnectionError)),
     )
     def _scrape_doi(self, url_publisher):
         try:
             response = requests.get(url_publisher)
             soup = BeautifulSoup(response.content, "html.parser")
-            doi_link = soup.find(
-                "a", href=lambda href: href and "doi.org" in href
-            )
+            doi_link = soup.find("a", href=lambda href: href and "doi.org" in href)
             doi = doi_link.get("href").split("doi.org/")[-1]
             return doi
         except Exception as e:
@@ -249,13 +233,9 @@ class ArXivEngine(BaseDOIEngine):
     @retry(
         stop=stop_after_attempt(3),
         wait=wait_exponential(multiplier=1, min=2, max=10),
-        retry=retry_if_exception_type(
-            (requests.HTTPError, requests.ConnectionError)
-        ),
+        retry=retry_if_exception_type((requests.HTTPError, requests.ConnectionError)),
     )
-    def _extract_metadata_from_entry(
-        self, entry, return_as: str
-    ) -> Optional[Dict]:
+    def _extract_metadata_from_entry(self, entry, return_as: str) -> Optional[Dict]:
         """Extract metadata from ArXiv entry"""
         arxiv_id = entry.id.split("/abs/")[-1].split("v")[0]
         year = entry.get("published", "")[:4]
@@ -377,9 +357,7 @@ if __name__ == "__main__":
 
     # Search by title
     outputs["metadata_by_title_dict"] = engine.search(title=TITLE)
-    outputs["metadata_by_title_json"] = engine.search(
-        title=TITLE, return_as="json"
-    )
+    outputs["metadata_by_title_json"] = engine.search(title=TITLE, return_as="json")
 
     # Search by DOI
     outputs["metadata_by_doi_dict"] = engine.search(doi=DOI)

scitex/scholar/metadata_engines/individual/CrossRefEngine.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -56,9 +57,7 @@ class CrossRefEngine(BaseDOIEngine):
 
     def _search_by_doi(self, doi: str, return_as: str) -> Optional[Dict]:
         """Search by DOI directly"""
-        doi = doi.replace("https://doi.org/", "").replace(
-            "http://doi.org/", ""
-        )
+        doi = doi.replace("https://doi.org/", "").replace("http://doi.org/", "")
         url = f"{self.base_url}/{doi}"
 
         try:
@@ -106,9 +105,7 @@ class CrossRefEngine(BaseDOIEngine):
                 "dict",
                 "json",
             ], "return_as must be either of 'dict' or 'json'"
-            response = self.session.get(
-                self.base_url, params=params, timeout=30
-            )
+            response = self.session.get(self.base_url, params=params, timeout=30)
             response.raise_for_status()
             data = response.json()
 
@@ -145,9 +142,7 @@ class CrossRefEngine(BaseDOIEngine):
                 return_as=return_as,
             )
 
-    def _extract_metadata_from_item(
-        self, item, return_as: str
-    ) -> Optional[Dict]:
+    def _extract_metadata_from_item(self, item, return_as: str) -> Optional[Dict]:
         """Extract metadata from CrossRef item"""
         item_title = " ".join(item.get("title", []))
         if item_title.endswith("."):
@@ -171,9 +166,7 @@ class CrossRefEngine(BaseDOIEngine):
         container_titles = item.get("container-title", [])
         short_container_titles = item.get("short-container-title", [])
         journal = container_titles[0] if container_titles else None
-        short_journal = (
-            short_container_titles[0] if short_container_titles else None
-        )
+        short_journal = short_container_titles[0] if short_container_titles else None
         issn_list = item.get("ISSN", [])
         issn = issn_list[0] if issn_list else None
 
@@ -190,12 +183,8 @@ class CrossRefEngine(BaseDOIEngine):
                 "title_engines": [self.name] if item_title else None,
                 "year": pub_year if pub_year else None,
                 "year_engines": [self.name] if pub_year else None,
-                "abstract": (
-                    item.get("abstract") if item.get("abstract") else None
-                ),
-                "abstract_engines": (
-                    [self.name] if item.get("abstract") else None
-                ),
+                "abstract": (item.get("abstract") if item.get("abstract") else None),
+                "abstract_engines": ([self.name] if item.get("abstract") else None),
                 "authors": extracted_authors if extracted_authors else None,
                 "authors_engines": [self.name] if extracted_authors else None,
             },
@@ -207,15 +196,9 @@ class CrossRefEngine(BaseDOIEngine):
                 "journal": journal if journal else None,
                 "journal_engines": [self.name] if journal else None,
                 "short_journal": short_journal if short_journal else None,
-                "short_journal_engines": (
-                    [self.name] if short_journal else None
-                ),
-                "publisher": (
-                    item.get("publisher") if item.get("publisher") else None
-                ),
-                "publisher_engines": (
-                    [self.name] if item.get("publisher") else None
-                ),
+                "short_journal_engines": ([self.name] if short_journal else None),
+                "publisher": (item.get("publisher") if item.get("publisher") else None),
+                "publisher_engines": ([self.name] if item.get("publisher") else None),
                 "volume": item.get("volume") if item.get("volume") else None,
                 "volume_engines": [self.name] if item.get("volume") else None,
                 "issue": item.get("issue") if item.get("issue") else None,
@@ -225,9 +208,7 @@ class CrossRefEngine(BaseDOIEngine):
             },
             "url": {
                 "doi": (
-                    "https://doi.org/" + item.get("DOI")
-                    if item.get("DOI")
-                    else None
+                    "https://doi.org/" + item.get("DOI") if item.get("DOI") else None
                 ),
                 "doi_engines": [self.name] if item.get("DOI") else None,
             },
@@ -259,23 +240,15 @@ if __name__ == "__main__":
 
         # Search by title
         outputs["metadata_by_title_dict"] = engine.search(title=TITLE)
-        outputs["metadata_by_title_json"] = engine.search(
-            title=TITLE, return_as="json"
-        )
+        outputs["metadata_by_title_json"] = engine.search(title=TITLE, return_as="json")
 
         # Search by DOI
         outputs["metadata_by_doi_dict"] = engine.search(doi=DOI)
-        outputs["metadata_by_doi_json"] = engine.search(
-            doi=DOI, return_as="json"
-        )
+        outputs["metadata_by_doi_json"] = engine.search(doi=DOI, return_as="json")
 
         # Empty Result
-        outputs["empty_dict"] = engine._create_minimal_metadata(
-            return_as="dict"
-        )
-        outputs["empty_json"] = engine._create_minimal_metadata(
-            return_as="json"
-        )
+        outputs["empty_dict"] = engine._create_minimal_metadata(return_as="dict")
+        outputs["empty_json"] = engine._create_minimal_metadata(return_as="json")
 
         for k, v in outputs.items():
             print("----------------------------------------")

scitex/scholar/metadata_engines/individual/CrossRefLocalEngine.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -41,7 +42,9 @@ class CrossRefLocalEngine(BaseDOIEngine):
         self.api_url = api_url.rstrip("/")
 
         # Detect API type: external (public) vs internal (Docker/local)
-        self._is_external_api = "/api/crossref" in self.api_url or "scitex.ai" in self.api_url
+        self._is_external_api = (
+            "/api/crossref" in self.api_url or "scitex.ai" in self.api_url
+        )
 
     @property
     def name(self) -> str:
@@ -85,9 +88,7 @@ class CrossRefLocalEngine(BaseDOIEngine):
         params = {}
 
         if doi:
-            doi = doi.replace("https://doi.org/", "").replace(
-                "http://doi.org/", ""
-            )
+            doi = doi.replace("https://doi.org/", "").replace("http://doi.org/", "")
             params["doi"] = doi
 
         if title:
@@ -107,9 +108,7 @@ class CrossRefLocalEngine(BaseDOIEngine):
 
         return self._make_search_request(params, return_as)
 
-    def _make_search_request(
-        self, params: dict, return_as: str
-    ) -> Optional[Dict]:
+    def _make_search_request(self, params: dict, return_as: str) -> Optional[Dict]:
         """Make search request to local or external API"""
         url = self._build_endpoint_url("search")
 
@@ -123,42 +122,32 @@ class CrossRefLocalEngine(BaseDOIEngine):
             response.raise_for_status()
             data = response.json()
 
-            if (
-                "doi" in params
-                and isinstance(data, dict)
-                and not data.get("error")
-            ):
-                return self._extract_metadata_from_crossref_data(
-                    data, return_as
-                )
+            if "doi" in params and isinstance(data, dict) and not data.get("error"):
+                return self._extract_metadata_from_crossref_data(data, return_as)
 
             elif "results" in data and data["results"]:
                 first_result = data["results"][0]
                 if first_result.get("doi"):
-                    return self._search_by_doi_only(
-                        first_result["doi"], return_as
-                    )
+                    return self._search_by_doi_only(first_result["doi"], return_as)
 
             elif isinstance(data, dict) and not data.get("error"):
-                return self._extract_metadata_from_crossref_data(
-                    data, return_as
-                )
+                return self._extract_metadata_from_crossref_data(data, return_as)
 
             return self._create_minimal_metadata(return_as=return_as)
 
         except Exception as e:
             # Shorten verbose connection error messages
             if "Connection refused" in str(e) or "Max retries exceeded" in str(e):
-                logger.warning(f"CrossRef Local server not available at {self.api_url} (connection refused)")
+                logger.warning(
+                    f"CrossRef Local server not available at {self.api_url} (connection refused)"
+                )
             else:
                 logger.warning(f"CrossRef Local search error: {e}")
             return self._create_minimal_metadata(return_as=return_as)
 
     def _search_by_doi_only(self, doi: str, return_as: str) -> Optional[Dict]:
         """Get full metadata for DOI"""
-        doi = doi.replace("https://doi.org/", "").replace(
-            "http://doi.org/", ""
-        )
+        doi = doi.replace("https://doi.org/", "").replace("http://doi.org/", "")
         url = self._build_endpoint_url("search")
         params = {"doi": doi}
 
@@ -170,7 +159,9 @@ class CrossRefLocalEngine(BaseDOIEngine):
         except Exception as exc:
             # Shorten verbose connection error messages
             if "Connection refused" in str(exc) or "Max retries exceeded" in str(exc):
-                logger.warning(f"CrossRef Local server not available at {self.api_url} (connection refused)")
+                logger.warning(
+                    f"CrossRef Local server not available at {self.api_url} (connection refused)"
+                )
             else:
                 logger.warning(f"CrossRef Local DOI lookup error: {exc}")
             return self._create_minimal_metadata(doi=doi, return_as=return_as)
@@ -205,9 +196,7 @@ class CrossRefLocalEngine(BaseDOIEngine):
         container_titles = data.get("container-title", [])
         short_container_titles = data.get("short-container-title", [])
         journal = container_titles[0] if container_titles else None
-        short_journal = (
-            short_container_titles[0] if short_container_titles else None
-        )
+        short_journal = short_container_titles[0] if short_container_titles else None
 
         issn_list = data.get("ISSN", [])
         issn = issn_list[0] if issn_list else None
@@ -229,15 +218,9 @@ class CrossRefLocalEngine(BaseDOIEngine):
                 "journal": journal if journal else None,
                 "journal_engines": [self.name] if journal else None,
                 "short_journal": short_journal if short_journal else None,
-                "short_journal_engines": (
-                    [self.name] if short_journal else None
-                ),
-                "publisher": (
-                    data.get("publisher") if data.get("publisher") else None
-                ),
-                "publisher_engines": (
-                    [self.name] if data.get("publisher") else None
-                ),
+                "short_journal_engines": ([self.name] if short_journal else None),
+                "publisher": (data.get("publisher") if data.get("publisher") else None),
+                "publisher_engines": ([self.name] if data.get("publisher") else None),
                 "volume": data.get("volume") if data.get("volume") else None,
                 "volume_engines": [self.name] if data.get("volume") else None,
                 "issue": data.get("issue") if data.get("issue") else None,
@@ -247,9 +230,7 @@ class CrossRefLocalEngine(BaseDOIEngine):
             },
             "url": {
                 "doi": (
-                    f"https://doi.org/{data.get('DOI')}"
-                    if data.get("DOI")
-                    else None
+                    f"https://doi.org/{data.get('DOI')}" if data.get("DOI") else None
                 ),
                 "doi_engines": [self.name] if data.get("DOI") else None,
             },
@@ -279,8 +260,7 @@ if __name__ == "__main__":
     print("INTERNAL API EXAMPLE")
     print("=" * 60)
     engine_internal = CrossRefLocalEngine(
-        "test@example.com",
-        api_url="http://crossref:3333"
+        "test@example.com", api_url="http://crossref:3333"
     )
     print(f"API URL: {engine_internal.api_url}")
     print(f"Is External: {engine_internal._is_external_api}")
@@ -291,8 +271,7 @@ if __name__ == "__main__":
     print("EXTERNAL API EXAMPLE")
     print("=" * 60)
     engine_external = CrossRefLocalEngine(
-        "test@example.com",
-        api_url="https://scitex.ai/scholar/api/crossref"
+        "test@example.com", api_url="https://scitex.ai/scholar/api/crossref"
     )
     print(f"API URL: {engine_external.api_url}")
     print(f"Is External: {engine_external._is_external_api}")

scitex/scholar/metadata_engines/individual/OpenAlexEngine.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -56,9 +57,7 @@ class OpenAlexEngine(BaseDOIEngine):
 
     def _search_by_doi(self, doi: str, return_as: str) -> Optional[Dict]:
         """Search by DOI directly"""
-        doi = doi.replace("https://doi.org/", "").replace(
-            "http://doi.org/", ""
-        )
+        doi = doi.replace("https://doi.org/", "").replace("http://doi.org/", "")
 
         params = {
             "filter": f"doi:{doi}",
@@ -70,9 +69,7 @@ class OpenAlexEngine(BaseDOIEngine):
                 "dict",
                 "json",
             ], "return_as must be either of 'dict' or 'json'"
-            response = self.session.get(
-                self.base_url, params=params, timeout=30
-            )
+            response = self.session.get(self.base_url, params=params, timeout=30)
             response.raise_for_status()
 
             data = response.json()
@@ -121,9 +118,7 @@ class OpenAlexEngine(BaseDOIEngine):
                 "dict",
                 "json",
             ], "return_as must be either of 'dict' or 'json'"
-            response = self.session.get(
-                self.base_url, params=params, timeout=30
-            )
+            response = self.session.get(self.base_url, params=params, timeout=30)
             response.raise_for_status()
 
             data = response.json()
@@ -151,9 +146,7 @@ class OpenAlexEngine(BaseDOIEngine):
                 return_as=return_as,
             )
 
-    def _extract_metadata_from_work(
-        self, work, return_as: str
-    ) -> Optional[Dict]:
+    def _extract_metadata_from_work(self, work, return_as: str) -> Optional[Dict]:
         """Extract metadata from OpenAlex work"""
         work_title = work.get("title", "")
         if work_title and work_title.endswith("."):
@@ -223,8 +216,7 @@ class OpenAlexEngine(BaseDOIEngine):
         citation_count_by_year = work.get("counts_by_year")
         if citation_count_by_year:
             citation_count_by_year = {
-                str(dd["year"]): dd["cited_by_count"]
-                for dd in citation_count_by_year
+                str(dd["year"]): dd["cited_by_count"] for dd in citation_count_by_year
             }
             citation_counts = {
                 "total": citation_count,
@@ -262,9 +254,7 @@ class OpenAlexEngine(BaseDOIEngine):
                     if work.get("publication_year")
                     else None
                 ),
-                "year_engines": (
-                    [self.name] if work.get("publication_year") else None
-                ),
+                "year_engines": ([self.name] if work.get("publication_year") else None),
                 "authors": extracted_authors if extracted_authors else None,
                 "authors_engines": [self.name] if extracted_authors else None,
                 "keywords": keywords if keywords else None,
@@ -299,7 +289,9 @@ class OpenAlexEngine(BaseDOIEngine):
                 "publisher": url_publisher if url_publisher else None,
                 "publisher_engines": [self.name] if url_publisher else None,
             },
-            "citation_count": citation_counts if citation_count_by_year else {
+            "citation_count": citation_counts
+            if citation_count_by_year
+            else {
                 "count": citation_count if citation_count else None,
                 "count_engines": [self.name] if citation_count else None,
             },
@@ -326,9 +318,7 @@ if __name__ == "__main__":
 
     # Search by title
     outputs["metadata_by_title_dict"] = engine.search(title=TITLE)
-    outputs["metadata_by_title_json"] = engine.search(
-        title=TITLE, return_as="json"
-    )
+    outputs["metadata_by_title_json"] = engine.search(title=TITLE, return_as="json")
 
     # Search by DOI
     outputs["metadata_by_doi_dict"] = engine.search(doi=DOI)

scitex/scholar/metadata_engines/individual/PubMedEngine.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -84,9 +85,7 @@ class PubMedEngine(BaseDOIEngine):
             query_parts.append(f"{year}[pdat]")
         query = " AND ".join(query_parts)
 
-        search_url = (
-            "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
-        )
+        search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
         search_params = {
             "db": "pubmed",
             "term": query,
@@ -94,9 +93,7 @@ class PubMedEngine(BaseDOIEngine):
             "retmax": 5,
             "email": self.email,
         }
-        response = self.session.get(
-            search_url, params=search_params, timeout=30
-        )
+        response = self.session.get(search_url, params=search_params, timeout=30)
         response.raise_for_status()
         data = response.json()
         pmids = data.get("esearchresult", {}).get("idlist", [])
@@ -108,9 +105,7 @@ class PubMedEngine(BaseDOIEngine):
                 metadata
                 and metadata.get("basic")
                 and metadata.get("basic").get("title")
-                and self._is_title_match(
-                    title, metadata.get("basic").get("title")
-                )
+                and self._is_title_match(title, metadata.get("basic").get("title"))
             ):
                 if return_as == "dict":
                     return metadata
@@ -123,13 +118,9 @@ class PubMedEngine(BaseDOIEngine):
         return_as: Optional[str] = "dict",
     ) -> Optional[Dict[str, Any]]:
         """Search by DOI using PubMed database"""
-        doi = doi.replace("https://doi.org/", "").replace(
-            "http://doi.org/", ""
-        )
+        doi = doi.replace("https://doi.org/", "").replace("http://doi.org/", "")
 
-        search_url = (
-            "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
-        )
+        search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
         search_params = {
             "db": "pubmed",
             "term": f'"{doi}"[doi]',
@@ -138,9 +129,7 @@ class PubMedEngine(BaseDOIEngine):
             "email": self.email,
         }
 
-        response = self.session.get(
-            search_url, params=search_params, timeout=30
-        )
+        response = self.session.get(search_url, params=search_params, timeout=30)
         response.raise_for_status()
         data = response.json()
         pmids = data.get("esearchresult", {}).get("idlist", [])
@@ -255,9 +244,7 @@ class PubMedEngine(BaseDOIEngine):
                 "journal": journal,
                 "journal_engines": [self.name] if journal else None,
                 "short_journal": short_journal,
-                "short_journal_engines": (
-                    [self.name] if short_journal else None
-                ),
+                "short_journal_engines": ([self.name] if short_journal else None),
                 "issn": issn,
                 "issn_engines": [self.name] if issn else None,
                 "volume": volume,
@@ -299,9 +286,7 @@ if __name__ == "__main__":
 
     # Search by title
     outputs["metadata_by_title_dict"] = engine.search(title=TITLE)
-    outputs["metadata_by_title_json"] = engine.search(
-        title=TITLE, return_as="json"
-    )
+    outputs["metadata_by_title_json"] = engine.search(title=TITLE, return_as="json")
 
     # Search by DOI
     outputs["metadata_by_doi_dict"] = engine.search(doi=DOI)
@@ -309,9 +294,7 @@ if __name__ == "__main__":
 
     # Search by PubMed ID
     outputs["metadata_by_pmid_dict"] = engine.search(pmid=PMID)
-    outputs["metadata_by_pmid_json"] = engine.search(
-        pmid=PMID, return_as="json"
-    )
+    outputs["metadata_by_pmid_json"] = engine.search(pmid=PMID, return_as="json")
 
     # Emptry Result
     outputs["empty_dict"] = engine._create_minimal_metadata(return_as="dict")