fix article labels (#32)

* Label is actually required

* Update version

Author: odarbelaeze

src/bibx/__init__.py

@@ -25,7 +25,7 @@
     "read_wos",
 ]
 
-__version__ = "0.3.0"
+__version__ = "0.3.1"
 
 
 def query_openalex(query: str, limit: int = 600) -> Collection:

src/bibx/_entities/article.py

@@ -9,8 +9,13 @@ def _keep(a: T, b: T) -> T:
     return a if a is not None else b
 
 
+def _keep_longest(a: str, b: str) -> str:
+    return a if len(a) > len(b) else b
+
+
 @dataclass
 class Article:
+    label: str
     ids: set[str]
     authors: list[str] = field(default_factory=list)
     year: Optional[int] = None
@@ -20,7 +25,6 @@ class Article:
     issue: Optional[str] = None
     page: Optional[str] = None
     doi: Optional[str] = None
-    _label: Optional[str] = None
     _permalink: Optional[str] = None
     times_cited: Optional[int] = None
     references: list["Article"] = field(default_factory=list)
@@ -31,6 +35,7 @@ class Article:
     def merge(self, other: "Article") -> "Article":
         """Merge two articles into a new one."""
         return Article(
+            label=_keep_longest(self.label, other.label),
             ids=self.ids.union(other.ids),
             authors=self.authors if self.authors else other.authors,
             year=_keep(self.year, other.year),
@@ -40,7 +45,6 @@ def merge(self, other: "Article") -> "Article":
             issue=_keep(self.issue, other.issue),
             page=_keep(self.page, other.page),
             doi=_keep(self.doi, other.doi),
-            _label=_keep(self._label, other._label),
             _permalink=_keep(self._permalink, other._permalink),
             times_cited=_keep(self.times_cited, other.times_cited),
             references=self.references or other.references,
@@ -54,17 +58,17 @@ def key(self) -> str:
         return next(iter(sorted(self.ids)))
 
     @property
-    def label(self) -> str:
-        if self._label is not None:
-            return self._label
+    def simple_label(self) -> Optional[str]:
         pieces = {
-            "AU": self.authors[0].replace(",", "") if self.authors else "anonymous",
+            "AU": self.authors[0].replace(",", "") if self.authors else None,
             "PY": str(self.year) if self.year else None,
             "J9": str(self.journal) if self.journal else None,
             "VL": f"V{self.volume}" if self.volume else None,
             "BP": f"P{self.page}" if self.page else None,
             "DI": f"DOI {self.doi}" if self.doi else None,
         }
+        if not any(pieces.values()):
+            return None
         return ", ".join(value for value in pieces.values() if value)
 
     @property
@@ -85,10 +89,17 @@ def simple_id(self) -> Optional[str]:
     def __repr__(self) -> str:
         return f"Article(ids={self.ids!r}, authors={self.authors!r})"
 
-    def add_simple_id(self) -> None:
+    def add_simple_id(self) -> "Article":
         if self.simple_id is None:
-            return
+            return self
         self.ids.add(f"simple:{self.simple_id}")
+        return self
+
+    def set_simple_label(self) -> "Article":
+        if self.simple_label is None:
+            return self
+        self.label = self.simple_label
+        return self
 
     def info(
         self,

src/bibx/_entities/collection_builders/openalex.py

@@ -75,6 +75,7 @@ def _extract_doi(url: str) -> str:
     @classmethod
     def _work_to_article(cls, work: Work) -> Article:
         article = Article(
+            label=work.id,
             ids={
                 f"{source}:{id_}"
                 if source != "doi"
@@ -93,7 +94,6 @@ def _work_to_article(cls, work: Work) -> Article:
             issue=work.biblio.issue,
             page=work.biblio.first_page,
             doi=cls._extract_doi(work.doi) if work.doi else None,
-            _label=work.id,
             _permalink=work.primary_location and work.primary_location.landing_page_url,
             times_cited=work.cited_by_count,
             references=[cls._reference_to_article(r) for r in work.referenced_works],
@@ -108,6 +108,7 @@ def _work_to_article(cls, work: Work) -> Article:
     @staticmethod
     def _reference_to_article(reference: str) -> Article:
         return Article(
+            label=reference,
             ids={f"openalex:{reference}"},
             _permalink=reference,
             sources={"openalex"},

src/bibx/_entities/collection_builders/scopus_bib.py

@@ -41,24 +41,29 @@ def _article_from_entry(self, entry: dict) -> Article:
         doi = entry.get("doi")
         if doi is not None:
             ids.add(f"doi:{doi}")
-        article = Article(
-            ids=ids,
-            authors=entry["author"].split(" and "),
-            year=int(entry["year"]),
-            title=entry.get("title"),
-            journal=entry.get("journal"),
-            volume=entry.get("volume"),
-            issue=entry.get("issue"),
-            page=entry.get("art_number"),
-            doi=entry.get("doi"),
-            references=list(self._articles_from_references(entry.get("references"))),
-            keywords=entry.get("keywords", "").split("; "),
-            extra=entry,
-            sources={json.dumps(entry)},
-            times_cited=times_cited,
+        return (
+            Article(
+                label=doi or entry.get("title", "replaceme"),
+                ids=ids,
+                authors=entry["author"].split(" and "),
+                year=int(entry["year"]),
+                title=entry.get("title"),
+                journal=entry.get("journal"),
+                volume=entry.get("volume"),
+                issue=entry.get("issue"),
+                page=entry.get("art_number"),
+                doi=entry.get("doi"),
+                references=list(
+                    self._articles_from_references(entry.get("references"))
+                ),
+                keywords=entry.get("keywords", "").split("; "),
+                extra=entry,
+                sources={json.dumps(entry)},
+                times_cited=times_cited,
+            )
+            .add_simple_id()
+            .set_simple_label()
         )
-        article.add_simple_id()
-        return article
 
     def _articles_from_references(self, references: Optional[str]) -> Iterable[Article]:
         if references is None:
@@ -76,13 +81,11 @@ def _article_from_reference(reference: str) -> Article:
         author = reference.split(",", maxsplit=2)[0].strip()
         match = re.search(r"(10.\d{4,9}/[-._;()/:A-Z0-9]+)", reference)
         doi = match.groups()[0] if match else None
-        article = Article(
+        return Article(
+            label=reference,
             ids=set() if doi is None else {f"doi:{doi}"},
             authors=[author],
             year=year,
-            _label=reference,
             doi=doi,
             sources={reference},
-        )
-        article.add_simple_id()
-        return article
+        ).add_simple_id()

src/bibx/_entities/collection_builders/scopus_ris.py

@@ -102,7 +102,8 @@ def _article_form_reference(cls, scopusref: str) -> Article:
         doi, _ = cls._find_doi(scopusref)
         if not authors or not year:
             raise MissingCriticalInformationError()
-        article = Article(
+        return Article(
+            label=scopusref,
             ids=set() if doi is None else {f"doi:{doi}"},
             authors=[f"{first_name} {last_name.replace(' ', '').replace('.', '')}"],
             year=int(year),
@@ -114,9 +115,7 @@ def _article_form_reference(cls, scopusref: str) -> Article:
             volume=volume_info.get("volume"),
             page=volume_info.get("page"),
             doi=doi,
-        )
-        article.add_simple_id()
-        return article
+        ).add_simple_id()
 
     @classmethod
     def _parse_references(cls, refs: list[str]) -> list[Article]:
@@ -134,7 +133,6 @@ def _parse_references(cls, refs: list[str]) -> list[Article]:
     def _ris_to_dict(record: str) -> dict[str, list[str]]:
         parsed = defaultdict(list)
         current = None
-
         for line in record.split("\n"):
             match = _RIS_PATTERN.match(line)
             if not match:
@@ -163,25 +161,29 @@ def _article_from_record(cls, record: str) -> Article:
         authors = data.get("AU", [])
         if not authors or not year:
             raise MissingCriticalInformationError()
-        doi = data.get("DO")
-        article = Article(
-            ids=set() if doi is None else {f"doi:{doi}"},
-            title=_joined(data.get("TI")),
-            authors=authors,
-            year=year,
-            journal=_joined(data.get("J2")),
-            volume=_joined(data.get("VL")),
-            issue=_joined(data.get("IS")),
-            page=_joined(data.get("SP")),
-            doi=_joined(data.get("DO")),
-            keywords=data.get("KW", []),
-            references=cls._parse_references(data.get("N1:References", [])),
-            sources={"scopus"},
-            extra=data,
-            times_cited=times_cited,
+        doi_list = data.get("DO")
+        doi = doi_list[0] if doi_list else None
+        return (
+            Article(
+                label=doi or "replaceme",
+                ids=set() if doi is None else {f"doi:{doi}"},
+                title=_joined(data.get("TI")),
+                authors=authors,
+                year=year,
+                journal=_joined(data.get("J2")),
+                volume=_joined(data.get("VL")),
+                issue=_joined(data.get("IS")),
+                page=_joined(data.get("SP")),
+                doi=doi,
+                keywords=data.get("KW", []),
+                references=cls._parse_references(data.get("N1:References", [])),
+                sources={"scopus"},
+                extra=data,
+                times_cited=times_cited,
+            )
+            .add_simple_id()
+            .set_simple_label()
         )
-        article.add_simple_id()
-        return article
 
     @classmethod
     def _parse_file(cls, file: TextIO) -> Iterable[Article]:

src/bibx/_entities/collection_builders/wos.py

@@ -297,26 +297,29 @@ def _parse_article_from_str(cls, article_as_str: str) -> Article:
             article_data[field].append(parsed["value"])
         processed = cls._parse_all(dict(article_data))
         doi = processed.get("DOI")
-        article = Article(
-            ids=set() if doi is None else {f"doi:{doi}"},
-            authors=processed.get("authors", []),
-            year=processed.get("year"),
-            title=processed.get("title"),
-            journal=processed.get("source_abbreviation"),
-            volume=processed.get("volume"),
-            issue=processed.get("issue"),
-            page=processed.get("beginning_page"),
-            doi=doi,
-            times_cited=processed.get("times_cited"),
-            references=list(
-                cls._get_articles_from_references(processed.get("references"))
-            ),
-            keywords=processed.get("keywords", []),
-            extra=processed,
-            sources={article_as_str},
+        return (
+            Article(
+                label=doi or "replaceme",
+                ids=set() if doi is None else {f"doi:{doi}"},
+                authors=processed.get("authors", []),
+                year=processed.get("year"),
+                title=processed.get("title"),
+                journal=processed.get("source_abbreviation"),
+                volume=processed.get("volume"),
+                issue=processed.get("issue"),
+                page=processed.get("beginning_page"),
+                doi=doi,
+                times_cited=processed.get("times_cited"),
+                references=list(
+                    cls._get_articles_from_references(processed.get("references"))
+                ),
+                keywords=processed.get("keywords", []),
+                extra=processed,
+                sources={article_as_str},
+            )
+            .add_simple_id()
+            .set_simple_label()
         )
-        article.add_simple_id()
-        return article
 
     @classmethod
     def _parse_reference_from_str(cls, reference: str) -> Article:
@@ -327,8 +330,8 @@ def _parse_reference_from_str(cls, reference: str) -> Article:
         processed = cls._parse_all(data)
         doi = processed.get("DOI")
         article = Article(
+            label=reference,
             ids=set() if doi is None else {f"doi:{doi}"},
-            _label=reference,
             title=processed.get("title"),
             authors=processed.get("authors", []),
             # FIXME: Year is required here