Merging staging branch into prod branch

backend/cellguide/pipeline/canonical_marker_genes/canonical_markers.py

@@ -12,14 +12,12 @@
     ParsedAsctbTableEntry,
     Reference,
 )
-from backend.cellguide.pipeline.canonical_marker_genes.utils import (
-    clean_doi,
-    get_title_and_citation_from_doi,
-)
 from backend.cellguide.pipeline.constants import ASCTB_MASTER_SHEET_URL, CELLGUIDE_PIPELINE_NUM_CPUS
 from backend.common.census_cube.data.ontology_labels import ontology_term_label
 from backend.common.census_cube.utils import setup_retry_session
+from backend.common.doi import clean_doi
 from backend.common.marker_genes.marker_gene_files.gene_metadata import get_gene_id_to_name_and_symbol
+from backend.common.providers.crossref_provider import CrossrefProvider
 
 logger = logging.getLogger(__name__)
 
@@ -53,6 +51,7 @@ def __init__(self, *, wmg_tissues: list[str], wmg_human_genes: list[str]):
 
         gene_metadata = get_gene_id_to_name_and_symbol()
         self.gene_id_to_name = gene_metadata.gene_id_to_name
+        self.crossref_provider = CrossrefProvider()
 
     def _get_tissue_id(self, anatomical_structures: list[AnatomicalStructure]) -> str:
         """
@@ -132,7 +131,7 @@ def fetch_doi_info(ref):
             doi = clean_doi(ref.doi)
             if doi:
                 if doi not in doi_to_citation:
-                    title = get_title_and_citation_from_doi(doi)
+                    title = self.crossref_provider.get_title_and_citation_from_doi(doi)
                     doi_to_citation[doi] = title
                 else:
                     title = doi_to_citation[doi]

backend/cellguide/pipeline/source_collections/source_collections_generator.py

@@ -1,10 +1,10 @@
-from backend.cellguide.pipeline.canonical_marker_genes.utils import format_citation_dp
 from backend.cellguide.pipeline.source_collections.types import SourceCollectionsData
 from backend.common.census_cube.utils import (
     descendants,
     get_collections_from_discover_api,
     get_datasets_from_discover_api,
 )
+from backend.common.citation import format_citation_dp
 
 
 def generate_source_collections_data(all_cell_type_ids_in_corpus: list[str]) -> dict[str, list[SourceCollectionsData]]:

backend/common/citation.py

@@ -0,0 +1,52 @@
+def format_citation_dp(message: dict) -> str:
+    """
+    Formats the citation message.
+
+    Parameters
+    ----------
+    message : dict
+        The message containing publisher_metadata from the /collections API.
+
+    Returns
+    -------
+    str
+        The formatted citation string.
+    """
+    author_str_suffix = ""
+    if len(message["authors"]) > 1:
+        author_str_suffix = " et al."
+    first_author = message["authors"][0]
+    author_str = f"{first_author['family']}" if "family" in first_author else f"{first_author['name']}"
+    author_str += author_str_suffix
+
+    journal = message["journal"] if message["journal"] else ""
+    year = f"{message['published_year']}"
+
+    return f"{author_str} ({year}) {journal}"
+
+
+def format_citation_crossref(message: dict) -> str:
+    """
+    Formats the citation message.
+
+    Parameters
+    ----------
+    message : dict
+        The message containing citation details output from CrossRef.
+
+    Returns
+    -------
+    str
+        The formatted citation string.
+    """
+    author_str_suffix = ""
+    if len(message["author"]) > 1:
+        author_str_suffix = " et al."
+    first_author = message["author"][0]
+    author_str = f"{first_author['family']}" if "family" in first_author else f"{first_author['name']}"
+    author_str += author_str_suffix
+
+    journal = message["container-title"][0] if len(message["container-title"]) else ""
+    year = message["created"]["date-parts"][0][0]
+
+    return f"{author_str} ({year}) {journal}"

backend/layers/common/doi.py → backend/common/doi.py

@@ -51,3 +51,29 @@ def portal_get_normalized_doi_url(doi_node: dict, errors: list) -> Optional[str]
             return None
         doi_url = f"https://doi.org/{parsed_doi}"
     return doi_url
+
+
+def clean_doi(doi: str) -> str:
+    """
+    Cleans the DOI string.
+
+    Parameters
+    ----------
+    doi : str
+        The DOI string to be cleaned.
+
+    Returns
+    -------
+    str
+        The cleaned DOI string.
+    """
+    doi = doi.strip()
+    if doi == "No DOI":
+        return ""
+
+    if doi != "" and doi[-1] == ".":
+        doi = doi[:-1]
+    if " " in doi:
+        doi = doi.split(" ")[1]  # this handles cases where the DOI string is "DOI: {doi}"
+    doi = doi.strip()
+    return doi