Merge pull request #761 from alliance-genome/SCRUM-4458-sw

fixed to missing data for 'authors', 'mod_corpus_associations', 'mesh…

agr_literature_service/api/crud/reference_crud.py

@@ -427,14 +427,13 @@ def show(db: Session, curie_or_reference_id: str):  # noqa
                     mod_reference_type_id=ref_mod_referencetype.reference_mod_referencetype_id,
                     reference_type=ref_mod_referencetype.mod_referencetype.referencetype.label,
                     mod_abbreviation=ref_mod_referencetype.mod_referencetype.mod.abbreviation)))
-    if "obsolete_reference" in reference_data:
-        reference_data["obsolete_references"] = [obs_reference["curie"] for obs_reference in
-                                                 reference_data["obsolete_reference"]]
-        del reference_data["obsolete_reference"]
+    reference_data["obsolete_references"] = [obs_reference["curie"] for obs_reference in
+                                             reference_data["obsolete_reference"]]
+    del reference_data["obsolete_reference"]
 
     # So thisis wierd, we check reference.mod_corpus_association BUT
     # use reference_data["mod_corpus_association"]
-    if reference.mod_corpus_association and "mod_corpus_association" in reference_data:
+    if reference.mod_corpus_association:
         for i in range(len(reference_data["mod_corpus_association"])):
             del reference_data["mod_corpus_association"][i]["reference_id"]
             reference_data["mod_corpus_association"][i]["mod_abbreviation"] = reference_data[
@@ -451,12 +450,12 @@ def show(db: Session, curie_or_reference_id: str):  # noqa
 
             reference_data["workflow_tags"].append(ont_json)
 
-    if reference.mesh_term and "mesh_term" in reference_data:
+    if reference.mesh_term:
         for mesh_term in reference_data["mesh_term"]:
             del mesh_term["reference_id"]
         reference_data['mesh_terms'] = reference_data['mesh_term']
 
-    if reference.author and "author" in reference_data:
+    if reference.author:
         authors = []
         for author in reference_data["author"]:
             del author["reference_id"]

agr_literature_service/api/crud/reference_utils.py

@@ -4,7 +4,7 @@
 
 from fastapi import HTTPException, status
 from sqlalchemy import or_
-from sqlalchemy.orm import Session, Load
+from sqlalchemy.orm import Session, subqueryload, joinedload
 
 from agr_literature_service.api.models import ReferenceModel, ObsoleteReferenceModel, ReferencefileModel
 
@@ -108,23 +108,27 @@ def get_reference(db: Session, curie_or_reference_id: str, load_referencefiles:
                   load_authors: bool = False, load_mod_corpus_associations: bool = False,
                   load_mesh_terms: bool = False, load_obsolete_references: bool = False):
     reference_id = int(curie_or_reference_id) if curie_or_reference_id.isdigit() else None
-    options = None
+    options = []
     query = db.query(ReferenceModel)
-    if load_referencefiles or load_authors or load_mod_corpus_associations or load_mesh_terms or \
-            load_obsolete_references:
-        options = Load(ReferenceModel)
-        if load_referencefiles:
-            options.subqueryload(ReferenceModel.referencefiles).subqueryload(
-                ReferencefileModel.referencefile_mods)
-        if load_authors:
-            options.joinedload(ReferenceModel.author)
-        if load_mod_corpus_associations:
-            options.joinedload(ReferenceModel.mod_corpus_association)
-        if load_mesh_terms:
-            options.joinedload(ReferenceModel.mesh_term)
-        if load_obsolete_references:
-            options.joinedload(ReferenceModel.obsolete_reference)
-        query = query.options(options)
+
+    if load_referencefiles:
+        options.append(subqueryload(ReferenceModel.referencefiles).subqueryload(ReferencefileModel.referencefile_mods))
+
+    if load_authors:
+        options.append(joinedload(ReferenceModel.author))
+
+    if load_mod_corpus_associations:
+        options.append(joinedload(ReferenceModel.mod_corpus_association))
+
+    if load_mesh_terms:
+        options.append(joinedload(ReferenceModel.mesh_term))
+
+    if load_obsolete_references:
+        options.append(joinedload(ReferenceModel.obsolete_reference))
+
+    if options:
+        query = query.options(*options)
+
     reference = query.filter(or_(ReferenceModel.curie == curie_or_reference_id,
                                  ReferenceModel.reference_id == reference_id)).one_or_none()
     if reference is None and reference_id is None: