[FIX] ignore string if doi/pmid/name string is empty (#598)

* do not create new base study if string is empty

* update openapi

Author: jdkent

store/neurostore/resources/data.py

@@ -1,9 +1,13 @@
+import string
+
 from flask import request
 from marshmallow import EXCLUDE
 from webargs.flaskparser import parser
 from webargs import fields
 import sqlalchemy.sql.expression as sae
 from sqlalchemy.orm import joinedload
+from sqlalchemy.sql import func
+
 
 from .utils import view_maker
 from .base import BaseView, ObjectView, ListView
@@ -216,7 +220,7 @@ def post(self):
             filter_params = {
                 k: study_data.get(k)
                 for k in search_keys
-                if study_data.get(k) is not None
+                if study_data.get(k)
             }
             if "name" in filter_params and (set(filter_params) - {"name"}) != set():
                 del filter_params["name"]
@@ -393,28 +397,34 @@ def pre_nested_record_update(record):
             return record
 
         query = BaseStudy.query
-        has_doi = has_pmid = False
+        has_doi = has_pmid = has_name = False
         base_study = None
         if record.doi:
             query = query.filter_by(doi=record.doi)
             has_doi = True
         if record.pmid:
             query = query.filter_by(pmid=record.pmid)
             has_pmid = True
+        if record.name and not record.doi and not record.pmid:
+            name_search = func.regexp_replace(
+                record.name, r'[' + string.punctuation + ']', '', 'g'
+            )
+            query = query.filter(BaseStudy.name.ilike(f"%{name_search}%"))
+            has_name = True
 
-        if query.count() >= 1 and (has_doi or has_pmid):
+        if query.count() >= 1 and (has_doi or has_pmid or has_name):
             base_study = query.first()
         elif has_doi or has_pmid:
             base_study = BaseStudy(
                 name=record.name,
-                doi=record.doi,
+                doi=record.doi if record.doi else None,
                 pmid=record.pmid,
                 description=record.description,
                 publication=record.publication,
                 year=record.year,
-                level=record.level,
                 authors=record.authors,
                 metadata_=record.metadata_,
+                level=record.level if record.level else "group",
             )
         else:
             # there is no published study to associate

store/neurostore/tests/api/test_base_studies.py

@@ -15,6 +15,13 @@ def test_post_list_of_studies(auth_client, ingest_neuroquery):
             "doi": "new_doi",
             "name": "new name",
         },
+        {
+            "pmid": base_studies[1].pmid,
+            "doi": "",
+        },
+        {
+            "name": "another new name",
+        },
     ]
 
     result = auth_client.post("/api/base-studies/", data=test_input)