Try to make research_database_info less singleton-like; fix test suit…

…e for RNC environment

crate_anon/anonymise/tests/researcher_report_tests.py

@@ -27,26 +27,24 @@
 
 """
 
+import os.path
 import random
-from tempfile import NamedTemporaryFile
+from tempfile import TemporaryDirectory
 from typing import List, TYPE_CHECKING
 from unittest import mock
 
 import factory
 from pypdf import PdfReader
 import pytest
-
 from sqlalchemy import (
     Column,
     DateTime,
     ForeignKey,
     Integer,
     Text,
 )
-
 from sqlalchemy.orm import relationship
 
-
 from crate_anon.anonymise.researcher_report import (
     mk_researcher_report_pdf,
     ResearcherReportConfig,
@@ -160,6 +158,8 @@ def setUp(self) -> None:
         )
         self.anon_dbsession.commit()
 
+        self.tempdir = TemporaryDirectory()
+
     @pytest.mark.usefixtures("django_test_settings")
     def test_report_has_pages_for_each_table(self) -> None:
         def index_of_list_substring(items: List[str], substr: str) -> int:
@@ -171,7 +171,9 @@ def index_of_list_substring(items: List[str], substr: str) -> int:
 
         anon_config = mock.Mock()
 
-        with NamedTemporaryFile(delete=False, mode="w") as f:
+        reportfilename = os.path.join(self.tempdir.name, "tmpreport.pdf")
+
+        with open(reportfilename, mode="w") as f:
             mock_db = mock.Mock(
                 table_names=["anon_patient", "anon_note"],
                 metadata=AnonTestBase.metadata,
@@ -182,15 +184,15 @@ def index_of_list_substring(items: List[str], substr: str) -> int:
                 __post_init__=mock.Mock(),
             ):
                 report_config = ResearcherReportConfig(
-                    output_filename=f.name,
+                    output_filename=reportfilename,
                     anonconfig=anon_config,
                     use_dd=False,
                 )
                 report_config.db_session = self.anon_dbsession
                 report_config.db = mock_db
                 mk_researcher_report_pdf(report_config)
 
-        with open(f.name, "rb") as f:
+        with open(reportfilename, "rb") as f:
             reader = PdfReader(f)
 
             patient_found = False
@@ -212,7 +214,7 @@ def index_of_list_substring(items: List[str], substr: str) -> int:
                 num_rows = int(lines[rows_index + 1])
                 table_name = lines[0]
 
-                if table_name == "patient":
+                if table_name == "anon_patient":
                     patient_found = True
                     self.assertEqual(num_rows, self.num_patients)
 

crate_anon/crateweb/anonymise_api/tests.py

@@ -49,6 +49,8 @@
 
 @override_settings(ANONYMISE_API=DEFAULT_SETTINGS)
 class AnonymisationTests(TestCase):
+    databases = {"default", "research"}
+
     def setUp(self) -> None:
         super().setUp()
 

crate_anon/crateweb/config/urls.py

@@ -79,9 +79,10 @@
     and EnvVar.RUNNING_TESTS not in os.environ
 ):
     from crate_anon.crateweb.research.research_db_info import (
-        research_database_info,
+        get_research_db_info,
     )
 
+    research_database_info = get_research_db_info()
     research_database_info.get_colinfolist()
 
 log = logging.getLogger(__name__)

crate_anon/crateweb/consent/models.py

@@ -111,7 +111,7 @@
 )
 from crate_anon.crateweb.research.models import get_mpid
 from crate_anon.crateweb.research.research_db_info import (
-    research_database_info,
+    get_research_db_info,
 )
 from crate_anon.crateweb.userprofile.models import UserProfile
 
@@ -2038,6 +2038,7 @@ def process_request_main(self) -> None:
         )  # delayed import
 
         # Translate to an NHS number
+        research_database_info = get_research_db_info()
         dbinfo = research_database_info.dbinfo_for_contact_lookup
         if self.lookup_nhs_number is not None:
             self.nhs_number = self.lookup_nhs_number

crate_anon/crateweb/consent/views.py

@@ -85,7 +85,7 @@
 )
 from crate_anon.crateweb.extra.pdf import serve_html_or_pdf
 from crate_anon.crateweb.research.research_db_info import (
-    research_database_info,
+    get_research_db_info,
 )
 from crate_anon.crateweb.research.models import PidLookup, get_mpid
 from crate_anon.crateweb.userprofile.models import UserProfile
@@ -504,6 +504,7 @@ def submit_contact_request(request: HttpRequest) -> HttpResponse:
     Args:
         request: the :class:`django.http.request.HttpRequest`
     """
+    research_database_info = get_research_db_info()
     dbinfo = research_database_info.dbinfo_for_contact_lookup
     if request.user.is_superuser:
         form = SuperuserSubmitContactRequestForm(
@@ -579,6 +580,7 @@ def clinician_initiated_contact_request(request: HttpRequest) -> HttpResponse:
     Args:
         request: the :class:`django.http.request.HttpRequest`
     """
+    research_database_info = get_research_db_info()
     dbinfo = research_database_info.dbinfo_for_contact_lookup
     email = request.user.email
     userprofile = UserProfile.objects.get(user=request.user)

crate_anon/crateweb/research/archive_func.py

@@ -46,7 +46,7 @@
     archive_template_url,
 )
 from crate_anon.crateweb.research.research_db_info import (
-    research_database_info,
+    get_research_db_info,
 )
 from crate_anon.crateweb.research.views import (
     FN_SRCDB,
@@ -151,6 +151,7 @@ def delimit_sql_identifier(identifer: str) -> str:
     """
     Delimits (quotes) an SQL identifier, if required.
     """
+    research_database_info = get_research_db_info()
     return research_database_info.grammar.quote_identifier_if_required(
         identifer
     )

crate_anon/crateweb/research/models.py

@@ -48,7 +48,7 @@
     register_for_json,
 )
 from cardinal_pythonlib.reprfunc import simple_repr
-from cardinal_pythonlib.sql.sql_grammar import format_sql, SqlGrammar
+from cardinal_pythonlib.sql.sql_grammar import format_sql
 from cardinal_pythonlib.tsv import make_tsv_row
 from cardinal_pythonlib.django.function_cache import django_cache_function
 from django.db import connections, DatabaseError, models
@@ -82,7 +82,7 @@
 )
 from crate_anon.crateweb.research.research_db_info import (
     RESEARCH_DB_CONNECTION_NAME,
-    research_database_info,
+    get_research_db_info,
     SingleResearchDatabase,
 )
 from crate_anon.crateweb.research.sql_writer import (
@@ -185,6 +185,7 @@ def database_last_updated(dbname: str) -> Optional[datetime.datetime]:
     are null, the function will return the minimum date possible. If there
     are no such tables, the function will return None.
     """
+    research_database_info = get_research_db_info()
     try:
         dbinfo = research_database_info.get_dbinfo_by_name(dbname)
     except ValueError:
@@ -1704,7 +1705,7 @@ def _get_select_mrid_column(self) -> Optional[ColumnId]:
         """
         if not self._patient_conditions:
             return None
-        return research_database_info.get_linked_mrid_column(
+        return self._research_database_info.get_linked_mrid_column(
             self._patient_conditions[0].table_id
         )
 
@@ -1748,7 +1749,6 @@ def patient_id_query(self, with_order_by: bool = True) -> str:
         if not self._patient_conditions:
             return ""
 
-        grammar = research_database_info.grammar
         select_mrid_column = self._get_select_mrid_column()
         if not select_mrid_column.is_valid:
             log.warning(
@@ -1758,6 +1758,10 @@ def patient_id_query(self, with_order_by: bool = True) -> str:
             # One way this can happen: (1) a user saves a PMQ; (2) the
             # administrator removes one of the databases!
             return ""
+
+        research_database_info = get_research_db_info()
+        grammar = research_database_info.grammar
+
         mrid_alias = "_mrid"
         sql = add_to_select(
             "",
@@ -1847,7 +1851,7 @@ def all_queries(self, mrids: List[Any] = None) -> List[TableQueryArgs]:
         return queries
 
     def where_patient_clause(
-        self, table_id: TableId, grammar: SqlGrammar, mrids: List[Any] = None
+        self, table_id: TableId, mrids: List[Any] = None
     ) -> SqlArgsTupleType:
         """
         Returns an SQL WHERE clauses similar to ``sometable.mrid IN (1, 2, 3)``
@@ -1857,15 +1861,13 @@ def where_patient_clause(
         Args:
             table_id: :class:`crate_anon.common.sql.TableId` for the table
                 whose MRID column we will apply the ``WHERE`` clause to
-            grammar: :class:`cardinal_pythonlib.sql.sql_grammar.SqlGrammar`
-                to use
             mrids: list of MRIDs; if this is ``None`` or empty, use the
                 patients fetched (live) by our :meth:`patient_id_query`.
 
         Returns:
             tuple: ``sql, args``
         """
-        mrid_column = research_database_info.get_mrid_column_from_table(
+        mrid_column = self._research_database_info.get_mrid_column_from_table(
             table_id
         )
         if mrids:
@@ -1881,6 +1883,8 @@ def where_patient_clause(
             # derived tables, subqueries, ... unless TOP, OFFSET or FOR XML
             # is specified."
             args = []  # type: List[Any]
+        research_database_info = get_research_db_info()
+        grammar = research_database_info.grammar
         sql = f"{mrid_column.identifier(grammar)} IN ({in_clause})"
         return sql, args
 
@@ -1914,6 +1918,7 @@ def make_query(
         """
         if not columns:
             raise ValueError("No columns specified")
+        research_database_info = get_research_db_info()
         grammar = research_database_info.grammar
         mrid_column = research_database_info.get_mrid_column_from_table(
             table_id
@@ -1922,9 +1927,7 @@ def make_query(
         for c in columns:
             if c not in all_columns:
                 all_columns.append(c)
-        where_clause, args = self.where_patient_clause(
-            table_id, grammar, mrids
-        )
+        where_clause, args = self.where_patient_clause(table_id, mrids)
         select_elements = [SelectElement(column_id=col) for col in all_columns]
         where_conditions = [WhereCondition(raw_sql=where_clause)]
         sql = add_to_select(
@@ -1946,6 +1949,7 @@ def output_cols_html(self) -> str:
         """
         Returns all our output columns in HTML format.
         """
+        research_database_info = get_research_db_info()
         grammar = research_database_info.grammar
         return prettify_sql_html(
             "\n".join(
@@ -1961,6 +1965,7 @@ def pt_conditions_html(self) -> str:
         """
         Returns all our patient WHERE conditions in HTML format.
         """
+        research_database_info = get_research_db_info()
         grammar = research_database_info.grammar
         return prettify_sql_html(
             "\nAND ".join([wc.sql(grammar) for wc in self.patient_conditions])
@@ -2030,6 +2035,7 @@ def gen_data_finder_queries(
             :class:`TableQueryArgs` objects (q.v.)
 
         """
+        research_database_info = get_research_db_info()
         grammar = research_database_info.grammar
         mrid_alias = "master_research_id"
         table_name_alias = "table_name"
@@ -2053,9 +2059,7 @@ def gen_data_finder_queries(
                 max_date = "NULL"
                 # ... OK (at least in MySQL) to do:
                 # SELECT col1, COUNT(*), NULL FROM table GROUP BY col1;
-            where_clause, args = self.where_patient_clause(
-                table_id, grammar, mrids
-            )
+            where_clause, args = self.where_patient_clause(table_id, mrids)
             table_identifier = table_id.identifier(grammar)
             select_elements = [
                 SelectElement(column_id=mrid_col, alias=mrid_alias),
@@ -2116,16 +2120,15 @@ def gen_monster_queries(
             :class:`TableQueryArgs` objects (q.v.)
 
         """
+        research_database_info = get_research_db_info()
         grammar = research_database_info.grammar
         for (
             table_id
         ) in research_database_info.get_mrid_linkable_patient_tables():
             mrid_col = research_database_info.get_mrid_column_from_table(
                 table=table_id
             )
-            where_clause, args = self.where_patient_clause(
-                table_id, grammar, mrids
-            )
+            where_clause, args = self.where_patient_clause(table_id, mrids)
             # We add the WHERE using our magic query machine, to get the joins
             # right:
             select_elements = [