Merge branch 'master' into develop

portal/migrations/versions/6120fcfc474a_add_missing_indexes.py

@@ -0,0 +1,67 @@
+"""add missing indexes
+
+Revision ID: 6120fcfc474a
+Revises: cf586ed4f043
+Create Date: 2024-08-06 17:49:02.447759
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '6120fcfc474a'
+down_revision = 'cf586ed4f043'
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_index(op.f('ix_audit_context'), 'audit', ['context'], unique=False)
+    op.create_index(op.f('ix_audit_subject_id'), 'audit', ['subject_id'], unique=False)
+    op.create_index(op.f('ix_audit_user_id'), 'audit', ['user_id'], unique=False)
+    op.create_index(op.f('ix_communications_communication_request_id'), 'communications', ['communication_request_id'], unique=False)
+    op.create_index(op.f('ix_communications_status'), 'communications', ['status'], unique=False)
+    op.create_index(op.f('ix_communications_user_id'), 'communications', ['user_id'], unique=False)
+    op.create_index(op.f('ix_email_messages_recipients'), 'email_messages', ['recipients'], unique=False)
+    op.create_index(op.f('ix_encounter_codings_encounter_id'), 'encounter_codings', ['encounter_id'], unique=False)
+    op.create_index(op.f('ix_encounters_status'), 'encounters', ['status'], unique=False)
+    op.create_index(op.f('ix_encounters_user_id'), 'encounters', ['user_id'], unique=False)
+    op.create_index(op.f('ix_questionnaire_responses_encounter_id'), 'questionnaire_responses', ['encounter_id'], unique=False)
+    op.create_index(op.f('ix_questionnaire_responses_subject_id'), 'questionnaire_responses', ['subject_id'], unique=False)
+    op.create_index(op.f('ix_tou_audit_id'), 'tou', ['audit_id'], unique=False)
+    op.create_index(op.f('ix_user_observations_audit_id'), 'user_observations', ['audit_id'], unique=False)
+    op.create_index(op.f('ix_user_observations_observation_id'), 'user_observations', ['observation_id'], unique=False)
+    op.create_index(op.f('ix_user_observations_user_id'), 'user_observations', ['user_id'], unique=False)
+
+# The following are added by hand, as the syntax for JSONB indexes isn't available in active version
+    op.execute("CREATE INDEX IF NOT EXISTS idx_qnr_identifier_val2 ON questionnaire_responses(((document->'identifier')->'value'))")
+    op.execute("CREATE INDEX IF NOT EXISTS idx_qnr_identifier_sys2 ON questionnaire_responses(((document->'identifier')->'system'))")
+    op.execute("CREATE INDEX IF NOT EXISTS idx_qnr_authored ON questionnaire_responses((document->'authored'))")
+
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f('ix_tou_audit_id'), table_name='tou')
+    op.drop_index(op.f('ix_questionnaire_responses_subject_id'), table_name='questionnaire_responses')
+    op.drop_index(op.f('ix_questionnaire_responses_encounter_id'), table_name='questionnaire_responses')
+    op.drop_index(op.f('ix_encounters_user_id'), table_name='encounters')
+    op.drop_index(op.f('ix_encounters_status'), table_name='encounters')
+    op.drop_index(op.f('ix_encounter_codings_encounter_id'), table_name='encounter_codings')
+    op.drop_index(op.f('ix_email_messages_recipients'), table_name='email_messages')
+    op.drop_index(op.f('ix_communications_user_id'), table_name='communications')
+    op.drop_index(op.f('ix_communications_status'), table_name='communications')
+    op.drop_index(op.f('ix_communications_communication_request_id'), table_name='communications')
+    op.drop_index(op.f('ix_audit_user_id'), table_name='audit')
+    op.drop_index(op.f('ix_audit_subject_id'), table_name='audit')
+    op.drop_index(op.f('ix_audit_context'), table_name='audit')
+    op.drop_index(op.f('ix_user_observations_audit_id'), table_name='user_observations')
+    op.drop_index(op.f('ix_user_observations_observation_id'), table_name='user_observations')
+    op.drop_index(op.f('ix_user_observations_user_id'), table_name='user_observations')
+
+    # and the ones added by hand
+    op.drop_index(op.f('idx_qnr_identifier_val2'), table_name='questionnaire_responses')
+    op.drop_index(op.f('idx_qnr_identifier_sys2'), table_name='questionnaire_responses')
+    op.drop_index(op.f('idx_qnr_authored'), table_name='questionnaire_responses')
+    # ### end Alembic commands ###

portal/models/audit.py

@@ -29,9 +29,9 @@ class Audit(db.Model):
 
     """
     id = db.Column(db.Integer, primary_key=True)
-    user_id = db.Column(db.ForeignKey('users.id'), nullable=False)
-    subject_id = db.Column(db.ForeignKey('users.id'), nullable=False)
-    _context = db.Column('context', db.Text, default='other', nullable=False)
+    user_id = db.Column(db.ForeignKey('users.id'), index=True, nullable=False)
+    subject_id = db.Column(db.ForeignKey('users.id'), index=True, nullable=False)
+    _context = db.Column('context', db.Text, default='other', index=True, nullable=False)
     timestamp = db.Column(db.DateTime, default=datetime.utcnow, nullable=False)
     version = db.Column(db.Text, default=lookup_version, nullable=False)
     comment = db.Column(db.Text)

portal/models/communication.py

@@ -268,16 +268,16 @@ class Communication(db.Model):
     """
     __tablename__ = 'communications'
     id = db.Column(db.Integer, primary_key=True)
-    status = db.Column('status', event_status_types, nullable=False)
+    status = db.Column('status', event_status_types, index=True, nullable=False)
 
     # FHIR Communication spec says `basedOn` can return to any
     # object.  For current needs, this is always a CommunicationRequest
     communication_request_id = db.Column(
-        db.ForeignKey('communication_requests.id'), nullable=False)
+        db.ForeignKey('communication_requests.id'), index=True, nullable=False)
     communication_request = db.relationship('CommunicationRequest')
 
     user_id = db.Column(db.ForeignKey(
-        'users.id', ondelete='cascade'), nullable=False)
+        'users.id', ondelete='cascade'), index=True, nullable=False)
 
     # message_id is null until sent
     message_id = db.Column(db.ForeignKey(

portal/models/encounter.py

@@ -21,7 +21,7 @@ class EncounterCodings(db.Model):
 
     __tablename__ = 'encounter_codings'
     id = db.Column(db.Integer, primary_key=True)
-    encounter_id = db.Column(db.ForeignKey('encounters.id'), nullable=False)
+    encounter_id = db.Column(db.ForeignKey('encounters.id'), index=True, nullable=False)
     coding_id = db.Column(db.ForeignKey('codings.id'), nullable=False)
 
 
@@ -48,11 +48,12 @@ class Encounter(db.Model):
     """
     __tablename__ = 'encounters'
     id = db.Column(db.Integer, primary_key=True)
-    status = db.Column('status', status_types, nullable=False)
+    status = db.Column('status', status_types, index=True, nullable=False)
     user_id = db.Column(
         db.ForeignKey(
             'users.id',
             name='encounters_user_id_fk'),
+        index=True,
         nullable=False)
     start_time = db.Column(db.DateTime, nullable=False)
     """required whereas end_time is optional

portal/models/message.py

@@ -98,7 +98,7 @@ class EmailMessage(db.Model):
     __tablename__ = 'email_messages'
     id = db.Column(db.Integer, primary_key=True)
     subject = db.Column(db.String(255), nullable=False)
-    _recipients = db.Column("recipients", db.Text, nullable=False)
+    _recipients = db.Column("recipients", db.Text, index=True, nullable=False)
     sender = db.Column(db.String(255), nullable=False)
     sent_at = db.Column(db.DateTime, default=datetime.utcnow)
     body = db.Column(db.Text, nullable=False)

portal/models/observation.py

@@ -137,13 +137,13 @@ class UserObservation(db.Model):
     __tablename__ = 'user_observations'
     id = db.Column(db.Integer, primary_key=True)
     user_id = db.Column(db.ForeignKey(
-        'users.id', ondelete='CASCADE'), nullable=False)
+        'users.id', ondelete='CASCADE'), index=True, nullable=False)
     observation_id = db.Column(
-        db.ForeignKey('observations.id'), nullable=False)
+        db.ForeignKey('observations.id'), index=True, nullable=False)
     encounter_id = db.Column(db.ForeignKey(
         'encounters.id', name='user_observation_encounter_id_fk'),
         nullable=False)
-    audit_id = db.Column(db.ForeignKey('audit.id'), nullable=False)
+    audit_id = db.Column(db.ForeignKey('audit.id'), index=True, nullable=False)
     audit = db.relationship('Audit', cascade="save-update, delete")
     encounter = db.relationship('Encounter', cascade='delete')
     # There was a time when UserObservations were constrained to

portal/models/questionnaire_response.py

@@ -49,11 +49,12 @@ def default_status(context):
 
     __tablename__ = 'questionnaire_responses'
     id = db.Column(db.Integer, primary_key=True)
-    subject_id = db.Column(db.ForeignKey('users.id'), nullable=False)
+    subject_id = db.Column(db.ForeignKey('users.id'), index=True, nullable=False)
     subject = db.relationship("User", back_populates="questionnaire_responses")
     document = db.Column(JSONB)
     encounter_id = db.Column(
         db.ForeignKey('encounters.id', name='qr_encounter_id_fk'),
+        index=True,
         nullable=False)
     questionnaire_bank_id = db.Column(
         db.ForeignKey('questionnaire_banks.id'), nullable=True)

portal/models/tou.py

@@ -19,7 +19,7 @@ class ToU(db.Model):
     id = db.Column(db.Integer(), primary_key=True)
     agreement_url = db.Column(
         db.Text, server_default='predates agreement_url', nullable=False)
-    audit_id = db.Column(db.ForeignKey('audit.id'), nullable=False)
+    audit_id = db.Column(db.ForeignKey('audit.id'), index=True, nullable=False)
     organization_id = db.Column(db.ForeignKey('organizations.id'))
     type = db.Column('type', tou_types, nullable=False)
     active = db.Column(db.Boolean(), nullable=False, server_default='1')