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Update for SQL Alchemy 2 #385

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Update for SQL Alchemy 2 #385

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@martinburchell martinburchell commented Jan 31, 2025 •
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Fixes #322

@martinburchell
Update pytest
bbc1a91
@martinburchell
Turn on SQLAlchemy 2.0 warnings in tests
19933e1
@martinburchell
Fix Perinatal POEM tests for SQLAlchemy 2.0
3bb1cf9
@martinburchell
Add flake8 and black to setup.py for convenience
4558946
@martinburchell
Remove alembic __init__.py to fix import error
f078f1f 
This started to cause problems with pytest with:

from alembic.config import Config

Python was looking in server/camcops_server/alembic
@martinburchell
Remove SQL Alchemy warnings flag from pytest.ini
0910cba 
This doesn't have any effect because SQL Alchemy is loaded first with -W error::sqlalchemy.exc.RemovedIn20Warning on the command line
@martinburchell
Turn cascade_backrefs off for TaskSchedule relationships
cc7b342 
Removed in SQLAlchemy 2.0
@martinburchell
Use new-style select() in reports for SQL Alchemy 2.0
3a494a4
@martinburchell
Update code documentation for database test cases
e0f5526
@martinburchell
Fix SQLAlchemy column types tests for 2.0
daa1fda
@martinburchell
Use cardinal_pythonlib compatible with SQLAlchemy 2.0
7dce0c7 
Note that this won't work unmodified with SQL Alchemy 1.4 because of the failed import of Double
from sqlalchemy.types
@martinburchell
Use get_rows_field_names_from_select()
b285076 
get_rows_fieldnames_from_query() no longer supported with SQLAlchemy 2.0
@martinburchell
Disable reverse cascade for SQLAlchemy 2.0
4a43625
@martinburchell
Fix number of login failures for SQLAlchemy 2.0
a34f7e6
@martinburchell
Disable reverse_cascade for group relationships for SQL Alchemy 2.0
dcfb7ef
@martinburchell
Use 2.0 style select in apeq_cpft_perinatal reports
359ecbf
@martinburchell
Use temporarily patched cardinal_pythonlib to workaround Double import
2647b47
@martinburchell
Update help docs for ddl now we have databricks
4afeb4f
@martinburchell
Temporarily disable SQLServer constraint disabling
d416e7f
@martinburchell
Use SQLAlchemy 2.0 select() in get_dirty_tables()
dfe2e3d
@martinburchell
Test invalid pknameinfo in API upload tests
094a668
@martinburchell
More consistent test class name
638b1a1
@martinburchell
Test invalid dbdata in API upload tests [no ci]
4b4e26b
@martinburchell
Test table mismatch in API upload tests [no ci]
f8de523
@martinburchell
Test refactoring [no ci]
acd5af0
@martinburchell
Fix flaky mock arg comparison in test [no ci]
e21a993
@martinburchell
Test tables not existing in API upload tests [no ci]
939c4fe
@martinburchell
Use new-style select() in get_server_live_records()
c0d2137
@martinburchell
Test API for empty entire database upload
53592aa
@martinburchell
Test validate patients API fails for patient info not a list
3fca743
@martinburchell
Update docs
529f03a
@martinburchell
Change BoolColumn to bool_column now it is a function
215144e
@martinburchell
Fix getting of blob relationship to use info dict
18863e8
@martinburchell
Fix HAMD task to get permitted value checker from info dict
75a4396
@martinburchell
Fix dummy database generation to get permitted value checker from inf…
3c2f359 
…o dict
@martinburchell
Add explicit configuration for Read the Docs
663f24c
@martinburchell
Get blob relationship from info dict when writing task XML
d6b8a49
@martinburchell
Bump cryptography to fix CVE-2024-12797
1c3c5fe
@martinburchell
Fix metadata lock when migrating database from scratch
7f81990 
Include fixed cardinal_pythonlib which closes the connection to the database after getting the version table.
@martinburchell
Pin cardinal_pythonlib to a commit now the branch is deleted
19a460f
@martinburchell
Merge branch 'dump-tests' into sqlalchemy2
b5bd4db
@martinburchell
Use the per-test table creation session in SQLA_coltypes tests
ad93c07 
and rename it to temp_session (and temp_engine).
@martinburchell
Add a non-mapped equivalent to camcops_column
8b5b93c 
It looks like we can't use MappedColumn in places where we are setting the type in the
arguments, so we need a non-mapped version as well.
@martinburchell
Ignore more third party imports when type-checking with MyPy
ab3caba
@martinburchell
MyPy fixes in cc_proquint.py
ada67c5
@martinburchell
MyPy type checking fixes in cc_dump_tests.py
54e9091
@martinburchell
Type hint fixes
298b0be
@martinburchell
Fix retrieval of camcops_column info properties
04792b4
@martinburchell
More typing fixes (return values)
9f441ee
@martinburchell
Improve test for missing columns/tables
2ecab91
@martinburchell
Add return types in Alembic template
df98a9e
@martinburchell
Add type hints to migrations
b4982e4
@martinburchell
Fix type checker errors for cc_blob.py
718c7bd
@martinburchell
Fix type chcker warnings for cc_config.py
8aff908
@martinburchell
Fix type checker warnings in cc_dummy_database.py
3757aec
@martinburchell
Fix type checker warnings in cc_exportrecipient.py
9396132
@martinburchell
Fix type checker warnings in cc_patient.py
5cd4e12
@martinburchell
Fix type checker warnings in cc_patientidnum.py
35a0422
@martinburchell
Fix type checker warnings in cc_user.py
4c562e1
@martinburchell
Merge branch 'master' into sqlalchemy2
ca60bcb
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Update to SQLAlchemy 2.0
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@martinburchell