Dashboard fixes (#140)

* small fixes and initial alembic scripts

* Add timestamp to callresponse

CHANGELOG.md

@@ -7,6 +7,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.4.6] - 2024-10-29
+
+### Fixed
+- Removed TTL in patient list in calling dashboard and also show patient that were called today to prevent patients from disappearing during calls
+- Corrected database column types so databases are identical over different environments
+
+### Added
+- Added Alembic for database migrations
+- Added a timestamp for call response, so we can track when patients were called
+
+
 ## [1.4.5] - 2024-10-21
 
 ### Fixed

alembic.ini

@@ -0,0 +1,113 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+# Use forward slashes (/) also on windows to provide an os agnostic path
+script_location = alembic
+
+# template used to generate migration file names; The default value is %%(rev)s_%%(slug)s
+# Uncomment the line below if you want the files to be prepended with date and time
+# see https://alembic.sqlalchemy.org/en/latest/tutorial.html#editing-the-ini-file
+# for all available tokens
+# file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.
+prepend_sys_path = .
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python>=3.9 or backports.zoneinfo library.
+# Any required deps can installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to ZoneInfo()
+# leave blank for localtime
+# timezone =
+
+# max length of characters to apply to the "slug" field
+# truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# version location specification; This defaults
+# to alembic/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path.
+# The path separator used here should be the separator specified by "version_path_separator" below.
+# version_locations = %(here)s/bar:%(here)s/bat:alembic/versions
+
+# version path separator; As mentioned above, this is the character used to split
+# version_locations. The default within new alembic.ini files is "os", which uses os.pathsep.
+# If this key is omitted entirely, it falls back to the legacy behavior of splitting on spaces and/or commas.
+# Valid values for version_path_separator are:
+#
+# version_path_separator = :
+# version_path_separator = ;
+# version_path_separator = space
+# version_path_separator = newline
+version_path_separator = os  # Use os.pathsep. Default configuration used for new projects.
+
+# set to 'true' to search source files recursively
+# in each "version_locations" directory
+# new in Alembic version 1.10
+# recursive_version_locations = false
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+sqlalchemy.url = 
+
+
+[post_write_hooks]
+hooks = ruff, ruff_format
+
+# lint with attempts to fix using "ruff"
+ruff.type = exec
+ruff.executable = %(here)s/.venv/bin/ruff
+ruff.options = check --fix REVISION_SCRIPT_FILENAME
+
+# format using "ruff" - use the exec runner, execute a binary
+ruff_format.type = exec
+ruff_format.executable = %(here)s/.venv/bin/ruff
+ruff_format.options = format REVISION_SCRIPT_FILENAME
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

alembic/README

@@ -0,0 +1,14 @@
+Generic single-database configuration.
+
+Used to run database migrations.
+
+To generate migration scripts use:
+```
+alembic revision --autogenerate -m "message"
+```
+
+Then to apply the migrations run:
+```
+alembic upgrade head
+```
+Though this should be part of the CI/CD or deploy pipeline

alembic/env.py

@@ -0,0 +1,80 @@
+from logging.config import fileConfig
+
+from alembic import context
+
+from noshow.database.connection import get_connection_string, get_engine
+from noshow.database.models import Base
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+target_metadata = Base.metadata
+target_metadata.schema = "noshow"
+
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+CONNECT_STRING = get_connection_string()
+
+
+def run_migrations_offline() -> None:
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    context.configure(
+        url=CONNECT_STRING,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+        include_schemas=True,
+        version_table_schema=target_metadata.schema,
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    connectable = get_engine(CONNECT_STRING)
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            include_schemas=True,
+            version_table_schema=target_metadata.schema,
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

alembic/script.py.mako

@@ -0,0 +1,26 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision: str = ${repr(up_revision)}
+down_revision: Union[str, None] = ${repr(down_revision)}
+branch_labels: Union[str, Sequence[str], None] = ${repr(branch_labels)}
+depends_on: Union[str, Sequence[str], None] = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    ${downgrades if downgrades else "pass"}

alembic/versions/20f444146781_add_timestamp.py

@@ -0,0 +1,34 @@
+"""add timestamp
+
+Revision ID: 20f444146781
+Revises:
+Create Date: 2024-10-30 09:56:46.886479
+
+"""
+
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "20f444146781"
+down_revision: Union[str, None] = None
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column(
+        "apicallresponse",
+        sa.Column("timestamp", sa.DateTime(), nullable=True),
+        schema="noshow",
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("apicallresponse", "timestamp", schema="noshow")
+    # ### end Alembic commands ###

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "noshow"
-version = "1.4.5"
+version = "1.4.6"
 authors = [
   { name="Ruben Peters", email="[email protected]" },
   { name="Eric Wolters", email="[email protected]" }
@@ -54,6 +54,8 @@ dev-dependencies = [
     "uvicorn~=0.28.0",
     "pytest-asyncio~=0.23.6",
     "pytest-cov>=5.0.0",
+    "alembic>=1.13.3",
+    "ruff>=0.7.1",
 ]
 
 [tool.isort]

requirements.txt

@@ -36,7 +36,7 @@ diskcache==5.6.3
 distro==1.9.0
 dpath==2.2.0
 dulwich==0.22.3
-dvc==3.55.2
+dvc==3.56.0
 dvc-data==3.16.6
 dvc-http==2.32.0
 dvc-objects==5.1.0
@@ -45,12 +45,12 @@ dvc-studio-client==0.21.0
 dvc-task==0.40.2
 dvclive==3.48.0
 entrypoints==0.4
-fastapi==0.115.2
+fastapi==0.115.3
 filelock==3.16.1
 flatten-dict==0.4.2
 flufl-lock==8.1.0
 fonttools==4.54.1
-frozenlist==1.4.1
+frozenlist==1.5.0
 fsspec==2024.10.0
 funcy==2.0
 gitdb==4.0.11
@@ -76,15 +76,15 @@ narwhals==1.10.0
 networkx==3.4.2
 numpy==1.26.4
 omegaconf==2.3.0
-orjson==3.10.9 ; implementation_name == 'cpython'
+orjson==3.10.10 ; implementation_name == 'cpython'
 packaging==24.1
 pandas==2.2.3
 pathspec==0.12.1
 pillow==10.4.0
 platformdirs==3.11.0
 prompt-toolkit==3.0.48
 propcache==0.2.0
-protobuf==5.28.2
+protobuf==5.28.3
 psutil==6.1.0
 pyarrow==14.0.2
 pycparser==2.22
@@ -106,7 +106,7 @@ pyyaml==6.0.2
 referencing==0.35.1
 relplot==1.0
 requests==2.32.3
-rich==13.9.2
+rich==13.9.3
 rpds-py==0.20.0
 ruamel-yaml==0.18.6
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
@@ -124,7 +124,7 @@ smmap==5.0.1
 sniffio==1.3.1
 sqlalchemy==2.0.36
 sqltrie==0.11.1
-starlette==0.40.0
+starlette==0.41.0
 streamlit==1.39.0
 tabulate==0.9.0
 tenacity==9.0.0
@@ -142,5 +142,5 @@ vine==5.1.0
 voluptuous==0.15.2
 watchdog==5.0.3 ; platform_system != 'Darwin'
 wcwidth==0.2.13
-yarl==1.15.5
+yarl==1.16.0
 zc-lockfile==3.0.post1

run/calling_dash.py

@@ -245,12 +245,18 @@ def main():
             ),
             type="primary",
         )
+        if current_response.timestamp is not None:
+            st.caption(
+                f"Laatst opgeslagen om: {current_response.timestamp:%Y-%m-%d %H:%M:%S}"
+            )
     st.button(
         "Vorige",
         on_click=previous_preds,
     )
     st.divider()
-    st.write(f"Laatste update: {last_updated:%Y-%m-%d %H:%M:%S}")
+    st.caption(
+        f"Laatste voorspellingen gegenereerd om: {last_updated:%Y-%m-%d %H:%M:%S}"
+    )
 
 
 if __name__ == "__main__":