list medical card base

alembic.ini

@@ -0,0 +1,110 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+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-dateutil library that can be
+# installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to dateutil.tz.gettz()
+# 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 = 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 = postgresql://barbie:redStar4,1@localhost:5432/medical_info_db
+
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.  See the documentation for further
+# detail and examples
+
+# format using "black" - use the console_scripts runner, against the "black" entrypoint
+# hooks = black
+# black.type = console_scripts
+# black.entrypoint = black
+# black.options = -l 79 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 @@
+Generic single-database configuration.

alembic/env.py

@@ -0,0 +1,79 @@
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+
+from alembic import context
+
+from medical_info.db.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 = mymodel.Base.metadata
+target_metadata = Base.metadata
+
+# 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.
+
+
+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.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    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 = engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection, target_metadata=target_metadata
+        )
+
+        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 +1,24 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    ${downgrades if downgrades else "pass"}

alembic/versions/8282d5b2badc_initial.py

@@ -0,0 +1,70 @@
+"""initial
+
+Revision ID: 8282d5b2badc
+Revises: 
+Create Date: 2023-07-21 22:53:46.768440
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '8282d5b2badc'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('medical_cards',
+    sa.Column('number', sa.String(length=100), nullable=False),
+    sa.Column('confidant_persons', postgresql.ARRAY(sa.UUID()), nullable=True),
+    sa.Column('id', sa.UUID(), nullable=False),
+    sa.Column('created_at', sa.TIMESTAMP(), nullable=False),
+    sa.Column('updated_at', sa.TIMESTAMP(), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_medical_cards_id'), 'medical_cards', ['id'], unique=False)
+    op.create_table('checkups',
+    sa.Column('medical_card_id', sa.UUID(), nullable=False),
+    sa.Column('medic_id', sa.UUID(), nullable=True),
+    sa.Column('claims', postgresql.ARRAY(sa.String()), nullable=True),
+    sa.Column('allergies', postgresql.ARRAY(sa.String()), nullable=True),
+    sa.Column('diseases', postgresql.ARRAY(sa.String()), nullable=True),
+    sa.Column('medicines', postgresql.ARRAY(sa.String()), nullable=True),
+    sa.Column('disease_process', sa.Text(), nullable=True),
+    sa.Column('visual_inspection', postgresql.ARRAY(sa.String()), nullable=True),
+    sa.Column('dental_formula', postgresql.JSONB(astext_type=sa.Text()), nullable=True),
+    sa.Column('dental_formula_ext', postgresql.JSONB(astext_type=sa.Text()), nullable=True),
+    sa.Column('id', sa.UUID(), nullable=False),
+    sa.Column('created_at', sa.TIMESTAMP(), nullable=False),
+    sa.Column('updated_at', sa.TIMESTAMP(), nullable=False),
+    sa.ForeignKeyConstraint(['medical_card_id'], ['medical_cards.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_checkups_id'), 'checkups', ['id'], unique=False)
+    op.create_table('health_maps',
+    sa.Column('comment', sa.Text(), nullable=True),
+    sa.Column('attachments', postgresql.ARRAY(sa.String()), nullable=True),
+    sa.Column('medical_card_id', sa.UUID(), nullable=False),
+    sa.Column('id', sa.UUID(), nullable=False),
+    sa.Column('created_at', sa.TIMESTAMP(), nullable=False),
+    sa.Column('updated_at', sa.TIMESTAMP(), nullable=False),
+    sa.ForeignKeyConstraint(['medical_card_id'], ['medical_cards.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_health_maps_id'), 'health_maps', ['id'], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f('ix_health_maps_id'), table_name='health_maps')
+    op.drop_table('health_maps')
+    op.drop_index(op.f('ix_checkups_id'), table_name='checkups')
+    op.drop_table('checkups')
+    op.drop_index(op.f('ix_medical_cards_id'), table_name='medical_cards')
+    op.drop_table('medical_cards')
+    # ### end Alembic commands ###

alembic/versions/aa4d531271c0_add_person_id.py

@@ -0,0 +1,28 @@
+"""add person_id
+
+Revision ID: aa4d531271c0
+Revises: 8282d5b2badc
+Create Date: 2023-07-22 00:58:19.689019
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'aa4d531271c0'
+down_revision = '8282d5b2badc'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('medical_cards', sa.Column('person_id', sa.UUID(), nullable=False))
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('medical_cards', 'person_id')
+    # ### end Alembic commands ###

notes.txt

@@ -1,3 +1,14 @@
 export PYTHONPATH='/home/dd/astra/medical_information/src'
+export POSTGRES_DB='medical_info_db'
+CREATE DATABASE medical_info_db;
+
+alembic revision --autogenerate -m 'initial'
+
+alembic init alembic  
+в alembic.ini правим sqlalchemy.url  
+alembic revision -m "add columns to checkup table"
+alembic revision --autogenerate -m "person, address, contact, document v1"
+
+alembic upgrade ae1 (можно часть версии, лишь бы однозначно указывала)
 
 uvicorn --reload --port 8000 medical_info.main:app

src/db/models.py

@@ -1,36 +0,0 @@
-import uuid
-from typing import Any
-import datetime
-
-import sqlalchemy as sa
-from sqlalchemy.dialects.postgresql import UUID, ARRAY
-from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import relationship, DeclarativeBase
-from sqlalchemy.sql.schema import ForeignKey
-
-class Base(DeclarativeBase):
-  pass
-
-class BaseModel(Base):
-  __abstract__ = True
-
-  id = sa.Column(UUID(as_uuid=True), primary_key=True, default=uuid.uuid4, index=True)
-  created_at = sa.Column(sa.TIMESTAMP, nullable=False, default=datetime.datetime.now())
-  updated_at = sa.Column(sa.TIMESTAMP, nullable=False, default=datetime.datetime.now(), onupdate=datetime.datetime.now())
-
-class MedicalCard(BaseModel):
-  number = sa.Column(sa.String(100), nullable=False)
-  checkups = relationship('Checkup', back_populates='medical_card')
-  confidant_persons = sa.Column(ARRAY(UUID(as_uuid=True)))
-  
-
-class Checkup(BaseModel):
-  medical_card_id = sa.Column(UUID(as_uuid=True), sa.ForeignKey("medical_cards.id"), nullable=False)
-  medical_card = relationship('MedicalCard', back_populates='medical_cards')
-  medic_id = sa.Column(UUID(as_uuid=True))
-  claims = sa.Column(ARRAY(String)) # жалобы
-  allergies = sa.Column(ARRAY(String)) # аллергологический анамнез
-  diseases = sa.Column(ARRAY(String)) # перенесенные и сопутствующие заболевания
-  medicines = sa.Column(ARRAY(String)) # принимаемые лекарственные препараты
-  disease_process = sa.Column(sa.Text) # Развитие настоящего заболевания
-  visual_inspection = sa.Column(ARRAY(String)) # внешний осмотр

src/medical_info/config.py

@@ -0,0 +1,33 @@
+from functools import lru_cache
+from typing import Optional
+from os import getenv
+from pydantic import BaseSettings, PostgresDsn
+
+class Settings(BaseSettings):
+  database_url: Optional[PostgresDsn]
+
+@lru_cache
+def get_settings() -> Settings:
+  settings = Settings()  # type: ignore
+  
+  if (db := getenv("POSTGRES_DB")) is not None:
+    # settings.database_url = PostgresDsn.build(
+    #       scheme="postgresql",
+    #       user=settings.database_url.user,
+    #       password=settings.database_url.password,
+    #       host=settings.database_url.host,
+    #       port=settings.database_url.port,
+    #       path=f"/{db}",
+    # )
+    settings.database_url = PostgresDsn.build(
+          scheme="postgresql",
+          user='barbie',
+          password='redStar4,1',
+          host='localhost',
+          port='5432',
+          path=f"/{db}",
+    )
+  elif (db := getenv("CONNECTION_STRING")) is not None:
+    settings.database_url = getenv("CONNECTION_STRING")
+  
+  return settings

src/medical_info/db/models.py

@@ -0,0 +1,53 @@
+import uuid
+from typing import Any
+import datetime
+
+import sqlalchemy as sa
+from sqlalchemy.dialects.postgresql import UUID, ARRAY, JSONB
+from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import relationship, DeclarativeBase
+from sqlalchemy.sql.schema import ForeignKey
+
+class Base(DeclarativeBase):
+  pass
+
+class BaseModel(Base):
+  __abstract__ = True
+
+  id = sa.Column(UUID(as_uuid=True), primary_key=True, default=uuid.uuid4, index=True)
+  created_at = sa.Column(sa.TIMESTAMP, nullable=False, default=datetime.datetime.now())
+  updated_at = sa.Column(sa.TIMESTAMP, nullable=False, default=datetime.datetime.now(), onupdate=datetime.datetime.now())
+
+class MedicalCard(BaseModel):
+  __tablename__ = 'medical_cards'
+
+  number = sa.Column(sa.String(100), nullable=False)
+  checkups = relationship('Checkup', back_populates='medical_card')
+  health_maps = relationship('HealthMap', back_populates='medical_card')
+  confidant_persons = sa.Column(ARRAY(UUID(as_uuid=True)))
+  person_id = sa.Column(UUID(as_uuid=True), nullable=False)
+  
+
+class Checkup(BaseModel):
+  __tablename__ = 'checkups'
+
+  medical_card_id = sa.Column(UUID(as_uuid=True), sa.ForeignKey("medical_cards.id"), nullable=False)
+  medical_card = relationship('MedicalCard', back_populates='checkups')
+  medic_id = sa.Column(UUID(as_uuid=True))
+  claims = sa.Column(ARRAY(sa.String)) # жалобы
+  allergies = sa.Column(ARRAY(sa.String)) # аллергологический анамнез
+  diseases = sa.Column(ARRAY(sa.String)) # перенесенные и сопутствующие заболевания
+  medicines = sa.Column(ARRAY(sa.String)) # принимаемые лекарственные препараты
+  disease_process = sa.Column(sa.Text) # Развитие настоящего заболевания
+  visual_inspection = sa.Column(ARRAY(sa.String)) # внешний осмотр
+
+  dental_formula = sa.Column(JSONB)
+  dental_formula_ext = sa.Column(JSONB)
+
+class HealthMap(BaseModel):
+  __tablename__ = 'health_maps'
+
+  comment = sa.Column(sa.Text)
+  attachments = sa.Column(ARRAY(sa.String))
+  medical_card_id = sa.Column(UUID(as_uuid=True), sa.ForeignKey("medical_cards.id"), nullable=False)
+  medical_card = relationship('MedicalCard', back_populates='health_maps')

src/medical_info/db/schemas/__init__.py

@@ -0,0 +1 @@
+from .medical_card import *

src/medical_info/db/schemas/medical_card.py

@@ -0,0 +1,11 @@
+from pydantic import BaseModel
+
+class MedicalCard(BaseModel):
+  number: str
+  person_id: str
+
+  class Config:
+    orm_mode = True
+
+class MedicalCardCreate(BaseModel):
+  person_id: str

src/medical_info/db/session.py

@@ -0,0 +1,23 @@
+from functools import lru_cache
+from typing import Generator
+
+from sqlalchemy import create_engine
+from sqlalchemy.orm import scoped_session, sessionmaker
+
+from medical_info.config import get_settings
+
+engine = create_engine(get_settings().database_url, pool_pre_ping=True)
+
+@lru_cache
+def create_session() -> scoped_session:
+  Session = scoped_session(
+    sessionmaker(autocommit=False, autoflush=False, bind=engine)
+  )
+  return Session
+
+def get_session() -> Generator[scoped_session, None, None]:
+  Session = create_session()
+  try:
+    yield Session
+  finally:
+    Session.remove()

src/medical_info/routers/medical_cards.py

@@ -1,9 +1,16 @@
 from fastapi import Depends
 from fastapi.routing import APIRouter
+from typing import List
+
+from medical_info.db import models
+from medical_info.db.schemas import MedicalCard
+from medical_info.services import MedicalCardService, get_medical_cards_service
 
 router = APIRouter(prefix='/medical_cards')
 
-@router.get('/')
+@router.get('/', response_model=List[MedicalCard])
-def list_persons():
+def list_medical_cards(
-  return "ok"
+  medical_cards_service: MedicalCardService = Depends(get_medical_cards_service)
+) -> List[models.MedicalCard]:
+  return medical_cards_service.list()
 

src/medical_info/services/__init__.py

@@ -0,0 +1,11 @@
+from fastapi import Depends
+from sqlalchemy.orm import Session
+
+from medical_info.db.session import get_session
+
+from .medical_cards import MedicalCardService
+
+def get_medical_cards_service(db_session: Session = Depends(get_session)) -> MedicalCardService:
+  return MedicalCardService(db_session)
+
+__all__ = ('get_medical_cards_service')

src/medical_info/services/base.py

@@ -0,0 +1,52 @@
+from typing import Any, Generic, List, Optional, Type, TypeVar
+
+import sqlalchemy
+from pydantic import BaseModel
+from sqlalchemy.orm import Session
+from starlette.exceptions import HTTPException
+
+from medical_info.db.models import Base
+
+ModelType = TypeVar('ModelType', bound=Base)
+CreateSchemaType = TypeVar('CreateSchemaType', bound=BaseModel)
+UpdateSchemaType = TypeVar('UpdateSchemaType', bound=BaseModel)
+
+class BaseService(Generic[ModelType, CreateSchemaType, UpdateSchemaType]):
+  def __init__(self, model: Type[ModelType], db_session: Session):
+    self.model = model
+    self.db_session = db_session
+
+  def get(self, id: Any) -> Optional[ModelType]:
+    obj: Optional[ModelType] = self.db_session.get(self.model, id)
+    if obj is None:
+      raise HTTPException(status_code=404, detail='NotFound')
+    return obj
+
+  def list(self) -> List[ModelType]:
+    objs: List[ModelType] = self.db_session.query(self.model).all()
+    return objs
+
+  def create(self, obj: CreateSchemaType) -> ModelType:
+    db_obj: ModelType = self.model(**obj.dict())
+    self.db_session.add(db_obj)
+    try:
+      self.db_session.commit()
+    except sqlalchemy.exc.IntegrityError as e:
+      self.db_session.rollback()
+      if 'duplicate key' in str(e):
+        raise HTTPException(status_code=409, detail='Conflict Error')
+      else:
+        raise e
+    return db_obj
+
+  def update(self, id: Any, obj: UpdateSchemaType) -> Optional[ModelType]:
+    db_obj = self.get(id)
+    for column, value in obj.dict(exclude_unset=True).items():
+      setattr(db_obj, column, value)
+    self.db_session.commit()
+    return db_obj
+
+  def delete(self, id: Any) -> None:
+    db_obj = self.db_session.get(self.model, id)
+    self.db_session.delete(db_obj)
+    self.db_session.commit()

src/medical_info/services/medical_cards.py

@@ -0,0 +1,9 @@
+from typing import Any
+from medical_info.db.models import MedicalCard
+from medical_info.db.schemas import MedicalCardCreate
+from medical_info.services.base import BaseService
+from sqlalchemy.orm import Session
+
+class MedicalCardService(BaseService[MedicalCard, MedicalCardCreate, Any]):
+  def __init__(self, db_session: Session):
+    super(MedicalCardService, self).__init__(MedicalCard, db_session)