Merge branch 'master' into issue-166-360Page

# Conflicts:
#	src/server/api/common_api.py

Author: urirot

src/docker-compose.yml

@@ -10,6 +10,7 @@ services:
       - postgres:/var/lib/postgresql/data
     environment:
       POSTGRES_PASSWORD: thispasswordisverysecure
+      POSTGRES_DB: paws
 
   server:
     container_name: paws-compose-server
@@ -23,7 +24,6 @@ services:
     environment: 
       FLASK_ENV: development
 
-
   client:
     build: ./client
     container_name: paws-compose-client
@@ -35,8 +35,12 @@ services:
       - CHOKIDAR_USEPOLLING=true
     stdin_open: true
 
+
 #using named volumes fixs a windows docker bug relating to container permissions
 #https://stackoverflow.com/questions/49148754/docker-container-shuts-down-giving-data-directory-has-wrong-ownership-error-wh
 volumes:
   postgres:
-  src_archive:
+  src_archive:
+
+
+

src/server/Dockerfile

@@ -1,5 +1,7 @@
 FROM python:3.7
 
+RUN apt-get update && apt-get install -y vim
+
 WORKDIR /app
 
 ENV PYTHONDONTWRITEBYTECODE 1
@@ -32,6 +34,14 @@ RUN chmod 777 /paws-data-pipeline/server
 
 WORKDIR /app
 
-CMD python app.py
+# we may want to switch this to a script which logs output, etc?
+# CMD python app.py
+
+RUN set FLASK_APP=server/app.py
+RUN export FLASK_APP
 
+# This abomination ensures that the PG server has finished its restart cycle
+CMD echo "SLEEPING 10"; sleep 10; echo "WAKING"; alembic upgrade head ; python -m flask run --host=0.0.0.0 --no-reload
 
+# --no-reload prevents Flask restart, which usually happens in middle of create_base_users()
+#TODO: SECURITY - ensure we are not running in debug mode in production

src/server/alembic.ini

@@ -0,0 +1,89 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = alembic
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# timezone to use when rendering the date
+# within the migration file as well as the filename.
+# 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
+# version_locations = %(here)s/bar %(here)s/bat alembic/versions
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+# Container
+sqlalchemy.url = postgresql://postgres:thispasswordisverysecure@paws-compose-db/paws
+
+# Local
+# sqlalchemy.url = postgresql://postgres:thispasswordisverysecure@localhost/paws
+
+
+[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
+
+# 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

src/server/alembic/README

@@ -0,0 +1 @@
+Generic single-database configuration.

src/server/alembic/env.py

@@ -0,0 +1,77 @@
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+
+from alembic import context
+
+# 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.
+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 = None
+
+# 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():
+    """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():
+    """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()

src/server/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():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}

src/server/alembic/versions/36c4ecbfd11a_add_pdp_users_full_name.py

@@ -0,0 +1,24 @@
+"""Add pdp_users full_name
+
+Revision ID: 36c4ecbfd11a
+Revises: 7138d52f92d6
+Create Date: 2020-12-18 15:28:17.367718
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "36c4ecbfd11a"
+down_revision = "7138d52f92d6"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.add_column("pdp_users", sa.Column("full_name", sa.String))
+
+
+def downgrade():
+    pass

src/server/alembic/versions/41da831646e4_pdp_users_role_fk_from_roles.py

@@ -0,0 +1,27 @@
+"""pdp_users.role FK from roles
+
+Revision ID: 41da831646e4
+Revises: 72d50d531bd5
+Create Date: 2020-12-16 15:53:28.514053
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "41da831646e4"
+down_revision = "72d50d531bd5"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.drop_column("pdp_users", "role")
+    op.add_column(
+        "pdp_users", sa.Column("role", sa.Integer, sa.ForeignKey("pdp_user_roles._id"))
+    )
+
+
+def downgrade():
+    pass

src/server/alembic/versions/6b8cf99be000_add_user_journal_table.py

@@ -0,0 +1,32 @@
+"""Add user journal table
+
+Revision ID: 6b8cf99be000
+Revises: 36c4ecbfd11a
+Create Date: 2020-12-21 15:08:07.784568
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.sql import func
+
+
+# revision identifiers, used by Alembic.
+revision = "6b8cf99be000"
+down_revision = "36c4ecbfd11a"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.create_table(
+        "pdp_user_journal",
+        sa.Column("_id", sa.Integer, primary_key=True),
+        sa.Column("stamp", sa.DateTime, nullable=False, server_default=func.now()),
+        sa.Column("username", sa.String(50), nullable=False),
+        sa.Column("event_type", sa.String(50)),
+        sa.Column("detail", sa.String(120)),
+    )
+
+
+def downgrade():
+    pass

src/server/alembic/versions/7138d52f92d6_add_uniqueness_constraints.py

@@ -0,0 +1,25 @@
+"""add uniqueness constraints
+
+Revision ID: 7138d52f92d6
+Revises: f3d30db17bed
+Create Date: 2020-12-17 17:31:29.154789
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "7138d52f92d6"
+down_revision = "f3d30db17bed"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.create_unique_constraint("uq_username", "pdp_users", ["username"])
+    op.create_unique_constraint("uq_role", "pdp_user_roles", ["role"])
+
+
+def downgrade():
+    pass