Release/1.3.20240909 (#354)

.env

@@ -1,5 +1,8 @@
 PYTHONPATH=/app
 
+# REST API
+AIOD_REST_PORT=8000
+
 #MYSQL
 MYSQL_ROOT_PASSWORD=ok
 
@@ -10,17 +13,28 @@ KEYCLOAK_ADMIN_PASSWORD=password
 KEYCLOAK_CLIENT_SECRET="QJiOGn09eCEfnqAmcPP2l4vMU8grlmVQ"
 REDIRECT_URIS=http://${HOSTNAME}/docs/oauth2-redirect
 POST_LOGOUT_REDIRECT_URIS=http://${HOSTNAME}/aiod-auth/realms/aiod/protocol/openid-connect/logout
+AIOD_KEYCLOAK_PORT=8080
+
+EGICHECKINALIAS=
 
 #ELASTICSEARCH
 ES_USER=elastic
 ES_PASSWORD=changeme
 ES_DISCOVERY_TYPE=single-node
 ES_ROLE="edit_aiod_resources"
 ES_JAVA_OPTS="-Xmx256m -Xms256m"
+AIOD_ES_HTTP_PORT=9200
+AIOD_ES_TRANSPORT_PORT=9300
 
 #LOGSTASH
 LS_JAVA_OPTS="-Xmx256m -Xms256m"
+AIOD_LOGSTASH_BEATS_PORT=5044
+AIOD_LOGSTASH_PORT=5000
+AIOD_LOGSTASH_API_PORT=9600
+
+#NGINX
+AIOD_NGINX_PORT=80
 
 #DATA STORAGE
 DATA_PATH=./data
-BACKUP_PATH=./data/backups
+BACKUP_PATH=./data/backups

README.md

@@ -287,4 +287,9 @@ To create a new release,
    release branch. Look at all closed PRs and create a changelog
 6. Create a PR from release branch to master
 7. After that's merged, create a PR from master to develop
-8. Notify everyone (e.g., in the API channel in Slack) and update the code on the server(s). 
+8. Deploy on the server(s):
+   - Check which services currently work (before the update). It's a sanity check for if a service _doesn't_ work later.
+   - Update the code on the server by checking out the release
+   - Merge configurations as necessary
+   - Make sure the latest database migrations are applied: see ["Schema Migrations"](alembic/readme.md#update-the-database)
+9. Notify everyone (e.g., in the API channel in Slack). 

alembic/Dockerfile

@@ -0,0 +1,5 @@
+FROM aiod_metadata_catalogue
+RUN python -m pip install alembic
+ENV PYTHONPATH="$PYTHONPATH:/app"
+WORKDIR /alembic
+ENTRYPOINT ["alembic", "upgrade", "head"]

alembic/README.md

@@ -0,0 +1,32 @@
+# Database Schema Migrations
+
+We use [Alembic](https://alembic.sqlalchemy.org/en/latest/tutorial.html#running-our-first-migration) to automate database schema migrations
+(e.g., adding a table, altering a column, and so on).
+Please refer to the Alembic documentation for more information.
+
+## Usage
+Commands below assume that the root directory of the project is your current working directory.
+
+Build the image with:
+```commandline
+docker build -f alembic/Dockerfile . -t aiod-migration
+```
+
+With the sqlserver container running, you can migrate to the latest schema with:
+
+```commandline
+docker run -v $(pwd)/alembic:/alembic:ro  -v $(pwd)/src:/app -it --network aiod_default  aiod-migration
+```
+Make sure that the specifid `--network` is the docker network that has the `sqlserver` container.
+The alembic directory is mounted to ensure the latest migrations are available, 
+the src directory is mounted so the migration scripts can use defined classes and variable from the project.
+
+## Update the Database
+> [!Caution]
+> Database migrations may be irreversible. Always make sure there is a backup of the old database.
+
+Following the usage commands above, on a new release we should run alembic to ensure the latest schema changes are applied.
+The default entrypoint of the container specifies to upgrade the database to the latest schema.
+
+## TODO
+ - set up support for auto-generating migration scripts: https://alembic.sqlalchemy.org/en/latest/autogenerate.html

alembic/alembic.ini

@@ -0,0 +1,116 @@
+# 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 = 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]
+# 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
+
+# lint with attempts to fix using "ruff" - use the exec runner, execute a binary
+# hooks = ruff
+# ruff.type = exec
+# ruff.executable = %(here)s/.venv/bin/ruff
+# ruff.options = --fix 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/alembic/README

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

alembic/alembic/env.py

@@ -0,0 +1,72 @@
+from logging.config import fileConfig
+
+from alembic import context
+
+# Assumes /src is in the Python path, so we can re-use logic for constructing db connections
+from database.session import db_url
+from database.session import EngineSingleton
+
+# 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 = 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() -> 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 = db_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 = EngineSingleton().engine
+    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/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/alembic/versions/0a23b40cc09c_extend_max_length_of_text_in_note.py

@@ -0,0 +1,48 @@
+"""Extend max length of text in note
+
+Revision ID: 0a23b40cc09c
+Revises: 
+Create Date: 2024-08-29 11:37:20.827291
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+from sqlalchemy import String
+
+from database.model.field_length import VERY_LONG
+
+# revision identifiers, used by Alembic.
+revision: str = "0a23b40cc09c"
+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:
+    # All models that derive from AIResourceBase
+    for table in [
+        "news",
+        "team",
+        "person",
+        "organisation",
+        "event",
+        "project",
+        "service",
+        "dataset",
+        "case_study",
+        "publication",
+        "computational_asset",
+        "ml_model",
+        "experiment",
+        "educational_resource",
+    ]:
+        op.alter_column(
+            f"note_{table}",
+            "value",
+            type_=String(VERY_LONG),
+        )
+
+
+def downgrade() -> None:
+    pass

data/keycloak/import/realm-export.json → data/keycloak/data/import/realm-export.json

@@ -1527,6 +1527,7 @@
     "strictTransportSecurity": "max-age=31536000; includeSubDomains"
   },
   "smtpServer": {},
+  "loginTheme" : "aiod",
   "eventsEnabled": false,
   "eventsListeners": [
     "jboss-logging"