Initial Alembic configuration

schema/README

+Generic single-database configuration.
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schema/alembic.ini

+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = .
+
+# 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 ./versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path
+# version_locations = %(here)s/bar %(here)s/bat ./versions
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+
+[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

schema/create_ws_tables.sql

-create table workflows (
-    workflow_id serial primary key ,
-    name        varchar
-);
-comment on table workflows is 'A listing of the available workflows in the system.  ';
-comment on column workflows.workflow_id is 'the unique id of the workflow.  auto-generated.';
-comment on column workflows.name is 'a human-readable name for the workflow.';
-
-create table workflow_requests (
-    workflow_request_id serial  primary key ,
-    job_id              int,
-    workflow_id         int references workflows(workflow_id),
-    argument            json
-);
-comment on table workflow_requests is 'A listing of requests for workflows and te resulting job ids.';
-comment on column workflow_requests.workflow_request_id is 'the unique id of the request.  auto-generated';
-comment on column workflow_requests.job_id is 'the id of the job that this request generted in the ? system.';
-comment on column workflow_requests.workflow_id is 'the id of the workflow used in this request.';
-comment on column workflow_requests.argument is 'the argument(s) used for the workflow in this request.';
-
-create table workflow_request_files (
-    workflow_request_id int references workflow_requests(workflow_request_id),
-    file_id int references files(file_id),
-    primary key (workflow_request_id, file_id)
-);
-comment on table workflow_request_files is 'A man-to-many mapping table tracking which files were used for workflow requests.';
-comment on column workflow_request_files.workflow_request_id is 'the id of the workflow request.';
-comment on column workflow_request_files.file_id is 'the id of the file referenced by the workflow request.';
-
-create table capabilities (
-    capability_id   serial primary key ,
-    name            varchar not null ,
-    template_files  varchar,
-    steps           varchar not null
-);
-comment on table capabilities is 'A listing of the available capabilities in the system.';
-comment on column capabilities.capability_id is 'the unique id of the capability.  auto-generated.';
-comment on column capabilities.name is 'the human-readable name of the capability.';
-comment on column capabilities.template_files is '?';
-comment on column capabilities.steps is 'the unique id of the capability.  auto-generated.';
-
-create table capability_requests (
-    capability_request_id serial primary key ,
-    capability_id int references capabilities(capability_id),
-    user_id int not null ,
-    argument json
-);
-
-comment on table capability_requests is 'A listing of requests for capabilities, with the id of the requesting user.';
-comment on column capability_requests.capability_request_id is 'The unique id of the request.  auto-generated.';
-comment on column capability_requests.capability_id is 'the id of the capability being requested.';
-comment on column capability_requests.user_id is 'the id of the user requesting the capability.';
-comment on column capability_requests.argument is 'the JSON holding the details of the request.';
\ No newline at end of file

schema/env.py

+from logging.config import fileConfig
+
+from sqlalchemy import create_engine
+from sqlalchemy import pool
+
+from alembic import context
+
+from pycapo import CapoConfig
+
+# 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 = lookup_url()
+
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def lookup_url():
+    capo = CapoConfig().settings('metadataDatabase')
+    url = capo.jdbcUrl.replace('jdbc:', '').replace('://', f'://{capo.jdbcUsername}:{capo.jdbcPassword}@')
+    return url
+
+
+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 = create_engine(lookup_url())
+
+    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()

schema/script.py.mako

+"""${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"}

schema/versions/44d5bbbf2615_workspaces_init.py

+"""workspaces-init
+
+Revision ID: 44d5bbbf2615
+Revises: 
+Create Date: 2020-09-02 11:25:01.571392
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '44d5bbbf2615'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.create_table('workflows',
+                    sa.Column('workflow_id', sa.Integer, primary_key=True, autoincrement=True,
+                              comment='the unique id of the workflow. auto-generated.'),
+                    sa.Column('name', sa.String, unique=True, comment='a human-readable name for the workflow.'),
+                    comment='A listing of the available workflows in the system.')
+
+    """
+    create table workflow_requests (
+        workflow_request_id serial  primary key ,
+                                            job_id              int,
+                                                                workflow_id         int references workflows(workflow_id),
+                                                                                                   argument            json
+    );
+    comment on table workflow_requests is 'A listing of requests for workflows and te resulting job ids.';
+    comment on column workflow_requests.workflow_request_id is 'the unique id of the request.  auto-generated';
+    comment on column workflow_requests.job_id is 'the id of the job that this request generted in the ? system.';
+    comment on column workflow_requests.workflow_id is 'the id of the workflow used in this request.';
+    comment on column workflow_requests.argument is 'the argument(s) used for the workflow in this request.';
+
+    create table workflow_request_files (
+        workflow_request_id int references workflow_requests(workflow_request_id),
+                                           file_id int references files(file_id),
+                                                                  primary key (workflow_request_id, file_id)
+    );
+    comment on table workflow_request_files is 'A man-to-many mapping table tracking which files were used for workflow requests.';
+    comment on column workflow_request_files.workflow_request_id is 'the id of the workflow request.';
+    comment on column workflow_request_files.file_id is 'the id of the file referenced by the workflow request.';
+
+    create table capabilities (
+        capability_id   serial primary key ,
+                                       name            varchar not null ,
+                                                               template_files  varchar,
+                                                                               steps           varchar not null
+    );
+    comment on table capabilities is 'A listing of the available capabilities in the system.';
+    comment on column capabilities.capability_id is 'the unique id of the capability.  auto-generated.';
+    comment on column capabilities.name is 'the human-readable name of the capability.';
+    comment on column capabilities.template_files is '?';
+    comment on column capabilities.steps is 'the unique id of the capability.  auto-generated.';
+
+    create table capability_requests (
+        capability_request_id serial primary key ,
+                                             capability_id int references capabilities(capability_id),
+                                                                          user_id int not null ,
+                                                                                      argument json
+    );
+
+    comment on table capability_requests is 'A listing of requests for capabilities, with the id of the requesting user.';
+    comment on column capability_requests.capability_request_id is 'The unique id of the request.  auto-generated.';
+    comment on column capability_requests.capability_id is 'the id of the capability being requested.';
+    comment on column capability_requests.user_id is 'the id of the user requesting the capability.';
+    comment on column capability_requests.argument is 'the JSON holding the details of the request.';
+    """
+
+
+def downgrade():
+    op.drop_table('workflows')
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