seamm_datastore package

Subpackages

• seamm_datastore.database package
  • Submodules
  • seamm_datastore.database.build module
    • import_datastore()
  • seamm_datastore.database.models module
    • Flowchart
      • Flowchart.conceptdoi
      • Flowchart.create()
      • Flowchart.create_from_file()
      • Flowchart.creators
      • Flowchart.description
      • Flowchart.doi
      • Flowchart.flowchart_metadata
      • Flowchart.flowchart_version
      • Flowchart.get_or_create_from_file()
      • Flowchart.group
      • Flowchart.group_id
      • Flowchart.group_permissions
      • Flowchart.id
      • Flowchart.jobs
      • Flowchart.json
      • Flowchart.keywords
      • Flowchart.other_permissions
      • Flowchart.owner
      • Flowchart.owner_id
      • Flowchart.owner_permissions
      • Flowchart.parse_flowchart_file()
      • Flowchart.projects
      • Flowchart.sha256
      • Flowchart.sha256_strict
      • Flowchart.title
    • Group
      • Group.create()
      • Group.id
      • Group.name
      • Group.special_projects
      • Group.users
    • GroupProjectAssociation
      • GroupProjectAssociation.entity_id
      • GroupProjectAssociation.groups
      • GroupProjectAssociation.permissions
      • GroupProjectAssociation.projects
      • GroupProjectAssociation.resource_id
    • Job
      • Job.create()
      • Job.create_from_file()
      • Job.description
      • Job.finished
      • Job.flowchart
      • Job.flowchart_id
      • Job.group
      • Job.group_id
      • Job.group_permissions
      • Job.id
      • Job.last_update
      • Job.other_permissions
      • Job.owner
      • Job.owner_id
      • Job.owner_permissions
      • Job.parameters
      • Job.parse_job_data()
      • Job.path
      • Job.projects
      • Job.started
      • Job.status
      • Job.submitted
      • Job.title
      • Job.update()
    • Project
      • Project.create()
      • Project.description
      • Project.flowcharts
      • Project.group
      • Project.group_id
      • Project.group_permissions
      • Project.id
      • Project.jobs
      • Project.name
      • Project.other_permissions
      • Project.owner
      • Project.owner_id
      • Project.owner_permissions
      • Project.path
      • Project.permissions_query()
      • Project.special_groups
      • Project.special_users
      • Project.update()
    • Resource
      • Resource.get()
      • Resource.get_by_id()
      • Resource.permissions_query()
    • Role
      • Role.id
      • Role.name
      • Role.users
    • User
      • User.added
      • User.create()
      • User.email
      • User.first_name
      • User.groups
      • User.id
      • User.last_name
      • User.password
      • User.password_hash
      • User.roles
      • User.special_projects
      • User.status
      • User.username
      • User.verify_password()
    • UserProjectAssociation
      • UserProjectAssociation.entity_id
      • UserProjectAssociation.permissions
      • UserProjectAssociation.projects
      • UserProjectAssociation.resource_id
      • UserProjectAssociation.users
    • utc_now()
  • seamm_datastore.database.schema module
    • FlowchartSchema
      • FlowchartSchema.Meta
      • FlowchartSchema.instance
      • FlowchartSchema.opts
    • GroupSchema
      • GroupSchema.Meta
      • GroupSchema.instance
      • GroupSchema.opts
    • JobSchema
      • JobSchema.Meta
      • JobSchema.instance
      • JobSchema.opts
    • LocalDateTime
    • ProjectSchema
      • ProjectSchema.Meta
      • ProjectSchema.instance
      • ProjectSchema.opts
    • RoleSchema
      • RoleSchema.Meta
      • RoleSchema.instance
      • RoleSchema.opts
    • UserSchema
      • UserSchema.Meta
      • UserSchema.instance
      • UserSchema.opts
  • Module contents
• seamm_datastore.tests package
  • Submodules
  • seamm_datastore.tests.conftest module
    • admin_connection()
    • connection()
    • filled_db()
    • session()
  • seamm_datastore.tests.test_build module
    • test_build()
    • test_import_datastore_duplicate_project_name_recovers()
  • seamm_datastore.tests.test_create module
    • test_add_job()
    • test_create_user()
    • test_flowchart_duplicate_hash_raises()
    • test_flowchart_from_file()
    • test_flowchart_get_or_create_concurrent_race()
    • test_flowchart_parse()
    • test_flowchart_sha256_strict_unique_constraint()
    • test_job_create_shared_flowchart_reuses_row()
    • test_project_create()
    • test_project_create_group()
    • test_project_exists()
    • test_project_no_user()
  • seamm_datastore.tests.test_errors module
  • seamm_datastore.tests.test_methods module
    • test_get_queries()
    • test_job_update()
    • test_job_update_error()
  • seamm_datastore.tests.test_seamm_datastore module
    • test_connected()
    • test_connection_logout()
  • Module contents

Submodules

seamm_datastore.connect module

Class and functions for connection to database.

class seamm_datastore.connect.SEAMMDatastore(database_uri: str = 'sqlite:///:memory:', initialize: bool = False, permissions: dict = None, username: str = None, password: str = None, datastore_location: str = None, default_project: str = 'default', timeout: float = 20.0)

Bases: object

add_job(id, flowchart_filename, project_names=['default'], path=None, title='', description='', submitted=None, started=None, finished=None, parameters=None, status='submitted')

current_user()

finish_job(job_id, finish_time, status='finished')

Set the status and time that the job finished.

Parameters:

• job_id (int) – The ID of the job, eg. 209

• finish_time (datetime.datetime) – The UTC time when the job finished.

• status (str) – The status, such as “error” or the default, “finished”

• as_json (bool = False) – Ignored

• current_user (str or User = None) – Ignored

Returns:

True if the finish time was successfully set, False otherwise.

Return type:

bool

import_datastore(*args, **kwargs)

login(username, password)

logout()

class seamm_datastore.connect.current_app(config)

Bases: object

Fake current_app

seamm_datastore.connect.login_required(method)

Decorator for actions requiring current user

seamm_datastore.connect.manage_session(function)

Decorator for closing sqlalchemy sessions when attached to SEAMMDatastore class.

seamm_datastore.connect.session_scope(session, timeout=20.0)

Provide a transactional scope around a series of operations.

Parameters:

• session (callable) – A session factory (e.g. a scoped_session) returning a new session.

• timeout (float) – Seconds to keep retrying the commit while the (SQLite) database is locked by another process. Together with the connection-level PRAGMA busy_timeout this lets many jobs register in the datastore at the same time – e.g. a batch of SLURM jobs starting together – without failing with “database is locked”. Default: 20 s.

seamm_datastore.flask_authorize_patch module

Patch for flask_authorize.

Flask authorize and the functions defined here can only be used with an application context.

class seamm_datastore.flask_authorize_patch.AccessControlPermissionsMixin

Bases: PermissionsMixin

classmethod authorized(check)

Query operator for permissions mixins. This operator can be used in SQLAlchemy query statements, and will automatically decorate queries with appropriate owner/group and permissionc checks.

Arguments:

check (str): Permission to authorize (i.e. read, update)

Examples:

Query all articles where the current user is read-authorized:

Article.query.filter(Article.authorized('read')).all()

Query by multiple parameters, including authorization:

Article.query.filter(or_(
    Article.name.contains('open article'),
    Article.authorized('read')
))

seamm_datastore.flask_authorize_patch.generate_association_table(entity_name, resource_name, entity_tablename=None, resource_tablename=None)

seamm_datastore.util module

Util Functions and classes

exception seamm_datastore.util.LoginRequiredError

Bases: Exception

exception seamm_datastore.util.NotAuthorizedError

Bases: Exception

Module contents

seamm_datastore The database models for the seamm datastore

seamm_datastore.connect

alias of SEAMMDatastore