seamm_datastore.database package

Submodules

seamm_datastore.database.build module

Automatic import of projects and jobs from directories.

seamm_datastore.database.build.import_datastore(session, location, as_json=True)[source]

Import all the projects and jobs at <location>.

Parameters:

  • session (SQLAlchemy or flask session)

  • location (str or path) – The location to check for jobs or projects. Usually the projects directory in a datastore.

Returns:

(n_projects, n_jobs) – The number of projects and jobs added to the database.

Return type:

int, integer

seamm_datastore.database.models module

Table models for SEAMM datastore SQLAlchemy database.

class seamm_datastore.database.models.Flowchart(**kwargs)[source]

Bases: Base, Resource

conceptdoi
classmethod create(**flowchart_info)[source]
classmethod create_from_file(path)[source]
creators
description
doi
flowchart_metadata
flowchart_version
group
group_id
group_permissions
id
jobs
json
keywords
other_permissions
owner
owner_id
owner_permissions
static parse_flowchart_file(path)[source]

Function for parsing information from flowchart

Parameters:

path (str) – The path to the flowchart.

Returns:

metadata – A json containing flowchart information to be added to the database.

Return type:

dict

projects
sha256
sha256_strict
title
class seamm_datastore.database.models.Group(**kwargs)[source]

Bases: Base

classmethod create(name, users)[source]

Add a project to the database.

Parameters:

  • name (str) – The name of the project, used for display and directory name.

  • users (list) – A list of usernames to add to the group

Returns:

A Group object

Return type:

Group

id
name
special_projects
users
class seamm_datastore.database.models.GroupProjectAssociation(**kwargs)[source]

Bases: Base, PermissionsAssociationMixin

entity_id
groups
permissions
projects
resource_id
class seamm_datastore.database.models.Job(**kwargs)[source]

Bases: Base, Resource

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

Create a new job to add to the datastore.

This method requires a user to be logged in and to have appropriate permissions for the project.

Parameters:

  • id (int) – The id of the job, an integer > 0.

  • flowchart_filename (str or pathlib.Path) – The path to the file containing the flowchart.

  • project_names ([str]) – A list of projects that the flowchart belongs to.

  • path (str) – The directory path for the job.

  • title (str = “”) – The title of the job, used for display.

  • description (str = “”) – A longer, textual description of the job.

  • submitted (datetime.datetime = now()) – When the job was submitted as a datetime object. Defaults to now in UTC.

  • started (datetime.datetime = None) – When the job was started, if it was. Preferably in UTC.

  • finished (datetime.datetime = None) – When the job finished, if it has. Preferably in UTC.

  • parameters (dict) – The command-line parameters for the job.

  • status (str = “submitted”) – The status of the job: “submitted”, “running”, “finished”, “error”, etc.

Returns:

The json of the job data, or the Job object, depending on “as_json”.

Return type:

json or Job

classmethod create_from_file(job_data_file)[source]
description
finished
flowchart
flowchart_id
group
group_id
group_permissions
id
last_update
other_permissions
owner
owner_id
owner_permissions
parameters
static parse_job_data(path)[source]

Parse job_data.json at path

path
projects
started
status
submitted
title
classmethod update(id, description=None, title=None, path=None, submitted=None, started=None, finished=None, status=None, project_names=None)[source]

Update method for existing jobs

class seamm_datastore.database.models.Project(**kwargs)[source]

Bases: Base, Resource

classmethod create(name, description='', path=None, group=None)[source]

Create a project to add to the database.

Parameters:

  • name (str) – The name of the project, used for display and directory name.

  • description (str) – A textual description of the project.

  • path (str = None) – The path on disk to the project files.

  • group (str or Group = None) – The group for the project. Defaults to user’s primary group.

Returns:

A Project object.

Return type:

Project

description
flowcharts
group
group_id
group_permissions
id
jobs
name
other_permissions
owner
owner_id
owner_permissions
path
classmethod permissions_query(permission)[source]
special_groups
special_users
classmethod update(id, description=None, name=None, path=None)[source]

Update method for existing jobs

class seamm_datastore.database.models.Resource[source]

Bases: AccessControlPermissionsMixin

classmethod get(permission='read', description=None, title=None, offset=None, limit=None, sort_by='id', order='asc', only='all')[source]

General get method for jobs, flowcharts, projects

classmethod get_by_id(id, permission='read')[source]

General get method for retrieving by ID

classmethod permissions_query(permission)[source]
class seamm_datastore.database.models.Role(**kwargs)[source]

Bases: Base

id
name
users
class seamm_datastore.database.models.User(**kwargs)[source]

Bases: Base

added
classmethod create(username, password, first_name=None, last_name=None, email=None, roles=['user'], groups=None)[source]

Create a new user to be added to the database.

Parameters:

  • username (str) – The username that identifies the user.

  • password (str) – The secret password for the user.

  • first_name (str = None) – The user’s first (given) name.

  • last_name (str = None) – The user’s last (family) name.

  • email (str = None) – The user’s principal email address.

  • roles ([str] = [“user”]) – A list of roles for the user. Defaults to just “user”.

  • groups ([str] = None) – A list of groups that the user belongs to. Defaults to the first group in the database.

email
first_name
groups
id
last_name
property password
password_hash
roles
special_projects
status
username
verify_password(password)[source]
class seamm_datastore.database.models.UserProjectAssociation(**kwargs)[source]

Bases: Base, PermissionsAssociationMixin

entity_id
permissions
projects
resource_id
users

seamm_datastore.database.schema module

Marshmallow models for serialization and deserialization.

class seamm_datastore.database.schema.FlowchartSchema(*args, **kwargs)[source]

Bases: SQLAlchemyAutoSchema

class Meta[source]

Bases: object

exclude = ('json', 'owner_permissions', 'group_permissions', 'other_permissions', 'sha256')
include_fk = True
include_relationships = True
model

alias of Flowchart

dump_fields: Dict[str, ma_fields.Field]
exclude: set[Any] | MutableSet[Any]
fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]
opts: SchemaOpts = <marshmallow_sqlalchemy.schema.SQLAlchemyAutoSchemaOpts object>
class seamm_datastore.database.schema.GroupSchema(*args, **kwargs)[source]

Bases: SQLAlchemyAutoSchema

class Meta[source]

Bases: object

include_fk = True
include_relationships = True
model

alias of Group

dump_fields: Dict[str, ma_fields.Field]
exclude: set[Any] | MutableSet[Any]
fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]
opts: SchemaOpts = <marshmallow_sqlalchemy.schema.SQLAlchemyAutoSchemaOpts object>
class seamm_datastore.database.schema.JobSchema(*args, **kwargs)[source]

Bases: SQLAlchemyAutoSchema

class Meta[source]

Bases: object

exclude = ('flowchart', 'owner_permissions', 'group_permissions', 'other_permissions')
include_fk = True
include_relationships = True
model

alias of Job

dump_fields: Dict[str, ma_fields.Field]
exclude: set[Any] | MutableSet[Any]
fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]
opts: SchemaOpts = <marshmallow_sqlalchemy.schema.SQLAlchemyAutoSchemaOpts object>
class seamm_datastore.database.schema.LocalDateTime(format: str | None = None, **kwargs)[source]

Bases: DateTime

class seamm_datastore.database.schema.ProjectSchema(*args, **kwargs)[source]

Bases: SQLAlchemyAutoSchema

class Meta[source]

Bases: object

exclude = ('owner_permissions', 'group_permissions', 'other_permissions')
include_fk = True
include_relationships = True
model

alias of Project

dump_fields: Dict[str, ma_fields.Field]
exclude: set[Any] | MutableSet[Any]
fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]
opts: SchemaOpts = <marshmallow_sqlalchemy.schema.SQLAlchemyAutoSchemaOpts object>
class seamm_datastore.database.schema.RoleSchema(*args, **kwargs)[source]

Bases: SQLAlchemyAutoSchema

class Meta[source]

Bases: object

include_fk = True
include_relationships = True
model

alias of Role

dump_fields: Dict[str, ma_fields.Field]
exclude: set[Any] | MutableSet[Any]
fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]
opts: SchemaOpts = <marshmallow_sqlalchemy.schema.SQLAlchemyAutoSchemaOpts object>
class seamm_datastore.database.schema.UserSchema(*args, **kwargs)[source]

Bases: SQLAlchemyAutoSchema

class Meta[source]

Bases: object

exclude = ('password_hash',)
include_fk = True
include_relationships = True
model

alias of User

dump_fields: Dict[str, ma_fields.Field]
exclude: set[Any] | MutableSet[Any]
fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]
opts: SchemaOpts = <marshmallow_sqlalchemy.schema.SQLAlchemyAutoSchemaOpts object>

Module contents