path: root/gn_auth/auth/authorisation/resources/models.py

"""Handle the management of resources."""
import json
import sqlite3
from uuid import UUID, uuid4
from functools import reduce, partial
from typing import Any, Dict, Sequence, Optional, NamedTuple

from gn_auth.auth.db import sqlite3 as db
from gn_auth.auth.dictify import dictify
from gn_auth.auth.authentication.users import User
from gn_auth.auth.db.sqlite3 import with_db_connection

from .checks import authorised_for

from ..checks import authorised_p
from ..errors import NotFoundError, AuthorisationError
from ..groups.models import (
    Group, GroupRole, user_group, group_by_id, is_group_leader)

class MissingGroupError(AuthorisationError):
    """Raised for any resource operation without a group."""

class ResourceCategory(NamedTuple):
    """Class representing a resource category."""
    resource_category_id: UUID
    resource_category_key: str
    resource_category_description: str

    def dictify(self) -> dict[str, Any]:
        """Return a dict representation of `ResourceCategory` objects."""
        return {
            "resource_category_id": self.resource_category_id,
            "resource_category_key": self.resource_category_key,
            "resource_category_description": self.resource_category_description
        }

class Resource(NamedTuple):
    """Class representing a resource."""
    group: Group
    resource_id: UUID
    resource_name: str
    resource_category: ResourceCategory
    public: bool
    resource_data: Sequence[dict[str, Any]] = tuple()

    def dictify(self) -> dict[str, Any]:
        """Return a dict representation of `Resource` objects."""
        return {
            "group": dictify(self.group), "resource_id": self.resource_id,
            "resource_name": self.resource_name,
            "resource_category": dictify(self.resource_category),
            "public": self.public,
            "resource_data": self.resource_data
        }

def __assign_resource_owner_role__(cursor, resource, user):
    """Assign `user` the 'Resource Owner' role for `resource`."""
    cursor.execute(
        "SELECT gr.* FROM group_roles AS gr INNER JOIN roles AS r "
        "ON gr.role_id=r.role_id WHERE r.role_name='resource-owner' "
        "AND gr.group_id=?",
        (str(resource.group.group_id),))
    role = cursor.fetchone()
    if not role:
        cursor.execute("SELECT * FROM roles WHERE role_name='resource-owner'")
        role = cursor.fetchone()
        cursor.execute(
            "INSERT INTO group_roles VALUES "
            "(:group_role_id, :group_id, :role_id)",
            {"group_role_id": str(uuid4()),
             "group_id": str(resource.group.group_id),
             "role_id": role["role_id"]})

    cursor.execute(
            "INSERT INTO group_user_roles_on_resources "
            "VALUES ("
            ":group_id, :user_id, :role_id, :resource_id"
            ")",
            {"group_id": str(resource.group.group_id),
             "user_id": str(user.user_id),
             "role_id": role["role_id"],
             "resource_id": str(resource.resource_id)})

@authorised_p(("group:resource:create-resource",),
              error_description="Insufficient privileges to create a resource",
              oauth2_scope="profile resource")
def create_resource(
        conn: db.DbConnection, resource_name: str,
        resource_category: ResourceCategory, user: User,
        public: bool) -> Resource:
    """Create a resource item."""
    with db.cursor(conn) as cursor:
        group = user_group(conn, user).maybe(
            False, lambda grp: grp)# type: ignore[misc, arg-type]
        if not group:
            raise MissingGroupError(
                "User with no group cannot create a resource.")
        resource = Resource(
            group, uuid4(), resource_name, resource_category, public)
        cursor.execute(
            "INSERT INTO resources VALUES (?, ?, ?, ?, ?)",
            (str(resource.group.group_id), str(resource.resource_id),
             resource_name,
             str(resource.resource_category.resource_category_id),
             1 if resource.public else 0))
        __assign_resource_owner_role__(cursor, resource, user)

    return resource

def resource_category_by_id(
        conn: db.DbConnection, category_id: UUID) -> ResourceCategory:
    """Retrieve a resource category by its ID."""
    with db.cursor(conn) as cursor:
        cursor.execute(
            "SELECT * FROM resource_categories WHERE "
            "resource_category_id=?",
            (str(category_id),))
        results = cursor.fetchone()
        if results:
            return ResourceCategory(
                UUID(results["resource_category_id"]),
                results["resource_category_key"],
                results["resource_category_description"])

    raise NotFoundError(
        f"Could not find a ResourceCategory with ID '{category_id}'")

def resource_categories(conn: db.DbConnection) -> Sequence[ResourceCategory]:
    """Retrieve all available resource categories"""
    with db.cursor(conn) as cursor:
        cursor.execute("SELECT * FROM resource_categories")
        return tuple(
            ResourceCategory(UUID(row[0]), row[1], row[2])
            for row in cursor.fetchall())
    return tuple()

def public_resources(conn: db.DbConnection) -> Sequence[Resource]:
    """List all resources marked as public"""
    categories = {
        str(cat.resource_category_id): cat for cat in resource_categories(conn)
    }
    with db.cursor(conn) as cursor:
        cursor.execute("SELECT * FROM resources WHERE public=1")
        results = cursor.fetchall()
        group_uuids = tuple(row[0] for row in results)
        query = ("SELECT * FROM groups WHERE group_id IN "
                 f"({', '.join(['?'] * len(group_uuids))})")
        cursor.execute(query, group_uuids)
        groups = {
            row[0]: Group(
                UUID(row[0]), row[1], json.loads(row[2] or "{}"))
            for row in cursor.fetchall()
        }
        return tuple(
            Resource(groups[row[0]], UUID(row[1]), row[2], categories[row[3]],
                     bool(row[4]))
            for row in results)

def group_leader_resources(
        conn: db.DbConnection, user: User, group: Group,
        res_categories: Dict[UUID, ResourceCategory]) -> Sequence[Resource]:
    """Return all the resources available to the group leader"""
    if is_group_leader(conn, user, group):
        with db.cursor(conn) as cursor:
            cursor.execute("SELECT * FROM resources WHERE group_id=?",
                           (str(group.group_id),))
            return tuple(
                Resource(group, UUID(row[1]), row[2],
                         res_categories[UUID(row[3])], bool(row[4]))
                for row in cursor.fetchall())
    return tuple()

def user_resources(conn: db.DbConnection, user: User) -> Sequence[Resource]:
    """List the resources available to the user"""
    categories = { # Repeated in `public_resources` function
        cat.resource_category_id: cat for cat in resource_categories(conn)
    }
    with db.cursor(conn) as cursor:
        def __all_resources__(group) -> Sequence[Resource]:
            gl_resources = group_leader_resources(conn, user, group, categories)

            cursor.execute(
                ("SELECT resources.* FROM group_user_roles_on_resources "
                 "LEFT JOIN resources "
                 "ON group_user_roles_on_resources.resource_id=resources.resource_id "
                 "WHERE group_user_roles_on_resources.group_id = ? "
                 "AND group_user_roles_on_resources.user_id = ?"),
                (str(group.group_id), str(user.user_id)))
            rows = cursor.fetchall()
            private_res = tuple(
                Resource(group, UUID(row[1]), row[2], categories[UUID(row[3])],
                         bool(row[4]))
                for row in rows)
            return tuple({
                res.resource_id: res
                for res in
                (private_res + gl_resources + public_resources(conn))# type: ignore[operator]
            }.values())

        # Fix the typing here
        return user_group(conn, user).map(__all_resources__).maybe(# type: ignore[arg-type,misc]
            public_resources(conn), lambda res: res)# type: ignore[arg-type,return-value]

def resource_data(conn, resource, offset: int = 0, limit: Optional[int] = None) -> tuple[dict, ...]:
    """
    Retrieve the data for `resource`, optionally limiting the number of items.
    """
    resource_data_function = {
        "mrna": mrna_resource_data,
        "genotype": genotype_resource_data,
        "phenotype": phenotype_resource_data
    }
    with db.cursor(conn) as cursor:
        return tuple(
            dict(data_row) for data_row in
            resource_data_function[
                resource.resource_category.resource_category_key](
                    cursor, resource.resource_id, offset, limit))

def attach_resource_data(cursor: db.DbCursor, resource: Resource) -> Resource:
    """Attach the linked data to the resource"""
    resource_data_function = {
        "mrna": mrna_resource_data,
        "genotype": genotype_resource_data,
        "phenotype": phenotype_resource_data
    }
    category = resource.resource_category
    data_rows = tuple(
        dict(data_row) for data_row in
        resource_data_function[category.resource_category_key](
            cursor, resource.resource_id))
    return Resource(
        resource.group, resource.resource_id, resource.resource_name,
        resource.resource_category, resource.public, data_rows)

def mrna_resource_data(cursor: db.DbCursor,
                       resource_id: UUID,
                       offset: int = 0,
                       limit: Optional[int] = None) -> Sequence[sqlite3.Row]:
    """Fetch data linked to a mRNA resource"""
    cursor.execute(
        (("SELECT * FROM mrna_resources AS mr "
          "INNER JOIN linked_mrna_data AS lmr "
          "ON mr.data_link_id=lmr.data_link_id "
          "WHERE mr.resource_id=?") + (
              f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")),
        (str(resource_id),))
    return cursor.fetchall()

def genotype_resource_data(
        cursor: db.DbCursor,
        resource_id: UUID,
        offset: int = 0,
        limit: Optional[int] = None) -> Sequence[sqlite3.Row]:
    """Fetch data linked to a Genotype resource"""
    cursor.execute(
        (("SELECT * FROM genotype_resources AS gr "
          "INNER JOIN linked_genotype_data AS lgd "
          "ON gr.data_link_id=lgd.data_link_id "
          "WHERE gr.resource_id=?") + (
              f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")),
        (str(resource_id),))
    return cursor.fetchall()

def phenotype_resource_data(
        cursor: db.DbCursor,
        resource_id: UUID,
        offset: int = 0,
        limit: Optional[int] = None) -> Sequence[sqlite3.Row]:
    """Fetch data linked to a Phenotype resource"""
    cursor.execute(
        ("SELECT * FROM phenotype_resources AS pr "
         "INNER JOIN linked_phenotype_data AS lpd "
         "ON pr.data_link_id=lpd.data_link_id "
         "WHERE pr.resource_id=?") + (
             f" LIMIT {limit} OFFSET {offset}" if bool(limit) else ""),
        (str(resource_id),))
    return cursor.fetchall()

def resource_by_id(
        conn: db.DbConnection, user: User, resource_id: UUID) -> Resource:
    """Retrieve a resource by its ID."""
    if not authorised_for(
            conn, user, ("group:resource:view-resource",),
            (resource_id,))[resource_id]:
        raise AuthorisationError(
            "You are not authorised to access resource with id "
            f"'{resource_id}'.")

    with db.cursor(conn) as cursor:
        cursor.execute("SELECT * FROM resources WHERE resource_id=:id",
                       {"id": str(resource_id)})
        row = cursor.fetchone()
        if row:
            return Resource(
                group_by_id(conn, UUID(row["group_id"])),
                UUID(row["resource_id"]), row["resource_name"],
                resource_category_by_id(conn, row["resource_category_id"]),
                bool(int(row["public"])))

    raise NotFoundError(f"Could not find a resource with id '{resource_id}'")

def __link_mrna_data_to_resource__(
        conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict:
    """Link mRNA Assay data with a resource."""
    with db.cursor(conn) as cursor:
        params = {
            "group_id": str(resource.group.group_id),
            "resource_id": str(resource.resource_id),
            "data_link_id": str(data_link_id)
        }
        cursor.execute(
            "INSERT INTO mrna_resources VALUES"
            "(:group_id, :resource_id, :data_link_id)",
            params)
        return params

def __link_geno_data_to_resource__(
        conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict:
    """Link Genotype data with a resource."""
    with db.cursor(conn) as cursor:
        params = {
            "group_id": str(resource.group.group_id),
            "resource_id": str(resource.resource_id),
            "data_link_id": str(data_link_id)
        }
        cursor.execute(
            "INSERT INTO genotype_resources VALUES"
            "(:group_id, :resource_id, :data_link_id)",
            params)
        return params

def __link_pheno_data_to_resource__(
        conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict:
    """Link Phenotype data with a resource."""
    with db.cursor(conn) as cursor:
        params = {
            "group_id": str(resource.group.group_id),
            "resource_id": str(resource.resource_id),
            "data_link_id": str(data_link_id)
        }
        cursor.execute(
            "INSERT INTO phenotype_resources VALUES"
            "(:group_id, :resource_id, :data_link_id)",
            params)
        return params

def link_data_to_resource(
        conn: db.DbConnection, user: User, resource_id: UUID, dataset_type: str,
        data_link_id: UUID) -> dict:
    """Link data to resource."""
    if not authorised_for(
            conn, user, ("group:resource:edit-resource",),
            (resource_id,))[resource_id]:
        raise AuthorisationError(
            "You are not authorised to link data to resource with id "
            f"{resource_id}")

    resource = with_db_connection(partial(
        resource_by_id, user=user, resource_id=resource_id))
    return {
        "mrna": __link_mrna_data_to_resource__,
        "genotype": __link_geno_data_to_resource__,
        "phenotype": __link_pheno_data_to_resource__,
    }[dataset_type.lower()](conn, resource, data_link_id)

def __unlink_mrna_data_to_resource__(
        conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict:
    """Unlink data from mRNA Assay resources"""
    with db.cursor(conn) as cursor:
        cursor.execute("DELETE FROM mrna_resources "
                       "WHERE resource_id=? AND data_link_id=?",
                       (str(resource.resource_id), str(data_link_id)))
        return {
            "resource_id": str(resource.resource_id),
            "dataset_type": resource.resource_category.resource_category_key,
            "data_link_id": data_link_id
        }

def __unlink_geno_data_to_resource__(
        conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict:
    """Unlink data from Genotype resources"""
    with db.cursor(conn) as cursor:
        cursor.execute("DELETE FROM genotype_resources "
                       "WHERE resource_id=? AND data_link_id=?",
                       (str(resource.resource_id), str(data_link_id)))
        return {
            "resource_id": str(resource.resource_id),
            "dataset_type": resource.resource_category.resource_category_key,
            "data_link_id": data_link_id
        }

def __unlink_pheno_data_to_resource__(
        conn: db.DbConnection, resource: Resource, data_link_id: UUID) -> dict:
    """Unlink data from Phenotype resources"""
    with db.cursor(conn) as cursor:
        cursor.execute("DELETE FROM phenotype_resources "
                       "WHERE resource_id=? AND data_link_id=?",
                       (str(resource.resource_id), str(data_link_id)))
        return {
            "resource_id": str(resource.resource_id),
            "dataset_type": resource.resource_category.resource_category_key,
            "data_link_id": str(data_link_id)
        }

def unlink_data_from_resource(
        conn: db.DbConnection, user: User, resource_id: UUID, data_link_id: UUID):
    """Unlink data from resource."""
    if not authorised_for(
            conn, user, ("group:resource:edit-resource",),
            (resource_id,))[resource_id]:
        raise AuthorisationError(
            "You are not authorised to link data to resource with id "
            f"{resource_id}")

    resource = with_db_connection(partial(
        resource_by_id, user=user, resource_id=resource_id))
    dataset_type = resource.resource_category.resource_category_key
    return {
        "mrna": __unlink_mrna_data_to_resource__,
        "genotype": __unlink_geno_data_to_resource__,
        "phenotype": __unlink_pheno_data_to_resource__,
    }[dataset_type.lower()](conn, resource, data_link_id)

def organise_resources_by_category(resources: Sequence[Resource]) -> dict[
        ResourceCategory, tuple[Resource]]:
    """Organise the `resources` by their categories."""
    def __organise__(accumulator, resource):
        category = resource.resource_category
        return {
            **accumulator,
            category: accumulator.get(category, tuple()) + (resource,)
        }
    return reduce(__organise__, resources, {})

def __attach_data__(
        data_rows: Sequence[sqlite3.Row],
        resources: Sequence[Resource]) -> Sequence[Resource]:
    def __organise__(acc, row):
        resource_id = UUID(row["resource_id"])
        return {
            **acc,
            resource_id: acc.get(resource_id, tuple()) + (dict(row),)
        }
    organised: dict[UUID, tuple[dict, ...]] = reduce(__organise__, data_rows, {})
    return tuple(
        Resource(
            resource.group, resource.resource_id, resource.resource_name,
            resource.resource_category, resource.public,
            organised.get(resource.resource_id, tuple()))
        for resource in resources)

def attach_mrna_resources_data(
        cursor, resources: Sequence[Resource]) -> Sequence[Resource]:
    """Attach linked data to mRNA Assay resources"""
    placeholders = ", ".join(["?"] * len(resources))
    cursor.execute(
        "SELECT * FROM mrna_resources AS mr INNER JOIN linked_mrna_data AS lmd"
        " ON mr.data_link_id=lmd.data_link_id "
        f"WHERE mr.resource_id IN ({placeholders})",
        tuple(str(resource.resource_id) for resource in resources))
    return __attach_data__(cursor.fetchall(), resources)

def attach_genotype_resources_data(
        cursor, resources: Sequence[Resource]) -> Sequence[Resource]:
    """Attach linked data to Genotype resources"""
    placeholders = ", ".join(["?"] * len(resources))
    cursor.execute(
        "SELECT * FROM genotype_resources AS gr "
        "INNER JOIN linked_genotype_data AS lgd "
        "ON gr.data_link_id=lgd.data_link_id "
        f"WHERE gr.resource_id IN ({placeholders})",
        tuple(str(resource.resource_id) for resource in resources))
    return __attach_data__(cursor.fetchall(), resources)

def attach_phenotype_resources_data(
        cursor, resources: Sequence[Resource]) -> Sequence[Resource]:
    """Attach linked data to Phenotype resources"""
    placeholders = ", ".join(["?"] * len(resources))
    cursor.execute(
        "SELECT * FROM phenotype_resources AS pr "
        "INNER JOIN linked_phenotype_data AS lpd "
        "ON pr.data_link_id=lpd.data_link_id "
        f"WHERE pr.resource_id IN ({placeholders})",
        tuple(str(resource.resource_id) for resource in resources))
    return __attach_data__(cursor.fetchall(), resources)

def attach_resources_data(
        conn: db.DbConnection, resources: Sequence[Resource]) -> Sequence[
            Resource]:
    """Attach linked data for each resource in `resources`"""
    resource_data_function = {
        "mrna": attach_mrna_resources_data,
        "genotype": attach_genotype_resources_data,
        "phenotype": attach_phenotype_resources_data
    }
    organised = organise_resources_by_category(resources)
    with db.cursor(conn) as cursor:
        return tuple(
            resource for categories in
            (resource_data_function[category.resource_category_key](
                cursor, rscs)
             for category, rscs in organised.items())
            for resource in categories)

@authorised_p(
    ("group:user:assign-role",),
    "You cannot assign roles to users for this group.",
    oauth2_scope="profile group role resource")
def assign_resource_user(
        conn: db.DbConnection, resource: Resource, user: User,
        role: GroupRole) -> dict:
    """Assign `role` to `user` for the specific `resource`."""
    with db.cursor(conn) as cursor:
        cursor.execute(
            "INSERT INTO "
            "group_user_roles_on_resources(group_id, user_id, role_id, "
            "resource_id) "
            "VALUES (?, ?, ?, ?) "
            "ON CONFLICT (group_id, user_id, role_id, resource_id) "
            "DO NOTHING",
            (str(resource.group.group_id), str(user.user_id),
             str(role.role.role_id), str(resource.resource_id)))
        return {
            "resource": dictify(resource),
            "user": dictify(user),
            "role": dictify(role),
            "description": (
                f"The user '{user.name}'({user.email}) was assigned the "
                f"'{role.role.role_name}' role on resource with ID "
                f"'{resource.resource_id}'.")}

@authorised_p(
    ("group:user:assign-role",),
    "You cannot assign roles to users for this group.",
    oauth2_scope="profile group role resource")
def unassign_resource_user(
        conn: db.DbConnection, resource: Resource, user: User,
        role: GroupRole) -> dict:
    """Assign `role` to `user` for the specific `resource`."""
    with db.cursor(conn) as cursor:
        cursor.execute(
            "DELETE FROM group_user_roles_on_resources "
            "WHERE group_id=? AND user_id=? AND role_id=? AND resource_id=?",
            (str(resource.group.group_id), str(user.user_id),
             str(role.role.role_id), str(resource.resource_id)))
        return {
            "resource": dictify(resource),
            "user": dictify(user),
            "role": dictify(role),
            "description": (
                f"The user '{user.name}'({user.email}) had the "
                f"'{role.role.role_name}' role on resource with ID "
                f"'{resource.resource_id}' taken away.")}

def save_resource(
        conn: db.DbConnection, user: User, resource: Resource) -> Resource:
    """Update an existing resource."""
    resource_id = resource.resource_id
    authorised = authorised_for(
        conn, user, ("group:resource:edit-resource",), (resource_id,))
    if authorised[resource_id]:
        with db.cursor(conn) as cursor:
            cursor.execute(
                "UPDATE resources SET "
                "resource_name=:resource_name, "
                "public=:public "
                "WHERE group_id=:group_id "
                "AND resource_id=:resource_id",
                {
                    "resource_name": resource.resource_name,
                    "public": 1 if resource.public else 0,
                    "group_id": str(resource.group.group_id),
                    "resource_id": str(resource.resource_id)
                })
            return resource

    raise AuthorisationError(
        "You do not have the appropriate privileges to edit this resource.")