diff options
Diffstat (limited to 'gn_auth/auth')
| -rw-r--r-- | gn_auth/auth/authorisation/resources/inbredset/models.py | 96 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/inbredset/views.py | 82 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/models.py | 54 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/views.py | 16 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/users/collections/views.py | 1 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/users/views.py | 4 | ||||
| -rw-r--r-- | gn_auth/auth/views.py | 2 |
7 files changed, 221 insertions, 34 deletions
diff --git a/gn_auth/auth/authorisation/resources/inbredset/models.py b/gn_auth/auth/authorisation/resources/inbredset/models.py new file mode 100644 index 0000000..de1c18a --- /dev/null +++ b/gn_auth/auth/authorisation/resources/inbredset/models.py @@ -0,0 +1,96 @@ +"""Functions to handle the low-level details regarding populations auth.""" +from uuid import UUID, uuid4 + +import sqlite3 + +from gn_auth.auth.errors import NotFoundError +from gn_auth.auth.authentication.users import User +from gn_auth.auth.authorisation.resources.groups.models import Group +from gn_auth.auth.authorisation.resources.base import Resource, ResourceCategory +from gn_auth.auth.authorisation.resources.models import ( + create_resource as _create_resource) + +def create_resource( + cursor: sqlite3.Cursor, + resource_name: str, + user: User, + group: Group, + public: bool +) -> Resource: + """Convenience function to create a resource of type 'inbredset-group'.""" + cursor.execute("SELECT * FROM resource_categories " + "WHERE resource_category_key='inbredset-group'") + category = cursor.fetchone() + if category: + return _create_resource(cursor, + resource_name, + ResourceCategory( + resource_category_id=UUID( + category["resource_category_id"]), + resource_category_key="inbredset-group", + resource_category_description=category[ + "resource_category_description"]), + user, + group, + public) + raise NotFoundError("Could not find a 'inbredset-group' resource category.") + + +def assign_inbredset_group_owner_role( + cursor: sqlite3.Cursor, + resource: Resource, + user: User +) -> Resource: + """ + Assign `user` as `InbredSet Group Owner` is resource category is + 'inbredset-group'. + """ + if resource.resource_category.resource_category_key == "inbredset-group": + cursor.execute( + "SELECT * FROM roles WHERE role_name='inbredset-group-owner'") + role = cursor.fetchone() + cursor.execute( + "INSERT INTO user_roles " + "VALUES(:user_id, :role_id, :resource_id) " + "ON CONFLICT (user_id, role_id, resource_id) DO NOTHING", + { + "user_id": str(user.user_id), + "role_id": str(role["role_id"]), + "resource_id": str(resource.resource_id) + }) + + return resource + + +def link_data_to_resource(# pylint: disable=[too-many-arguments] + cursor: sqlite3.Cursor, + resource_id: UUID, + species_id: int, + population_id: int, + population_name: str, + population_fullname: str +) -> dict: + """Link a species population to a resource for auth purposes.""" + params = { + "resource_id": str(resource_id), + "data_link_id": str(uuid4()), + "species_id": species_id, + "population_id": population_id, + "population_name": population_name, + "population_fullname": population_fullname + } + cursor.execute( + "INSERT INTO linked_inbredset_groups " + "VALUES(" + " :data_link_id," + " :species_id," + " :population_id," + " :population_name," + " :population_fullname" + ")", + params) + cursor.execute( + "INSERT INTO inbredset_group_resources " + "VALUES (:resource_id, :data_link_id)", + params) + return params diff --git a/gn_auth/auth/authorisation/resources/inbredset/views.py b/gn_auth/auth/authorisation/resources/inbredset/views.py index 444c442..b559105 100644 --- a/gn_auth/auth/authorisation/resources/inbredset/views.py +++ b/gn_auth/auth/authorisation/resources/inbredset/views.py @@ -1,12 +1,22 @@ """Views for InbredSet resources.""" -from flask import jsonify, Response, Blueprint +from pymonad.either import Left, Right, Either +from flask import jsonify, Response, Blueprint, current_app as app + from gn_auth.auth.db import sqlite3 as db +from gn_auth.auth.requests import request_json from gn_auth.auth.db.sqlite3 import with_db_connection +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth +from gn_auth.auth.authorisation.resources.groups.models import user_group + +from .models import (create_resource, + link_data_to_resource, + assign_inbredset_group_owner_role) -iset = Blueprint("inbredset", __name__) +popbp = Blueprint("populations", __name__) -@iset.route("/resource-id/<int:speciesid>/<int:inbredsetid>") +@popbp.route("/populations/resource-id/<int:speciesid>/<int:inbredsetid>", + methods=["GET"]) def resource_id_by_inbredset_id(speciesid: int, inbredsetid: int) -> Response: """Retrieve the resource ID for resource attached to the inbredset.""" def __res_by_iset_id__(conn): @@ -34,3 +44,69 @@ def resource_id_by_inbredset_id(speciesid: int, inbredsetid: int) -> Response: resp.status_code = 404 return resp + + +@popbp.route("/populations/create", methods=["POST"]) +@require_oauth("profile group resource") +def create_population_resource(): + """Create a resource of type 'inbredset-group'.""" + with (require_oauth.acquire("profile group resource") as _token, + db.connection(app.config["AUTH_DB"]) as conn, + db.cursor(conn) as cursor): + + def __check_form__(form, usergroup) -> Either: + """Check form for errors.""" + errors: tuple[str, ...] = tuple() + + species_id = form.get("species_id") + if not bool(species_id): + errors = errors + ("Missing `species_id` value.",) + + population_id = form.get("population_id") + if not bool(population_id): + errors = errors + ("Missing `population_id` value.",) + + population_name = form.get("population_name") + if not bool(population_name): + errors = errors + ("Missing `population_name` value.",) + + population_fullname = form.get("population_fullname") + if not bool(population_fullname): + errors = errors + ("Missing `population_fullname` value.",) + + if bool(errors): + error_messages = "\n\t - ".join(errors) + return Left({ + "error": "Invalid Request Data!", + "error_description": error_messages + }) + + return Right({"formdata": form, "group": usergroup}) + + return user_group(conn, _token.user).then( + lambda group: __check_form__(request_json(), group) + ).then( + lambda formdata: { + **formdata, + "resource": create_resource( + cursor, + f"Population — {formdata['formdata']['population_name']}", + _token.user, + formdata["group"], + formdata["formdata"].get("public", "on") == "on")} + ).then( + lambda resource: { + **resource, + "resource": assign_inbredset_group_owner_role( + cursor, resource["resource"], _token.user)} + ).then( + lambda resource: link_data_to_resource( + cursor, + resource["resource"].resource_id, + resource["formdata"]["species_id"], + resource["formdata"]["population_id"], + resource["formdata"]["population_name"], + resource["formdata"]["population_fullname"]) + ).either( + lambda error: (jsonify(error), 400), + jsonify) diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py index c7c8352..fa7797b 100644 --- a/gn_auth/auth/authorisation/resources/models.py +++ b/gn_auth/auth/authorisation/resources/models.py @@ -17,7 +17,7 @@ from gn_auth.auth.errors import NotFoundError, AuthorisationError from .checks import authorised_for from .base import Resource, ResourceCategory -from .groups.models import Group, user_group, is_group_leader +from .groups.models import Group, is_group_leader from .mrna import ( resource_data as mrna_resource_data, attach_resources_data as mrna_attach_resources_data, @@ -34,8 +34,6 @@ from .phenotype import ( link_data_to_resource as phenotype_link_data_to_resource, unlink_data_from_resource as phenotype_unlink_data_from_resource) -from .errors import MissingGroupError - def __assign_resource_owner_role__(cursor, resource, user): """Assign `user` the 'Resource Owner' role for `resource`.""" cursor.execute("SELECT * FROM roles WHERE role_name='resource-owner'") @@ -66,28 +64,36 @@ def resource_from_dbrow(row: sqlite3.Row): @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: +def create_resource(# pylint: disable=[too-many-arguments] + cursor: sqlite3.Cursor, + resource_name: str, + resource_category: ResourceCategory, + user: User, + group: Group, + 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(# Not all resources require an owner group - "User with no group cannot create a resource.") - resource = Resource(uuid4(), resource_name, resource_category, public) - cursor.execute( - "INSERT INTO resources VALUES (?, ?, ?, ?)", - (str(resource.resource_id), - resource_name, - str(resource.resource_category.resource_category_id), - 1 if resource.public else 0)) - cursor.execute("INSERT INTO resource_ownership (group_id, resource_id) " - "VALUES (?, ?)", - (str(group.group_id), str(resource.resource_id))) - __assign_resource_owner_role__(cursor, resource, user) + resource = Resource(uuid4(), resource_name, resource_category, public) + cursor.execute( + "INSERT INTO resources VALUES (?, ?, ?, ?)", + (str(resource.resource_id), + resource_name, + str(resource.resource_category.resource_category_id), + 1 if resource.public else 0)) + # TODO: @fredmanglis,@rookie101 + # 1. Move the actions below into a (the?) hooks system + # 2. Do more checks: A resource can have varying hooks depending on type + # e.g. if mRNA, pheno or geno resource, assign: + # - "resource-owner" + # if inbredset-group, assign: + # - "resource-owner", + # - "inbredset-group-owner" etc. + # if resource is of type "group", assign: + # - group-leader + cursor.execute("INSERT INTO resource_ownership (group_id, resource_id) " + "VALUES (?, ?)", + (str(group.group_id), str(resource.resource_id))) + __assign_resource_owner_role__(cursor, resource, user) return resource diff --git a/gn_auth/auth/authorisation/resources/views.py b/gn_auth/auth/authorisation/resources/views.py index 494fde9..3f972f6 100644 --- a/gn_auth/auth/authorisation/resources/views.py +++ b/gn_auth/auth/authorisation/resources/views.py @@ -40,15 +40,18 @@ from gn_auth.auth.authentication.oauth2.resource_server import require_oauth from gn_auth.auth.authentication.users import User, user_by_id, user_by_email from .checks import authorised_for +from .inbredset.views import popbp +from .errors import MissingGroupError +from .groups.models import Group, user_group from .models import ( Resource, resource_data, resource_by_id, public_resources, resource_categories, assign_resource_user, link_data_to_resource, unassign_resource_user, resource_category_by_id, user_roles_on_resources, unlink_data_from_resource, create_resource as _create_resource, get_resource_id) -from .groups.models import Group resources = Blueprint("resources", __name__) +resources.register_blueprint(popbp, url_prefix="/") @resources.route("/categories", methods=["GET"]) @require_oauth("profile group resource") @@ -68,13 +71,20 @@ def create_resource() -> Response: resource_name = form.get("resource_name") resource_category_id = UUID(form.get("resource_category")) db_uri = app.config["AUTH_DB"] - with db.connection(db_uri) as conn: + with (db.connection(db_uri) as conn, + db.cursor(conn) as cursor): try: + group = user_group(conn, the_token.user).maybe( + False, lambda grp: grp)# type: ignore[misc, arg-type] + if not group: + raise MissingGroupError(# Not all resources require an owner group + "User with no group cannot create a resource.") resource = _create_resource( - conn, + cursor, resource_name, resource_category_by_id(conn, resource_category_id), the_token.user, + group, (form.get("public") == "on")) return jsonify(asdict(resource)) except sqlite3.IntegrityError as sql3ie: diff --git a/gn_auth/auth/authorisation/users/collections/views.py b/gn_auth/auth/authorisation/users/collections/views.py index eeae91d..f619c3d 100644 --- a/gn_auth/auth/authorisation/users/collections/views.py +++ b/gn_auth/auth/authorisation/users/collections/views.py @@ -113,6 +113,7 @@ def import_anonymous() -> Response: anon_id = UUID(request.json.get("anon_id"))#type: ignore[union-attr] anon_colls = user_collections(redisconn, User( anon_id, "anon@ymous.user", "Anonymous User")) + anon_colls = tuple(coll for coll in anon_colls if coll['num_members'] > 0) save_collections( redisconn, token.user, diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py index 2a6ff29..7adcd06 100644 --- a/gn_auth/auth/authorisation/users/views.py +++ b/gn_auth/auth/authorisation/users/views.py @@ -152,8 +152,8 @@ def send_verification_email( timedelta( minutes=expiration_minutes)).timestamp()) }) - send_message(smtp_user=current_app.config["SMTP_USER"], - smtp_passwd=current_app.config["SMTP_PASSWORD"], + send_message(smtp_user=current_app.config.get("SMTP_USER", ""), + smtp_passwd=current_app.config.get("SMTP_PASSWORD", ""), message=build_email_message( from_address=current_app.config["EMAIL_ADDRESS"], to_addresses=(user_address(user),), diff --git a/gn_auth/auth/views.py b/gn_auth/auth/views.py index 17fc94b..6867f38 100644 --- a/gn_auth/auth/views.py +++ b/gn_auth/auth/views.py @@ -11,7 +11,6 @@ from .authorisation.resources.views import resources from .authorisation.privileges.views import privileges from .authorisation.resources.groups.views import groups from .authorisation.resources.system.views import system -from .authorisation.resources.inbredset.views import iset oauth2 = Blueprint("oauth2", __name__) @@ -24,4 +23,3 @@ oauth2.register_blueprint(groups, url_prefix="/group") oauth2.register_blueprint(system, url_prefix="/system") oauth2.register_blueprint(resources, url_prefix="/resource") oauth2.register_blueprint(privileges, url_prefix="/privileges") -oauth2.register_blueprint(iset, url_prefix="/resource/inbredset") |