diff options
Diffstat (limited to 'gn_auth')
6 files changed, 221 insertions, 69 deletions
diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py index d3df6dc..8d3cfc3 100644 --- a/gn_auth/auth/authorisation/resources/models.py +++ b/gn_auth/auth/authorisation/resources/models.py @@ -29,7 +29,7 @@ from .genotypes.models import ( attach_resources_data as genotype_attach_resources_data, link_data_to_resource as genotype_link_data_to_resource, unlink_data_from_resource as genotype_unlink_data_from_resource) -from .phenotype import ( +from .phenotypes.models import ( resource_data as phenotype_resource_data, attach_resources_data as phenotype_attach_resources_data, link_data_to_resource as phenotype_link_data_to_resource, diff --git a/gn_auth/auth/authorisation/resources/phenotype.py b/gn_auth/auth/authorisation/resources/phenotype.py deleted file mode 100644 index 7005db3..0000000 --- a/gn_auth/auth/authorisation/resources/phenotype.py +++ /dev/null @@ -1,68 +0,0 @@ -"""Phenotype data resources functions and utilities.""" -import uuid -from typing import Optional, Sequence - -import sqlite3 - -import gn_auth.auth.db.sqlite3 as db - -from .base import Resource -from .data import __attach_data__ - -def resource_data( - cursor: db.DbCursor, - resource_id: uuid.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 link_data_to_resource( - conn: db.DbConnection, - resource: Resource, - data_link_id: uuid.UUID) -> dict: - """Link Phenotype data with a resource.""" - with db.cursor(conn) as cursor: - params = { - "resource_id": str(resource.resource_id), - "data_link_id": str(data_link_id) - } - cursor.execute( - "INSERT INTO phenotype_resources VALUES" - "(:resource_id, :data_link_id)", - params) - return params - -def unlink_data_from_resource( - conn: db.DbConnection, - resource: Resource, - data_link_id: uuid.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 attach_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) diff --git a/gn_auth/auth/authorisation/resources/phenotypes/__init__.py b/gn_auth/auth/authorisation/resources/phenotypes/__init__.py new file mode 100644 index 0000000..0d4dbfa --- /dev/null +++ b/gn_auth/auth/authorisation/resources/phenotypes/__init__.py @@ -0,0 +1 @@ +"""The phenotypes package.""" diff --git a/gn_auth/auth/authorisation/resources/phenotypes/models.py b/gn_auth/auth/authorisation/resources/phenotypes/models.py new file mode 100644 index 0000000..d4a516a --- /dev/null +++ b/gn_auth/auth/authorisation/resources/phenotypes/models.py @@ -0,0 +1,142 @@ +"""Phenotype data resources functions and utilities.""" +import uuid +from functools import reduce +from typing import Optional, Sequence + +import sqlite3 +from pymonad.maybe import Just, Maybe, Nothing +from pymonad.tools import monad_from_none_or_value + +import gn_auth.auth.db.sqlite3 as db +from gn_auth.auth.authorisation.resources.data import __attach_data__ +from gn_auth.auth.authorisation.resources.base import Resource, resource_from_dbrow + +def resource_data( + cursor: db.DbCursor, + resource_id: uuid.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 link_data_to_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.UUID) -> dict: + """Link Phenotype data with a resource.""" + with db.cursor(conn) as cursor: + params = { + "resource_id": str(resource.resource_id), + "data_link_id": str(data_link_id) + } + cursor.execute( + "INSERT INTO phenotype_resources VALUES" + "(:resource_id, :data_link_id)", + params) + return params + +def unlink_data_from_resource( + conn: db.DbConnection, + resource: Resource, + data_link_id: uuid.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 attach_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 individual_linked_resource( + conn: db.DbConnection, + species_id: int, + population_id: int, + dataset_id: int, + xref_id: str) -> Maybe: + """Given the data details, return the linked resource, if one is defined.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT " + "rsc.*, rc.*, lpd.SpeciesId AS species_id, " + "lpd.InbredSetId AS population_id, lpd.PublishXRefId AS xref_id, " + "lpd.dataset_name, lpd.dataset_fullname, lpd.dataset_shortname " + "FROM linked_phenotype_data AS lpd " + "INNER JOIN phenotype_resources AS pr " + "ON lpd.data_link_id=pr.data_link_id " + "INNER JOIN resources AS rsc ON pr.resource_id=rsc.resource_id " + "INNER JOIN resource_categories AS rc " + "ON rsc.resource_category_id=rc.resource_category_id " + "WHERE " + "(lpd.SpeciesId, lpd.InbredSetId, lpd.PublishFreezeId, lpd.PublishXRefId) = " + "(?, ?, ?, ?)", + (species_id, population_id, dataset_id, xref_id)) + return monad_from_none_or_value( + Nothing, Just, cursor.fetchone()).then(resource_from_dbrow) + + +def all_linked_resources( + conn: db.DbConnection, + species_id: int, + population_id: int, + dataset_id: int) -> Maybe: + """Given the data details, return the linked resource, if one is defined.""" + with db.cursor(conn) as cursor: + cursor.execute( + "SELECT rsc.*, rc.resource_category_key, " + "rc.resource_category_description, lpd.SpeciesId AS species_id, " + "lpd.InbredSetId AS population_id, lpd.PublishXRefId AS xref_id, " + "lpd.dataset_name, lpd.dataset_fullname, lpd.dataset_shortname " + "FROM linked_phenotype_data AS lpd " + "INNER JOIN phenotype_resources AS pr " + "ON lpd.data_link_id=pr.data_link_id INNER JOIN resources AS rsc " + "ON pr.resource_id=rsc.resource_id " + "INNER JOIN resource_categories AS rc " + "ON rsc.resource_category_id=rc.resource_category_id " + "WHERE " + "(lpd.SpeciesId, lpd.InbredSetId, lpd.PublishFreezeId) = (?, ?, ?)", + (species_id, population_id, dataset_id)) + + _rscdatakeys = ( + "species_id", "population_id", "xref_id", "dataset_name", + "dataset_fullname", "dataset_shortname") + def __organise__(resources, row): + _rscid = uuid.UUID(row["resource_id"]) + _resource = resources.get(_rscid, resource_from_dbrow(row)) + return { + **resources, + _rscid: Resource( + _resource.resource_id, + _resource.resource_name, + _resource.resource_category, + _resource.public, + _resource.resource_data + ( + {key: row[key] for key in _rscdatakeys},)) + } + results: dict[uuid.UUID, Resource] = reduce( + __organise__, cursor.fetchall(), {}) + if len(results) == 0: + return Nothing + return Just(tuple(results.values())) diff --git a/gn_auth/auth/authorisation/resources/phenotypes/views.py b/gn_auth/auth/authorisation/resources/phenotypes/views.py new file mode 100644 index 0000000..a971d2b --- /dev/null +++ b/gn_auth/auth/authorisation/resources/phenotypes/views.py @@ -0,0 +1,75 @@ +"""Views for the phenotype resources.""" +from pymonad.either import Left, Right +from flask import jsonify, 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.authorisation.resources.request_utils import check_form +from gn_auth.auth.authorisation.roles.models import user_roles_on_resource + +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth + +from .models import all_linked_resources, individual_linked_resource + +phenobp = Blueprint("phenotypes", __name__) + +@phenobp.route("/phenotypes/individual/linked-resource", methods=["POST"]) +def get_individual_linked_resource(): + """Get the linked resource for a particular phenotype within the dataset. + + Phenotypes are a tad tricky. Each phenotype could technically be a resource + on its own, and thus a user could have access to only a subset of phenotypes + within the entire dataset.""" + with (require_oauth.acquire("profile group resource") as _token, + db.connection(app.config["AUTH_DB"]) as conn): + return check_form( + request_json(), + "species_id", + "population_id", + "dataset_id", + "xref_id" + ).then( + lambda formdata: individual_linked_resource( + conn, + int(formdata["species_id"]), + int(formdata["population_id"]), + int(formdata["dataset_id"]), + formdata["xref_id"] + ).maybe(Left("No linked resource!"), + lambda lrsc: Right({ + "formdata": formdata, + "resource": lrsc + })) + ).then( + lambda fdlrsc: { + **fdlrsc, + "roles": user_roles_on_resource( + conn, _token.user.user_id, fdlrsc["resource"].resource_id) + } + ).either(lambda error: (jsonify(error), 400), + lambda res: jsonify({ + key: value for key, value in res.items() + if key != "formdata" + })) + + +@phenobp.route("/phenotypes/linked-resources", methods=["POST"]) +def get_all_linked_resources(): + """Get all the linked resources for all phenotypes within a dataset. + + See `get_individual_linked_resource(…)` documentation.""" + with (require_oauth.acquire("profile group resource") as _token, + db.connection(app.config["AUTH_DB"]) as conn): + return check_form( + request_json(), + "species_id", + "population_id", + "dataset_id" + ).then( + lambda formdata: all_linked_resources( + conn, + int(formdata["species_id"]), + int(formdata["population_id"]), + int(formdata["dataset_id"])).maybe( + Left("No linked resource!"), Right) + ).either(lambda error: (jsonify(error), 400), jsonify) diff --git a/gn_auth/auth/authorisation/resources/views.py b/gn_auth/auth/authorisation/resources/views.py index 31421f4..3d590a3 100644 --- a/gn_auth/auth/authorisation/resources/views.py +++ b/gn_auth/auth/authorisation/resources/views.py @@ -42,6 +42,7 @@ 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 .genotypes.views import genobp +from .phenotypes.views import phenobp from .errors import MissingGroupError from .groups.models import Group, user_group from .models import ( @@ -54,6 +55,7 @@ from .models import ( resources = Blueprint("resources", __name__) resources.register_blueprint(popbp, url_prefix="/") resources.register_blueprint(genobp, url_prefix="/") +resources.register_blueprint(phenobp, url_prefix="/") @resources.route("/categories", methods=["GET"]) @require_oauth("profile group resource") |