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-rw-r--r--gn_auth/auth/authorisation/resources/models.py2
-rw-r--r--gn_auth/auth/authorisation/resources/phenotype.py68
-rw-r--r--gn_auth/auth/authorisation/resources/phenotypes/__init__.py1
-rw-r--r--gn_auth/auth/authorisation/resources/phenotypes/models.py142
-rw-r--r--gn_auth/auth/authorisation/resources/phenotypes/views.py75
-rw-r--r--gn_auth/auth/authorisation/resources/views.py2
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")