Copy over files from GN3 repository.

1 files changed, 310 insertions, 0 deletions

diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py
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+++ b/gn_auth/auth/authorisation/data/views.py
@@ -0,0 +1,310 @@
+"""Handle data endpoints."""
+import sys
+import uuid
+import json
+from typing import Any
+from functools import partial
+
+import redis
+from MySQLdb.cursors import DictCursor
+from authlib.integrations.flask_oauth2.errors import _HTTPException
+from flask import request, jsonify, Response, Blueprint, current_app as app
+
+import gn3.db_utils as gn3db
+from gn3 import jobs
+from gn3.commands import run_async_cmd
+from gn3.db.traits import build_trait_name
+
+from gn3.auth import db
+from gn3.auth.db_utils import with_db_connection
+
+from gn3.auth.authorisation.checks import require_json
+from gn3.auth.authorisation.errors import InvalidData, NotFoundError
+
+from gn3.auth.authorisation.groups.models import group_by_id
+
+from gn3.auth.authorisation.users.models import user_resource_roles
+
+from gn3.auth.authorisation.resources.checks import authorised_for
+from gn3.auth.authorisation.resources.models import (
+    user_resources, public_resources, attach_resources_data)
+
+from gn3.auth.authentication.users import User
+from gn3.auth.authentication.oauth2.resource_server import require_oauth
+
+from gn3.auth.authorisation.data.phenotypes import link_phenotype_data
+from gn3.auth.authorisation.data.mrna import link_mrna_data, ungrouped_mrna_data
+from gn3.auth.authorisation.data.genotypes import (
+    link_genotype_data, ungrouped_genotype_data)
+
+data = Blueprint("data", __name__)
+
+@data.route("species")
+def list_species() -> Response:
+    """List all available species information."""
+    with (gn3db.database_connection(app.config["SQL_URI"]) as gn3conn,
+          gn3conn.cursor(DictCursor) as cursor):
+        cursor.execute("SELECT * FROM Species")
+        return jsonify(tuple(dict(row) for row in cursor.fetchall()))
+
+@data.route("/authorisation", methods=["POST"])
+@require_json
+def authorisation() -> Response:
+    """Retrive the authorisation level for datasets/traits for the user."""
+    # Access endpoint with something like:
+    # curl -X POST http://127.0.0.1:8080/api/oauth2/data/authorisation \
+    #    -H "Content-Type: application/json" \
+    #    -d '{"traits": ["HC_M2_0606_P::1442370_at", "BXDGeno::01.001.695",
+    #        "BXDPublish::10001"]}'
+    db_uri = app.config["AUTH_DB"]
+    privileges = {}
+    user = User(uuid.uuid4(), "anon@ymous.user", "Anonymous User")
+    with db.connection(db_uri) as auth_conn:
+        try:
+            with require_oauth.acquire("profile group resource") as the_token:
+                user = the_token.user
+                resources = attach_resources_data(
+                    auth_conn, user_resources(auth_conn, the_token.user))
+                resources_roles = user_resource_roles(auth_conn, the_token.user)
+                privileges = {
+                    resource_id: tuple(
+                        privilege.privilege_id
+                        for roles in resources_roles[resource_id]
+                        for privilege in roles.privileges)#("group:resource:view-resource",)
+                    for resource_id, is_authorised
+                    in authorised_for(
+                        auth_conn, the_token.user,
+                        ("group:resource:view-resource",), tuple(
+                            resource.resource_id for resource in resources)).items()
+                    if is_authorised
+                }
+        except _HTTPException as exc:
+            err_msg = json.loads(exc.body)
+            if err_msg["error"] == "missing_authorization":
+                resources = attach_resources_data(
+                    auth_conn, public_resources(auth_conn))
+            else:
+                raise exc from None
+
+        def __gen_key__(resource, data_item):
+            if resource.resource_category.resource_category_key.lower() == "phenotype":
+                return (
+                    f"{resource.resource_category.resource_category_key.lower()}::"
+                    f"{data_item['dataset_name']}::{data_item['PublishXRefId']}")
+            return (
+                f"{resource.resource_category.resource_category_key.lower()}::"
+                f"{data_item['dataset_name']}")
+
+        data_to_resource_map = {
+            __gen_key__(resource, data_item): resource.resource_id
+            for resource in resources
+            for data_item in resource.resource_data
+        }
+        privileges = {
+            **{
+                resource.resource_id: ("system:resource:public-read",)
+                for resource in resources if resource.public
+            },
+            **privileges}
+
+        args = request.get_json()
+        traits_names = args["traits"] # type: ignore[index]
+        def __translate__(val):
+            return {
+                "Temp": "Temp",
+                "ProbeSet": "mRNA",
+                "Geno": "Genotype",
+                "Publish": "Phenotype"
+            }[val]
+
+        def __trait_key__(trait):
+            dataset_type = __translate__(trait['db']['dataset_type']).lower()
+            dataset_name = trait["db"]["dataset_name"]
+            if dataset_type == "phenotype":
+                return f"{dataset_type}::{dataset_name}::{trait['trait_name']}"
+            return f"{dataset_type}::{dataset_name}"
+
+        return jsonify(tuple(
+            {
+                "user": user._asdict(),
+                **{key:trait[key] for key in ("trait_fullname", "trait_name")},
+                "dataset_name": trait["db"]["dataset_name"],
+                "dataset_type": __translate__(trait["db"]["dataset_type"]),
+                "resource_id": data_to_resource_map.get(__trait_key__(trait)),
+                "privileges": privileges.get(
+                    data_to_resource_map.get(
+                        __trait_key__(trait),
+                        uuid.UUID("4afa415e-94cb-4189-b2c6-f9ce2b6a878d")),
+                    tuple()) + (
+                        # Temporary traits do not exist in db: Set them
+                        # as public-read
+                        ("system:resource:public-read",)
+                        if trait["db"]["dataset_type"] == "Temp"
+                        else tuple())
+            } for trait in
+            (build_trait_name(trait_fullname)
+             for trait_fullname in traits_names)))
+
+def __search_mrna__():
+    query = __request_key__("query", "")
+    limit = int(__request_key__("limit", 10000))
+    offset = int(__request_key__("offset", 0))
+    with gn3db.database_connection(app.config["SQL_URI"]) as gn3conn:
+        __ungrouped__ = partial(
+            ungrouped_mrna_data, gn3conn=gn3conn, search_query=query,
+            selected=__request_key_list__("selected"),
+            limit=limit, offset=offset)
+        return jsonify(with_db_connection(__ungrouped__))
+
+def __request_key__(key: str, default: Any = ""):
+    if bool(request.json):
+        return request.json.get(#type: ignore[union-attr]
+            key, request.args.get(key, request.form.get(key, default)))
+    return request.args.get(key, request.form.get(key, default))
+
+def __request_key_list__(key: str, default: tuple[Any, ...] = tuple()):
+    if bool(request.json):
+        return (request.json.get(key,[])#type: ignore[union-attr]
+                or request.args.getlist(key) or request.form.getlist(key)
+                or list(default))
+    return (request.args.getlist(key)
+            or request.form.getlist(key) or list(default))
+
+def __search_genotypes__():
+    query = __request_key__("query", "")
+    limit = int(__request_key__("limit", 10000))
+    offset = int(__request_key__("offset", 0))
+    with gn3db.database_connection(app.config["SQL_URI"]) as gn3conn:
+        __ungrouped__ = partial(
+            ungrouped_genotype_data, gn3conn=gn3conn, search_query=query,
+            selected=__request_key_list__("selected"),
+            limit=limit, offset=offset)
+        return jsonify(with_db_connection(__ungrouped__))
+
+def __search_phenotypes__():
+    # launch the external process to search for phenotypes
+    redisuri = app.config["REDIS_URI"]
+    with redis.Redis.from_url(redisuri, decode_responses=True) as redisconn:
+        job_id = uuid.uuid4()
+        selected = __request_key__("selected_traits", [])
+        command =[
+            sys.executable, "-m", "scripts.search_phenotypes",
+            __request_key__("species_name"),
+            __request_key__("query"),
+            str(job_id),
+            f"--host={__request_key__('gn3_server_uri')}",
+            f"--auth-db-uri={app.config['AUTH_DB']}",
+            f"--gn3-db-uri={app.config['SQL_URI']}",
+            f"--redis-uri={redisuri}",
+            f"--per-page={__request_key__('per_page')}"] +(
+                [f"--selected={json.dumps(selected)}"]
+                if len(selected) > 0 else [])
+        jobs.create_job(redisconn, {
+            "job_id": job_id, "command": command, "status": "queued",
+            "search_results": tuple()})
+        return jsonify({
+            "job_id": job_id,
+            "command_id": run_async_cmd(
+                redisconn, app.config.get("REDIS_JOB_QUEUE"), command),
+            "command": command
+        })
+
+@data.route("/search", methods=["GET"])
+@require_oauth("profile group resource")
+def search_unlinked_data():
+    """Search for various unlinked data."""
+    dataset_type = request.json["dataset_type"]
+    search_fns = {
+        "mrna": __search_mrna__,
+        "genotype": __search_genotypes__,
+        "phenotype": __search_phenotypes__
+    }
+    return search_fns[dataset_type]()
+
+@data.route("/search/phenotype/<uuid:job_id>", methods=["GET"])
+def pheno_search_results(job_id: uuid.UUID) -> Response:
+    """Get the search results from the external script"""
+    def __search_error__(err):
+        raise NotFoundError(err["error_description"])
+    redisuri = app.config["REDIS_URI"]
+    with redis.Redis.from_url(redisuri, decode_responses=True) as redisconn:
+        return jobs.job(redisconn, job_id).either(
+            __search_error__, jsonify)
+
+@data.route("/link/genotype", methods=["POST"])
+def link_genotypes() -> Response:
+    """Link genotype data to group."""
+    def __values__(form) -> dict[str, Any]:
+        if not bool(form.get("species_name", "").strip()):
+            raise InvalidData("Expected 'species_name' not provided.")
+        if not bool(form.get("group_id")):
+            raise InvalidData("Expected 'group_id' not provided.",)
+        try:
+            _group_id = uuid.UUID(form.get("group_id"))
+        except TypeError as terr:
+            raise InvalidData("Expected a UUID for 'group_id' value.") from terr
+        if not bool(form.get("selected")):
+            raise InvalidData("Expected at least one dataset to be provided.")
+        return {
+            "group_id": uuid.UUID(form.get("group_id")),
+            "datasets": form.get("selected")
+        }
+
+    def __link__(conn: db.DbConnection, group_id: uuid.UUID, datasets: dict):
+        return link_genotype_data(conn, group_by_id(conn, group_id), datasets)
+
+    return jsonify(with_db_connection(
+        partial(__link__, **__values__(request.json))))
+
+@data.route("/link/mrna", methods=["POST"])
+def link_mrna() -> Response:
+    """Link mrna data to group."""
+    def __values__(form) -> dict[str, Any]:
+        if not bool(form.get("species_name", "").strip()):
+            raise InvalidData("Expected 'species_name' not provided.")
+        if not bool(form.get("group_id")):
+            raise InvalidData("Expected 'group_id' not provided.",)
+        try:
+            _group_id = uuid.UUID(form.get("group_id"))
+        except TypeError as terr:
+            raise InvalidData("Expected a UUID for 'group_id' value.") from terr
+        if not bool(form.get("selected")):
+            raise InvalidData("Expected at least one dataset to be provided.")
+        return {
+            "group_id": uuid.UUID(form.get("group_id")),
+            "datasets": form.get("selected")
+        }
+
+    def __link__(conn: db.DbConnection, group_id: uuid.UUID, datasets: dict):
+        return link_mrna_data(conn, group_by_id(conn, group_id), datasets)
+
+    return jsonify(with_db_connection(
+        partial(__link__, **__values__(request.json))))
+
+@data.route("/link/phenotype", methods=["POST"])
+def link_phenotype() -> Response:
+    """Link phenotype data to group."""
+    def __values__(form):
+        if not bool(form.get("species_name", "").strip()):
+            raise InvalidData("Expected 'species_name' not provided.")
+        if not bool(form.get("group_id")):
+            raise InvalidData("Expected 'group_id' not provided.",)
+        try:
+            _group_id = uuid.UUID(form.get("group_id"))
+        except TypeError as terr:
+            raise InvalidData("Expected a UUID for 'group_id' value.") from terr
+        if not bool(form.get("selected")):
+            raise InvalidData("Expected at least one dataset to be provided.")
+        return {
+            "group_id": uuid.UUID(form["group_id"]),
+            "traits": form["selected"]
+        }
+
+    with gn3db.database_connection(app.config["SQL_URI"]) as gn3conn:
+        def __link__(conn: db.DbConnection, group_id: uuid.UUID,
+                     traits: tuple[dict, ...]) -> dict:
+            return link_phenotype_data(
+                conn, gn3conn, group_by_id(conn, group_id), traits)
+
+        return jsonify(with_db_connection(
+            partial(__link__, **__values__(request.json))))