From 7fd2a24e72316cc75e954eeb11074d0faf09eee3 Mon Sep 17 00:00:00 2001 From: Victor Rocheleau Date: Mon, 16 Sep 2024 20:56:05 +0000 Subject: [PATCH 01/35] chore: init action to publish json schemas as release artifacts --- .github/workflows/build.yml | 13 +++++++++ .../chord/management/commands/schemas.py | 27 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 chord_metadata_service/chord/management/commands/schemas.py diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index b2c9bf1ae..4915471ef 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -33,3 +33,16 @@ jobs: image-name: ghcr.io/bento-platform/katsu development-dockerfile: bento.dev.Dockerfile dockerfile: bento.Dockerfile + + # TODO: test, maybe just add to a protected build directory? + - name: Make release artifacts + run: | + ./manage.py schema phenopacket >> ./dist/schemas/phenopacket_schema.json + ./manage.py schema experiment >> ./dist/schemas/experiment_schema.json + ./manage.py schema discovery >> ./dist/schemas/discovery.json + + - name: Upload release artifacts + uses: actions/upload-artifact@v4 + with: + name: JSON-schemas + path: ./dist/schemas diff --git a/chord_metadata_service/chord/management/commands/schemas.py b/chord_metadata_service/chord/management/commands/schemas.py new file mode 100644 index 000000000..9914987dd --- /dev/null +++ b/chord_metadata_service/chord/management/commands/schemas.py @@ -0,0 +1,27 @@ +import json +from typing import Any +from django.core.management.base import BaseCommand, CommandParser + +from chord_metadata_service.chord.data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_PHENOPACKET +from chord_metadata_service.discovery.schemas import DISCOVERY_SCHEMA +from chord_metadata_service.experiments.schemas import EXPERIMENT_SCHEMA +from chord_metadata_service.phenopackets.schemas import PHENOPACKET_SCHEMA + +NAME_TO_SCHEMA: dict[str, object] = { + DATA_TYPE_PHENOPACKET: PHENOPACKET_SCHEMA, + DATA_TYPE_EXPERIMENT: EXPERIMENT_SCHEMA, + "discovery": DISCOVERY_SCHEMA, +} + +class Command(BaseCommand): + help = """ + Compiles and returns a JSON-schema in a single JSON file for artifact. + Use in GitHub Actions in order to publish usable schemas on releases. + """ + + def add_arguments(self, parser: CommandParser) -> None: + parser.add_argument("schema", action="store", type=str, choices=NAME_TO_SCHEMA.keys()) + + def handle(self, *args: Any, **options: Any) -> str | None: + schema = NAME_TO_SCHEMA[options["schema"]] + self.stdout.write(json.dumps(schema)) From 3ecf74aab68bcb8ca4af04f34896bd88e49e6b57 Mon Sep 17 00:00:00 2001 From: Victor Rocheleau Date: Mon, 16 Sep 2024 21:03:09 +0000 Subject: [PATCH 02/35] lint --- .../chord/management/commands/schemas.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/chord_metadata_service/chord/management/commands/schemas.py b/chord_metadata_service/chord/management/commands/schemas.py index 9914987dd..8a13c5a08 100644 --- a/chord_metadata_service/chord/management/commands/schemas.py +++ b/chord_metadata_service/chord/management/commands/schemas.py @@ -13,15 +13,16 @@ "discovery": DISCOVERY_SCHEMA, } + class Command(BaseCommand): - help = """ - Compiles and returns a JSON-schema in a single JSON file for artifact. - Use in GitHub Actions in order to publish usable schemas on releases. - """ + help = """ + Compiles and returns a JSON-schema in a single JSON file for artifact. + Use in GitHub Actions in order to publish usable schemas on releases. + """ - def add_arguments(self, parser: CommandParser) -> None: - parser.add_argument("schema", action="store", type=str, choices=NAME_TO_SCHEMA.keys()) + def add_arguments(self, parser: CommandParser) -> None: + parser.add_argument("schema", action="store", type=str, choices=NAME_TO_SCHEMA.keys()) - def handle(self, *args: Any, **options: Any) -> str | None: - schema = NAME_TO_SCHEMA[options["schema"]] - self.stdout.write(json.dumps(schema)) + def handle(self, *args: Any, **options: Any) -> str | None: + schema = NAME_TO_SCHEMA[options["schema"]] + self.stdout.write(json.dumps(schema)) From a40ebdca19bfee4aa0e43f063ec059e8d9087dd1 Mon Sep 17 00:00:00 2001 From: Victor Rocheleau Date: Mon, 16 Sep 2024 21:04:19 +0000 Subject: [PATCH 03/35] init artifact dir --- .github/workflows/build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 4915471ef..bd9b7f9f3 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -37,6 +37,7 @@ jobs: # TODO: test, maybe just add to a protected build directory? - name: Make release artifacts run: | + mkdir -p ./dist/schemas ./manage.py schema phenopacket >> ./dist/schemas/phenopacket_schema.json ./manage.py schema experiment >> ./dist/schemas/experiment_schema.json ./manage.py schema discovery >> ./dist/schemas/discovery.json From 93eb6b6ebdde61de9bcde7eb355cebfa79ea1a57 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 17 Sep 2024 11:23:48 -0400 Subject: [PATCH 04/35] chore!: remove Django admin interface (was debug only) This isn't used and provides a potential security hole, and probably will not play nice with the Bento authorization scheme. --- chord_metadata_service/chord/admin.py | 13 ------ chord_metadata_service/metadata/urls.py | 20 ---------- chord_metadata_service/patients/admin.py | 9 ----- chord_metadata_service/phenopackets/admin.py | 42 -------------------- chord_metadata_service/resources/admin.py | 8 ---- 5 files changed, 92 deletions(-) delete mode 100644 chord_metadata_service/chord/admin.py delete mode 100644 chord_metadata_service/patients/admin.py delete mode 100644 chord_metadata_service/phenopackets/admin.py delete mode 100644 chord_metadata_service/resources/admin.py diff --git a/chord_metadata_service/chord/admin.py b/chord_metadata_service/chord/admin.py deleted file mode 100644 index 6a8df2f35..000000000 --- a/chord_metadata_service/chord/admin.py +++ /dev/null @@ -1,13 +0,0 @@ -from django.contrib import admin - -from .models import Project, Dataset - - -@admin.register(Project) -class ProjectAdmin(admin.ModelAdmin): - pass - - -@admin.register(Dataset) -class DatasetAdmin(admin.ModelAdmin): - pass diff --git a/chord_metadata_service/metadata/urls.py b/chord_metadata_service/metadata/urls.py index 0787c91b2..623660635 100644 --- a/chord_metadata_service/metadata/urls.py +++ b/chord_metadata_service/metadata/urls.py @@ -1,32 +1,12 @@ -"""metadata URL Configuration - -The `urlpatterns` list routes URLs to views. For more information please see: - https://docs.djangoproject.com/en/2.2/topics/http/urls/ -Examples: -Function views - 1. Add an import: from my_app import views - 2. Add a URL to urlpatterns: path('', views.home, name='home') -Class-based views - 1. Add an import: from other_app.views import Home - 2. Add a URL to urlpatterns: path('', Home.as_view(), name='home') -Including another URLconf - 1. Import the include() function: from django.urls import include, path - 2. Add a URL to urlpatterns: path('blog/', include('blog.urls')) -""" -from django.contrib import admin from django.urls import path, include from chord_metadata_service.restapi import api_views, urls as restapi_urls from chord_metadata_service.chord import urls as chord_urls from drf_spectacular.views import SpectacularAPIView, SpectacularSwaggerView -# TODO: django.conf.settings breaks reverse(), how to import properly? -from .settings import DEBUG - urlpatterns = [ path('api/', include(restapi_urls)), path('service-info', api_views.service_info, name="service-info"), *chord_urls.urlpatterns, # TODO: Use include? can we double up? - *([path('admin/', admin.site.urls)] if DEBUG else []), # OpenAPI 3 documentation with Swagger UI path('schema/', SpectacularAPIView.as_view(), name="schema"), path('', SpectacularSwaggerView.as_view(), name="swagger-ui"), diff --git a/chord_metadata_service/patients/admin.py b/chord_metadata_service/patients/admin.py deleted file mode 100644 index f11157807..000000000 --- a/chord_metadata_service/patients/admin.py +++ /dev/null @@ -1,9 +0,0 @@ -from django.contrib import admin -from .models import Individual - -# TODO: This should not be available outside of development mode. - - -@admin.register(Individual) -class IndividualAdmin(admin.ModelAdmin): - pass diff --git a/chord_metadata_service/phenopackets/admin.py b/chord_metadata_service/phenopackets/admin.py deleted file mode 100644 index 211576f7f..000000000 --- a/chord_metadata_service/phenopackets/admin.py +++ /dev/null @@ -1,42 +0,0 @@ -from django.contrib import admin -from . import models as m - - -@admin.register(m.MetaData) -class MetaDataAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.PhenotypicFeature) -class PhenotypicFeatureAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.Disease) -class DiseaseAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.Biosample) -class BiosampleAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.Phenopacket) -class PhenopacketAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.GenomicInterpretation) -class GenomicInterpretationAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.Diagnosis) -class DiagnosisAdmin(admin.ModelAdmin): - pass - - -@admin.register(m.Interpretation) -class InterpretationAdmin(admin.ModelAdmin): - pass diff --git a/chord_metadata_service/resources/admin.py b/chord_metadata_service/resources/admin.py deleted file mode 100644 index a646858bd..000000000 --- a/chord_metadata_service/resources/admin.py +++ /dev/null @@ -1,8 +0,0 @@ -from django.contrib import admin - -from .models import Resource - - -@admin.register(Resource) -class ResourceAdmin(admin.ModelAdmin): - pass From fe02f362e9c005d74d71842ddc9f3972e973bd2a Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 13:39:47 -0400 Subject: [PATCH 05/35] chore: release gh actions workflow test --- .github/workflows/build.yml | 14 --------- .github/workflows/release.yml | 59 +++++++++++++++++++++++++++++++++++ 2 files changed, 59 insertions(+), 14 deletions(-) create mode 100644 .github/workflows/release.yml diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index bd9b7f9f3..b2c9bf1ae 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -33,17 +33,3 @@ jobs: image-name: ghcr.io/bento-platform/katsu development-dockerfile: bento.dev.Dockerfile dockerfile: bento.Dockerfile - - # TODO: test, maybe just add to a protected build directory? - - name: Make release artifacts - run: | - mkdir -p ./dist/schemas - ./manage.py schema phenopacket >> ./dist/schemas/phenopacket_schema.json - ./manage.py schema experiment >> ./dist/schemas/experiment_schema.json - ./manage.py schema discovery >> ./dist/schemas/discovery.json - - - name: Upload release artifacts - uses: actions/upload-artifact@v4 - with: - name: JSON-schemas - path: ./dist/schemas diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 000000000..d15d0f1f6 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,59 @@ +name: Create and upload release artifacts +on: + release: + types: [published, prereleased] + # temporary PR trigger for test + pull_request: + branches: + - develop + - 'features/**' + +jobs: + release-artifacts: + runs-on: ubuntu-latest + + permissions: + contents: read + + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + submodules: true + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install Poetry + run: python -m pip install poetry + - name: Install dependencies + run: poetry install + - name: Make release artifacts + run: | + mkdir -p ./dist/schemas + ./manage.py schema phenopacket >> ./dist/schemas/phenopacket_schema.json + ./manage.py schema experiment >> ./dist/schemas/experiment_schema.json + ./manage.py schema discovery >> ./dist/schemas/discovery.json + - name: Upload release artifacts + uses: actions/github-scripts@v7 + with: + script: | + const fs = require(fs); + + # temporary hardcoding for test + const tag = "v8.0.2-test" + # const tag = context.ref.replace("refs/tags/", ""); + console.log("tag = ", tag); + + const release = await github.rest.repos.getReleaseByTag({ + owner: context.repo.owner, + repo: context.repo.repo, + tag + }); + await github.rest.repos.uploadReleaseAsset({ + owner: context.repo.owner, + repo: context.repo.repo, + release_id: release.data.id, + name: "JSON Schemas", + data: await fs.readdirSync("./dist/schemas") + }); From cebe42784a888d6dc3adad353db8801600a46147 Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 13:41:19 -0400 Subject: [PATCH 06/35] fix: release actions typo --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index d15d0f1f6..c5fa82e52 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -35,7 +35,7 @@ jobs: ./manage.py schema experiment >> ./dist/schemas/experiment_schema.json ./manage.py schema discovery >> ./dist/schemas/discovery.json - name: Upload release artifacts - uses: actions/github-scripts@v7 + uses: actions/github-script@v7 with: script: | const fs = require(fs); From 8bda0ff1f03c59fda126ace8f4aeb757daa6fef9 Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 13:43:28 -0400 Subject: [PATCH 07/35] fix: release action uses poetry to create schemas --- .github/workflows/release.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index c5fa82e52..1bc00a039 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -31,9 +31,9 @@ jobs: - name: Make release artifacts run: | mkdir -p ./dist/schemas - ./manage.py schema phenopacket >> ./dist/schemas/phenopacket_schema.json - ./manage.py schema experiment >> ./dist/schemas/experiment_schema.json - ./manage.py schema discovery >> ./dist/schemas/discovery.json + poetry run ./manage.py schema phenopacket >> ./dist/schemas/phenopacket_schema.json + poetry run ./manage.py schema experiment >> ./dist/schemas/experiment_schema.json + poetry run ./manage.py schema discovery >> ./dist/schemas/discovery.json - name: Upload release artifacts uses: actions/github-script@v7 with: From 7789a08d68300a64ed61c6427a0d222c875566c0 Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 13:45:47 -0400 Subject: [PATCH 08/35] fix: release workflow schemas typo --- .github/workflows/release.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 1bc00a039..52965ce84 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -31,9 +31,9 @@ jobs: - name: Make release artifacts run: | mkdir -p ./dist/schemas - poetry run ./manage.py schema phenopacket >> ./dist/schemas/phenopacket_schema.json - poetry run ./manage.py schema experiment >> ./dist/schemas/experiment_schema.json - poetry run ./manage.py schema discovery >> ./dist/schemas/discovery.json + poetry run ./manage.py schemas phenopacket >> ./dist/schemas/phenopacket_schema.json + poetry run ./manage.py schemas experiment >> ./dist/schemas/experiment_schema.json + poetry run ./manage.py schemas discovery >> ./dist/schemas/discovery.json - name: Upload release artifacts uses: actions/github-script@v7 with: From 7b2b0cc45c6adb2efe26211d9472498a5fae7245 Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 13:55:12 -0400 Subject: [PATCH 09/35] debug get release --- .github/workflows/release.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 52965ce84..8e910c4cb 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -40,20 +40,21 @@ jobs: script: | const fs = require(fs); - # temporary hardcoding for test - const tag = "v8.0.2-test" - # const tag = context.ref.replace("refs/tags/", ""); + // temporary hardcoding for test + const tag = "v8.0.2-test"; + // const tag = context.ref.replace("refs/tags/", ""); console.log("tag = ", tag); const release = await github.rest.repos.getReleaseByTag({ owner: context.repo.owner, repo: context.repo.repo, - tag + tag: tag, }); + console.log("release id = ", release.data.id) await github.rest.repos.uploadReleaseAsset({ owner: context.repo.owner, repo: context.repo.repo, release_id: release.data.id, name: "JSON Schemas", - data: await fs.readdirSync("./dist/schemas") + data: await fs.readdirSync("./dist/schemas"), }); From f171f733791f75770571cd2f8432928902a12657 Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 13:56:56 -0400 Subject: [PATCH 10/35] fix: release action script fs import --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 8e910c4cb..360d0de03 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -38,7 +38,7 @@ jobs: uses: actions/github-script@v7 with: script: | - const fs = require(fs); + const fs = require("fs"); // temporary hardcoding for test const tag = "v8.0.2-test"; From 04d84cee94403f46a5b41eff339e7ad4d2623229 Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 14:03:26 -0400 Subject: [PATCH 11/35] fix: release workflow permissions --- .github/workflows/release.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 360d0de03..186cd38d3 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -13,7 +13,8 @@ jobs: runs-on: ubuntu-latest permissions: - contents: read + contents: write + repository-projects: write steps: - name: Checkout From 178077575a0795fc71a53c9183a7494c9702be10 Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 14:19:27 -0400 Subject: [PATCH 12/35] upload schemas as zip --- .github/workflows/release.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 186cd38d3..13f5aeb26 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -35,6 +35,7 @@ jobs: poetry run ./manage.py schemas phenopacket >> ./dist/schemas/phenopacket_schema.json poetry run ./manage.py schemas experiment >> ./dist/schemas/experiment_schema.json poetry run ./manage.py schemas discovery >> ./dist/schemas/discovery.json + zip -r json-schemas.zip ./dist/schemas - name: Upload release artifacts uses: actions/github-script@v7 with: @@ -56,6 +57,6 @@ jobs: owner: context.repo.owner, repo: context.repo.repo, release_id: release.data.id, - name: "JSON Schemas", - data: await fs.readdirSync("./dist/schemas"), + name: "json-schemas.zip", + data: await fs.readFile("./json-schemas.zip"), }); From c618ff36b79870cf16ecbcb958fc3e08b7d14f8f Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 14:23:38 -0400 Subject: [PATCH 13/35] fix: release action read file no cb --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 13f5aeb26..225df504b 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -58,5 +58,5 @@ jobs: repo: context.repo.repo, release_id: release.data.id, name: "json-schemas.zip", - data: await fs.readFile("./json-schemas.zip"), + data: await fs.readFileSync("./json-schemas.zip"), }); From d0819aaececa8204e5cd44a3b6b6ceebbb9ccc6e Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 14:42:00 -0400 Subject: [PATCH 14/35] fix: pretty JSON artifact --- .github/workflows/release.yml | 5 +++-- chord_metadata_service/chord/management/commands/schemas.py | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 225df504b..a3bd30a56 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -35,7 +35,8 @@ jobs: poetry run ./manage.py schemas phenopacket >> ./dist/schemas/phenopacket_schema.json poetry run ./manage.py schemas experiment >> ./dist/schemas/experiment_schema.json poetry run ./manage.py schemas discovery >> ./dist/schemas/discovery.json - zip -r json-schemas.zip ./dist/schemas + pushd ./dist/schemas + zip -r ../../json-schemas.zip * - name: Upload release artifacts uses: actions/github-script@v7 with: @@ -57,6 +58,6 @@ jobs: owner: context.repo.owner, repo: context.repo.repo, release_id: release.data.id, - name: "json-schemas.zip", + name: "json-schemas-clean.zip", data: await fs.readFileSync("./json-schemas.zip"), }); diff --git a/chord_metadata_service/chord/management/commands/schemas.py b/chord_metadata_service/chord/management/commands/schemas.py index 8a13c5a08..c20e1a6ef 100644 --- a/chord_metadata_service/chord/management/commands/schemas.py +++ b/chord_metadata_service/chord/management/commands/schemas.py @@ -25,4 +25,4 @@ def add_arguments(self, parser: CommandParser) -> None: def handle(self, *args: Any, **options: Any) -> str | None: schema = NAME_TO_SCHEMA[options["schema"]] - self.stdout.write(json.dumps(schema)) + self.stdout.write(json.dumps(schema, indent=2)) From 4dac6510540586619df58d38f1a1437a9888bc31 Mon Sep 17 00:00:00 2001 From: v-rocheleau Date: Tue, 17 Sep 2024 15:02:29 -0400 Subject: [PATCH 15/35] chore: release workflow trigger on published and prereleased only --- .github/workflows/release.yml | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index a3bd30a56..5c5f2f5aa 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -2,11 +2,6 @@ name: Create and upload release artifacts on: release: types: [published, prereleased] - # temporary PR trigger for test - pull_request: - branches: - - develop - - 'features/**' jobs: release-artifacts: @@ -43,21 +38,19 @@ jobs: script: | const fs = require("fs"); - // temporary hardcoding for test - const tag = "v8.0.2-test"; - // const tag = context.ref.replace("refs/tags/", ""); - console.log("tag = ", tag); + // get tag + const tag = context.ref.replace("refs/tags/", ""); + // get release from tag const release = await github.rest.repos.getReleaseByTag({ owner: context.repo.owner, repo: context.repo.repo, tag: tag, }); - console.log("release id = ", release.data.id) await github.rest.repos.uploadReleaseAsset({ owner: context.repo.owner, repo: context.repo.repo, release_id: release.data.id, - name: "json-schemas-clean.zip", + name: "json-schemas.zip", data: await fs.readFileSync("./json-schemas.zip"), }); From b12fd9a9de79a293a544f6cec227ebc18a6ca8c7 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 17 Sep 2024 16:39:12 -0400 Subject: [PATCH 16/35] fix: proper permissions for schema endpoints --- chord_metadata_service/experiments/api_views.py | 6 +++--- chord_metadata_service/phenopackets/api_views.py | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/chord_metadata_service/experiments/api_views.py b/chord_metadata_service/experiments/api_views.py index 2f67b9e44..e7b17aaf6 100644 --- a/chord_metadata_service/experiments/api_views.py +++ b/chord_metadata_service/experiments/api_views.py @@ -3,13 +3,13 @@ from rest_framework import mixins, serializers, status, viewsets from rest_framework.settings import api_settings from rest_framework.decorators import api_view, permission_classes -from rest_framework.permissions import AllowAny from rest_framework.response import Response from .serializers import ExperimentSerializer, ExperimentResultSerializer from .models import Experiment, ExperimentResult from .schemas import EXPERIMENT_SCHEMA, experiment_resolver, experiment_base_uri from .filters import ExperimentFilter, ExperimentResultFilter +from chord_metadata_service.authz.permissions import BentoAllowAny from chord_metadata_service.restapi.constants import MODEL_ID_PATTERN from chord_metadata_service.restapi.pagination import LargeResultsSetPagination, BatchResultsSetPagination @@ -140,7 +140,7 @@ def dispatch(self, *args, **kwargs): } ) @api_view(["GET"]) -@permission_classes([AllowAny]) +@permission_classes([BentoAllowAny]) def get_experiment_schema(_request): """ get: @@ -151,7 +151,7 @@ def get_experiment_schema(_request): @api_view(["GET"]) -@permission_classes([AllowAny]) +@permission_classes([BentoAllowAny]) def get_experiment_subschema(_request, subschema: str): """ get: diff --git a/chord_metadata_service/phenopackets/api_views.py b/chord_metadata_service/phenopackets/api_views.py index 426b68dc8..3749e52e5 100644 --- a/chord_metadata_service/phenopackets/api_views.py +++ b/chord_metadata_service/phenopackets/api_views.py @@ -2,9 +2,9 @@ from rest_framework import viewsets from rest_framework.settings import api_settings from rest_framework.decorators import api_view, permission_classes -from rest_framework.permissions import AllowAny from rest_framework.response import Response +from chord_metadata_service.authz.permissions import BentoAllowAny from chord_metadata_service.restapi.api_renderers import ( PhenopacketsRenderer, FHIRRenderer, @@ -231,7 +231,7 @@ class InterpretationViewSet(PhenopacketsModelViewSet): } ) @api_view(["GET"]) -@permission_classes([AllowAny]) +@permission_classes([BentoAllowAny]) def get_chord_phenopacket_schema(_request): """ get: @@ -242,7 +242,7 @@ def get_chord_phenopacket_schema(_request): @api_view(["GET"]) -@permission_classes([AllowAny]) +@permission_classes([BentoAllowAny]) def get_chord_phenopacket_subschema(_request, subschema: str): """ get: From 32dc7ea928bf13c582a7d392513465e389cc3542 Mon Sep 17 00:00:00 2001 From: Victor Rocheleau Date: Thu, 19 Sep 2024 16:25:31 -0400 Subject: [PATCH 17/35] fix(actions): single release workflow trigger for pre-release and stable --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 5c5f2f5aa..40c0a1a78 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -1,7 +1,7 @@ name: Create and upload release artifacts on: release: - types: [published, prereleased] + types: [published] jobs: release-artifacts: From 4606a8bdbb841fb20d8582ff2919b814f1b74ddb Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 27 Sep 2024 12:08:58 -0400 Subject: [PATCH 18/35] fix(chord): fix bad logic for checking if dataset project changed adds a test which catches this. --- chord_metadata_service/authz/tests/helpers.py | 11 +++++ chord_metadata_service/chord/api_views.py | 2 +- .../chord/tests/test_api.py | 41 ++++++++++++------- 3 files changed, 38 insertions(+), 16 deletions(-) diff --git a/chord_metadata_service/authz/tests/helpers.py b/chord_metadata_service/authz/tests/helpers.py index ccb70d861..9ec625723 100644 --- a/chord_metadata_service/authz/tests/helpers.py +++ b/chord_metadata_service/authz/tests/helpers.py @@ -76,6 +76,17 @@ def one_no_authz_put(self, url: str, *args, **kwargs): """ return self._one_authz_put(False, url, *args, **kwargs) + def _one_authz_patch(self, authz_res: bool, url: str, *args, **kwargs): + with aioresponses() as m: + mock_authz_eval_one_result(m, authz_res) + return self.client.patch(url, *args, content_type="application/json", **kwargs) + + def one_authz_patch(self, url: str, *args, **kwargs): + """ + Mocks a single True response from the authorization service and executes a JSON PATCH request. + """ + return self._one_authz_patch(True, url, *args, **kwargs) + def _one_authz_delete(self, authz_res: bool, url: str, *args, **kwargs): with aioresponses() as m: mock_authz_eval_one_result(m, authz_res) diff --git a/chord_metadata_service/chord/api_views.py b/chord_metadata_service/chord/api_views.py index 16c3495dd..8038dce89 100644 --- a/chord_metadata_service/chord/api_views.py +++ b/chord_metadata_service/chord/api_views.py @@ -251,7 +251,7 @@ async def update(self, request, *args, **kwargs): return forbidden(request) # side effect: sets authz done flag # Do not allow datasets to change project - if request.data["project"] != dataset_project_id: + if "project" in request.data and request.data["project"] != dataset_project_id: return bad_request(request, "Dataset project ID cannot change") authz.mark_authz_done(request) diff --git a/chord_metadata_service/chord/tests/test_api.py b/chord_metadata_service/chord/tests/test_api.py index d5be94229..d50391001 100644 --- a/chord_metadata_service/chord/tests/test_api.py +++ b/chord_metadata_service/chord/tests/test_api.py @@ -236,9 +236,17 @@ def setUp(self): def test_update_dataset(self): r = self.one_authz_put(f"/api/datasets/{self.dataset.identifier}", data=json.dumps(self.valid_update)) - assert r.status_code == status.HTTP_200_OK + self.assertEqual(r.status_code, status.HTTP_200_OK) + self.dataset.refresh_from_db() + self.assertEqual(self.dataset.title, self.valid_update["title"]) + + def test_update_dataset_partial(self): + r = self.one_authz_patch( + f"/api/datasets/{self.dataset.identifier}", data=json.dumps({"title": self.valid_update["title"]}) + ) + self.assertEqual(r.status_code, status.HTTP_200_OK) self.dataset.refresh_from_db() - assert self.dataset.title == self.valid_update["title"] + self.assertEqual(self.dataset.title, self.valid_update["title"]) def test_update_dataset_changed_project(self): r = self.one_authz_put( @@ -248,50 +256,53 @@ def test_update_dataset_changed_project(self): "project": str(self.project_2.identifier), }) ) - assert r.status_code == status.HTTP_400_BAD_REQUEST + self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) res = r.json() - assert res["message"] == "Bad Request" - assert res["errors"][0]["message"] == "Dataset project ID cannot change" + self.assertEqual(res["message"], "Bad Request") + self.assertEqual(res["errors"][0]["message"], "Dataset project ID cannot change") def test_update_dataset_bad_dats_json(self): r = self.one_authz_put( f"/api/datasets/{self.dataset.identifier}", data=json.dumps({**self.valid_update, "dats_file": "asdf"}), # asdf is not JSON ) - assert r.status_code == status.HTTP_400_BAD_REQUEST + self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) res = r.json() - assert res["message"] == "Bad Request" - assert res["errors"][0]["message"] == ( - "Submitted dataset.dats_file data is not a valid JSON string. Make sure the string value is JSON " - "compatible, or submit dats_file as a JSON object." + self.assertEqual(res["message"], "Bad Request") + self.assertEqual( + res["errors"][0]["message"], + ( + "Submitted dataset.dats_file data is not a valid JSON string. Make sure the string value is JSON " + "compatible, or submit dats_file as a JSON object." + ) ) def test_update_dataset_forbidden(self): r = self.one_no_authz_put(f"/api/datasets/{self.dataset.identifier}", data=json.dumps(self.valid_update)) - assert r.status_code == status.HTTP_403_FORBIDDEN + self.assertEqual(r.status_code, status.HTTP_403_FORBIDDEN) def test_update_dataset_not_found(self): r = self.one_authz_put(f"/api/datasets/{uuid.uuid4()}", data=json.dumps(self.valid_update)) - assert r.status_code == status.HTTP_404_NOT_FOUND + self.assertEqual(r.status_code, status.HTTP_404_NOT_FOUND) class DeleteDatasetTest(AuthzAPITestCase, ProjectTestCase): def test_delete_dataset(self): r = self.one_authz_delete(f"/api/datasets/{self.dataset.identifier}") - assert r.status_code == status.HTTP_204_NO_CONTENT + self.assertEqual(r.status_code, status.HTTP_204_NO_CONTENT) with self.assertRaises(Dataset.DoesNotExist): # must not exist in DB anymore self.dataset.refresh_from_db() def test_delete_dataset_forbidden(self): r = self.one_no_authz_delete(f"/api/datasets/{self.dataset.identifier}") - assert r.status_code == status.HTTP_403_FORBIDDEN + self.assertEqual(r.status_code, status.HTTP_403_FORBIDDEN) self.dataset.refresh_from_db() # must not raise DoesNotExist def test_delete_dataset_not_found(self): r = self.client.delete(f"/api/datasets/{uuid.uuid4()}") - assert r.status_code == status.HTTP_404_NOT_FOUND + self.assertEqual(r.status_code, status.HTTP_404_NOT_FOUND) class CreateProjectJsonSchema(AuthzAPITestCaseWithProjectJSON): From a64af85b238cd82db8d390b319b7da3044b9362b Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 30 Sep 2024 13:22:00 -0400 Subject: [PATCH 19/35] feat(chord): allow downloading DATS JSON as attachment --- chord_metadata_service/chord/api_views.py | 8 ++-- chord_metadata_service/patients/api_views.py | 19 +++++---- chord_metadata_service/restapi/utils.py | 41 +++++++++++++++++++- 3 files changed, 54 insertions(+), 14 deletions(-) diff --git a/chord_metadata_service/chord/api_views.py b/chord_metadata_service/chord/api_views.py index 8038dce89..ff8fea820 100644 --- a/chord_metadata_service/chord/api_views.py +++ b/chord_metadata_service/chord/api_views.py @@ -28,12 +28,13 @@ from chord_metadata_service.resources.serializers import ResourceSerializer from chord_metadata_service.restapi.api_renderers import PhenopacketsRenderer, JSONLDDatasetRenderer, RDFDatasetRenderer from chord_metadata_service.restapi.pagination import LargeResultsSetPagination +from chord_metadata_service.restapi.utils import response_optionally_as_attachment from .models import Project, Dataset, ProjectJsonSchema from .serializers import ( ProjectJsonSchemaSerializer, ProjectSerializer, - DatasetSerializer + DatasetSerializer, ) from .filters import AuthorizedDatasetFilter @@ -142,7 +143,7 @@ class DatasetViewSet(CHORDPublicModelViewSet): queryset = Dataset.objects.all().order_by("title") @action(detail=True, methods=['get']) - def dats(self, request, *_args, **_kwargs): + def dats(self, request: DrfRequest, *_args, **_kwargs): """ Retrieve a specific DATS file for a given dataset. @@ -154,7 +155,8 @@ def dats(self, request, *_args, **_kwargs): return not_found(request) # side effect: sets authz done flag authz.mark_authz_done(request) - return Response(dataset.dats_file) + + return response_optionally_as_attachment(dataset.dats_file, f"{dataset.identifier}_dats.json") @action(detail=True, methods=["get"]) def resources(self, request, *_args, **_kwargs): diff --git a/chord_metadata_service/patients/api_views.py b/chord_metadata_service/patients/api_views.py index 2c38d5eac..8af66534e 100644 --- a/chord_metadata_service/patients/api_views.py +++ b/chord_metadata_service/patients/api_views.py @@ -1,5 +1,4 @@ import asyncio -import re from adrf.views import APIView from bento_lib.responses import errors @@ -48,7 +47,11 @@ from chord_metadata_service.restapi.constants import MODEL_ID_PATTERN from chord_metadata_service.restapi.pagination import LargeResultsSetPagination, BatchResultsSetPagination from chord_metadata_service.restapi.negociation import FormatInPostContentNegotiation -from chord_metadata_service.restapi.utils import build_experiments_by_subject, get_biosamples_with_experiment_details +from chord_metadata_service.restapi.utils import ( + build_experiments_by_subject, + get_biosamples_with_experiment_details, + response_optionally_as_attachment, +) from .filters import IndividualFilter from .models import Individual @@ -121,8 +124,7 @@ def list(self, request, *args, **kwargs): return super().list(request, *args, **kwargs) @action(detail=True, methods=["GET", "POST"]) - def phenopackets(self, request, *_args, **_kwargs): - as_attachment = request.query_params.get("attachment", "") in ("1", "true", "yes") + def phenopackets(self, request: DrfRequest, *_args, **_kwargs): individual = self.get_object() phenopackets = ( @@ -132,13 +134,10 @@ def phenopackets(self, request, *_args, **_kwargs): .order_by("id") ) - filename_safe_id = re.sub(r"[\\/:*?\"<>|]", "_", individual.id) - return Response( + return response_optionally_as_attachment( + request, PhenopacketSerializer(phenopackets, many=True).data, - headers=( - {"Content-Disposition": f"attachment; filename=\"{filename_safe_id}_phenopackets.json\""} - if as_attachment else {} - ), + f"{individual.id}_phenopackets.json" ) diff --git a/chord_metadata_service/restapi/utils.py b/chord_metadata_service/restapi/utils.py index 64f236d44..29c63a823 100644 --- a/chord_metadata_service/restapi/utils.py +++ b/chord_metadata_service/restapi/utils.py @@ -1,9 +1,28 @@ from __future__ import annotations -from chord_metadata_service.phenopackets.models import Biosample + +import re + from collections import defaultdict from django.db.models import F +from rest_framework.request import Request as DrfRequest +from rest_framework.response import Response from typing import Any +from chord_metadata_service.phenopackets.models import Biosample + +__all__ = [ + "COMPUTED_PROPERTY_PREFIX", + "camel_case_field_names", + "transform_keys", + "computed_property", + "remove_computed_properties", + "get_biosamples_with_experiment_details", + "build_experiments_by_subject", + "response_as_attachment", + "attachment_content_disposition", + "response_optionally_as_attachment", +] + COMPUTED_PROPERTY_PREFIX = "__" @@ -88,3 +107,23 @@ def build_experiments_by_subject(biosamples_experiments_details: list[dict]) -> } }) return experiments_with_biosamples + + +def response_as_attachment(request: DrfRequest) -> bool: + """ + Helper function for processing the as_attachment query parameter, for consistent behaviour when returning JSON + responses as file attachments. + """ + return request.query_params.get("attachment", "").strip().lower() in ("1", "true", "yes") + + +FILENAME_REPLACE_PATTERN = re.compile(r"[\\/:*?\"<>|]") + + +def attachment_content_disposition(filename: str) -> dict[str, str]: + filename_safe = FILENAME_REPLACE_PATTERN.sub("_", filename) + return {"Content-Disposition": f"attachment; filename=\"{filename_safe}\""} + + +def response_optionally_as_attachment(request: DrfRequest, data, filename: str) -> Response: + return Response(data, headers=attachment_content_disposition(filename) if response_as_attachment(request) else {}) From e979cc550fd968e7fd8e00e35f7b094c8440bf69 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 30 Sep 2024 13:25:42 -0400 Subject: [PATCH 20/35] fix --- chord_metadata_service/chord/api_views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chord_metadata_service/chord/api_views.py b/chord_metadata_service/chord/api_views.py index ff8fea820..31e3dde86 100644 --- a/chord_metadata_service/chord/api_views.py +++ b/chord_metadata_service/chord/api_views.py @@ -156,7 +156,7 @@ def dats(self, request: DrfRequest, *_args, **_kwargs): authz.mark_authz_done(request) - return response_optionally_as_attachment(dataset.dats_file, f"{dataset.identifier}_dats.json") + return response_optionally_as_attachment(request, dataset.dats_file, f"{dataset.identifier}_dats.json") @action(detail=True, methods=["get"]) def resources(self, request, *_args, **_kwargs): From 07150101b22167b1e59f3d116a7d1ca741e2b2e2 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 30 Sep 2024 13:47:40 -0400 Subject: [PATCH 21/35] test: dats as attachment --- chord_metadata_service/chord/tests/test_api.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/chord_metadata_service/chord/tests/test_api.py b/chord_metadata_service/chord/tests/test_api.py index d50391001..212c826e0 100644 --- a/chord_metadata_service/chord/tests/test_api.py +++ b/chord_metadata_service/chord/tests/test_api.py @@ -184,6 +184,24 @@ def test_dats(self): response = self.client.get("/api/datasets/does-not-exist/dats") self.assertEqual(response.status_code, status.HTTP_404_NOT_FOUND) + def test_dats_as_attachment(self): + payload = {**self.dats_valid_payload, 'dats_file': {}} + + r = self.one_authz_post('/api/datasets', data=json.dumps(payload)) + + self.assertEqual(r.status_code, status.HTTP_201_CREATED) + dataset_id = Dataset.objects.first().identifier + + response = self.client.get(f"/api/datasets/{dataset_id}/dats?attachment=true") + self.assertEqual(response.status_code, status.HTTP_200_OK) + self.assertDictEqual(response.data, payload['dats_file']) + self.assertEqual(response.headers["Content-Disposition"], f"attachment; filename=\"{dataset_id}_dats.json\"") + + response = self.client.get(f"/api/datasets/{dataset_id}/dats?attachment=false") + self.assertEqual(response.status_code, status.HTTP_200_OK) + self.assertDictEqual(response.data, payload['dats_file']) + self.assertNotIn("Content-Disposition", response.headers) + def test_resources(self): resource = { "id": "NCBITaxon:2023-09-14", From e5a3a8e29cf9e0bf7149bd9dfba4ada616564fbc Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 30 Sep 2024 14:39:58 -0400 Subject: [PATCH 22/35] address review comments --- .../chord/tests/test_api.py | 26 +++++++++++++------ chord_metadata_service/restapi/utils.py | 6 +---- 2 files changed, 19 insertions(+), 13 deletions(-) diff --git a/chord_metadata_service/chord/tests/test_api.py b/chord_metadata_service/chord/tests/test_api.py index 212c826e0..e7c5676d7 100644 --- a/chord_metadata_service/chord/tests/test_api.py +++ b/chord_metadata_service/chord/tests/test_api.py @@ -192,15 +192,25 @@ def test_dats_as_attachment(self): self.assertEqual(r.status_code, status.HTTP_201_CREATED) dataset_id = Dataset.objects.first().identifier - response = self.client.get(f"/api/datasets/{dataset_id}/dats?attachment=true") - self.assertEqual(response.status_code, status.HTTP_200_OK) - self.assertDictEqual(response.data, payload['dats_file']) - self.assertEqual(response.headers["Content-Disposition"], f"attachment; filename=\"{dataset_id}_dats.json\"") + subtest_params = [ + ("?attachment=true", True), + ("?attachment=false", False), + ("?attachment=", False), + ("", False), + ] - response = self.client.get(f"/api/datasets/{dataset_id}/dats?attachment=false") - self.assertEqual(response.status_code, status.HTTP_200_OK) - self.assertDictEqual(response.data, payload['dats_file']) - self.assertNotIn("Content-Disposition", response.headers) + for params in subtest_params: + with self.subTest(params=params): + response = self.client.get(f"/api/datasets/{dataset_id}/dats{params[0]}") + self.assertEqual(response.status_code, status.HTTP_200_OK) + self.assertDictEqual(response.data, payload['dats_file']) + if params[1]: + self.assertEqual( + response.headers["Content-Disposition"], + f"attachment; filename=\"{dataset_id}_dats.json\"" + ) + else: + self.assertNotIn("Content-Disposition", response.headers) def test_resources(self): resource = { diff --git a/chord_metadata_service/restapi/utils.py b/chord_metadata_service/restapi/utils.py index 29c63a823..442d3d303 100644 --- a/chord_metadata_service/restapi/utils.py +++ b/chord_metadata_service/restapi/utils.py @@ -11,8 +11,6 @@ from chord_metadata_service.phenopackets.models import Biosample __all__ = [ - "COMPUTED_PROPERTY_PREFIX", - "camel_case_field_names", "transform_keys", "computed_property", "remove_computed_properties", @@ -25,6 +23,7 @@ COMPUTED_PROPERTY_PREFIX = "__" +FILENAME_REPLACE_PATTERN = re.compile(r"[\\/:*?\"<>|]") def camel_case_field_names(string) -> str: @@ -117,9 +116,6 @@ def response_as_attachment(request: DrfRequest) -> bool: return request.query_params.get("attachment", "").strip().lower() in ("1", "true", "yes") -FILENAME_REPLACE_PATTERN = re.compile(r"[\\/:*?\"<>|]") - - def attachment_content_disposition(filename: str) -> dict[str, str]: filename_safe = FILENAME_REPLACE_PATTERN.sub("_", filename) return {"Content-Disposition": f"attachment; filename=\"{filename_safe}\""} From 74be8414a4ed488df4ba87e4b6211c6a9d0ed736 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 1 Oct 2024 10:25:18 -0400 Subject: [PATCH 23/35] chore: update base image (with built-in uvicorn) + lockfile deps --- bento.Dockerfile | 5 +- bento.dev.Dockerfile | 2 +- poetry.lock | 1179 +++++++++++++++++++++--------------------- 3 files changed, 606 insertions(+), 580 deletions(-) diff --git a/bento.Dockerfile b/bento.Dockerfile index 28acf531b..239070d53 100644 --- a/bento.Dockerfile +++ b/bento.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.06.01 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.10.01 SHELL ["/bin/bash", "-c"] @@ -6,8 +6,7 @@ SHELL ["/bin/bash", "-c"] # Install Poetry for dependency management and uvicorn to serve the API RUN apt-get update -y && \ apt-get install -y postgresql-client && \ - rm -rf /var/lib/apt/lists/* && \ - pip install --no-cache-dir "uvicorn[standard]==0.30.1" + rm -rf /var/lib/apt/lists/* # Backwards-compatible with old BentoV2 container layout WORKDIR /app diff --git a/bento.dev.Dockerfile b/bento.dev.Dockerfile index 001b51844..a2588da40 100644 --- a/bento.dev.Dockerfile +++ b/bento.dev.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.06.01 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.10.01 LABEL org.opencontainers.image.description="Local development image for Katsu." 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1 - 4 files changed, 4 insertions(+), 80 deletions(-) diff --git a/chord_metadata_service/authz/middleware.py b/chord_metadata_service/authz/middleware.py index 6574c6a4d..d4abda9a7 100644 --- a/chord_metadata_service/authz/middleware.py +++ b/chord_metadata_service/authz/middleware.py @@ -17,7 +17,7 @@ # be protected by the gateway. include_pattern_public = ( re.compile(r"^(GET|POST|PUT|DELETE)$"), - re.compile(r"^/api/(projects|datasets|public|public_overview|public_search_fields|public_dataset|public_rules)$"), + re.compile(r"^/api/(projects|datasets|public|public_overview|public_search_fields|public_rules)$"), ) include_pattern_workflows = (pattern_get, re.compile(r"^(/workflows$|/workflows/)")) include_pattern_si = (pattern_get, re.compile(r"^/service-info")) diff --git a/chord_metadata_service/discovery/api_views.py b/chord_metadata_service/discovery/api_views.py index 3a9a7e516..e06d635ec 100644 --- a/chord_metadata_service/discovery/api_views.py +++ b/chord_metadata_service/discovery/api_views.py @@ -2,7 +2,6 @@ from adrf.decorators import api_view from bento_lib.responses import errors -from django.conf import settings from drf_spectacular.utils import extend_schema, inline_serializer from functools import partial from operator import is_not @@ -11,12 +10,11 @@ from rest_framework.request import Request as DrfRequest from rest_framework.response import Response +from chord_metadata_service.authz.permissions import BentoAllowAny +from chord_metadata_service.chord import data_types as dts from chord_metadata_service.discovery.exceptions import DiscoveryScopeException from chord_metadata_service.discovery.utils import get_request_discovery_scope, get_public_model_scoped_queryset - -from ..authz.permissions import BentoAllowAny -from ..chord import data_types as dts, models as cm -from ..logger import logger +from chord_metadata_service.logger import logger from .fields import get_field_options, get_range_stats, get_categorical_stats, get_date_stats from .model_lookups import PUBLIC_MODEL_NAMES_TO_DATA_TYPE, PUBLIC_MODEL_NAMES_TO_MODEL, PublicModelName @@ -203,36 +201,6 @@ async def _get_field_response(field: str) -> dict: return Response(response) -@api_view(["GET"]) -@permission_classes([BentoAllowAny]) -async def public_dataset(_request: DrfRequest): - """ - get: - Properties of the datasets - """ - - # For now, we don't have any permissions checks for this. - # In the future, we could introduce a view:dataset permission or something. - - if not settings.CONFIG_PUBLIC: - return Response(dres.NO_PUBLIC_DATA_AVAILABLE, status=status.HTTP_404_NOT_FOUND) - - # Datasets provenance metadata - datasets = cm.Dataset.objects.values( - "title", "description", "contact_info", - "dates", "stored_in", "spatial_coverage", - "types", "privacy", "distributions", - "dimensions", "primary_publications", "citations", - "produced_by", "creators", "licenses", - "acknowledges", "keywords", "version", "dats_file", - "extra_properties", "identifier", "discovery" - ) - - return Response({ - "datasets": datasets - }) - - @api_view(["GET"]) @permission_classes([BentoAllowAny]) async def discovery_schema(_request: DrfRequest): diff --git a/chord_metadata_service/discovery/tests/test_api.py b/chord_metadata_service/discovery/tests/test_api.py index a863ae81e..62dc82792 100644 --- a/chord_metadata_service/discovery/tests/test_api.py +++ b/chord_metadata_service/discovery/tests/test_api.py @@ -428,49 +428,6 @@ def test_overview_response(self): self.assertEqual(8, response_obj["fields"]["baseline_creatinine"]["data"][-1]["value"]) -class PublicDatasetsMetadataTest(AuthzAPITestCase): - - def setUp(self) -> None: - project = ch_m.Project.objects.create(title="Test project", description="test description") - dats_path = os.path.join(os.path.dirname(__file__), "example_dats_provenance.json") - with open(dats_path) as f: - dats_content = json.loads(f.read()) - - ch_m.Dataset.objects.create( - title="Dataset 1", - description="Test dataset", - contact_info="Test contact info", - types=["test type 1", "test type 2"], - privacy="Open", - keywords=["test keyword 1", "test keyword 2"], - data_use=ch_c.VALID_DATA_USE_1, - project=project, - dats_file=dats_content - ) - - @override_settings(CONFIG_PUBLIC=DISCOVERY_CONFIG_TEST) - def test_public_dataset(self): - response = self.dt_authz_counts_get(reverse("public-dataset")) - response_obj = response.json() - self.assertEqual(response.status_code, status.HTTP_200_OK) - self.assertIsInstance(response_obj, dict) - - # datasets - self.assertIsInstance(response_obj["datasets"], list) - for i, dataset in enumerate(response_obj["datasets"]): - self.assertIn("title", dataset.keys()) - self.assertIsNotNone(dataset["title"]) - if i == 0: - self.assertTrue("keywords" in dataset["dats_file"]) - - @override_settings(CONFIG_PUBLIC={}) - def test_public_dataset_response_no_config(self): - response = self.dt_authz_counts_get(reverse("public-dataset")) - response_obj = response.json() - self.assertIsInstance(response_obj, dict) - self.assertEqual(response_obj, dres.NO_PUBLIC_DATA_AVAILABLE) - - class DiscoverySchemaTest(AuthzAPITestCase): @override_settings(CONFIG_PUBLIC=DISCOVERY_CONFIG_TEST) def test_discover_schema(self): diff --git a/chord_metadata_service/restapi/urls.py b/chord_metadata_service/restapi/urls.py index 43078d229..a7d71631f 100644 --- a/chord_metadata_service/restapi/urls.py +++ b/chord_metadata_service/restapi/urls.py @@ -89,6 +89,5 @@ name='public',), path('public_search_fields', public_search_fields, name='public-search-fields'), path('public_overview', public_overview, name='public-overview',), - path('public_dataset', public_dataset, name='public-dataset'), path('public_rules', public_rules, name='public-rules'), ] From ed6b2a279175d1fd0152069414e682839b3cefe6 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 1 Oct 2024 10:31:49 -0400 Subject: [PATCH 25/35] lint: cleanup --- chord_metadata_service/discovery/tests/test_api.py | 2 -- chord_metadata_service/restapi/urls.py | 1 - 2 files changed, 3 deletions(-) diff --git a/chord_metadata_service/discovery/tests/test_api.py b/chord_metadata_service/discovery/tests/test_api.py index 62dc82792..f3a13576f 100644 --- a/chord_metadata_service/discovery/tests/test_api.py +++ b/chord_metadata_service/discovery/tests/test_api.py @@ -1,5 +1,3 @@ -import json -import os from copy import deepcopy import uuid diff --git a/chord_metadata_service/restapi/urls.py b/chord_metadata_service/restapi/urls.py index a7d71631f..da795ce96 100644 --- a/chord_metadata_service/restapi/urls.py +++ b/chord_metadata_service/restapi/urls.py @@ -6,7 +6,6 @@ public_rules, public_search_fields, public_overview, - public_dataset, discovery_schema ) from chord_metadata_service.experiments import api_views as experiment_views From 8064918159308b356f4ed6d5c505129024c83861 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 26 Oct 2024 00:28:27 +0000 Subject: [PATCH 26/35] chore(deps): bump werkzeug from 3.0.4 to 3.0.6 Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.0.4 to 3.0.6. - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/werkzeug/compare/3.0.4...3.0.6) --- updated-dependencies: - dependency-name: werkzeug dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index def078d77..357e75c49 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2367,13 +2367,13 @@ tests = ["coverage[toml]"] [[package]] name = "werkzeug" -version = "3.0.4" +version = "3.0.6" description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.8" files = [ - {file = "werkzeug-3.0.4-py3-none-any.whl", hash = "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c"}, - {file = "werkzeug-3.0.4.tar.gz", hash = "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"}, + {file = "werkzeug-3.0.6-py3-none-any.whl", hash = "sha256:1bc0c2310d2fbb07b1dd1105eba2f7af72f322e1e455f2f93c993bee8c8a5f17"}, + {file = "werkzeug-3.0.6.tar.gz", hash = "sha256:a8dd59d4de28ca70471a34cba79bed5f7ef2e036a76b3ab0835474246eb41f8d"}, ] [package.dependencies] From 9a195d7dde675e2138f2a9663c264be413c0e3ca Mon Sep 17 00:00:00 2001 From: Julian Date: Tue, 29 Oct 2024 11:24:59 -0400 Subject: [PATCH 27/35] add HTML support to document ingestion workflow --- chord_metadata_service/chord/workflows/metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chord_metadata_service/chord/workflows/metadata.py b/chord_metadata_service/chord/workflows/metadata.py index 81e416568..74d91b999 100644 --- a/chord_metadata_service/chord/workflows/metadata.py +++ b/chord_metadata_service/chord/workflows/metadata.py @@ -147,7 +147,7 @@ def boolean_input(id_: str, required: bool = True): wm.WorkflowFileArrayInput( id="document_files", required=True, - pattern=r"^.*\.(pdf|csv|tsv|txt|docx|xlsx|jpeg|jpg|png|gif|md|markdown|mp3|m4a|mp4)$", + pattern=r"^.*\.(pdf|csv|tsv|txt|docx|xlsx|jpeg|jpg|png|gif|md|html|markdown|mp3|m4a|mp4)$", ), ], )) From 491d13eefb3d689dcb51cce545933592401afeda Mon Sep 17 00:00:00 2001 From: Julian Date: Tue, 29 Oct 2024 11:25:39 -0400 Subject: [PATCH 28/35] expand experiment result schema for html --- chord_metadata_service/experiments/schemas.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chord_metadata_service/experiments/schemas.py b/chord_metadata_service/experiments/schemas.py index cad38f7c4..0ab643503 100644 --- a/chord_metadata_service/experiments/schemas.py +++ b/chord_metadata_service/experiments/schemas.py @@ -86,7 +86,7 @@ "file_format": { "type": "string", "enum": ["SAM", "BAM", "CRAM", "VCF", "BCF", "MAF", "GVCF", "BigWig", "BigBed", "FASTA", "FASTQ", "TAB", - "SRA", "SRF", "SFF", "GFF", "PDF", "CSV", "TSV", "JPEG", "PNG", "GIF", "MARKDOWN", "MP3", "M4A", + "SRA", "SRF", "SFF", "GFF", "PDF", "CSV", "TSV", "JPEG", "PNG", "GIF", "HTML", "MARKDOWN", "MP3", "M4A", "MP4", "DOCX", "XLS", "XLSX", "UNKNOWN", "OTHER"] }, "data_output_type": { From 3967cafb642bb9024cb6e10b0e12ec92d9984c25 Mon Sep 17 00:00:00 2001 From: Julian Date: Tue, 29 Oct 2024 11:32:32 -0400 Subject: [PATCH 29/35] lint --- chord_metadata_service/experiments/schemas.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/chord_metadata_service/experiments/schemas.py b/chord_metadata_service/experiments/schemas.py index 0ab643503..798a7decf 100644 --- a/chord_metadata_service/experiments/schemas.py +++ b/chord_metadata_service/experiments/schemas.py @@ -86,8 +86,8 @@ "file_format": { "type": "string", "enum": ["SAM", "BAM", "CRAM", "VCF", "BCF", "MAF", "GVCF", "BigWig", "BigBed", "FASTA", "FASTQ", "TAB", - "SRA", "SRF", "SFF", "GFF", "PDF", "CSV", "TSV", "JPEG", "PNG", "GIF", "HTML", "MARKDOWN", "MP3", "M4A", - "MP4", "DOCX", "XLS", "XLSX", "UNKNOWN", "OTHER"] + "SRA", "SRF", "SFF", "GFF", "PDF", "CSV", "TSV", "JPEG", "PNG", "GIF", "HTML", "MARKDOWN", + "MP3", "M4A", "MP4", "DOCX", "XLS", "XLSX", "UNKNOWN", "OTHER"] }, "data_output_type": { "type": "string", From 1ba0364616f2712bdb1d97db6dbcb311fe9240c2 Mon Sep 17 00:00:00 2001 From: Julian Date: Tue, 29 Oct 2024 11:57:52 -0400 Subject: [PATCH 30/35] reorder files extension in regex pattern --- chord_metadata_service/chord/workflows/metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chord_metadata_service/chord/workflows/metadata.py b/chord_metadata_service/chord/workflows/metadata.py index 74d91b999..48a353e87 100644 --- a/chord_metadata_service/chord/workflows/metadata.py +++ b/chord_metadata_service/chord/workflows/metadata.py @@ -147,7 +147,7 @@ def boolean_input(id_: str, required: bool = True): wm.WorkflowFileArrayInput( id="document_files", required=True, - pattern=r"^.*\.(pdf|csv|tsv|txt|docx|xlsx|jpeg|jpg|png|gif|md|html|markdown|mp3|m4a|mp4)$", + pattern=r"^.*\.(pdf|csv|tsv|txt|docx|xlsx|jpeg|jpg|png|gif|md|markdown|html|mp3|m4a|mp4)$", ), ], )) From 2123496953061c9f6a770ed303a9330ede2c1d0c Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 29 Oct 2024 13:03:24 -0400 Subject: [PATCH 31/35] fix: wrong search count for some searches across nested properties --- chord_metadata_service/discovery/utils.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/chord_metadata_service/discovery/utils.py b/chord_metadata_service/discovery/utils.py index d5647f35a..df6dc13ea 100644 --- a/chord_metadata_service/discovery/utils.py +++ b/chord_metadata_service/discovery/utils.py @@ -242,9 +242,14 @@ def get_public_model_scoped_queryset(scope: ValidatedDiscoveryScope, mn: PublicM filter_scope = "project" value = scope.project_id else: - return PUBLIC_MODEL_NAMES_TO_MODEL[mn].objects.all() + return PUBLIC_MODEL_NAMES_TO_MODEL[mn].objects.distinct() filter_query = PUBLIC_MODEL_NAMES_TO_SCOPE_FILTERS[mn][filter_scope]["filter"] prefetch = PUBLIC_MODEL_NAMES_TO_SCOPE_FILTERS[mn][filter_scope]["prefetch_related"] - return PUBLIC_MODEL_NAMES_TO_MODEL[mn].objects.prefetch_related(*prefetch).filter(**{filter_query: value}) + return ( + PUBLIC_MODEL_NAMES_TO_MODEL[mn].objects + .distinct() + .prefetch_related(*prefetch) + .filter(**{filter_query: value}) + ) From ca323493383bb927b64bd11f856d9e42c3d721a2 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 29 Oct 2024 14:31:56 -0400 Subject: [PATCH 32/35] fix: summary stats should not be accessed thru phenopackets --- chord_metadata_service/discovery/stats.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/chord_metadata_service/discovery/stats.py b/chord_metadata_service/discovery/stats.py index 336eeed82..9d5a045e8 100644 --- a/chord_metadata_service/discovery/stats.py +++ b/chord_metadata_service/discovery/stats.py @@ -29,8 +29,8 @@ async def individual_experiment_type_stats( """ return await bento_public_format_count_and_stats_list( queryset - .values(label=F("phenopackets__biosamples__experiment__experiment_type")) - .annotate(value=Count("phenopackets__biosamples__experiment", distinct=True)), + .values(label=F("biosamples__experiment__experiment_type")) + .annotate(value=Count("biosamples__experiment", distinct=True)), discovery, field_permissions, ) @@ -45,8 +45,8 @@ async def individual_biosample_tissue_stats( """ return await bento_public_format_count_and_stats_list( queryset - .values(label=F("phenopackets__biosamples__sampled_tissue__label")) - .annotate(value=Count("phenopackets__biosamples", distinct=True)), + .values(label=F("biosamples__sampled_tissue__label")) + .annotate(value=Count("biosamples", distinct=True)), discovery, field_permissions, ) From 91ce64511d5b11a4c07ddc983fe5d48e131e1412 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 29 Oct 2024 14:32:22 -0400 Subject: [PATCH 33/35] test: nested search counts --- .../discovery/tests/constants.py | 12 +++++++++- .../patients/tests/test_api.py | 24 ++++++++++++++++--- 2 files changed, 32 insertions(+), 4 deletions(-) diff --git a/chord_metadata_service/discovery/tests/constants.py b/chord_metadata_service/discovery/tests/constants.py index de236dccc..1595e04a5 100644 --- a/chord_metadata_service/discovery/tests/constants.py +++ b/chord_metadata_service/discovery/tests/constants.py @@ -23,7 +23,7 @@ "search": [ { "section_title": "First Section", - "fields": ["sex", "age", "tissues"] + "fields": ["sex", "age", "tissues", "extraction_protocol"] } ], "fields": { @@ -87,6 +87,16 @@ "units": "mm" } }, + "extraction_protocol": { + "mapping": "experiment/extraction_protocol", + "mapping_for_search_filter": "individual/biosamples/experiment/extraction_protocol", + "title": "Experiment Extraction Protocol", + "description": "experiment extraction protocol", + "datatype": "string", + "config": { + "enum": ["NGS"] + }, + }, }, "rules": { "count_threshold": 5, diff --git a/chord_metadata_service/patients/tests/test_api.py b/chord_metadata_service/patients/tests/test_api.py index 8c7c7e8ee..001e6862b 100644 --- a/chord_metadata_service/patients/tests/test_api.py +++ b/chord_metadata_service/patients/tests/test_api.py @@ -20,6 +20,8 @@ CONFIG_PUBLIC_TEST_SEARCH_SEX_ONLY ) from chord_metadata_service.discovery.types import DiscoveryConfig +from chord_metadata_service.experiments import models as ex_m +from chord_metadata_service.experiments.tests import constants as ex_c from chord_metadata_service.patients.models import Individual from chord_metadata_service.phenopackets import models as ph_m from chord_metadata_service.phenopackets.tests import constants as ph_c @@ -380,13 +382,13 @@ def setUp(self): project=self.project_2, ) - individuals = [ + self.individuals = [ c.generate_valid_individual(date_of_consent_range=(2020, 2023)) for _ in range(self.num_individuals) ] - individual_objs = [Individual.objects.create(**individual) for individual in individuals] - ph_m.Biosample.objects.create(**ph_c.valid_biosample_1(Individual.objects.all()[0])) + individual_objs = [Individual.objects.create(**individual) for individual in self.individuals] + biosample = ph_m.Biosample.objects.create(**ph_c.valid_biosample_1(Individual.objects.all()[0])) for idx, individual in enumerate(individual_objs, 1): self.meta_data = ph_m.MetaData.objects.create(**ph_c.VALID_META_DATA_1) @@ -396,6 +398,13 @@ def setUp(self): meta_data=self.meta_data, dataset=self.dataset, ) + if idx == 1: + self.phenopacket.biosamples.add(biosample) + self.phenopacket.save() + + instrument = ex_m.Instrument.objects.create(**ex_c.valid_instrument()) + ex_m.Experiment.objects.create(**ex_c.valid_experiment(biosample, instrument, self.dataset, 1)) + ex_m.Experiment.objects.create(**ex_c.valid_experiment(biosample, instrument, self.dataset, 2)) random.seed(self.random_seed) @@ -694,6 +703,15 @@ def test_public_filtering_mapping_for_search_filter(self): response_obj = response.json() self.assertEqual(1, response_obj["count"]) + @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST_NO_THRESHOLD) + def test_public_filtering_two_experiments(self): + response = self.dt_authz_counts_get(f"/api/public?sex={self.individuals[0]['sex']}&extraction_protocol=NGS") + self.assertEqual(response.status_code, status.HTTP_200_OK) + response_obj = response.json() + self.assertEqual(response_obj["count"], 1) + self.assertEqual(response_obj["biosamples"]["count"], 1) + self.assertEqual(response_obj["experiments"]["count"], 2) + @override_settings(CONFIG_PUBLIC=DISCOVERY_CONFIG_TEST) def test_public_overview_sex(self): response = self.dt_authz_counts_get('/api/public_search_fields') From 07981957a7ced720ea08a6fb508c27f52708a4a3 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 30 Oct 2024 09:43:32 -0400 Subject: [PATCH 34/35] chore: docstring for get_public_model_scoped_queryset(...) --- chord_metadata_service/discovery/utils.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/chord_metadata_service/discovery/utils.py b/chord_metadata_service/discovery/utils.py index df6dc13ea..aef006f94 100644 --- a/chord_metadata_service/discovery/utils.py +++ b/chord_metadata_service/discovery/utils.py @@ -234,6 +234,19 @@ def get_discovery_field_set_permissions( def get_public_model_scoped_queryset(scope: ValidatedDiscoveryScope, mn: PublicModelName) -> QuerySet: + """ + Discovery models can be scoped to either a project or dataset; for downstream filtering, we need to pre-scope the + model queryset to the project/dataset being queried. + + Since downstream filtering may be applied to (possibly deeply)nested fields/models (e.g., biosamples, experiments), + we use `.distinct()` instead of `.all()`. Otherwise, there may be multiple instances of the same top-level object + (individual especially, which has this deep nesting) for each nested instance, for example, in the case of multiple + experiments for a biosample for an individual. + + :param scope: The scope to filter the queryset to. + :param mn: The discovery/"public" model name for + """ + filter_scope: PublicScopeFilterKeys if scope.dataset_id: filter_scope = "dataset" From e6b15ce027d5d02a7455453dede36fdbabce02ce Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 30 Oct 2024 09:55:17 -0400 Subject: [PATCH 35/35] chore(discovery): note modifications for discovery stats lookups --- chord_metadata_service/discovery/stats.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/chord_metadata_service/discovery/stats.py b/chord_metadata_service/discovery/stats.py index 9d5a045e8..a86bfa1c0 100644 --- a/chord_metadata_service/discovery/stats.py +++ b/chord_metadata_service/discovery/stats.py @@ -25,8 +25,12 @@ async def individual_experiment_type_stats( """ Used for a fixed-response public API and beacon. returns count and bento_public format list of stats for experiment type - note that queryset_stats_for_field() does not count "missing" correctly when the field has multiple foreign keys + Note: queryset_stats_for_field() does not count "missing" correctly when the field has multiple foreign keys. """ + + # Note: the queryset used to join through phenopackets, but individuals can be created without a phenopacket (which + # occurs sometimes in tests or in the case of a new packet model), which would cause this to return the wrong stats. + return await bento_public_format_count_and_stats_list( queryset .values(label=F("biosamples__experiment__experiment_type")) @@ -43,6 +47,10 @@ async def individual_biosample_tissue_stats( Used for a fixed-response public API and beacon. returns count and bento_public format list of stats for biosample sampled_tissue """ + + # Note: the queryset used to join through phenopackets, but individuals can be created without a phenopacket (which + # occurs sometimes in tests or in the case of a new packet model), which would cause this to return the wrong stats. + return await bento_public_format_count_and_stats_list( queryset .values(label=F("biosamples__sampled_tissue__label"))