Merge branch 'dev' into add-graphql-to-navbar

Author: danielreti

.github/workflows/lint.yaml

@@ -4,22 +4,52 @@ on: push
 jobs:
   lint:
     runs-on: ubuntu-latest
+    env:
+      DOCKER_BUILDKIT: 1
+      BUILDKIT_PROGRESS: plain
+      CLOUDSDK_CORE_DISABLE_PROMPTS: 1
+      # used for generating API
+      SM_DOCKER: samplemetadata:dev
     defaults:
       run:
         shell: bash -eo pipefail -l {0}
-
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@main
 
       - uses: actions/setup-python@v2
         with:
           python-version: "3.10"
-          cache: "pip"
 
-      - name: Install packages
+      - uses: actions/setup-java@v2
+        with:
+          distribution: "temurin" # See 'Supported distributions' for available options
+          java-version: "17"
+
+      - name: Setup build env
+        run: |
+          set -euxo pipefail
+
+          pip install -r requirements-dev.txt
+          pip install -r requirements.txt
+
+          # openapi-generator
+          wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/5.3.0/openapi-generator-cli-5.3.0.jar -O openapi-generator-cli.jar
+
+      - name: "build image"
+        run: |
+          docker build \
+            --build-arg SM_ENVIRONMENT=local \
+            --tag $SM_DOCKER \
+            -f deploy/api/Dockerfile \
+            .
+
+      - name: Build + install packages
         run: |
+          export OPENAPI_COMMAND="java -jar openapi-generator-cli.jar"
+          python regenerate_api.py
           pip install -r requirements-dev.txt
           pip install .
+          mkdir .mypy_cache
 
       - name: pre-commit
         run: pre-commit run --all-files

.pre-commit-config.yaml

@@ -1,92 +1,98 @@
 repos:
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
-      hooks:
-          - id: check-yaml
-            exclude: '\.*conda/.*'
-          - id: end-of-file-fixer
-          - id: trailing-whitespace
-            exclude: '\.txt$|\.tsv$'
-          - id: check-case-conflict
-          - id: check-merge-conflict
-          - id: detect-private-key
-          - id: debug-statements
-          - id: check-added-large-files
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+        exclude: '\.*conda/.*'
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: '\.txt$|\.tsv$'
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: detect-private-key
+      - id: debug-statements
+      - id: check-added-large-files
 
-    - repo: https://github.com/igorshubovych/markdownlint-cli
-      rev: v0.33.0
-      hooks:
-          - id: markdownlint
-            args: ["--config", ".markdownlint.json"]
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.33.0
+    hooks:
+      - id: markdownlint
+        args: ["--config", ".markdownlint.json"]
 
-    - repo: https://github.com/ambv/black
-      rev: 23.3.0
-      hooks:
-          - id: black
-            args: [.]
-            pass_filenames: false
-            always_run: true
-            exclude: ^metamist/
+  - repo: https://github.com/ambv/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        args: [.]
+        pass_filenames: false
+        always_run: true
+        exclude: ^metamist/
 
-    - repo: https://github.com/PyCQA/flake8
-      rev: "6.0.0"
-      hooks:
-          - id: flake8
-            additional_dependencies: [flake8-bugbear, flake8-quotes]
+  - repo: https://github.com/PyCQA/flake8
+    rev: "6.0.0"
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8-bugbear, flake8-quotes]
 
-    # Using system installation of pylint to support checking python module imports
-    - repo: local
-      hooks:
-          - id: pylint
-            name: pylint
-            entry: pylint
-            language: system
-            types: [python]
+  # Using system installation of pylint to support checking python module imports
+  - repo: local
+    hooks:
+      - id: pylint
+        name: pylint
+        entry: pylint
+        language: system
+        types: [python]
 
-    # mypy
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.961
-      hooks:
-          - id: mypy
-            args:
-                [
-                    --pretty,
-                    --show-error-codes,
-                    --no-strict-optional,
-                    --ignore-missing-imports,
-                    --install-types,
-                    --non-interactive,
-                ]
-            additional_dependencies:
-                - strawberry-graphql[fastapi]==0.138.1
+  # mypy
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.5.1
+    hooks:
+      - id: mypy
+        args:
+          [
+            --pretty,
+            --show-error-codes,
+            --no-strict-optional,
+            --ignore-missing-imports,
+            --install-types,
+            --non-interactive,
+            --show-error-context,
+            --check-untyped-defs,
+            --explicit-package-bases,
+            --disable-error-code,
+            operator,
+          ]
+        additional_dependencies:
+          - strawberry-graphql[fastapi]==0.206.0
+          - types-PyMySQL==1.1.0.1
 
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: "v3.0.0-alpha.4"
-      hooks:
-          - id: prettier
-            # I'm not exactly sure why it changes behaviour, but
-            # calling `cd web`, then calling `ls src/**/*.tsx`
-            # returns different results to `cd web && ls src/**/*.tsx`
-            # so just include both patterns here
-            entry: bash -c 'cd web && prettier --write --ignore-unknown --check src/*.{ts,tsx,css} src/**/*.{ts,tsx,css}'
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.0-alpha.4"
+    hooks:
+      - id: prettier
+        # I'm not exactly sure why it changes behaviour, but
+        # calling `cd web`, then calling `ls src/**/*.tsx`
+        # returns different results to `cd web && ls src/**/*.tsx`
+        # so just include both patterns here
+        entry: bash -c 'cd web && prettier --write --ignore-unknown --check src/*.{ts,tsx,css} src/**/*.{ts,tsx,css}'
 
-    - repo: https://github.com/pre-commit/mirrors-eslint
-      rev: "v8.33.0"
-      hooks:
-          - id: eslint
-            entry: bash -c 'cd web && eslint'
-            files: \.[jt]sx?$
-            types: [file]
-            additional_dependencies:
-                - eslint@^7.32.0
-                - eslint-config-airbnb@^19.0.4
-                - eslint-config-airbnb-base@^15.0.0
-                - eslint-config-airbnb-typescript@^17.0.0
-                - eslint-config-prettier@^8.6.0
-                - eslint-plugin-import@^2.26.0
-                - eslint-plugin-jsx-a11y@^6.6.1
-                - eslint-plugin-prettier@^4.2.1
-                - eslint-plugin-react@^7.31.11
-                - eslint-plugin-react-hooks@^4.6.0
-                - "@typescript-eslint/eslint-plugin@^5.48.0"
-                - "@typescript-eslint/parser@^5.48.0"
+  - repo: https://github.com/pre-commit/mirrors-eslint
+    rev: "v8.33.0"
+    hooks:
+      - id: eslint
+        entry: bash -c 'cd web && eslint'
+        files: \.[jt]sx?$
+        types: [file]
+        additional_dependencies:
+          - eslint@^7.32.0
+          - eslint-config-airbnb@^19.0.4
+          - eslint-config-airbnb-base@^15.0.0
+          - eslint-config-airbnb-typescript@^17.0.0
+          - eslint-config-prettier@^8.6.0
+          - eslint-plugin-import@^2.26.0
+          - eslint-plugin-jsx-a11y@^6.6.1
+          - eslint-plugin-prettier@^4.2.1
+          - eslint-plugin-react@^7.31.11
+          - eslint-plugin-react-hooks@^4.6.0
+          - "@typescript-eslint/eslint-plugin@^5.48.0"
+          - "@typescript-eslint/parser@^5.48.0"

api/graphql/loaders.py

@@ -13,26 +13,26 @@
 from db.python.connect import NotFoundError
 from db.python.layers import (
     AnalysisLayer,
-    SampleLayer,
     AssayLayer,
+    FamilyLayer,
     ParticipantLayer,
+    SampleLayer,
     SequencingGroupLayer,
-    FamilyLayer,
 )
 from db.python.tables.analysis import AnalysisFilter
 from db.python.tables.assay import AssayFilter
 from db.python.tables.project import ProjectPermissionsTable
 from db.python.tables.sample import SampleFilter
 from db.python.tables.sequencing_group import SequencingGroupFilter
-from db.python.utils import ProjectId, GenericFilter
+from db.python.utils import GenericFilter, ProjectId
 from models.models import (
-    AssayInternal,
-    SampleInternal,
-    SequencingGroupInternal,
     AnalysisInternal,
-    ParticipantInternal,
+    AssayInternal,
     FamilyInternal,
+    ParticipantInternal,
     Project,
+    SampleInternal,
+    SequencingGroupInternal,
 )
 
 
@@ -53,6 +53,8 @@ class LoaderKeys(enum.Enum):
     SAMPLES_FOR_PARTICIPANTS = 'samples_for_participants'
     SAMPLES_FOR_PROJECTS = 'samples_for_projects'
 
+    PHENOTYPES_FOR_PARTICIPANTS = 'phenotypes_for_participants'
+
     PARTICIPANTS_FOR_IDS = 'participants_for_ids'
     PARTICIPANTS_FOR_FAMILIES = 'participants_for_families'
     PARTICIPANTS_FOR_PROJECTS = 'participants_for_projects'
@@ -291,9 +293,7 @@ async def load_participants_for_ids(
     p_by_id = {p.id: p for p in persons}
     missing_pids = set(participant_ids) - set(p_by_id.keys())
     if missing_pids:
-        raise NotFoundError(
-            f'Could not find participants with ids {missing_pids}'
-        )
+        raise NotFoundError(f'Could not find participants with ids {missing_pids}')
     return [p_by_id.get(p) for p in participant_ids]
 
 
@@ -400,7 +400,23 @@ async def load_analyses_for_sequencing_groups(
     return by_sg_id
 
 
-async def get_context(request: Request, connection=get_projectless_db_connection):  # pylint: disable=unused-argument
+@connected_data_loader(LoaderKeys.PHENOTYPES_FOR_PARTICIPANTS)
+async def load_phenotypes_for_participants(
+    participant_ids: list[int], connection
+) -> list[dict]:
+    """
+    Data loader for phenotypes for participants
+    """
+    player = ParticipantLayer(connection)
+    participant_phenotypes = await player.get_phenotypes_for_participants(
+        participant_ids=participant_ids
+    )
+    return [participant_phenotypes.get(pid, {}) for pid in participant_ids]
+
+
+async def get_context(
+    request: Request, connection=get_projectless_db_connection
+):  # pylint: disable=unused-argument
     """Get loaders / cache context for strawberyy GraphQL"""
     mapped_loaders = {k: fn(connection) for k, fn in loaders.items()}
     return {

api/graphql/schema.py

@@ -14,16 +14,10 @@
 from strawberry.fastapi import GraphQLRouter
 from strawberry.types import Info
 
-from api.graphql.filters import (
-    GraphQLFilter,
-    GraphQLMetaFilter,
-)
-from api.graphql.loaders import (
-    get_context,
-    LoaderKeys,
-)
+from api.graphql.filters import GraphQLFilter, GraphQLMetaFilter
+from api.graphql.loaders import LoaderKeys, get_context
 from db.python import enum_tables
-from db.python.layers import AnalysisLayer, SequencingGroupLayer, SampleLayer
+from db.python.layers import AnalysisLayer, SampleLayer, SequencingGroupLayer
 from db.python.layers.assay import AssayLayer
 from db.python.layers.family import FamilyLayer
 from db.python.tables.analysis import AnalysisFilter
@@ -34,21 +28,19 @@
 from db.python.utils import GenericFilter
 from models.enums import AnalysisStatus
 from models.models import (
-    SampleInternal,
-    ParticipantInternal,
-    Project,
     AnalysisInternal,
+    AssayInternal,
     FamilyInternal,
+    ParticipantInternal,
+    Project,
+    SampleInternal,
     SequencingGroupInternal,
-    AssayInternal,
 )
 from models.models.sample import sample_id_transform_to_raw
-from models.utils.sample_id_format import (
-    sample_id_format,
-)
+from models.utils.sample_id_format import sample_id_format
 from models.utils.sequencing_group_id_format import (
-    sequencing_group_id_transform_to_raw,
     sequencing_group_id_format,
+    sequencing_group_id_transform_to_raw,
 )
 
 enum_methods = {}
@@ -336,6 +328,13 @@ async def samples(
         samples = await info.context[LoaderKeys.SAMPLES_FOR_PARTICIPANTS].load(q)
         return [GraphQLSample.from_internal(s) for s in samples]
 
+    @strawberry.field
+    async def phenotypes(
+        self, info: Info, root: 'GraphQLParticipant'
+    ) -> strawberry.scalars.JSON:
+        loader = info.context[LoaderKeys.PHENOTYPES_FOR_PARTICIPANTS]
+        return await loader.load(root.id)
+
     @strawberry.field
     async def families(
         self, info: Info, root: 'GraphQLParticipant'