Address mypy errors

.pre-commit-config.yaml

@@ -1,92 +1,96 @@
 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,
+            --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/routes/analysis.py

@@ -8,12 +8,11 @@
 from pydantic import BaseModel
 from starlette.responses import StreamingResponse
 
-from api.utils.dates import parse_date_only_string
 from api.utils.db import (
-    get_projectless_db_connection,
+    Connection,
     get_project_readonly_connection,
     get_project_write_connection,
-    Connection,
+    get_projectless_db_connection,
 )
 from api.utils.export import ExportType
 from db.python.layers.analysis import AnalysisLayer
@@ -22,20 +21,17 @@
 from db.python.utils import GenericFilter
 from models.enums import AnalysisStatus
 from models.models.analysis import (
+    Analysis,
     AnalysisInternal,
     ProjectSizeModel,
-    SequencingGroupSizeModel,
-    DateSizeModel,
-    Analysis,
 )
 from models.utils.sample_id_format import (
     sample_id_transform_to_raw_list,
-    sample_id_format,
 )
 from models.utils.sequencing_group_id_format import (
+    sequencing_group_id_format,
     sequencing_group_id_format_list,
     sequencing_group_id_transform_to_raw_list,
-    sequencing_group_id_format,
 )
 
 router = APIRouter(prefix='/analysis', tags=['analysis'])
@@ -326,40 +322,42 @@ async def get_sequencing_group_file_sizes(
     """
     Get the per sample file size by type over the given projects and date range
     """
-    atable = AnalysisLayer(connection)
-
-    # Check access to projects
-    project_ids = None
-    pt = ProjectPermissionsTable(connection=connection.connection)
-    project_ids = await pt.get_project_ids_from_names_and_user(
-        connection.author, project_names, readonly=True
-    )
-
-    # Map from internal pids to project name
-    prj_name_map = dict(zip(project_ids, project_names))
-
-    # Convert dates
-    start = parse_date_only_string(start_date)
-    end = parse_date_only_string(end_date)
-
-    # Get results with internal ids as keys
-    results = await atable.get_sequencing_group_file_sizes(
-        project_ids=project_ids, start_date=start, end_date=end
-    )
-
-    # Convert to the correct output type, converting internal ids to external
-    fixed_pids: list[Any] = [
-        ProjectSizeModel(
-            project=prj_name_map[project_data['project']],
-            samples=[
-                SequencingGroupSizeModel(
-                    sample=sample_id_format(s['sample']),
-                    dates=[DateSizeModel(**d) for d in s['dates']],
-                )
-                for s in project_data['samples']
-            ],
-        )
-        for project_data in results
-    ]
 
-    return fixed_pids
+    raise NotImplementedError('This route is broken, and not properly implemented yet')
+    # atable = AnalysisLayer(connection)
+
+    # # Check access to projects
+    # project_ids = None
+    # pt = ProjectPermissionsTable(connection=connection.connection)
+    # project_ids = await pt.get_project_ids_from_names_and_user(
+    #     connection.author, project_names, readonly=True
+    # )
+
+    # # Map from internal pids to project name
+    # prj_name_map = dict(zip(project_ids, project_names))
+
+    # # Convert dates
+    # start = parse_date_only_string(start_date)
+    # end = parse_date_only_string(end_date)
+
+    # # Get results with internal ids as keys
+    # results = await atable.get_sequencing_group_file_sizes(
+    #     project_ids=project_ids, start_date=start, end_date=end
+    # )
+
+    # # Convert to the correct output type, converting internal ids to external
+    # fixed_pids: list[Any] = [
+    #     ProjectSizeModel(
+    #         project=prj_name_map[project_data['project']],
+    #         samples=[
+    #             SequencingGroupSizeModel(
+    #                 sample=sample_id_format(s['sample']),
+    #                 dates=[DateSizeModel(**d) for d in s['dates']],
+    #             )
+    #             for s in project_data['samples']
+    #         ],
+    #     )
+    #     for project_data in results
+    # ]
+
+    # return fixed_pids

db/python/connect.py

@@ -121,7 +121,9 @@ def get_connection_string(self):
         if self.port:
             _host += f':{self.port}'
 
-        options = {}  # {'min_size': self.min_pool_size, 'max_size': self.max_pool_size}
+        options: dict[
+            str, str | int
+        ] = {}  # {'min_size': self.min_pool_size, 'max_size': self.max_pool_size}
         _options = '&'.join(f'{k}={v}' for k, v in options.items())
 
         url = f'mysql://{u_p}@{_host}/{self.dbname}?{_options}'

db/python/enum_tables/enums.py

@@ -1,6 +1,7 @@
-import re
 import abc
+import re
 from functools import lru_cache
+
 from async_lru import alru_cache
 
 from db.python.connect import DbBase
@@ -36,7 +37,8 @@ def _get_table_name(cls):
         matcher = table_name_matcher.match(tn)
         if not matcher:
             raise ValueError(
-                f'The tablename {tn} is not valid (must match {table_name_matcher.pattern})'
+                f'The tablename {tn} is not valid (must match '
+                f'{table_name_matcher.pattern})'
             )
         return tn
 
@@ -47,9 +49,9 @@ async def get(self) -> list[str]:
         """
         _query = f'SELECT DISTINCT name FROM {self._get_table_name()}'
         rows = await self.connection.fetch_all(_query)
-        rows = [r['name'] for r in rows]
+        nrows = [r['name'] for r in rows]
 
-        return rows
+        return nrows
 
     async def insert(self, value: str):
         """

db/python/layers/seqr.py

@@ -1,8 +1,8 @@
 # pylint: disable=unnecessary-lambda-assignment,too-many-locals,broad-exception-caught
 
+import asyncio
 import os
 import re
-import asyncio
 import traceback
 from collections import defaultdict
 from datetime import datetime
@@ -15,29 +15,29 @@
 from cpg_utils.cloud import get_google_identity_token
 
 from api.settings import (
-    SEQR_URL,
     SEQR_AUDIENCE,
     SEQR_MAP_LOCATION,
     SEQR_SLACK_NOTIFICATION_CHANNEL,
+    SEQR_URL,
     get_slack_token,
 )
 from db.python.connect import Connection
+from db.python.enum_tables import SequencingTypeTable
 from db.python.layers.analysis import AnalysisLayer
 from db.python.layers.base import BaseLayer
 from db.python.layers.family import FamilyLayer
 from db.python.layers.participant import ParticipantLayer
 from db.python.layers.sequencing_group import SequencingGroupLayer
 from db.python.tables.analysis import AnalysisFilter
 from db.python.tables.project import ProjectPermissionsTable
-from db.python.enum_tables import SequencingTypeTable
-from db.python.utils import ProjectId, GenericFilter
+from db.python.utils import GenericFilter, ProjectId
 from models.enums import AnalysisStatus
 
 # literally the most temporary thing ever, but for complete
 # automation need to have sample inclusion / exclusion
 from models.utils.sequencing_group_id_format import (
-    sequencing_group_id_format_list,
     sequencing_group_id_format,
+    sequencing_group_id_format_list,
 )
 
 SEQUENCING_GROUPS_TO_IGNORE = {22735, 22739}
@@ -421,9 +421,9 @@ async def update_es_index(
         )
 
         if len(es_index_analyses) == 0:
-            return [f'No ES index to synchronise']
+            return ['No ES index to synchronise']
 
-        with AnyPath(fn_path).open('w+') as f:
+        with AnyPath(fn_path).open('w+') as f:  # type: ignore
             f.write('\n'.join(rows_to_write))
 
         es_index = es_index_analyses[-1].output