Merge pull request #215 from Caleydo/release-v13.1.0

Makefile

@@ -1,9 +1,13 @@
 .DEFAULT_GOAL := help
 pkg_src = tdp_publicdb
 
-flake8 = flake8 $(pkg_src) setup.py
-isort = isort $(pkg_src) setup.py
 black = black --line-length 140 $(pkg_src) setup.py
+pyright = echo 'pyright not used' # pyright $(pkg_src) setup.py
+ruff = ruff $(pkg_src) setup.py --line-length 140 --select E,W,F,N,I,C,B,UP,PT,SIM,RUF --ignore E501,C901,B008,C417
+
+.PHONY: start  ## Start the development server
+start:
+	python $(pkg_src)
 
 .PHONY: all  ## Perform the most common development-time rules
 all: format lint test
@@ -13,25 +17,25 @@ ci: check-format lint test
 
 .PHONY: format  ## Auto-format the source code
 format:
-	$(isort)
+	$(ruff) --fix
 	$(black)
 
 .PHONY: check-format  ## Check the source code format without changes
 check-format:
-	$(isort) --check-only
 	$(black) --check
 
-.PHONY: lint  ## Run flake8
+.PHONY: lint  ## Run flake8 and pyright
 lint:
-	$(flake8)
+	$(ruff) --format=github
+	$(pyright)
 
 .PHONY: test  ## Run tests
 test:
 	pytest $(pkg_src)
 
 .PHONEY: documentation ## Generate docs
-documentation: 
-	mkdocs build
+documentation:
+	echo "TODO"
 
 .PHONY: install  ## Install the requirements
 install:
@@ -41,6 +45,20 @@ install:
 develop:
 	pip install -e .[develop]
 
+.PHONY: env_encrypt ## Encrypts the current ./<app>/.env
+env_encrypt:
+	openssl aes-256-cbc -pbkdf2 -in ./$(pkg_src)/.env -out ./$(pkg_src)/.env.enc
+
+.PHONY: env_decrypt ## Decrypts the ./<app>/.env.enc
+env_decrypt:
+	@if [ -z "${ENV_PASSWORD}" ]; then \
+		echo "No ENV_PASSWORD set, prompting for password..."; \
+		openssl aes-256-cbc -pbkdf2 -d -in ./$(pkg_src)/.env.enc -out ./$(pkg_src)/.env; \
+	else \
+		echo "ENV_PASSWORD set, using it..."; \
+		openssl aes-256-cbc -pbkdf2 -d -in ./$(pkg_src)/.env.enc -out ./$(pkg_src)/.env -pass env:ENV_PASSWORD; \
+	fi
+
 .PHONY: build  ## Build a wheel
 build:
 	python setup.py sdist bdist_wheel --dist-dir dist_python
@@ -55,4 +73,4 @@ help:
 	@grep -E \
 		'^.PHONY: .*?## .*$$' $(MAKEFILE_LIST) | \
 		sort | \
-		awk 'BEGIN {FS = ".PHONY: |## "}; {printf "\033[36m%-20s\033[0m %s\n", $$2, $$3}'
+		awk 'BEGIN {FS = ".PHONY: |## "}; {printf "\033[36m%-20s\033[0m %s\n", $$2, $$3}'

package.json

@@ -1,7 +1,7 @@
 {
   "name": "tdp_publicdb",
   "description": "",
-  "version": "13.0.3",
+  "version": "13.1.0",
   "author": {
     "name": "The Caleydo Team",
     "email": "contact@caleydo.org",
@@ -62,7 +62,7 @@
     "react-select": "^4.1.0",
     "react-select-async-paginate": "^0.5.3",
     "react-virtualized": "^9.22.3",
-    "tdp_core": "^16.2.2",
+    "tdp_core": "^17.0.0",
     "visyn_scripts": "^1.1.1"
   },
   "optionalDependencies": {

requirements.txt

@@ -1 +1 @@
-tdp_core>=16.2.2,<17.0.0
+tdp_core>=16.0.1,<17.0.0

requirements_dev.txt

@@ -1,9 +1,5 @@
-black~=22.3.0
-debugpy~=1.5.1
-flake8~=4.0.1
-isort~=5.10.1
-mkdocs-material~=8.2.8
-pep8-naming~=0.12.1
+black~=22.12.0
+pyright~=1.1.285
 pytest-runner~=6.0.0
-pytest~=7.1.1
-recommonmark~=0.7.1
+pytest~=7.2.0
+ruff==0.0.218

setup.py

@@ -57,7 +57,7 @@ def requirements(file):
     package_data={},
     # Although 'package_data' is the preferred approach, in some case you may
     # need to place data files outside of your packages. See:
-    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa
+    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files
     # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
     data_files=[],  # [('my_data', ['data/data_file'])],
 )

src/common/GeneUtils.ts

@@ -125,7 +125,7 @@ export class GeneUtils {
   static formatDrug(item: ISelect3Item<IDrugData>, node: HTMLElement, mode: 'result' | 'selection', currentSearchQuery?: RegExp) {
     if (mode === 'result') {
       // show scientific name if is different from the drug id
-      const showScientificName = item.id.toLocaleLowerCase() !== item.data.scientificname.toLocaleLowerCase();
+      const showScientificName = item.data.scientificname && item.id.toLocaleLowerCase() !== item.data.scientificname.toLocaleLowerCase();
       // highlight match
       return `${item.id.replace(currentSearchQuery!, Select3Utils.highlightMatch)}<br>
       ${

src/common/config.ts

@@ -136,6 +136,7 @@ export const tissue: IDataSourceConfig = {
       ColumnDescUtils.numberCol('height', 0, find('height').max, { label: 'Height', visible: false }),
       ColumnDescUtils.numberCol('weight', 0, find('weight').max, { label: 'Weight', visible: false }),
       ColumnDescUtils.numberCol('bmi', 0, find('bmi').max, { label: 'Body Mass Index (BMI)', visible: false }),
+      ColumnDescUtils.numberCol('tumorpurity', 0, find('tumorpurity').max, { label: 'Tumor Purity', visible: false }),
       ColumnDescUtils.categoricalCol('microsatellite_stability_class', find('microsatellite_stability_class').categories, {
         label: 'Micro Satellite Instability (MSI) Status',
         visible: false,
@@ -157,7 +158,17 @@ export const tissue: IDataSourceConfig = {
   },
   columnInfo: {
     string: ['id', 'tumortype_adjacent'],
-    number: ['age', 'days_to_death', 'days_to_last_followup', 'height', 'weight', 'bmi', 'microsatellite_stability_score', 'mutational_fraction'],
+    number: [
+      'age',
+      'days_to_death',
+      'days_to_last_followup',
+      'height',
+      'weight',
+      'bmi',
+      'tumorpurity',
+      'microsatellite_stability_score',
+      'mutational_fraction',
+    ],
     categorical: [
       'organ',
       'gender',

tdp_publicdb/__init__.py

@@ -3,10 +3,6 @@
 # Copyright (c) The Caleydo Team. All rights reserved.
 # Licensed under the new BSD license, available at http://caleydo.org/license
 ###############################################################################
-
-
-from typing import Type
-
 from pydantic import BaseModel
 from tdp_core.plugin.model import AVisynPlugin, RegHelper
 
@@ -15,7 +11,7 @@
 
 class VisynPlugin(AVisynPlugin):
     def register(self, registry: RegHelper):
-        registry.append("tdp-sql-database-definition", "publicdb", "tdp_publicdb.sql", dict(configKey="tdp_publicdb"))
+        registry.append("tdp-sql-database-definition", "publicdb", "tdp_publicdb.sql", {"configKey": "tdp_publicdb"})
 
         registry.append(
             "tdp_proxy",
@@ -39,5 +35,5 @@ def register(self, registry: RegHelper):
         )
 
     @property
-    def setting_class(self) -> Type[BaseModel]:
+    def setting_class(self) -> type[BaseModel]:
         return TDPPublicDBSettings

tdp_publicdb/entity.py

@@ -56,6 +56,7 @@ def _tissue_columns(query):
         .column("height", type="number")
         .column("weight", type="number")
         .column("bmi", type="number")
+        .column("tumorpurity", type="number")
         .column("microsatellite_stability_score", type="number")
         .column("microsatellite_stability_class", type="categorical")
         .column("mutational_fraction", type="number")
@@ -87,6 +88,7 @@ def _tissue_columns(query):
         "height",
         "weight",
         "bmi",
+        "tumorpurity",
         "microsatellite_stability_class",
         "microsatellite_stability_score",
         "hla_a_allele1",

tdp_publicdb/migration/env.py

@@ -1,3 +1,3 @@
-import tdp_core.dbmigration.env  # NOQA
+import tdp_core.dbmigration.env
 
 tdp_core.dbmigration.env.run_migrations_online()

tdp_publicdb/settings.py

@@ -1,5 +1,3 @@
-from typing import Dict
-
 from pydantic import BaseModel
 from tdp_core import manager
 
@@ -8,7 +6,7 @@ class TDPPublicDBSettings(BaseModel):
     dburl: str = "postgresql://publicdb:publicdb@publicdb:5432/publicdb"
     statement_timeout: str = "'5min'"
     statement_timeout_query: str = "set statement_timeout to {}"
-    engine: Dict = {"pool_pre_ping": True}
+    engine: dict = {"pool_pre_ping": True}
 
 
 def get_settings() -> TDPPublicDBSettings:

tdp_publicdb/tests/conftest.py

@@ -6,12 +6,12 @@
 from tdp_core.server.visyn_server import create_visyn_server
 
 
-@pytest.fixture
+@pytest.fixture()
 def app() -> Generator[FastAPI, Any, None]:
-    yield create_visyn_server()
+    return create_visyn_server()
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture()
 def client(app: FastAPI) -> Generator[TestClient, Any, None]:
     with TestClient(app) as client:
         yield client