Upgrade python deps

.gitignore

@@ -37,3 +37,6 @@ package-lock.json
 !.yarn/releases
 !.yarn/sdks
 !.yarn/versions
+
+# venv
+.venv/

Makefile

@@ -1,9 +1,13 @@
 .DEFAULT_GOAL := help
 pkg_src = coral
 
-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
+
+.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

coral/__init__.py

@@ -4,9 +4,7 @@
 # Licensed under the new BSD license, available at http://caleydo.org/license
 ###############################################################################
 from os import path
-from typing import Type
 
-from pydantic import BaseModel
 from tdp_core.plugin.model import AVisynPlugin, RegHelper
 
 from .settings import CoralSettings
@@ -34,5 +32,5 @@ def register(self, registry: RegHelper):
         )
 
     @property
-    def setting_class(self) -> Type[BaseModel]:
+    def setting_class(self) -> type[CoralSettings]:
         return CoralSettings

coral/db.py

@@ -12,7 +12,7 @@
 _log.info("Setting up the db view.")
 
 # main dictionary containing all views registered for this plugin
-views = dict()
+views = {}
 schema = "cohort"
 
 # create a view + idtype for each available table

coral/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()

coral/settings.py

@@ -1,5 +1,3 @@
-from typing import Dict
-
 from pydantic import BaseModel
 from tdp_core import manager
 
@@ -11,7 +9,7 @@ class CoralSettings(BaseModel):
     statement_timeout: str = "300000"
     supp_statement_timeout: str = "40000"
     statement_timeout_query: str = "set statement_timeout to {}"
-    logging: Dict = {"version": 1, "disable_existing_loggers": False, "loggers": {"coral": {"level": "DEBUG"}}}
+    logging: dict = {"version": 1, "disable_existing_loggers": False, "loggers": {"coral": {"level": "DEBUG"}}}
 
 
 def get_settings() -> CoralSettings:

coral/sql_query_mapper.py

@@ -95,7 +95,7 @@ def to_dict(self, row):
         try:
             return {c.key: getattr(row, c.key) for c in inspect(row).mapper.column_attrs}
         except NoInspectionAvailable:  # this exception is raised when the result is not of a registered sqlalchemy type due to which the inspection fails
-            result = dict()
+            result = {}
             result[COLUMN_LABEL_SCORE] = row[0]
             result[COLUMN_LABEL_ID] = row[1]
             return result
@@ -145,10 +145,7 @@ def get_cohorts_by_id_sql(self, args, error_msg):
                 str_values = str_values + ("{val}, ".format(val=curr_val))
                 cnt += 1
 
-        if cnt > 0:
-            str_values = str_values[:-2]  # remove the last ', ' from the value list
-        else:
-            str_values = "-1"  # returns no cohorts -> ids are only positiv
+        str_values = str_values[:-2] if cnt > 0 else "-1"  # returns no cohorts -> ids are only positiv
 
         sql_text = "SELECT id, name, is_initial, previous_cohort, entity_database, entity_schema, entity_table FROM cohort.cohort c WHERE c.id IN ({str_values})".format(
             str_values=str_values
@@ -173,7 +170,7 @@ def update_cohort_name_sql(self, args, error_msg):
 
             session_data.query(Cohort).filter(Cohort.id == cohort_id).update({Cohort.name: name}, synchronize_session=False)
             # synchronize_session
-            # False - don’t synchronize the session. This option is the most efficient and is reliable once the session is expired,
+            # False - don`t synchronize the session. This option is the most efficient and is reliable once the session is expired,
             # which typically occurs after a commit(), or explicitly using expire_all(). Before the expiration,
             # updated objects may still remain in the session with stale values on their attributes, which can lead to confusing results.
 
@@ -341,19 +338,13 @@ def equals_filter_statement(self, prefix, attribute, values, numeric):
                 if val.startswith("!"):
                     add_equals_not_value = True
                     val = val[1:]
-                    if numeric in ["true"]:  # determine if the values are strings or numbers
-                        curr_val = "{val}".format(val=val)
-                    else:
-                        curr_val = "'{val}'".format(val=val)
+                    curr_val = "{val}".format(val=val) if numeric in ["true"] else "'{val}'".format(val=val)
 
                     str_not_values = str_not_values + ("{val}, ".format(val=curr_val))
 
                 else:
                     add_equals_value = True
-                    if numeric in ["true"]:  # determine if the values are strings or numbers
-                        curr_val = "{val}".format(val=val)
-                    else:
-                        curr_val = "'{val}'".format(val=val)
+                    curr_val = "{val}".format(val=val) if numeric in ["true"] else "'{val}'".format(val=val)
 
                     str_values = str_values + ("{val}, ".format(val=curr_val))
 
@@ -455,10 +446,7 @@ def create_cohort_treatment_filtered(self, args, cohort, error_msg):
             raise RuntimeError(error_msg)
 
         array_operation = "="
-        if base_agent in ["true"]:  # determine if the values are strings or numbers
-            array_operation = "@>"
-        else:
-            array_operation = "="
+        array_operation = "@>" if base_agent in ["true"] else "="
 
         entity_id_col = ""
         if cohort.entity_table == "tdp_tissue":
@@ -508,10 +496,7 @@ def create_cohort_treatment_filtered(self, args, cohort, error_msg):
         # regimen is defined
         if regimen is not None:
             reg_sql = ("tmp.rn::int = {val}").format(val=regimen)
-            if agent is not None:
-                sql_where = sql_where + " AND " + reg_sql
-            else:
-                sql_where = reg_sql
+            sql_where = sql_where + " AND " + reg_sql if agent is not None else reg_sql
 
         # SQL with the combined filter (actual agent values, null values)
         sql_refiend = ""
@@ -555,10 +540,7 @@ def create_cohort_treatment_filtered(self, args, cohort, error_msg):
                 base_table=cohort.entity_table,
             )
 
-            if agent_exists:
-                sql_refiend = sql_refiend + " UNION " + sql_null
-            else:
-                sql_refiend = sql_refiend + sql_null
+            sql_refiend = sql_refiend + " UNION " + sql_null if agent_exists else sql_refiend + sql_null
 
         # complete SQL statement that filters the data based on the given cohort
         new_sql_text = """SELECT cohort.* FROM ({entities}) cohort

coral/tests/conftest.py

@@ -0,0 +1,34 @@
+import pytest
+from fastapi import FastAPI
+from fastapi.testclient import TestClient
+from tdp_core.security.manager import SecurityManager
+from tdp_core.security.model import User
+from tdp_core.server.visyn_server import create_visyn_server
+from tdp_core.tests.fixtures.postgres_db import postgres_db
+
+assert postgres_db  # silence unused import warning
+
+
+@pytest.fixture(scope="session")
+def app(postgres_db) -> FastAPI:
+    server = create_visyn_server(
+        workspace_config={
+            "tdp_core": {"enabled_plugins": ["tdp_core", "coral"]},
+            "coral": {
+                "dburl": postgres_db.url,
+            },
+        }
+    )
+
+    return server
+
+
+@pytest.fixture()
+def client(monkeypatch, app: FastAPI):
+    def mock_current_user_in_manager(self):
+        return User(id="admin")
+
+    monkeypatch.setattr(SecurityManager, "current_user", property(mock_current_user_in_manager))
+
+    with TestClient(app) as client:
+        yield client

coral/tests/test_api.py

@@ -0,0 +1,5 @@
+from fastapi.testclient import TestClient
+
+
+def test_loggedinas(client: TestClient):
+    assert client.get("/loggedinas").json()["name"] == "admin"

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'])],
 )