Merge pull request #324 from helxplatform/develop

Develop Merge

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.9.17-slim-bullseye
+FROM python:3.9.18-slim-bullseye
 
 ENV PYTHONDONTWRITEBYTECODE 1
 ENV PYTHONUNBUFFERED 1

Makefile

@@ -5,7 +5,7 @@ COMMIT_HASH      := $(shell git rev-parse --short HEAD)
 SHELL            := /bin/bash
 
 # If env defines a registry, use it, else use the default
-DEFAULT_REGISTRY := docker.io
+DEFAULT_REGISTRY := containers.renci.org
 ifdef DOCKER_REGISTRY
 ifeq "$(origin DOCKER_REGISTRY)" "environment"
 DOCKER_REGISTRY := ${DOCKER_REGISTRY}
@@ -143,7 +143,7 @@ start:	build.postgresql.local
 #build: Build the Docker image
 build:
 	if [ -z "$(VER)" ]; then echo "Please provide a value for the VER variable like this:"; echo "make VER=4 build"; false; fi;
-	docker build --no-cache --pull -t ${DOCKER_IMAGE} -f Dockerfile .
+	docker build --no-cache --platform=linux/amd64 --pull -t ${DOCKER_IMAGE} -f Dockerfile .
 	docker tag ${DOCKER_IMAGE} ${DOCKER_REGISTRY}/${DOCKER_IMAGE}
 	docker tag ${DOCKER_IMAGE} ${DOCKER_REGISTRY}/${DOCKER_IMAGE}-${COMMIT_HASH}
 

README.md

@@ -177,7 +177,7 @@ make install
 #### With Tycho cloned locally
 
 > NOTE: To work with Tycho and appstore locally comment
-> `tycho-api` in requirements.txt and setup.cfg.
+> `tycho-api` in requirements.txt.
 
 Clone Tycho repo locally outside the appstore project.
 
@@ -448,8 +448,7 @@ python setup.py publish
 
 #### Updating Appstore
 
-1. Go to appstore code base and update tycho version in following files `requirements.txt`
-and `setup.cfg` created in the publishing step
+1. Go to appstore code base and update tycho version in following files `requirements.txt` created in the publishing step
 
 2. Build and publish appstore
 

appstore/appstore/settings/base.py

@@ -6,6 +6,7 @@
 
 import os
 import logging
+import json
 from pathlib import Path
 
 logger = logging.getLogger(__name__)
@@ -44,6 +45,9 @@
 DEV_PHASE = os.environ.get("DEV_PHASE", "local")
 TYCHO_MODE = os.environ.get("TYCHO_MODE", "null" if DEV_PHASE == "stub" else "live")
 
+# Needs to be JSON-encoded since expressions can contain basically any character that would be used as a delimiter. 
+AUTO_WHITELIST_PATTERNS = json.loads(os.environ.get("AUTO_WHITELIST_PATTERNS", "[]"))
+
 # Variables used for an external Tycho app registry.
 # ToDo: Consider setting the default value of TYCHO_APP_REGISTRY_REPO to 
 # "https://github.com/helxplatform/helx-apps/raw" and remove any other similar
@@ -88,6 +92,9 @@
     "drf_spectacular",
 ]
 
+##  Setting to allow for a seamless login that was breaking at django-allauth 0.47.
+SOCIALACCOUNT_LOGIN_ON_GET=True
+
 LOCAL_APPS = [
     "api",
     "core",

appstore/middleware/filter_whitelist_middleware.py

@@ -1,4 +1,5 @@
 import logging
+import re
 
 from django.conf import settings
 from django.contrib.auth.models import Group
@@ -60,12 +61,24 @@ def is_whitelisted(user):
         if user.groups.filter(name="whitelisted").exists():
             return True
         return False
+
+    @staticmethod
+    def is_auto_whitelisted_email(user):
+        email = user.email
+        for pattern in settings.AUTO_WHITELIST_PATTERNS:
+            if re.match(pattern, email) is not None:
+                return True
+        return False
 
     @staticmethod
     def is_authorized(user):
         if AuthorizedUser.objects.filter(email=user.email).exists():
             logger.debug(f"found user email {user.email} in AuthorizedUser")
             return True
+        if AllowWhiteListedUserOnly.is_auto_whitelisted_email(user):
+            # authorize the user automatically, and allow them through.
+            AuthorizedUser.objects.create(email=user.email)
+            return True
         logger.debug(f"user email {user.email} not found in AuthorizedUser")
         return False
 

requirements.txt

@@ -15,9 +15,9 @@ python3-openid==3.1.0
 requests==2.31.0
 requests-oauthlib
 selenium==3.141.0
-tycho-api>=1.17.2
+tycho-api>=1.17
 webdriver-manager==3.2.1
 sqlparse==0.4.2
 asgiref==3.4.1
 psycopg2-binary
-python-irodsclient==1.1.5
+python-irodsclient==1.1.5