From a8fc561c01e6a98e262f07d7f60d79779d43fe83 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Wed, 6 Sep 2023 14:37:05 +0200
Subject: [PATCH] refactor: port to python for backend
---
.github/workflows/ci.yml | 4 +-
Dockerfile | 48 +-
backend/.gitignore | 3 +
backend/app/_store.py | 142 +
backend/app/app.py | 50 +
backend/app/auth.py | 67 +
backend/app/bkwdcompat.py | 248 +
backend/app/config.py | 39 +
backend/app/const.py | 21 +
backend/app/dev_banner.py | 22 +
backend/app/index_html.py | 45 +
backend/app/logger.py | 42 +
backend/app/plugin.py | 80 +
backend/app/quickstart.py | 55 +
backend/app/sane_url.py | 152 +
backend/app/sxplr_iam.py | 6 +
backend/app/user.py | 63 +
backend/app/util.py | 54 +
{deploy => backend/app}/well-known/robot.txt | 0
.../app}/well-known/security.txt | 0
backend/requirements.txt | 12 +
check_all.sh | 47 -
deploy/.gitignore | 3 -
deploy/README.md | 18 -
deploy/api-test/Jenkinsfile | 58 -
.../api-test/datasets/mouse.2015.e2e-spec.js | 13 -
.../api-test/datasets/mouse.2017.e2e-spec.js | 13 -
.../api-test/datasets/rat.v1_01.e2e-spec.js | 13 -
deploy/api-test/datasets/rat.v2.e2e-spec.js | 13 -
deploy/api-test/datasets/rat.v3.e2e-spec.js | 13 -
deploy/api-test/datasets/ratMouse.util.js | 77 -
deploy/api-test/datasets/util.js | 15 -
deploy/app.js | 228 -
deploy/app.spec.js | 90 -
deploy/auth/hbp-oidc-v2.js | 81 -
deploy/auth/index.js | 38 -
deploy/auth/index.spec.js | 109 -
deploy/auth/oidc.js | 52 -
deploy/auth/spec-helper.js | 66 -
deploy/auth/util.js | 26 -
deploy/auth/util.spec.js | 151 -
deploy/bkwdCompat/index.js | 24 -
deploy/bkwdCompat/ngLinks.json | 705 ---
deploy/bkwdCompat/urlState.js | 287 -
deploy/bkwdCompat/urlState.spec.js | 18 -
deploy/catchError.js | 13 -
deploy/constants.js | 21 -
deploy/csp/index.js | 147 -
deploy/csp/index.spec.js | 109 -
deploy/devBanner/index.js | 29 -
deploy/logging/index.js | 35 -
deploy/lruStore/index.js | 164 -
deploy/package-lock.json | 5133 -----------------
deploy/package.json | 44 -
deploy/plugins/index.js | 84 -
deploy/quickstart/index.js | 58 -
deploy/saneUrl/depcObjStore.js | 26 -
deploy/saneUrl/index.js | 134 -
deploy/saneUrl/index.spec.js | 327 --
deploy/saneUrl/store.js | 100 -
deploy/saneUrl/util.js | 70 -
deploy/saneUrl/util.spec.js | 206 -
deploy/server.js | 90 -
deploy/server.spec.js | 112 -
deploy/user/index.js | 86 -
deploy/user/index.spec.js | 245 -
deploy/user/store.js | 68 -
deploy/util/streamHandleError.js | 4 -
deploy_env.md | 67 +-
e2e/screenshots/gen.js | 1 +
netlify.toml | 7 -
src/util/fn.ts | 3 -
72 files changed, 1126 insertions(+), 9568 deletions(-)
create mode 100644 backend/.gitignore
create mode 100644 backend/app/_store.py
create mode 100644 backend/app/app.py
create mode 100644 backend/app/auth.py
create mode 100644 backend/app/bkwdcompat.py
create mode 100644 backend/app/config.py
create mode 100644 backend/app/const.py
create mode 100644 backend/app/dev_banner.py
create mode 100644 backend/app/index_html.py
create mode 100644 backend/app/logger.py
create mode 100644 backend/app/plugin.py
create mode 100644 backend/app/quickstart.py
create mode 100644 backend/app/sane_url.py
create mode 100644 backend/app/sxplr_iam.py
create mode 100644 backend/app/user.py
create mode 100644 backend/app/util.py
rename {deploy => backend/app}/well-known/robot.txt (100%)
rename {deploy => backend/app}/well-known/security.txt (100%)
create mode 100644 backend/requirements.txt
delete mode 100755 check_all.sh
delete mode 100644 deploy/.gitignore
delete mode 100644 deploy/README.md
delete mode 100644 deploy/api-test/Jenkinsfile
delete mode 100644 deploy/api-test/datasets/mouse.2015.e2e-spec.js
delete mode 100644 deploy/api-test/datasets/mouse.2017.e2e-spec.js
delete mode 100644 deploy/api-test/datasets/rat.v1_01.e2e-spec.js
delete mode 100644 deploy/api-test/datasets/rat.v2.e2e-spec.js
delete mode 100644 deploy/api-test/datasets/rat.v3.e2e-spec.js
delete mode 100644 deploy/api-test/datasets/ratMouse.util.js
delete mode 100644 deploy/api-test/datasets/util.js
delete mode 100644 deploy/app.js
delete mode 100644 deploy/app.spec.js
delete mode 100644 deploy/auth/hbp-oidc-v2.js
delete mode 100644 deploy/auth/index.js
delete mode 100644 deploy/auth/index.spec.js
delete mode 100644 deploy/auth/oidc.js
delete mode 100644 deploy/auth/spec-helper.js
delete mode 100644 deploy/auth/util.js
delete mode 100644 deploy/auth/util.spec.js
delete mode 100644 deploy/bkwdCompat/index.js
delete mode 100644 deploy/bkwdCompat/ngLinks.json
delete mode 100644 deploy/bkwdCompat/urlState.js
delete mode 100644 deploy/bkwdCompat/urlState.spec.js
delete mode 100644 deploy/catchError.js
delete mode 100644 deploy/constants.js
delete mode 100644 deploy/csp/index.js
delete mode 100644 deploy/csp/index.spec.js
delete mode 100644 deploy/devBanner/index.js
delete mode 100644 deploy/logging/index.js
delete mode 100644 deploy/lruStore/index.js
delete mode 100644 deploy/package-lock.json
delete mode 100644 deploy/package.json
delete mode 100644 deploy/plugins/index.js
delete mode 100644 deploy/quickstart/index.js
delete mode 100644 deploy/saneUrl/depcObjStore.js
delete mode 100644 deploy/saneUrl/index.js
delete mode 100644 deploy/saneUrl/index.spec.js
delete mode 100644 deploy/saneUrl/store.js
delete mode 100644 deploy/saneUrl/util.js
delete mode 100644 deploy/saneUrl/util.spec.js
delete mode 100644 deploy/server.js
delete mode 100644 deploy/server.spec.js
delete mode 100644 deploy/user/index.js
delete mode 100644 deploy/user/index.spec.js
delete mode 100644 deploy/user/store.js
delete mode 100644 deploy/util/streamHandleError.js
delete mode 100644 netlify.toml
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 25a2cd761..1b17f4974 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -69,7 +69,5 @@ jobs:
with:
node-version: 16.x
- run: |
- cd deploy
- npm i
- npm run test
+ echo "busybody"
diff --git a/Dockerfile b/Dockerfile
index a6277e7b7..26aa7f570 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -40,48 +40,28 @@ RUN node ./src/environments/parseEnv.js
RUN npm run build
RUN node third_party/matomo/processMatomo.js
-# RUN npm run build-storybook
-
-# gzipping container
-FROM ubuntu:22.04 as compressor
-RUN apt upgrade -y && apt update && apt install brotli
-
-RUN mkdir /iv
-COPY --from=builder /iv/dist/aot /iv
-# COPY --from=builder /iv/storybook-static /iv/storybook-static
-
-# Remove duplicated assets. Use symlink instead.
-# WORKDIR /iv/storybook-static
-RUN rm -rf ./assets
-RUN ln -s ../assets ./assets
-
-WORKDIR /iv
-
-RUN for f in $(find . -type f); do gzip < $f > $f.gz && brotli < $f > $f.br; done
# prod container
-FROM node:16-alpine
+FROM python:3.10-alpine
+
+RUN adduser --disabled-password nonroot
-ENV NODE_ENV=production
+# Needed for the requirement as git, otherwise, not needed
+RUN apk update
+RUN apk add git curl
-RUN apk --no-cache add ca-certificates
RUN mkdir /iv-app
WORKDIR /iv-app
-# Copy common folder
-COPY --from=builder /iv/common /common
-
-# Copy the express server
-COPY --from=builder /iv/deploy .
+# Copy the fastapi server
+COPY --from=builder /iv/backend .
+RUN pip install -r requirements.txt
+COPY --from=builder /iv/dist/aot /iv/backend/public
-# Copy built siibra explorer
-COPY --from=compressor /iv ./public
+ENV PATH_TO_PUBLIC=/iv/backend/public
-RUN chown -R node:node /iv-app
-
-USER node
-RUN npm i
+RUN chown -R nonroot:nonroot /iv-app
+USER nonroot
EXPOSE 8080
-ENV PORT 8080
-ENTRYPOINT [ "node", "server.js" ]
+ENTRYPOINT uvicorn app.app:app --host 0.0.0.0 --port 8080
diff --git a/backend/.gitignore b/backend/.gitignore
new file mode 100644
index 000000000..2fb9ba976
--- /dev/null
+++ b/backend/.gitignore
@@ -0,0 +1,3 @@
+venv
+__pycache__
+.env
diff --git a/backend/app/_store.py b/backend/app/_store.py
new file mode 100644
index 000000000..63ddd248d
--- /dev/null
+++ b/backend/app/_store.py
@@ -0,0 +1,142 @@
+from abc import ABC, abstractmethod
+from ebrains_drive import BucketApiClient
+from io import StringIO
+import requests
+from .logger import logger
+
+class Store(ABC):
+ @abstractmethod
+ def set(self, key: str, value: str): ...
+
+ @abstractmethod
+ def get(self, key: str): ...
+
+ @abstractmethod
+ def delete(self, key: str): ...
+
+ def is_healthy(self) -> bool:
+ raise NotImplementedError
+
+class FallbackStore(Store):
+ _mem = {}
+ def set(self, key: str, value: str):
+ self._mem[key] = value
+
+ def get(self, key: str):
+ return self._mem.get(key)
+
+ def delete(self, key: str):
+ self._mem.pop(key, None)
+
+ def is_healthy(self) -> bool:
+ return True
+
+ _instance: 'FallbackStore' = None
+ @classmethod
+ def Ephemeral(cls):
+ if cls._instance is None:
+ cls._instance = cls()
+ return cls._instance
+
+
+class RedisEphStore(Store):
+
+ _persistent_store: "RedisEphStore" = None
+ _ephemeral_store: "RedisEphStore" = None
+
+ def __init__(self, host: str="localhost", port: int=6379, username: str=None, password: str=None, expiry_s: int=60*60*24) -> None:
+ super().__init__()
+ from redis import Redis
+ self._redis = Redis(host, port, password=password, username=username)
+ self.expiry_s = expiry_s
+
+ def set(self, key: str, value: str):
+ self._redis.set(key, value, ex=self.expiry_s)
+
+ def delete(self, key: str):
+ self._redis.delete(key)
+
+ def get(self, key: str):
+ return self._redis.get(key)
+
+ def is_healthy(self) -> bool:
+ try:
+ self._redis.ping()
+ return True
+ except Exception as e:
+ logger.error(f"redis store is not healthy! {str(e)}")
+ return False
+
+ @classmethod
+ def Persistent(cls):
+ from .config import REDIS_ADDR, REDIS_PASSWORD, REDIS_PORT, REDIS_USERNAME
+ if cls._persistent_store is None:
+ cls._persistent_store = cls(REDIS_ADDR, REDIS_PORT, REDIS_USERNAME, REDIS_PASSWORD, expiry_s=None)
+ return cls._persistent_store
+
+ @classmethod
+ def Ephemeral(cls):
+ from .config import REDIS_ADDR, REDIS_PASSWORD, REDIS_PORT, REDIS_USERNAME
+ if cls._ephemeral_store is None:
+ _store = cls(REDIS_ADDR, REDIS_PORT, REDIS_USERNAME, REDIS_PASSWORD)
+ if not _store.is_healthy():
+ logger.warn(f"ephstore is not healthy, fall back to mem store instead.")
+ return FallbackStore.Ephemeral()
+ cls._ephemeral_store = _store
+ return cls._ephemeral_store
+
+ @classmethod
+ def Get(cls, key: str):
+ store = cls.Persistent()
+ return store.get(key)
+
+class DataproxyStore(Store):
+
+ class NotFound(Exception): ...
+ class GenericException(Exception): ...
+
+ ENDPOINT = "https://data-proxy.ebrains.eu/api/v1/buckets/{bucket_name}/{object_name}"
+
+ def __init__(self, token: str, bucket_name: str):
+ super().__init__()
+ self.token = token
+ self.bucket_name = bucket_name
+
+
+ def update_token(self, token: str):
+ self.token = token
+
+
+ def _get_bucket(self):
+ client = BucketApiClient(token=self.token)
+ return client.buckets.get_bucket(self.bucket_name)
+
+
+ def delete(self, key: str):
+ bucket = self._get_bucket()
+ file = bucket.get_file(key)
+ file.delete()
+
+
+ def set(self, key: str, value: str):
+ bucket = self._get_bucket()
+
+ sio = StringIO()
+ sio.write(value)
+ sio.seek(0)
+ bucket.upload(sio, key)
+
+
+ def get(self, key: str):
+ try:
+ resp = requests.get(DataproxyStore.ENDPOINT.format(bucket_name=self.bucket_name, object_name=key))
+ resp.raise_for_status()
+ return resp.content.decode("utf-8")
+ except DataproxyStore.NotFound as e:
+ raise e from e
+ except requests.exceptions.HTTPError as e:
+ if e.response.status_code == 404:
+ raise DataproxyStore.NotFound(str(e)) from e
+ raise DataproxyStore.GenericException(str(e)) from e
+ except Exception as e:
+ raise DataproxyStore.GenericException(str(e)) from e
diff --git a/backend/app/app.py b/backend/app/app.py
new file mode 100644
index 000000000..ca7dfcaac
--- /dev/null
+++ b/backend/app/app.py
@@ -0,0 +1,50 @@
+from pathlib import Path
+from fastapi import FastAPI, Request
+from fastapi.responses import RedirectResponse
+from fastapi.staticfiles import StaticFiles
+from starlette.middleware.sessions import SessionMiddleware
+
+from app.quickstart import router as quickstart_router
+from app.sane_url import router as saneurl_router, vip_routes
+from app.config import HOST_PATHNAME, SESSION_SECRET, PATH_TO_PUBLIC
+from app.dev_banner import router as devbanner_router
+from app.index_html import router as index_router
+from app.plugin import router as plugin_router
+from app.auth import router as auth_router
+from app.user import router as user_router
+from app.config import HOST_PATHNAME
+
+app = FastAPI()
+
+app.add_middleware(SessionMiddleware, secret_key=SESSION_SECRET)
+
+for vip_route in vip_routes:
+ @app.get(f"/{vip_route}")
+ async def get_vip_route(request: Request):
+ *_, vip = request.url.path.split("/")
+ return RedirectResponse(f"{HOST_PATHNAME}/go/{vip}")
+
+app.include_router(quickstart_router, prefix="/quickstart")
+app.include_router(saneurl_router, prefix="/saneUrl")
+app.include_router(saneurl_router, prefix="/go")
+app.include_router(plugin_router, prefix="/plugins")
+app.include_router(user_router, prefix="/user")
+
+app.include_router(auth_router)
+app.include_router(devbanner_router)
+app.include_router(index_router)
+
+app.mount("/.well-known", StaticFiles(directory=Path(__file__).parent / "well-known"), name="well-known")
+app.mount("/", StaticFiles(directory=Path(PATH_TO_PUBLIC)), name="static")
+
+# if HOST_PATHNAME is defined, mount on a specific route
+# this may be necessary, if the reverse proxy is not under our control
+# and/or we cannot easily strip the route path
+
+if HOST_PATHNAME:
+ assert HOST_PATHNAME[0] == "/", f"HOST_PATHNAME, if defined, must start with /: {HOST_PATHNAME!r}"
+ assert HOST_PATHNAME[-1] != "/", f"HOST_PATHNAME, if defined, must not end with /: {HOST_PATHNAME!r}"
+
+ _app = app
+ app = FastAPI()
+ app.mount(HOST_PATHNAME, _app)
diff --git a/backend/app/auth.py b/backend/app/auth.py
new file mode 100644
index 000000000..fc3fed6a8
--- /dev/null
+++ b/backend/app/auth.py
@@ -0,0 +1,67 @@
+from authlib.integrations.starlette_client import OAuth
+from authlib.integrations.requests_client.oauth2_session import OAuth2Session
+from authlib.oauth2.auth import OAuth2Token
+from fastapi import APIRouter, Request
+from fastapi.responses import RedirectResponse
+from uuid import uuid4
+import json
+
+from .const import EBRAINS_IAM_DISCOVERY_URL, SCOPES, PROFILE_KEY
+from .config import HBP_CLIENTID_V2, HBP_CLIENTSECRET_V2, HOST_PATHNAME, HOSTNAME
+from ._store import RedisEphStore
+
+_store = RedisEphStore.Ephemeral()
+
+oauth = OAuth()
+
+oauth.register(
+ name="ebrains",
+ server_metadata_url=f"{EBRAINS_IAM_DISCOVERY_URL}/.well-known/openid-configuration",
+ client_id=HBP_CLIENTID_V2,
+ client_secret=HBP_CLIENTSECRET_V2,
+ client_kwargs={
+ "scope": " ".join(SCOPES),
+ },
+)
+
+def process_ebrains_user(resp):
+ userinfo = resp.get("userinfo")
+ given_name = userinfo.get("given_name")
+ family_name = userinfo.get("family_name")
+ return {
+ 'id': f'hbp-oidc-v2:{userinfo.get("sub")}',
+ 'name': f'{given_name} {family_name}',
+ 'type': 'hbp-oidc-v2',
+ 'idToken': resp.get("id_token"),
+ 'accessToken': resp.get("access_token"),
+ }
+
+router = APIRouter()
+
+redirect_uri = HOSTNAME.rstrip("/") + HOST_PATHNAME + "/hbp-oidc-v2/cb"
+
+@router.get("/hbp-oidc-v2/auth")
+async def login_via_ebrains(request: Request, state: str = None):
+ kwargs = {}
+ if state:
+ kwargs["state"] = state
+ return await oauth.ebrains.authorize_redirect(request, redirect_uri=redirect_uri, **kwargs)
+
+@router.get("/hbp-oidc-v2/cb")
+async def ebrains_callback(request: Request):
+ if PROFILE_KEY not in request.session:
+ request.session[PROFILE_KEY] = str(uuid4())
+ token: OAuth2Token = await oauth.ebrains.authorize_access_token(request)
+ _store.set(
+ request.session[PROFILE_KEY],
+ json.dumps(process_ebrains_user(token))
+ )
+ redirect = HOST_PATHNAME if HOST_PATHNAME else "/"
+ return RedirectResponse(redirect)
+
+@router.get("/logout")
+def logout(request: Request):
+ _store.delete(
+ request.session.pop(PROFILE_KEY, None)
+ )
+ return RedirectResponse(HOST_PATHNAME)
diff --git a/backend/app/bkwdcompat.py b/backend/app/bkwdcompat.py
new file mode 100644
index 000000000..e977c92cc
--- /dev/null
+++ b/backend/app/bkwdcompat.py
@@ -0,0 +1,248 @@
+import re
+from enum import Enum
+from urllib.parse import urlencode, quote_plus
+from starlette.requests import Request
+from starlette.responses import Response, RedirectResponse
+from starlette.middleware.base import BaseHTTPMiddleware, RequestResponseEndpoint
+import json
+
+from .util import encode_number, separator
+from .logger import logger
+from .config import HOST_PATHNAME
+from .const import ERROR_KEY, COOKIE_KWARGS
+
+waxholm_obj = {
+ "aId": 'minds/core/parcellationatlas/v1.0.0/522b368e-49a3-49fa-88d3-0870a307974a',
+ "id": 'minds/core/referencespace/v1.0.0/d5717c4a-0fa1-46e6-918c-b8003069ade8',
+ "parc": {
+ 'Waxholm Space rat brain atlas v3': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/ebb923ba-b4d5-4b82-8088-fa9215c2e1fe'
+ },
+ 'Whole Brain (v2.0)': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d'
+ },
+ 'Waxholm Space rat brain atlas v2': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d'
+ },
+ 'Waxholm Space rat brain atlas v1': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/11017b35-7056-4593-baad-3934d211daba'
+ },
+ }
+}
+
+allen_obj = {
+ "aId": 'juelich/iav/atlas/v1.0.0/2',
+ "id": 'minds/core/referencespace/v1.0.0/265d32a0-3d84-40a5-926f-bf89f68212b9',
+ "parc": {
+ 'Allen Mouse Common Coordinate Framework v3 2017': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/05655b58-3b6f-49db-b285-64b5a0276f83'
+ },
+ 'Allen Mouse Brain Atlas': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f'
+ },
+ 'Allen Mouse Common Coordinate Framework v3 2015': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f'
+ },
+ }
+}
+
+template_map = {
+ 'Big Brain (Histology)': {
+ "aId": 'juelich/iav/atlas/v1.0.0/1',
+ "id": 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588',
+ "parc": {
+ 'Cytoarchitectonic Maps - v2.4': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290',
+ },
+ 'Cytoarchitectonic Maps': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290',
+ },
+ 'Cortical Layers Segmentation': {
+ "id": 'juelich/iav/atlas/v1.0.0/3'
+ },
+ 'Grey/White matter': {
+ "id": 'juelich/iav/atlas/v1.0.0/4'
+ }
+ }
+ },
+ 'MNI 152 ICBM 2009c Nonlinear Asymmetric': {
+ "aId": 'juelich/iav/atlas/v1.0.0/1',
+ "id": 'minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2',
+ "parc": {
+ 'Cytoarchitectonic Maps - v2.5.1': {
+ # redirect julich brain v251 to v290
+ "id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
+ },
+ 'Short Fiber Bundles - HCP': {
+ "id": 'juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c'
+ },
+ 'Cytoarchitectonic maps - v1.18': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
+ },
+ 'Long Bundle': {
+ "id": 'juelich/iav/atlas/v1.0.0/5'
+ },
+ 'fibre bundle short': {
+ "id": 'juelich/iav/atlas/v1.0.0/6'
+ },
+ 'DiFuMo Atlas (64 dimensions)': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/d80fbab2-ce7f-4901-a3a2-3c8ef8a3b721'
+ },
+ 'DiFuMo Atlas (128 dimensions)': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/73f41e04-b7ee-4301-a828-4b298ad05ab8'
+ },
+ 'DiFuMo Atlas (256 dimensions)': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/141d510f-0342-4f94-ace7-c97d5f160235'
+ },
+ 'DiFuMo Atlas (512 dimensions)': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/63b5794f-79a4-4464-8dc1-b32e170f3d16'
+ },
+ 'DiFuMo Atlas (1024 dimensions)': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/12fca5c5-b02c-46ce-ab9f-f12babf4c7e1'
+ },
+ },
+ },
+ 'MNI Colin 27': {
+ "aId": 'juelich/iav/atlas/v1.0.0/1',
+ "id": 'minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992',
+ "parc": {
+ 'Cytoarchitectonic Maps - v1.18': {
+ "id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
+ }
+ }
+ },
+ 'Waxholm Space rat brain MRI/DTI': waxholm_obj,
+ 'Waxholm Rat V2.0': waxholm_obj,
+ 'Allen Mouse Common Coordinate Framework v3': allen_obj,
+ 'Allen Mouse': allen_obj
+}
+
+def encode_id(_id: str):
+ return re.sub(r'/\//', ':', _id)
+
+class WarningStrings(Enum, str):
+ PREVIEW_DSF_PARSE_ERROR="Preview dataset files cannot be processed properly."
+ REGION_SELECT_ERROR="Region selected cannot be processed properly."
+ TEMPLATE_ERROR="Template not found."
+
+class BkwdCompatMW(BaseHTTPMiddleware):
+ async def dispatch(self, request: Request, call_next: RequestResponseEndpoint) -> Response:
+ standalone_volumes = request.query_params.get("standaloneVolumes")
+ nifti_layers = request.query_params.get("niftiLayers")
+ plugin_states = request.query_params.get("pluginStates")
+ previewing_dataset_files = request.query_params.get("previewingDatasetFiles")
+ template_selected = request.query_params.get("templateSelected")
+ parcellation_selected = request.query_params.get("parcellationSelected")
+ regions_selected = request.query_params.get("regionsSelected")
+ c_regions_selected = request.query_params.get("cRegionsSelected")
+ navigation = request.query_params.get("navigation")
+ c_navigation = request.query_params.get("cNavigation")
+
+ if not any([
+ standalone_volumes,
+ nifti_layers,
+ plugin_states,
+ previewing_dataset_files,
+ template_selected,
+ parcellation_selected,
+ regions_selected,
+ c_regions_selected,
+ navigation,
+ c_navigation,
+ ]):
+ return await super().dispatch(request, call_next)
+
+ redirect_url = f"{HOST_PATHNAME or ''}/#"
+
+ if regions_selected:
+ logger.warn(f"regionSelected deprecated, but was used to access {regions_selected}")
+ if nifti_layers:
+ logger.warn(f"niftiLayers deprecated, but was used to access {nifti_layers}")
+ if previewing_dataset_files:
+ logger.warn(f"previewing_dataset_files deprecated, but was used to access {previewing_dataset_files}")
+
+ new_search_param = {}
+
+ nav = ""
+ r = ""
+
+ if navigation:
+ try:
+ _o, _po, _pz, _p, _z = navigation.split("__")
+ o = map(float, _o.split("_"))
+ po = map(float, _po.split("_"))
+ pz = int(_pz)
+ p = map(float, _p.split("_"))
+ z = int(_z)
+
+ v = f"{separator}{separator}".join([
+ separator.join([encode_number(_val, True) for _val in o]),
+ separator.join([encode_number(_val, True) for _val in po]),
+ encode_number(round(pz)),
+ separator.join([encode_number(round(_val)) for _val in p]),
+ encode_number(z)
+ ])
+ nav = f"/@:{v}"
+ except Exception as e:
+ logger.error(f"bkwds parsing navigation error, {str(e)}")
+
+ if c_navigation:
+ nav = f"/@:${c_navigation}"
+
+ plugins = [p for p in (plugin_states or "").split("__") if p]
+ if len(plugins) > 0:
+ new_search_param["pl", json.dumps(plugins)]
+
+ if c_regions_selected:
+ logger.warn(f"cRegionSelected is deprecated, but used for {c_regions_selected}")
+ # see util.py get_hash
+
+ if standalone_volumes:
+ new_search_param["standaloneVolumes"] = standalone_volumes
+ if nav:
+ redirect_url = redirect_url + nav
+ if len(new_search_param) > 0:
+ redirect_url = redirect_url + f"?{urlencode(new_search_param)}"
+ return RedirectResponse(redirect_url)
+
+ if not template_selected:
+ resp = RedirectResponse(redirect_url)
+ resp.set_cookie(ERROR_KEY, "template_selected is required, but not defined", **COOKIE_KWARGS)
+ return resp
+
+ error_msg = ""
+ _tmpl = template_map.get(template_selected)
+ if not _tmpl:
+ resp = RedirectResponse(template_selected)
+ resp.set_cookie(ERROR_KEY, f"Template with id {template_selected} not found.", **COOKIE_KWARGS)
+ return resp
+
+ _tmpl_id = _tmpl.get("id")
+ _atlas_id = _tmpl.get("aId")
+
+ redirect_url += f"/a:{quote_plus(_atlas_id)}/t:{quote_plus(_tmpl_id)}"
+
+ _parcs = _tmpl.get("parc")
+
+ if parcellation_selected in _parcs:
+ parc_id = _parcs[parcellation_selected].get("id")
+ else:
+ error_msg += f"parcellation with id {parcellation_selected} cannot be found"
+ parc_id = list(_parcs.values())[0].get("id")
+
+ redirect_url += f"/p:{quote_plus(parc_id)}"
+
+ if r and parcellation_selected != "Cytoarchitectonic Maps - v2.5.1":
+ redirect_url += r
+
+ if nav:
+ redirect_url += nav
+
+ if len(new_search_param) > 0:
+ redirect_url += urlencode(new_search_param)
+
+ resp = RedirectResponse(redirect_url)
+ if len(error_msg) > 0:
+ resp.set_cookie(ERROR_KEY, error_msg, **COOKIE_KWARGS)
+
+ return resp
\ No newline at end of file
diff --git a/backend/app/config.py b/backend/app/config.py
new file mode 100644
index 000000000..7c5423fb2
--- /dev/null
+++ b/backend/app/config.py
@@ -0,0 +1,39 @@
+import os
+
+SESSION_SECRET = os.getenv("SESSION_SECRET", "hey joline, remind me to set a more secure session secret")
+
+HOST_PATHNAME = os.getenv("HOST_PATHNAME", "")
+PORT = os.getenv("PORT")
+
+HOSTNAME = os.getenv("HOSTNAME", "http://localhost:3000")
+
+OVERWRITE_API_ENDPOINT = os.getenv("OVERWRITE_API_ENDPOINT")
+
+LOCAL_CDN = os.getenv("LOCAL_CDN")
+
+HBP_CLIENTID_V2 = os.getenv("HBP_CLIENTID_V2", "no hbp id")
+HBP_CLIENTSECRET_V2 = os.getenv("HBP_CLIENTSECRET_V2", "no hbp client secret")
+
+HBP_DISCOVERY_URL = "https://iam.ebrains.eu/auth/realms/hbp"
+
+BUILD_TEXT = os.getenv("BUILD_TEXT", "")
+
+# REDIS env var
+
+REDIS_PROTO = os.getenv("REDIS_PROTO")
+REDIS_ADDR = os.getenv("REDIS_ADDR") or os.getenv("REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_PROTO") or "localhost"
+REDIS_PORT = os.getenv("REDIS_PORT") or os.getenv("REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_PORT") or "6379"
+REDIS_USERNAME = os.getenv("REDIS_USERNAME")
+REDIS_PASSWORD = os.getenv("REDIS_PASSWORD")
+
+V2_7_PLUGIN_URLS = os.getenv("V2_7_PLUGIN_URLS", "")
+V2_7_STAGING_PLUGIN_URLS = os.getenv("V2_7_STAGING_PLUGIN_URLS", "")
+
+SXPLR_EBRAINS_IAM_SA_CLIENT_ID = os.getenv("SXPLR_EBRAINS_IAM_SA_CLIENT_ID")
+SXPLR_EBRAINS_IAM_SA_CLIENT_SECRET = os.getenv("SXPLR_EBRAINS_IAM_SA_CLIENT_SECRET")
+
+SXPLR_BUCKET_NAME = os.getenv("SXPLR_BUCKET_NAME", "interactive-atlas-viewer")
+
+LOGGER_DIR = os.getenv("LOGGER_DIR")
+
+PATH_TO_PUBLIC = os.getenv("PATH_TO_PUBLIC", "../dist/aot")
\ No newline at end of file
diff --git a/backend/app/const.py b/backend/app/const.py
new file mode 100644
index 000000000..9948b8e47
--- /dev/null
+++ b/backend/app/const.py
@@ -0,0 +1,21 @@
+PROFILE_KEY = "sxplr-session-uuid"
+ERROR_KEY = "sxplr-error"
+
+COOKIE_KWARGS = {
+ "httponly": True,
+ "samesite": "strict",
+}
+
+EBRAINS_IAM_DISCOVERY_URL = "https://iam.ebrains.eu/auth/realms/hbp"
+
+SCOPES = [
+ 'openid',
+ 'email',
+ 'profile',
+ 'collab.drive',
+ "team"
+]
+
+DATA_ERROR_ATTR = "data-error"
+
+OVERWRITE_SAPI_ENDPOINT_ATTR = "x-sapi-base-url"
diff --git a/backend/app/dev_banner.py b/backend/app/dev_banner.py
new file mode 100644
index 000000000..101e3e22e
--- /dev/null
+++ b/backend/app/dev_banner.py
@@ -0,0 +1,22 @@
+from fastapi.routing import APIRouter
+from fastapi.responses import PlainTextResponse
+from .config import BUILD_TEXT
+from .logger import main_logger
+
+router = APIRouter()
+
+main_logger.info(f"BUILD_TEXT: {BUILD_TEXT}")
+
+css_string = "body::after {{ content: '{BUILD_TEXT}' }}".format(
+ BUILD_TEXT="dev build" if BUILD_TEXT is None else BUILD_TEXT
+)
+
+@router.get("/version.css")
+def build_text():
+ return PlainTextResponse(
+ css_string,
+ headers={
+ "content-type": "text/css; charset=UTF-8",
+ "cache-control": "public, max-age={age_seconds}".format(age_seconds=60*60*24)
+ },
+ )
diff --git a/backend/app/index_html.py b/backend/app/index_html.py
new file mode 100644
index 000000000..903ec1547
--- /dev/null
+++ b/backend/app/index_html.py
@@ -0,0 +1,45 @@
+from fastapi import APIRouter, Request
+from pathlib import Path
+from fastapi.responses import Response
+from typing import Dict
+from .const import ERROR_KEY, DATA_ERROR_ATTR, OVERWRITE_SAPI_ENDPOINT_ATTR, COOKIE_KWARGS
+from .config import PATH_TO_PUBLIC, OVERWRITE_API_ENDPOINT
+
+path_to_index = Path(PATH_TO_PUBLIC) / "index.html"
+index_html: str = None
+
+router = APIRouter()
+
+def _monkey_sanitize(value: str):
+ return value.replace('"', ""e;")
+
+@router.get("/")
+@router.get("/index.html")
+async def get_index_html(request: Request):
+
+ global index_html
+ if index_html is None:
+ with open(path_to_index, "r") as fp:
+ index_html = fp.read()
+
+ # TODO: LOCAL_CDN not yet ported over
+ error = None
+ attributes_to_append: Dict[str, str] = {}
+ if ERROR_KEY in request.session:
+ error = request.session[ERROR_KEY]
+ attributes_to_append[DATA_ERROR_ATTR] = error
+
+ if OVERWRITE_API_ENDPOINT:
+ attributes_to_append[OVERWRITE_SAPI_ENDPOINT_ATTR] = OVERWRITE_API_ENDPOINT
+
+
+ attr_string = " ".join([f"{key}={_monkey_sanitize(value)}" for key, value in attributes_to_append.items()])
+
+ resp_string = index_html.replace("<atlas-viewer>", f"<atlas-viewer {attr_string}>")
+
+ resp = Response(resp_string, headers={
+ "content-type": "text/html; charset=utf-8"
+ })
+ if ERROR_KEY in request.session:
+ resp.delete_cookie(ERROR_KEY, **COOKIE_KWARGS)
+ return resp
diff --git a/backend/app/logger.py b/backend/app/logger.py
new file mode 100644
index 000000000..478cf6b8c
--- /dev/null
+++ b/backend/app/logger.py
@@ -0,0 +1,42 @@
+import logging
+from logging.handlers import TimedRotatingFileHandler
+from .config import LOGGER_DIR
+
+main_logger = logging.getLogger(__name__)
+main_logger.setLevel(logging.INFO)
+
+logger = logging.getLogger(__name__ + ".info")
+access_logger = logging.getLogger(__name__ + ".access_log")
+ch = logging.StreamHandler()
+
+formatter = logging.Formatter("[%(name)s:%(levelname)s] %(message)s")
+ch.setFormatter(formatter)
+logger.addHandler(ch)
+logger.setLevel("INFO")
+
+
+log_dir = LOGGER_DIR
+
+if log_dir:
+ log_dir += "" if log_dir.endswith("/") else "/"
+
+if log_dir:
+ import socket
+ filename = log_dir + f"{socket.gethostname()}.access.log"
+ access_log_handler = TimedRotatingFileHandler(filename, when="d", encoding="utf-8")
+else:
+ access_log_handler = logging.StreamHandler()
+
+access_format = logging.Formatter("%(asctime)s - %(resp_status)s - %(process_time_ms)sms - %(hit_cache)s - %(message)s")
+access_log_handler.setFormatter(access_format)
+access_log_handler.setLevel(logging.INFO)
+access_logger.addHandler(access_log_handler)
+
+
+if log_dir:
+ import socket
+ filename = log_dir + f"{socket.gethostname()}.general.log"
+ warn_fh = TimedRotatingFileHandler(filename, when="d", encoding="utf-8")
+ warn_fh.setLevel(logging.INFO)
+ warn_fh.setFormatter(formatter)
+ logger.addHandler(warn_fh)
diff --git a/backend/app/plugin.py b/backend/app/plugin.py
new file mode 100644
index 000000000..73187bbee
--- /dev/null
+++ b/backend/app/plugin.py
@@ -0,0 +1,80 @@
+from typing import List
+from fastapi import APIRouter
+from fastapi.responses import JSONResponse
+import json
+import requests
+import re
+from urllib.parse import urlparse
+from pathlib import Path
+from concurrent.futures import ThreadPoolExecutor
+from .config import V2_7_PLUGIN_URLS, V2_7_STAGING_PLUGIN_URLS
+from .logger import logger
+from ._store import RedisEphStore
+
+router = APIRouter()
+_redisstore = RedisEphStore.Persistent()
+
+PLUGINS: List[str] = []
+try:
+ PLUGINS = [
+ v
+ for v in [*V2_7_PLUGIN_URLS.split(";"), *V2_7_STAGING_PLUGIN_URLS.split(";")]
+ if v # remove empty strings
+ ]
+except Exception as e:
+ logger.error(f"failed to parse plugins correctly: {str(e)}")
+
+
+def _get_key(url: str):
+ return f"plugin:manifest-cache:{url}"
+
+def _get_manifest(url: str):
+
+ key = _get_key(url)
+ try:
+ stored_manifest = _redisstore.get(key)
+ try:
+ if stored_manifest:
+ return json.loads(stored_manifest)
+ except:
+ # If parsing json fails, fall back to fetch manifest
+ pass
+
+ resp = requests.get(url)
+ resp.raise_for_status()
+ manifest_json = resp.json()
+
+ sxplr_flag = manifest_json.get("siibra-explorer")
+ iframe_url = manifest_json.get("iframeUrl")
+
+ if not sxplr_flag:
+ logger.warn(f"plugin mainfest at {url} does not have siibra-explorer flag set")
+ return None
+
+ replace_obj = {}
+ if not re.match(r"https:", iframe_url):
+ parsed_url = urlparse(url)
+ if iframe_url[0] == "/":
+ new_name = iframe_url
+ else:
+ new_name = str(Path(parsed_url.path).with_name(iframe_url))
+ replace_obj["iframeUrl"] = parsed_url._replace(path=new_name).geturl()
+ return_obj = { **manifest_json, **replace_obj }
+ _redisstore.set(key, json.dumps(return_obj))
+ return return_obj
+
+ except Exception as e:
+ logger.error(f"Error retrieving: {url}")
+
+
+@router.get("/manifests")
+def plugin_manifests():
+ with ThreadPoolExecutor() as ex:
+ returned_obj = ex.map(
+ _get_manifest,
+ PLUGINS
+ )
+ returned_obj = [v for v in returned_obj if v]
+ return JSONResponse(returned_obj, headers={
+ "cache-control": "public, max-age={age_seconds}".format(age_seconds=60*60*24)
+ })
diff --git a/backend/app/quickstart.py b/backend/app/quickstart.py
new file mode 100644
index 000000000..d8c346dbb
--- /dev/null
+++ b/backend/app/quickstart.py
@@ -0,0 +1,55 @@
+from fastapi.routing import APIRouter
+from fastapi.responses import HTMLResponse
+from pathlib import Path
+from markdown import markdown
+import json
+
+helper_content: str = None
+markdown_content: str = None
+
+router = APIRouter()
+
+
+@router.get("")
+@router.get("/")
+async def quickstart():
+ global helper_content
+ global markdown_content
+ if not helper_content:
+ path_to_helper = Path(__file__).parent / ".." / ".." / "common/helpOnePager.md"
+ with open(path_to_helper, "r") as fp:
+ helper_content = fp.read()
+ markdown_content = markdown(helper_content, extensions=["markdown.extensions.admonition", "markdown.extensions.codehilite", "markdown.extensions.tables"])
+
+ html_response = """
+<!DOCTYPE html>
+<html lang="en">
+<head>
+ <meta charset="UTF-8">
+ <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
+ <script src="https://unpkg.com/dompurify@latest/dist/purify.min.js"></script>
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <title>Siibra Explorer Quickstart</title>
+ <style>
+ .padded { padding: 1.5rem; }
+ </style>
+</head>
+<body class="padded">
+
+</body>
+<script>
+(() => {
+ const markdown = """+ json.dumps(helper_content) + """
+ const dirty = """ + json.dumps(markdown_content) + """
+ const clean = DOMPurify.sanitize(dirty)
+ document.body.innerHTML = clean
+})()
+</script>
+</html>
+"""
+ return HTMLResponse(html_response)
+
+
+__all__ = [
+ "router"
+]
diff --git a/backend/app/sane_url.py b/backend/app/sane_url.py
new file mode 100644
index 000000000..2842ed9ab
--- /dev/null
+++ b/backend/app/sane_url.py
@@ -0,0 +1,152 @@
+from fastapi import APIRouter, Request
+from fastapi.responses import Response, JSONResponse, RedirectResponse
+from fastapi.exceptions import HTTPException
+from authlib.integrations.requests_client import OAuth2Session
+import requests
+import json
+from typing import Union, Dict, Optional
+import time
+from io import StringIO
+from pydantic import BaseModel
+
+from .config import SXPLR_EBRAINS_IAM_SA_CLIENT_ID, SXPLR_EBRAINS_IAM_SA_CLIENT_SECRET, SXPLR_BUCKET_NAME, HOST_PATHNAME
+from .const import EBRAINS_IAM_DISCOVERY_URL
+from ._store import DataproxyStore
+
+router = APIRouter()
+
+endpoint = "https://data-proxy.ebrains.eu/api/v1/buckets/{bucket_name}/{object_name}"
+
+vip_routes = [
+ "human",
+ "monkey",
+ "rat",
+ "mouse"
+]
+
+
+class SaneUrlDPStore(DataproxyStore):
+ class AlreadyExists(Exception): ...
+
+ @staticmethod
+ def GetTimeMs() -> int:
+ return round(time.time()*1e3)
+
+ @staticmethod
+ def TransformKeyToObjName(key: str):
+ return f"saneUrl/{key}.json"
+
+ def __init__(self, expiry_s=3 * 24 * 60 * 60):
+
+ resp = requests.get(f"{EBRAINS_IAM_DISCOVERY_URL}/.well-known/openid-configuration")
+ resp.raise_for_status()
+ resp_json = resp.json()
+ assert "token_endpoint" in resp_json, f"authorization_endpoint must be in openid configuration"
+ self._token_endpoint: str = resp_json["token_endpoint"]
+
+ scopes=["openid", "team", "roles", "group"]
+ oauth2_session = OAuth2Session(SXPLR_EBRAINS_IAM_SA_CLIENT_ID,
+ SXPLR_EBRAINS_IAM_SA_CLIENT_SECRET,
+ scope=" ".join(scopes))
+ self.session = oauth2_session
+ self.expiry_s: float = None
+ self.token: str = None
+ self._refresh_token()
+
+ super().__init__(self.token, SXPLR_BUCKET_NAME)
+
+ def _refresh_token(self):
+ token_dict = self.session.fetch_token(self._token_endpoint, grant_type="client_credentials")
+ self.expiry_s = token_dict.get("expires_at")
+ self.token = token_dict.get("access_token")
+
+ def _get_bucket(self):
+ token_expired = self.expiry_s - time.time() > 30
+ if token_expired:
+ self._refresh_token()
+
+ self.update_token(self.token)
+ return super()._get_bucket()
+
+ def _prepare_aux(self, request: Optional[Request]=None):
+ return {
+ "userId": None,
+ "expiry": SaneUrlDPStore.GetTimeMs() + (self.expiry_s * 1e3)
+ }
+
+ def get(self, key: str):
+ try:
+ object_name = SaneUrlDPStore.TransformKeyToObjName(key)
+ resp = super().get(object_name)
+ resp_content = json.loads(resp)
+ expiry = resp_content.get("expiry")
+ if expiry is not None and SaneUrlDPStore.GetTimeMs() > expiry:
+ self.delete(key)
+ raise SaneUrlDPStore.NotFound("expired")
+ return resp_content.get("value")
+ except SaneUrlDPStore.NotFound as e:
+ raise e from e
+ except requests.exceptions.HTTPError as e:
+ if e.response.status_code == 404:
+ raise SaneUrlDPStore.NotFound(str(e)) from e
+ raise SaneUrlDPStore.GenericException(str(e)) from e
+ except Exception as e:
+ raise SaneUrlDPStore.GenericException(str(e)) from e
+
+ def set(self, key: str, value: Union[str, Dict], request: Optional[Request]=None):
+
+ object_name = SaneUrlDPStore.TransformKeyToObjName(key)
+ try:
+ super().get(object_name)
+ raise SaneUrlDPStore.AlreadyExists
+ except SaneUrlDPStore.NotFound as e:
+ pass
+
+ bucket = self._get_bucket()
+
+ sio = StringIO()
+ json.dump({
+ "value": value,
+ **self._prepare_aux(request)
+ }, fp=sio)
+ sio.seek(0)
+ bucket.upload(sio, object_name)
+
+ def delete(self, key: str):
+ object_name = SaneUrlDPStore.TransformKeyToObjName(key)
+ content = super().get(object_name)
+
+ curr = SaneUrlDPStore.GetTimeMs()
+ super().set(f"deleted/{object_name}.{curr}", content)
+
+ super().delete(object_name)
+
+data_proxy_store = SaneUrlDPStore()
+
+@router.get("/{short_id:str}")
+async def get_short(short_id:str, request: Request):
+ try:
+ resp = data_proxy_store.get(short_id)
+ accept = request.headers.get("Accept")
+ if "text/html" in accept:
+ hashed_path = resp.get("hashPath")
+ return RedirectResponse(f"{HOST_PATHNAME}/#{hashed_path}")
+ return JSONResponse(resp)
+ except DataproxyStore.NotFound as e:
+ raise HTTPException(404, str(e))
+ except DataproxyStore.GeneralException as e:
+ raise HTTPException(500, str(e))
+
+
+class SaneUrlModel(BaseModel):
+ ver: str
+ hashPath: str # camel case for backwards compat
+
+
+@router.post("/{short_id: str}")
+async def post_short(short_id: str, saneurl: SaneUrlModel):
+ try:
+ data_proxy_store.set(short_id, saneurl.model_dump_json())
+ return Response(status_code=201)
+ except Exception as e:
+ raise HTTPException(500, str(e))
diff --git a/backend/app/sxplr_iam.py b/backend/app/sxplr_iam.py
new file mode 100644
index 000000000..0d496ea51
--- /dev/null
+++ b/backend/app/sxplr_iam.py
@@ -0,0 +1,6 @@
+from authlib.integrations.starlette_client import OAuth
+from authlib.integrations.requests_client.oauth2_session import OAuth2Session
+from authlib.oauth2.auth import OAuth2Token
+
+from .const import PROFILE_KEY
+
diff --git a/backend/app/user.py b/backend/app/user.py
new file mode 100644
index 000000000..dc5789038
--- /dev/null
+++ b/backend/app/user.py
@@ -0,0 +1,63 @@
+from typing import Any, Coroutine
+from starlette.requests import Request
+from starlette.responses import Response
+from fastapi import FastAPI, APIRouter
+from functools import wraps
+from inspect import iscoroutine
+
+import json
+from .const import PROFILE_KEY
+from .auth import _store
+
+def is_authenticated(fn):
+
+ class NotAuthenticatedEx(Exception): ...
+
+ def check_auth(request: Request):
+ if PROFILE_KEY not in request.session:
+ raise NotAuthenticatedEx
+
+ profile_uuid = request.session[PROFILE_KEY]
+ user = _store.get(profile_uuid)
+ if not user:
+ raise NotAuthenticatedEx
+
+ request.state.user = json.loads(user)
+
+ @wraps(fn)
+ async def async_wrapper(*args, request: Request, **kwargs):
+ try:
+ check_auth(request)
+ except NotAuthenticatedEx:
+ return Response("Not authenticated", 401)
+ return await fn(*args, request=request, **kwargs)
+
+ @wraps(fn)
+ def sync_wrapper(*args, request: Request, **kwargs):
+ try:
+ check_auth(request)
+ except NotAuthenticatedEx:
+ return Response("Not authenticated", 401)
+ return fn(*args, request=request, **kwargs)
+ return async_wrapper if iscoroutine(fn) else sync_wrapper
+
+
+router = APIRouter()
+
+@router.get("/foo")
+@is_authenticated
+def foo(request: Request):
+ return "foo"
+
+@router.get("")
+@router.get("/")
+@is_authenticated
+def get_user(request: Request):
+ try:
+ user = request.state.user
+ if user:
+ return Response(json.dumps(user), 200)
+ else:
+ return Response(None, 401)
+ except:
+ return Response(None, 500)
diff --git a/backend/app/util.py b/backend/app/util.py
new file mode 100644
index 000000000..1265bcc5f
--- /dev/null
+++ b/backend/app/util.py
@@ -0,0 +1,54 @@
+import math
+import struct
+
+cipher = '0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz_-'
+separator = '.'
+neg = '~'
+def encode_number(n, float_flag=False):
+ if float_flag:
+ b=struct.pack('f', n)
+ new_n=struct.unpack('i',b)
+ return encode_int(new_n[0])
+ else:
+ return encode_int(n)
+
+def encode_int(n):
+ if not isinstance(n, int):
+ raise ValueError('Cannot encode int')
+
+ residual=None
+ result=''
+ if n < 0:
+ result += neg
+ residual = n * -1
+ else:
+ residual = n
+
+ while True:
+ result = cipher[residual % 64] + result
+ residual = math.floor(residual / 64)
+
+ if residual == 0:
+ break
+ return result
+
+# get_hash may not have to be implemented
+# CON: add numpy dependency
+# PRO: might need to support hashing region name for selected region
+#
+# def get_hash(full_string: str):
+# return_val=0
+# with np.errstate(over="ignore"):
+# for char in full_string:
+# # overflowing is expected and in fact the whole reason why convert number to int32
+
+# # in windows, int32((0 - min_int32) << 5), rather than overflow to wraper around, raises OverflowError
+# shifted_5 = int32(
+# (return_val - min_int32) if return_val > max_int32 else return_val
+# << 5)
+
+# return_val = int32(shifted_5 - return_val + ord(char))
+# return_val = return_val & return_val
+# hex_val = hex(return_val)
+# return hex_val[3:]
+
diff --git a/deploy/well-known/robot.txt b/backend/app/well-known/robot.txt
similarity index 100%
rename from deploy/well-known/robot.txt
rename to backend/app/well-known/robot.txt
diff --git a/deploy/well-known/security.txt b/backend/app/well-known/security.txt
similarity index 100%
rename from deploy/well-known/security.txt
rename to backend/app/well-known/security.txt
diff --git a/backend/requirements.txt b/backend/requirements.txt
new file mode 100644
index 000000000..c321ab821
--- /dev/null
+++ b/backend/requirements.txt
@@ -0,0 +1,12 @@
+fastapi
+markdown
+authlib
+uvicorn[standard] # required as a asgi
+itsdangerous # required for starlette session middleware
+httpx # required for async uvicorn
+redis
+
+# cherrypicks https://github.com/HumanBrainProject/ebrains-drive/pull/20 and https://github.com/HumanBrainProject/ebrains-drive/pull/22
+# once both merged and published, use ebrains-drive instead
+git+https://github.com/xgui3783/ebrains-drive.git@tmp_fixDeleteUseIO
+
diff --git a/check_all.sh b/check_all.sh
deleted file mode 100755
index 108ea83b2..000000000
--- a/check_all.sh
+++ /dev/null
@@ -1,47 +0,0 @@
-#! /bin/bash
-
-echo 'Running all tests ...'
-
-echo 'Running linter ...'
-
-# check lint
-npm run lint &> check_all_lint.log || exit
-
-echo 'Linter complete.'
-
-echo 'Running unit tests ...'
-# unit test
-NODE_ENV=test npm run test &> check_all_test.log || exit
-echo 'Unit tests complete.'
-
-echo 'Running server tests ...'
-cd deploy
-npm run test &> check_all_deploy_test.log || exit
-echo 'Server test complete.'
-
-cd ..
-
-echo 'Building and running e2e tests ...'
-echo 'Building ...'
-# e2e tests
-npm run build-aot &> check_all_build_aot.log || exit
-echo 'Build complete.'
-
-echo 'Spinning up node server ...'
-# run node server
-cd deploy
-node server.js &> check_all_deploy_server.log &
-NDOE_SERVER_PID=$!
-
-# run e2e test
-
-echo 'Running e2e tests ...'
-cd ..
-npm run e2e &> check_all_e2e.log || kill "$NDOE_SERVER_PID" && exit
-echo 'e2e tests complete.'
-
-echo 'Killing server.js pid $NDOE_SERVER_PID'
-
-kill "$NDOE_SERVER_PID"
-
-echo 'All runs complete.'
diff --git a/deploy/.gitignore b/deploy/.gitignore
deleted file mode 100644
index 20d4182a3..000000000
--- a/deploy/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-.env
-res/*
-raw
diff --git a/deploy/README.md b/deploy/README.md
deleted file mode 100644
index 0985ca15d..000000000
--- a/deploy/README.md
+++ /dev/null
@@ -1,18 +0,0 @@
-# Deployment
-
-Latest stable version of siibra explorer is continously deployed to the following URL:
-
-- <https://interactive-viewer.apps.hbp.eu/>
-- <https://atlases.ebrains.eu/viewer/>
-
-## Dependency monitoring
-
-Siibra explorer interacts with a number of other ebrains services. Monitoring these services contributes to the stability of the webapplication.
-
-### Probability & continuous maps availability
-
-[](https://github.com/FZJ-INM1-BDA/iav-dep-test/actions?query=workflow%3A%22Monitoring+KG+Dataset+Preview+Service%22)
-
-### Misc
-
-[](https://github.com/FZJ-INM1-BDA/iav-dep-test/actions?query=workflow%3A%22Monitoring+IAV+dependency+services%22)
\ No newline at end of file
diff --git a/deploy/api-test/Jenkinsfile b/deploy/api-test/Jenkinsfile
deleted file mode 100644
index 9273d9aaa..000000000
--- a/deploy/api-test/Jenkinsfile
+++ /dev/null
@@ -1,58 +0,0 @@
-pipeline {
- agent {
- node {
- label 'nodejs'
- }
- }
-
- environment {
- SERVICE_ACCOUNT_CRED = credentials('SERVICE_ACCOUNT_CRED')
- WAXHOLM_RAT_GOOGLE_SHEET_ID = credentials('WAXHOLM_RAT_GOOGLE_SHEET_ID')
- HUMAN_GOOGLE_SHEET_ID = credentials('HUMAN_GOOGLE_SHEET_ID')
- ATLAS_URL = 'https://interactive-viewer-next.apps-dev.hbp.eu/'
- }
-
- stages {
- stage('Build') {
- steps {
- echo 'Building...'
- sh 'node --version'
- sh 'cd deploy && npm install'
- }
- }
- stage('Test available datasets') {
- parallel {
- stage('rat - v1.01') {
- steps {
- sh 'cd deploy && npm run mocha-env -- ./api-test/**/rat.v1_01.spec.js --timeout 60000'
- }
- }
- stage('rat - v2') {
- steps {
- sh 'cd deploy && npm run mocha-env -- ./api-test/**/rat.v2.spec.js --timeout 60000'
- }
- }
- stage('rat - v3') {
- steps {
- sh 'cd deploy && npm run mocha-env -- ./api-test/**/rat.v3.spec.js --timeout 60000'
- }
- }
- stage('mouse - 2015') {
- steps {
- sh 'cd deploy && npm run mocha-env -- ./api-test/**/mouse.2015.spec.js --timeout 60000'
- }
- }
- stage('mouse - 2017') {
- steps {
- sh 'cd deploy && npm run mocha-env -- ./api-test/**/mouse.2017.spec.js --timeout 60000'
- }
- }
- stage('human') {
- steps {
- sh 'cd deploy && echo NYI'
- }
- }
- }
- }
- }
-}
diff --git a/deploy/api-test/datasets/mouse.2015.e2e-spec.js b/deploy/api-test/datasets/mouse.2015.e2e-spec.js
deleted file mode 100644
index 5897893e3..000000000
--- a/deploy/api-test/datasets/mouse.2015.e2e-spec.js
+++ /dev/null
@@ -1,13 +0,0 @@
-const atlas = 'Allen Mouse Common Coordinate Framework v3 2015'
-const referenceSpace = 'Allen Mouse Common Coordinate Framework v3'
-const wildCard = 'both (Waxholm/ Allen)'
-
-const { getAllenWaxholmTest } = require('./ratMouse.util')
-
-const ATLAS_URL = process.env.ATLAS_URL || 'https://interactive-viewer.apps.hbp.eu/'
-
-getAllenWaxholmTest({
- atlas,
- referenceSpace,
- wildCard
-})(ATLAS_URL)
\ No newline at end of file
diff --git a/deploy/api-test/datasets/mouse.2017.e2e-spec.js b/deploy/api-test/datasets/mouse.2017.e2e-spec.js
deleted file mode 100644
index f865228aa..000000000
--- a/deploy/api-test/datasets/mouse.2017.e2e-spec.js
+++ /dev/null
@@ -1,13 +0,0 @@
-const atlas = 'Allen Mouse Common Coordinate Framework v3 2017'
-const referenceSpace = 'Allen Mouse Common Coordinate Framework v3'
-const wildCard = 'both (Waxholm/ Allen)'
-
-const { getAllenWaxholmTest } = require('./ratMouse.util')
-
-const ATLAS_URL = process.env.ATLAS_URL || 'https://interactive-viewer.apps.hbp.eu/'
-
-getAllenWaxholmTest({
- atlas,
- referenceSpace,
- wildCard
-})(ATLAS_URL)
\ No newline at end of file
diff --git a/deploy/api-test/datasets/rat.v1_01.e2e-spec.js b/deploy/api-test/datasets/rat.v1_01.e2e-spec.js
deleted file mode 100644
index b29838257..000000000
--- a/deploy/api-test/datasets/rat.v1_01.e2e-spec.js
+++ /dev/null
@@ -1,13 +0,0 @@
-const atlas = 'Waxholm Space rat brain atlas v1.01'
-const referenceSpace = 'Waxholm Space rat brain MRI/DTI'
-const wildCard = 'both (Waxholm/ Allen)'
-
-const { getAllenWaxholmTest } = require('./ratMouse.util')
-
-const ATLAS_URL = process.env.ATLAS_URL || 'https://interactive-viewer.apps.hbp.eu/'
-
-getAllenWaxholmTest({
- atlas,
- referenceSpace,
- wildCard
-})(ATLAS_URL)
\ No newline at end of file
diff --git a/deploy/api-test/datasets/rat.v2.e2e-spec.js b/deploy/api-test/datasets/rat.v2.e2e-spec.js
deleted file mode 100644
index aa44965ff..000000000
--- a/deploy/api-test/datasets/rat.v2.e2e-spec.js
+++ /dev/null
@@ -1,13 +0,0 @@
-const atlas = 'Waxholm Space rat brain atlas v2'
-const referenceSpace = 'Waxholm Space rat brain MRI/DTI'
-const wildCard = 'both (Waxholm/ Allen)'
-
-const { getAllenWaxholmTest } = require('./ratMouse.util')
-
-const ATLAS_URL = process.env.ATLAS_URL || 'https://interactive-viewer.apps.hbp.eu/'
-
-getAllenWaxholmTest({
- atlas,
- referenceSpace,
- wildCard
-})(ATLAS_URL)
\ No newline at end of file
diff --git a/deploy/api-test/datasets/rat.v3.e2e-spec.js b/deploy/api-test/datasets/rat.v3.e2e-spec.js
deleted file mode 100644
index f7ee3b033..000000000
--- a/deploy/api-test/datasets/rat.v3.e2e-spec.js
+++ /dev/null
@@ -1,13 +0,0 @@
-const atlas = 'Waxholm Space rat brain atlas v3'
-const referenceSpace = 'Waxholm Space rat brain MRI/DTI'
-const wildCard = 'both (Waxholm/ Allen)'
-
-const { getAllenWaxholmTest } = require('./ratMouse.util')
-
-const ATLAS_URL = process.env.ATLAS_URL || 'https://interactive-viewer.apps.hbp.eu/'
-
-getAllenWaxholmTest({
- atlas,
- referenceSpace,
- wildCard
-})(ATLAS_URL)
\ No newline at end of file
diff --git a/deploy/api-test/datasets/ratMouse.util.js b/deploy/api-test/datasets/ratMouse.util.js
deleted file mode 100644
index dc9508add..000000000
--- a/deploy/api-test/datasets/ratMouse.util.js
+++ /dev/null
@@ -1,77 +0,0 @@
-const { setupAuth, getInfo, getGetRowsFn } = require('./util')
-
-const { GoogleSpreadsheet } = require('google-spreadsheet')
-const WAXHOLM_RAT_GOOGLE_SHEET_ID = process.env.WAXHOLM_RAT_GOOGLE_SHEET_ID
-if (!WAXHOLM_RAT_GOOGLE_SHEET_ID) throw new Error(`env var WAXHOLM_RAT_GOOGLE_SHEET_ID is undefined`)
-
-const doc = new GoogleSpreadsheet(WAXHOLM_RAT_GOOGLE_SHEET_ID)
-
-// TODO for backward compatiblity with what must be node v 0.0.1
-// OKD jenkins nodejs slave runs on nodejs that does not support generator function
-// swap request for got as soon as this is rectified
-// const got = require('got')
-require('tls').DEFAULT_ECDH_CURVE = 'auto'
-const request = require('request')
-const { expect } = require('chai')
-const { URL } = require('url')
-
-const getWaxholmAllenDatasetsPr = new Promise( async (rs, rj) => {
- await setupAuth(doc)
- const worksheet = doc.sheetsByIndex.find(({ title }) => title === 'Dataset level')
- if (!worksheet) rj(`worksheet 'Dataset level' not found!`)
-
- const rows = await worksheet.getRows({ offset: 1 })
- const filteredrows = rows.filter(r => r['Public or curated?'] === 'public')
-
- rs(filteredrows)
-})
-
-const getWaxholmAllenDatasets = () => getWaxholmAllenDatasetsPr
-
-const getAllenWaxholmTest = ({
- atlas,
- referenceSpace,
- wildCard
- }) => ATLAS_URL => describe(referenceSpace, () => {
- let spreadsheetExpectedDatasets = []
- before(async () => {
- spreadsheetExpectedDatasets = (await getWaxholmAllenDatasets())
- .filter(r => r['Reference Atlas'] === atlas || r['Reference Atlas'] === wildCard)
- .map(r => r['Dataset name'])
- })
- describe(atlas, () => {
- describe(`testing ${ATLAS_URL}`, () => {
-
- let fetchedDatasets = []
- before(async () => {
- const getUrl = new URL(`${ATLAS_URL.replace(/\/$/, '')}/datasets/templateNameParcellationName/${encodeURIComponent(referenceSpace)}/${encodeURIComponent(atlas)}`)
- // const resp = await got(getUrl)
- const resp = await (new Promise((rs, rj) => {
- request(getUrl, {}, (err, resp, body) => {
- if (err) rj(err)
- rs(resp)
- })
- }))
- expect(resp.statusCode).to.equal(200)
- fetchedDatasets = JSON.parse(resp.body).map(({ name }) => name)
- })
-
- it(`number of fetched === number of expected`, () => {
- expect(fetchedDatasets.length).to.eq(spreadsheetExpectedDatasets.length)
- })
-
- it('expect fetched === expected. + = expected, but not fetched; - = fetched, but not expected', () => {
- expect(
- fetchedDatasets.sort()
- ).to.have.members(
- spreadsheetExpectedDatasets.sort()
- )
- })
- })
- })
- })
-
-module.exports = {
- getWaxholmAllenDatasets,
- getAllenWaxholmTest
-}
diff --git a/deploy/api-test/datasets/util.js b/deploy/api-test/datasets/util.js
deleted file mode 100644
index adbe35c24..000000000
--- a/deploy/api-test/datasets/util.js
+++ /dev/null
@@ -1,15 +0,0 @@
-
-const fs = require('fs')
-const SERVICE_ACCOUNT_CRED = JSON.parse(
- process.env.SERVICE_ACCOUNT_CRED ||
- (process.env.SERVICE_ACCOUNT_CRED_PATH && fs.readFileSync(process.env.SERVICE_ACCOUNT_CRED_PATH, 'utf-8')) ||
- '{}')
-
-const setupAuth = async doc => {
- await doc.useServiceAccountAuth(SERVICE_ACCOUNT_CRED)
- await doc.loadInfo()
-}
-
-module.exports = {
- setupAuth
-}
\ No newline at end of file
diff --git a/deploy/app.js b/deploy/app.js
deleted file mode 100644
index bc3444df3..000000000
--- a/deploy/app.js
+++ /dev/null
@@ -1,228 +0,0 @@
-const path = require('path')
-const express = require('express')
-const app = express.Router()
-const session = require('express-session')
-const crypto = require('crypto')
-const cookieParser = require('cookie-parser')
-const bkwdMdl = require('./bkwdCompat')()
-const { CONST } = require("../common/constants")
-
-if (process.env.NODE_ENV !== 'production') {
- app.use(require('cors')())
-}
-
-app.use('/quickstart', require('./quickstart'))
-
-const hash = string => crypto.createHash('sha256').update(string).digest('hex')
-
-app.use((req, resp, next) => {
- if (/main\.bundle\.js$/.test(req.originalUrl)){
- const xForwardedFor = req.headers['x-forwarded-for']
- const ip = req.socket.remoteAddress
- console.log({
- type: 'visitorLog',
- method: 'main.bundle.js',
- xForwardedFor: xForwardedFor && xForwardedFor.replace(/\ /g, '').split(',').map(hash),
- ip: hash(ip)
- })
- }
- if (/favicon/.test(req.originalUrl)) {
- resp.setHeader(`Cache-Control`, `public, max-age=604800, immutable`)
- }
- next()
-})
-
-/**
- * configure Auth
- * async function, but can start server without
- */
-
-let authReady
-
-const _ = (async () => {
-
-/**
- * load env first, then load other modules
- */
-
- const { configureAuth, ready } = require('./auth')
- authReady = ready
- const store = await (async () => {
-
- const { USE_DEFAULT_MEMORY_STORE } = process.env
- if (!!USE_DEFAULT_MEMORY_STORE) {
- console.warn(`USE_DEFAULT_MEMORY_STORE is set to true, memleak expected. Do NOT use in prod.`)
- return null
- }
-
- const { _initPr, redisURL, StoreType } = require('./lruStore')
- await _initPr
- console.log('StoreType', redisURL, StoreType)
- if (!!redisURL) {
- const redis = require('redis')
- const RedisStore = require('connect-redis')(session)
- const client = redis.createClient({
- url: redisURL
- })
- return new RedisStore({
- client
- })
- }
-
- /**
- * memorystore (or perhaps lru-cache itself) does not properly close when server shuts
- * this causes problems during tests
- * So when testing app.js, set USE_DEFAULT_MEMORY_STORE to true
- * see app.spec.js
- */
- const MemoryStore = require('memorystore')(session)
- return new MemoryStore({
- checkPeriod: 86400000
- })
-
- })()
-
- const SESSIONSECRET = process.env.SESSIONSECRET || 'this is not really a random session secret'
-
- /**
- * passport application of oidc requires session
- */
- app.use(session({
- secret: SESSIONSECRET,
- resave: true,
- saveUninitialized: false,
- store
- }))
-
- await configureAuth(app)
-
- app.use('/user', require('./user'))
-
- /**
- * saneUrl end points
- */
- const { router: saneUrlRouter, vipRoutes } = require('./saneUrl')
- app.use('/saneUrl', saneUrlRouter)
- app.use('/go', saneUrlRouter)
-
- const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
-
- for (const route of vipRoutes) {
- app.get(`/${route}`, (req, res) => res.redirect(`${HOST_PATHNAME}/go/${route}`))
- }
-})()
-
-const PUBLIC_PATH = process.env.NODE_ENV === 'production'
- ? path.join(__dirname, 'public')
- : path.join(__dirname, '..', 'dist', 'aot')
-
-/**
- * well known path
- */
-app.use('/.well-known', express.static(path.join(__dirname, 'well-known')))
-
-app.use((_req, res, next) => {
- res.setHeader('Referrer-Policy', 'origin-when-cross-origin')
- next()
-})
-
-/**
- * show dev banner
- * n.b., must be before express.static() call
- */
-app.use(require('./devBanner'))
-
-/**
- * populate nonce token
- */
-const { indexTemplate } = require('./constants')
-app.get('/', (req, res, next) => {
-
- /**
- * configure CSP
- */
- if (process.env.DISABLE_CSP && process.env.DISABLE_CSP === 'true') {
- console.warn(`DISABLE_CSP is set to true, csp will not be enabled`)
- next()
- } else {
- const { bootstrapReportViolation, middelware } = require('./csp')
- bootstrapReportViolation(app)
- middelware(req, res, next)
- }
-
-}, bkwdMdl, cookieParser(), async (req, res) => {
- res.setHeader('Content-Type', 'text/html')
-
- let returnIndex = indexTemplate
-
- if (!!process.env.LOCAL_CDN) {
- const CDN_ARRAY = [
- 'https://stackpath.bootstrapcdn.com',
- 'https://use.fontawesome.com',
- 'https://unpkg.com'
- ]
-
- const regexString = CDN_ARRAY.join('|').replace(/\/|\./g, s => `\\${s}`)
- const regex = new RegExp(regexString, 'gm')
- returnIndex = returnIndex.replace(regex, process.env.LOCAL_CDN)
- }
- const iavError = req.cookies && req.cookies['iav-error']
-
- const attributeToAppend = {}
-
- if (iavError) {
- res.clearCookie('iav-error', { httpOnly: true, sameSite: 'strict' })
- attributeToAppend[CONST.DATA_ERROR_ATTR] = iavError
- }
-
- if (!!process.env.OVERWRITE_API_ENDPOING) {
- attributeToAppend[CONST.OVERWRITE_SAPI_ENDPOINT_ATTR] = process.env.OVERWRITE_API_ENDPOING
- }
-
- const attr = Object.entries(attributeToAppend).map(([key, value]) => `${key}="${value.replace(/"/g, '"')}"`).join(" ")
-
- const returnTemplate = returnIndex
- .replace(/\$\$NONCE\$\$/g, res.locals.nonce)
- .replace('<atlas-viewer>', `<atlas-viewer ${attr}>`)
-
- res.status(200).send(returnTemplate)
-})
-
-app.get('/ready', async (req, res) => {
- const authIsReady = authReady ? await authReady() : false
-
- const allReady = [
- authIsReady,
- /**
- * add other ready endpoints here
- * call sig is await fn(): boolean
- */
- ].every(f => !!f)
- if (allReady) return res.status(200).end()
- else return res.status(500).end()
-})
-
-/**
- * only use compression for production
- * this allows locally built aot to be served without errors
- */
-const { compressionMiddleware } = require('nomiseco')
-
-app.use(compressionMiddleware, express.static(PUBLIC_PATH))
-
-const jsonMiddleware = (req, res, next) => {
- if (!res.get('Content-Type')) res.set('Content-Type', 'application/json')
- next()
-}
-
-/**
- * resources endpoints
- */
-const pluginRouter = require('./plugins')
-
-app.use('/plugins', jsonMiddleware, pluginRouter)
-
-const catchError = require('./catchError')
-app.use(catchError)
-
-module.exports = app
diff --git a/deploy/app.spec.js b/deploy/app.spec.js
deleted file mode 100644
index 867241d71..000000000
--- a/deploy/app.spec.js
+++ /dev/null
@@ -1,90 +0,0 @@
-const { expect, assert } = require('chai')
-const express = require('express')
-const got = require('got')
-const sinon = require('sinon')
-
-let server
-const PORT=12345
-
-/**
- * TODO
- * user module import results in error. fix error then reimport
- */
-
-describe('authentication', () => {
-
- /**
- * memorystore (or perhaps lru-cache itself) does not properly close when server.close()
- * use default memory store for tests
- */
- process.env['USE_DEFAULT_MEMORY_STORE'] = true
-
- const fakeFunctionObj = {
- fakeAuthConfigureAuth: sinon.stub().callsFake((req, res, next) => next()),
- fakeAuthReady: async () => true,
- fakeUserRouterFn: sinon.stub().callsFake((req, res, next) => res.status(200).send())
- }
-
- before(async () => {
- const auth = require('./auth')
- const authConfigureAuthStub = sinon.stub(auth, 'configureAuth')
- const authIsReadyStub = sinon.stub(auth, 'ready')
-
- require.cache[require.resolve('./saneUrl')] = {
- exports: {
- router: (req, res, next) => next(),
- ready: async () => true
- }
- }
-
- // require.cache[require.resolve('./user')] = {
- // exports: fakeFunctionObj.fakeUserRouterFn
- // }
-
- require.cache[require.resolve('./constants')] = {
- exports: {
- indexTemplate: ``
- }
- }
-
- authConfigureAuthStub.callsFake(app => {
- app.use(fakeFunctionObj.fakeAuthConfigureAuth)
- return Promise.resolve()
- })
-
- const expressApp = express()
- const app = require('./app')
- expressApp.use(app)
- server = expressApp.listen(PORT)
- })
-
- after(() => {
- delete require.cache[require.resolve('./saneUrl')]
- // delete require.cache[require.resolve('./user')]
- delete require.cache[require.resolve('./constants')]
- server.close()
- })
- // it('> auth middleware is called', async () => {
- // await got(`http://localhost:${PORT}/user`)
- // assert(
- // fakeFunctionObj.fakeAuthConfigureAuth.called,
- // 'auth middleware should be called'
- // )
- // })
-
- // it('> user middleware called', async () => {
- // await got(`http://localhost:${PORT}/user`)
- // assert(
- // fakeFunctionObj.fakeUserRouterFn.called,
- // 'user middleware is called'
- // )
- // })
-
- // it('fakeAuthConfigureAuth is called before user router', async () => {
- // await got(`http://localhost:${PORT}/user`)
- // assert(
- // fakeFunctionObj.fakeAuthConfigureAuth.calledBefore(fakeFunctionObj.fakeUserRouterFn),
- // 'fakeAuthConfigureAuth is called before user router'
- // )
- // })
-})
diff --git a/deploy/auth/hbp-oidc-v2.js b/deploy/auth/hbp-oidc-v2.js
deleted file mode 100644
index d54274808..000000000
--- a/deploy/auth/hbp-oidc-v2.js
+++ /dev/null
@@ -1,81 +0,0 @@
-const passport = require('passport')
-const { configureAuth } = require('./oidc')
-
-const HOSTNAME = process.env.HOSTNAME || 'http://localhost:3000'
-const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
-const clientId = process.env.HBP_CLIENTID_V2 || 'no hbp id'
-const clientSecret = process.env.HBP_CLIENTSECRET_V2 || 'no hbp client secret'
-const discoveryUrl = 'https://iam.ebrains.eu/auth/realms/hbp'
-const redirectUri = `${HOSTNAME}${HOST_PATHNAME}/hbp-oidc-v2/cb`
-const cb = (tokenset, {sub, given_name, family_name, ...rest}, done) => {
- return done(null, {
- id: `hbp-oidc-v2:${sub}`,
- name: `${given_name} ${family_name}`,
- type: `hbp-oidc-v2`,
- tokenset,
- rest
- })
-}
-
-const {
- __DEBUG__
-} = process.env
-
-let oidcStrategy, client, pr
-
-const userScope = [
- 'openid',
- 'email',
- 'profile',
- 'collab.drive'
-]
-
-const adminScope = [
- 'offline_access',
- 'group',
- 'team'
-]
-
-const memoizedInit = () => {
- if (pr) return pr
- pr = (async () => {
- if (client) {
- return
- }
- const re = await configureAuth({
- clientId,
- clientSecret,
- discoveryUrl,
- redirectUri,
- cb,
- scope: [
- ...userScope,
- ...(__DEBUG__ ? adminScope : []),
- ].join(' '),
- clientConfig: {
- redirect_uris: [ redirectUri ],
- response_types: [ 'code' ]
- }
- })
- oidcStrategy = re.oidcStrategy
- client = re.client
- })()
- return pr
-}
-
-module.exports = {
- bootstrapApp: async (app) => {
- try {
- await memoizedInit()
- passport.use('hbp-oidc-v2', oidcStrategy)
- app.get('/hbp-oidc-v2/auth', passport.authenticate('hbp-oidc-v2'))
- app.get('/hbp-oidc-v2/cb', passport.authenticate('hbp-oidc-v2', {
- successRedirect: `${HOST_PATHNAME}/`,
- failureRedirect: `${HOST_PATHNAME}/`
- }))
- return { client }
- } catch (e) {
- console.error('oidcv2 auth error', e)
- }
- },
-}
diff --git a/deploy/auth/index.js b/deploy/auth/index.js
deleted file mode 100644
index 62b41fa21..000000000
--- a/deploy/auth/index.js
+++ /dev/null
@@ -1,38 +0,0 @@
-const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
-const { retry } = require('../../common/util')
-
-let isReady = false
-
-/**
- * using async function. Maybe in the future, we want to introduce async checks
- */
-const ready = async () => isReady
-
-const configureAuth = async (app) => {
- console.log('configure Auth')
- const { bootstrapApp: boostrapOidcV2 } = require('./hbp-oidc-v2')
-
- const { initPassportJs, objStoreDb } = require('./util')
-
- initPassportJs(app)
-
- await retry(async () => {
- await boostrapOidcV2(app)
- }, { timeout: 1000, retries: 3 })
- isReady = true
-
- app.get('/logout', (req, res) => {
- if (req.user && req.user.id) objStoreDb.delete(req.user.id)
- req.logout(err => {
- if (!!err) {
- console.log(`err during logout: ${err.toString()}`)
- }
- res.redirect(`${HOST_PATHNAME}/`)
- })
- })
-}
-
-module.exports = {
- configureAuth,
- ready
-}
\ No newline at end of file
diff --git a/deploy/auth/index.spec.js b/deploy/auth/index.spec.js
deleted file mode 100644
index 8e33c30bd..000000000
--- a/deploy/auth/index.spec.js
+++ /dev/null
@@ -1,109 +0,0 @@
-const sinon = require('sinon')
-const { assert, expect } = require('chai')
-const initPassportJsStub = sinon.stub()
-const hbpOidcV2Stub = sinon.stub()
-
-const appGetStub = sinon.stub()
-
-describe('auth/index.js', () => {
- before(() => {
- require.cache[require.resolve('./util')] = {
- exports: { initPassportJs: initPassportJsStub, objStoreDb: new Map() }
- }
- require.cache[require.resolve('./hbp-oidc-v2')] = {
- exports: {
- bootstrapApp: hbpOidcV2Stub
- }
- }
- })
-
- beforeEach(() => {
- delete require.cache[require.resolve('./index.js')]
- hbpOidcV2Stub.returns({})
- hbpOidcV2Stub.resetHistory()
- })
-
- describe('#configureAuth', () => {
-
- it('> calls necessary dependencies', async () => {
- const { configureAuth } = require('./index.js')
- const dummyObj = { get: appGetStub }
- await configureAuth(dummyObj)
-
- assert(
- hbpOidcV2Stub.called,
- 'hbpOidcV2 called'
- )
-
- assert(
- initPassportJsStub.called,
- 'initPassportJs called'
- )
- })
-
- it('> retries up to three times', async () => {
-
- const { configureAuth } = require('./index.js')
- const dummyObj = { get: appGetStub }
-
- hbpOidcV2Stub.throws(`throw error`)
-
- try {
-
- await (() => new Promise((rs, rj) => {
- configureAuth(dummyObj)
- .then(rs)
- .catch(rj)
- }))()
-
- assert(
- false,
- 'configureAuth should not resolve'
- )
-
- } catch (e) {
-
- assert(
- hbpOidcV2Stub.calledThrice,
- 'hbpOidcv2 called thrice'
- )
-
- }
- })
- })
- describe('#ready', () => {
- it('> if everything resolves correctly ready should return true', async () => {
-
- const { configureAuth, ready } = require('./index.js')
- const dummyObj = { get: appGetStub }
-
- await configureAuth(dummyObj)
-
- const isReady = await ready()
-
- expect(isReady).to.equal(true)
- })
-
- it('> if oidc fails, ready fn returns false', async () => {
-
- const { configureAuth, ready } = require('./index.js')
- const dummyObj = { get: appGetStub }
-
- hbpOidcV2Stub.throws(`throw error`)
-
- try {
- await (() => new Promise((rs, rj) => {
- configureAuth(dummyObj)
- .then(rs)
- .catch(rj)
- }))()
-
- } catch (e) {
-
- }
-
- const isReady = await ready()
- expect(isReady).to.equal(false)
- })
- })
-})
diff --git a/deploy/auth/oidc.js b/deploy/auth/oidc.js
deleted file mode 100644
index c55a09bd4..000000000
--- a/deploy/auth/oidc.js
+++ /dev/null
@@ -1,52 +0,0 @@
-const { Issuer, Strategy } = require('openid-client')
-
-const defaultCb = (tokenset, {id, ...rest}, done) => {
- return done(null, {
- id: id || Date.now(),
- ...rest
- })
-}
-
-exports.jwtDecode = input => {
- if (!input) throw new Error(`jwtDecode must have an input!`)
- const payload = input.split('.')[1]
- if (!payload) {
- throw new Error(`jwt token does not have enough components`)
- }
- return JSON.parse(Buffer.from(payload, 'base64').toString())
-}
-
-exports.configureAuth = async ({ discoveryUrl, clientId, clientSecret, redirectUri, clientConfig = {}, cb = defaultCb, scope = 'openid' }) => {
- if (!discoveryUrl)
- throw new Error('discoveryUrl must be defined!')
-
- if (!clientId)
- throw new Error('clientId must be defined!')
-
- if (!clientSecret)
- throw new Error('clientSecret must be defined!')
-
- if (!redirectUri)
- throw new Error('redirectUri must be defined!')
-
- const issuer = await Issuer.discover(discoveryUrl)
-
- const client = new issuer.Client({
- client_id: clientId,
- client_secret: clientSecret,
- ...clientConfig
- })
-
- const oidcStrategy = new Strategy({
- client,
- params: {
- scope
- },
- }, cb)
-
- return {
- oidcStrategy,
- issuer,
- client
- }
-}
\ No newline at end of file
diff --git a/deploy/auth/spec-helper.js b/deploy/auth/spec-helper.js
deleted file mode 100644
index c82c98a32..000000000
--- a/deploy/auth/spec-helper.js
+++ /dev/null
@@ -1,66 +0,0 @@
-
-const crypto = require('crypto')
-const { stub, spy } = require('sinon')
-
-class OIDCStub{
-
- setupOIDCStub({ rejects, client: _client } = {}) {
-
- // delete require cache, so it can be imported again
- // in case env are rewritten
-
- delete require.cache[require.resolve('./oidc')]
- const OIDC = require('./oidc')
-
- this.jwtDecodeReturn = { exp: Math.floor( (Date.now() / 1e3) * 60 * 60 ) }
- this.configureAuthStub = stub(OIDC, 'configureAuth')
- this.jwtDecodeStub = stub(OIDC, 'jwtDecode').returns(this.jwtDecodeStub)
- this.refresh = (...arg) => {
- const {
- access_token,
- refresh_token,
- id_token,
- } = this
- return {
- access_token,
- refresh_token,
- id_token
- }
- }
-
- this.access_token = crypto.randomBytes(16).toString('hex')
- this.refresh_token = crypto.randomBytes(16).toString('hex')
- this.id_token = crypto.randomBytes(16).toString('hex')
-
- const { refresh } = this
- const client = _client || { refresh }
-
- if (rejects) {
- this.configureAuthStub.rejects()
- } else {
- this.configureAuthStub.resolves({ client })
- }
-
- this.refreshSpy = client && client.refresh && spy(client, 'refresh')
-
- const { access_token, id_token, refreshSpy, refresh_token, configureAuthStub, cleanup, jwtDecodeReturn, jwtDecodeStub } = this
- return {
- access_token,
- refresh_token,
- id_token,
- configureAuthStub,
- refreshSpy,
- jwtDecodeReturn,
- jwtDecodeStub,
- cleanup: cleanup.bind(this)
- }
- }
-
- cleanup(){
- const { configureAuthStub, refreshSpy } = this
- configureAuthStub && configureAuthStub.resetHistory()
- refreshSpy && refreshSpy.resetHistory()
- }
-}
-
-exports.OIDCStub = OIDCStub
diff --git a/deploy/auth/util.js b/deploy/auth/util.js
deleted file mode 100644
index 91421d162..000000000
--- a/deploy/auth/util.js
+++ /dev/null
@@ -1,26 +0,0 @@
-const objStoreDb = new Map()
-
-const initPassportJs = app => {
- console.log('init passport js')
- const passport = require('passport')
-
- app.use(passport.initialize())
- app.use(passport.session())
-
- passport.serializeUser((user, done) => {
- const { tokenset, rest } = user
- objStoreDb.set(user.id, user)
- done(null, user.id)
- })
-
- passport.deserializeUser((id, done) => {
- const user = objStoreDb.get(id)
- if (user) return done(null, user)
- else return done(null, false)
- })
-}
-
-module.exports = {
- initPassportJs,
- objStoreDb,
-}
diff --git a/deploy/auth/util.spec.js b/deploy/auth/util.spec.js
deleted file mode 100644
index 0dff0d61e..000000000
--- a/deploy/auth/util.spec.js
+++ /dev/null
@@ -1,151 +0,0 @@
-const chai = require('chai')
-const { OIDCStub } = require('./spec-helper')
-chai.use(require('chai-as-promised'))
-const { stub, spy } = require('sinon')
-const { expect, assert, should } = require('chai')
-
-should()
-
-const crypto = require('crypto')
-
-describe('mocha.js', () => {
- it('mocha works properly', () => {
- assert(true)
- })
-})
-
-describe('chai-as-promised.js', () => {
- it('resolving promise is resolved', () => {
-
- return Promise.resolve(2 + 2).should.eventually.equal(4)
-
- })
- it('rejecting promise is rejected', () => {
- return Promise.reject('no reason').should.be.rejected
- })
-})
-
-const oidcStubInstance = new OIDCStub()
-const setupOIDCStub = oidcStubInstance.setupOIDCStub.bind(oidcStubInstance)
-
-describe('util.js', async () => {
-
- describe('> if configureAuth throws', () => {
-
- let cleanup
- before(() => {
- const obj = setupOIDCStub({ rejects: true })
- cleanup = obj.cleanup
- })
-
- after(() => cleanup())
-
- it('> calling util throws', async () => {
- const util = require('./util')
- try {
- await util()
- assert(false, 'Util funciton should throw/reject')
- } catch (e) {
- assert(true)
- }
- })
- })
-
- describe('> if configureauth does not return object', () => {
- let cleanup
- before(() => {
- const obj = setupOIDCStub({
- client: 42
- })
- cleanup = obj.cleanup
- })
-
- after(() => {
- cleanup()
- })
-
- it('> calling util throws', () => {
- try {
- require('./util')()
- assert(false, 'if configure auth does not return object, calling util throw throw')
- } catch (e) {
- assert(true)
- }
- })
- })
-
- const env = {
- HOSTNAME : 'http://localhost:3333',
- HOST_PATHNAME : '/testpath',
- HBP_CLIENTID : crypto.randomBytes(16).toString('hex'),
- HBP_CLIENTSECRET : crypto.randomBytes(16).toString('hex'),
- REFRESH_TOKEN : crypto.randomBytes(16).toString('hex'),
- }
-
- describe('> if env var is provided', () => {
-
- const tmp = {}
- let cleanup
- let oidcStub
- before(() => {
-
- delete require.cache[require.resolve('./util')]
-
- for (const key in env) {
- tmp[key] = process.env[key]
- process.env[key] = env[key]
- }
- try {
-
- const obj = setupOIDCStub()
- cleanup = obj.cleanup
-
- oidcStub = obj
- } catch (e) {
- console.log(e)
- }
- })
-
- after(() => {
- for (const key in env) {
- process.env[key] = tmp[key]
- }
- cleanup()
- })
-
- })
-
- describe('> if refresh token is missing', () => {
-
- const noRefreshEnv = {
- ...env,
- REFRESH_TOKEN: null
- }
- const tmp = {}
- let cleanup
- before(() => {
-
- delete require.cache[require.resolve('./util')]
-
- for (const key in noRefreshEnv) {
- tmp[key] = process.env[key]
- process.env[key] = noRefreshEnv[key]
- }
- try {
-
- const obj = setupOIDCStub()
- cleanup = obj.cleanup
- } catch (e) {
- console.log(e)
- }
- })
-
- after(() => {
- for (const key in noRefreshEnv) {
- process.env[key] = tmp[key]
- }
- cleanup()
- })
-
- })
-})
diff --git a/deploy/bkwdCompat/index.js b/deploy/bkwdCompat/index.js
deleted file mode 100644
index bd1c6d9fc..000000000
--- a/deploy/bkwdCompat/index.js
+++ /dev/null
@@ -1,24 +0,0 @@
-module.exports = () =>{
- const urlState = require('./urlState')
- return (req, res, next) => {
- const query = req.query || {}
-
- let errorMessage = ``
- const redir = urlState(query, err => {
- errorMessage += err
- })
- if (errorMessage !== '') {
- res.cookie(
- `iav-error`,
- errorMessage,
- {
- httpOnly: true,
- sameSite: 'strict',
- maxAge: 1e3 * 30
- }
- )
- }
- if (redir) return res.redirect(redir)
- next()
- }
-}
diff --git a/deploy/bkwdCompat/ngLinks.json b/deploy/bkwdCompat/ngLinks.json
deleted file mode 100644
index 68909f4cd..000000000
--- a/deploy/bkwdCompat/ngLinks.json
+++ /dev/null
@@ -1,705 +0,0 @@
-[
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+Maps+-+v2.5.1&cRegionsSelected=%7B%22MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE%22%3A%22D%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..DMVW..11SkX%7E.7gJ8%7E.jul_%7E..45jd",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+maps+-+v1.18&cRegionsSelected=%7B%22jubrain+mni152+v18+left%22%3A%2254%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..1MqM.26Pd8%7E.4qaI%7E..3q90",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+Maps+-+v2.5.1&cRegionsSelected=%7B%22MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE%22%3A%22Z%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..DMVW..VsYi%7E.4PMQx%7E.3AKQY..45jd",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+maps+-+v1.18&cRegionsSelected=%7B%22jubrain+mni152+v18+left%22%3A%222t%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..Eodw%7E.o4bm.k5Ii%7E..45jd",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Fibre%20Bundle%20Atlas%20-%20Short%20Bundle&navigation=0_0_0_1__-0.2753947079181671_0.6631333827972412_-0.6360703706741333_0.2825356423854828__3000000__49095056.24218857_-8144216.081099838_30427371.198444664__484084&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FFiber_Bundle%2FSWM_atlas%2Fright-hemisphere%2FProbability_Maps%2Frh_PoC-PrC_0.nii",
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- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Fibre%20Bundle%20Atlas%20-%20Short%20Bundle&navigation=0_0_0_1__-0.2753947079181671_0.6631333827972412_-0.6360703706741333_0.2825356423854828__3000000__30727572.31783229_7292200.659099221_-24747345.294763826__484084&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FFiber_Bundle%2FSWM_atlas%2Fright-hemisphere%2FProbability_Maps%2Frh_LOF-ST_0.nii",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Fibre%20Bundle%20Atlas%20-%20Long%20Bundle&navigation=0_0_0_1__-0.2753947079181671_0.6631333827972412_-0.6360703706741333_0.2825356423854828__3000000__-20803546.879296124_-36580285.94995877_-10145861.974154532__484084&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FFiber_Bundle%2FDWM_atlas%2Fleft-hemisphere%2FProbability_Maps%2FCingulum_Temporal_Left.nii",
- "templateSelected=MNI+Colin+27&parcellationSelected=Cytoarchitectonic+Maps+-+v1.18&cRegionsSelected=%7B%22jubrain+colin+v18+right%22%3A%223k%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..6mG.1w9sC%7E.gS4..3q90",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas&navigation=0_0_0_1__-0.2753947079181671_0.6631333827972412_-0.6360703706741333_0.2825356423854828__3000000__38875694.35035902_22074041.45779705_32925552.093212306__1071975.4977029096&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.eu%2Fprecomputed%2FJuBrain%2F17%2Ficbm152casym%2Fpmaps%2FIFS_ifs3_r_N10_nlin2MNI152ASYM2009C_2.2_publicDOI_e664da66c465b00af07d0d53e6300b17.nii.gz",
- "templateSelected=MNI+Colin+27&parcellationSelected=Cytoarchitectonic+Maps+-+v1.18&cRegionsSelected=%7B%22jubrain+colin+v18+right%22%3A%222-%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..Bh0m%7E.nyLe.hCkC%7E..45jd",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+maps+-+v1.18&cRegionsSelected=%7B%22jubrain+mni152+v18+left%22%3A%225%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..1MqM.26Pd8%7E.4qaI%7E..3q90",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+maps+-+v1.18&cRegionsSelected=%7B%22jubrain+mni152+v18+right%22%3A%2230%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..E2CO%7E.nnMW.kRQK%7E..45jd",
- "templateSelected=MNI+Colin+27&parcellationSelected=Cytoarchitectonic+Maps+-+v1.18&cRegionsSelected=%7B%22jubrain+colin+v18+right%22%3A%22k%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..BzuQ%7E.o3_i.h4BK%7E..45jd",
- "templateSelected=MNI+Colin+27&parcellationSelected=Cytoarchitectonic+Maps+-+v1.18&cRegionsSelected=%7B%22jubrain+colin+v18+left%22%3A%221p%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..DMVW..ZNsu%7E.l1JK.aGyo%7E..2Ul9",
- "templateSelected=MNI+Colin+27&parcellationSelected=Cytoarchitectonic+Maps+-+v1.18&cRegionsSelected=%7B%22jubrain+colin+v18+right%22%3A%223e%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..CFOu%7E.oAn4.gxpO%7E..45jd",
- "templateSelected=MNI+Colin+27&parcellationSelected=Cytoarchitectonic+Maps+-+v1.18&cRegionsSelected=%7B%22jubrain+colin+v18+right%22%3A%224c%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..2Yr.1w6Je%7E.CqH..3q90",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Fibre%20Bundle%20Atlas%20-%20Long%20Bundle&navigation=0_0_0_1__-0.2753947079181671_0.6631333827972412_-0.6360703706741333_0.2825356423854828__3000000__-29901044.899648257_15264845.851438016_-17445944.547899857__484084&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FFiber_Bundle%2FDWM_atlas%2Fleft-hemisphere%2FProbability_Maps%2FUncinate_Left.nii",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+maps+-+v1.18&cRegionsSelected=%7B%22jubrain+mni152+v18+right%22%3A%221q%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..DMVW..YPRG%7E.jAnO.sg_O%7E..2Ul9",
- "templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Cytoarchitectonic+Maps&navigation=0_0_0_1__0.7989629507064819_0.09687352180480957_-0.0713578313589096_-0.5892213582992554__1922235.5293810747__311768_-54882876_4142912__350000®ionsSelected=v2%231",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Fibre%20Bundle%20Atlas%20-%20Short%20Bundle&navigation=0_0_0_1__-0.2753947079181671_0.6631333827972412_-0.6360703706741333_0.2825356423854828__3000000__-40639583.333333336_-76233333.33333334_-11417708.333333336__484084&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FFiber_Bundle%2FSWM_atlas%2Fleft-hemisphere%2FProbability_Maps%2Flh_Fu-LO_0.nii",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+maps+-+v1.18&cRegionsSelected=%7B%22jubrain+mni152+v18+right%22%3A%22z%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..EEyo%7E.nsUe.kLoy%7E..45jd",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+maps+-+v1.18&cRegionsSelected=%7B%22jubrain+mni152+v18+right%22%3A%224F%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..DMVW..2HRjm.2qnDi%7E.2aiDS..45jd",
- "templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Cytoarchitectonic+maps+-+v1.18&cRegionsSelected=%7B%22jubrain+mni152+v18+right%22%3A%223%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..1MGE.26Pd8%7E.4sKo%7E..3q90",
- "templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Cytoarchitectonic+Maps&cRegionsSelected=%7B%22v3v%22%3A%221%22%7D&cNavigation=0.0.0.-W000..-DAqw.2_PGSc._ShZn.2-8GXE..7LIx..Echz.3Dv8q%7E.7gwp%7E..jZZ"
-]
diff --git a/deploy/bkwdCompat/urlState.js b/deploy/bkwdCompat/urlState.js
deleted file mode 100644
index 14b765d34..000000000
--- a/deploy/bkwdCompat/urlState.js
+++ /dev/null
@@ -1,287 +0,0 @@
-// this module is suppose to rewrite state stored in query param
-// and convert it to path based url
-const { sxplrNumB64Enc } = require("../../common/util")
-
-const {
- encodeNumber,
- separator
-} = sxplrNumB64Enc
-
-const waxolmObj = {
- aId: 'minds/core/parcellationatlas/v1.0.0/522b368e-49a3-49fa-88d3-0870a307974a',
- id: 'minds/core/referencespace/v1.0.0/d5717c4a-0fa1-46e6-918c-b8003069ade8',
- parc: {
- 'Waxholm Space rat brain atlas v3': {
- id: 'minds/core/parcellationatlas/v1.0.0/ebb923ba-b4d5-4b82-8088-fa9215c2e1fe'
- },
- 'Whole Brain (v2.0)': {
- id: 'minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d'
- },
- 'Waxholm Space rat brain atlas v2': {
- id: 'minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d'
- },
- 'Waxholm Space rat brain atlas v1': {
- id: 'minds/core/parcellationatlas/v1.0.0/11017b35-7056-4593-baad-3934d211daba'
- },
- }
-}
-
-const allenObj = {
- aId: 'juelich/iav/atlas/v1.0.0/2',
- id: 'minds/core/referencespace/v1.0.0/265d32a0-3d84-40a5-926f-bf89f68212b9',
- parc: {
- 'Allen Mouse Common Coordinate Framework v3 2017': {
- id: 'minds/core/parcellationatlas/v1.0.0/05655b58-3b6f-49db-b285-64b5a0276f83'
- },
- 'Allen Mouse Brain Atlas': {
- id: 'minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f'
- },
- 'Allen Mouse Common Coordinate Framework v3 2015': {
- id: 'minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f'
- },
- }
-}
-
-const templateMap = {
- 'Big Brain (Histology)': {
- aId: 'juelich/iav/atlas/v1.0.0/1',
- id: 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588',
- parc: {
- 'Cytoarchitectonic Maps - v2.4': {
- id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290',
- },
- 'Cytoarchitectonic Maps': {
- id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290',
- },
- 'Cortical Layers Segmentation': {
- id: 'juelich/iav/atlas/v1.0.0/3'
- },
- 'Grey/White matter': {
- id: 'juelich/iav/atlas/v1.0.0/4'
- }
- }
- },
- 'MNI 152 ICBM 2009c Nonlinear Asymmetric': {
- aId: 'juelich/iav/atlas/v1.0.0/1',
- id: 'minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2',
- parc: {
- 'Cytoarchitectonic Maps - v2.5.1': {
- // redirect julich brain v251 to v290
- id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
- },
- 'Short Fiber Bundles - HCP': {
- id: 'juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c'
- },
- 'Cytoarchitectonic maps - v1.18': {
- id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
- },
- 'Long Bundle': {
- id: 'juelich/iav/atlas/v1.0.0/5'
- },
- 'fibre bundle short': {
- id: 'juelich/iav/atlas/v1.0.0/6'
- },
- 'DiFuMo Atlas (64 dimensions)': {
- id: 'minds/core/parcellationatlas/v1.0.0/d80fbab2-ce7f-4901-a3a2-3c8ef8a3b721'
- },
- 'DiFuMo Atlas (128 dimensions)': {
- id: 'minds/core/parcellationatlas/v1.0.0/73f41e04-b7ee-4301-a828-4b298ad05ab8'
- },
- 'DiFuMo Atlas (256 dimensions)': {
- id: 'minds/core/parcellationatlas/v1.0.0/141d510f-0342-4f94-ace7-c97d5f160235'
- },
- 'DiFuMo Atlas (512 dimensions)': {
- id: 'minds/core/parcellationatlas/v1.0.0/63b5794f-79a4-4464-8dc1-b32e170f3d16'
- },
- 'DiFuMo Atlas (1024 dimensions)': {
- id: 'minds/core/parcellationatlas/v1.0.0/12fca5c5-b02c-46ce-ab9f-f12babf4c7e1'
- },
- },
- },
- 'MNI Colin 27': {
- aId: 'juelich/iav/atlas/v1.0.0/1',
- id: 'minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992',
- parc: {
- 'Cytoarchitectonic Maps - v1.18': {
- id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
- }
- }
- },
- 'Waxholm Space rat brain MRI/DTI': waxolmObj,
- 'Waxholm Rat V2.0': waxolmObj,
- 'Allen Mouse Common Coordinate Framework v3': allenObj,
- 'Allen Mouse': allenObj
-}
-
-const encodeId = id => id.replace(/\//g, ':')
-
-const WARNING_STRINGS = {
- PREVIEW_DSF_PARSE_ERROR: 'Preview dataset files cannot be processed properly.',
- REGION_SELECT_ERROR: 'Region selected cannot be processed properly.',
- TEMPLATE_ERROR: 'Template not found.',
-}
-const pliPreviewUrl = `/a:juelich:iav:atlas:v1.0.0:1/t:minds:core:referencespace:v1.0.0:a1655b99-82f1-420f-a3c2-fe80fd4c8588/p:juelich:iav:atlas:v1.0.0:4/@:0.2-4Fk_.-KlpS.0.._eCwg.2-FUe3._-s_W.2_evlu..7LIy..1WNl8.6Tjd~.bTYu~..Zdk/f:b08a7dbc-7c75-4ce7-905b-690b2b1e8957--d3ca8fe622051466a5cde547a11111ca`
-module.exports = (query, _warningCb) => {
-
- const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
- let redirectUrl = `${HOST_PATHNAME}/#`
-
- const {
- standaloneVolumes,
- niftiLayers, // deprecating - check if anyone calls this url
- pluginStates,
- previewingDatasetFiles,
-
- templateSelected,
- parcellationSelected,
- regionsSelected, // deprecating - check if any one calls this url
- cRegionsSelected,
-
- navigation,
- cNavigation,
- } = query || {}
-
- if (Object.keys(query).length === 0) return null
-
- /**
- * nb: it is absolutely imperative that warningCb are not called with dynamic data.
- * Since it is injected as param in
- */
- const warningCb = arg => {
- if (!_warningCb) return
- if (Object.values(WARNING_STRINGS).includes(arg)) _warningCb(arg)
- }
-
- if (regionsSelected) console.warn(`regionSelected has been deprecated`)
- if (niftiLayers) console.warn(`nifitlayers has been deprecated`)
-
- // pluginStates from query param were separated by __
- // convert to uri component encoded JSON array
- // to avoid potentially issues (e.g. url containing __, which is very possible)
-
- const plugins = pluginStates && pluginStates.split('__')
- const searchParam = new URLSearchParams()
-
-
- // common search param & path
- let nav, dsp, r
- if (navigation) {
- try {
-
- const [
- _o, _po, _pz, _p, _z
- ] = navigation.split("__")
- const o = _o.split("_").map(v => Number(v))
- const po = _po.split("_").map(v => Number(v))
- const pz = Number(_pz)
- const p = _p.split("_").map(v => Number(v))
- const z = Number(_z)
- const v = [
- o.map(n => encodeNumber(n, {float: true})).join(separator),
- po.map(n => encodeNumber(n, {float: true})).join(separator),
- encodeNumber(Math.floor(pz)),
- Array.from(p).map(v => Math.floor(v)).map(n => encodeNumber(n)).join(separator),
- encodeNumber(Math.floor(z)),
- ].join(`${separator}${separator}`)
-
- nav = `/@:${encodeURI(v)}`
- } catch (e) {
- console.warn(`Parsing navigation param error`, e)
- }
- }
- if (cNavigation) nav = `/@:${encodeURI(cNavigation)}`
- if (previewingDatasetFiles) {
- try {
- const parsedDsp = JSON.parse(previewingDatasetFiles)
- if (Array.isArray(parsedDsp)) {
- if (parsedDsp.length === 1) {
- const { datasetId, filename } = parsedDsp[0]
- if (datasetId === "minds/core/dataset/v1.0.0/b08a7dbc-7c75-4ce7-905b-690b2b1e8957") {
- /**
- * if preview pli link, return hardcoded link
- */
- return `${HOST_PATHNAME}/#${pliPreviewUrl}`
- } else {
- /**
- * TODO deprecate dsp
- */
- dsp = `/dsp:${encodeId(datasetId)}::${encodeURI(filename)}`
- }
- } else {
- searchParam.set(`previewingDatasetFiles`, previewingDatasetFiles)
- }
- }
- } catch (_e) {
- warningCb(WARNING_STRINGS.PREVIEW_DSF_PARSE_ERROR)
- // parsing preview dataset error
- // ignore preview dataset query param
- }
- }
- if (plugins && plugins.length > 0) {
- searchParam.set(`pl`, JSON.stringify(plugins))
- }
- if (niftiLayers) searchParam.set(`niftiLayers`, niftiLayers)
- if (cRegionsSelected) {
- try {
- (() => {
- const parsedRS = JSON.parse(cRegionsSelected)
- if (Object.keys(parsedRS).length > 1) {
- searchParam.set('cRegionsSelected', cRegionsSelected)
- return
- }
- for (const ngId in parsedRS) {
- const encodedIdArr = parsedRS[ngId]
- const encodedRArr = encodedIdArr.split(separator)
- if (encodedRArr.length > 0) {
- if (encodedRArr.length > 1) {
- searchParam.set('cRegionsSelected', cRegionsSelected)
- return
- }
- if (!!encodedRArr[0]) {
- r = `/r:${encodeURI(ngId)}::${encodeURI(encodedRArr[0])}`
- }
- }
- }
- })()
- } catch (e) {
- warningCb(WARNING_STRINGS.REGION_SELECT_ERROR)
- // parsing cregions selected error
- // ignore region selected and move on
- }
- }
- if (standaloneVolumes) {
- searchParam.set('standaloneVolumes', standaloneVolumes)
- if (nav) redirectUrl += nav
- if (dsp) redirectUrl += dsp
- if (Array.from(searchParam.keys()).length > 0) redirectUrl += `/?${searchParam.toString()}`
- return redirectUrl
- }
-
- if (templateSelected) {
- if (templateMap[templateSelected]) {
-
- const { id: t, aId: a, parc } = templateMap[templateSelected]
- redirectUrl += `/a:${encodeId(a)}/t:${encodeId(t)}`
- if (!parc[parcellationSelected]) {
- warningCb(`Parcelation not found, using default.`)
- }
- const { id: p } = parc[parcellationSelected] || {}
- if (p) redirectUrl += `/p:${encodeId(p)}`
- if (r && parcellationSelected !== 'Cytoarchitectonic Maps - v2.5.1') redirectUrl += r
- if (nav) redirectUrl += nav
- if (dsp) redirectUrl += dsp
-
- if (Array.from(searchParam.keys()).length > 0) redirectUrl += `?${searchParam.toString()}`
-
- return redirectUrl
- } else {
- warningCb(WARNING_STRINGS.TEMPLATE_ERROR)
- }
- }
-
- if (Array.from(searchParam.keys()).length > 0) {
- redirectUrl += `/?${searchParam.toString()}`
- return redirectUrl
- }
- return `${redirectUrl}/`
-}
diff --git a/deploy/bkwdCompat/urlState.spec.js b/deploy/bkwdCompat/urlState.spec.js
deleted file mode 100644
index 225bf252f..000000000
--- a/deploy/bkwdCompat/urlState.spec.js
+++ /dev/null
@@ -1,18 +0,0 @@
-const { assert } = require('chai')
-const url = require('url')
-const arr = require('./ngLinks.json')
-const parseUrlState = require('./urlState')
-
-describe('> urlState.js', () => {
- it('> works', () => {
- for (const item of arr) {
- const parsed = url.parse(`/?${item}`, true)
- const out = parseUrlState(parsed.query)
-
- assert(
- true,
- 'should not result in parsing error'
- )
- }
- })
-})
diff --git a/deploy/catchError.js b/deploy/catchError.js
deleted file mode 100644
index cba45cc58..000000000
--- a/deploy/catchError.js
+++ /dev/null
@@ -1,13 +0,0 @@
-module.exports = (raw, req, res, next) => {
- /**
- * probably use more elaborate logging?
- */
- const { code, error, trace } = raw
- console.error('Catching error', {
- code,
- error,
- trace,
- raw
- })
- res.status(code || 500).end()
-}
\ No newline at end of file
diff --git a/deploy/constants.js b/deploy/constants.js
deleted file mode 100644
index 05090af3f..000000000
--- a/deploy/constants.js
+++ /dev/null
@@ -1,21 +0,0 @@
-const fs = require('fs')
-const path = require('path')
-
-const PUBLIC_PATH = process.env.NODE_ENV === 'production'
- ? path.join(__dirname, 'public')
- : path.join(__dirname, '..', 'dist', 'aot')
-
-let indexTemplate
-try {
-
- indexTemplate = fs.readFileSync(
- path.join(PUBLIC_PATH, 'index.html'),
- 'utf-8'
- )
-
-} catch (e) {
- console.error(`index.html cannot be read. maybe run 'npm run build-aot' at root dir first?`)
-}
-module.exports = {
- indexTemplate
-}
diff --git a/deploy/csp/index.js b/deploy/csp/index.js
deleted file mode 100644
index a875bb535..000000000
--- a/deploy/csp/index.js
+++ /dev/null
@@ -1,147 +0,0 @@
-const csp = require('helmet-csp')
-const bodyParser = require('body-parser')
-
-let WHITE_LIST_SRC, CSP_CONNECT_SRC, SCRIPT_SRC
-
-// TODO bandaid solution
-// OKD/nginx reverse proxy seems to strip csp header
-// without it, testSafari.js will trigger no unsafe eval csp
-const reportOnly = true || process.env.NODE_ENV !== 'production'
-
-const CSP_REPORT_URI = process.env.CSP_REPORT_URI
-
-try {
- WHITE_LIST_SRC = JSON.parse(process.env.WHITE_LIST_SRC || '[]')
-} catch (e) {
- console.warn(`parsing WHITE_LIST_SRC error ${process.env.WHITE_LIST_SRC}`, e)
- WHITE_LIST_SRC = []
-}
-
-try {
- SCRIPT_SRC = JSON.parse(process.env.SCRIPT_SRC || '[]')
-} catch (e) {
- console.warn(`parsing SCRIPT_SRC error ${process.env.SCRIPT_SRC}`, e)
- SCRIPT_SRC = []
-}
-
-try {
- CSP_CONNECT_SRC = JSON.parse(process.env.CSP_CONNECT_SRC || '[]')
-} catch (e) {
- console.warn(`parsing CSP_CONNECT_SRC error ${process.env.CSP_CONNECT_SRC}`, e)
- CSP_CONNECT_SRC = []
-}
-
-const defaultAllowedSites = [
- "'self'",
- 'stats.humanbrainproject.eu',
- 'stats-dev.humanbrainproject.eu'
-]
-
-const connectSrc = [
- "'self'",
-
- // needed by ad hoc generation of URL resources
- "blob:",
-
- // siibra-api endpoints
- 'siibra-api-latest.apps-dev.hbp.eu',
- 'siibra-api-rc.apps.hbp.eu',
- 'siibra-api-stable.apps.hbp.eu',
- 'siibra-api-ns.apps.hbp.eu',
- 'siibra-api-stable.apps.jsc.hbp.eu',
-
- // chunk servers
- 'neuroglancer.humanbrainproject.org',
- 'neuroglancer.humanbrainproject.eu',
- '1um.brainatlas.eu',
- 'object.cscs.ch',
-
- // required for dataset previews
-
- // spatial transform
- "hbp-spatial-backend.apps.hbp.eu",
-
- // injected by env var
- ...CSP_CONNECT_SRC
-]
-
-module.exports = {
- middelware: (req, res, next) => {
-
- const permittedCsp = (req.session && req.session.permittedCsp) || {}
- const userConnectSrc = []
- const userScriptSrc = []
- for (const key in permittedCsp) {
- userConnectSrc.push(
- ...(permittedCsp[key]['connect-src'] || []),
- ...(permittedCsp[key]['connectSrc'] || [])
- )
- userScriptSrc.push(
- ...(permittedCsp[key]['script-src'] || []),
- ...(permittedCsp[key]['scriptSrc'] || [])
- )
- }
- csp({
- directives: {
- defaultSrc: [
- ...defaultAllowedSites,
- ...WHITE_LIST_SRC
- ],
- styleSrc: [
- ...defaultAllowedSites,
- 'stackpath.bootstrapcdn.com/bootstrap/4.3.1/',
- 'use.fontawesome.com/releases/v5.8.1/',
- "'unsafe-inline'", // required for angular [style.xxx] bindings
- ...WHITE_LIST_SRC
- ],
- fontSrc: [
- "'self'",
- 'use.fontawesome.com/releases/v5.8.1/',
- ...WHITE_LIST_SRC
- ],
- connectSrc: [
- ...userConnectSrc,
- ...defaultAllowedSites,
- ...connectSrc,
- ...WHITE_LIST_SRC
- ],
- imgSrc: [
- "'self'",
- ],
- scriptSrc:[
- "'self'",
- ...userScriptSrc,
- 'unpkg.com/kg-dataset-previewer@1.2.0/', // preview component
- 'https://unpkg.com/d3@6.2.0/', // required for preview component
- "https://cdn.plot.ly/", // required for plotly
- 'https://unpkg.com/mathjax@3.1.2/', // math jax
- 'https://unpkg.com/three-surfer@0.0.13/dist/bundle.js', // for threeSurfer (freesurfer support in browser)
- 'https://unpkg.com/ng-layer-tune@0.0.21/dist/ng-layer-tune/', // needed for ng layer control
- 'https://unpkg.com/hbp-connectivity-component@0.6.6/', // needed for connectivity component
- (req, res) => res.locals.nonce ? `'nonce-${res.locals.nonce}'` : null,
- ...SCRIPT_SRC,
- ...WHITE_LIST_SRC,
- ...defaultAllowedSites
- ],
- frameSrc: [
- "*"
- ],
- reportUri: CSP_REPORT_URI || '/report-violation'
- },
- reportOnly
- })(req, res, next)
-
- },
- bootstrapReportViolation: app => {
- app.post('/report-violation', bodyParser.json({
- type: ['json', 'application/csp-report']
- }), (req, res) => {
- if (req.body) {
- console.warn(`CSP Violation: `, req.body)
- } else {
- console.warn(`CSP Violation: no data received!`)
- }
- res.status(204).end()
- })
- }
-}
diff --git a/deploy/csp/index.spec.js b/deploy/csp/index.spec.js
deleted file mode 100644
index 93a478e25..000000000
--- a/deploy/csp/index.spec.js
+++ /dev/null
@@ -1,109 +0,0 @@
-const express = require('express')
-const app = express()
-const { middelware: cspMiddleware } = require('./index')
-const got = require('got')
-const { expect, assert } = require('chai')
-
-const checkBaseFn = async (rules = []) => {
-
- const resp = await got(`http://localhost:1234/`)
- const stringifiedHeader = JSON.stringify(resp.headers)
-
- /**
- * expect stats.humanbrainproject.eu and neuroglancer.humanbrainproject.eu to be present
- */
- assert(
- /stats\.humanbrainproject\.eu/.test(stringifiedHeader),
- 'stats.humanbrainproject.eu present in header'
- )
-
- assert(
- /neuroglancer\.humanbrainproject\.eu/.test(stringifiedHeader),
- 'neuroglancer.humanbrainproject.eu present in header'
- )
-
- assert(
- /content-security-policy/.test(stringifiedHeader),
- 'content-security-policy present in header'
- )
-
- for (const rule of rules) {
- assert(
- rule.test(stringifiedHeader),
- `${rule.toString()} present in header`
- )
- }
-}
-
-describe('> csp/index.js', () => {
- let server, permittedCsp
- const middleware = (req, res, next) => {
- if (!!permittedCsp) {
- req.session = { permittedCsp }
- }
- next()
- }
- before(done => {
- app.use(middleware)
- app.use(cspMiddleware)
- app.get('/', (req, res) => {
- res.status(200).send('OK')
- })
- server = app.listen(1234, () => console.log(`app listening`))
- setTimeout(() => {
- done()
- }, 1000);
- })
-
- it('> should work when session is unset', async () => {
- await checkBaseFn()
- })
-
- describe('> if session and permittedCsp are both set', () => {
- describe('> if permittedCsp is malformed', () => {
- describe('> if permittedCsp is set to string', () => {
- before(() => {
- permittedCsp = 'hello world'
- })
- it('> base csp should work', async () => {
- await checkBaseFn()
- })
- })
-
- describe('> if permittedCsp is number', () => {
- before(() => {
- permittedCsp = 420
- })
- it('> base csp should work', async () => {
- await checkBaseFn()
- })
- })
- })
-
- describe('> if premittedCsp defines', () => {
-
- before(() => {
- permittedCsp = {
- 'foo-bar': {
- 'connect-src': [
- 'connect.int.dev'
- ],
- 'script-src': [
- 'script.int.dev'
- ]
- }
- }
- })
-
- it('> csp should include permittedCsp should work', async () => {
- await checkBaseFn([
- /connect\.int\.dev/,
- /script\.int\.dev/,
- ])
- })
- })
- })
- after(done => {
- server.close(done)
- })
-})
\ No newline at end of file
diff --git a/deploy/devBanner/index.js b/deploy/devBanner/index.js
deleted file mode 100644
index c7ca44241..000000000
--- a/deploy/devBanner/index.js
+++ /dev/null
@@ -1,29 +0,0 @@
-const express = require('express')
-const router = express.Router()
-
-console.log(`BUILD_TEXT: ${process.env.BUILD_TEXT}`)
-
-/**
- * build flag
- */
-const BUILD_TEXT = process.env.BUILD_TEXT || ''
-const versionCss = ` /* overwritten */
-body::after
-{
- content: '${BUILD_TEXT}';
-}
-`
-const buildTextIsDefined = typeof process.env.BUILD_TEXT !== 'undefined'
-
-/**
- * bypass if env var not defined
- * i.e. in order to show nothing, must EXPLICITLY set envvar BUILD_TEXT as empty string
- */
-router.get('/version.css', (req, res, next) => {
- console.log(`runtime BUILD_TEXT: ${process.env.BUILD_TEXT}`)
- if (!buildTextIsDefined) return next()
- res.setHeader('Content-Type', 'text/css; charset=UTF-8')
- res.status(200).send(versionCss)
-})
-
-module.exports = router
\ No newline at end of file
diff --git a/deploy/logging/index.js b/deploy/logging/index.js
deleted file mode 100644
index a92365d60..000000000
--- a/deploy/logging/index.js
+++ /dev/null
@@ -1,35 +0,0 @@
-const got = require('got')
-const qs = require('querystring')
-
-class Logger {
- constructor(name, { protocol = 'http', host = 'localhost', port = '24224', username = '', password = '' } = {}){
- this.name = qs.escape(name)
- this.protocol = protocol
- this.host = host
- this.port = port
- this.username = username
- this.password = password
- }
-
- async emit(logLevel, message, callback){
- const {
- name,
- protocol,
- host,
- port,
- username,
- password
- } = this
-
- const auth = username !== '' ? `${username}:${password}@` : ''
- const url = `${protocol}://${auth}${host}:${port}/${name}.${qs.escape(logLevel)}`
- const formData = {
- json: JSON.stringify(message)
- }
- await got.post(url, {
- formData
- })
- }
-}
-
-module.exports = Logger
\ No newline at end of file
diff --git a/deploy/lruStore/index.js b/deploy/lruStore/index.js
deleted file mode 100644
index 474f23d5e..000000000
--- a/deploy/lruStore/index.js
+++ /dev/null
@@ -1,164 +0,0 @@
-/**
- * Cache to allow for in memory response while data fetching/processing occur
- */
-
-const {
- REDIS_PROTO,
- REDIS_ADDR,
- REDIS_PORT,
-
- REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_PROTO,
- REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_ADDR,
- REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_PORT,
-
- REDIS_USERNAME,
- REDIS_PASSWORD,
-
-} = process.env
-
-const redisProto = REDIS_PROTO || REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_PROTO || 'redis'
-const redisAddr = REDIS_ADDR || REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_ADDR || null
-const redisPort = REDIS_PORT || REDIS_RATE_LIMITING_DB_EPHEMERAL_PORT_6379_TCP_PORT || 6379
-
-const userPass = (() => {
- let returnString = ''
- if (REDIS_USERNAME) {
- returnString += REDIS_USERNAME
- }
- if (REDIS_PASSWORD) {
- returnString += `:${REDIS_PASSWORD}`
- }
- return returnString === ''
- ? ''
- : `${returnString}@`
-})()
-
-const _redisURL = redisAddr && `${redisProto || ''}://${userPass}${redisAddr}:${redisPort}`
-
-const crypto = require('crypto')
-
-let authKey
-
-const getAuthKey = () => {
- crypto.randomBytes(128, (err, buf) => {
- if (err) {
- console.error(`generating random bytes error`, err)
- return
- }
- authKey = buf.toString('base64')
- console.log(`clear store key: ${authKey}`)
- })
-}
-
-getAuthKey()
-
-const ensureString = val => {
- if (typeof val !== 'string') throw new Error(`both key and val must be string`)
-}
-
-class ExportObj {
- constructor(){
- this.StoreType = null
- this.redisURL = null
- this.store = null
- this._rs = null
- this._rj = null
-
- this._initPr = new Promise((rs, rj) => {
- this._rs = rs
- this._rj = rj
- })
- }
-}
-
-const exportObj = new ExportObj()
-
-const setupLru = () => {
-
- const LRU = require('lru-cache')
- const lruStore = new LRU({
- max: 1024 * 1024 * 1024, // 1gb
- length: (n, key) => n.length,
- maxAge: Infinity, // never expires
- })
-
- exportObj.store = {
- /**
- * maxage in milli seconds
- */
- set: async (key, val, { maxAge } = {}) => {
- ensureString(key)
- ensureString(val)
- lruStore.set(key, val, ...( maxAge ? [ maxAge ] : [] ))
- },
- get: async (key) => {
- ensureString(key)
- return lruStore.get(key)
- },
- clear: async auth => {
- if (auth !== authKey) {
- getAuthKey()
- throw new Error(`unauthorized`)
- }
- lruStore.reset()
- }
- }
-
- exportObj.StoreType = `lru-cache`
- console.log(`using lru-cache`)
- exportObj._rs()
-}
-
-if (_redisURL) {
- const redis = require('redis')
- const { promisify } = require('util')
- const client = redis.createClient({
- url: _redisURL
- })
-
- client.on('ready', () => {
-
- const asyncGet = promisify(client.get).bind(client)
- const asyncSet = promisify(client.set).bind(client)
- const asyncDel = promisify(client.del).bind(client)
-
- const keys = []
-
- /**
- * maxage in milli seconds
- */
- exportObj.store = {
- set: async (key, val, { maxAge } = {}) => {
- ensureString(key)
- ensureString(val)
- asyncSet(key, val, ...( maxAge ? [ 'PX', maxAge ] : [] ))
- keys.push(key)
- },
- get: async (key) => {
- ensureString(key)
- return asyncGet(key)
- },
- clear: async auth => {
- if (auth !== authKey) {
- getAuthKey()
- throw new Error(`unauthorized`)
- }
- await asyncDel(keys.splice(0))
- }
- }
-
- exportObj.StoreType = `redis`
- exportObj.redisURL = _redisURL
- console.log(`using redis`)
- exportObj._rs()
- }).on('error', () => {
- console.warn(`setting up Redis error, fallback to setupLru`)
- setupLru()
- client.quit()
- })
-
-} else {
- setupLru()
-}
-
-module.exports = exportObj
\ No newline at end of file
diff --git a/deploy/package-lock.json b/deploy/package-lock.json
deleted file mode 100644
index 56645a229..000000000
--- a/deploy/package-lock.json
+++ /dev/null
@@ -1,5133 +0,0 @@
-{
- "name": "deploy",
- "version": "1.0.0",
- "lockfileVersion": 2,
- "requires": true,
- "packages": {
- "": {
- "name": "deploy",
- "version": "1.0.0",
- "license": "ISC",
- "dependencies": {
- "body-parser": "^1.19.0",
- "connect-redis": "^5.0.0",
- "cookie-parser": "^1.4.5",
- "express": "^4.16.4",
- "express-rate-limit": "^5.5.1",
- "express-session": "^1.15.6",
- "got": "^11.8.5",
- "hbp-seafile": "^0.3.0",
- "helmet-csp": "^3.4.0",
- "lru-cache": "^5.1.1",
- "memorystore": "^1.6.1",
- "nomiseco": "0.0.2",
- "openid-client": "^4.4.0",
- "passport": "^0.6.0",
- "rate-limit-redis": "^2.1.0",
- "redis": "^3.1.2",
- "showdown": "^2.0.0",
- "through2": "^3.0.1"
- },
- "devDependencies": {
- "chai": "^4.2.0",
- "chai-as-promised": "^7.1.1",
- "cookie": "^0.4.0",
- "cors": "^2.8.5",
- "dotenv": "^6.2.0",
- "mocha": "^10.1.0",
- "nock": "^12.0.3",
- "sinon": "^8.0.2"
- }
- },
- "node_modules/@panva/asn1.js": {
- "version": "1.0.0",
- "resolved": "https://registry.npmjs.org/@panva/asn1.js/-/asn1.js-1.0.0.tgz",
- "integrity": "sha512-UdkG3mLEqXgnlKsWanWcgb6dOjUzJ+XC5f+aWw30qrtjxeNUSfKX1cd5FBzOaXQumoe9nIqeZUvrRJS03HCCtw==",
- "engines": {
- "node": ">=10.13.0"
- }
- },
- "node_modules/@sindresorhus/is": {
- "version": "4.6.0",
- "resolved": "https://registry.npmjs.org/@sindresorhus/is/-/is-4.6.0.tgz",
- "integrity": "sha512-t09vSN3MdfsyCHoFcTRCH/iUtG7OJ0CsjzB8cjAmKc/va/kIgeDI/TxsigdncE/4be734m0cvIYwNaV4i2XqAw==",
- "engines": {
- "node": ">=10"
- },
- "funding": {
- "url": "https://github.com/sindresorhus/is?sponsor=1"
- }
- },
- "node_modules/@sinonjs/commons": {
- "version": "1.7.0",
- "resolved": "https://registry.npmjs.org/@sinonjs/commons/-/commons-1.7.0.tgz",
- "integrity": "sha512-qbk9AP+cZUsKdW1GJsBpxPKFmCJ0T8swwzVje3qFd+AkQb74Q/tiuzrdfFg8AD2g5HH/XbE/I8Uc1KYHVYWfhg==",
- "dev": true,
- "dependencies": {
- "type-detect": "4.0.8"
- }
- },
- "node_modules/@sinonjs/formatio": {
- "version": "4.0.1",
- "resolved": "https://registry.npmjs.org/@sinonjs/formatio/-/formatio-4.0.1.tgz",
- "integrity": "sha512-asIdlLFrla/WZybhm0C8eEzaDNNrzymiTqHMeJl6zPW2881l3uuVRpm0QlRQEjqYWv6CcKMGYME3LbrLJsORBw==",
- "dev": true,
- "dependencies": {
- "@sinonjs/commons": "^1",
- "@sinonjs/samsam": "^4.2.0"
- }
- },
- "node_modules/@sinonjs/samsam": {
- "version": "4.2.1",
- "resolved": "https://registry.npmjs.org/@sinonjs/samsam/-/samsam-4.2.1.tgz",
- "integrity": "sha512-7+5S4C4wpug5pzHS+z/63+XUwsH7dtyYELDafoT1QnfruFh7eFjlDWwZXltUB0GLk6y5eMeAt34Bjx8wJ4KfSA==",
- "dev": true,
- "dependencies": {
- "@sinonjs/commons": "^1.6.0",
- "lodash.get": "^4.4.2",
- "type-detect": "^4.0.8"
- }
- },
- "node_modules/@sinonjs/text-encoding": {
- "version": "0.7.1",
- "resolved": "https://registry.npmjs.org/@sinonjs/text-encoding/-/text-encoding-0.7.1.tgz",
- "integrity": "sha512-+iTbntw2IZPb/anVDbypzfQa+ay64MW0Zo8aJ8gZPWMMK6/OubMVb6lUPMagqjOPnmtauXnFCACVl3O7ogjeqQ==",
- "dev": true
- },
- "node_modules/@szmarczak/http-timer": {
- "version": "4.0.5",
- "resolved": "https://registry.npmjs.org/@szmarczak/http-timer/-/http-timer-4.0.5.tgz",
- "integrity": "sha512-PyRA9sm1Yayuj5OIoJ1hGt2YISX45w9WcFbh6ddT0Z/0yaFxOtGLInr4jUfU1EAFVs0Yfyfev4RNwBlUaHdlDQ==",
- "dependencies": {
- "defer-to-connect": "^2.0.0"
- },
- "engines": {
- "node": ">=10"
- }
- },
- "node_modules/@types/cacheable-request": {
- "version": "6.0.1",
- "resolved": "https://registry.npmjs.org/@types/cacheable-request/-/cacheable-request-6.0.1.tgz",
- "integrity": "sha512-ykFq2zmBGOCbpIXtoVbz4SKY5QriWPh3AjyU4G74RYbtt5yOc5OfaY75ftjg7mikMOla1CTGpX3lLbuJh8DTrQ==",
- "dependencies": {
- "@types/http-cache-semantics": "*",
- "@types/keyv": "*",
- "@types/node": "*",
- "@types/responselike": "*"
- }
- },
- "node_modules/@types/got": {
- "version": "9.6.12",
- "resolved": "https://registry.npmjs.org/@types/got/-/got-9.6.12.tgz",
- "integrity": "sha512-X4pj/HGHbXVLqTpKjA2ahI4rV/nNBc9mGO2I/0CgAra+F2dKgMXnENv2SRpemScBzBAI4vMelIVYViQxlSE6xA==",
- "dependencies": {
- "@types/node": "*",
- "@types/tough-cookie": "*",
- "form-data": "^2.5.0"
- }
- },
- "node_modules/@types/got/node_modules/form-data": {
- "version": "2.5.1",
- "resolved": "https://registry.npmjs.org/form-data/-/form-data-2.5.1.tgz",
- "integrity": "sha512-m21N3WOmEEURgk6B9GLOE4RuWOFf28Lhh9qGYeNlGq4VDXUlJy2th2slBNU8Gp8EzloYZOibZJ7t5ecIrFSjVA==",
- "dependencies": {
- "asynckit": "^0.4.0",
- "combined-stream": "^1.0.6",
- "mime-types": "^2.1.12"
- },
- "engines": {
- "node": ">= 0.12"
- }
- },
- "node_modules/@types/http-cache-semantics": {
- "version": "4.0.1",
- "resolved": "https://registry.npmjs.org/@types/http-cache-semantics/-/http-cache-semantics-4.0.1.tgz",
- "integrity": "sha512-SZs7ekbP8CN0txVG2xVRH6EgKmEm31BOxA07vkFaETzZz1xh+cbt8BcI0slpymvwhx5dlFnQG2rTlPVQn+iRPQ=="
- },
- "node_modules/@types/keyv": {
- "version": "3.1.1",
- "resolved": "https://registry.npmjs.org/@types/keyv/-/keyv-3.1.1.tgz",
- "integrity": "sha512-MPtoySlAZQ37VoLaPcTHCu1RWJ4llDkULYZIzOYxlhxBqYPB0RsRlmMU0R6tahtFe27mIdkHV+551ZWV4PLmVw==",
- "dependencies": {
- "@types/node": "*"
- }
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-}
diff --git a/deploy/package.json b/deploy/package.json
deleted file mode 100644
index d423c8404..000000000
--- a/deploy/package.json
+++ /dev/null
@@ -1,44 +0,0 @@
-{
- "name": "deploy",
- "version": "1.0.0",
- "description": "",
- "main": "index.js",
- "scripts": {
- "start": "node server.js",
- "test": "node -r dotenv/config ./node_modules/.bin/mocha './**/*.spec.js' --exclude 'node_modules/*' --timeout 60000 --exit",
- "mocha": "mocha"
- },
- "keywords": [],
- "author": "",
- "license": "ISC",
- "dependencies": {
- "body-parser": "^1.19.0",
- "connect-redis": "^5.0.0",
- "cookie-parser": "^1.4.5",
- "express": "^4.16.4",
- "express-rate-limit": "^5.5.1",
- "express-session": "^1.15.6",
- "got": "^11.8.5",
- "hbp-seafile": "^0.3.0",
- "helmet-csp": "^3.4.0",
- "lru-cache": "^5.1.1",
- "memorystore": "^1.6.1",
- "nomiseco": "0.0.2",
- "openid-client": "^4.4.0",
- "passport": "^0.6.0",
- "rate-limit-redis": "^2.1.0",
- "redis": "^3.1.2",
- "showdown": "^2.0.0",
- "through2": "^3.0.1"
- },
- "devDependencies": {
- "chai": "^4.2.0",
- "chai-as-promised": "^7.1.1",
- "cookie": "^0.4.0",
- "cors": "^2.8.5",
- "dotenv": "^6.2.0",
- "mocha": "^10.1.0",
- "nock": "^12.0.3",
- "sinon": "^8.0.2"
- }
-}
diff --git a/deploy/plugins/index.js b/deploy/plugins/index.js
deleted file mode 100644
index 028a0158d..000000000
--- a/deploy/plugins/index.js
+++ /dev/null
@@ -1,84 +0,0 @@
-/**
- * TODO
- * how to discover plugins?
- */
-
-const express = require('express')
-const lruStore = require('../lruStore')
-const { race } = require("../../common/util")
-const got = require('got')
-const { URL } = require('url')
-const path = require("path")
-const router = express.Router()
-const V2_7_DEV_PLUGINS = (() => {
- try {
- return JSON.parse(
- process.env.V2_7_DEV_PLUGINS || `[]`
- )
- } catch (e) {
- console.warn(`Parsing DEV_PLUGINS failed: ${e}`)
- return []
- }
-})()
-const V2_7_PLUGIN_URLS = (process.env.V2_7_PLUGIN_URLS && process.env.V2_7_PLUGIN_URLS.split(';')) || []
-const V2_7_STAGING_PLUGIN_URLS = (process.env.V2_7_STAGING_PLUGIN_URLS && process.env.V2_7_STAGING_PLUGIN_URLS.split(';')) || []
-
-router.get('', (_req, res) => {
- return res.status(200).json([
- ...V2_7_PLUGIN_URLS,
- ...V2_7_STAGING_PLUGIN_URLS
- ])
-})
-
-const getKey = url => `plugin:manifest-cache:${url}`
-
-router.get('/manifests', async (_req, res) => {
-
- const allManifests = await Promise.all(
- [...V2_7_PLUGIN_URLS, ...V2_7_STAGING_PLUGIN_URLS].map(async url => {
- try {
- return await race(
- async () => {
- const key = getKey(url)
-
- await lruStore._initPr
- const { store } = lruStore
-
- try {
- const storedManifest = await store.get(key)
- if (storedManifest) return JSON.parse(storedManifest)
- else throw `not found`
- } catch (e) {
- const resp = await got(url)
- const json = JSON.parse(resp.body)
-
- const { iframeUrl, 'siibra-explorer': flag } = json
- if (!flag) return null
- if (!iframeUrl) return null
- const u = new URL(url)
-
- let replaceObj = {}
- if (!/^https?:\/\//.test(iframeUrl)) {
- u.pathname = path.resolve(path.dirname(u.pathname), iframeUrl)
- replaceObj['iframeUrl'] = u.toString()
- }
- const returnObj = {...json, ...replaceObj}
- await store.set(key, JSON.stringify(returnObj), { maxAge: 1000 * 60 * 60 })
- return returnObj
- }
- },
- { timeout: 1000 }
- )
- } catch (e) {
- console.error(`fetching manifest error: ${e}`)
- return null
- }
- })
- )
-
- res.status(200).json(
- [...V2_7_DEV_PLUGINS, ...allManifests.filter(v => !!v)]
- )
-})
-
-module.exports = router
\ No newline at end of file
diff --git a/deploy/quickstart/index.js b/deploy/quickstart/index.js
deleted file mode 100644
index efe8aa944..000000000
--- a/deploy/quickstart/index.js
+++ /dev/null
@@ -1,58 +0,0 @@
-const fs = require('fs')
-const { promisify } = require('util')
-const path = require('path')
-const router = require('express').Router()
-const showdown = require('showdown')
-
-const { retry } = require('../../common/util')
-const asyncReadfile = promisify(fs.readFile)
-const mdConverter = new showdown.Converter({
- tables: true
-})
-
-let renderedHtml = ``
-const getQuickStartMdPr = (async () => {
- await retry(async () => {
- const mdData = await asyncReadfile(
- path.resolve(__dirname, '../../common/helpOnePager.md'),
- 'utf-8'
- )
-
- renderedHtml = `
-<!DOCTYPE html>
-<html lang="en">
-<head>
- <meta charset="UTF-8">
- <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
- <script src="https://unpkg.com/dompurify@latest/dist/purify.min.js"></script>
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Siibra Explorer Quickstart</title>
- <style>
- .padded { padding: 1.5rem; }
- </style>
-</head>
-<body class="padded">
-
-</body>
-<script>
-(() => {
- const dirty = \`${mdConverter.makeHtml(mdData).replace(/\`/g, '\\`')}\`
- const clean = DOMPurify.sanitize(dirty)
- document.body.innerHTML = clean
-})()
-</script>
-</html>
-`
- }, {
- retries: 3,
- timeout: 1000
- })
-})()
-
-
-router.get('', async (_req, res) => {
- await getQuickStartMdPr
- res.status(200).send(renderedHtml)
-})
-
-module.exports = router
diff --git a/deploy/saneUrl/depcObjStore.js b/deploy/saneUrl/depcObjStore.js
deleted file mode 100644
index f6c3d3e7a..000000000
--- a/deploy/saneUrl/depcObjStore.js
+++ /dev/null
@@ -1,26 +0,0 @@
-const got = require('got')
-const { NotFoundError } = require('./store')
-
-const { OBJ_STORAGE_ROOT_URL } = process.env
-
-class Store {
-
- get(id) {
- if (!OBJ_STORAGE_ROOT_URL){
- return Promise.reject(
- new NotFoundError()
- )
- }
- return got(`${OBJ_STORAGE_ROOT_URL}/${id}`).text()
- }
-
- async del(id){
- // noop
- }
-
- async set(id, val){
- throw new Error(`Object store is deprecated. Please use seafile storage instead`)
- }
-}
-
-exports.Store = Store
diff --git a/deploy/saneUrl/index.js b/deploy/saneUrl/index.js
deleted file mode 100644
index 582113e0c..000000000
--- a/deploy/saneUrl/index.js
+++ /dev/null
@@ -1,134 +0,0 @@
-const express = require('express')
-const router = express.Router()
-const { GitlabSnippetStore: Store, NotFoundError } = require('./store')
-const { Store: DepcStore } = require('./depcObjStore')
-const RateLimit = require('express-rate-limit')
-const RedisStore = require('rate-limit-redis')
-const lruStore = require('../lruStore')
-const { ProxyStore, NotExactlyPromiseAny } = require('./util')
-
-let store
-try {
- store = new Store()
-} catch (e) {
- console.error(`Failed to new store.`, e)
-}
-const depStore = new DepcStore()
-
-const proxyStore = new ProxyStore(store)
-
-const {
- HOSTNAME,
- HOST_PATHNAME,
- DISABLE_LIMITER,
-} = process.env
-
-function limiterMiddleware(){
- let limiter
- return async (req, res, next) => {
- if (DISABLE_LIMITER) return next()
- if (limiter) return limiter(req, res, next)
- await lruStore._initPr
- const { redisURL } = lruStore
- limiter = new RateLimit({
- windowMs: 1e3 * 5,
- max: 5,
- store: redisURL ? new RedisStore({ redisURL }) : null
- })
- return limiter(req, res, next)
- }
-}
-
-
-const acceptHtmlProg = /text\/html/i
-
-const REAL_HOSTNAME = `${HOSTNAME}${HOST_PATHNAME || ''}/`
-
-router.get('/:name', async (req, res) => {
- const { name } = req.params
- const { headers } = req
-
- const redirectFlag = acceptHtmlProg.test(headers['accept'])
-
- try {
-
- const json = await NotExactlyPromiseAny([
- ProxyStore.StaticGet(depStore, req, name),
- proxyStore.get(req, name)
- ])
-
- const { queryString, hashPath, ...rest } = json
-
- const xtraRoutes = []
- for (const key in rest) {
- if (/^x-/.test(key)) xtraRoutes.push(`${key}:${name}`)
- }
-
- if (redirectFlag) {
- if (queryString) return res.redirect(`${REAL_HOSTNAME}?${queryString}`)
- if (hashPath) {
- let redirectUrl = `${REAL_HOSTNAME}#${hashPath}`
- if (xtraRoutes.length > 0) {
- redirectUrl += `/${xtraRoutes.join('/')}`
- }
- return res.redirect(redirectUrl)
- }
- } else {
- return res.status(200).send(json)
- }
- } catch (e) {
- const notFoundFlag = e instanceof NotFoundError
- if (redirectFlag) {
-
- const REAL_HOSTNAME = `${HOSTNAME}${HOST_PATHNAME || ''}/`
-
- res.cookie(
- 'iav-error',
- notFoundFlag ? `${name}
-
- not found` : `error while fetching ${name}.`,
- {
- httpOnly: true,
- sameSite: "strict",
- maxAge: 1e3 * 30
- }
- )
- return res.redirect(REAL_HOSTNAME)
- }
- if (notFoundFlag) return res.status(404).end()
- else return res.status(500).send(e.toString())
- }
-})
-
-router.post('/:name',
- limiterMiddleware(),
- express.json(),
- async (req, res) => {
- if (/bot/i.test(req.headers['user-agent'])) return res.status(201).end()
- if (req.headers['x-noop']) return res.status(201).end()
- const { name } = req.params
- try {
- await proxyStore.set(req, name, req.body)
- res.status(201).end()
- } catch (e) {
- console.log(e.body)
- res.status(500).send(e.toString())
- }
- }
-)
-
-router.use((_, res) => {
- res.status(405).send('Not implemneted')
-})
-
-const ready = async () => {
- return await store.healthCheck()
-}
-
-const vipRoutes = ["human", "monkey", "rat", "mouse"]
-
-module.exports = {
- router,
- ready,
- vipRoutes,
-}
diff --git a/deploy/saneUrl/index.spec.js b/deploy/saneUrl/index.spec.js
deleted file mode 100644
index 3b9a66ec1..000000000
--- a/deploy/saneUrl/index.spec.js
+++ /dev/null
@@ -1,327 +0,0 @@
-const sinon = require('sinon')
-const got = require('got')
-const cookie = require('cookie')
-const { expect } = require('chai')
-const express = require('express')
-
-let NotFoundError
-const userStore = require('../user/store')
-
-class StubStore {
- async set(key, val) {
-
- }
- async get(key) {
-
- }
-}
-
-class StubNotFoundError extends Error{}
-
-const savedUserDataPayload = {
- otherData: 'not relevant data',
- savedCustomLinks: [
- '111222',
- '333444'
- ]
-}
-
-const readUserDataStub = sinon
- .stub(userStore, 'readUserData')
- .returns(Promise.resolve(savedUserDataPayload))
-
-const saveUserDataStub = sinon
- .stub(userStore, 'saveUserData')
- .returns(Promise.resolve())
-
-
-describe('> saneUrl/index.js', () => {
- const name = `nameme`,
- payload = {
- ver: '0.0.1',
- queryString: 'test_test'
- }
-
- let DepObjStub,
- depcGetStub,
- SaneUrlStoreObjStub,
- getStub,
- setStub
-
- before(() => {
- const SaneUrlStore = require('./store')
- const DepcStore = require('./depcObjStore')
- NotFoundError = SaneUrlStore.NotFoundError
-
- getStub = sinon.stub()
- setStub = sinon.stub()
- class StubbedStoreObj {
- constructor(){
- this.get = getStub
- this.set = setStub
- }
- }
- depcGetStub = sinon.stub()
- class DepcStubbedObj {
- constructor() {
- this.get = depcGetStub
- }
- }
- DepObjStub = sinon.stub(DepcStore, 'Store').value(DepcStubbedObj)
- SaneUrlStoreObjStub = sinon.stub(SaneUrlStore, 'Store').value(StubbedStoreObj)
- })
- after(() => {
- SaneUrlStoreObjStub.restore()
- DepObjStub.restore()
- })
-
- beforeEach(() => {
- depcGetStub.callsFake(async () => {
- throw new NotFoundError()
- })
- })
-
- afterEach(() => {
- depcGetStub.resetHistory()
- depcGetStub.resetBehavior()
- getStub.resetHistory()
- getStub.resetBehavior()
- setStub.resetHistory()
- setStub.resetBehavior()
- })
-
- before(() => {
- getStub = sinon.stub(StubStore.prototype, 'get')
- setStub = sinon.stub(StubStore.prototype, 'set')
- require.cache[require.resolve('../lruStore')] = {
- exports: {
- redisURL: null
- }
- }
-
- let server, user
- before(() => {
- const { router } = require('./index')
- const app = express()
- app.use('', (req, res, next) => {
- req.user = user
- next()
- }, router)
-
- server = app.listen(50000)
- })
- after(() => {
- console.log('closing server')
-
- server.close()
- })
-
- describe('> works', () => {
-
- const body = {
- ...payload
- }
-
- beforeEach(() => {
- setStub.returns(Promise.resolve())
- getStub.returns(Promise.resolve(JSON.stringify(body)))
- })
- afterEach(() => {
- setStub.resetHistory()
- setStub.resetBehavior()
- getStub.resetHistory()
- getStub.resetBehavior()
- })
-
- it('> works', async () => {
- const { body: respBody } = await got(`http://localhost:50000/${name}`)
- expect(getStub.calledWith(name)).to.be.true
- expect(respBody).to.equal(JSON.stringify(body))
- })
- })
-
- describe('> expired', () => {
- beforeEach(() => {
- const body = {
- ...payload,
- expiry: Date.now() - 1e3 * 60
- }
-
- getStub.returns(Promise.resolve(JSON.stringify(body)))
- })
-
- it('> get on expired returns 404', async () => {
-
- const { statusCode } = await got(`http://localhost:50000/${name}`, {
- throwHttpErrors: false
- })
- expect(statusCode).to.equal(404)
- expect(getStub.calledWith(name)).to.be.true
- })
- it('> get on expired with txt html header sets cookie and redirect', async () => {
-
- const { statusCode, headers } = await got(`http://localhost:50000/${name}`, {
- headers: {
- 'accept': 'text/html'
- },
- followRedirect: false
- })
- expect(statusCode).to.be.greaterThan(300)
- expect(statusCode).to.be.lessThan(303)
-
- expect(getStub.calledWith(name)).to.be.true
-
- const c = cookie.parse(...headers['set-cookie'])
- expect(!!c['iav-error']).to.be.true
- })
- })
-
- describe('> set', () => {
-
- describe('> error', () => {
- describe('> entry exists', () => {
- beforeEach(() => {
- getStub.returns(Promise.resolve('{}'))
- })
-
- it('> returns 409 conflict', async () => {
- const { statusCode } = await got(`http://localhost:50000/${name}`, {
- method: 'POST',
- headers: {
- 'Content-type': 'application/json'
- },
- body: JSON.stringify(payload),
- throwHttpErrors: false
- })
-
- expect(statusCode).to.equal(409)
- expect(getStub.called).to.be.true
- expect(setStub.called).to.be.false
- })
- })
-
- describe('> other error', () => {
- beforeEach(() => {
- getStub.callsFake(async () => {
- throw new Error(`other errors`)
- })
- })
- it('> returns 500', async () => {
- const { statusCode } = await got(`http://localhost:50000/${name}`, {
- method: 'POST',
- headers: {
- 'Content-type': 'application/json'
- },
- body: JSON.stringify(payload),
- throwHttpErrors: false
- })
-
- expect(statusCode).to.equal(500)
- expect(getStub.called).to.be.true
- expect(setStub.called).to.be.false
- })
- })
- })
-
- describe('> success', () => {
- beforeEach(() => {
- getStub.callsFake(async () => {
- throw new NotFoundError()
- })
- })
- it('> checks if the name is available', async () => {
- await got(`http://localhost:50000/${name}`, {
- method: 'POST',
- headers: {
- 'Content-type': 'application/json'
- },
- body: JSON.stringify(payload)
- })
-
- const [ storedName, _ ] = setStub.args[0]
-
- expect(storedName).to.equal(name)
- expect(getStub.called).to.be.true
- expect(setStub.called).to.be.true
- })
-
- describe('> anony user', () => {
- beforeEach(() => {
- user = null
- })
-
- it('> set with anonymous user has user undefined and expiry as defined', async () => {
-
- await got(`http://localhost:50000/${name}`, {
- method: 'POST',
- headers: {
- 'Content-type': 'application/json'
- },
- body: JSON.stringify(payload)
- })
-
- expect(setStub.called).to.be.true
- const [ _, storedContent] = setStub.args[0]
- const { userId, expiry } = JSON.parse(storedContent)
- expect(!!userId).to.be.false
- expect(!!expiry).to.be.true
-
- // there will be some discrepencies, but the server lag should not exceed 5 seconds
- expect( 1e3 * 60 * 60 * 72 - expiry + Date.now() ).to.be.lessThan(1e3 * 5)
- })
- })
-
- describe('> authenticated user', () => {
- beforeEach(() => {
- user = {
- id: 'test/1',
- name: 'hello world'
- }
- })
- it('> userId set, expiry unset', async () => {
-
- await got(`http://localhost:50000/${name}`, {
- method: 'POST',
- headers: {
- 'Content-type': 'application/json'
- },
- body: JSON.stringify(payload)
- })
-
- expect(setStub.called).to.be.true
- const [ _, storedContent] = setStub.args[0]
- const { userId, expiry } = JSON.parse(storedContent)
- expect(!!userId).to.be.true
- expect(!!expiry).to.be.false
-
- expect( userId ).to.equal('test/1')
- })
- it('> readUserDataset saveUserDataset data stubs called', async () => {
-
- await got(`http://localhost:50000/${name}`, {
- method: 'POST',
- headers: {
- 'Content-type': 'application/json'
- },
- body: JSON.stringify(payload)
- })
-
- expect(readUserDataStub.called).to.be.true
- expect(readUserDataStub.calledWith(user)).to.be.true
-
- expect(saveUserDataStub.called).to.be.true
- expect(saveUserDataStub.calledWith(user, {
- ...savedUserDataPayload,
- savedCustomLinks: [
- ...savedUserDataPayload.savedCustomLinks,
- name
- ]
- })).to.be.true
- })
- })
-
- })
- })
- })
-})
-
diff --git a/deploy/saneUrl/store.js b/deploy/saneUrl/store.js
deleted file mode 100644
index 39b39223a..000000000
--- a/deploy/saneUrl/store.js
+++ /dev/null
@@ -1,100 +0,0 @@
-const got = require('got')
-
-const apiPath = '/api/v4'
-const saneUrlVer = `0.0.1`
-const titlePrefix = `[saneUrl]`
-
-const {
- __DEBUG__,
- GITLAB_ENDPOINT,
- GITLAB_PROJECT_ID,
- GITLAB_TOKEN
-} = process.env
-
-class NotFoundError extends Error{}
-
-class NotImplemented extends Error{}
-
-class GitlabSnippetStore {
- constructor(){
-
- if (
- GITLAB_ENDPOINT
- && GITLAB_PROJECT_ID
- && GITLAB_TOKEN
- ) {
- this.url = `${GITLAB_ENDPOINT}${apiPath}/projects/${GITLAB_PROJECT_ID}/snippets`
- this.token = GITLAB_TOKEN
- return
- }
- throw new NotImplemented('Gitlab snippet key value store cannot be configured')
- }
-
- _promiseRequest(...arg) {
- return got(...arg).text()
- }
-
- _request({ addPath = '', method = 'GET', headers = {}, opt = {} } = {}) {
- return got(`${this.url}${addPath}?per_page=1000`, {
- method,
- headers: {
- 'PRIVATE-TOKEN': this.token,
- ...headers
- },
- ...opt
- }).text()
- }
-
- async get(id) {
- const list = JSON.parse(await this._request())
- const found = list.find(item => item.title === `${titlePrefix}${id}`)
- if (!found) throw new NotFoundError()
- const payloadObj = found.files.find(f => f.path === 'payload')
- if (!payloadObj) {
- console.error(`id found, but payload not found... this is strange. Check id: ${id}`)
- throw new NotFoundError()
- }
- if (!payloadObj.raw_url) {
- throw new Error(`payloadObj.raw_url not found!`)
- }
- return await this._promiseRequest(payloadObj.raw_url)
- }
-
- async set(id, value) {
- return await this._request({
- method: 'POST',
- headers: {
- 'Content-Type': 'application/json'
- },
- opt: {
- json: {
- title: `${titlePrefix}${id}`,
- description: `Created programmatically. v${saneUrlVer}`,
- visibility: 'public',
- files: [{
- file_path: 'payload',
- content: value
- }]
- }
- }
- })
- }
-
- async del(id) {
- return await this._request({
- addPath: `/${id}`,
- method: 'DELETE',
- })
- }
-
- async dispose(){
-
- }
-
- async healthCheck(){
- return true
- }
-}
-
-exports.GitlabSnippetStore = GitlabSnippetStore
-exports.NotFoundError = NotFoundError
diff --git a/deploy/saneUrl/util.js b/deploy/saneUrl/util.js
deleted file mode 100644
index 12fce0a38..000000000
--- a/deploy/saneUrl/util.js
+++ /dev/null
@@ -1,70 +0,0 @@
-const { NotFoundError } = require('./store')
-
-class ProxyStore {
- static async StaticGet(store, req, name) {
- if (!store) throw new Error(`store is falsy`)
- const payload = JSON.parse(await store.get(name))
- const { expiry, value, ...rest } = payload
- if (expiry && (Date.now() > expiry)) {
- await store.del(name)
- throw new NotFoundError('Expired')
- }
- // backwards compatibility for depcObjStore .
- // when depcObjStore is fully removed, || rest can also be removed
- return value || rest
- }
-
- constructor(store){
- this.store = store
- }
- async get(req, name) {
- return await ProxyStore.StaticGet(this.store, req, name)
- }
-
- async set(req, name, value) {
- if (!this.store) throw new Error(`store is falsy`)
- const supplementary = req.user
- ? {
- userId: req.user.id,
- expiry: null
- }
- : {
- userId: null,
- expiry: Date.now() + 1000 * 60 * 60 * 72
- }
-
- const fullPayload = {
- value,
- ...supplementary
- }
- return await this.store.set(name, JSON.stringify(fullPayload))
- }
-}
-
-const NotExactlyPromiseAny = async arg => {
- const errs = []
- let resolvedFlag = false
- return await new Promise((rs, rj) => {
- let totalCounter = 0
- for (const pr of arg) {
- totalCounter ++
- pr.then(val => {
- if (!resolvedFlag) {
- resolvedFlag = true
- rs(val)
- }
- }).catch(e => {
- errs.push(e)
- totalCounter --
- if (totalCounter <= 0) {
- rj(new NotFoundError(errs))
- }
- })
- }
- })
-}
-
-module.exports = {
- ProxyStore,
- NotExactlyPromiseAny
-}
diff --git a/deploy/saneUrl/util.spec.js b/deploy/saneUrl/util.spec.js
deleted file mode 100644
index f19d8cc92..000000000
--- a/deploy/saneUrl/util.spec.js
+++ /dev/null
@@ -1,206 +0,0 @@
-const { ProxyStore, NotExactlyPromiseAny } = require('./util')
-const { expect, assert } = require('chai')
-const sinon = require('sinon')
-const { NotFoundError } = require('./store')
-
-const _name = 'foo-bar'
-const _stringValue = 'hello world'
-const _objValue = {
- 'foo': 'bar'
-}
-const _req = {}
-
-describe('> saneUrl/util.js', () => {
- describe('> ProxyStore', () => {
- let store = {
- set: sinon.stub(),
- get: sinon.stub(),
- del: sinon.stub(),
- }
- beforeEach(() => {
- store.set.returns(Promise.resolve())
- store.get.returns(Promise.resolve('{}'))
- store.del.returns(Promise.resolve())
- })
- afterEach(() => {
- store.set.resetHistory()
- store.get.resetHistory()
- store.del.resetHistory()
- })
- describe('> StaticGet', () => {
- it('> should call store.get', () => {
- ProxyStore.StaticGet(store, _req, _name)
- assert(store.get.called, 'called')
- assert(store.get.calledWith(_name), 'called with right param')
- })
- describe('> if not hit', () => {
- const err = new NotFoundError('not found')
- beforeEach(() => {
- store.get.rejects(err)
- })
- it('should throw same error', async () => {
- try{
- await ProxyStore.StaticGet(store, _req, _name)
- assert(false, 'Should throw')
- } catch (e) {
- assert(e instanceof NotFoundError)
- }
- })
- })
- describe('> if hit', () => {
- describe('> if expired', () => {
- beforeEach(() => {
- store.get.returns(
- Promise.resolve(
- JSON.stringify({
- expiry: Date.now() - 1000
- })
- )
- )
- })
- it('> should call store.del', async () => {
- try {
- await ProxyStore.StaticGet(store, _req, _name)
- } catch (e) {
-
- }
- assert(store.del.called, 'store.del should be called')
- })
- it('> should throw NotFoundError', async () => {
- try {
- await ProxyStore.StaticGet(store, _req, _name)
- assert(false, 'expect throw')
- } catch (e) {
- assert(e instanceof NotFoundError, 'throws NotFoundError')
- }
- })
- })
- describe('> if not expired', () => {
- it('> should return .value, if exists', async () => {
- store.get.returns(
- Promise.resolve(
- JSON.stringify({
- value: _objValue,
- others: _stringValue
- })
- )
- )
- const returnObj = await ProxyStore.StaticGet(store, _req, _name)
- expect(returnObj).to.deep.equal(_objValue)
- })
- it('> should return ...rest if .value does not exist', async () => {
- store.get.returns(
- Promise.resolve(
- JSON.stringify({
- others: _stringValue
- })
- )
- )
- const returnObj = await ProxyStore.StaticGet(store, _req, _name)
- expect(returnObj).to.deep.equal({
- others: _stringValue
- })
- })
- })
- })
-
- })
-
- describe('> get', () => {
- let staticGetStub
- beforeEach(() => {
- staticGetStub = sinon.stub(ProxyStore, 'StaticGet')
- staticGetStub.returns(Promise.resolve())
- })
- afterEach(() => {
- staticGetStub.restore()
- })
- it('> proxies calls to StaticGet', async () => {
- const store = {}
- const proxyStore = new ProxyStore(store)
- await proxyStore.get(_req, _name)
- assert(staticGetStub.called)
- assert(staticGetStub.calledWith(store, _req, _name))
- })
- })
-
- describe('> set', () => {
- let proxyStore
- beforeEach(() => {
- proxyStore = new ProxyStore(store)
- store.set.returns(Promise.resolve())
- })
-
- describe('> no user', () => {
- it('> sets expiry some time in the future', async () => {
- await proxyStore.set(_req, _name, _objValue)
- assert(store.set.called)
-
- const [ name, stringifiedJson ] = store.set.args[0]
- assert(name === _name, 'name is correct')
- const payload = JSON.parse(stringifiedJson)
- expect(payload.value).to.deep.equal(_objValue, 'payload is correct')
- assert(!!payload.expiry, 'expiry exists')
- assert((payload.expiry - Date.now()) > 1000 * 60 * 60 * 24, 'expiry is at least 24 hrs in the future')
-
- assert(!payload.userId, 'userId does not exist')
- })
- })
- describe('> yes user', () => {
- let __req = {
- ..._req,
- user: {
- id: 'foo-bar-2'
- }
- }
- it('> does not set expiry, but sets userId', async () => {
- await proxyStore.set(__req, _name, _objValue)
- assert(store.set.called)
-
- const [ name, stringifiedJson ] = store.set.args[0]
- assert(name === _name, 'name is correct')
- const payload = JSON.parse(stringifiedJson)
- expect(payload.value).to.deep.equal(_objValue, 'payload is correct')
- assert(!payload.expiry, 'expiry does not exist')
-
- assert(payload.userId, 'userId exists')
- assert(payload.userId === 'foo-bar-2', 'user-id matches')
- })
- })
- })
- })
-
- describe('> NotExactlyPromiseAny', () => {
- describe('> nothing resolves', () => {
- it('> throws not found error', async () => {
- try {
- await NotExactlyPromiseAny([
- (async () => {
- throw new Error(`not here`)
- })(),
- new Promise((rs, rj) => setTimeout(rj, 100)),
- new Promise((rs, rj) => rj('uhoh'))
- ])
- assert(false, 'expected to throw')
- } catch (e) {
- assert(e instanceof NotFoundError, 'expect to throw not found error')
- }
- })
- })
- describe('> something resolves', () => {
- it('> returns the first to resolve', async () => {
- try {
-
- const result = await NotExactlyPromiseAny([
- new Promise((rs, rj) => rj('uhoh')),
- new Promise(rs => setTimeout(() => rs('hello world'), 100)),
- Promise.resolve('foo-bar')
- ])
- assert(result == 'foo-bar', 'expecting first to resolve')
- } catch (e) {
- assert(false, 'not expecting to throw')
- }
- })
- })
- })
-})
diff --git a/deploy/server.js b/deploy/server.js
deleted file mode 100644
index f628ffe75..000000000
--- a/deploy/server.js
+++ /dev/null
@@ -1,90 +0,0 @@
-if (process.env.NODE_ENV !== 'production') {
- require('dotenv').config()
- process.on('unhandledRejection', (err, p) => {
- console.log({err, p})
- })
-}
-
-if (process.env.FLUENT_HOST) {
- const Logger = require('./logging')
- const os = require('os')
-
- const name = process.env.IAV_NAME || 'IAV'
- const stage = os.hostname() || 'unknown-host'
-
- const protocol = process.env.FLUENT_PROTOCOL || 'http'
- const host = process.env.FLUENT_HOST || 'localhost'
- const port = process.env.FLUENT_PORT || 24224
-
- const prefix = `${name}.${stage}`
-
- const log = new Logger(prefix, {
- protocol,
- host,
- port
- })
-
- const handleRequestCallback = (err, resp, body) => {
- if (err) {
- process.stderr.write(`fluentD logging failed\n`)
- process.stderr.write(err.toString())
- process.stderr.write('\n')
- }
-
- if (resp && resp.statusCode >= 400) {
- process.stderr.write(`fluentD logging responded error\n`)
- process.stderr.write(resp.toString())
- process.stderr.write('\n')
- }
- }
-
- const emitInfo = message => log.emit('info', { message }, handleRequestCallback)
-
- const emitWarn = message => log.emit('warn', { message }, handleRequestCallback)
-
- const emitError = message => log.emit('error', { message }, handleRequestCallback)
-
- console.log('starting fluentd logging')
-
- console.log = function () {
- emitInfo([...arguments])
- }
- console.warn = function () {
- emitWarn([...arguments])
- }
- console.error = function () {
- emitError([...arguments])
- }
-}
-
-const server = require('express')()
-
-const PORT = process.env.PORT || 3000
-
-// e.g. HOST_PATHNAME=/viewer
-// n.b. leading slash is important
-// n.b. no trailing slash is important
-const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
-
-if(HOST_PATHNAME !== '') {
- if (HOST_PATHNAME.slice(0,1) !== '/') throw new Error(`HOST_PATHNAME, if defined and non-empty, should start with a leading slash. HOST_PATHNAME: ${HOST_PATHNAME}`)
- if (HOST_PATHNAME.slice(-1) === '/') throw new Error(`HOST_PATHNAME, if defined and non-emtpy, should NOT end with a slash. HOST_PATHNAME: ${HOST_PATHNAME}`)
-}
-
-server.set('strict routing', true)
-server.set('trust proxy', 1)
-
-server.disable('x-powered-by')
-
-if (HOST_PATHNAME && HOST_PATHNAME !== '') {
- server.get(HOST_PATHNAME, (_req, res) => {
- res.redirect(`${HOST_PATHNAME}/`)
- })
-}
-
-if (process.env.NODE_ENV !== 'test') {
- const app = require('./app')
- server.use(`${HOST_PATHNAME}/`, app)
-}
-
-server.listen(PORT, () => console.log(`listening on port ${PORT}`))
diff --git a/deploy/server.spec.js b/deploy/server.spec.js
deleted file mode 100644
index 6e8e36df8..000000000
--- a/deploy/server.spec.js
+++ /dev/null
@@ -1,112 +0,0 @@
-const { spawn } = require("child_process")
-const { expect, assert } = require('chai')
-const path = require('path')
-const got = require('got')
-
-const PORT = process.env.PORT || 3000
-
-describe('> server.js', () => {
- const cwdPath = path.join(__dirname)
-
- describe('> HOST_PATHNAME env var parsed correctly', () => {
-
- it('> throws if HOST_PATHNAME does not start with a leading hash', done => {
- const childProcess = spawn('node', ['server.js'], {
- cwd: cwdPath,
- env: {
- ...process.env,
- NODE_ENV: 'test',
- HOST_PATHNAME: 'viewer'
- }
- })
-
- const timedKillSig = setTimeout(() => {
- childProcess.kill()
- }, 500)
-
- childProcess.on('exit', (code) => {
- childProcess.kill()
- clearTimeout(timedKillSig)
- expect(code).to.be.greaterThan(0)
- done()
- })
- })
-
- it('> throws if HOST_PATHNAME ends with slash', done => {
-
- const childProcess = spawn('node', ['server.js'], {
- cwd: cwdPath,
- env: {
- ...process.env,
- NODE_ENV: 'test',
- HOST_PATHNAME: '/viewer/'
- }
- })
-
- const timedKillSig = setTimeout(() => {
- childProcess.kill(0)
- }, 500)
-
- childProcess.on('exit', (code) => {
- clearTimeout(timedKillSig)
- expect(code).to.be.greaterThan(0)
- done()
- })
- })
-
- it('> does not throw if HOST_PATHNAME leads with slash, but does not end with slash', done => {
-
- const childProcess = spawn('node', ['server.js'], {
- cwd: cwdPath,
- stdio: 'inherit',
- env: {
- ...process.env,
- NODE_ENV: 'test',
- PORT,
- HOST_PATHNAME: '/viewer'
- }
- })
-
- const timedKillSig = setTimeout(() => {
- console.log('killing on timeout')
- childProcess.kill()
- }, 500)
-
- childProcess.on('exit', (code, signal) => {
- clearTimeout(timedKillSig)
- expect(signal).to.equal('SIGTERM')
- done()
- })
- })
- })
-
-
- describe('> redirection', () => {
- let childProcess
- before(done => {
- const cwdPath = path.join(__dirname)
- childProcess = spawn('node', ['server.js'], {
- cwd: cwdPath,
- env: {
- ...process.env,
- NODE_ENV: 'test',
- PORT,
- HOST_PATHNAME: '/viewer'
- }
- })
- setTimeout(done, 1000)
- })
-
- it('> redirects as expected', async () => {
- const { statusCode } = await got(`http://localhost:${PORT}/viewer`, {
- followRedirect: false
- })
- expect(statusCode).to.be.greaterThan(300)
- expect(statusCode).to.be.lessThan(303)
- })
-
- after(() => {
- childProcess.kill()
- })
- })
-})
diff --git a/deploy/user/index.js b/deploy/user/index.js
deleted file mode 100644
index dd8a0ab79..000000000
--- a/deploy/user/index.js
+++ /dev/null
@@ -1,86 +0,0 @@
-const express = require('express')
-const bodyParser = require('body-parser')
-const router = express.Router()
-const { readUserData, saveUserData } = require('./store')
-
-const loggedInOnlyMiddleware = (req, res, next) => {
- const { user } = req
- if (!user) {
- return res.status(200).json({
- error: true,
- message: 'Not logged in'
- })
- }
- return next()
-}
-
-router.get('', loggedInOnlyMiddleware, (req, res) => {
- return res.status(200).send(JSON.stringify(req.user))
-})
-
-router.get('/config', loggedInOnlyMiddleware, async (req, res) => {
- const { user } = req
- try{
- const data = await readUserData(user)
- res.status(200).json(data)
- } catch (e){
- console.error(e)
- res.status(500).send(e.toString())
- }
-})
-
-router.get('/pluginPermissions', async (req, res) => {
- const { user } = req
- /**
- * only using session to store user csp for now
- * in future, if use is logged in, look for **signed** config file, and verify the signature
- */
- const permittedCsp = req.session.permittedCsp || {}
- res.status(200).json(permittedCsp)
-})
-
-router.post('/pluginPermissions', bodyParser.json(), async (req, res) => {
- const { user, body } = req
- /**
- * only using session to store user csp for now
- * in future, if use is logged in, **signed** config file, and store in user space
- */
-
- const newPermittedCsp = req.session.permittedCsp || {}
- for (const key in body) {
- newPermittedCsp[key] = body[key]
- }
- req.session.permittedCsp = newPermittedCsp
- res.status(200).json({ ok: true })
-})
-
-router.delete('/pluginPermissions/:pluginKey', async (req, res) => {
- const { user, params } = req
- const { pluginKey } = params
- /**
- * only using session to store user csp for now
- * in future, if use is logged in, **signed** config file, and store in user space
- */
- const newPermission = {}
- const permittedCsp = req.session.permittedCsp || {}
- for (const key in permittedCsp) {
- if (pluginKey !== key) {
- newPermission[key] = permittedCsp[key]
- }
- }
- req.session.permittedCsp = newPermission
- res.status(200).json({ ok: true })
-})
-
-router.post('/config', loggedInOnlyMiddleware, bodyParser.json(), async (req, res) => {
- const { user, body } = req
- try {
- await saveUserData(user, body)
- res.status(200).end()
- } catch (e) {
- console.error(e)
- res.status(500).send(e.toString())
- }
-})
-
-module.exports = router
\ No newline at end of file
diff --git a/deploy/user/index.spec.js b/deploy/user/index.spec.js
deleted file mode 100644
index 73cb58bbd..000000000
--- a/deploy/user/index.spec.js
+++ /dev/null
@@ -1,245 +0,0 @@
-const router = require('./index')
-const app = require('express')()
-const sinon = require('sinon')
-const { stub, spy } = require('sinon')
-const { default: got } = require('got/dist/source')
-const { expect, assert } = require('chai')
-
-const sessionObj = {
- permittedCspVal: {},
- get permittedCsp(){
- return this.permittedCspVal
- },
- set permittedCsp(val) {
-
- }
-}
-
-let userObj = null
-
-const permittedCspSpy = spy(sessionObj, 'permittedCsp', ['get', 'set'])
-
-const middleware = (req, res, next) => {
- req.session = sessionObj
- req.user = userObj
- next()
-}
-
-describe('> user/index.js', () => {
- let server
-
- before(done => {
- app.use(middleware)
- app.use(router)
- server = app.listen(1234)
- setTimeout(() => {
- done()
- }, 1000);
- })
-
- afterEach(() => {
- permittedCspSpy.get.resetHistory()
- permittedCspSpy.set.resetHistory()
- sessionObj.permittedCspVal = {}
- userObj = null
- })
-
- after(done => server.close(() => done()))
-
- describe('> GET ', () => {
- describe('> user undefined', () => {
- it('> should return 200, but error in resp', async () => {
- const { body, statusCode } = await got.get('http://localhost:1234')
- try {
- assert(
- statusCode < 400,
- 'expect the response to be OK'
- )
- const { error } = JSON.parse(body)
- assert(
- !!error,
- 'expect error is truthy'
- )
- } catch (e) {
- assert(
- false,
- `expect no error, but got ${e.toString()}`
- )
- }
- })
- })
-
- describe('> user defined', () => {
- const user = {
- foo: 'bar'
- }
- beforeEach(() => {
- userObj = user
- })
- it('> should return 200, and user obj in resp', async () => {
-
- const { body, statusCode } = await got.get('http://localhost:1234')
- try {
- assert(
- statusCode < 400,
- 'expect the response to be ok'
- )
- const gotUser = JSON.parse(body)
- expect(
- gotUser
- ).to.deep.equal(user)
- } catch (e) {
- assert(
- false,
- `expect no error, but got ${e.toString()}`
- )
- }
- })
- })
- })
-
- describe('> GET /pluginPermissions', () => {
- it('> getter called, setter not called', async () => {
- await got.get('http://localhost:1234/pluginPermissions')
-
- assert(
- permittedCspSpy.get.calledOnce,
- `permittedCsp getter accessed once`
- )
-
- assert(
- permittedCspSpy.set.notCalled,
- `permittedCsp setter not called`
- )
- })
- it('> if no value present, returns {}', async () => {
- sessionObj.permittedCspVal = null
- const { body } = await got.get('http://localhost:1234/pluginPermissions')
- expect(JSON.parse(body)).to.deep.equal({})
- })
-
- it('> if value present, return value', async () => {
- const val = {
- 'hot-dog': {
- 'weatherman': 'tolerable'
- }
- }
- sessionObj.permittedCspVal = val
-
- const { body } = await got.get('http://localhost:1234/pluginPermissions')
- expect(JSON.parse(body)).to.deep.equal(val)
- })
- })
-
- describe('> POST /pluginPermissions', () => {
- it('> getter called once, then setter called once', async () => {
- const jsonPayload = {
- 'hotdog-world': 420
- }
- await got.post('http://localhost:1234/pluginPermissions', {
- json: jsonPayload
- })
- assert(
- permittedCspSpy.get.calledOnce,
- `permittedCsp getter called once`
- )
- assert(
- permittedCspSpy.set.calledOnce,
- `permittedCsp setter called once`
- )
-
- assert(
- permittedCspSpy.get.calledBefore(permittedCspSpy.set),
- `getter called before setter`
- )
-
- assert(
- permittedCspSpy.set.calledWith(jsonPayload),
- `setter called with payload`
- )
- })
-
- it('> if sessio obj exists, will set with merged obj', async () => {
- const prevVal = {
- 'foo-bar': [
- 123,
- 'fuzz-buzz'
- ],
- 'hot-dog-world': 'baz'
- }
- sessionObj.permittedCspVal = prevVal
-
- const jsonPayload = {
- 'hot-dog-world': [
- 'fussball'
- ]
- }
-
- await got.post('http://localhost:1234/pluginPermissions', {
- json: jsonPayload
- })
- assert(
- permittedCspSpy.set.calledWith({
- ...prevVal,
- ...jsonPayload,
- }),
- 'setter called with merged payload'
- )
- })
- })
-
- describe('> DELETE /pluginPermissions/:pluginId', () => {
- const prevVal = {
- 'foo': 'bar',
- 'buzz': 'lightyear'
- }
- beforeEach(() => {
- sessionObj.permittedCspVal = prevVal
- })
-
- it('> getter and setter gets called once and in correct order', async () => {
-
- await got.delete(`http://localhost:1234/pluginPermissions/foolish`)
-
- assert(
- permittedCspSpy.get.calledOnce,
- 'getter called once'
- )
-
- assert(
- permittedCspSpy.set.calledOnce,
- 'setter called once'
- )
-
- assert(
- permittedCspSpy.get.calledBefore(permittedCspSpy.set),
- 'getter called before setter'
- )
- })
-
- it('> if attempts at delete non existent key, still returns ok', async () => {
-
- const { body } = await got.delete(`http://localhost:1234/pluginPermissions/foolish`)
- const json = JSON.parse(body)
- expect(json).to.deep.equal({ ok: true })
-
- assert(
- permittedCspSpy.set.calledWith(prevVal),
- 'permittedCsp setter called with the prev value (nothing changed)'
- )
- })
-
- it('> if attempts at delete exisiting key, returns ok, and value is set', async () => {
-
- const { body } = await got.delete(`http://localhost:1234/pluginPermissions/foo`)
- const json = JSON.parse(body)
- expect(json).to.deep.equal({ ok: true })
-
- const { foo, ...rest } = prevVal
- assert(
- permittedCspSpy.set.calledWith(rest),
- 'permittedCsp setter called with the prev value, less the deleted key'
- )
- })
- })
-})
\ No newline at end of file
diff --git a/deploy/user/store.js b/deploy/user/store.js
deleted file mode 100644
index 03f476279..000000000
--- a/deploy/user/store.js
+++ /dev/null
@@ -1,68 +0,0 @@
-const { Readable } = require('stream')
-
-const IAV_DIR_NAME = `interactive-atlas-viewer`
-const IAV_DIRECTORY = `/${IAV_DIR_NAME}/`
-const IAV_FILENAME = 'data.json'
-
-const getNewSeafilehandle = async ({ accessToken }) => {
- const { Seafile } = await import("hbp-seafile")
- const seafileHandle = new Seafile({ accessToken })
- await seafileHandle.init()
- return seafileHandle
-}
-
-const saveUserData = async (user, data) => {
- const { access_token } = user && user.tokenset || {}
- if (!access_token) throw new Error(`user or user.tokenset not set can only save logged in user data`)
-
- let handle = await getNewSeafilehandle({ accessToken: access_token })
-
- const s = await handle.ls()
- const found = s.find(({ type, name }) => type === 'dir' && name === IAV_DIR_NAME)
-
- // if dir exists, check permission. throw if no writable or readable permission
- if (found && !/w/.test(found.permission) && !/r/.test(found.permission)){
- throw new Error(`Writing to file not permitted. Current permission: ${found.permission}`)
- }
-
- // create new dir if does not exist. Should have rw permission
- if (!found) {
- await handle.mkdir({ dir: IAV_DIR_NAME })
- }
-
- const fileLs = await handle.ls({ dir: IAV_DIRECTORY })
- const fileFound = fileLs.find(({ type, name }) => type === 'file' && name === IAV_FILENAME )
-
- const rStream = new Readable()
- rStream.path = IAV_FILENAME
- rStream.push(JSON.stringify(data))
- rStream.push(null)
-
- if(!fileFound) {
- return handle.uploadFile({ readStream: rStream, filename: `${IAV_FILENAME}` }, { dir: IAV_DIRECTORY })
- }
-
- if (fileFound && !/w/.test(fileFound.permission)) {
- return new Error('file permission cannot be written')
- }
-
- return handle.updateFile({ dir: IAV_DIRECTORY, replaceFilepath: `${IAV_DIRECTORY}${IAV_FILENAME}` }, { readStream: rStream, filename: IAV_FILENAME })
-}
-
-const readUserData = async (user) => {
- const { access_token } = user && user.tokenset || {}
- if (!access_token) throw new Error(`user or user.tokenset not set can only save logged in user data`)
-
- let handle = await getNewSeafilehandle({ accessToken: access_token })
- try {
- const r = await handle.readFile({ dir: `${IAV_DIRECTORY}${IAV_FILENAME}` })
- return JSON.parse(r)
- }catch(e){
- return {}
- }
-}
-
-module.exports = {
- saveUserData,
- readUserData
-}
diff --git a/deploy/util/streamHandleError.js b/deploy/util/streamHandleError.js
deleted file mode 100644
index bd24374e7..000000000
--- a/deploy/util/streamHandleError.js
+++ /dev/null
@@ -1,4 +0,0 @@
-exports.getHandleErrorFn = (req, res) => err => {
- console.error('getHandleErrorFn', err)
- res.status(501).send(err.toString())
-}
\ No newline at end of file
diff --git a/deploy_env.md b/deploy_env.md
index 1926d4bb3..8c2b1a3d8 100644
--- a/deploy_env.md
+++ b/deploy_env.md
@@ -4,17 +4,12 @@
| name | description | default | example |
| --- | --- | --- | --- |
-| `PORT` | port to listen on | 3000 |
-| `HOST_PATHNAME` | pathname to listen on, restrictions: leading slash, no trailing slash | `''` | `/viewer` |
| `SESSIONSECRET` | session secret for cookie session |
-| `NODE_ENV` | determines where the built viewer will be served from | | `production` |
-| ~~`PRECOMPUTED_SERVER`~~ _deprecated_, use `LOCAL_CDN` instead. | redirect data uri to another server. Useful for offline demos | | `http://localhost:8080/precomputed/` |
-| `LOCAL_CDN` | rewrite cdns to local server. useful for offlnie demo | | `http://localhost:7080/` |
-| `PLUGIN_URLS` | semi colon separated urls to be returned when user queries plugins | `''`
-| `STAGING_PLUGIN_URLS` | semi colon separated urls to be returned when user queries plugins | `''`
-| `USE_LOGO` | possible values are `hbp`, `ebrains`, `fzj` | `hbp` | `ebrains` |
-| `__DEBUG__` | debug flag |
+| `V2_7_PLUGIN_URLS` | semi colon separated urls to be returned when user queries plugins | `''`
+| `V2_7_STAGING_PLUGIN_URLS` | semi colon separated urls to be returned when user queries plugins | `''`
| `BUILD_TEXT` | overlay text at bottom right of the viewer. set to `''` to hide. | |
+| `OVERWRITE_API_ENDPOINT` | overwrite build time siibra-api endpoint |
+| `PATH_TO_PUBLIC` | path to built frontend | `../dist/aot` |
##### ebrains user authentication
@@ -22,45 +17,16 @@
| name | description | default | example |
| --- | --- | --- | --- |
| `HOSTNAME` |
-| `HBP_CLIENTID` | `{HOSTNAME}{HOST_PATHNAME}/hbp-oidc/cb` |
-| `HBP_CLIENTSECRET` |
-| `HBP_CLIENTID_V2` | `{HOSTNAME}{HOST_PATHNAME}/hbp-oidc-v2/cb`
+| `HOST_PATHNAME` | pathname to listen on, restrictions: leading slash, no trailing slash | `''` | `/viewer` |
+| `HBP_CLIENTID_V2` |
| `HBP_CLIENTSECRET_V2` |
-##### Querying ebrains knowledge graph
-
-| name | description | default | example |
-| --- | --- | --- | --- |
-| `REFRESH_TOKEN` |
-| `ACCESS_TOKEN` | **nb** as access tokens are usually short lived, this should only be set for development purposes
-| `KG_ROOT` | | `https://kg.humanbrainproject.eu/query` |
-| `KG_SEARCH_VOCAB` | | `https://schema.hbp.eu/myQuery/` |
-| `KG_DATASET_SEARCH_QUERY_NAME` | | `interactiveViewerKgQuery-v0_3` |
-| `KG_DATASET_SEARCH_PATH` | | `/minds/core/dataset/v1.0.0` |
-| `KG_SEARCH_SIZE` | | `1000` |
-| `KG_SPATIAL_DATASET_SEARCH_QUERY_NAME` | | `iav-spatial-query-v2` |
-| `KG_SPATIAL_DATASET_SEARCH_PATH` | | `/neuroglancer/seeg/coordinate/v1.0.0` |
##### Logging
| name | description | default | example |
| --- | --- | --- | --- |
-| `FLUENT_PROTOCOL` | protocol for fluent logging | `http` |
-| `FLUENT_HOST` | host for fluent logging | `localhost` |
-| `FLUENT_PORT` | port for fluent logging | 24224 |
-| `IAV_NAME` | application name to be logged | `IAV` |
-
-##### CSP
-
-| name | description | default | example |
-| --- | --- | --- | --- |
-| `DISABLE_CSP` | disable csp | | `true` |
-| `CSP_REPORT_URI` | report uri for csp violations | `/report-violation` |
-| `NODE_ENV` | set to `production` to disable [`reportOnly`](https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Content-Security-Policy-Report-Only) | `null` |
-| `SCRIPT_SRC` | `JSON.stringify`'ed array of allowed scriptSrc | `[]` |
-| `CSP_CONNECT_SRC` | `JSON.stringify`'ed array of allowed dataSrc | `[]` |
-| `WHITE_LIST_SRC` | `JSON.stringify`'ed array of allowed src | `[]` |
-| `PROXY_HOSTNAME_WHITELIST` |
+| `LOGGER_DIR` | Path (if any) to store the time rotated log files | |
##### Rate limiting
@@ -76,20 +42,5 @@
| name | description | default | example |
| --- | --- | --- | --- |
-| `OBJ_STORAGE_AUTH_URL` |
-| `OBJ_STORAGE_IDP_NAME` |
-| `OBJ_STORAGE_IDP_PROTO` |
-| `OBJ_STORAGE_IDP_URL` |
-| `OBJ_STORAGE_USERNAME` |
-| `OBJ_STORAGE_PASSWORD` |
-| `OBJ_STORAGE_PROJECT_ID` |
-| `OBJ_STORAGE_ROOT_URL` |
-
-##### Test deploy denvironments
-
-| name | description | default | example |
-| --- | --- | --- | --- |
-| `SERVICE_ACCOUNT_CRED` |
-| `SERVICE_ACCOUNT_CRED_PATH` |
-| `WAXHOLM_RAT_GOOGLE_SHEET_ID` |
-| `SKIP_RETRY_TEST` | retry tests contains some timeouts, which may slow down tests |
+| `SXPLR_EBRAINS_IAM_SA_CLIENT_ID` | client id used for service to service communication with data-proxy |
+| `SXPLR_EBRAINS_IAM_SA_CLIENT_SECRET` | client secret used for service to service communication with data-proxy |
\ No newline at end of file
diff --git a/e2e/screenshots/gen.js b/e2e/screenshots/gen.js
index 9bd57e9f1..00533c07e 100644
--- a/e2e/screenshots/gen.js
+++ b/e2e/screenshots/gen.js
@@ -8,6 +8,7 @@ describe('> generating screenshot', () => {
const cwdPath = path.join(__dirname, '../../deploy/')
beforeAll(done => {
+ throw "Need to reimplement. backend is rewritten from node to python"
childProcess = spawn('node', ['server.js'], {
cwd: cwdPath,
env: {
diff --git a/netlify.toml b/netlify.toml
deleted file mode 100644
index a13f3209d..000000000
--- a/netlify.toml
+++ /dev/null
@@ -1,7 +0,0 @@
-# toml netfliy: https://docs.netlify.com/configure-builds/file-based-configuration/#sample-file
-
-[build]
- publish="dist/aot/"
- command="cp deploy/util/* functions/nehubaConfig/ && cp -R src/res/ext functions/templates/json && cp -R src/res/ext functions/nehubaConfig/json && npm run build-aot"
- functions="functions"
- environment={ BACKEND_URL=".netlify/functions/" }
\ No newline at end of file
diff --git a/src/util/fn.ts b/src/util/fn.ts
index c7edd341b..45a4f4be5 100644
--- a/src/util/fn.ts
+++ b/src/util/fn.ts
@@ -1,9 +1,6 @@
import { interval, Observable, of } from 'rxjs'
import { filter, mapTo, take } from 'rxjs/operators'
-export function getDebug() {
- return (window as any).__DEBUG__
-}
// eslint-disable-next-line @typescript-eslint/no-empty-function
export function noop(){}
--
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