Merge branch 'release_22.05' into dev

2026-09-24 16:30:27 +08:00 · 2022-07-15 14:24:30 +01:00
parent ef8fc56dee 08d4e9d373
commit 71b1a9ced4
10 changed files with 88 additions and 8 deletions
@@ -20,6 +20,7 @@ lib/galaxy.egg-info
 lib/galaxy/web/framework/static/maps
 lib/galaxy/web/framework/static/scripts
 lib/galaxy/web/framework/static/style
+lib/galaxy/web/framework/meta.json

 # Database stuff
 /database/
@@ -44,6 +44,7 @@
    "date-fns-tz": "^1.3.3",
    "decode-uri-component": "^0.2.0",
    "dom-to-image": "^2.6.0",
+    "dumpmeta-webpack-plugin": "^0.2.0",
    "elkjs": "^0.7.1",
    "file-saver": "^2.0.5",
    "flush-promises": "^1.0.2",
@@ -5,6 +5,7 @@ const VueLoaderPlugin = require("vue-loader/lib/plugin");
 const MiniCssExtractPlugin = require("mini-css-extract-plugin");
 const CssMinimizerPlugin = require("css-minimizer-webpack-plugin");
 const DuplicatePackageCheckerPlugin = require("@cerner/duplicate-package-checker-webpack-plugin");
+const { DumpMetaPlugin } = require("dumpmeta-webpack-plugin");

 const scriptsBase = path.join(__dirname, "src");
 const testsBase = path.join(__dirname, "tests");
@@ -24,6 +25,8 @@ const modulesExcludedFromLibs = [
    "citeproc",
 ].join("|");

+const buildDate = new Date();
+
 module.exports = (env = {}, argv = {}) => {
    // environment name based on -d, -p, webpack flag
    const targetEnv = process.env.NODE_ENV == "production" || argv.mode == "production" ? "production" : "development";
@@ -193,13 +196,21 @@ module.exports = (env = {}, argv = {}) => {
            }),
            new webpack.DefinePlugin({
                __targetEnv__: JSON.stringify(targetEnv),
-                __buildTimestamp__: JSON.stringify(new Date().toISOString()),
+                __buildTimestamp__: JSON.stringify(buildDate.toISOString()),
            }),
            new VueLoaderPlugin(),
            new MiniCssExtractPlugin({
                filename: "[name].css",
            }),
            new DuplicatePackageCheckerPlugin(),
+            new DumpMetaPlugin({
+                filename: path.join(__dirname, "../lib/galaxy/web/framework/meta.json"),
+                prepare: (stats) => ({
+                    // add any other information you need to dump
+                    hash: stats.hash,
+                    epoch: Date.parse(buildDate),
+                }),
+            }),
        ],
        devServer: {
            client: {
@@ -1661,6 +1661,14 @@
    "@types/eslint" "*"
    "@types/estree" "*"

+"@types/eslint-scope@^3.7.3":
+  version "3.7.4"
+  resolved "https://registry.yarnpkg.com/@types/eslint-scope/-/eslint-scope-3.7.4.tgz#37fc1223f0786c39627068a12e94d6e6fc61de16"
+  integrity sha512-9K4zoImiZc3HlIp6AVUDE4CWYx22a+lhSZMYNpbjW04+YF0KWj4pJXnEMjdnFTiQibFFmElcsasJXDbdI/EPhA==
+  dependencies:
+    "@types/eslint" "*"
+    "@types/estree" "*"
+
 "@types/eslint@*":
  version "8.4.1"
  resolved "https://registry.yarnpkg.com/@types/eslint/-/eslint-8.4.1.tgz#c48251553e8759db9e656de3efc846954ac32304"
@@ -1674,6 +1682,11 @@
  resolved "https://registry.yarnpkg.com/@types/estree/-/estree-0.0.50.tgz#1e0caa9364d3fccd2931c3ed96fdbeaa5d4cca83"
  integrity sha512-C6N5s2ZFtuZRj54k2/zyRhNDjJwwcViAM3Nbm8zjBpbqAdZ00mr0CFxvSKeO8Y/e03WVFLpQMdHYVfUd6SB+Hw==

+"@types/estree@^0.0.51":
+  version "0.0.51"
+  resolved "https://registry.yarnpkg.com/@types/estree/-/estree-0.0.51.tgz#cfd70924a25a3fd32b218e5e420e6897e1ac4f40"
+  integrity sha512-CuPgU6f3eT/XgKKPqKd/gLZV1Xmvf1a2R5POBOGQa6uv82xpls89HU5zKeVoyR8XzHd1RGNOlQlvUe3CFkjWNQ==
+
 "@types/express-serve-static-core@*", "@types/express-serve-static-core@^4.17.18":
  version "4.17.28"
  resolved "https://registry.yarnpkg.com/@types/express-serve-static-core/-/express-serve-static-core-4.17.28.tgz#c47def9f34ec81dc6328d0b1b5303d1ec98d86b8"
@@ -3855,6 +3868,13 @@ dot-case@^3.0.4:
    no-case "^3.0.4"
    tslib "^2.0.3"

+dumpmeta-webpack-plugin@^0.2.0:
+  version "0.2.0"
+  resolved "https://registry.yarnpkg.com/dumpmeta-webpack-plugin/-/dumpmeta-webpack-plugin-0.2.0.tgz#c3a9da7d163ad3bb1d0373fb2c0bf5bb9b626b8f"
+  integrity sha512-9oxLTPvYVtk7HOmOq2rGQlvajCNiXtIKLInIrdNpdgzeoMMELaAsRsRBZfm6xf0JuwyBfytdJxsmtM6luTeqzA==
+  dependencies:
+    webpack ">=4.0.0 <6.0.0"
+
 duplexify@^3.6.0:
  version "3.7.1"
  resolved "https://registry.yarnpkg.com/duplexify/-/duplexify-3.7.1.tgz#2a4df5317f6ccfd91f86d6fd25d8d8a103b88309"
@@ -3961,6 +3981,14 @@ enhanced-resolve@^5.8.3:
    graceful-fs "^4.2.4"
    tapable "^2.2.0"

+enhanced-resolve@^5.9.3:
+  version "5.10.0"
+  resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.10.0.tgz#0dc579c3bb2a1032e357ac45b8f3a6f3ad4fb1e6"
+  integrity sha512-T0yTFjdpldGY8PmuXXR0PyQ1ufZpEGiHVrp7zHKB7jdR4qlmZHhONVM5AQOAWXuF/w3dnHbEQVrNptJgt7F+cQ==
+  dependencies:
+    graceful-fs "^4.2.4"
+    tapable "^2.2.0"
+
 ent@~2.2.0:
  version "2.2.0"
  resolved "https://registry.yarnpkg.com/ent/-/ent-2.2.0.tgz#e964219325a21d05f44466a2f686ed6ce5f5dd1d"
@@ -6330,7 +6358,7 @@ json-parse-better-errors@^1.0.2:
  resolved "https://registry.yarnpkg.com/json-parse-better-errors/-/json-parse-better-errors-1.0.2.tgz#bb867cfb3450e69107c131d1c514bab3dc8bcaa9"
  integrity sha512-mrqyZKfX5EhL7hvqcV6WG1yYjnjeuYDzDhhcAAUrq8Po85NBQBJP+ZDUT75qZQ98IkUoBqdkExkukOU7Ts2wrw==

-json-parse-even-better-errors@^2.3.0:
+json-parse-even-better-errors@^2.3.0, json-parse-even-better-errors@^2.3.1:
  version "2.3.1"
  resolved "https://registry.yarnpkg.com/json-parse-even-better-errors/-/json-parse-even-better-errors-2.3.1.tgz#7c47805a94319928e05777405dc12e1f7a4ee02d"
  integrity sha512-xyFwyhro/JEof6Ghe2iz2NcXoj2sloNsWr/XsERDK/oiPCfaNhl5ONfp+jQdAZRQQ0IJWNzH9zIZF7li91kh2w==
@@ -10026,6 +10054,36 @@ webpack-sources@^3.2.3:
  resolved "https://registry.yarnpkg.com/webpack-sources/-/webpack-sources-3.2.3.tgz#2d4daab8451fd4b240cc27055ff6a0c2ccea0cde"
  integrity sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w==

+"webpack@>=4.0.0 <6.0.0":
+  version "5.73.0"
+  resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.73.0.tgz#bbd17738f8a53ee5760ea2f59dce7f3431d35d38"
+  integrity sha512-svjudQRPPa0YiOYa2lM/Gacw0r6PvxptHj4FuEKQ2kX05ZLkjbVc5MnPs6its5j7IZljnIqSVo/OsY2X0IpHGA==
+  dependencies:
+    "@types/eslint-scope" "^3.7.3"
+    "@types/estree" "^0.0.51"
+    "@webassemblyjs/ast" "1.11.1"
+    "@webassemblyjs/wasm-edit" "1.11.1"
+    "@webassemblyjs/wasm-parser" "1.11.1"
+    acorn "^8.4.1"
+    acorn-import-assertions "^1.7.6"
+    browserslist "^4.14.5"
+    chrome-trace-event "^1.0.2"
+    enhanced-resolve "^5.9.3"
+    es-module-lexer "^0.9.0"
+    eslint-scope "5.1.1"
+    events "^3.2.0"
+    glob-to-regexp "^0.4.1"
+    graceful-fs "^4.2.9"
+    json-parse-even-better-errors "^2.3.1"
+    loader-runner "^4.2.0"
+    mime-types "^2.1.27"
+    neo-async "^2.6.2"
+    schema-utils "^3.1.0"
+    tapable "^2.1.1"
+    terser-webpack-plugin "^5.1.3"
+    watchpack "^2.3.1"
+    webpack-sources "^3.2.3"
+
 webpack@^5.68.0:
  version "5.68.0"
  resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.68.0.tgz#a653a58ed44280062e47257f260117e4be90d560"
@@ -123,6 +123,7 @@ from galaxy.web import (
    legacy_url_for,
    url_for,
 )
+from galaxy.web.framework.base import server_starttime
 from galaxy.web.proxy import ProxyManager
 from galaxy.web.short_term_storage import (
    ShortTermStorageAllocator,
@@ -739,7 +740,7 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
        self.url_for = url_for
        self.legacy_url_for = legacy_url_for

-        self.server_starttime = int(time.time())  # used for cachebusting
+        self.server_starttime = server_starttime  # used for cachebusting
        # Limit lifetime of tool shed repository cache to app startup
        self.tool_shed_repository_cache = None
        self.api_spec = None
@@ -62,7 +62,7 @@ docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (
 ecdsa==0.17.0; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
 edam-ontology==1.25.2
 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
-fastapi==0.78.0; python_full_version >= "3.6.1"
+fastapi==0.79.0; python_full_version >= "3.6.1"
 fluent-logger==0.10.0; python_version >= "3.5"
 fonttools==4.33.3; python_version >= "3.7"
 fs==2.4.16
@@ -52,7 +52,7 @@ docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (
 ecdsa==0.17.0; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
 edam-ontology==1.25.2
 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
-fastapi==0.78.0; python_full_version >= "3.6.1"
+fastapi==0.79.0; python_full_version >= "3.6.1"
 fs==2.4.16
 funcsigs==1.0.2
 future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
@@ -2,6 +2,7 @@
 A simple WSGI application/framework.
 """
 import io
+import json
 import logging
 import os
 import socket
@@ -25,11 +26,17 @@ import webob.exc as httpexceptions
 from paste.response import HeaderDict

 from galaxy.util import smart_str
+from galaxy.util.resources import resource_string

 log = logging.getLogger(__name__)

 #: time of the most recent server startup
 server_starttime = int(time.time())
+try:
+    meta_json = json.loads(resource_string(__package__, "meta.json"))
+    server_starttime = meta_json.get("epoch") or server_starttime
+except Exception:
+    meta_json = {}


 def __resource_with_deleted(self, member_name, collection_name, **kwargs):
@@ -567,6 +574,7 @@ __all__ = (
    "httpexceptions",
    "lazy_property",
    "routes",
+    "server_starttime",
    "walk_controller_modules",
    "WebApplication",
 )
@@ -151,7 +151,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
            raise web.httpexceptions.HTTPNotFound(f"Invalid reference dataset id: {str(hda_id)}.")
        if not self._can_access_dataset(trans, data):
            return trans.show_error_message("You are not allowed to access this dataset")
-        if data.purged:
+        if data.purged or data.dataset.purged:
            return trans.show_error_message("The dataset you are attempting to view has been purged.")
        elif data.deleted and not (trans.user_is_admin or (data.history and trans.get_user() == data.history.user)):
            return trans.show_error_message("The dataset you are attempting to view has been deleted.")
@@ -32,7 +32,6 @@ from fastapi.encoders import jsonable_encoder
 from fastapi.openapi.constants import (
    METHODS_WITH_BODY,
    REF_PREFIX,
-    STATUS_CODES_WITH_NO_BODY,
 )
 from fastapi.openapi.models import OpenAPI
 from fastapi.params import (
@@ -44,6 +43,7 @@ from fastapi.utils import (
    deep_dict_update,
    generate_operation_id_for_path,
    get_model_definitions,
+    is_body_allowed_for_status_code,
 )
 from pydantic import BaseModel
 from pydantic.fields import (
@@ -266,7 +266,7 @@ def get_openapi_path(
            operation.setdefault("responses", {}).setdefault(status_code, {})[
                "description"
            ] = route.response_description
-            if route_response_media_type and route.status_code not in STATUS_CODES_WITH_NO_BODY:
+            if route_response_media_type and is_body_allowed_for_status_code(route.status_code):
                response_schema = {"type": "string"}
                if lenient_issubclass(current_response_class, JSONResponse):
                    if route.response_field: