From 6228314f700c56e4d81f05ee51d61c3ab2764923 Mon Sep 17 00:00:00 2001 From: Mikko Nieminen Date: Thu, 12 Sep 2024 16:32:07 +0200 Subject: [PATCH] upgrade dependencies (#1959), update docs (#1991) --- CHANGELOG.rst | 37 ++++++++ docs_manual/source/conf.py | 2 +- docs_manual/source/sodar_release_notes.rst | 45 ++++++++++ samplesheets/vueapp/package-lock.json | 98 ++++++++++++---------- samplesheets/vueapp/package.json | 2 +- 5 files changed, 139 insertions(+), 45 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index e671b553..9c15337c 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -5,6 +5,43 @@ Changelog for the SODAR project. Loosely follows the `Keep a Changelog `_ guidelines. +Unreleased +========== + +Added +----- + +- **General** + - Python v3.11 support (#1922, #1978) +- **Landingzones** + - REST API list view pagination (#1994) +- **Samplesheets** + - REST API list view pagination (#1994) + +Changed +------- + +- **General** + - Upgrade to django-sodar-core v1.0.2 (#1922) + - Upgrade to Postgres v16 (#1922) + - Upgrade Python and Vue app dependencies (#1922, #1959) +- **Irodsinfo** + - Update REST API versioning (#1936) +- **Landingzones** + - Update REST API versioning (#1936) + - Update REST API views for OpenAPI compatibility (#1951) +- **Samplesheets** + - Update REST API versioning (#1936) + - Update REST API views for OpenAPI compatibility (#1951) + +Removed +------- + +- **General** + - Python v3.8 support (#1922) + - Postgres `. +v1.0.0 (WIP) +============ + +Release for SODAR Core v1.0 upgrade and feature updates. + +- Add Python v3.11 support +- Add REST API list view pagination +- Update REST API versioning +- Update REST API views for OpenAPI support +- Upgrade to Postgres v16 +- Upgrade to SODAR Core v1.0.2 +- SODAR Core v1.0 updates: OIDC auth support, new REST API versioning, + owner/delegate remote sync controls etc. +- Upgrade to Django v4.2 +- Remove Python v3.8 support +- Remove Postgres <12 support + +Migration Guide +--------------- + +Python Version Support + Python v3.11 is now the recommended Python version. Support for v3.8 has + been dropped. It is recommended to upgrade your deployment for Python v3.11. +PostgreSQL Version Support + This release drops support for Postgres versions below v12. The recommended + version is v16. Note that if you run both the SODAR Server and the iRODS + iCAT server on the same PostgreSQL database server, you may need to upgrade + your iRODS server. The CUBI iRODS v4.2 Docker image does not support + Postgres >11. See the latest dev version of sodar-docker-compose for more + information. +REST API Versioning Changes + REST API versioning has changed in SODAR Core v1.0 and SODAR Server v1.0. + Accept header versioning is now specific to each Django app providing their + own API. The APIs now use semantic versioning and have individual version + numbers starting at ``1.0``. There is no backwards compatibility for old + version numbers. If your clients or scripts make use of the versioning, you + will need to consult the REST API documentation and update them accordingly. + +.. warning:: + + It is strongly recommended to backup your SODAR and iRODS databases before + upgrading to this version due to the changed database requirements. Also it + is strongly recommended to go through all documentation before upgrading. + + v0.15.1 (2024-09-12) ==================== diff --git a/samplesheets/vueapp/package-lock.json b/samplesheets/vueapp/package-lock.json index da69140a..48e8984a 100644 --- a/samplesheets/vueapp/package-lock.json +++ b/samplesheets/vueapp/package-lock.json @@ -1,12 +1,12 @@ { "name": "samplesheets", - "version": "0.15.1", + "version": "1.0.0-WIP", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "samplesheets", - "version": "0.15.1", + "version": "1.0.0-WIP", "dependencies": { "bootstrap-vue": "^2.22.0", "core-js": "^3.23.5", @@ -5240,9 +5240,9 @@ "dev": true }, "node_modules/body-parser": { - "version": "1.20.2", - "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.2.tgz", - "integrity": "sha512-ml9pReCu3M61kGlqoTm2umSXTlRTuGTx0bfYj+uIUKKYycG5NtSbeetV3faSU6R7ajOPw0g/J1PvK4qNy7s5bA==", + "version": "1.20.3", + "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.3.tgz", + "integrity": "sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g==", "dev": true, "dependencies": { "bytes": "3.1.2", @@ -5253,7 +5253,7 @@ "http-errors": "2.0.0", "iconv-lite": "0.4.24", "on-finished": "2.4.1", - "qs": "6.11.0", + "qs": "6.13.0", "raw-body": "2.5.2", "type-is": "~1.6.18", "unpipe": "1.0.0" @@ -7092,9 +7092,9 @@ } }, "node_modules/encodeurl": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-1.0.2.tgz", - "integrity": "sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w==", + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-2.0.0.tgz", + "integrity": "sha512-Q0n9HRi4m6JuGIV1eFlmvJB7ZEVxu93IrMyiMsGC0lrMJMWzRgx6WGquyfQgZVb31vhGgXnfmPNNXmxnOkRBrg==", "dev": true, "engines": { "node": ">= 0.8" @@ -8253,37 +8253,37 @@ } }, "node_modules/express": { - "version": "4.19.2", - "resolved": "https://registry.npmjs.org/express/-/express-4.19.2.tgz", - "integrity": "sha512-5T6nhjsT+EOMzuck8JjBHARTHfMht0POzlA60WV2pMD3gyXw2LZnZ+ueGdNxG+0calOJcWKbpFcuzLZ91YWq9Q==", + "version": "4.21.0", + "resolved": "https://registry.npmjs.org/express/-/express-4.21.0.tgz", + "integrity": "sha512-VqcNGcj/Id5ZT1LZ/cfihi3ttTn+NJmkli2eZADigjq29qTlWi/hAQ43t/VLPq8+UX06FCEx3ByOYet6ZFblng==", "dev": true, "dependencies": { "accepts": "~1.3.8", "array-flatten": "1.1.1", - "body-parser": "1.20.2", + "body-parser": "1.20.3", "content-disposition": "0.5.4", "content-type": "~1.0.4", "cookie": "0.6.0", "cookie-signature": "1.0.6", "debug": "2.6.9", "depd": "2.0.0", - "encodeurl": "~1.0.2", + "encodeurl": "~2.0.0", "escape-html": "~1.0.3", "etag": "~1.8.1", - "finalhandler": "1.2.0", + "finalhandler": "1.3.1", "fresh": "0.5.2", "http-errors": "2.0.0", - "merge-descriptors": "1.0.1", + "merge-descriptors": "1.0.3", "methods": "~1.1.2", "on-finished": "2.4.1", "parseurl": "~1.3.3", - "path-to-regexp": "0.1.7", + "path-to-regexp": "0.1.10", "proxy-addr": "~2.0.7", - "qs": "6.11.0", + "qs": "6.13.0", "range-parser": "~1.2.1", "safe-buffer": "5.2.1", - "send": "0.18.0", - "serve-static": "1.15.0", + "send": "0.19.0", + "serve-static": "1.16.2", "setprototypeof": "1.2.0", "statuses": "2.0.1", "type-is": "~1.6.18", @@ -8310,9 +8310,9 @@ "dev": true }, "node_modules/express/node_modules/path-to-regexp": { - "version": "0.1.7", - "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.7.tgz", - "integrity": "sha512-5DFkuoqlv1uYQKxy8omFBeJPQcdoE07Kv2sferDCrAq1ohOU+MSDswDIbnx3YAM60qIOnYa53wBhXW0EbMonrQ==", + "version": "0.1.10", + "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.10.tgz", + "integrity": "sha512-7lf7qcQidTku0Gu3YDPc8DJ1q7OOucfa/BSsIwjuh56VU7katFvuM8hULfkwB3Fns/rsVF7PwPKVw1sl5KQS9w==", "dev": true }, "node_modules/extend-shallow": { @@ -8503,13 +8503,13 @@ } }, "node_modules/finalhandler": { - "version": "1.2.0", - "resolved": "https://registry.npmjs.org/finalhandler/-/finalhandler-1.2.0.tgz", - "integrity": "sha512-5uXcUVftlQMFnWC9qu/svkWv3GTd2PfUhK/3PLkYNAe7FbqJMt3515HaxE6eRL74GdsriiwujiawdaB1BpEISg==", + "version": "1.3.1", + "resolved": "https://registry.npmjs.org/finalhandler/-/finalhandler-1.3.1.tgz", + "integrity": "sha512-6BN9trH7bp3qvnrRyzsBz+g3lZxTNZTbVO2EV1CS0WIcDbawYVdYvGflME/9QP0h0pYlCDBCTjYa9nZzMDpyxQ==", "dev": true, "dependencies": { "debug": "2.6.9", - "encodeurl": "~1.0.2", + "encodeurl": "~2.0.0", "escape-html": "~1.0.3", "on-finished": "2.4.1", "parseurl": "~1.3.3", @@ -13130,10 +13130,13 @@ "dev": true }, "node_modules/merge-descriptors": { - "version": "1.0.1", - "resolved": "https://registry.npmjs.org/merge-descriptors/-/merge-descriptors-1.0.1.tgz", - "integrity": "sha512-cCi6g3/Zr1iqQi6ySbseM1Xvooa98N0w31jzUYrXPX2xqObmFGHJ0tQ5u74H3mVh7wLouTseZyYIq39g8cNp1w==", - "dev": true + "version": "1.0.3", + "resolved": "https://registry.npmjs.org/merge-descriptors/-/merge-descriptors-1.0.3.tgz", + "integrity": "sha512-gaNvAS7TZ897/rVaZ0nMtAyxNyi/pdbjbAwUpFQpN70GqnVfOiXpeUUMKRBmzXaSQ8DdTX4/0ms62r2K+hE6mQ==", + "dev": true, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } }, "node_modules/merge-source-map": { "version": "1.1.0", @@ -14942,12 +14945,12 @@ } }, "node_modules/qs": { - "version": "6.11.0", - "resolved": "https://registry.npmjs.org/qs/-/qs-6.11.0.tgz", - "integrity": "sha512-MvjoMCJwEarSbUYk5O+nmoSzSutSsTwF85zcHPQ9OrlFoZOYIjaqBAJIqIXjptyD5vThxGq52Xu/MaJzRkIk4Q==", + "version": "6.13.0", + "resolved": "https://registry.npmjs.org/qs/-/qs-6.13.0.tgz", + "integrity": "sha512-+38qI9SOr8tfZ4QmJNplMUxqjbe7LKvvZgWdExBOmd+egZTtjLB67Gu0HRX3u/XOq7UU2Nx6nsjvS16Z9uwfpg==", "dev": true, "dependencies": { - "side-channel": "^1.0.4" + "side-channel": "^1.0.6" }, "engines": { "node": ">=0.6" @@ -15506,9 +15509,9 @@ } }, "node_modules/send": { - "version": "0.18.0", - "resolved": "https://registry.npmjs.org/send/-/send-0.18.0.tgz", - "integrity": "sha512-qqWzuOjSFOuqPjFe4NOsMLafToQQwBSOEpS+FwEt3A2V3vKubTquT3vmLTQpFgMXp8AlFWFuP1qKaJZOtPpVXg==", + "version": "0.19.0", + "resolved": "https://registry.npmjs.org/send/-/send-0.19.0.tgz", + "integrity": "sha512-dW41u5VfLXu8SJh5bwRmyYUbAoSB3c9uQh6L8h/KtsFREPWpbX1lrljJo186Jc4nmci/sGUZ9a0a0J2zgfq2hw==", "dev": true, "dependencies": { "debug": "2.6.9", @@ -15544,6 +15547,15 @@ "integrity": "sha512-Tpp60P6IUJDTuOq/5Z8cdskzJujfwqfOTkrwIwj7IRISpnkJnT6SyJ4PCPnGMoFjC9ddhal5KVIYtAt97ix05A==", "dev": true }, + "node_modules/send/node_modules/encodeurl": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-1.0.2.tgz", + "integrity": "sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w==", + "dev": true, + "engines": { + "node": ">= 0.8" + } + }, "node_modules/send/node_modules/ms": { "version": "2.1.3", "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz", @@ -15638,15 +15650,15 @@ } }, "node_modules/serve-static": { - "version": "1.15.0", - "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.15.0.tgz", - "integrity": "sha512-XGuRDNjXUijsUL0vl6nSD7cwURuzEgglbOaFuZM9g3kwDXOWVTck0jLzjPzGD+TazWbboZYu52/9/XPdUgne9g==", + "version": "1.16.2", + "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.16.2.tgz", + "integrity": "sha512-VqpjJZKadQB/PEbEwvFdO43Ax5dFBZ2UECszz8bQ7pi7wt//PWe1P6MN7eCnjsatYtBT6EuiClbjSWP2WrIoTw==", "dev": true, "dependencies": { - "encodeurl": "~1.0.2", + "encodeurl": "~2.0.0", "escape-html": "~1.0.3", "parseurl": "~1.3.3", - "send": "0.18.0" + "send": "0.19.0" }, "engines": { "node": ">= 0.8.0" diff --git a/samplesheets/vueapp/package.json b/samplesheets/vueapp/package.json index 1acb3387..e1f003c5 100644 --- a/samplesheets/vueapp/package.json +++ b/samplesheets/vueapp/package.json @@ -1,6 +1,6 @@ { "name": "samplesheets", - "version": "0.15.1", + "version": "1.0.0-WIP", "private": true, "scripts": { "serve": "vue-cli-service serve",