Merge branch 'master' into user-resolver-find-by-orcid

README.md

@@ -33,12 +33,18 @@ GOOGLE_CLIENT_SECRET=
 
 [podman-compose](https://github.com/containers/podman-compose) is used to run a local copy of all required services together.
 
+#### macOS Development Setup 
+If you're working on macOS and encounter issues with file watching in Vite, use the following environment variables (in config.env):
 
+```
+CHOKIDAR_USEPOLLING=true
+```
 
-macOS Development Setup - If you're working on macOS and encounter issues with file watching in Vite, use the following environment variables (in config.env):
+If you're working on macOS and encounter issues with elastic search, use the following environment variables (in config.env):
 
 ```
-CHOKIDAR_USEPOLLING=true
+ES_JAVA_OPTS: -XX:UseSVE=0
+CLI_JAVA_OPTS: -XX:UseSVE=0
 ```
 
 ```shell

cli/deno.json

@@ -1,7 +1,7 @@
 {
   "name": "@openneuro/cli",
   "license": "MIT",
-  "version": "4.29.8",
+  "version": "4.29.9",
   "exports": "./mod.ts",
   "publish": {
     "include": [

config.env.example

@@ -21,6 +21,9 @@ GLOBUS_CLIENT_SECRET=
 # macOS Development Setup - Fixes issues with Vite file watching - set to CHOKIDAR_USEPOLLING=true
 CHOKIDAR_USEPOLLING=false
 CHOKIDAR_INTERVAL=1000
+# macOS Development Setup - Fixes issues with elastic search container - set to ES_JAVA_OPTS: -XX:UseSVE=0 and CLI_JAVA_OPTS: -XX:UseSVE=0
+# ES_JAVA_OPTS: -XX:UseSVE=0
+# CLI_JAVA_OPTS: -XX:UseSVE=0
 
 # Relay for enabling mail - leave blank to disable email
 CRN_SERVER_MAIL_API_KEY=

docker-compose.yml

@@ -141,7 +141,6 @@ services:
       cluster.routing.allocation.disk.watermark.high: 5gb
       xpack.security.enabled: false
       xpack.security.enrollment.enabled: false
-      ES_JAVA_OPTS: "-Xms750m -Xmx750m"
     healthcheck:
       test: "curl -s -f http://localhost:9200 || exit 1"
       interval: 10s

helm/openneuro/Chart.yaml

@@ -5,7 +5,7 @@ description: OpenNeuro production deployment chart
 home: https://openneuro.org
 sources:
   - https://github.com/openNeuroOrg/openneuro
-appVersion: 4.29.8
+appVersion: 4.29.9
 dependencies:
   - name: redis
     version: 17.1.4

helm/openneuro/values-production.yaml

@@ -54,7 +54,7 @@ workerDiskSize:
   - id: projects/hs-openneuro/zones/us-west1-c/disks/openneuro-prod-datasets-0
     size: 47000Gi
   - id: projects/hs-openneuro/zones/us-west1-c/disks/openneuro-prod-datasets-1
-    size: 38000Gi
+    size: 40000Gi
   - id: projects/hs-openneuro/zones/us-west1-c/disks/openneuro-prod-datasets-2
     size: 31000Gi
   - id: projects/hs-openneuro/zones/us-west1-c/disks/openneuro-prod-datasets-3

lerna.json

@@ -5,5 +5,5 @@
   ],
   "npmClient": "yarn",
   "useWorkspaces": true,
-  "version": "4.29.8"
+  "version": "4.29.9"
 }

packages/openneuro-app/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/app",
-  "version": "4.29.8",
+  "version": "4.29.9",
   "description": "React JS web frontend for the OpenNeuro platform.",
   "license": "MIT",
   "main": "public/client.js",
@@ -20,7 +20,7 @@
     "@emotion/react": "11.11.1",
     "@emotion/styled": "11.11.0",
     "@niivue/niivue": "0.45.1",
-    "@openneuro/components": "^4.29.8",
+    "@openneuro/components": "^4.29.9",
     "@sentry/react": "^8.25.0",
     "@tanstack/react-table": "^8.9.3",
     "buffer": "^6.0.3",

packages/openneuro-cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/cli",
-  "version": "4.29.8",
+  "version": "4.29.9",
   "description": "OpenNeuro command line uploader / editor.",
   "main": "index.js",
   "repository": "[email protected]:OpenNeuroOrg/openneuro.git",
@@ -16,7 +16,7 @@
   },
   "dependencies": {
     "@apollo/client": "3.11.8",
-    "@openneuro/client": "^4.29.8",
+    "@openneuro/client": "^4.29.9",
     "bids-validator": "1.14.8",
     "cli-progress": "^3.8.2",
     "commander": "7.2.0",

packages/openneuro-client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/client",
-  "version": "4.29.8",
+  "version": "4.29.9",
   "description": "OpenNeuro shared client library.",
   "main": "dist/index.js",
   "browser": "src/index.js",
@@ -27,7 +27,7 @@
   },
   "devDependencies": {
     "@graphql-tools/schema": "^10.0.0",
-    "@openneuro/server": "^4.29.8",
+    "@openneuro/server": "^4.29.9",
     "core-js": "^3.10.1",
     "ioredis-mock": "^8.8.1",
     "vitest": "2.1.2"

packages/openneuro-components/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/components",
-  "version": "4.29.8",
+  "version": "4.29.9",
   "description": "OpenNeuro component library and Storybook configuration",
   "main": "dist/index.js",
   "browser": "src/index.js",

packages/openneuro-indexer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/indexer",
-  "version": "4.29.8",
+  "version": "4.29.9",
   "description": "OpenNeuro elastic search indexing tool",
   "main": "./dist/index.js",
   "types": "./src/index.d.ts",
@@ -11,8 +11,8 @@
   "dependencies": {
     "@apollo/client": "3.11.8",
     "@elastic/elasticsearch": "8.13.1",
-    "@openneuro/client": "^4.29.8",
-    "@openneuro/search": "^4.29.8",
+    "@openneuro/client": "^4.29.9",
+    "@openneuro/search": "^4.29.9",
     "graphql": "16.8.1",
     "ts-node": "10.9.2",
     "typescript": "5.6.3"

packages/openneuro-search/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/search",
-  "version": "4.29.8",
+  "version": "4.29.9",
   "description": "OpenNeuro search client functions.",
   "main": "dist/index.js",
   "browser": "src/index.ts",

packages/openneuro-server/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "4.29.8",
+  "version": "4.29.9",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -21,7 +21,7 @@
     "@elastic/elasticsearch": "8.13.1",
     "@graphql-tools/schema": "^10.0.0",
     "@keyv/redis": "^2.7.0",
-    "@openneuro/search": "^4.29.8",
+    "@openneuro/search": "^4.29.9",
     "@sentry/node": "^8.25.0",
     "@sentry/profiling-node": "^8.25.0",
     "base64url": "^3.0.0",

services/datalad/datalad_service/tasks/validator.py

@@ -10,7 +10,7 @@
 
 logger = logging.getLogger('datalad_service.' + __name__)
 
-DENO_VALIDATOR_VERSION = '2.0.0'
+DENO_VALIDATOR_VERSION = '2.0.1'
 
 DENO_METADATA = {
     'validator': 'schema',
@@ -76,6 +76,10 @@ def issues_mutation(dataset_id, ref, issues, validator_metadata):
     """
     Return the OpenNeuro mutation to update any validation issues.
     """
+    # Workaround for bad "affects" values - drop them
+    for issue in issues["issues"]:
+        if "affects" in issue and not isinstance(issue["affects"], str):
+            del issue["affects"]
     validatorInput = {
         'datasetId': dataset_id,
         'id': ref,

services/datalad/hooks/pre-receive

@@ -121,6 +121,27 @@ function main() {
       continue
     fi
 
+    IFS=$'\n'
+    for file in $large_files; do
+      if [[ "$status" == 0 ]]; then
+        echo ""
+        echo "-------------------------------------------------------------------------"
+        echo "Your push was rejected because it contains files larger than 10MB."
+        echo "Please use git-annex to store larger files."
+        echo "-------------------------------------------------------------------------"
+        echo ""
+        echo "Offending files:"
+        status="$EXIT_FAILURE"
+      fi
+      echo " - ${file} (ref: ${refname})"
+    done
+    unset IFS
+
+    if [[ "$branch" == "git-annex" || "$branch" == "synced/git-annex" ]]; then
+      continue
+    fi
+    # Additional validation and filtering of main/master branches
+
     filterDotFiles
 
     # Check if .bidsignore is in the new tree
@@ -130,6 +151,9 @@ function main() {
     python -m bidsschematools pre-receive-hook <<END
 bids-hook-v2
 $( git show "${newref}:dataset_description.json" | tr -d '\r\n' )
+.datalad/config
+.gitattributes
+.bidsignore
 ${bidsignore}
 0001
 $( git ls-tree --name-only -r "${newref}" )
@@ -144,22 +168,6 @@ END
       exit $EXIT_FAILURE
     fi
 
-    IFS=$'\n'
-    for file in $large_files; do
-      if [[ "$status" == 0 ]]; then
-        echo ""
-        echo "-------------------------------------------------------------------------"
-        echo "Your push was rejected because it contains files larger than 10MB."
-        echo "Please use git-annex to store larger files."
-        echo "-------------------------------------------------------------------------"
-        echo ""
-        echo "Offending files:"
-        status="$EXIT_FAILURE"
-      fi
-      echo " - ${file} (ref: ${refname})"
-    done
-    unset IFS
-
     validateGitAttributes
   done
 

yarn.lock

@@ -5915,7 +5915,7 @@ __metadata:
     "@emotion/react": "npm:11.11.1"
     "@emotion/styled": "npm:11.11.0"
     "@niivue/niivue": "npm:0.45.1"
-    "@openneuro/components": "npm:^4.29.8"
+    "@openneuro/components": "npm:^4.29.9"
     "@sentry/react": "npm:^8.25.0"
     "@tanstack/react-table": "npm:^8.9.3"
     "@testing-library/jest-dom": "npm:6.4.2"
@@ -5971,7 +5971,7 @@ __metadata:
   resolution: "@openneuro/cli@workspace:packages/openneuro-cli"
   dependencies:
     "@apollo/client": "npm:3.11.8"
-    "@openneuro/client": "npm:^4.29.8"
+    "@openneuro/client": "npm:^4.29.9"
     "@types/mkdirp": "npm:1.0.2"
     "@types/node": "npm:20.12.7"
     bids-validator: "npm:1.14.8"
@@ -5994,14 +5994,14 @@ __metadata:
   languageName: unknown
   linkType: soft
 
-"@openneuro/client@npm:^4.29.8, @openneuro/client@workspace:packages/openneuro-client":
+"@openneuro/client@npm:^4.29.9, @openneuro/client@workspace:packages/openneuro-client":
   version: 0.0.0-use.local
   resolution: "@openneuro/client@workspace:packages/openneuro-client"
   dependencies:
     "@apollo/client": "npm:3.11.8"
     "@graphql-tools/mock": "npm:^9.0.0"
     "@graphql-tools/schema": "npm:^10.0.0"
-    "@openneuro/server": "npm:^4.29.8"
+    "@openneuro/server": "npm:^4.29.9"
     core-js: "npm:^3.10.1"
     crypto-hash: "npm:^1.3.0"
     graphql: "npm:16.8.1"
@@ -6013,7 +6013,7 @@ __metadata:
   languageName: unknown
   linkType: soft
 
-"@openneuro/components@npm:^4.29.8, @openneuro/components@workspace:packages/openneuro-components":
+"@openneuro/components@npm:^4.29.9, @openneuro/components@workspace:packages/openneuro-components":
   version: 0.0.0-use.local
   resolution: "@openneuro/components@workspace:packages/openneuro-components"
   dependencies:
@@ -6054,8 +6054,8 @@ __metadata:
   dependencies:
     "@apollo/client": "npm:3.11.8"
     "@elastic/elasticsearch": "npm:8.13.1"
-    "@openneuro/client": "npm:^4.29.8"
-    "@openneuro/search": "npm:^4.29.8"
+    "@openneuro/client": "npm:^4.29.9"
+    "@openneuro/search": "npm:^4.29.9"
     "@types/jsonwebtoken": "npm:^8"
     "@types/node": "npm:20.12.7"
     "@types/tsc-watch": "npm:^4"
@@ -6069,7 +6069,7 @@ __metadata:
   languageName: unknown
   linkType: soft
 
-"@openneuro/search@npm:^4.29.8, @openneuro/search@workspace:packages/openneuro-search":
+"@openneuro/search@npm:^4.29.9, @openneuro/search@workspace:packages/openneuro-search":
   version: 0.0.0-use.local
   resolution: "@openneuro/search@workspace:packages/openneuro-search"
   dependencies:
@@ -6084,7 +6084,7 @@ __metadata:
   languageName: unknown
   linkType: soft
 
-"@openneuro/server@npm:^4.29.8, @openneuro/server@workspace:packages/openneuro-server":
+"@openneuro/server@npm:^4.29.9, @openneuro/server@workspace:packages/openneuro-server":
   version: 0.0.0-use.local
   resolution: "@openneuro/server@workspace:packages/openneuro-server"
   dependencies:
@@ -6094,7 +6094,7 @@ __metadata:
     "@elastic/elasticsearch": "npm:8.13.1"
     "@graphql-tools/schema": "npm:^10.0.0"
     "@keyv/redis": "npm:^2.7.0"
-    "@openneuro/search": "npm:^4.29.8"
+    "@openneuro/search": "npm:^4.29.9"
     "@sentry/node": "npm:^8.25.0"
     "@sentry/profiling-node": "npm:^8.25.0"
     "@types/cors": "npm:^2"