diff --git a/.gitignore b/.gitignore index 0cd4843612..d48f05a4e8 100644 --- a/.gitignore +++ b/.gitignore @@ -19,3 +19,4 @@ dist !.yarn/sdks !.yarn/versions .*.sw[po] +.venv/ diff --git a/.pnp.cjs b/.pnp.cjs index a097f0461a..d13d05820e 100755 --- a/.pnp.cjs +++ b/.pnp.cjs @@ -10247,6 +10247,14 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { ["debug", "virtual:428f325a939c2653ad822eb3d75efb02ac311523dd0d4f9645afc39ea00bd86eceac35a9d59c9b6977d76b670a4ef0ae057ea572338a44729aa592711a8c05a3#npm:4.3.2"]\ ],\ "linkType": "HARD"\ + }],\ + ["npm:7.1.0", {\ + "packageLocation": "./.yarn/cache/agent-base-npm-7.1.0-4b12ba5111-f7828f9914.zip/node_modules/agent-base/",\ + "packageDependencies": [\ + ["agent-base", "npm:7.1.0"],\ + ["debug", "virtual:58471071b1e0e7981e3318280660861b4dec874aaf0d60e144b70657cb5ce0af059ae16711a2af10f4d1ff0536527e350e6e47a8f79db2d8d37ff2ec84865bbc#npm:4.3.4"]\ + ],\ + "linkType": "HARD"\ }]\ ]],\ ["agentkeepalive", [\ @@ -10817,11 +10825,11 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { }]\ ]],\ ["async-mutex", [\ - ["npm:0.3.2", {\ - "packageLocation": "./.yarn/cache/async-mutex-npm-0.3.2-600f6c46a1-620b771dfd.zip/node_modules/async-mutex/",\ + ["npm:0.4.0", {\ + "packageLocation": "./.yarn/cache/async-mutex-npm-0.4.0-f5a25d4255-813a71728b.zip/node_modules/async-mutex/",\ "packageDependencies": [\ - ["async-mutex", "npm:0.3.2"],\ - ["tslib", "npm:2.4.1"]\ + ["async-mutex", "npm:0.4.0"],\ + ["tslib", "npm:2.6.1"]\ ],\ "linkType": "HARD"\ }]\ @@ -10930,6 +10938,15 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { "linkType": "HARD"\ }]\ ]],\ + ["b4a", [\ + ["npm:1.6.4", {\ + "packageLocation": "./.yarn/cache/b4a-npm-1.6.4-080bcba845-81b086f9af.zip/node_modules/b4a/",\ + "packageDependencies": [\ + ["b4a", "npm:1.6.4"]\ + ],\ + "linkType": "HARD"\ + }]\ + ]],\ ["babel-jest", [\ ["npm:29.7.0", {\ "packageLocation": "./.yarn/cache/babel-jest-npm-29.7.0-273152fbe9-ee6f8e0495.zip/node_modules/babel-jest/",\ @@ -11447,6 +11464,13 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { ["buffer", "npm:5.7.1"]\ ],\ "linkType": "HARD"\ + }],\ + ["npm:5.5.1", {\ + "packageLocation": "./.yarn/cache/bson-npm-5.5.1-d8774a4337-f49730504e.zip/node_modules/bson/",\ + "packageDependencies": [\ + ["bson", "npm:5.5.1"]\ + ],\ + "linkType": "HARD"\ }]\ ]],\ ["btoa-lite", [\ @@ -15314,6 +15338,15 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { "linkType": "HARD"\ }]\ ]],\ + ["fast-fifo", [\ + ["npm:1.3.2", {\ + "packageLocation": "./.yarn/cache/fast-fifo-npm-1.3.2-391cc25df4-6bfcba3e4d.zip/node_modules/fast-fifo/",\ + "packageDependencies": [\ + ["fast-fifo", "npm:1.3.2"]\ + ],\ + "linkType": "HARD"\ + }]\ + ]],\ ["fast-glob", [\ ["npm:2.2.7", {\ "packageLocation": "./.yarn/cache/fast-glob-npm-2.2.7-f211fb26f4-304ccff1d4.zip/node_modules/fast-glob/",\ @@ -15771,12 +15804,19 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { ],\ "linkType": "SOFT"\ }],\ - ["virtual:0f2c58533d5ae53fe8d3b1cb5e5cb8e43e3e2d7669343628c0e0e3ec650e92c188661a07c62bd0e049a683d03ad0f5f7911a33a29316bd3959b8724b5aeada68#npm:1.15.2", {\ - "packageLocation": "./.yarn/__virtual__/follow-redirects-virtual-9f20bb700a/0/cache/follow-redirects-npm-1.15.2-1ec1dd82be-faa66059b6.zip/node_modules/follow-redirects/",\ + ["npm:1.15.3", {\ + "packageLocation": "./.yarn/cache/follow-redirects-npm-1.15.3-ca69c47b72-584da22ec5.zip/node_modules/follow-redirects/",\ "packageDependencies": [\ - ["follow-redirects", "virtual:0f2c58533d5ae53fe8d3b1cb5e5cb8e43e3e2d7669343628c0e0e3ec650e92c188661a07c62bd0e049a683d03ad0f5f7911a33a29316bd3959b8724b5aeada68#npm:1.15.2"],\ + ["follow-redirects", "npm:1.15.3"]\ + ],\ + "linkType": "SOFT"\ + }],\ + ["virtual:35a845e191d5a8a7376e256c81e9e855732385142c5dc9e26f0b8393c2fb4673b81fed201d5f2c5ab96fb727142683ac03329eab760f2c4870779d4bda6abe8f#npm:1.15.2", {\ + "packageLocation": "./.yarn/__virtual__/follow-redirects-virtual-2e83874824/0/cache/follow-redirects-npm-1.15.2-1ec1dd82be-faa66059b6.zip/node_modules/follow-redirects/",\ + "packageDependencies": [\ + ["follow-redirects", "virtual:35a845e191d5a8a7376e256c81e9e855732385142c5dc9e26f0b8393c2fb4673b81fed201d5f2c5ab96fb727142683ac03329eab760f2c4870779d4bda6abe8f#npm:1.15.2"],\ ["@types/debug", null],\ - ["debug", "virtual:58471071b1e0e7981e3318280660861b4dec874aaf0d60e144b70657cb5ce0af059ae16711a2af10f4d1ff0536527e350e6e47a8f79db2d8d37ff2ec84865bbc#npm:4.3.4"]\ + ["debug", null]\ ],\ "packagePeers": [\ "@types/debug",\ @@ -15784,12 +15824,12 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { ],\ "linkType": "HARD"\ }],\ - ["virtual:35a845e191d5a8a7376e256c81e9e855732385142c5dc9e26f0b8393c2fb4673b81fed201d5f2c5ab96fb727142683ac03329eab760f2c4870779d4bda6abe8f#npm:1.15.2", {\ - "packageLocation": "./.yarn/__virtual__/follow-redirects-virtual-2e83874824/0/cache/follow-redirects-npm-1.15.2-1ec1dd82be-faa66059b6.zip/node_modules/follow-redirects/",\ + ["virtual:6f48908c3af8c754fea38f10057cfc0081ca24b9ec51933d35d3ad791bb3860f2b56d8b63b6851dbeaa8a9ef39ad5034c7710c92d6dad744acf332331717e74b#npm:1.15.3", {\ + "packageLocation": "./.yarn/__virtual__/follow-redirects-virtual-12c73923b5/0/cache/follow-redirects-npm-1.15.3-ca69c47b72-584da22ec5.zip/node_modules/follow-redirects/",\ "packageDependencies": [\ - ["follow-redirects", "virtual:35a845e191d5a8a7376e256c81e9e855732385142c5dc9e26f0b8393c2fb4673b81fed201d5f2c5ab96fb727142683ac03329eab760f2c4870779d4bda6abe8f#npm:1.15.2"],\ + ["follow-redirects", "virtual:6f48908c3af8c754fea38f10057cfc0081ca24b9ec51933d35d3ad791bb3860f2b56d8b63b6851dbeaa8a9ef39ad5034c7710c92d6dad744acf332331717e74b#npm:1.15.3"],\ ["@types/debug", null],\ - ["debug", null]\ + ["debug", "virtual:58471071b1e0e7981e3318280660861b4dec874aaf0d60e144b70657cb5ce0af059ae16711a2af10f4d1ff0536527e350e6e47a8f79db2d8d37ff2ec84865bbc#npm:4.3.4"]\ ],\ "packagePeers": [\ "@types/debug",\ @@ -17344,11 +17384,11 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { ],\ "linkType": "HARD"\ }],\ - ["npm:5.0.1", {\ - "packageLocation": "./.yarn/cache/https-proxy-agent-npm-5.0.1-42d65f358e-571fccdf38.zip/node_modules/https-proxy-agent/",\ + ["npm:7.0.2", {\ + "packageLocation": "./.yarn/cache/https-proxy-agent-npm-7.0.2-83ea6a5d42-088969a0dd.zip/node_modules/https-proxy-agent/",\ "packageDependencies": [\ - ["https-proxy-agent", "npm:5.0.1"],\ - ["agent-base", "npm:6.0.2"],\ + ["https-proxy-agent", "npm:7.0.2"],\ + ["agent-base", "npm:7.1.0"],\ ["debug", "virtual:428f325a939c2653ad822eb3d75efb02ac311523dd0d4f9645afc39ea00bd86eceac35a9d59c9b6977d76b670a4ef0ae057ea572338a44729aa592711a8c05a3#npm:4.3.2"]\ ],\ "linkType": "HARD"\ @@ -20787,15 +20827,6 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { "linkType": "HARD"\ }]\ ]],\ - ["md5-file", [\ - ["npm:5.0.0", {\ - "packageLocation": "./.yarn/cache/md5-file-npm-5.0.0-e5f59abc62-c606a00ff5.zip/node_modules/md5-file/",\ - "packageDependencies": [\ - ["md5-file", "npm:5.0.0"]\ - ],\ - "linkType": "HARD"\ - }]\ - ]],\ ["measured-core", [\ ["npm:1.51.1", {\ "packageLocation": "./.yarn/cache/measured-core-npm-1.51.1-3a43a565f1-b8c7cd5495.zip/node_modules/measured-core/",\ @@ -21391,16 +21422,44 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { ],\ "linkType": "HARD"\ }],\ - ["npm:4.17.1", {\ - "packageLocation": "./.yarn/cache/mongodb-npm-4.17.1-a2fe811ff1-e7f280570d.zip/node_modules/mongodb/",\ + ["npm:5.9.1", {\ + "packageLocation": "./.yarn/cache/mongodb-npm-5.9.1-7e427c6de3-a827937120.zip/node_modules/mongodb/",\ "packageDependencies": [\ - ["mongodb", "npm:4.17.1"],\ - ["@aws-sdk/credential-providers", "npm:3.212.0"],\ + ["mongodb", "npm:5.9.1"]\ + ],\ + "linkType": "SOFT"\ + }],\ + ["virtual:6f48908c3af8c754fea38f10057cfc0081ca24b9ec51933d35d3ad791bb3860f2b56d8b63b6851dbeaa8a9ef39ad5034c7710c92d6dad744acf332331717e74b#npm:5.9.1", {\ + "packageLocation": "./.yarn/__virtual__/mongodb-virtual-01716b6021/0/cache/mongodb-npm-5.9.1-7e427c6de3-a827937120.zip/node_modules/mongodb/",\ + "packageDependencies": [\ + ["mongodb", "virtual:6f48908c3af8c754fea38f10057cfc0081ca24b9ec51933d35d3ad791bb3860f2b56d8b63b6851dbeaa8a9ef39ad5034c7710c92d6dad744acf332331717e74b#npm:5.9.1"],\ + ["@aws-sdk/credential-providers", null],\ ["@mongodb-js/saslprep", "npm:1.1.0"],\ - ["bson", "npm:4.7.2"],\ + ["@mongodb-js/zstd", null],\ + ["@types/aws-sdk__credential-providers", null],\ + ["@types/kerberos", null],\ + ["@types/mongodb-client-encryption", null],\ + ["@types/mongodb-js__zstd", null],\ + ["@types/snappy", null],\ + ["bson", "npm:5.5.1"],\ + ["kerberos", null],\ + ["mongodb-client-encryption", null],\ ["mongodb-connection-string-url", "npm:2.6.0"],\ + ["snappy", null],\ ["socks", "npm:2.7.1"]\ ],\ + "packagePeers": [\ + "@aws-sdk/credential-providers",\ + "@mongodb-js/zstd",\ + "@types/aws-sdk__credential-providers",\ + "@types/kerberos",\ + "@types/mongodb-client-encryption",\ + "@types/mongodb-js__zstd",\ + "@types/snappy",\ + "kerberos",\ + "mongodb-client-encryption",\ + "snappy"\ + ],\ "linkType": "HARD"\ }]\ ]],\ @@ -21425,35 +21484,32 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { }]\ ]],\ ["mongodb-memory-server", [\ - ["npm:8.15.1", {\ - "packageLocation": "./.yarn/unplugged/mongodb-memory-server-npm-8.15.1-52153cb2c7/node_modules/mongodb-memory-server/",\ + ["npm:9.0.1", {\ + "packageLocation": "./.yarn/unplugged/mongodb-memory-server-npm-9.0.1-cf910b6df5/node_modules/mongodb-memory-server/",\ "packageDependencies": [\ - ["mongodb-memory-server", "npm:8.15.1"],\ - ["mongodb-memory-server-core", "npm:8.15.1"],\ + ["mongodb-memory-server", "npm:9.0.1"],\ + ["mongodb-memory-server-core", "npm:9.0.1"],\ ["tslib", "npm:2.6.2"]\ ],\ "linkType": "HARD"\ }]\ ]],\ ["mongodb-memory-server-core", [\ - ["npm:8.15.1", {\ - "packageLocation": "./.yarn/cache/mongodb-memory-server-core-npm-8.15.1-0f2c58533d-2e47663a65.zip/node_modules/mongodb-memory-server-core/",\ + ["npm:9.0.1", {\ + "packageLocation": "./.yarn/cache/mongodb-memory-server-core-npm-9.0.1-6f48908c3a-41ed9b1c6c.zip/node_modules/mongodb-memory-server-core/",\ "packageDependencies": [\ - ["mongodb-memory-server-core", "npm:8.15.1"],\ - ["async-mutex", "npm:0.3.2"],\ + ["mongodb-memory-server-core", "npm:9.0.1"],\ + ["async-mutex", "npm:0.4.0"],\ ["camelcase", "npm:6.3.0"],\ ["debug", "virtual:58471071b1e0e7981e3318280660861b4dec874aaf0d60e144b70657cb5ce0af059ae16711a2af10f4d1ff0536527e350e6e47a8f79db2d8d37ff2ec84865bbc#npm:4.3.4"],\ ["find-cache-dir", "npm:3.3.2"],\ - ["follow-redirects", "virtual:0f2c58533d5ae53fe8d3b1cb5e5cb8e43e3e2d7669343628c0e0e3ec650e92c188661a07c62bd0e049a683d03ad0f5f7911a33a29316bd3959b8724b5aeada68#npm:1.15.2"],\ - ["get-port", "npm:5.1.1"],\ - ["https-proxy-agent", "npm:5.0.1"],\ - ["md5-file", "npm:5.0.0"],\ - ["mongodb", "npm:4.17.1"],\ + ["follow-redirects", "virtual:6f48908c3af8c754fea38f10057cfc0081ca24b9ec51933d35d3ad791bb3860f2b56d8b63b6851dbeaa8a9ef39ad5034c7710c92d6dad744acf332331717e74b#npm:1.15.3"],\ + ["https-proxy-agent", "npm:7.0.2"],\ + ["mongodb", "virtual:6f48908c3af8c754fea38f10057cfc0081ca24b9ec51933d35d3ad791bb3860f2b56d8b63b6851dbeaa8a9ef39ad5034c7710c92d6dad744acf332331717e74b#npm:5.9.1"],\ ["new-find-package-json", "npm:2.0.0"],\ ["semver", "npm:7.5.4"],\ - ["tar-stream", "npm:2.2.0"],\ + ["tar-stream", "npm:3.1.6"],\ ["tslib", "npm:2.6.2"],\ - ["uuid", "npm:9.0.0"],\ ["yauzl", "npm:2.10.0"]\ ],\ "linkType": "HARD"\ @@ -24349,6 +24405,15 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { "linkType": "HARD"\ }]\ ]],\ + ["queue-tick", [\ + ["npm:1.0.1", {\ + "packageLocation": "./.yarn/cache/queue-tick-npm-1.0.1-10bd6eaf3d-57c3292814.zip/node_modules/queue-tick/",\ + "packageDependencies": [\ + ["queue-tick", "npm:1.0.1"]\ + ],\ + "linkType": "HARD"\ + }]\ + ]],\ ["quick-format-unescaped", [\ ["npm:4.0.4", {\ "packageLocation": "./.yarn/cache/quick-format-unescaped-npm-4.0.4-7e22c9b7dc-7bc32b9935.zip/node_modules/quick-format-unescaped/",\ @@ -26857,6 +26922,17 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { "linkType": "HARD"\ }]\ ]],\ + ["streamx", [\ + ["npm:2.15.5", {\ + "packageLocation": "./.yarn/cache/streamx-npm-2.15.5-08568dca5b-52e0ec9402.zip/node_modules/streamx/",\ + "packageDependencies": [\ + ["streamx", "npm:2.15.5"],\ + ["fast-fifo", "npm:1.3.2"],\ + ["queue-tick", "npm:1.0.1"]\ + ],\ + "linkType": "HARD"\ + }]\ + ]],\ ["strict-uri-encode", [\ ["npm:2.0.0", {\ "packageLocation": "./.yarn/cache/strict-uri-encode-npm-2.0.0-1ec3189376-eaac4cf978.zip/node_modules/strict-uri-encode/",\ @@ -27495,6 +27571,16 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { ["readable-stream", "npm:3.6.0"]\ ],\ "linkType": "HARD"\ + }],\ + ["npm:3.1.6", {\ + "packageLocation": "./.yarn/cache/tar-stream-npm-3.1.6-ce3ac17e49-f3627f9185.zip/node_modules/tar-stream/",\ + "packageDependencies": [\ + ["tar-stream", "npm:3.1.6"],\ + ["b4a", "npm:1.6.4"],\ + ["fast-fifo", "npm:1.3.2"],\ + ["streamx", "npm:2.15.5"]\ + ],\ + "linkType": "HARD"\ }]\ ]],\ ["teeny-request", [\ @@ -29269,7 +29355,7 @@ function $$SETUP_STATE(hydrateRuntimeState, basePath) { "packageDependencies": [\ ["vitest-mongodb", "npm:0.0.5"],\ ["debug", "virtual:58471071b1e0e7981e3318280660861b4dec874aaf0d60e144b70657cb5ce0af059ae16711a2af10f4d1ff0536527e350e6e47a8f79db2d8d37ff2ec84865bbc#npm:4.3.4"],\ - ["mongodb-memory-server", "npm:8.15.1"]\ + ["mongodb-memory-server", "npm:9.0.1"]\ ],\ "linkType": "HARD"\ }]\ diff --git a/Dockerfile b/Dockerfile index 39bdcb0849..08fee52f93 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM node:18.17.1-bullseye as dependencies +FROM docker.io/library/node:18.17.1-bullseye as dependencies WORKDIR /srv diff --git a/README.md b/README.md index 2076113541..537d30f8f9 100644 --- a/README.md +++ b/README.md @@ -31,14 +31,14 @@ GOOGLE_CLIENT_ID= GOOGLE_CLIENT_SECRET= ``` -[docker-compose](https://docs.docker.com/compose/overview/) is used to run a local copy of all required services together. +[podman-compose](https://github.com/containers/podman-compose) is used to run a local copy of all required services together. ```shell -# This will run docker-compose in the background (-d flag is --detach) -docker-compose up -d +# This will run podman-compose in the background (-d flag is --detach) +podman-compose up -d ``` -For example, you can restart the server container with `docker-compose restart server` or view logs with `docker-compose logs -f --tail=10 server`. +For example, you can restart the server container with `podman-compose restart server` or view logs with `podman-compose logs -f --tail=10 server`. ## Major Components diff --git a/docker-compose.yml b/docker-compose.yml index 2752978214..63247b07e8 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,48 +1,10 @@ # docker compose versions version: '2.3' -volumes: - node_deps: - dist: - driver_opts: - type: tmpfs - device: tmpfs - dist_app: - driver_opts: - type: tmpfs - device: tmpfs - dist_client: - driver_opts: - type: tmpfs - device: tmpfs - dist_cli: - driver_opts: - type: tmpfs - device: tmpfs - dist_components: - driver_opts: - type: tmpfs - device: tmpfs - dist_indexer: - driver_opts: - type: tmpfs - device: tmpfs - dist_server: - driver_opts: - type: tmpfs - device: tmpfs - dist_search: - driver_opts: - type: tmpfs - device: tmpfs - typescript_build_cache: - node_modules_app: - node_modules_components: - services: # This dummy service provides shared configuration for all Node deps node: - image: node:18.17.1-bullseye + image: docker.io/library/node:18.17.1-bullseye env_file: ./config.env working_dir: /srv command: bash -c 'yarn install && yarn pnpify tsc-watch -b --onSuccess "touch /watch/done"' @@ -52,23 +14,10 @@ services: retries: 60 tmpfs: - /watch - - /srv/.build-cache volumes: - - ./:/srv - - node_deps:/srv/.yarn - - ./.yarn/cache:/srv/.yarn/cache:ro - - ./.yarn/releases:/srv/.yarn/releases:cached - - ./.yarn/plugins:/srv/.yarn/plugins:cached - - dist:/srv/dist - - dist_app:/srv/packages/openneuro-app/dist - - dist_cli:/srv/packages/openneuro-cli/dist - - dist_client:/srv/packages/openneuro-client/dist - - dist_components:/srv/packages/openneuro-components/dist - - dist_search:/srv/packages/openneuro-search/dist - - dist_indexer:/srv/packages/openneuro-indexer/dist - - dist_server:/srv/packages/openneuro-server/dist - - node_modules_app:/srv/packages/openneuro-app/node_modules - - node_modules_components:/srv/packages/openneuro-components/node_modules + - ./:/srv:rw,z + - /srv/dist + - /srv/.build-cache # web app bundle build app: @@ -126,20 +75,20 @@ services: # mongodb mongo: - image: mongo:5.0 + image: docker.io/library/mongo:5.0 volumes: - - ${PERSISTENT_DIR}/mongo:/data/db:delegated + - ${PERSISTENT_DIR}/mongo:/data/db:z # Redis redis: - image: redis:alpine + image: docker.io/library/redis:alpine # datalad Python backend datalad: build: context: services/datalad volumes: - - ${PERSISTENT_DIR}/datalad:/datalad:delegated + - ${PERSISTENT_DIR}/datalad:/datalad:z - ./services/datalad/datalad_service:/srv/datalad_service env_file: ./config.env init: true @@ -169,11 +118,10 @@ services: # nginx + app web: - image: nginx:1.16.1 + image: docker.io/library/nginx:1.16.1 volumes: - ./nginx/nginx.dev.conf:/etc/nginx/conf.d/default.conf:ro ports: - - '80:80' - '8110:8110' - '9876:80' depends_on: @@ -197,11 +145,3 @@ services: - '9200:9200' - '9300:9300' -# comment out `x-disabled` to enable kibana service -x-disabled: - kibana: - image: kibana:7.10.1 - depends_on: - - elasticsearch - ports: - - '5601:5601' diff --git a/nginx/nginx.dev.conf b/nginx/nginx.dev.conf index bb7f62a769..c88233f7f9 100644 --- a/nginx/nginx.dev.conf +++ b/nginx/nginx.dev.conf @@ -1,6 +1,3 @@ -# Override docker-compose 600s TTL -resolver 127.0.0.11 valid=10s; - server { listen 80; @@ -8,11 +5,6 @@ server { gzip_proxied any; gzip_types text/html application/json text/css; - # Use a variable to allow for IP changes when a new container starts - # https://www.nginx.com/blog/dns-service-discovery-nginx-plus/#domain-name-proxy_pass - set $openneuro_server server; - set $datalad_service datalad; - location /uploads { client_max_body_size 0; proxy_set_header Host $host; @@ -20,7 +12,7 @@ server { proxy_set_header Connection ""; proxy_http_version 1.1; proxy_request_buffering off; - proxy_pass http://$datalad_service:80; + proxy_pass http://datalad:80; } location /git { @@ -30,7 +22,7 @@ server { proxy_set_header Connection ""; proxy_http_version 1.1; proxy_request_buffering off; - proxy_pass http://$datalad_service:80; + proxy_pass http://datalad:80; } # crn-server proxy @@ -41,7 +33,7 @@ server { proxy_set_header Connection ""; proxy_http_version 1.1; proxy_request_buffering off; - proxy_pass http://$openneuro_server:8111; + proxy_pass http://server:8111; } # Sitemap path @@ -52,11 +44,11 @@ server { proxy_set_header Connection ""; proxy_http_version 1.1; proxy_request_buffering off; - proxy_pass http://$openneuro_server:8111/crn/sitemap; + proxy_pass http://server:8111/crn/sitemap; } location /graphql-subscriptions { - proxy_pass http://$openneuro_server:8111/graphql-subscriptions; + proxy_pass http://server:8111/graphql-subscriptions; proxy_http_version 1.1; proxy_set_header Upgrade $http_upgrade; proxy_set_header Connection "upgrade"; diff --git a/package.json b/package.json index 5bc9953e08..4d4207bd4a 100644 --- a/package.json +++ b/package.json @@ -66,7 +66,8 @@ } }, "resolutions": { - "react-router-dom": "6.3.0" + "react-router-dom": "6.3.0", + "mongodb-memory-server": "9.0.1" }, "packageManager": "yarn@3.6.3", "dependencies": { diff --git a/packages/openneuro-app/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap b/packages/openneuro-app/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap index e872da249e..b03d7be6ad 100644 --- a/packages/openneuro-app/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap +++ b/packages/openneuro-app/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap @@ -258,7 +258,7 @@ exports[`SnapshotContainer component > renders successfully 1`] = ` >

/participants.tsv @@ -269,7 +269,7 @@ exports[`SnapshotContainer component > renders successfully 1`] = ` class="e-meta" >

Tabular file contains custom columns not described in a data dictionary diff --git a/packages/openneuro-app/src/scripts/dataset/files/viewers/__tests__/__snapshots__/file-viewer-json.spec.jsx.snap b/packages/openneuro-app/src/scripts/dataset/files/viewers/__tests__/__snapshots__/file-viewer-json.spec.jsx.snap index 6cc92e5718..a1f7dce83d 100644 --- a/packages/openneuro-app/src/scripts/dataset/files/viewers/__tests__/__snapshots__/file-viewer-json.spec.jsx.snap +++ b/packages/openneuro-app/src/scripts/dataset/files/viewers/__tests__/__snapshots__/file-viewer-json.spec.jsx.snap @@ -1,29 +1,5 @@ // Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html -exports[`File Viewer - JSON > renders with invalid JSON 1`] = ` - -

- Tree -

-
-

- JSON failed to parse -

- 
-    Unexpected token ; in JSON at position 4
-
-

- Raw -

-
- 
-    1234;
-
- -`; - exports[`File Viewer - JSON > renders with valid JSON 1`] = `

diff --git a/packages/openneuro-app/src/scripts/pages/metadata/dataset-metadata.tsx b/packages/openneuro-app/src/scripts/pages/metadata/dataset-metadata.tsx index a13a5d271d..9c91a2a7eb 100644 --- a/packages/openneuro-app/src/scripts/pages/metadata/dataset-metadata.tsx +++ b/packages/openneuro-app/src/scripts/pages/metadata/dataset-metadata.tsx @@ -80,8 +80,7 @@ export function DatasetMetadata(): React.ReactElement { "affirmedDefaced", "affirmedConsent", ]} - > - + /> ) } diff --git a/packages/openneuro-server/src/libs/authentication/__tests__/jwt.spec.ts b/packages/openneuro-server/src/libs/authentication/__tests__/jwt.spec.ts index 42a4bfc8e5..c62e3d9f5b 100644 --- a/packages/openneuro-server/src/libs/authentication/__tests__/jwt.spec.ts +++ b/packages/openneuro-server/src/libs/authentication/__tests__/jwt.spec.ts @@ -16,7 +16,7 @@ describe("jwt auth", () => { }, }, } - const user = User({ email: "test@example.com" }) + const user = new User({ email: "test@example.com" }) const obj = addJWT(config)(user) expect(obj).toHaveProperty("token") }) diff --git a/services/datalad/Dockerfile b/services/datalad/Dockerfile index 09cd717b38..7701586071 100644 --- a/services/datalad/Dockerfile +++ b/services/datalad/Dockerfile @@ -1,5 +1,5 @@ -FROM denoland/deno:bin-1.33.1 AS deno -FROM python:3.11-slim as production +FROM docker.io/denoland/deno:bin-1.33.1 AS deno +FROM docker.io/library/python:3.11-slim as production WORKDIR /srv diff --git a/yarn.lock b/yarn.lock index d1fbbce1ae..57562b684f 100644 --- a/yarn.lock +++ b/yarn.lock @@ -8439,6 +8439,15 @@ __metadata: languageName: node linkType: hard +"agent-base@npm:^7.0.2": + version: 7.1.0 + resolution: "agent-base@npm:7.1.0" + dependencies: + debug: ^4.3.4 + checksum: f7828f991470a0cc22cb579c86a18cbae83d8a3cbed39992ab34fc7217c4d126017f1c74d0ab66be87f71455318a8ea3e757d6a37881b8d0f2a2c6aa55e5418f + languageName: node + linkType: hard + "agent-base@npm:~4.2.1": version: 4.2.1 resolution: "agent-base@npm:4.2.1" @@ -8948,12 +8957,12 @@ __metadata: languageName: node linkType: hard -"async-mutex@npm:^0.3.2": - version: 0.3.2 - resolution: "async-mutex@npm:0.3.2" +"async-mutex@npm:^0.4.0": + version: 0.4.0 + resolution: "async-mutex@npm:0.4.0" dependencies: - tslib: ^2.3.1 - checksum: 620b771dfdea1cad0a6b712915c31a1e3ca880a8cf1eae92b4590f435995e0260929c6ebaae0b9126b1456790ea498064b5bb9a506948cda760f48d3d0dcc4c8 + tslib: ^2.4.0 + checksum: 813a71728b35a4fbfd64dba719f04726d9133c67b577fcd951b7028c4a675a13ee34e69beb82d621f87bf81f5d4f135c4c44be0448550c7db728547244ef71fc languageName: node linkType: hard @@ -9051,6 +9060,13 @@ __metadata: languageName: node linkType: hard +"b4a@npm:^1.6.4": + version: 1.6.4 + resolution: "b4a@npm:1.6.4" + checksum: 81b086f9af1f8845fbef4476307236bda3d660c158c201db976f19cdce05f41f93110ab6b12fd7a2696602a490cc43d5410ee36a56d6eef93afb0d6ca69ac3b2 + languageName: node + linkType: hard + "babel-jest@npm:^29.7.0": version: 29.7.0 resolution: "babel-jest@npm:29.7.0" @@ -9483,6 +9499,13 @@ __metadata: languageName: node linkType: hard +"bson@npm:^5.5.0": + version: 5.5.1 + resolution: "bson@npm:5.5.1" + checksum: f49730504e8362e2c8d1eb0c272e5e125392c41fb7196fc35ccbc39718ee62569a1d197bd2342c3334cd420073d3fd5dc7dea764a7f219dcd79e0ce473dd2772 + languageName: node + linkType: hard + "btoa-lite@npm:^1.0.0": version: 1.0.0 resolution: "btoa-lite@npm:1.0.0" @@ -12839,6 +12862,13 @@ __metadata: languageName: node linkType: hard +"fast-fifo@npm:^1.1.0, fast-fifo@npm:^1.2.0": + version: 1.3.2 + resolution: "fast-fifo@npm:1.3.2" + checksum: 6bfcba3e4df5af7be3332703b69a7898a8ed7020837ec4395bb341bd96cc3a6d86c3f6071dd98da289618cf2234c70d84b2a6f09a33dd6f988b1ff60d8e54275 + languageName: node + linkType: hard + "fast-glob@npm:3.2.7, fast-glob@npm:^3.1.1, fast-glob@npm:^3.2.2": version: 3.2.7 resolution: "fast-glob@npm:3.2.7" @@ -13243,7 +13273,7 @@ __metadata: languageName: node linkType: hard -"follow-redirects@npm:^1.15.0, follow-redirects@npm:^1.15.2": +"follow-redirects@npm:^1.15.0": version: 1.15.2 resolution: "follow-redirects@npm:1.15.2" peerDependenciesMeta: @@ -13253,6 +13283,16 @@ __metadata: languageName: node linkType: hard +"follow-redirects@npm:^1.15.3": + version: 1.15.3 + resolution: "follow-redirects@npm:1.15.3" + peerDependenciesMeta: + debug: + optional: true + checksum: 584da22ec5420c837bd096559ebfb8fe69d82512d5585004e36a3b4a6ef6d5905780e0c74508c7b72f907d1fa2b7bd339e613859e9c304d0dc96af2027fd0231 + languageName: node + linkType: hard + "for-each@npm:^0.3.3": version: 0.3.3 resolution: "for-each@npm:0.3.3" @@ -13674,7 +13714,7 @@ fsevents@~2.3.2: languageName: node linkType: hard -"get-port@npm:5.1.1, get-port@npm:^5.1.1": +"get-port@npm:5.1.1": version: 5.1.1 resolution: "get-port@npm:5.1.1" checksum: 0162663ffe5c09e748cd79d97b74cd70e5a5c84b760a475ce5767b357fb2a57cb821cee412d646aa8a156ed39b78aab88974eddaa9e5ee926173c036c0713787 @@ -14675,13 +14715,13 @@ fsevents@~2.3.2: languageName: node linkType: hard -"https-proxy-agent@npm:^5.0.1": - version: 5.0.1 - resolution: "https-proxy-agent@npm:5.0.1" +"https-proxy-agent@npm:^7.0.2": + version: 7.0.2 + resolution: "https-proxy-agent@npm:7.0.2" dependencies: - agent-base: 6 + agent-base: ^7.0.2 debug: 4 - checksum: 571fccdf38184f05943e12d37d6ce38197becdd69e58d03f43637f7fa1269cf303a7d228aa27e5b27bbd3af8f09fd938e1c91dcfefff2df7ba77c20ed8dfc765 + checksum: 088969a0dd476ea7a0ed0a2cf1283013682b08f874c3bc6696c83fa061d2c157d29ef0ad3eb70a2046010bb7665573b2388d10fdcb3e410a66995e5248444292 languageName: node linkType: hard @@ -17750,15 +17790,6 @@ fsevents@~2.3.2: languageName: node linkType: hard -"md5-file@npm:^5.0.0": - version: 5.0.0 - resolution: "md5-file@npm:5.0.0" - bin: - md5-file: cli.js - checksum: c606a00ff58adf5428e8e2f36d86e5d3c7029f9688126faca302cd83b5e92cac183a62e1d1f05fae7c2614e80f993326fd0a8d6a3a913c41ec7ea0eefc25aa76 - languageName: node - linkType: hard - "measured-core@npm:^1.51.1": version: 1.51.1 resolution: "measured-core@npm:1.51.1" @@ -18334,36 +18365,33 @@ fsevents@~2.3.2: languageName: node linkType: hard -"mongodb-memory-server-core@npm:8.15.1": - version: 8.15.1 - resolution: "mongodb-memory-server-core@npm:8.15.1" +"mongodb-memory-server-core@npm:9.0.1": + version: 9.0.1 + resolution: "mongodb-memory-server-core@npm:9.0.1" dependencies: - async-mutex: ^0.3.2 + async-mutex: ^0.4.0 camelcase: ^6.3.0 debug: ^4.3.4 find-cache-dir: ^3.3.2 - follow-redirects: ^1.15.2 - get-port: ^5.1.1 - https-proxy-agent: ^5.0.1 - md5-file: ^5.0.0 - mongodb: ^4.16.0 + follow-redirects: ^1.15.3 + https-proxy-agent: ^7.0.2 + mongodb: ^5.9.0 new-find-package-json: ^2.0.0 semver: ^7.5.4 - tar-stream: ^2.1.4 - tslib: ^2.6.1 - uuid: ^9.0.0 + tar-stream: ^3.0.0 + tslib: ^2.6.2 yauzl: ^2.10.0 - checksum: 2e47663a65575f4d067f8acf47a00aa7f2cfd8040854034f72e2ca35ab3d708fbe45feff556eff9d9d8fce5a9618a57c4d01c8a9c267b810470962fd5e126823 + checksum: 41ed9b1c6c3d56e637594e250ccd151cdf2b958b77551e9e8616f39f1d4ceb22376def390f3bbedff5417b3b448ec235a108e9022da1ab88458719baaf11d8c6 languageName: node linkType: hard -"mongodb-memory-server@npm:^8.12.0": - version: 8.15.1 - resolution: "mongodb-memory-server@npm:8.15.1" +"mongodb-memory-server@npm:9.0.1": + version: 9.0.1 + resolution: "mongodb-memory-server@npm:9.0.1" dependencies: - mongodb-memory-server-core: 8.15.1 - tslib: ^2.6.1 - checksum: ad1f1cba52925556274786414c9267056dac6a7463789a13ebb3722a840fdbe45131a50d964ec5ee215460518dc0966050c8f118b70ea97d8de5d4276da44c6b + mongodb-memory-server-core: 9.0.1 + tslib: ^2.6.2 + checksum: 0f54d26edde117a6e87423461445be094a6af6e7d87d3bf2c98607683c41bed4f2e5a0175dfa8ffd9b6d0bf6fcea11bf3a18aaf66f5ccc619a0a6a4417ebdfce languageName: node linkType: hard @@ -18385,21 +18413,35 @@ fsevents@~2.3.2: languageName: node linkType: hard -"mongodb@npm:^4.16.0": - version: 4.17.1 - resolution: "mongodb@npm:4.17.1" +"mongodb@npm:^5.9.0": + version: 5.9.1 + resolution: "mongodb@npm:5.9.1" dependencies: - "@aws-sdk/credential-providers": ^3.186.0 "@mongodb-js/saslprep": ^1.1.0 - bson: ^4.7.2 + bson: ^5.5.0 mongodb-connection-string-url: ^2.6.0 socks: ^2.7.1 + peerDependencies: + "@aws-sdk/credential-providers": ^3.188.0 + "@mongodb-js/zstd": ^1.0.0 + kerberos: ^1.0.0 || ^2.0.0 + mongodb-client-encryption: ">=2.3.0 <3" + snappy: ^7.2.2 dependenciesMeta: + "@mongodb-js/saslprep": + optional: true + peerDependenciesMeta: "@aws-sdk/credential-providers": optional: true - "@mongodb-js/saslprep": + "@mongodb-js/zstd": + optional: true + kerberos: optional: true - checksum: e7f280570d0f23d60c308b2a484ed55762ec8e523946c0de1a0b3b398f24efcf1916a745e5407f32cd1c105b2f19d8ac75474c92f73cdf651affe3430a963f54 + mongodb-client-encryption: + optional: true + snappy: + optional: true + checksum: a827937120cd7eecafc0ad5657b40536774f0b09582a9363db0a192149ba20eae80a33fccf573f5ce69a20aca6759c40b4961d9d1d4de2a350c543030055e0f6 languageName: node linkType: hard @@ -21063,6 +21105,13 @@ fsevents@~2.3.2: languageName: node linkType: hard +"queue-tick@npm:^1.0.1": + version: 1.0.1 + resolution: "queue-tick@npm:1.0.1" + checksum: 57c3292814b297f87f792fbeb99ce982813e4e54d7a8bdff65cf53d5c084113913289d4a48ec8bbc964927a74b847554f9f4579df43c969a6c8e0f026457ad01 + languageName: node + linkType: hard + "quick-format-unescaped@npm:^4.0.3": version: 4.0.4 resolution: "quick-format-unescaped@npm:4.0.4" @@ -23231,6 +23280,16 @@ resolve@^2.0.0-next.3: languageName: node linkType: hard +"streamx@npm:^2.15.0": + version: 2.15.5 + resolution: "streamx@npm:2.15.5" + dependencies: + fast-fifo: ^1.1.0 + queue-tick: ^1.0.1 + checksum: 52e0ec94026d67c9e2e2e1090f05e5b138c2f2822462d9a8ef4a4805625a31d103e55ea5267fcd9bfe041374926424e42aec2dda28a85cb9de42c2a16d416d94 + languageName: node + linkType: hard + "strict-uri-encode@npm:^2.0.0": version: 2.0.0 resolution: "strict-uri-encode@npm:2.0.0" @@ -23758,7 +23817,18 @@ resolve@^2.0.0-next.3: languageName: node linkType: hard -"tar-stream@npm:^2.1.4, tar-stream@npm:~2.2.0": +"tar-stream@npm:^3.0.0": + version: 3.1.6 + resolution: "tar-stream@npm:3.1.6" + dependencies: + b4a: ^1.6.4 + fast-fifo: ^1.2.0 + streamx: ^2.15.0 + checksum: f3627f918581976e954ff03cb8d370551053796b82564f8c7ca8fac84c48e4d042026d0854fc222171a34ff9c682b72fae91be9c9b0a112d4c54f9e4f443e9c5 + languageName: node + linkType: hard + +"tar-stream@npm:~2.2.0": version: 2.2.0 resolution: "tar-stream@npm:2.2.0" dependencies: @@ -24342,7 +24412,7 @@ resolve@^2.0.0-next.3: languageName: node linkType: hard -"tslib@npm:^2.5.0, tslib@npm:^2.6.1": +"tslib@npm:^2.5.0, tslib@npm:^2.6.2": version: 2.6.2 resolution: "tslib@npm:2.6.2" checksum: 329ea56123005922f39642318e3d1f0f8265d1e7fcb92c633e0809521da75eeaca28d2cf96d7248229deb40e5c19adf408259f4b9640afd20d13aecc1430f3ad