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base repository: nomad-nmr/nomad-server
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base: v3.4.0
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head repository: nomad-nmr/nomad-server
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compare: v3.5.0
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Commits on Nov 24, 2023

  1. NMRium usage stats backend

    tomlebl committed Nov 24, 2023
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Commits on Nov 27, 2023

  1. Merge pull request #62 from nomad-nmr/stats

    NMRium usage stats backend
    tomlebl authored Nov 27, 2023
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  2. NMRium 0.45.0 update

    tomlebl committed Nov 27, 2023
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Commits on Dec 1, 2023

  1. collection modal done

    tomlebl committed Dec 1, 2023
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Commits on Dec 4, 2023

  1. collections table bare

    tomlebl committed Dec 4, 2023
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Commits on Dec 8, 2023

  1. collections table wired

    tomlebl committed Dec 8, 2023
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Commits on Dec 11, 2023

  1. edit collection meta frontend

    tomlebl committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. edit collection meta redux

    tomlebl committed Dec 12, 2023
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Commits on Dec 19, 2023

  1. improved datastore stats

    tomlebl committed Dec 19, 2023
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Commits on Dec 20, 2023

  1. Copy the full SHA
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Commits on Dec 21, 2023

  1. zipDataset util function

    tomlebl committed Dec 21, 2023
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Commits on Jan 5, 2024

  1. download collection

    tomlebl committed Jan 5, 2024
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Commits on Jan 12, 2024

  1. tag selection

    tomlebl committed Jan 12, 2024
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  2. NMRium 0.47.0

    tomlebl committed Jan 12, 2024
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  3. Redux update

    tomlebl committed Jan 12, 2024
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Commits on Jan 26, 2024

  1. GrpUsr form added

    tomlebl committed Jan 26, 2024
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Commits on Jan 29, 2024

  1. Copy the full SHA
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  2. npm update

    tomlebl committed Jan 29, 2024
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Commits on Jan 30, 2024

  1. auth token fix

    tomlebl committed Jan 30, 2024
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Commits on Feb 9, 2024

  1. checkAuthTimeout fix

    tomlebl committed Feb 9, 2024
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  2. nmrium v0.49.0 update

    tomlebl committed Feb 9, 2024
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Commits on Feb 12, 2024

  1. reject dataset save as

    tomlebl committed Feb 12, 2024
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Commits on Feb 14, 2024

  1. case sensitive paramsets

    tomlebl committed Feb 14, 2024
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Commits on Feb 20, 2024

  1. emails adding from csv

    tomlebl committed Feb 20, 2024
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  2. reverting vitest to 0.34.6

    tomlebl committed Feb 20, 2024
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  4. fixing api tests

    tomlebl committed Feb 20, 2024
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  5. add users from csv test

    tomlebl committed Feb 20, 2024
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Commits on Feb 26, 2024

  1. submit open rack works

    tomlebl committed Feb 26, 2024
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  2. nmrium 0.50.1 update

    tomlebl committed Feb 26, 2024
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Commits on Feb 27, 2024

  1. rack for all done

    tomlebl committed Feb 27, 2024
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Commits on Mar 5, 2024

  1. Copy the full SHA
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Commits on Mar 11, 2024

  1. batch-submit tests finished

    tomlebl committed Mar 11, 2024
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  2. mongoose update + test fix

    tomlebl committed Mar 11, 2024
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  3. vitest update

    tomlebl committed Mar 11, 2024
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  4. amending dev dependenies

    tomlebl committed Mar 11, 2024
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Commits on Mar 20, 2024

  1. collection tests

    tomlebl committed Mar 20, 2024
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  2. test api workflow

    tomlebl committed Mar 20, 2024
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    864be0d View commit details
  3. fixing working directory

    tomlebl committed Mar 20, 2024
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  4. fixing working directory 2

    tomlebl committed Mar 20, 2024
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  5. fixing working directory 3

    tomlebl committed Mar 20, 2024
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  6. fixing working directory 4

    tomlebl committed Mar 20, 2024
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  7. fixing working directory 5

    tomlebl committed Mar 20, 2024
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  8. fixing working directory 6

    tomlebl committed Mar 20, 2024
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  9. fixing working directory 7

    tomlebl committed Mar 20, 2024
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  10. fixing working directory 8

    tomlebl committed Mar 20, 2024
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Showing with 8,516 additions and 15,811 deletions.
  1. +15 −0 .github/workflows/deploy-api.yml
  2. +1 −0 .gitignore
  3. +1 −1 Dockerfile.api
  4. +2 −2 Dockerfile.serv
  5. +2 −2 Dockerfile.serv-tls
  6. +2 −0 docker-compose.yaml
  7. +35 −0 env-example/backend-test.env
  8. +1 −0 env-example/backend.env
  9. +5 −1 nginx.conf
  10. +4 −0 nginx.conf-tls
  11. +1 −1 nomad-front-end/Dockerfile
  12. +1,778 −6,068 nomad-front-end/package-lock.json
  13. +7 −7 nomad-front-end/package.json
  14. +12 −1 nomad-front-end/src/App.jsx
  15. BIN nomad-front-end/src/assets/folder-icon.png
  16. +1 −0 nomad-front-end/src/components/AddSampleDrawer/AddSampleDrawer.jsx
  17. +137 −0 nomad-front-end/src/components/CollectionsTable/CollectionsTable.jsx
  18. +2 −2 nomad-front-end/src/components/CopyLinkToClipboard/CopyLinkToClipboard.jsx
  19. +4 −3 nomad-front-end/src/components/DatasetTags/DatasetTags.jsx
  20. +121 −9 nomad-front-end/src/components/Forms/AddSampleForm/AddSampleForm.jsx
  21. +3 −3 nomad-front-end/src/components/Forms/SelectGrpUsr/SelectGrpUsr.jsx
  22. +8 −6 nomad-front-end/src/components/InfoCards/InfoCard/InfoCard.jsx
  23. +1 −0 nomad-front-end/src/components/InfoCards/InfoCard/InfoCard.module.css
  24. +45 −6 nomad-front-end/src/components/Modals/AddRackModal/AddRackModal.jsx
  25. +86 −0 nomad-front-end/src/components/Modals/CollectionMetaModal/CollectionMetaModal.jsx
  26. +73 −0 nomad-front-end/src/components/Modals/CollectionModal/CollectionModal.jsx
  27. +7 −1 nomad-front-end/src/components/Modals/DataSetModal/DataSetModal.jsx
  28. +9 −5 nomad-front-end/src/components/NavBar/MainMenu/MainMenu.jsx
  29. +30 −4 nomad-front-end/src/components/NavBar/PageHeader/Controls/BatchSubmitControls.jsx
  30. +87 −0 nomad-front-end/src/components/NavBar/PageHeader/Controls/CollectionControls.jsx
  31. +48 −7 nomad-front-end/src/components/NavBar/PageHeader/Controls/NMRiumControls.jsx
  32. +27 −13 nomad-front-end/src/components/NavBar/PageHeader/Controls/SearchDatasetControls.jsx
  33. +7 −1 nomad-front-end/src/components/NavBar/PageHeader/Controls/SearchExpsControls.jsx
  34. +41 −4 nomad-front-end/src/components/NavBar/PageHeader/PageHeader.jsx
  35. +1 −1 nomad-front-end/src/components/NavBar/PageHeader/PageHeader.module.css
  36. +13 −2 nomad-front-end/src/components/RackTabs/RackTable/RackTable.jsx
  37. +25 −5 nomad-front-end/src/components/SearchComponents/DatasetCard.jsx
  38. +13 −1 nomad-front-end/src/components/SearchComponents/DatasetCard.module.css
  39. +52 −44 nomad-front-end/src/components/SearchComponents/DatasetTable.jsx
  40. +3 −2 nomad-front-end/src/components/SearchComponents/SearchForm.jsx
  41. +1 −1 nomad-front-end/src/components/StatusDrawer/StatusDrawer.jsx
  42. +40 −12 nomad-front-end/src/containers/BatchSubmit/BatchSubmit.jsx
  43. +373 −0 nomad-front-end/src/containers/Collections/Collections.jsx
  44. +43 −0 nomad-front-end/src/containers/Collections/Collections.module.css
  45. +9 −3 nomad-front-end/src/containers/Groups/Groups.jsx
  46. +30 −10 nomad-front-end/src/containers/NMRium/NMRium.jsx
  47. +4 −0 nomad-front-end/src/containers/NMRium/NMRium.module.css
  48. +59 −19 nomad-front-end/src/containers/SearchDataset/SearchDataset.jsx
  49. +10 −2 nomad-front-end/src/index.jsx
  50. +395 −0 nomad-front-end/src/nmriumGlobal.css
  51. +16 −0 nomad-front-end/src/store/actions/actionTypes.js
  52. +7 −1 nomad-front-end/src/store/actions/auth.js
  53. +148 −0 nomad-front-end/src/store/actions/collections.js
  54. +50 −0 nomad-front-end/src/store/actions/datasets.js
  55. +16 −1 nomad-front-end/src/store/actions/index.js
  56. +10 −2 nomad-front-end/src/store/reducers/auth.js
  57. +120 −0 nomad-front-end/src/store/reducers/collections.js
  58. +52 −5 nomad-front-end/src/store/reducers/datasets.js
  59. +9 −8 nomad-front-end/src/store/reducers/groups.jsx
  60. +1 −1 nomad-rest-api/Dockerfile
  61. +4 −0 nomad-rest-api/app.js
  62. +6 −2 nomad-rest-api/controllers/admin/groups.js
  63. +1 −1 nomad-rest-api/controllers/admin/parameterSets.js
  64. +34 −0 nomad-rest-api/controllers/admin/stats.js
  65. +1 −1 nomad-rest-api/controllers/auth.js
  66. +38 −23 nomad-rest-api/controllers/batch-submit.js
  67. +277 −0 nomad-rest-api/controllers/collections.js
  68. +9 −0 nomad-rest-api/controllers/data.js
  69. +56 −81 nomad-rest-api/controllers/datasets.js
  70. +16 −5 nomad-rest-api/middleware/validateDataAccess.js
  71. +8 −4 nomad-rest-api/middleware/validateDataWriteAccess.js
  72. +24 −0 nomad-rest-api/models/collection.js
  73. +2 −1 nomad-rest-api/models/dataset.js
  74. +20 −4 nomad-rest-api/models/rack.js
  75. +14 −2 nomad-rest-api/models/user.js
  76. +2,948 −9,372 nomad-rest-api/package-lock.json
  77. +11 −11 nomad-rest-api/package.json
  78. +3 −8 nomad-rest-api/routes/admin/parameterSets.js
  79. +9 −0 nomad-rest-api/routes/admin/stats.js
  80. +3 −3 nomad-rest-api/routes/batch-submit.js
  81. +40 −0 nomad-rest-api/routes/collections.js
  82. +5 −0 nomad-rest-api/server.js
  83. +414 −0 nomad-rest-api/tests/batch-submit.test.js
  84. +12 −6 nomad-rest-api/tests/claim.test.js
  85. +251 −0 nomad-rest-api/tests/collections.test.js
  86. +5 −2 nomad-rest-api/tests/datasets.test.js
  87. +13 −0 nomad-rest-api/tests/fixtures/data/collections.js
  88. +2 −0 nomad-rest-api/tests/fixtures/data/datasets.js
  89. +25 −0 nomad-rest-api/tests/fixtures/data/experiments.js
  90. +1 −0 nomad-rest-api/tests/fixtures/data/groups.js
  91. +57 −0 nomad-rest-api/tests/fixtures/data/racks.js
  92. +19 −1 nomad-rest-api/tests/fixtures/db.js
  93. +10 −7 nomad-rest-api/tests/groups.test.js
  94. +2 −2 nomad-rest-api/tests/instruments.test.js
  95. +4 −4 nomad-rest-api/tests/parameterSets.test.js
  96. +1 −1 nomad-rest-api/tests/submit.test.js
  97. +3 −3 nomad-rest-api/tests/users.test.js
  98. +65 −0 nomad-rest-api/utils/zipDataset.js
15 changes: 15 additions & 0 deletions .github/workflows/deploy-api.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
name: Deploy API
on: push
jobs:
test:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Install dependencies
working-directory: nomad-rest-api
run: npm ci
- name: Test
working-directory: nomad-rest-api
run: echo "Testing...."
# npm test
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
/datastore
/downloads
/env

2 changes: 1 addition & 1 deletion Dockerfile.api
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM node:18.16.1-slim
FROM node:20.11.0-slim

WORKDIR /app

4 changes: 2 additions & 2 deletions Dockerfile.serv
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM node:lts-bullseye-slim as frontend
FROM node:20.11.0-slim as frontend

WORKDIR /app

@@ -20,7 +20,7 @@ ENV VITE_DATASTORE_ON=true
RUN npm run build


FROM nginx:1.25.3-alpine
FROM nginx:mainline-alpine

COPY --from=frontend /app/dist /react-builds/frontend

4 changes: 2 additions & 2 deletions Dockerfile.serv-tls
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM node:lts-bullseye-slim as frontend
FROM node:20.11.0-slim as frontend

WORKDIR /app

@@ -18,7 +18,7 @@ ENV VITE_DATASTORE_ON=true

RUN npm run build

FROM nginx:1.25.3-alpine
FROM nginx:mainline-alpine

COPY --from=frontend /app/dist /react-builds/frontend

2 changes: 2 additions & 0 deletions docker-compose.yaml
Original file line number Diff line number Diff line change
@@ -16,6 +16,7 @@ services:
volumes:
- ./nomad-rest-api:/app
- ./datastore:/app/datastore
- ./downloads:/app/downloads
- /app/node_modules
depends_on:
- mongodb
@@ -29,6 +30,7 @@ services:
volumes:
- ./nomad-front-end/src:/app/src
- /app/node_modules
- ./downloads:/app/downloads
depends_on:
- backend

35 changes: 35 additions & 0 deletions env-example/backend-test.env
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
PORT=8080
MONGODB_URL='mongodb://mongodb:27017/nomad'
HOST='0.0.0.0'
#Frontend host url
FRONT_HOST_URL='http://localhost:3003'

#Password for automatically generated admin user
ADMIN_PASSWORD=''

#JWT expiration time in seconds. Set to 10h for development
JWT_EXPIRATION=36000

#Secret word for generating JWT
JWT_SECRET=''

EMAIL_SUFFIX=''

#SMTP configuration
SMTP_HOST=''
SMTP_PORT=587
SMTP_SECURE=false
SMTP_REQUIRE_TLS=true
SMTP_USER=''
SMTP_PASS=''
SMTP_SENDER=''

#Set true if NOMAD submission is used
SUBMIT_ON=true

#Set true if NOMAD datastore is used
DATASTORE_ON=true,
DATASTORE_PATH='/app/datastore'
#timeout for upload data route connection
DATA_UPLOAD_TIMEOUT=30000

1 change: 1 addition & 0 deletions env-example/backend.env
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
NODE_ENV='dev'
PORT=8080
MONGODB_URL='mongodb://mongodb:27017/nomad'
HOST='0.0.0.0'
6 changes: 5 additions & 1 deletion nginx.conf
Original file line number Diff line number Diff line change
@@ -69,7 +69,11 @@ http {
proxy_set_header Connection "upgrade";

proxy_pass http://api:8080/socket.io/;
}
}

location /downloads {
alias /app/downloads;
}



4 changes: 4 additions & 0 deletions nginx.conf-tls
Original file line number Diff line number Diff line change
@@ -82,6 +82,10 @@ http {
proxy_pass http://api:8080/socket.io/;
}

location /downloads {
alias /app/downloads;
}


error_page 404 /404.html;
location = /404.html {
2 changes: 1 addition & 1 deletion nomad-front-end/Dockerfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM node:lts-bullseye-slim
FROM node:20.11.0-slim

WORKDIR /app

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