@openneuro/server 4.20.5 → 4.20.6-alpha.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (185) hide show
  1. package/package.json +4 -6
  2. package/src/__mocks__/{config.js → config.ts} +5 -5
  3. package/src/app.ts +32 -31
  4. package/src/cache/item.ts +6 -7
  5. package/src/cache/types.ts +8 -8
  6. package/src/{config.js → config.ts} +6 -6
  7. package/src/datalad/__tests__/changelog.spec.ts +83 -0
  8. package/src/datalad/__tests__/dataset.spec.ts +109 -0
  9. package/src/datalad/__tests__/description.spec.ts +141 -0
  10. package/src/datalad/__tests__/files.spec.ts +77 -0
  11. package/src/datalad/__tests__/pagination.spec.ts +136 -0
  12. package/src/datalad/__tests__/{snapshots.spec.js → snapshots.spec.ts} +17 -17
  13. package/src/datalad/{analytics.js → analytics.ts} +4 -4
  14. package/src/datalad/{changelog.js → changelog.ts} +17 -14
  15. package/src/datalad/{dataset.js → dataset.ts} +95 -93
  16. package/src/datalad/{description.js → description.ts} +37 -37
  17. package/src/datalad/draft.ts +38 -0
  18. package/src/datalad/files.ts +26 -20
  19. package/src/datalad/{pagination.js → pagination.ts} +47 -47
  20. package/src/datalad/{readme.js → readme.ts} +13 -11
  21. package/src/datalad/{reexporter.js → reexporter.ts} +4 -4
  22. package/src/datalad/{snapshots.js → snapshots.ts} +56 -62
  23. package/src/datalad/{upload.js → upload.ts} +7 -5
  24. package/src/elasticsearch/elastic-client.ts +11 -0
  25. package/src/elasticsearch/reindex-dataset.ts +7 -7
  26. package/src/graphql/__tests__/__snapshots__/permissions.spec.ts.snap +5 -0
  27. package/src/graphql/__tests__/{comment.spec.js → comment.spec.ts} +17 -17
  28. package/src/graphql/__tests__/permissions.spec.ts +113 -0
  29. package/src/graphql/{permissions.js → permissions.ts} +14 -14
  30. package/src/graphql/resolvers/__tests__/brainlife.spec.ts +11 -11
  31. package/src/graphql/resolvers/__tests__/{dataset-search.spec.js → dataset-search.spec.ts} +25 -23
  32. package/src/graphql/resolvers/__tests__/dataset.spec.ts +175 -0
  33. package/src/graphql/resolvers/__tests__/derivatives.spec.ts +19 -19
  34. package/src/graphql/resolvers/__tests__/importRemoteDataset.spec.ts +20 -20
  35. package/src/graphql/resolvers/__tests__/permssions.spec.ts +35 -0
  36. package/src/graphql/resolvers/__tests__/snapshots.spec.ts +59 -0
  37. package/src/graphql/resolvers/__tests__/user.spec.ts +18 -0
  38. package/src/graphql/resolvers/brainlife.ts +4 -4
  39. package/src/graphql/resolvers/cache.ts +4 -4
  40. package/src/graphql/resolvers/{comment.js → comment.ts} +16 -16
  41. package/src/graphql/resolvers/{dataset-search.js → dataset-search.ts} +45 -43
  42. package/src/graphql/resolvers/{dataset.js → dataset.ts} +38 -52
  43. package/src/graphql/resolvers/datasetType.ts +3 -3
  44. package/src/graphql/resolvers/derivatives.ts +11 -11
  45. package/src/graphql/resolvers/description.ts +18 -0
  46. package/src/graphql/resolvers/{draft.js → draft.ts} +13 -13
  47. package/src/graphql/resolvers/{flaggedFiles.js → flaggedFiles.ts} +4 -4
  48. package/src/graphql/resolvers/{follow.js → follow.ts} +1 -1
  49. package/src/graphql/resolvers/git.ts +3 -3
  50. package/src/graphql/resolvers/history.ts +13 -0
  51. package/src/graphql/resolvers/importRemoteDataset.ts +12 -11
  52. package/src/graphql/resolvers/index.ts +25 -0
  53. package/src/graphql/resolvers/{issues.js → issues.ts} +9 -9
  54. package/src/graphql/resolvers/metadata.ts +8 -8
  55. package/src/graphql/resolvers/{mutation.js → mutation.ts} +26 -26
  56. package/src/graphql/resolvers/{newsletter.js → newsletter.ts} +2 -2
  57. package/src/graphql/resolvers/permissions.ts +15 -21
  58. package/src/graphql/resolvers/publish.ts +17 -0
  59. package/src/graphql/resolvers/query.ts +21 -0
  60. package/src/graphql/resolvers/{readme.js → readme.ts} +3 -3
  61. package/src/graphql/resolvers/{reexporter.js → reexporter.ts} +2 -2
  62. package/src/graphql/resolvers/relation.ts +5 -5
  63. package/src/graphql/resolvers/{reset.js → reset.ts} +2 -2
  64. package/src/graphql/resolvers/reviewer.ts +4 -4
  65. package/src/graphql/resolvers/{snapshots.js → snapshots.ts} +49 -49
  66. package/src/graphql/resolvers/{stars.js → stars.ts} +1 -1
  67. package/src/graphql/resolvers/summary.ts +3 -3
  68. package/src/graphql/resolvers/{upload.js → upload.ts} +5 -5
  69. package/src/graphql/resolvers/{user.js → user.ts} +16 -18
  70. package/src/graphql/resolvers/{validation.js → validation.ts} +12 -14
  71. package/src/graphql/{schema.js → schema.ts} +4 -6
  72. package/src/graphql/utils/{file.js → file.ts} +2 -2
  73. package/src/handlers/{comments.js → comments.ts} +11 -11
  74. package/src/handlers/{config.js → config.ts} +1 -1
  75. package/src/handlers/{datalad.js → datalad.ts} +22 -22
  76. package/src/handlers/{doi.js → doi.ts} +6 -6
  77. package/src/handlers/reviewer.ts +6 -6
  78. package/src/handlers/{sitemap.js → sitemap.ts} +19 -19
  79. package/src/handlers/stars.ts +11 -10
  80. package/src/handlers/{subscriptions.js → subscriptions.ts} +17 -16
  81. package/src/handlers/{users.js → users.ts} +3 -3
  82. package/src/libs/__tests__/apikey.spec.ts +25 -0
  83. package/src/libs/__tests__/datalad-service.spec.ts +27 -0
  84. package/src/libs/__tests__/{dataset.spec.js → dataset.spec.ts} +9 -9
  85. package/src/libs/{apikey.js → apikey.ts} +5 -5
  86. package/src/libs/authentication/__tests__/jwt.spec.ts +59 -0
  87. package/src/libs/authentication/{crypto.js → crypto.ts} +16 -16
  88. package/src/libs/authentication/google.ts +18 -0
  89. package/src/libs/authentication/jwt.ts +40 -33
  90. package/src/libs/authentication/{orcid.js → orcid.ts} +11 -11
  91. package/src/libs/authentication/{passport.js → passport.ts} +45 -30
  92. package/src/libs/authentication/{states.js → states.ts} +17 -20
  93. package/src/libs/{counter.js → counter.ts} +1 -1
  94. package/src/libs/{datalad-service.js → datalad-service.ts} +4 -4
  95. package/src/libs/dataset.ts +9 -0
  96. package/src/libs/doi/__tests__/__snapshots__/doi.spec.ts.snap +17 -0
  97. package/src/libs/doi/__tests__/doi.spec.ts +25 -0
  98. package/src/libs/doi/__tests__/normalize.spec.ts +19 -19
  99. package/src/libs/doi/{index.js → index.ts} +27 -21
  100. package/src/libs/doi/normalize.ts +2 -2
  101. package/src/libs/email/__tests__/index.spec.ts +14 -14
  102. package/src/libs/email/index.ts +4 -4
  103. package/src/libs/email/templates/__tests__/comment-created.spec.ts +12 -12
  104. package/src/libs/email/templates/__tests__/dataset-deleted.spec.ts +6 -6
  105. package/src/libs/email/templates/__tests__/owner-unsubscribed.spec.ts +6 -6
  106. package/src/libs/email/templates/__tests__/snapshot-created.spec.ts +9 -9
  107. package/src/libs/email/templates/__tests__/snapshot-reminder.spec.ts +7 -7
  108. package/src/libs/email/templates/comment-created.ts +2 -1
  109. package/src/libs/email/templates/dataset-deleted.ts +2 -1
  110. package/src/libs/email/templates/dataset-import-failed.ts +2 -1
  111. package/src/libs/email/templates/dataset-imported.ts +2 -1
  112. package/src/libs/email/templates/owner-unsubscribed.ts +2 -1
  113. package/src/libs/email/templates/snapshot-created.ts +2 -1
  114. package/src/libs/email/templates/snapshot-reminder.ts +2 -1
  115. package/src/libs/{notifications.js → notifications.ts} +100 -113
  116. package/src/libs/{orcid.js → orcid.ts} +20 -20
  117. package/src/libs/{redis.js → redis.ts} +6 -6
  118. package/src/models/__tests__/ingestDataset.spec.ts +15 -15
  119. package/src/models/analytics.ts +2 -2
  120. package/src/models/badAnnexObject.ts +6 -6
  121. package/src/models/comment.ts +10 -10
  122. package/src/models/counter.ts +2 -2
  123. package/src/models/dataset.ts +16 -16
  124. package/src/models/deletion.ts +3 -3
  125. package/src/models/deprecatedSnapshot.ts +2 -2
  126. package/src/models/doi.ts +2 -2
  127. package/src/models/file.ts +2 -2
  128. package/src/models/ingestDataset.ts +4 -4
  129. package/src/models/issue.ts +2 -2
  130. package/src/models/key.ts +2 -2
  131. package/src/models/mailgunIdentifier.ts +2 -2
  132. package/src/models/metadata.ts +3 -3
  133. package/src/models/newsletter.ts +3 -3
  134. package/src/models/notification.ts +2 -2
  135. package/src/models/permission.ts +4 -4
  136. package/src/models/reviewer.ts +7 -7
  137. package/src/models/snapshot.ts +2 -2
  138. package/src/models/stars.ts +6 -6
  139. package/src/models/subscription.ts +2 -2
  140. package/src/models/summary.ts +2 -2
  141. package/src/models/upload.ts +3 -3
  142. package/src/models/user.ts +4 -4
  143. package/src/{routes.js → routes.ts} +62 -62
  144. package/src/server.ts +9 -9
  145. package/src/utils/__tests__/datasetOrSnapshot.spec.ts +25 -25
  146. package/src/utils/__tests__/validateUrl.spec.ts +10 -10
  147. package/src/utils/datasetOrSnapshot.ts +2 -2
  148. package/src/utils/validateUrl.ts +1 -1
  149. package/src/datalad/__tests__/changelog.spec.js +0 -82
  150. package/src/datalad/__tests__/dataset.spec.js +0 -109
  151. package/src/datalad/__tests__/description.spec.js +0 -137
  152. package/src/datalad/__tests__/files.spec.js +0 -75
  153. package/src/datalad/__tests__/pagination.spec.js +0 -136
  154. package/src/datalad/draft.js +0 -37
  155. package/src/elasticsearch/elastic-client.js +0 -11
  156. package/src/graphql/__tests__/permissions.spec.js +0 -107
  157. package/src/graphql/pubsub.js +0 -5
  158. package/src/graphql/resolvers/__tests__/dataset.spec.js +0 -175
  159. package/src/graphql/resolvers/__tests__/permssions.spec.js +0 -34
  160. package/src/graphql/resolvers/__tests__/snapshots.spec.js +0 -58
  161. package/src/graphql/resolvers/__tests__/user.spec.js +0 -17
  162. package/src/graphql/resolvers/description.js +0 -29
  163. package/src/graphql/resolvers/history.js +0 -11
  164. package/src/graphql/resolvers/index.js +0 -25
  165. package/src/graphql/resolvers/publish.js +0 -17
  166. package/src/graphql/resolvers/query.js +0 -21
  167. package/src/graphql/resolvers/subscriptions.js +0 -81
  168. package/src/graphql/utils/publish-draft-update.js +0 -13
  169. package/src/libs/__tests__/apikey.spec.js +0 -24
  170. package/src/libs/__tests__/datalad-service.spec.js +0 -26
  171. package/src/libs/authentication/__tests__/jwt.spec.js +0 -23
  172. package/src/libs/authentication/globus.js +0 -11
  173. package/src/libs/authentication/google.js +0 -19
  174. package/src/libs/bidsId.js +0 -68
  175. package/src/libs/dataset.js +0 -9
  176. package/src/libs/doi/__tests__/doi.spec.js +0 -24
  177. package/src/libs/redis-pubsub.js +0 -5
  178. package/src/libs/request.js +0 -155
  179. package/src/libs/scitran.js +0 -25
  180. package/src/libs/subscription-server.js +0 -20
  181. package/src/libs/testing-utils.js +0 -17
  182. package/src/persistent/datasets/.gitignore +0 -3
  183. package/src/persistent/temp/.gitignore +0 -3
  184. /package/src/libs/__mocks__/{notifications.js → notifications.ts} +0 -0
  185. /package/src/libs/authentication/{verifyUser.js → verifyUser.ts} +0 -0
package/src/libs/scitran.js DELETED
@@ -1,25 +0,0 @@
1
- import User from '../models/user'
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-
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- /**
4
- * Scitran
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- *
6
- * A library for interactions with the
7
- * scitran API.
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- */
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- export default {
10
- /**
11
- * Get User
12
- */
13
- getUser(userId, callback) {
14
- // Updated to use internal authentication
15
- User.findOne({ id: userId })
16
- .then(user => {
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- // Mock the SciTran response
18
- const userResponse = { body: { ...user, _id: user.id } }
19
- callback(null, { body: userResponse })
20
- })
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- .catch(err => {
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- callback(err)
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- })
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- },
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- }
package/src/libs/subscription-server.js DELETED
@@ -1,20 +0,0 @@
1
- /*import { execute, subscribe } from 'graphql'
2
- import { SubscriptionServer } from 'subscriptions-transport-ws'
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- import schema from '../graphql/schema.js'
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-
5
- const subscriptionServerFactory = httpserver =>
6
- new SubscriptionServer(
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- {
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- execute,
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- subscribe,
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- schema,
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- keepAlive: 30000,
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- },
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- {
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- server: httpserver,
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- path: '/graphql-subscriptions',
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- },
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- )
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-
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- export default subscriptionServerFactory
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- */
package/src/libs/testing-utils.js DELETED
@@ -1,17 +0,0 @@
1
- import http from 'http'
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-
3
- export default {
4
- ok(res) {
5
- if (res.status !== 200) {
6
- const b = http.STATUS_CODES[res.status]
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- return new Error(
8
- 'expected 200, got ' +
9
- res.status +
10
- ' "' +
11
- b +
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- '" with message: ' +
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- res.text,
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- )
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- }
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- },
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- }
package/src/persistent/datasets/.gitignore DELETED
@@ -1,3 +0,0 @@
1
- # Ignore everything in this directory except this file
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- *
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- !.gitignore
package/src/persistent/temp/.gitignore DELETED
@@ -1,3 +0,0 @@
1
- # Ignore everything in this directory except this file
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- *
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- !.gitignore