@apollo-annotation/cli 1.1.1 → 1.1.2

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 (161) hide show
  1. package/README.md +133 -87
  2. package/dist/ApolloConf.d.ts.map +1 -1
  3. package/dist/ApolloConf.js +14 -3
  4. package/dist/ApolloConf.js.map +1 -1
  5. package/dist/baseCommand.d.ts +37 -1
  6. package/dist/baseCommand.d.ts.map +1 -1
  7. package/dist/baseCommand.js +226 -9
  8. package/dist/baseCommand.js.map +1 -1
  9. package/dist/commands/assembly/add-from-fasta.d.ts +8 -8
  10. package/dist/commands/assembly/add-from-fasta.d.ts.map +1 -1
  11. package/dist/commands/assembly/add-from-fasta.js +20 -16
  12. package/dist/commands/assembly/add-from-fasta.js.map +1 -1
  13. package/dist/commands/assembly/add-from-gff.d.ts +5 -5
  14. package/dist/commands/assembly/add-from-gff.d.ts.map +1 -1
  15. package/dist/commands/assembly/add-from-gff.js +2 -4
  16. package/dist/commands/assembly/add-from-gff.js.map +1 -1
  17. package/dist/commands/assembly/check.d.ts +3 -3
  18. package/dist/commands/assembly/check.d.ts.map +1 -1
  19. package/dist/commands/assembly/check.js +10 -48
  20. package/dist/commands/assembly/check.js.map +1 -1
  21. package/dist/commands/assembly/delete.d.ts +2 -2
  22. package/dist/commands/assembly/delete.d.ts.map +1 -1
  23. package/dist/commands/assembly/delete.js +4 -5
  24. package/dist/commands/assembly/delete.js.map +1 -1
  25. package/dist/commands/assembly/get.d.ts +1 -1
  26. package/dist/commands/assembly/get.d.ts.map +1 -1
  27. package/dist/commands/assembly/get.js +3 -5
  28. package/dist/commands/assembly/get.js.map +1 -1
  29. package/dist/commands/assembly/sequence.d.ts +4 -4
  30. package/dist/commands/assembly/sequence.d.ts.map +1 -1
  31. package/dist/commands/assembly/sequence.js +9 -29
  32. package/dist/commands/assembly/sequence.js.map +1 -1
  33. package/dist/commands/change/get.d.ts +1 -1
  34. package/dist/commands/change/get.d.ts.map +1 -1
  35. package/dist/commands/change/get.js +3 -5
  36. package/dist/commands/change/get.js.map +1 -1
  37. package/dist/commands/config.d.ts +4 -4
  38. package/dist/commands/config.d.ts.map +1 -1
  39. package/dist/commands/config.js +12 -19
  40. package/dist/commands/config.js.map +1 -1
  41. package/dist/commands/export/gff3.d.ts +2 -2
  42. package/dist/commands/export/gff3.d.ts.map +1 -1
  43. package/dist/commands/export/gff3.js +4 -26
  44. package/dist/commands/export/gff3.js.map +1 -1
  45. package/dist/commands/feature/add-child.d.ts +4 -4
  46. package/dist/commands/feature/add-child.d.ts.map +1 -1
  47. package/dist/commands/feature/add-child.js +6 -32
  48. package/dist/commands/feature/add-child.js.map +1 -1
  49. package/dist/commands/feature/add.d.ts +7 -18
  50. package/dist/commands/feature/add.d.ts.map +1 -1
  51. package/dist/commands/feature/add.js +4 -57
  52. package/dist/commands/feature/add.js.map +1 -1
  53. package/dist/commands/feature/check.d.ts +3 -2
  54. package/dist/commands/feature/check.d.ts.map +1 -1
  55. package/dist/commands/feature/check.js +16 -35
  56. package/dist/commands/feature/check.js.map +1 -1
  57. package/dist/commands/feature/copy.d.ts +4 -4
  58. package/dist/commands/feature/copy.d.ts.map +1 -1
  59. package/dist/commands/feature/copy.js +6 -32
  60. package/dist/commands/feature/copy.js.map +1 -1
  61. package/dist/commands/feature/delete.d.ts +4 -3
  62. package/dist/commands/feature/delete.d.ts.map +1 -1
  63. package/dist/commands/feature/delete.js +25 -46
  64. package/dist/commands/feature/delete.js.map +1 -1
  65. package/dist/commands/feature/edit-attribute.d.ts +4 -4
  66. package/dist/commands/feature/edit-attribute.d.ts.map +1 -1
  67. package/dist/commands/feature/edit-attribute.js +4 -24
  68. package/dist/commands/feature/edit-attribute.js.map +1 -1
  69. package/dist/commands/feature/edit-coords.d.ts +3 -3
  70. package/dist/commands/feature/edit-coords.d.ts.map +1 -1
  71. package/dist/commands/feature/edit-coords.js +4 -24
  72. package/dist/commands/feature/edit-coords.js.map +1 -1
  73. package/dist/commands/feature/edit-type.d.ts +2 -2
  74. package/dist/commands/feature/edit-type.d.ts.map +1 -1
  75. package/dist/commands/feature/edit-type.js +4 -24
  76. package/dist/commands/feature/edit-type.js.map +1 -1
  77. package/dist/commands/feature/edit.d.ts +1 -1
  78. package/dist/commands/feature/edit.d.ts.map +1 -1
  79. package/dist/commands/feature/edit.js +2 -18
  80. package/dist/commands/feature/edit.js.map +1 -1
  81. package/dist/commands/feature/get-id.d.ts +1 -1
  82. package/dist/commands/feature/get-id.d.ts.map +1 -1
  83. package/dist/commands/feature/get-id.js +5 -15
  84. package/dist/commands/feature/get-id.js.map +1 -1
  85. package/dist/commands/feature/get-indexed-id.d.ts +3 -3
  86. package/dist/commands/feature/get-indexed-id.d.ts.map +1 -1
  87. package/dist/commands/feature/get-indexed-id.js +3 -20
  88. package/dist/commands/feature/get-indexed-id.js.map +1 -1
  89. package/dist/commands/feature/get.d.ts +4 -4
  90. package/dist/commands/feature/get.d.ts.map +1 -1
  91. package/dist/commands/feature/get.js +4 -21
  92. package/dist/commands/feature/get.js.map +1 -1
  93. package/dist/commands/feature/import.d.ts +4 -4
  94. package/dist/commands/feature/import.d.ts.map +1 -1
  95. package/dist/commands/feature/import.js +4 -21
  96. package/dist/commands/feature/import.js.map +1 -1
  97. package/dist/commands/feature/search.d.ts +2 -2
  98. package/dist/commands/feature/search.d.ts.map +1 -1
  99. package/dist/commands/feature/search.js +9 -28
  100. package/dist/commands/feature/search.js.map +1 -1
  101. package/dist/commands/file/delete.d.ts +2 -1
  102. package/dist/commands/file/delete.d.ts.map +1 -1
  103. package/dist/commands/file/delete.js +12 -21
  104. package/dist/commands/file/delete.js.map +1 -1
  105. package/dist/commands/file/download.d.ts +2 -2
  106. package/dist/commands/file/download.d.ts.map +1 -1
  107. package/dist/commands/file/download.js +3 -7
  108. package/dist/commands/file/download.js.map +1 -1
  109. package/dist/commands/file/get.d.ts +1 -1
  110. package/dist/commands/file/get.d.ts.map +1 -1
  111. package/dist/commands/file/get.js +2 -4
  112. package/dist/commands/file/get.js.map +1 -1
  113. package/dist/commands/file/upload.d.ts +4 -4
  114. package/dist/commands/file/upload.d.ts.map +1 -1
  115. package/dist/commands/file/upload.js +3 -7
  116. package/dist/commands/file/upload.js.map +1 -1
  117. package/dist/commands/jbrowse/desktop.d.ts +4 -4
  118. package/dist/commands/jbrowse/get-config.d.ts.map +1 -1
  119. package/dist/commands/jbrowse/get-config.js +1 -7
  120. package/dist/commands/jbrowse/get-config.js.map +1 -1
  121. package/dist/commands/jbrowse/set-config.d.ts +1 -1
  122. package/dist/commands/jbrowse/set-config.d.ts.map +1 -1
  123. package/dist/commands/jbrowse/set-config.js +1 -19
  124. package/dist/commands/jbrowse/set-config.js.map +1 -1
  125. package/dist/commands/login.d.ts +5 -5
  126. package/dist/commands/login.d.ts.map +1 -1
  127. package/dist/commands/login.js +8 -7
  128. package/dist/commands/login.js.map +1 -1
  129. package/dist/commands/logout.d.ts.map +1 -1
  130. package/dist/commands/logout.js +2 -6
  131. package/dist/commands/logout.js.map +1 -1
  132. package/dist/commands/refseq/add-alias.d.ts +2 -2
  133. package/dist/commands/refseq/add-alias.d.ts.map +1 -1
  134. package/dist/commands/refseq/add-alias.js +2 -21
  135. package/dist/commands/refseq/add-alias.js.map +1 -1
  136. package/dist/commands/refseq/get.d.ts +1 -1
  137. package/dist/commands/refseq/get.d.ts.map +1 -1
  138. package/dist/commands/refseq/get.js +3 -5
  139. package/dist/commands/refseq/get.js.map +1 -1
  140. package/dist/commands/status.d.ts.map +1 -1
  141. package/dist/commands/status.js +2 -6
  142. package/dist/commands/status.js.map +1 -1
  143. package/dist/commands/user/get.d.ts +2 -2
  144. package/dist/commands/user/get.d.ts.map +1 -1
  145. package/dist/commands/user/get.js +1 -4
  146. package/dist/commands/user/get.js.map +1 -1
  147. package/dist/fileCommand.d.ts +2 -1
  148. package/dist/fileCommand.d.ts.map +1 -1
  149. package/dist/fileCommand.js +18 -11
  150. package/dist/fileCommand.js.map +1 -1
  151. package/dist/test/test.js +154 -30
  152. package/dist/test/test.js.map +1 -1
  153. package/dist/test/utils.d.ts.map +1 -1
  154. package/dist/test/utils.js +15 -2
  155. package/dist/test/utils.js.map +1 -1
  156. package/dist/utils.d.ts +1 -21
  157. package/dist/utils.d.ts.map +1 -1
  158. package/dist/utils.js +1 -234
  159. package/dist/utils.js.map +1 -1
  160. package/oclif.manifest.json +820 -532
  161. package/package.json +14 -15
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@apollo-annotation/cli",
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- "version": "1.1.1",
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+ "version": "1.1.2",
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  "description": "Command line interface for the Apollo annotation server",
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  "repository": {
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  "type": "git",
@@ -70,37 +70,36 @@
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  }
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  },
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  "dependencies": {
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- "@inquirer/input": "^1.2.14",
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- "@inquirer/password": "^1.1.14",
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- "@inquirer/select": "^1.3.1",
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- "@oclif/core": "^3.18.2",
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- "@oclif/plugin-help": "^6.0.8",
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- "bson": "^6.3.0",
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+ "@inquirer/prompts": "^8.5.2",
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+ "@oclif/core": "^4.11.14",
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+ "@oclif/plugin-help": "^6.2.53",
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+ "bson": "^7.3.1",
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  "cli-progress": "^3.12.0",
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- "conf": "^12.0.0",
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+ "conf": "^15.1.0",
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  "joi": "^17.7.0",
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+ "ms": "^2.1.3",
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  "nanoid": "^4.0.2",
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- "open": "^10.1.0",
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+ "open": "^11.0.0",
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  "tslib": "^2.3.1",
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- "undici": "^6.7.0",
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+ "undici": "^8.7.0",
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  "yaml": "^2.3.4"
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  },
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  "devDependencies": {
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- "@apollo-annotation/mst": "^1.1.1",
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- "@apollo-annotation/shared": "^1.1.1",
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+ "@apollo-annotation/mst": "^1.1.2",
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+ "@apollo-annotation/shared": "^1.1.2",
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  "@istanbuljs/esm-loader-hook": "^0.2.0",
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  "@istanbuljs/nyc-config-typescript": "^1.0.2",
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- "@oclif/test": "^3.1.3",
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+ "@oclif/test": "^4.1.20",
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  "@types/chai": "^4.3.19",
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  "@types/cli-progress": "^3",
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  "@types/cross-spawn": "^6.0.6",
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- "@types/inquirer": "^9.0.7",
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+ "@types/ms": "^2",
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  "@types/node": "^24.10.9",
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  "babel-plugin-istanbul": "^6.1.1",
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  "cross-spawn": "^7.0.3",
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  "mongodb": "^4.7.0",
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  "nyc": "^15.1.0",
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- "oclif": "^4.4.2",
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+ "oclif": "^4.23.27",
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  "prettier": "^3.3.2",
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  "react-dom": "^18.2.0",
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  "rxjs": "^7.4.0",