@apollo-annotation/cli 0.1.10

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Files changed (81) hide show
  1. package/README.md +899 -0
  2. package/bin/dev.cmd +3 -0
  3. package/bin/dev.js +9 -0
  4. package/bin/run.cmd +3 -0
  5. package/bin/run.js +8 -0
  6. package/dist/Config.d.ts +43 -0
  7. package/dist/Config.js +233 -0
  8. package/dist/baseCommand.d.ts +21 -0
  9. package/dist/baseCommand.js +62 -0
  10. package/dist/commands/assembly/add-fasta.d.ts +15 -0
  11. package/dist/commands/assembly/add-fasta.js +98 -0
  12. package/dist/commands/assembly/add-gff.d.ts +16 -0
  13. package/dist/commands/assembly/add-gff.js +76 -0
  14. package/dist/commands/assembly/check.d.ts +15 -0
  15. package/dist/commands/assembly/check.js +148 -0
  16. package/dist/commands/assembly/delete.d.ts +14 -0
  17. package/dist/commands/assembly/delete.js +43 -0
  18. package/dist/commands/assembly/get.d.ts +9 -0
  19. package/dist/commands/assembly/get.js +33 -0
  20. package/dist/commands/assembly/get.test.d.ts +1 -0
  21. package/dist/commands/assembly/get.test.js +50 -0
  22. package/dist/commands/assembly/sequence.d.ts +16 -0
  23. package/dist/commands/assembly/sequence.js +117 -0
  24. package/dist/commands/change/get.d.ts +9 -0
  25. package/dist/commands/change/get.js +35 -0
  26. package/dist/commands/change/get.test.d.ts +1 -0
  27. package/dist/commands/change/get.test.js +22 -0
  28. package/dist/commands/config.d.ts +25 -0
  29. package/dist/commands/config.js +217 -0
  30. package/dist/commands/config.test.d.ts +1 -0
  31. package/dist/commands/config.test.js +188 -0
  32. package/dist/commands/feature/add-child.d.ts +17 -0
  33. package/dist/commands/feature/add-child.js +120 -0
  34. package/dist/commands/feature/check.d.ts +14 -0
  35. package/dist/commands/feature/check.js +97 -0
  36. package/dist/commands/feature/copy.d.ts +17 -0
  37. package/dist/commands/feature/copy.js +110 -0
  38. package/dist/commands/feature/delete.d.ts +11 -0
  39. package/dist/commands/feature/delete.js +99 -0
  40. package/dist/commands/feature/edit-attribute.d.ts +16 -0
  41. package/dist/commands/feature/edit-attribute.js +100 -0
  42. package/dist/commands/feature/edit-coords.d.ts +15 -0
  43. package/dist/commands/feature/edit-coords.js +109 -0
  44. package/dist/commands/feature/edit-type.d.ts +10 -0
  45. package/dist/commands/feature/edit-type.js +70 -0
  46. package/dist/commands/feature/edit.d.ts +13 -0
  47. package/dist/commands/feature/edit.js +81 -0
  48. package/dist/commands/feature/get-id.d.ts +14 -0
  49. package/dist/commands/feature/get-id.js +56 -0
  50. package/dist/commands/feature/get.d.ts +16 -0
  51. package/dist/commands/feature/get.js +87 -0
  52. package/dist/commands/feature/import.d.ts +15 -0
  53. package/dist/commands/feature/import.js +83 -0
  54. package/dist/commands/feature/search.d.ts +14 -0
  55. package/dist/commands/feature/search.js +91 -0
  56. package/dist/commands/login.d.ts +21 -0
  57. package/dist/commands/login.js +206 -0
  58. package/dist/commands/login.test.d.ts +1 -0
  59. package/dist/commands/login.test.js +52 -0
  60. package/dist/commands/logout.d.ts +10 -0
  61. package/dist/commands/logout.js +41 -0
  62. package/dist/commands/logout.test.d.ts +1 -0
  63. package/dist/commands/logout.test.js +67 -0
  64. package/dist/commands/refseq/get.d.ts +13 -0
  65. package/dist/commands/refseq/get.js +44 -0
  66. package/dist/commands/status.d.ts +6 -0
  67. package/dist/commands/status.js +38 -0
  68. package/dist/commands/status.test.d.ts +1 -0
  69. package/dist/commands/status.test.js +54 -0
  70. package/dist/commands/user/get.d.ts +14 -0
  71. package/dist/commands/user/get.js +46 -0
  72. package/dist/commands/user/get.test.d.ts +1 -0
  73. package/dist/commands/user/get.test.js +23 -0
  74. package/dist/index.d.ts +1 -0
  75. package/dist/index.js +1 -0
  76. package/dist/test/fixtures.d.ts +7 -0
  77. package/dist/test/fixtures.js +40 -0
  78. package/dist/utils.d.ts +54 -0
  79. package/dist/utils.js +373 -0
  80. package/oclif.manifest.json +1632 -0
  81. package/package.json +100 -0
package/package.json ADDED
@@ -0,0 +1,100 @@
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+ {
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+ "name": "@apollo-annotation/cli",
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+ "description": "Command line interface for the Apollo annotation server",
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+ "version": "0.1.10",
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+ "author": "Apollo Team",
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+ "repository": {
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+ "type": "git",
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+ "url": "https://github.com/GMOD/Apollo3.git",
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+ "directory": "packages/apollo-cli"
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+ },
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+ "bin": {
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+ "apollo": "./bin/run.js"
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+ },
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+ "type": "module",
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+ "main": "",
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+ "types": "dist/index.d.ts",
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+ "exports": "./dist/index.js",
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+ "engines": {
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+ "node": ">=18.0.0"
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+ },
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+ "files": [
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+ "/bin",
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+ "/dist",
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+ "/oclif.manifest.json"
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+ ],
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+ "scripts": {
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+ "build": "shx rm -rf dist && tsc -b",
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+ "dev": "tsx bin/dev.js",
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+ "postpack": "shx rm -f oclif.manifest.json",
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+ "posttest": "yarn lint",
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+ "prepack": "yarn build && oclif manifest && oclif readme",
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+ "prepare": "yarn build",
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+ "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
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+ "test:ci": "nyc mocha 'src/**/*.test.ts'",
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+ "version": "oclif readme && git add README.md"
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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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+ "joi": "^17.7.0",
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+ "open": "^10.1.0",
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+ "tslib": "^2.3.1",
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+ "undici": "^6.7.0",
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+ "yaml": "^2.3.4"
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+ },
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+ "devDependencies": {
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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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+ "@types/chai": "^4",
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+ "@types/inquirer": "^9.0.7",
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+ "@types/mocha": "^10",
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+ "@types/node": "^18.14.2",
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+ "babel-plugin-istanbul": "^6.1.1",
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+ "mocha": "^10.2.0",
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+ "nyc": "^15.1.0",
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+ "oclif": "^4.4.2",
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+ "shx": "^0.3.3",
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+ "ts-node": "^10.3.0",
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+ "tsx": "^4.6.2",
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+ "typescript": "^5.1.6"
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+ },
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+ "oclif": {
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+ "helpOptions": {
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+ "flagSortOrder": "none"
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+ },
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+ "bin": "apollo",
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+ "dirname": "apollo-cli",
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+ "commands": "./dist/commands",
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+ "plugins": [
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+ "@oclif/plugin-help"
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+ ],
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+ "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/packages/apollo-cli/<%- commandPath %>",
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+ "topicSeparator": " ",
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+ "topics": {
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+ "assembly": {
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+ "description": "Commands to handle assemblies"
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+ },
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+ "change": {
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+ "description": "Commands to handle the log of changes made to the database"
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+ },
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+ "feature": {
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+ "description": "Commands to handle features"
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+ },
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+ "refseq": {
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+ "description": "Commands to handle reference sequences"
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+ },
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+ "user": {
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+ "description": "Commands to handle users"
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+ }
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+ }
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+ },
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+ "publishConfig": {
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+ "access": "public"
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+ }
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+ }