Merge pull request #223 from lifeomic/PHC-3861-add-genomic-ingestion-commands

feat: PHC-3861 add genomic ingestion commands

Author: cluebbehusen

CHANGELOG.md

@@ -5,6 +5,32 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [13.9.0] - 2023-01-04
+
+### Added
+- Added a `lo genomics ingestions` command set with the following commands
+  - `lo genomics ingestions list` Lists genomic ingestions for a project
+  - `lo genomics ingestions get` Gets a genomic ingestions
+  - `lo genomics ingestions create-foundation` Creates a Foundation ingestion
+  - `lo genomics ingestions create-caris` Creates a Caris ingestion
+  - `lo genomics ingestions create-foundation-bam` Creates a Foundation BAM ingestion
+  - `lo genomics ingestions create-caris-bam` Creates a Caris BAM ingestion
+
+## [13.8.1] - 2022-07-25
+
+### Fixed
+- Added `maxBodyLength` for file uploads
+
+## [13.8.0] - 2022-05-24
+
+### Changed
+- `lo surveys export-responses` now supports an optional `query` parameter
+
+## [13.7.0] - 2022-04-06
+
+### Changed
+- Updated how project is published
+
 ## [13.6.0] - 2021-10-06
 
 ### Changed
@@ -891,6 +917,10 @@ and `create-nantomics-vcf-import`
 
 - Replaced the `defaults` command with a `setup` command
 
+[13.9.0]: https://github.com/lifeomic/cli/compare/v13.8.1..v13.9.0
+[13.8.1]: https://github.com/lifeomic/cli/compare/v13.8.0..v13.8.1
+[13.8.0]: https://github.com/lifeomic/cli/compare/v13.7.0..v13.8.0
+[13.7.0]: https://github.com/lifeomic/cli/compare/v13.6.0..v13.7.0
 [13.6.0]: https://github.com/lifeomic/cli/compare/v13.5.0..v13.6.0
 [13.5.0]: https://github.com/lifeomic/cli/compare/v13.4.0..v13.5.0
 [13.4.0]: https://github.com/lifeomic/cli/compare/v13.3.0..v13.4.0

lib/cmds/genomics_cmds/ingestions.js

@@ -0,0 +1,10 @@
+'use strict';
+
+const options = require('../../common-yargs');
+
+exports.command = 'ingestions <command>';
+exports.desc = 'Perform operations on genomic ingestions.';
+exports.builder = yargs => {
+  return options(yargs.commandDir('ingestions_cmds'));
+};
+exports.handler = function (argv) {};

lib/cmds/genomics_cmds/ingestions_cmds/create-caris-bam.js

@@ -0,0 +1,36 @@
+'use strict';
+
+const { post } = require('../../../api');
+const print = require('../../../print');
+
+exports.command = 'create-caris-bam <projectId> <bamFileId>';
+exports.desc = 'Create Caris BAM ingestion for <bamFileId> in <projectId>';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The project ID.',
+    type: 'string'
+  }).positional('bamFileId', {
+    describe: 'The ID of the BAM file.',
+    type: 'string'
+  }).option('succeededEmail', {
+    describe: 'An email address to notify if the ingestion succeeds',
+    type: 'string'
+  }).option('failedEmail', {
+    describe: 'An email address to notify if the ingestion fails',
+    type: 'string'
+  });
+};
+
+exports.handler = async argv => {
+  const response = await post(argv, `/v1/genomic-ingestion/projects/${argv.projectId}/ingestions`, {
+    ingestionType: 'CarisBam',
+    inputFiles: {
+      bam: argv.bamFileId
+    },
+    notificationConfig: {
+      succeededEmail: argv.succeededEmail,
+      failedEmail: argv.failedEmail
+    }
+  });
+  print(response.data, argv);
+};

lib/cmds/genomics_cmds/ingestions_cmds/create-caris.js

@@ -0,0 +1,36 @@
+'use strict';
+
+const { post } = require('../../../api');
+const print = require('../../../print');
+
+exports.command = 'create-caris <projectId> <tarFileId>';
+exports.desc = 'Create Caris ingestion for <tarFileId> in <projectId>';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The project ID.',
+    type: 'string'
+  }).positional('tarFileId', {
+    describe: 'The ID of the TAR file.',
+    type: 'string'
+  }).option('succeededEmail', {
+    describe: 'An email address to notify if the ingestion succeeds',
+    type: 'string'
+  }).option('failedEmail', {
+    describe: 'An email address to notify if the ingestion fails',
+    type: 'string'
+  });
+};
+
+exports.handler = async argv => {
+  const response = await post(argv, `/v1/genomic-ingestion/projects/${argv.projectId}/ingestions`, {
+    ingestionType: 'Caris',
+    inputFiles: {
+      tar: argv.tarFileId
+    },
+    notificationConfig: {
+      succeededEmail: argv.succeededEmail,
+      failedEmail: argv.failedEmail
+    }
+  });
+  print(response.data, argv);
+};

lib/cmds/genomics_cmds/ingestions_cmds/create-foundation-bam.js

@@ -0,0 +1,36 @@
+'use strict';
+
+const { post } = require('../../../api');
+const print = require('../../../print');
+
+exports.command = 'create-foundation-bam <projectId> <bamFileId>';
+exports.desc = 'Create Foundation BAM ingestion for <bamFileId> in <projectId>';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The project ID.',
+    type: 'string'
+  }).positional('bamFileId', {
+    describe: 'The ID of the BAM file.',
+    type: 'string'
+  }).option('succeededEmail', {
+    describe: 'An email address to notify if the ingestion succeeds',
+    type: 'string'
+  }).option('failedEmail', {
+    describe: 'An email address to notify if the ingestion fails',
+    type: 'string'
+  });
+};
+
+exports.handler = async argv => {
+  const response = await post(argv, `/v1/genomic-ingestion/projects/${argv.projectId}/ingestions`, {
+    ingestionType: 'FoundationBam',
+    inputFiles: {
+      bam: argv.bamFileId
+    },
+    notificationConfig: {
+      succeededEmail: argv.succeededEmail,
+      failedEmail: argv.failedEmail
+    }
+  });
+  print(response.data, argv);
+};

lib/cmds/genomics_cmds/ingestions_cmds/create-foundation.js

@@ -0,0 +1,44 @@
+'use strict';
+
+const { post } = require('../../../api');
+const print = require('../../../print');
+
+exports.command = 'create-foundation <projectId> <xmlFileId> <reportFileId> [vcfFileId]';
+exports.desc = 'Create Foundation ingestion for <xmlFileId>, <reportFileId>, and optionally [vcfFileId] in <projectId>';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The project ID.',
+    type: 'string'
+  }).positional('xmlFileId', {
+    describe: 'The ID of the XML file.',
+    type: 'string'
+  }).positional('reportFileId', {
+    describe: 'The ID of the report file.',
+    type: 'string'
+  }).positional('vcfFileId', {
+    describe: 'The ID of the VCF file.',
+    type: 'string'
+  }).option('succeededEmail', {
+    describe: 'An email address to notify if the ingestion succeeds',
+    type: 'string'
+  }).option('failedEmail', {
+    describe: 'An email address to notify if the ingestion fails',
+    type: 'string'
+  });
+};
+
+exports.handler = async argv => {
+  const response = await post(argv, `/v1/genomic-ingestion/projects/${argv.projectId}/ingestions`, {
+    ingestionType: 'Foundation',
+    inputFiles: {
+      xml: argv.xmlFileId,
+      vcf: argv.vcfFileId || null,
+      report: argv.reportFileId
+    },
+    notificationConfig: {
+      succeededEmail: argv.succeededEmail,
+      failedEmail: argv.failedEmail
+    }
+  });
+  print(response.data, argv);
+};

lib/cmds/genomics_cmds/ingestions_cmds/get.js

@@ -0,0 +1,21 @@
+'use strict';
+
+const { get } = require('../../../api');
+const print = require('../../../print');
+
+exports.command = 'get <projectId> <ingestionId>';
+exports.desc = 'Fetch ingestion details by <projectId> and <ingestionId>';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The project ID.',
+    type: 'string'
+  }).positional('ingestionId', {
+    describe: 'The ingestion ID.',
+    type: 'string'
+  });
+};
+
+exports.handler = async argv => {
+  const response = await get(argv, `/v1/genomic-ingestion/projects/${argv.projectId}/ingestions/${argv.ingestionId}`);
+  print(response.data, argv);
+};

lib/cmds/genomics_cmds/ingestions_cmds/list.js

@@ -0,0 +1,54 @@
+'use strict';
+
+const querystring = require('querystring');
+const { get, list } = require('../../../api');
+const print = require('../../../print');
+const formatPage = require('../../../formatPage');
+
+exports.command = 'list <projectId>';
+exports.desc = 'List ingestions by <projectId>';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The project ID.',
+    type: 'string'
+  }).option('page-size', {
+    describe: 'The page size.',
+    type: 'number',
+    alias: 'n',
+    default: 25
+  }).option('next-page-token', {
+    describe: 'The next page token.',
+    alias: 't',
+    type: 'string'
+  }).option('limit', {
+    describe: 'The maximum number of items to return.',
+    alias: 'l',
+    type: 'number'
+  }).option('name', {
+    describe: 'Filter ingestions where the ingestion name contains this',
+    type: 'string'
+  }).option('failed', {
+    describe: 'Filter ingestions that have failed',
+    type: 'boolean'
+  }).option('step', {
+    describe: 'Filter ingestions that are on this step',
+    type: 'string',
+    choices: ['AwaitingFiles', 'Submitted', 'Transformed', 'Normalized', 'TestCreated', 'TestNotCreated']
+  });
+};
+
+exports.handler = async argv => {
+  const opts = {
+    pageSize: argv.limit ? 1000 : argv.pageSize
+  };
+
+  if (argv.nextPageToken) opts.nextPageToken = argv.nextPageToken;
+  if (argv.name) opts.name = argv.name;
+  if (argv.failed) opts.failed = argv.failed;
+  if (argv.step) opts.steps = argv.step;
+
+  const path = `/v1/genomic-ingestion/projects/${argv.projectId}/ingestions?${querystring.stringify(opts)}`;
+
+  const response = await (argv.limit ? list(argv, path) : get(argv, path));
+  print(formatPage(response.data), argv);
+};