Include comments here #511 (review)

Use includeFASTA instead of withFasta and --include-fasta instead of
--with-fasta in cli

.github/workflows/pull_request.yml

@@ -42,7 +42,7 @@ jobs:
           yarn --cwd packages/apollo-shared start &
           ALLOW_ROOT_USER=true ROOT_USER_PASSWORD=pass yarn --cwd packages/apollo-collaboration-server start &
       - name: Run CLI tests
-        run: yarn tsx src/test/test.ts
+        run: yarn test:cli
         working-directory: packages/apollo-cli
       # - name: Run docker tests
       #   working-directory: packages/apollo-cli

packages/apollo-cli/README.md

@@ -352,25 +352,25 @@ _See code:
 
 ## `apollo export gff3 ASSEMBLY`
 
-Export the annotation of an assembly to stdout as gff3
+Export the annotations for an assembly to stdout as gff3
 
 ```
 USAGE
-  $ apollo export gff3 ASSEMBLY [--profile <value>] [--config-file <value>] [--with-fasta]
+  $ apollo export gff3 ASSEMBLY [--profile <value>] [--config-file <value>] [--include-fasta]
 
 ARGUMENTS
-  ASSEMBLY  Export features for this assembly name or id
+  ASSEMBLY  Export annotations for this assembly name or id
 
 FLAGS
   --config-file=<value>  Use this config file (mostly for testing)
+  --include-fasta        Include fasta sequence in output
   --profile=<value>      Use credentials from this profile
-  --with-fasta           Append fasta sequence to output
 
 DESCRIPTION
-  Export the annotation of an assembly to stdout as gff3
+  Export the annotations for an assembly to stdout as gff3
 
 EXAMPLES
-  Export annotation for myAssembly:
+  Export annotations for myAssembly:
 
     $ apollo export gff3 myAssembly > out.gff3
 ```

packages/apollo-cli/package.json

@@ -29,6 +29,7 @@
     "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
     "posttest": "yarn lint",
     "test:ci": "nyc mocha 'src/**/*.test.ts'",
+    "test:cli": "yarn tsx src/test/test.ts",
     "version": "oclif readme --multi --dir ../website/docs/admin/cli/ && oclif readme && git add README.md"
   },
   "oclif": {

packages/apollo-cli/src/commands/export/gff3.ts

@@ -12,25 +12,26 @@ import {
 import { Readable } from 'node:stream'
 
 export default class Get extends BaseCommand<typeof Get> {
-  static description = 'Export the annotation of an assembly to stdout as gff3'
+  static description =
+    'Export the annotations for an assembly to stdout as gff3'
 
   static examples = [
     {
-      description: 'Export annotation for myAssembly:',
+      description: 'Export annotations for myAssembly:',
       command: '<%= config.bin %> <%= command.id %> myAssembly > out.gff3',
     },
   ]
 
   static args = {
     assembly: Args.string({
-      description: 'Export features for this assembly name or id',
+      description: 'Export annotations for this assembly name or id',
       required: true,
     }),
   }
 
   static flags = {
-    'with-fasta': Flags.boolean({
-      description: 'Append fasta sequence to output',
+    'include-fasta': Flags.boolean({
+      description: 'Include fasta sequence in output',
       default: false,
     }),
   }
@@ -77,7 +78,7 @@ export default class Get extends BaseCommand<typeof Get> {
     const params: Record<string, string> = {
       exportID,
       assemblyId,
-      withFasta: this.flags['with-fasta'] ? 'True' : 'False',
+      includeFASTA: this.flags['include-fasta'] ? 'true' : 'false',
     }
     const exportSearchParams = new URLSearchParams(params)
     exportURL.search = exportSearchParams.toString()
@@ -95,6 +96,8 @@ export default class Get extends BaseCommand<typeof Get> {
     if (body) {
       const readable = Readable.from(body)
       readable.pipe(process.stdout)
+    } else {
+      this.error('Failed to export gff3')
     }
   }
 }

packages/apollo-cli/src/test/test.ts

@@ -9,7 +9,7 @@
  * USAGE
  * From package root directory (`packages/apollo-cli`). Run all tests:
  *
- * yarn tsx src/test/test.ts
+ * yarn test:cli
  *
  * Run only matching pattern:
  *
@@ -1371,7 +1371,7 @@ void describe('Test CLI', () => {
       `${apollo} assembly add-from-fasta ${P} test_data/tiny.fasta.gz -a vv1 -f --editable`,
     )
     new Shell(`${apollo} feature import ${P} test_data/tiny.fasta.gff3 -a vv1`)
-    let p = new Shell(`${apollo} export gff3 ${P} vv1 --with-fasta`)
+    let p = new Shell(`${apollo} export gff3 ${P} vv1 --include-fasta`)
     let gff = p.stdout
     assert.ok(gff.startsWith('##gff-version 3'))
     assert.ok(gff.includes('multivalue=val1,val2,val3'))
@@ -1395,12 +1395,12 @@ void describe('Test CLI', () => {
       `${apollo} assembly add-from-fasta ${P} test_data/tiny.fasta.gz -a vv1 -f`,
     )
     new Shell(`${apollo} feature import ${P} test_data/tiny.fasta.gff3 -a vv1`)
-    let p = new Shell(`${apollo} export gff3 ${P} vv1 --with-fasta`)
+    let p = new Shell(`${apollo} export gff3 ${P} vv1 --include-fasta`)
     let gff = p.stdout
     assert.ok(gff.startsWith('##gff-version 3'))
     assert.ok(gff.includes('multivalue=val1,val2,val3'))
     assert.ok(gff.includes('##FASTA\n'))
-    // We have end with two newlines because the test data does have an extra newline at the end.
+    // We end with two newlines because the test data does have an extra newline at the end.
     assert.deepStrictEqual(gff.slice(-7, gff.length), 'taccc\n\n')
 
     p = new Shell(`${apollo} export gff3 ${P} vv1`)
@@ -1415,12 +1415,12 @@ void describe('Test CLI', () => {
       `${apollo} assembly add-from-fasta ${P} https://raw.githubusercontent.com/GMOD/Apollo3/refs/heads/main/packages/apollo-cli/test_data/tiny.fasta.gz -a vv1 -f`,
     )
     new Shell(`${apollo} feature import ${P} test_data/tiny.fasta.gff3 -a vv1`)
-    let p = new Shell(`${apollo} export gff3 ${P} vv1 --with-fasta`)
+    let p = new Shell(`${apollo} export gff3 ${P} vv1 --include-fasta`)
     let gff = p.stdout
     assert.ok(gff.startsWith('##gff-version 3'))
     assert.ok(gff.includes('multivalue=val1,val2,val3'))
     assert.ok(gff.includes('##FASTA\n'))
-    // We have end with two newlines because the test data does have an extra newline at the end.
+    // We end with two newlines because the test data does have an extra newline at the end.
     assert.deepStrictEqual(gff.slice(-7, gff.length), 'taccc\n\n')
 
     p = new Shell(`${apollo} export gff3 ${P} vv1`)

packages/apollo-collaboration-server/src/export/export.controller.ts

@@ -1,8 +1,11 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import {
   Controller,
+  DefaultValuePipe,
   Get,
   Logger,
+  ParseBoolPipe,
+  ParseIntPipe,
   Query,
   Response,
   StreamableFile,
@@ -41,21 +44,17 @@ export class ExportController {
   @Validations(Role.None)
   @Get()
   async exportGFF3(
-    @Query()
-    request: {
-      exportID: string
-      withFasta: 'True' | 'False'
-      fastaWidth?: number
-    },
+    // @Query()
+    @Query('exportID') exportID: string,
+    @Query('includeFASTA', new DefaultValuePipe(false), ParseBoolPipe)
+    includeFASTA: boolean,
+    @Query('fastaWidth', new DefaultValuePipe(80), ParseIntPipe)
+    fastaWidth: number,
     @Response({ passthrough: true }) res: ExpressResponse,
   ) {
-    const { exportID, withFasta, ...rest } = request
-    if (!['True', 'False'].includes(withFasta)) {
-      throw new Error(`withFasta must be "True" or "False", got: ${withFasta}`)
-    }
     const [stream, assembly] = await this.exportService.exportGFF3(exportID, {
-      withFasta: withFasta === 'True',
-      ...rest,
+      includeFASTA,
+      fastaWidth,
     })
     const assemblyName = await this.exportService.getAssemblyName(assembly)
     res.set({

packages/apollo-collaboration-server/src/export/export.service.ts

@@ -153,13 +153,13 @@ export class ExportService {
 
   async exportGFF3(
     exportID: string,
-    opts: { withFasta?: boolean; fastaWidth?: number },
+    opts: { includeFASTA?: boolean; fastaWidth?: number },
   ): Promise<[Readable, string]> {
     const exportDoc = await this.exportModel.findById(exportID)
     if (!exportDoc) {
       throw new NotFoundException()
     }
-    const { fastaWidth, withFasta } = opts
+    const { fastaWidth, includeFASTA } = opts
     const { assembly } = exportDoc
     const refSeqs = await this.refSeqModel.find({ assembly }).exec()
     const refSeqIds = refSeqs.map((refSeq) => refSeq._id)
@@ -212,14 +212,14 @@ export class ExportService {
       gff.formatStream({ insertVersionDirective: true }),
       (error) => {
         if (error) {
-          this.logger.error('GFF3 export failed here')
+          this.logger.error('GFF3 export failed')
           this.logger.error(error)
         }
       },
     )
 
     let sequenceStream: Readable[] = []
-    if (withFasta) {
+    if (includeFASTA) {
       const assemblyDoc = await this.assemblyModel.findById(assembly.toString())
       if (!assemblyDoc) {
         throw new Error(

packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx

@@ -113,7 +113,7 @@ export function DownloadGFF3({ handleClose, session }: DownloadGFF3Props) {
     const exportURL = new URL('export', internetAccount.baseURL)
     const params: Record<string, string> = {
       exportID,
-      withFasta: 'True',
+      includeFASTA: 'true',
     }
     const exportSearchParams = new URLSearchParams(params)
     exportURL.search = exportSearchParams.toString()

packages/website/docs/admin/cli/export.md

@@ -6,25 +6,25 @@ Commands to export data
 
 ## `apollo export gff3 ASSEMBLY`
 
-Export the annotation of an assembly to stdout as gff3
+Export the annotations for an assembly to stdout as gff3
 
 ```
 USAGE
-  $ apollo export gff3 ASSEMBLY [--profile <value>] [--config-file <value>] [--with-fasta]
+  $ apollo export gff3 ASSEMBLY [--profile <value>] [--config-file <value>] [--include-fasta]
 
 ARGUMENTS
-  ASSEMBLY  Export features for this assembly name or id
+  ASSEMBLY  Export annotations for this assembly name or id
 
 FLAGS
   --config-file=<value>  Use this config file (mostly for testing)
+  --include-fasta        Include fasta sequence in output
   --profile=<value>      Use credentials from this profile
-  --with-fasta           Append fasta sequence to output
 
 DESCRIPTION
-  Export the annotation of an assembly to stdout as gff3
+  Export the annotations for an assembly to stdout as gff3
 
 EXAMPLES
-  Export annotation for myAssembly:
+  Export annotations for myAssembly:
 
     $ apollo export gff3 myAssembly > out.gff3
 ```