Allow uploading file separately from adding assembly in CLI #405
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dariober
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Jul 22, 2024
* CLI can upload and add assembly from gzip files (#405 and #407) * CLI can add assembly in non-editable mode with `--no-db` flag, i.e. without loading sequence to mongodb (#406). Only bgzip'd & indexed fasta file are supported, not plain fa/fai files. See tests in test.py: `testFeatureChecksIndexed`, `testFileUploadGzip`, `testAddAssemblyWithoutLoadingInMongo`
garrettjstevens
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Aug 30, 2024
* CLI can upload and add assembly from gzip files (#405 and #407) * CLI can add assembly in non-editable mode with `--no-db` flag, i.e. without loading sequence to mongodb (#406). Only bgzip'd & indexed fasta file are supported, not plain fa/fai files. See tests in test.py: `testFeatureChecksIndexed`, `testFileUploadGzip`, `testAddAssemblyWithoutLoadingInMongo`
garrettjstevens
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Sep 20, 2024
* CLI can upload and add assembly from gzip files (#405 and #407) * CLI can add assembly in non-editable mode with `--no-db` flag, i.e. without loading sequence to mongodb (#406). Only bgzip'd & indexed fasta file are supported, not plain fa/fai files. See tests in test.py: `testFeatureChecksIndexed`, `testFileUploadGzip`, `testAddAssemblyWithoutLoadingInMongo`
garrettjstevens
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Sep 21, 2024
…ssembly (#432) * Start implementing file upload|download|get * Add delete command and various small edits * Add FileCommand handling file operations * Handle default profile via undefined * Download file as stream * Handling of gzip input and bgzip'd & indexed fasta * CLI can upload and add assembly from gzip files (#405 and #407) * CLI can add assembly in non-editable mode with `--no-db` flag, i.e. without loading sequence to mongodb (#406). Only bgzip'd & indexed fasta file are supported, not plain fa/fai files. See tests in test.py: `testFeatureChecksIndexed`, `testFileUploadGzip`, `testAddAssemblyWithoutLoadingInMongo` * Fix linter * Formatting * Add description for file CLI topic * Deduplicate sequence fetching code * Reference File schema from Assembly schema * Rename commands * Remove -i option since file is positional * Rename option --no-db and some other fixes * Add additional type and make input arg required * Tmp commit * fix app start issue * fix lint * Tmp commit addressing #432 Fix #424 * Tmp commit * This should address comments in #432 But most likely there will be changes to clunky code * Temp commit to fix buffer * Fix filehandle type * Use files service to get filehandles * Fix fileId vs fileIds and other issues for #432 All tests except those for chekcs passing * Allow fasta input to be gzip * Fixes after rebase * Move LocalFileGzip to collab server package * Match selector to other updated tests --------- Co-authored-by: dariober <dario.beraldi@gmail.com> Co-authored-by: Shashank Budhanuru Ramaraju <shashank.b.r.gowda45587@gmail.com>
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Currently in the CLI, when adding an assembly from a file, the file is uploaded and then the file is used to add an assembly all in the same command. We should support a mode of operation where there is one command to upload a file, which returns a file ID, and another command to add an assembly using that file ID. This could help when people want to regularly clean out and re-add genomes so they don't have to re-upload the file each time.
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