AWS Omics store have capability to import files into it from s3 bucket, we also have such functionality on the server side, let's implement it on the UI as well.
Corresponding server API: GET /omcisstore/{id}/import
Body:
name - required, string
serviceRoleArn - optional, parameter if not present, server will get it from the region settings. Shouldn't be propagated on UI.
sourceFileType - required, for Ref Store - REFERENCE for Seq Store - one of [FASTQ, BAM, UBAM, CRAM]subjectId - required, string
sampleId - required, string
referencePath - only for Seq Store, optional for FASTQ and UBAM, required for BAM CRAM, should be valid path from Ref Store registered in the system
description - optional, string
generatedFrom - optional, string
sourceFiles - required, object with 2 fields. For Ref Store only source1 should be provided, source2 can be provided for FASTQ files
By navigating to the storage view and clicking a button Import in the right upper corner user should be able to start import procedure by filling out a form:
For Ref Store form should provide the next field to fill:
name - string
subjectId - string
sampleId - string
description - string
generatedFrom - string
sourceFiles- interactive control, allows user to navigate to any s3 bucket registered in the system and choose a file
For Seq Store form should provide the next field to fill:
name - string
subjectId - string
sampleId - string
sourceFileType - predefined list of FASTQ, BAM, UBAM, CRAM
referencePath - interactive control, allows user to navigate to any s3 bucket registered in the system and choose a file
description - string
generatedFrom - string
sourceFiles- interactive control, allows user to navigate to any s3 bucket registered in the system and choose a file, for FASTQ it should allow to choose 2 files
AWS Omics store have capability to import files into it from s3 bucket, we also have such functionality on the server side, let's implement it on the UI as well.
Corresponding server API:
GET /omcisstore/{id}/importBody:name- required, stringserviceRoleArn- optional, parameter if not present, server will get it from the region settings. Shouldn't be propagated on UI.sourceFileType- required, for Ref Store -REFERENCEfor Seq Store - one of[FASTQ, BAM, UBAM, CRAM]subjectId- required, stringsampleId- required, stringreferencePath- only for Seq Store, optional for FASTQ and UBAM, required for BAM CRAM, should be valid path from Ref Store registered in the systemdescription- optional, stringgeneratedFrom- optional, stringsourceFiles- required, object with 2 fields. For Ref Store onlysource1should be provided,source2can be provided forFASTQfilesBy navigating to the storage view and clicking a button
Importin the right upper corner user should be able to start import procedure by filling out a form:For Ref Store form should provide the next field to fill:
name- stringsubjectId- stringsampleId- stringdescription- stringgeneratedFrom- stringsourceFiles- interactive control, allows user to navigate to any s3 bucket registered in the system and choose a fileFor Seq Store form should provide the next field to fill:
name- stringsubjectId- stringsampleId- stringsourceFileType- predefined list of FASTQ, BAM, UBAM, CRAMreferencePath- interactive control, allows user to navigate to any s3 bucket registered in the system and choose a filedescription- stringgeneratedFrom- stringsourceFiles- interactive control, allows user to navigate to any s3 bucket registered in the system and choose a file, for FASTQ it should allow to choose 2 files