[BLAST Search] Database management - Githubissues

epam / NGB

New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support

MIT License

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[BLAST Search] Database management #397

Open mzueva opened 3 years ago

mzueva commented 3 years ago

Background For implementation of #381 NGB shall provide API to list available BLAST Databases.

Approach

NGB Server

NGB shall provide API for BLAST Database management

BLAST Database entity shall be stored in DB and have the following fields:
- Id - Long
- Name - String (unique)
- Path - String
- Type - Enum <PROTEIN, NUCLEOTIDE>
create, update, list, delete operations shall be supported, list operation shall support optional type filter
Database management API is allowed for ADMIN users only

NGB CLI

NGB CLI shall provide commands for DB management:
- _reg_blastdb rbd - creates a new DB, positional arguments: name path type:
```
ngb reg_blast_db RefSeq /opt/db/Refsec.fna NUCLEOTIDE
```
- _del_blastdb dbd - deletes DB by ID
```
ngb del_blast_db 1
```
- _list_blastdb lbd - lists all db with optional --type filter, json and table formats shall be supported
```
ngb list_blast_db 
1     RefSeq   /opt/db/Refsec.fna      NUCLEOTIDE
2     Genes    /opt/db/Genes.fna.n     PROTEIN
```

mzueva commented 3 years ago

@okolesn Could you please check two items:

Listing databases using CLI with table format gives an error ]./ngb lbd -

$ ./ngb lbd -t
[main] ERROR com.epam.ngb.cli.app.Application - Format specifier '%7s'

Let's also add a method for load database by path