Services API

The Services Application is responsible by execution of scripts and queries in annotation database. This page should list all requests available. It receives HTTP requests and answer in JSON content type, something like:

curl -H"content-type:application/json"  http://127.0.0.1:3000/SearchDatabase/GetPipeline | python -mjson.tool                                       
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   151  100   151    0     0    123      0  0:00:01  0:00:01 --:--:--   123

{
    "__CLASS__": "Report_HTML_DB::Models::Services::BaseResponse",
    "elapsed_ms": 0.268837,
    "message": "Ok",
    "response": {
        "pipeline_id": "4528"
    },
    "status_code": 200
}

Blast

This controller is responsible by execution of functions from BlastRepository.

Actions

/Blast/search

This action receives a POST Request and execute executeBlastSearch function from BlastRepository.
Returns a Report_HTML_DB::Models::Services::BaseResponse with BLAST result as response
This action receive a JSON object as body from request with the following properties:

Key	Value
PROGRAM	Program name (blastn, blastp, blastx, tblastn, tblastx)
DATALIB	Data lib(PMN_genome_1 for all genes - nucleotidic sequences, PMN_genes_1 for contigs in nucleotidic sequence, PMN_prot_1 for protein sequences)
QUERY_FROM	Set subsequence from
QUERY_TO	Set subsequence to
FILTER	Set filters(for low complexity use "L" value)
EXPECT	Read more here
MAT_PARAM	Read more here
UNGAPPED_ALIGNMENT	"is_set" if you want a ungapped alignment
GENETIC_CODE	Read more here
DB_GENETIC_CODE	Read more here
COST_OPEN_GAP	Read more here
COST_EXTEND_GAP	Read more here
WORD_SIZE	Word size for wordfinder algorithm (length of best perfect match)
ALIGNMENT_VIEW	Read more here
DESCRIPTIONS	Read more here
ALIGNMENTS	Read more here

/Blast/fancy

This action receives a POST request and execute fancy_blast function from BlastRepository.
Returns a Report_HTML_DB::Models::Services::BaseResponse with HTML and a encoded image in base 64 from fancy_blast.pl result as response
This action receive a JSON object as body from request with the following properties:

Parameters	Description
blast	blast result as a string

SearchDatabase

This controller is responsible by execution of function from SearchDatabaseRepository

Actions