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

/SearchDatabase/GetFeatureID

This method is used to get the feature ID from uniquename.
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has the feature ID from database.

Parameters	Description
uniquename	Scalar variable with uniquename

/SearchDatabase/GetPipeline

This method is used to get the pipeline ID from database.
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an object with the attribute “pipeline_id” from database.
Don’t need parameters.

/SearchDatabase/GetRibosomalRNAs

This method return ribosomal RNAs available in annotation database
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, which in response property, has a list with all ribosomal RNAs available in database.

Parameters	Description
pipeline	Pipeline ID

/SearchDatabase/rRNA_search

Method used to make search of rRNA annotations.
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of feature IDs sorted by locus tag.

Parameters	Description
pipeline	Pipeline ID
pageSize	Quantity of elements
offset	Offset of search
type	Type of rRNA
contig	Contig ID

/SearchDatabase/Gene

This method is used to realize search by all genes in database.
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of objects Report_HTML_DB::Models::Application::Feature.

Parameters	Description
pipeline	Pipeline ID
geneID	Search by genes with this locus tag
geneDescription	Search by genes with this description
noDescription	Search by genes which don't contain this description
individually	Match all terms, positive values can be "on", 1; set 0 if you don't want
featureId	Search by a list of genes with those feature ID; Should be a string with feature IDs separated by spaces
pageSize	Quantity of elements
offset	Offset of search

/SearchDatabase/GetGeneBasics

Method used to return basic data of genes from database: the beginning position from sequence, final position from the sequence, type, name.
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an list of objects Report_HTML_DB::Models::Application::Feature.

Parameters	Description
id	Feature ID
pipeline	Pipeline ID

/SearchDatabase/GetSubsequence

Method used to get subsequence stretch of gene

Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an list of objects Report_HTML_DB::Models::Application::Feature.

Parameters	Description
type	Type of sequence (CDS, or anything else)
contig	Contig's name, if you're using a type of sequence different of "CDS", contig's name is required
sequenceName	Sequence's name, if you're using a type of sequence equal "CDS", sequence's name is required
start	Start position
end	End position
pipeline	Pipeline ID

/SearchDatabase/subEvidences

Method used to get subevidences based on feature id
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an list of objects Report_HTML_DB::Models::Application::Subevidence.

Parameters	Description
feature	Feature ID
pipeline	Pipeline ID

/SearchDatabase/getIntervalEvidenceProperties

Method used to return properties of evidences that the type is interval and basic data of everything isn't CDS
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an list of hashes with keys and values from evidence.

Parameters	Description
feature	Feature ID
typeFeature	Component name from feature

/SearchDatabase/getSimilarityEvidenceProperties

Method used to return properties of evidence typed like similarity
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an list of hashes with keys and values from evidence.

Parameters	Description
feature	Feature ID

/SearchDatabase/getIdentifierAndDescriptionSimilarity

Method used to get identifier and description of similarity
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an hash with the properties "identifier" and "description".

Parameters	Description
feature_id	Feature ID

/SearchDatabase/analysesCDS

Method used to make search of analyses of protein-coding genes.
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of feature IDs sorted by locus tag.

Key	Description
pipeline	Scalar variable with pipeline ID
contig	Scalar variable with feature ID from contig
geneDesc	Scalar variable which realize search by all CDS with this description
noDesc	Scalar variable which realize search by all CDS that doesn’t have this description
individually	Scalar variable which make all terms from geneDesc and noDesc match
noGO	Scalar variable, if you don’t want to have results related to GO annotation
goID	Scalar variable with GO Identifier
goDesc	Scalar variable with GO Description
noTC	Scalar variable, if you don’t want to have results related to TCDB annotation
tcdbID	Scalar variable with TCDB ID
tcdbFam	Scalar variable with TCDB Family
tcdbSubclass	Scalar variable with TCDB subclass
tcdbClass	Scalar variable with TCDB class
tcdbDesc	Scalar variable with TCDB description
noBlast	Scalar variable, if you don’t want to have results related to BLAST annotations
blastID	Scalar variable with BLAST identifier
blastDesc	Scalar variable with BLAST description
noRps	Scalar variable, if you don’t want to have results related to RPS-BLAST annotations
rpsID	Scalar variable with RPS-BLAST Identifier
rpsDesc	Scalar variable with RPS-BLAST Description
noKEGG	Scalar variable, if you don’t want to have results related to KEGG annotations
koID	Scalar variable with KEGG Identifier
keggPath	Scalar variable with KEGG Pathway
keggDesc	Scalar variable with KEGG description
noOrth	Scalar variable, if you don’t want to see results related to orthology annotations.
orthID	Scalar variable with orthology Identifier
orthDesc	Scalar variable with orthology description
noIP	Scalar variable, if you don’t want to see results related to InterProScan annotations.
interproID	Scalar variable with InterProScan identifier
interproDesc	Scalar variable with InterProScan description
noTMHMM	Scalar variable, if you don’t want results related to TMHMM annotations.
TMHMMdom	Scalar variable with number of transmembrane domains
tmhmmQuant	Scalar variable which auxiliate search of TMHMMdom, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
noDGPI	Scalar variable, if you don’t want results related to DGPI annotations.
cleavageSiteDGPI	Scalar variable with cleavage site from DGPI
scoreDGPI	Scalar variable with score from DGPI
cleavageQuant	Scalar variable which auxiliate search of cleavageSiteDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
scoreQuant	Scalar variable which auxiliate search of scoreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
noPreDGPI	Scalar variable, if you don’t want results related to PreDGPI annotations.
namePreDGPI	Scalar variable with name of PreDGPI
positionPreDGPI	Scalar variable with position from PreDGPI
positionQuantPreDGPI	Scalar variable which auxiliate search of positionPreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
specificityPreDGPI	Scalar variable specifity from PreDGPI
specificityQuantPreDGPI	Scalar variable which auxiliate search of specificityPreDGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
sequencePreDGPI	Scalar variable with sequence to compare with PreDGPI annotations
noBigGPI	Scalar variable, if you don’t want results related to BiGPI annotations.
pvalueBigpi	Scalar variable value from BiGPI
pvalueQuantBigpi	Scalar variable which auxiliate search of quantity BiGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
positionBigpi	Scalar variable value with the position of BiGPI annotation
positionQuantBigpi	Scalar variable which auxiliate search of position BiGPI, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
noPhobius	Scalar variable, if you don’t want results related to Phobius annotations.
TMdom	Scalar vairable, quantity of transmembrane domains
tmQuant	Scalar variable which auxiliate search of parameter TMdom, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
sigP	Scalar variable if you want the phobius with result with signal peptide. If you don’t care: “sigPwhatever”, if you want: “sigPyes”, if you don’t want: “sigPno”
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
components	Scalar variable with annotation component names used

/SearchDatabase/trnaSearch

Method used to realize search of tRNA annotations.
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of feature IDs sorted by locus tag.

Parameters	Description
pipeline	Scalar variable with pipeline ID
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
tRNAaa	Scalar variable to search tRNA by amino acid
tRNAcd	Scalar variable to search tRNA by codon

/SearchDatabase/tandemRepeatsSearch

Method used to get data of tandem repeats
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of feature IDs sorted by locus tag.

Parameters	Description
pipeline	Scalar variable with pipeline ID
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
TRFrepSeq	Scalar variable with sequence in repetition unit
TRFrepSize	Scalar variable with repetition units of bases
TRFsize	Scalar variable which auxiliate search of repetition units of bases, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
TRFrepNumMin	Scalar variable with occurrences in this min value
TRFrepNumMax	Scalar variable with occurrences in this max value

/SearchDatabase/ncRNASearch

Method used to get data of non coding RNAs
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of feature IDs sorted by locus tag.

Parameters	Description
pipeline	Scalar variable with pipeline ID
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
ncRNAtargetID	Scalar variable with target ID from RFAM
ncRNAevalue	Scalar variable with evalue from result
ncRNAevM	Scalar variable which auxiliate search with evalue result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
ncRNAtargetName	Scalar variable with target name
ncRNAtargetClass	Scalar variable with target class
ncRNAtargetType	Scalar variable with target type
ncRNAtargetDesc	Scalar variable with target description

/SearchDatabase/transcriptionalTerminatorSearch

Method used to get data of transcriptional terminators
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of feature IDs sorted by locus tag.

Parameters	Description
pipeline	Scalar variable with pipeline ID
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
TTconf	Scalar variable with transcriptional termintators with confidence score
TTconfM	Scalar variable which auxiliate search with confidence score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
TThp	Scalar variable with transcriptional terminators with hairpin score
TThpM	Scalar variable which auxiliate search with hairpin score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
TTtail	Scalar variable with transcriptional terminators with tail score
TTtailM	Scalar variable which auxiliate search with tail score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"

/SearchDatabase/rbsSearch

Method used to get data of ribosomal binding sites
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of feature IDs sorted by locus tag.

Parameters	Description
pipeline	Scalar variable with pipeline ID
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
RBSpattern	Scalar variable with a sequence pattern
RBSshift	Scalar variable with "on" for true value or 0 for false, represents a search for all ribosomal binding site predictions that recommend a shift in start codon position
RBSshiftM	Scalar variable with option values, if you want upstream, value should be "neg"; if you want downstream, value should be "pos"; if you want either, value should be "both"
RBSnewcodon	Scalar variable with "on" for true value or 0 for false, represents a search for all ribosomal binding site predictions that recommend a change of start codon

/SearchDatabase/alienhunterSearch

Method used to get data of horizontal gene transfers
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::PagedResponse JSON, where in response property, has an list of feature IDs sorted by locus tag.

Parameters	Description
pipeline	Scalar variable with pipeline ID
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig
AHlen	Scalar variable with length of regions predicted
AHlenM	Scalar variable which auxiliate search with length of regions predicted result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
AHscore	Scalar variable with value to get regions of score
AHscM	Scalar variable which auxiliate search with regions of score result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"
AHthr	Scalar variable with value to get regions of threshold
AHthrM	Scalar variable which auxiliate search with regions of treshold result, if you want exatly value: “exact”, less: “orLess”, more: “orMore”, or none: "none"

/SearchDatabase/geneByPosition

Method used to get feature by position
Request method should be GET and must have an content-type header with the value "application/json".
Return a Report_HTML_DB::Models::Services::PagedResponse with a list of Report_HTML_DB::Models::Application::Feature as response

Parameters	Description
start	Start position
end	End position
pipeline	Scalar variable with pipeline ID
pageSize	Scalar variable with the page size
offset	Scalar variable with the offset
contig	Scalar variable with feature ID from contig

/SearchDatabase/targetClass

Method used to get target class
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an list of target class values.

Parameters	Description
pipeline_id	Pipeline ID

/SearchDatabase/getGOResultsByFeatureID

Method used to get GO results from feature ID
Request method should be GET and must have an content-type header with the value "application/json".
Returns a Report_HTML_DB::Models::Services::BaseResponse JSON, where in response property, has an list of GO results annotated.

Parameters	Description
feature_id	Feature ID
pipeline_id	Pipeline ID