Module: Sylfy::Service::LipidMap::REST

Defined in:
lib/sylfy/service/lipidmaprest.rb

Constant Summary collapse

@@baseuri = 
"http://www.lipidmaps.org/data"

Class Method Summary collapse

Class Method Details

.lmsdOntoSearch(onto, outputtype = "TSV") ⇒ Object

Method for setting inchi data member

Parameters:

onto

string = “<ontoStr>” <ontoStr> = <ParamName> <ParamModifier> <ParamName> = carbons, doublebonds, triplebonds, rings, OH, NH2, OOH, ketones, epoxides, COOH, methyls, SH, Br, Cl, F, Methylenes, CHO, OMe, OAc, COOMe, Ester, Ether <ParamModifier> = eq, ge, le <ParamValue> = integer example: “carbons eq 20, triplebonds ge 2” or “carbons eq 10”

option

:OutputType => TSV, CSV, SDF [defualt: TSV],




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# File 'lib/sylfy/service/lipidmaprest.rb', line 165

def lmsdOntoSearch(onto, outputtype = "TSV")
  
	paramName = ["carbons", "doublebonds", "triplebonds", "rings", "OH", "NH2", "OOH", "ketones", "epoxides"]
	paramName = paramName + ["COOH", "methyls", "SH", "Br", "Cl", "F", "Methylenes", "CHO", "OMe", "OAc", "COOMe", "Ester", "Ether"]
	
	paramModifier = ["eq", "ge", "le"]
	
	i = 1
	ontostr = ""
	
	onto.chomp.gsub(/, /, ',').split(/,/).each do |str|
		dat = str.split(/ /)
		if paramName.include?(dat[0]) && paramModifier.include?(dat[1]) && i < 5
			ontostr += '&' if i > 1
			ontostr += "OntologyParamName#{i}=#{dat[0]}&OntologyParamModifier#{i}=#{dat[1]}&OntologyParamValue#{i}=#{dat[2].to_i}"
			i += 1
		end
	end
	
	if ontostr != ''
		return lmsdSearch(ontostr, "ProcessTextOntologySearch", outputtype)
	else
		raise Sylfy::Service::ParameterError, "ontology string error."
	end
  
  
end

.lmsdRecord(id, outputtype = "TSV") ⇒ Object

Method for setting inchi data member

Parameters:

id

LipidMap id to search

outputtype

TSV, CSV, SDF or MDLMOL [defualt: TSV]



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# File 'lib/sylfy/service/lipidmaprest.rb', line 28

def lmsdRecord(id, outputtype = "TSV")
  
	uri = "#{@@baseuri}/LMSDRecord.php?LMID=#{id}"
	uri += "&Mode=File"
	uri += "&OutputType=#{["TSV", "CSV", "SDF"].include?(outputtype) ? outputtype : 'TSV'}"
	uri += "&OutputDelimiter=Comma&OutputQuote=Yes&OutputColumnHeader=Yes"
	
	begin
		doc = URI.parse(uri).read().strip()
		case outputtype
		when 'TSV', nil
			return CSV.parse(doc, :headers => true, :col_sep => "\t")
		when 'CSV'
			return CSV.parse(doc, :headers => true)
		else
			return doc
		end
	rescue OpenURI::HTTPError
		return nil
	end
	
end

.lmsdSearch(str, mode, outputtype = "TSV") ⇒ Object

Method for setting inchi data member

Parameters:

str

search string

mode

Search mode ProcessStrSearch, ProcessTextSearch or ProcessTextOntologySearch

outputtype

TSV, CSV, SDF or MDLMOL [defualt: TSV]



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# File 'lib/sylfy/service/lipidmaprest.rb', line 61

def lmsdSearch(str, mode, outputtype = "TSV")
  
	uri = "#{@@baseuri}/structure/LMSDSearch.php?#{str}&OutputMode=File&Mode=#{mode}"
	uri += "&OutputType=#{["TSV", "CSV", "SDF"].include?(outputtype) ? outputtype : 'TSV'}"
	uri += "&OutputDelimiter=Comma&OutputQuote=Yes&OutputColumnHeader=Yes"
	
	begin
		doc = URI.parse(uri).read().strip()
		case outputtype
		when 'TSV', nil
			return CSV.parse(doc, :headers => true, :col_sep => "\t")
		when 'CSV'
			return CSV.parse(doc, :headers => true)
		else
			return doc
		end
	rescue OpenURI::HTTPError
		return nil
	end
	
end

.lmsdStrSearch(string, field = 'LMID', exactMatch = true, outputtype = "TSV") ⇒ Object

Method for setting inchi data member

Parameters:

string

search string

field

field type: LMID, Name, Formula, SMILESString [defualt: LMID]

exactMatch

Boolean [defualt: yes]

outputtype

TSV, CSV, SDF or MDLMOL [defualt: TSV]



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# File 'lib/sylfy/service/lipidmaprest.rb', line 97

def lmsdStrSearch(string, field = 'LMID', exactMatch = true, outputtype = "TSV")
  
	searchType = exactMatch ? 'ExactMatch' : 'SubStructure'
	
	if ['LMID', 'Name', 'Formula', 'SMILESString'].include?(field)
		return lmsdSearch("#{field}=#{URI.encode(string)}&SearchType=#{searchType}", "ProcessStrSearch", outputtype)
	else
		raise Sylfy::Service::ParameterError, "#{field} field does not in service."
	end
end

.lmsdTxtSearch(hash, outputtype = "TSV") ⇒ Object

Method for setting inchi data member

Parameters:

hash

searh hash 

:LMID	=> LM_ID,
:Name	=> part of any common name,
:Formula => formula,
:ExactMass => positive number,
:ExactMassOffSet => positive number,
:CoreClass => integer [1 to 8],
  1=Fatty Acyls [FA] 
  2=Glycerolipids [GL] 
  3=Glycerophospholipids [GP] 
  4=Sphingolipids [SP] 
  5=Sterol Lipids [ST] 
  6=Prenol Lipids [PR] 
  7=Saccharolipids [SL] 
  8=Polyketides [PK]
:MainClass => integer,
  e.g.  FA10=101
        FA11=111
        ST05=505
:SubClass => integer
  e.g.  ST0402=50402

outputtype

TSV, CSV, SDF or MDLMOL [defualt: TSV]



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# File 'lib/sylfy/service/lipidmaprest.rb', line 139

def lmsdTxtSearch(hash, outputtype = "TSV")
  
	string = ''
	
	hash.each_pair do |k, v|
		string += '&' if string != ''
		string += "#{k.to_s}=#{v}"
	end
	
	return lmsdSearch(string, "ProcessTextSearch", outputtype)
end