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service-p2m2tools-api

Scala CI Docker image

API Service to parse the formats of the metabolomics data acquisition devices of the P2M2 platform

API

Path Description Return values Return values
/p2m2tools/api/format/sniffer returns the file type gcms, openlabcds, masslynx-txt, masslynx-xml, xcalibur { format : value}
/p2m2tools/api/format/parse parse a file from a metabolomics analysis by guessing its format compound { header : [sample, metabolite, retTime, area, height, injectedVolume, vial, acquisitionDate, exportDate], samples : list< list<string> > }
/p2m2tools/api/format/parse/gcms parse a GCMS metabolomics analysis file compound list { "class":"GCMS","format":"gcms","origin": "","header": <map> ,"results":<list<map>>, "request":{"size:":<int>} }
/p2m2tools/api/format/parse/openlabcds parse a openlab CDS metabolomics analysis file compound list { "class":"OpenLabCDS","format":"openlabcds","origin": "","header": <map> ,"results":<list<map>>, "request":{"size:":<int>} }
/p2m2tools/api/format/parse/masslynx parse a MassLynx metabolomics analysis file (Quantitative Summary File) compound list
/p2m2tools/api/format/parse/xcalibur parse a Xcalibur metabolomics analysis file compound list

prerequisites

curl -L https://github.com/com-lihaoyi/mill/releases/download/0.11.2/0.11.2 > mill && chmod +x mill

run tests

./mill app.test

run service

docker

docker pull inraep2m2/service-p2m2tools-api:latest
docker run -d -p 8080:8080 -t inraep2m2/service-p2m2tools-api:latest

OR

docker pull ghcr.io/<repository-user>/service-p2m2tools-api:latest
docker run -d -p 8080:8080 -t ghcr.io/<repository-user>/service-p2m2tools-api:latest

Replace <repository-user> with your github username

jar

./mill app.assembly
java -jar ./out/app/assembly.dest/out.jar

mill

or with mill

./mill -w app.runBackground

Curl examples

With String content

curl -X POST http://localhost:8080/p2m2tools/api/format/sniffer --data-raw '
[Header]
Data File Name	C:\Users\X\Desktop\Projets CR\P2M2\TQD\210510_13C\13CPROT2.qgd
Output Date	23/08/2021
Output Time	14:09:36

[MS Quantitative Results]
ID#	Name	Type	ISTD Group#	Mass	Ret.Time	Start Time	End Time	A/H	Area	Height	Conc.	Mode	Peak#	Std.Ret.Time	Calibration Curve	3rd	2nd	1st	Constant	Ref.Ion Area	Ref.Ion Height	Ref.Ion Set Ratio	Ref.Ion Ratio	Recovery	SI	Ref.Ion1 m/z	Ref.Ion1 Area	Ref.Ion1 Height	Ref.Ion1 Set Ratio	Ref.Ion1 Ratio	Ref.Ion2 m/z	Ref.Ion2 Area	Ref.Ion2 Height	Ref.Ion2 Set Ratio	Ref.Ion2 Ratio	Ref.Ion3 m/z	Ref.Ion3 Area	Ref.Ion3 Height	Ref.Ion3 Set Ratio	Ref.Ion3 Ratio	Ref.Ion4 m/z	Ref.Ion4 Area	Ref.Ion4 Height	Ref.Ion4 Set Ratio	Ref.Ion4 Ratio	Ref.Ion5 m/z	Ref.Ion5 Area	Ref.Ion5 Height	Ref.Ion5 Set Ratio	Ref.Ion5 Ratio	Ret. Index	S/N	Unit	Description	Threshold
1	Glyoxylate (1MEOX) (1TMS )m0	Target	1	160.00	6.405	6.393	6.423	1.080	14	13	0.00029	Auto	3	6.400	Default	0	0	0	0	0	0	84.50	0.00	0.00	18	73.00	0	0	84.50	0.00	59.00	142	129	49.59	1014.29	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1218	4.87	mg/L		0.00000
'

With file

curl -X POST http://localhost:8080/p2m2tools/api/format/sniffer --data-binary @app/test/resources/xcalibur.xls

Javascript examples

node example-requests-file.js
var fs = require('fs');

/*
    Example 1 - Obtain the information contained in the file in Xcalibur format
*/

(async() => {

    var contentFile = fs.readFileSync('app/test/resources/xcalibur.xls')
    var response = await fetch('http://localhost:8080/p2m2tools/api/format/parse/xcalibur', {
            method: 'POST',
            headers: {
                "Content-Type": "application/json"
            },
            body: contentFile
    })

    const data = await response.json();
    console.log(data);

})();

devel / memo

setting up IntelliJ IDEA

./mill -j 0 mill.idea.GenIdea/idea