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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,34 @@ | ||
| FROM ubuntu:16.04 | ||
| MAINTAINER Pradeeban Kathiravelu "[email protected]" | ||
| FROM alpine:3.8 | ||
| LABEL maintainer="[email protected]" | ||
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| ### update and include Shadow to manage users and groups | ||
| RUN apk update | ||
| RUN apk --no-cache add wget | ||
| RUN apk --no-cache add shadow | ||
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| # build with | ||
| # sudo docker build --rm=true -t="repo/imgname" . | ||
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| ### update | ||
| RUN apt-get -q update | ||
| RUN apt-get -q -y upgrade | ||
| RUN apt-get -q -y dist-upgrade | ||
| RUN apt-get install -q -y libcurl3 | ||
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| # Java | ||
| RUN mkdir /root/src | ||
| # Add group Bindaas and user Bindaas | ||
| RUN groupadd -g 9999 bindaas && \ | ||
| useradd -r -u 9999 -g bindaas bindaas | ||
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| WORKDIR /root/src | ||
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| RUN apt-get install -y openjdk-8-jre | ||
| RUN apk --no-cache add openjdk8-jre | ||
| WORKDIR /root/bindaas/ | ||
| RUN wget https://github.com/sharmalab/bindaas/releases/download/v3.3.5/bindaas-dist-3.3.5.tar.gz | ||
| RUN tar -xvf bindaas-dist-3.3.5.tar.gz && rm bindaas-dist-3.3.5.tar.gz | ||
| COPY bindaas.config.json /root/bindaas/bin/ | ||
| COPY run.sh /root/bindaas/bin/ | ||
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| # Add java to path | ||
| ENV PATH /root/src/jre1.8.0_171/bin:$PATH | ||
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| RUN chown -R bindaas:bindaas /root/ | ||
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| # Bindaas | ||
| RUN mkdir -p /root/bindaas | ||
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| ADD https://github.com/sharmalab/bindaas/releases/download/v3.0.2/bindaas-dist-3.0.2.tar.gz /root/bindaas/ | ||
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| WORKDIR /root/bindaas | ||
| RUN ls | ||
| RUN mv bindaas-dist-3.0.2.tar.gz bindaas.tar.gz 2>&1; exit 0 | ||
| RUN tar -xvf bindaas.tar.gz 2>&1; exit 0 | ||
| RUN rm bindaas.tar.gz 2>&1; exit 0 | ||
| WORKDIR /root/bindaas/bin | ||
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| COPY bindaas.config.json /root/bindaas/bin/ | ||
| USER bindaas | ||
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| EXPOSE 9099 | ||
| EXPOSE 8080 | ||
| WORKDIR /root/bindaas/bin | ||
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| COPY /run.sh /root/bindaas/bin/run.sh | ||
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| CMD ["sh", "run.sh"] |
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| @@ -1,4 +1,5 @@ | ||
| #!/bin/bash | ||
| #nohup /usr/bin/mongod & | ||
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| java -Dpid=BINDAAS_INSTANCE -Xmx1024m -jar org.eclipse.osgi_3.8.2.v20130124-134944.jar | ||
| java -jar -Dpid=BINDAAS_INSTANCE org.eclipse.osgi_3.10.100.v20150529-1857.jar | ||
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| while true; do sleep 1000; done |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,91 +1,89 @@ | ||
| //convert.js | ||
| // | ||
| var readline = require('readline'); | ||
| const readline = require('readline'); | ||
| const path = require('path') | ||
| const fs = require('fs'); | ||
| const inputFolder = process.argv[2] || './input'; | ||
| const outputFolder = process.argv[3] || './output'; | ||
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| const fileTemps = {}; | ||
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| let remainder = 0; | ||
| fs.readdirSync(inputFolder).forEach(fileName => { | ||
| //const filePath = `${fileName}`; | ||
| convert(fileName); | ||
| const ext = path.extname(`${inputFolder}/${fileName}`); | ||
| if(ext!=='.json') return; | ||
| fileTemps[fileName] = null; | ||
| convert(fileName) | ||
| }); | ||
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| let filename = process.argv[2] || "heatmap_TCGA-28-1751-01Z-00-DX1.low_res.json"; | ||
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| let tempObject; | ||
| function convert(filename){ | ||
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| function convert(filename) { | ||
| // read file | ||
| const myInterface = readline.createInterface({ | ||
| input: fs.createReadStream(`${inputFolder}/${filename}`) | ||
| }) | ||
| let lineno = 0; | ||
| let data = []; | ||
| let size = {}; | ||
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| let fields = []; | ||
| let ranges = [0, 1]; | ||
| let ranges = [0,1]; | ||
| // read file | ||
| const myInterface = readline.createInterface({ | ||
| input: fs.createReadStream(`${inputFolder}/${filename}`) | ||
| }); | ||
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| remainder++; | ||
| myInterface.on('line', function(line) { | ||
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| myInterface.on('line', function (line) { | ||
| const record = JSON.parse(line); | ||
| if (lineno == 1) { | ||
| tempObject = record; | ||
| if(record.properties.metric_value == 0)return; | ||
| ++lineno; | ||
| if(lineno==1) { | ||
| fileTemps[filename] = record; | ||
| }; | ||
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| if (record.properties.metric_value == 0) return; | ||
| lineno++; | ||
| data.push([ | ||
| record.bbox[0], | ||
| record.bbox[1], | ||
| ...record.properties.multiheat_param.metric_array | ||
| ]); | ||
| }).on('close', () => { | ||
| const content = generateDoc(data); | ||
| if (!fs.existsSync(outputFolder)) fs.mkdirSync(outputFolder); | ||
| fs.writeFile(`${outputFolder}/NEW_${filename}`, content, function(err) { | ||
| if (err) throw err; | ||
| remainder--; | ||
| console.log(`${filename} completed`); | ||
| if (remainder == 0) console.log('finished'); | ||
| else console.log(`${remainder} Files remaining`); | ||
| // | ||
| }); | ||
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| record.bbox[0], | ||
| record.bbox[1], | ||
| ...record.properties.multiheat_param.metric_array]); | ||
| }).on('close',()=>{ | ||
| const content = generateDoc(data,filename); | ||
| if(!fs.existsSync(outputFolder)) fs.mkdirSync(outputFolder); | ||
| fs.writeFile(`${outputFolder}/NEW_${filename}`, content, function(err) { | ||
| console.log('close'); | ||
| if (err) throw err; | ||
| remainder--; | ||
| console.log(`${filename} completed`); | ||
| if(remainder == 0) console.log('finished'); | ||
| else console.log(`${remainder} Files remaining`); | ||
| }); | ||
| }); | ||
| } | ||
|
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| function generateDoc(data) { | ||
| const [x, y, x1, y1] = tempObject.bbox; | ||
| const width = x1 - x; | ||
| const height = y1 - y; | ||
| const fields = tempObject.properties.multiheat_param.heatname_array.map(d => { | ||
| return { | ||
| name: d, | ||
| range: [0, 1] | ||
| } | ||
| }); | ||
| return `{ | ||
| "provenance":{ | ||
| "image":{ | ||
| "subject_id":"${tempObject.provenance.image.subject_id}", | ||
| "case_id":"${tempObject.provenance.image.case_id}", | ||
| "slide": "${tempObject.provenance.image.subject_id}", | ||
| "specimen": "", | ||
| function generateDoc(data,filename){ | ||
| const [x,y,x1,y1] = fileTemps[filename].bbox; | ||
| const width = x1 - x; | ||
| const height = y1 - y; | ||
| const fields = fileTemps[filename].properties.multiheat_param.heatname_array.map(d =>{ | ||
| return{ | ||
| name:d, | ||
| range:[0,1] | ||
| }}); | ||
| return `{ | ||
| "provenance":{ | ||
| "image":{ | ||
| "subject_id":"${fileTemps[filename].provenance.image.subject_id}", | ||
| "case_id":"${fileTemps[filename].provenance.image.case_id}", | ||
| "slide": "${fileTemps[filename].provenance.image.subject_id}", | ||
| "specimen": "", | ||
| "study": "" | ||
| }, | ||
| "analysis":{ | ||
| "study_id":"${tempObject.provenance.analysis.study_id}", | ||
| "analysis":{ | ||
| "study_id":"${fileTemps[filename].provenance.analysis.study_id}", | ||
| "computation":"heatmap", | ||
| "size": [${width},${height}], | ||
| "fields":${JSON.stringify(fields)}, | ||
| "execution_id":"${tempObject.provenance.analysis.execution_id}", | ||
| "execution_id":"${fileTemps[filename].provenance.analysis.execution_id}", | ||
| "source":"computer" | ||
| } | ||
| }, | ||
| "data":${JSON.stringify(data)} | ||
| }`; | ||
| } | ||
| } |
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