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tests.ts
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tests.ts
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import * as atomic from "./req/operations/atomicOperations";
import {registerOperations} from "./req/tests/registerOperations";
import {rebuildRTDirectory} from "./req/main/rebuildRTDirectory";
import {getUnSortedBam,getSam} from "./req/alignData";
import * as L6R1R1 from "./req/tests/L6R1R1";
import * as L6R1R2 from "./req/tests/L6R1R2";
import * as hpv16Ref from "./req/tests/hpv16Ref";
import * as hpv18Ref from "./req/tests/hpv18Ref";
import * as hpv16Figure from "./req/tests/hpv16Figure";
import * as L6R1HPV16Align from "./req/tests/L6R1HPV16Align";
import * as L6R1HPV18Align from "./req/tests/L6R1HPV18Align";
import * as L6R7R1 from "./req/tests/L6R7R1";
import * as L6R7R2 from "./req/tests/L6R7R2";
import * as L6R1HPV16AlignImported from "./req/tests/L6R1HPV16AlignImported";
import * as L6R1HPV18AlignImported from "./req/tests/L6R1HPV18AlignImported";
import {testVersionParser} from "./req/tests/testVersionParser";
import {testFastQCReportGeneration} from "./req/tests/testFastQCReportGeneration";
import {testHPV16Index} from "./req/tests/testHPV16Index";
import {testHPV18Index} from "./req/tests/testHPV18Index";
import {testHPV16IndexForVisualization} from "./req/tests/testHPV16IndexForVisualization";
import {testHPV18IndexForVisualization} from "./req/tests/testHPV18IndexForVisualization";
import {testL6R1HPV16Alignment} from "./req/tests/testL6R1HPV16Alignment";
import {testL6R1HPV18Alignment} from "./req/tests/testL6R1HPV18Alignment"
import {testL6R1HPV16CoverageTrackRenderer} from "./req/tests/testL6R1HPV16CoverageTrackRender";
import {testL6R1HPV16SNPTrackRenderer} from "./req/tests/testL6R1HPV16SNPTrackRender";
import {testL6R1HPV16CoverageTrackCompilation} from "./req/tests/testL6R1HPV16CoverageTrackCompilation";
import {testL6R1HPV16SNPTrackCompilation} from "./req/tests/testL6R1HPV16SNPTrackCompilation";
import {testL6R1HPV18CoverageTrackRenderer} from "./req/tests/testL6R1HPV18CoverageTrackRender";
import {testL6R1HPV18SNPTrackRenderer} from "./req/tests/testL6R1HPV18SNPTrackRender";
import {testL6R1HPV16AlignImportedImporting} from "./req/tests/testL6R1HPV16AlignImportedImporting";
import {testL6R1HPV16AlignImportedLinking} from "./req/tests/testL6R1HPV16AlignImportedLinking";
import {testL6R1HPV18AlignImportedImporting} from "./req/tests/testL6R1HPV18AlignImportedImporting";
import {testL6R1HPV18AlignImportedLinking} from "./req/tests/testL6R1HPV18AlignImportedLinking";
import {testL6R1HPV16NoHeaderSAMImporting} from "./req/tests/testL6R1HPV16NoHeaderSAMImporting";
import {testL6R7HPV16Alignment} from "./req/tests/testL6R7HPV16Alignment";
import {testL6R7HPV16CoverageTrackRenderer} from "./req/tests/testL6R7HPV16CoverageTrackRenderer";
import {testL6R7HPV16SNPTrackRenderer} from "./req/tests/testL6R7HPV16SNPTrackRender";
import {testL6R7HPV16CoverageTrackCompilation} from "./req/tests/testL6R7HPV16CoverageTrackCompilation";
import {testL6R7HPV16SNPTrackCompilation} from "./req/tests/testL6R7HPV16SNPTrackCompilation";
import {runBLASTSegmentTests} from "./req/tests/runBLASTSegmentTests";
const pjson = require("./resources/app/package.json");
import {isBeta,versionIsGreaterThan} from "./req/versionIsGreaterThan";
let opsRunner = setInterval(function(){atomic.runOperations(1);},1000);
async function runTests() : Promise<void>
{
return new Promise<void>(async (resolve,reject) => {
console.log("Testing version parsing");
try
{
await testVersionParser();
}
catch(err)
{
return reject();
}
console.log("Validating version in package.json")
try
{
let beta = isBeta(pjson.version);
}
catch(err)
{
console.log("Version in package.json is malformed");
return reject();
}
console.log("Generating FastQC report for L6R1R1");
atomic.addOperation("generateFastQCReport",L6R1R1.get());
try
{
await testFastQCReportGeneration();
}
catch(err)
{
console.log("failed to generate FastQC report for L6R1R1");
return reject();
}
console.log("Generating FastQC report for L6R1R2");
atomic.addOperation("generateFastQCReport",L6R1R2.get());
try
{
await testFastQCReportGeneration();
}
catch(err)
{
console.log("failed to generate FastQC report for L6R1R2");
return reject();
}
console.log("Starting to index hpv16");
atomic.addOperation("indexFastaForBowTie2Alignment",hpv16Ref.get());
try
{
await testHPV16Index();
}
catch(err)
{
console.log("test index threw exception");
return reject();
}
console.log("Starting to index hpv18");
atomic.addOperation("indexFastaForBowTie2Alignment",hpv18Ref.get());
try
{
await testHPV18Index();
}
catch(err)
{
console.log("test index threw exception");
return reject();
}
console.log("Starting to index hpv16 for visualization");
atomic.addOperation("indexFastaForVisualization",hpv16Ref.get());
try
{
await testHPV16IndexForVisualization();
}
catch(err)
{
console.log("test index for visualization threw exception");
return reject();
}
console.log("Starting to index hpv18 for visualization");
atomic.addOperation("indexFastaForVisualization",hpv18Ref.get());
try
{
await testHPV18IndexForVisualization();
}
catch(err)
{
console.log("test index for visualization threw exception");
return reject();
}
console.log("Starting to align L6R1R1, L6R1R2 against hpv16");
atomic.addOperation(
"runAlignment",
{
fasta : hpv16Ref.get(),
fastq1 : L6R1R1.get(),
fastq2 : L6R1R2.get()
}
);
try
{
await testL6R1HPV16Alignment();
}
catch(err)
{
console.log("test alignment threw exception");
return reject();
}
console.log("Starting to align L6R1R1, L6R1R2 against hpv18");
atomic.addOperation(
"runAlignment",
{
fasta : hpv18Ref.get(),
fastq1 : L6R1R1.get(),
fastq2 : L6R1R2.get()
}
);
try
{
await testL6R1HPV18Alignment();
}
catch(err)
{
console.log("test alignment threw exception");
return reject();
}
console.log("Rendering coverage track for L6R1 alignment against HPV16")
try
{
await testL6R1HPV16CoverageTrackRenderer();
}
catch(err)
{
console.log("coverage track rendering threw exception");
return reject();
}
console.log("Rendering SNP track for L6R1 alignment against HPV16")
try
{
await testL6R1HPV16SNPTrackRenderer();
}
catch(err)
{
console.log("SNP track rendering threw exception");
return reject();
}
console.log("Compiling coverage track for L6R1 alignment against HPV16");
try
{
await testL6R1HPV16CoverageTrackCompilation();
}
catch(err)
{
console.log("Coverage track compilation threw exception");
return reject();
}
console.log("Compiling SNP track for L6R1 alignment against HPV16");
try
{
await testL6R1HPV16SNPTrackCompilation();
}
catch(err)
{
console.log("SNP track compilation threw exception");
return reject();
}
console.log("Rendering coverage track for L6R1 alignment against HPV18")
try
{
await testL6R1HPV18CoverageTrackRenderer();
}
catch(err)
{
console.log("coverage track rendering threw exception");
return reject();
}
console.log("Rendering SNP track for L6R1 alignment against HPV18")
try
{
await testL6R1HPV18SNPTrackRenderer();
}
catch(err)
{
console.log("coverage track rendering threw exception");
return reject();
}
console.log("Importing binary alignment map from L6R1 HPV16 alignment");
atomic.addOperation("inputBamFile",{
bamPath : getUnSortedBam(L6R1HPV16Align.get())});
try
{
await testL6R1HPV16AlignImportedImporting();
}
catch(err)
{
console.log("bam importing threw exception");
return reject();
}
console.log("Linking imported L6R1 HPV16 binary alignment map to HPV16");
atomic.addOperation("linkRefSeqToAlignment",{
align : L6R1HPV16AlignImported.get(),
fasta : hpv16Ref.get()
});
try
{
await testL6R1HPV16AlignImportedLinking();
}
catch(err)
{
console.log("bam linking threw exception");
return reject();
}
console.log("Importing binary alignment map from L6R1 HPV18 alignment");
atomic.addOperation("inputBamFile",{
bamPath : getUnSortedBam(L6R1HPV18Align.get())
});
try
{
await testL6R1HPV18AlignImportedImporting();
}
catch(err)
{
console.log("bam importing threw exception "+err);
return reject();
}
console.log("Linking imported L6R1 HPV18 binary alignment map to HPv18");
atomic.addOperation("linkRefSeqToAlignment",{
align : L6R1HPV18AlignImported.get(),
fasta : hpv18Ref.get()
});
try
{
await testL6R1HPV18AlignImportedLinking();
}
catch(err)
{
console.log("bam linking threw exception");
return reject();
}
console.log("Importing sequence alignment map from L6R1 HPV16 alignment");
atomic.addOperation("inputBamFile",{
bamPath : getSam(L6R1HPV16Align.get())
});
try
{
await testL6R1HPV16AlignImportedImporting();
}
catch(err)
{
console.log("sam importing threw exception");
return reject();
}
console.log("Linking imported L6R1 HPV16 sequence alignment map to HPV16");
atomic.addOperation("linkRefSeqToAlignment",{
align : L6R1HPV16AlignImported.get(),
fasta : hpv16Ref.get()
});
try
{
await testL6R1HPV16AlignImportedLinking();
}
catch(err)
{
console.log("sam linking threw exception");
return reject();
}
console.log("Importing sequence alignment map from L6R1 HPV18 alignment");
atomic.addOperation("inputBamFile",{
bamPath : getSam(L6R1HPV18Align.get())
});
try
{
await testL6R1HPV18AlignImportedImporting();
}
catch(err)
{
console.log("sam importing threw exception "+err);
return reject();
}
console.log("Linking imported L6R1 HPV18 sequence alignment map to HPv18");
atomic.addOperation("linkRefSeqToAlignment",{
align : L6R1HPV18AlignImported.get(),
fasta : hpv18Ref.get()
});
try
{
await testL6R1HPV18AlignImportedLinking();
}
catch(err)
{
console.log("sam linking threw exception");
return reject();
}
console.log("Importing headerless sequence alignment map");
atomic.addOperation("inputBamFile",{
bamPath : "data/L6R1HPV16NoHeader.sam"
});
try
{
await testL6R1HPV16AlignImportedImporting();
}
catch(err)
{
console.log("importing headerless sam threw (expected) exception "+err);
}
console.log("Importing headerless sequence aligment map with ref seq")
atomic.addOperation("inputBamFile",{
bamPath : "data/L6R1HPV16NoHeader.sam",
fasta : hpv16Ref.get()
});
try
{
await testL6R1HPV16NoHeaderSAMImporting();
}
catch(err)
{
console.log("importing headerless sam with ref seq threw exception "+err);
return reject();
}
console.log("Starting to align L6R7R1, L6R7R2 against hpv16");
atomic.addOperation(
"runAlignment",
{
fasta : hpv16Ref.get(),
fastq1 : L6R7R1.get(),
fastq2 : L6R7R2.get()
}
);
try
{
await testL6R7HPV16Alignment();
}
catch(err)
{
console.log("test alignment threw exception");
return reject();
}
console.log("Rendering coverage track for L6R7 alignment against HPV16")
try
{
await testL6R7HPV16CoverageTrackRenderer();
}
catch(err)
{
console.log("coverage track rendering threw exception");
return reject();
}
console.log("Rendering SNP track for L6R7 alignment against HPV16")
try
{
await testL6R7HPV16SNPTrackRenderer();
}
catch(err)
{
console.log("SNP track rendering threw exception");
return reject();
}
console.log("Compiling coverage track for L6R7 alignment against HPV16");
try
{
await testL6R7HPV16CoverageTrackCompilation();
}
catch(err)
{
console.log("Coverage track compilation threw exception");
return reject();
}
console.log("Compiling SNP track for L6R7 alignment against HPV16");
try
{
await testL6R7HPV16SNPTrackCompilation();
}
catch(err)
{
console.log("SNP track compilation threw exception");
return reject();
}
resolve();
});
}
setTimeout(function(){
(async function(){
rebuildRTDirectory();
registerOperations();
L6R1R1.loadNoSpaces();
L6R1R2.loadNoSpaces();
hpv16Ref.loadNoSpaces();
hpv18Ref.loadNoSpaces();
L6R7R1.loadNoSpaces();
L6R7R2.loadNoSpaces();
try
{
await runTests();
//BLAST tests rely on NCBI BLAST actually being online and usuable.
//It's a full end-to-end integration test, actually making requests to NCBI.
//If NCBI is experiencing high-traffic or is having issues, it will be reflected in issues with these tests.
//We separate these tests out and ensure they only run once instead of once with and without spaces being present
//in resource paths.
await runBLASTSegmentTests();
}
catch(err)
{
console.log("run tests threw exception");
clearInterval(opsRunner);
process.exit(1);
}
L6R1R1.loadSpaces();
L6R1R2.loadSpaces();
hpv16Ref.loadNoSpaces();
hpv18Ref.loadNoSpaces();
L6R7R1.loadSpaces();
L6R7R2.loadSpaces();
try
{
await runTests();
}
catch(err)
{
console.log("run tests threw exception");
clearInterval(opsRunner);
process.exit(1);
}
clearInterval(opsRunner);
process.exit(0);
})();
},1000);