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Merge pull request #58 from metabolomics-us/QA
FIEHNLAB-1820/Calculate all possible adducts for spectra
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1 change: 1 addition & 0 deletions
1
backend/app/server/proxy/src/main/mona-web/src/app/mocks/user.model.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| export class User { | ||
| emailAddress: string; | ||
| id: string; | ||
| firstName: string; | ||
| lastName: string; | ||
| institution: string; | ||
|
|
||
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83 changes: 83 additions & 0 deletions
83
...a/edu/ucdavis/fiehnlab/mona/backend/curation/processor/metadata/CalculateAllAdducts.scala
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| package edu.ucdavis.fiehnlab.mona.backend.curation.processor.metadata | ||
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| import com.typesafe.scalalogging.LazyLogging | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.domain.{Compound, MetaData, Spectrum} | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.workflow.annotations.Step | ||
| import edu.ucdavis.fiehnlab.mona.backend.curation.util.chemical.AdductBuilder | ||
| import edu.ucdavis.fiehnlab.mona.backend.curation.util.{CommonMetaData, CurationUtilities} | ||
| import org.springframework.batch.item.ItemProcessor | ||
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| import scala.collection.mutable.ArrayBuffer | ||
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| @Step(description = "this step will calculate all possible adducts") | ||
| class CalculateAllAdducts extends ItemProcessor[Spectrum, Spectrum] with LazyLogging { | ||
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| private val PRECURSOR_MATCH_TOLERANCE: Double = 0.5 | ||
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| /** | ||
| * processes the given spectrum | ||
| * | ||
| * @param spectrum to be processed | ||
| * @return processed spectrum | ||
| */ | ||
| override def process(spectrum: Spectrum): Spectrum = { | ||
| // Get computed total exact mass from the biological compound if it exists | ||
| if(spectrum.tags.exists(x => x.text == "GC-MS")) { | ||
| logger.info(s"Process is only for LC-MS spectra") | ||
| spectrum | ||
| } else { | ||
| val biologicalIndex: Int = | ||
| if (spectrum.compound.exists(_.kind == "biological")) { | ||
| spectrum.compound.indexWhere(_.kind == "biological") | ||
| } else if (spectrum.compound.nonEmpty) { | ||
| 0 | ||
| } else { | ||
| -1 | ||
| } | ||
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| if (biologicalIndex == -1) { | ||
| logger.info(s"${spectrum.id}: Valid compound could not be found!") | ||
| spectrum | ||
| } else { | ||
| // Get total exact mass from biological compound | ||
| val theoreticalMass: Double = { | ||
| val x: String = CurationUtilities.findMetaDataValue(spectrum.compound(biologicalIndex).metaData, CommonMetaData.TOTAL_EXACT_MASS) | ||
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| if (x == null) { | ||
| -1 | ||
| } else { | ||
| x.toDouble | ||
| } | ||
| } | ||
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| val biologicalCompound = spectrum.compound(biologicalIndex) | ||
| val adductMap = AdductBuilder.LCMS_POSITIVE_ADDUCTS ++ AdductBuilder.LCMS_NEGATIVE_ADDUCTS | ||
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| val updatedMetadata: ArrayBuffer[MetaData] = new ArrayBuffer[MetaData]() | ||
| biologicalCompound.metaData.foreach(x => updatedMetadata.append(x)) | ||
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| val updatedCompoundSet: ArrayBuffer[Compound] = new ArrayBuffer[Compound]() | ||
| spectrum.compound.foreach(x => updatedCompoundSet.append(x)) | ||
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| if (theoreticalMass < 0) { | ||
| logger.info(s"${spectrum.id}: Computed exact mass was not found, unable to generate adduct information") | ||
| spectrum | ||
| } else { | ||
| adductMap.foreach { | ||
| case (x, f) => updatedMetadata.append(MetaData("theoretical adduct", true, true, x, null, null, null, f(theoreticalMass))) | ||
| } | ||
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| val updatedCompound = biologicalCompound.copy( | ||
| metaData = updatedMetadata.toArray | ||
| ) | ||
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| updatedCompoundSet.update(biologicalIndex, updatedCompound) | ||
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| spectrum.copy( | ||
| compound = updatedCompoundSet.toArray | ||
| ) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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24 changes: 24 additions & 0 deletions
24
...st/scala/edu/ucdavis/fiehnlab/mona/backend/curation/config/EmbeddedRestServerConfig.scala
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| package edu.ucdavis.fiehnlab.mona.backend.curation.config | ||
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| import com.typesafe.scalalogging.LazyLogging | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.auth.jwt.service.MongoLoginService | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.domain.service.LoginService | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.persistence.rest.server.config.RestServerConfig | ||
| import org.springframework.context.annotation.{Bean, Configuration, Import} | ||
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| /** | ||
| * Created by wohlg on 3/11/2016. | ||
| */ | ||
| @Configuration | ||
| @Import(Array(classOf[RestServerConfig])) | ||
| class EmbeddedRestServerConfig extends LazyLogging { | ||
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| /** | ||
| * the service which actually does the login for us | ||
| * | ||
| * @return | ||
| */ | ||
| @Bean | ||
| def loginService: LoginService = new MongoLoginService | ||
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| } |
27 changes: 27 additions & 0 deletions
27
...c/test/scala/edu/ucdavis/fiehnlab/mona/backend/curation/config/RestClientTestConfig.scala
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| package edu.ucdavis.fiehnlab.mona.backend.curation.config | ||
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| import edu.ucdavis.fiehnlab.mona.backend.core.auth.jwt.service.MongoLoginService | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.auth.rest.config.AuthSecurityConfig | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.domain.service.LoginService | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.persistence.rest.client.config.RestClientConfig | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.persistence.rest.client.service.RestLoginService | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.statistics.config.StatisticsRepositoryConfig | ||
| import org.springframework.beans.factory.annotation.Value | ||
| import org.springframework.boot.autoconfigure.SpringBootApplication | ||
| import org.springframework.context.annotation.{Bean, Import, Primary} | ||
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| /** | ||
| * Created by wohlgemuth on 3/15/16. | ||
| */ | ||
| @Import(Array(classOf[RestClientConfig], classOf[EmbeddedRestServerConfig], classOf[AuthSecurityConfig], classOf[StatisticsRepositoryConfig])) | ||
| @SpringBootApplication | ||
| class RestClientTestConfig { | ||
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| @Bean | ||
| @Primary | ||
| def loginService(@Value("${mona.rest.server.host}") host: String, @Value("${mona.rest.server.port}") port: Int): LoginService = | ||
| new RestLoginService("localhost", port) | ||
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| @Bean | ||
| def loginServiceDelegate: LoginService = new MongoLoginService | ||
| } |
35 changes: 35 additions & 0 deletions
35
...u/ucdavis/fiehnlab/mona/backend/curation/processor/metadata/CalculateAllAdductsTest.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| package edu.ucdavis.fiehnlab.mona.backend.curation.processor.metadata | ||
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| import com.typesafe.scalalogging.LazyLogging | ||
| import org.scalatest.matchers.should.Matchers | ||
| import org.scalatest.wordspec.AnyWordSpec | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.domain.Spectrum | ||
| import edu.ucdavis.fiehnlab.mona.backend.core.domain.io.json.JSONDomainReader | ||
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| import java.io.InputStreamReader | ||
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| class CalculateAllAdductsTest extends AnyWordSpec with Matchers with LazyLogging{ | ||
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| val reader: JSONDomainReader[Spectrum] = JSONDomainReader.create[Spectrum] | ||
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| "this processor" when { | ||
| val processor = new CalculateAllAdducts | ||
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| val exampleRecord: Spectrum = JSONDomainReader.create[Spectrum].read(new InputStreamReader(getClass.getResourceAsStream("/monaRecord2.json"))) | ||
| "given a spectra" must { | ||
| "correctly calculate adduct list" in { | ||
| val processedSpectrum = processor.process(exampleRecord) | ||
| logger.info(s"${processedSpectrum.compound(0).metaData.filter(x => x.category == "theoretical adduct")}") | ||
| assert(processedSpectrum.compound(0).metaData.filter(x => x.category == "theoretical adduct").length == 16) | ||
| } | ||
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| "spot check calculations" in { | ||
| val processedSpectrum = processor.process(exampleRecord) | ||
| val sortedMetaData = processedSpectrum.compound(0).metaData.filter(x => x.category == "theoretical adduct") | ||
| sortedMetaData.find(x => x.name == "[M+H]+").get.value shouldBe 165.041395368 | ||
| sortedMetaData.find(x => x.name == "[2M+NH4]+").get.value shouldBe 346.105430736 | ||
| sortedMetaData.find(x => x.name == "[2M+HAc-H]-").get.value shouldBe 387.110880736 | ||
| } | ||
| } | ||
| } | ||
| } |
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