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Correct the mapping on external resources links in supplementary info…
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…rmation page (#204)

* Decoupling external link resources from experiment

type

* Bump atlas-web-core

* Add autowired for link beans

* Refactor codes for arrayexpress

* Bump atlas-web-core

* [Chore] Bulk - Fix experiment design's memory issue  (#203)

* Remove experiment design field from Experiment

Temporary leave experimentDesign field on Experiment entity to pass the test. I am going to remove it in the last commit

* Refactor ExperimentsConditionsDetailsController

* Refactor BaselineExperimentAssayGroupsLines

* Refactor BaselineExperimentPageService

* Refactor HeatmapGroupingsService

* Refactor DifferentialExperimentPageService

* Refactor EvidenceService

* Refactor EvidenceService - left over

* Refactor ContrastSummaryController

* Refactor ExperimentPageContentService

* update with the latest atlas-web-core module changes

* Remove experimentDesign field from Experiment entity (latest core changes)

* Update to the latest atlas-web-core module changes

* Refactor getExperimentDesign method usage

* Refactor externalResourcesLinks

Co-authored-by: Károly Erdős <[email protected]>

* Bump atlas-web-core

* Refactor the external resources links

* Bump altas-web-core

* Decoupling external link resources from experiment

type

* Bump atlas-web-core

* Add autowired for link beans

* Refactor codes for arrayexpress

* Refactor externalResourcesLinks

Co-authored-by: Károly Erdős <[email protected]>

* Refactor the external resources links

---------

Co-authored-by: Károly Erdős <[email protected]>
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@lingyun1010 @ke4
lingyun1010 and ke4 authored Jul 23, 2024
1 parent c21eeba commit 3ec58e0
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200 changes: 85 additions & 115 deletions app/src/main/java/uk/ac/ebi/atlas/experimentpage/ExpressionAtlasContentService.java
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package uk.ac.ebi.atlas.experimentpage;

import com.google.common.collect.ImmutableList;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import uk.ac.ebi.atlas.experimentpage.differential.download.DifferentialSecondaryDataFiles;
import uk.ac.ebi.atlas.experimentpage.link.LinkToArrayExpress;
Expand All @@ -19,9 +20,10 @@

import javax.servlet.http.HttpServletResponse;
import java.net.URI;
import java.util.List;
import java.util.Map;
import java.util.function.Function;

import static com.google.common.collect.ImmutableList.toImmutableList;
import java.util.stream.Collectors;

@Component
public class ExpressionAtlasContentService {
Expand All @@ -33,26 +35,16 @@ public class ExpressionAtlasContentService {
bulkDifferentialExperimentExternallyAvailableContentService;
private final ExternallyAvailableContentService<MicroarrayExperiment>
microarrayExperimentExternallyAvailableContentService;
private final ExternallyAvailableContentService<BaselineExperiment>
rnaSeqBaselineExperimentExternallyAvailableContentServiceGeo;
private final ExternallyAvailableContentService<DifferentialExperiment>
rnaSeqDifferentialExperimentExternallyAvailableContentServiceGeo;
private final ExternallyAvailableContentService<MicroarrayExperiment>
microarrayExperimentExternallyAvailableContentServiceGeo;
private final ExternallyAvailableContentService<BaselineExperiment>
rnaSeqBaselineExperimentExternallyAvailableContentServiceEna;
private final ExternallyAvailableContentService<DifferentialExperiment>
bulkDifferentialExperimentExternallyAvailableContentServiceEna;
private final ExternallyAvailableContentService<MicroarrayExperiment>
microarrayExperimentExternallyAvailableContentServiceEna;
private final ExternallyAvailableContentService<BaselineExperiment>
bulkBaselineExperimentExternallyAvailableContentServiceEga;
private final ExternallyAvailableContentService<DifferentialExperiment>
bulkDifferentialExperimentExternallyAvailableContentServiceEga;
private final ExternallyAvailableContentService<MicroarrayExperiment>
microarrayExperimentExternallyAvailableContentServiceEga;

private final LinkToEna linkToEna;
private final LinkToEga linkToEga;
private final LinkToGeo linkToGeo;
private final LinkToPride linkToPride;
private final LinkToArrayExpress linkToArrayExpress;

private final ExperimentTrader experimentTrader;

@Autowired
public ExpressionAtlasContentService(
ExperimentDownloadSupplier.Proteomics proteomicsExperimentDownloadSupplier,
ExperimentDownloadSupplier.RnaSeqBaseline rnaSeqBaselineExperimentDownloadSupplier,
Expand All @@ -69,39 +61,31 @@ public ExpressionAtlasContentService(
ExperimentDesignFile.RnaSeq rnaSeqDifferentialExperimentDesignFile,
ExperimentDesignFile.Microarray microarrayExperimentDesignFile,
RnaSeqQcReport rnaSeqQCReport,
LinkToArrayExpress.RnaSeqBaseline rnaSeqBaselineLinkToArrayExpress,
LinkToArrayExpress.ProteomicsBaseline proteomicsBaselineLinkToArrayExpress,
LinkToArrayExpress.Differential differentialLinkToArrayExpress,
LinkToArrayExpress.Microarray microarrayLinkToArrayExpress,
LinkToArrayExpress linkToArrayExpress,
LinkToPride linkToPride,
LinkToEna.RnaSeqBaseline rnaSeqBaselineLinkToEna,
LinkToEna.Differential differentialLinkToEna,
LinkToEna.Microarray microarrayLinkToEna,
LinkToEga.RnaSeqBaseline rnaSeqBaselineLinkToEga,
LinkToEga.Differential differentialLinkToEga,
LinkToEga.Microarray microarrayLinkToEga,
LinkToGeo.RnaSeqBaseline rnaSeqBaselineLinkToGeo,
LinkToGeo.Differential differentialLinkToGeo,
LinkToGeo.Microarray microarrayLinkToGeo,
LinkToEna linkToEna,
LinkToEga linkToEga,
LinkToGeo linkToGeo,
ExperimentTrader experimentTrader) {
this.experimentTrader = experimentTrader;

this.linkToEna = linkToEna;
this.linkToEga = linkToEga;
this.linkToGeo = linkToGeo;
this.linkToPride = linkToPride;
this.linkToArrayExpress = linkToArrayExpress;
this.proteomicsBaselineExperimentExternallyAvailableContentService =
new ExternallyAvailableContentService<>(
ImmutableList.of(
proteomicsExperimentDownloadSupplier,
baselineStaticFilesDownload,
baselineExperimentDesignFile,
linkToPride,
proteomicsBaselineLinkToArrayExpress));
baselineExperimentDesignFile));

this.rnaSeqBaselineExperimentExternallyAvailableContentService =
new ExternallyAvailableContentService<>(
ImmutableList.of(
rnaSeqBaselineExperimentDownloadSupplier,
baselineStaticFilesDownload,
baselineExperimentDesignFile,
rnaSeqBaselineLinkToArrayExpress));
baselineExperimentDesignFile));

this.bulkDifferentialExperimentExternallyAvailableContentService =
new ExternallyAvailableContentService<>(
Expand All @@ -111,7 +95,6 @@ public ExpressionAtlasContentService(
rnaSeqDifferentialStaticFilesDownload,
rnaSeqDifferentialExperimentDesignFile,
rnaSeqQCReport,
differentialLinkToArrayExpress,
rnaSeqDifferentialContrastImageSupplier));

this.microarrayExperimentExternallyAvailableContentService =
Expand All @@ -121,35 +104,7 @@ public ExpressionAtlasContentService(
microarraySecondaryDataFiles,
microarrayStaticFilesDownload,
microarrayExperimentDesignFile,
microarrayLinkToArrayExpress,
microarrayContrastImageSupplier));

this.rnaSeqBaselineExperimentExternallyAvailableContentServiceGeo =
new ExternallyAvailableContentService<>(ImmutableList.of(rnaSeqBaselineLinkToGeo));

this.rnaSeqDifferentialExperimentExternallyAvailableContentServiceGeo =
new ExternallyAvailableContentService<>(ImmutableList.of(differentialLinkToGeo));

this.microarrayExperimentExternallyAvailableContentServiceGeo =
new ExternallyAvailableContentService<>(ImmutableList.of(microarrayLinkToGeo));

this.rnaSeqBaselineExperimentExternallyAvailableContentServiceEna =
new ExternallyAvailableContentService<>(ImmutableList.of(rnaSeqBaselineLinkToEna));

this.bulkDifferentialExperimentExternallyAvailableContentServiceEna =
new ExternallyAvailableContentService<>(ImmutableList.of(differentialLinkToEna));

this.microarrayExperimentExternallyAvailableContentServiceEna =
new ExternallyAvailableContentService<>(ImmutableList.of(microarrayLinkToEna));

this.bulkBaselineExperimentExternallyAvailableContentServiceEga =
new ExternallyAvailableContentService<>(ImmutableList.of(rnaSeqBaselineLinkToEga));

this.bulkDifferentialExperimentExternallyAvailableContentServiceEga =
new ExternallyAvailableContentService<>(ImmutableList.of(differentialLinkToEga));

this.microarrayExperimentExternallyAvailableContentServiceEga =
new ExternallyAvailableContentService<>(ImmutableList.of(microarrayLinkToEga));
}

public Function<HttpServletResponse, Void> stream(String experimentAccession, String accessKey, final URI uri) {
Expand All @@ -171,76 +126,91 @@ public Function<HttpServletResponse, Void> stream(String experimentAccession, St
}

public ImmutableList<ExternallyAvailableContent> list(String experimentAccession,
String accessKey,
ExternallyAvailableContent.ContentType contentType) {
String accessKey,
ExternallyAvailableContent.ContentType contentType) {
Experiment<?> experiment = experimentTrader.getExperiment(experimentAccession, accessKey);
String externalResourceType = externalResourceLinksPriority(experiment);
ImmutableList.Builder<ExternallyAvailableContent> arrayExpressAndOtherExternalResourcesLinks = ImmutableList.builder();
ImmutableList.Builder<ExternallyAvailableContent> otherExternalResourceLinks = ImmutableList.builder();
ImmutableList.Builder<ExternallyAvailableContent> externalResourcesLinks = ImmutableList.builder();
ImmutableList.Builder<ExternallyAvailableContent> otherExternalResourceLinks;

switch (experiment.getType()) {
case PROTEOMICS_BASELINE:
case PROTEOMICS_BASELINE_DIA:
arrayExpressAndOtherExternalResourcesLinks.addAll(
proteomicsBaselineExperimentExternallyAvailableContentService.list((BaselineExperiment) experiment, contentType));
externalResourcesLinks.addAll(proteomicsBaselineExperimentExternallyAvailableContentService.list((BaselineExperiment) experiment, contentType));
otherExternalResourceLinks = externalResourceLinks(experiment);
externalResourcesLinks.addAll(otherExternalResourceLinks.build());
break;
case RNASEQ_MRNA_BASELINE:
arrayExpressAndOtherExternalResourcesLinks.addAll(rnaSeqBaselineExperimentExternallyAvailableContentService.list(
externalResourcesLinks.addAll(rnaSeqBaselineExperimentExternallyAvailableContentService.list(
(BaselineExperiment) experiment, contentType));
otherExternalResourceLinks.addAll(externalResourceType.equals("geo") ?
rnaSeqBaselineExperimentExternallyAvailableContentServiceGeo.list(
(BaselineExperiment) experiment, contentType) :
externalResourceType.equals("ega") ?
bulkBaselineExperimentExternallyAvailableContentServiceEga.list(
(BaselineExperiment) experiment, contentType) :
rnaSeqBaselineExperimentExternallyAvailableContentServiceEna.list(
(BaselineExperiment) experiment, contentType));
arrayExpressAndOtherExternalResourcesLinks.addAll(otherExternalResourceLinks.build());
otherExternalResourceLinks = externalResourceLinks(experiment);
externalResourcesLinks.addAll(otherExternalResourceLinks.build());
break;
case RNASEQ_MRNA_DIFFERENTIAL:
case PROTEOMICS_DIFFERENTIAL:
arrayExpressAndOtherExternalResourcesLinks.addAll(bulkDifferentialExperimentExternallyAvailableContentService.list(
externalResourcesLinks.addAll(bulkDifferentialExperimentExternallyAvailableContentService.list(
(DifferentialExperiment) experiment, contentType));
otherExternalResourceLinks.addAll(externalResourceType.equals("geo") ?
rnaSeqDifferentialExperimentExternallyAvailableContentServiceGeo.list(
(DifferentialExperiment) experiment, contentType) :
externalResourceType.equals("ega") ?
bulkDifferentialExperimentExternallyAvailableContentServiceEga.list(
(DifferentialExperiment) experiment, contentType) :
bulkDifferentialExperimentExternallyAvailableContentServiceEna.list(
(DifferentialExperiment) experiment, contentType));
arrayExpressAndOtherExternalResourcesLinks.addAll(otherExternalResourceLinks.build());
otherExternalResourceLinks = externalResourceLinks(experiment);
externalResourcesLinks.addAll(otherExternalResourceLinks.build());
break;
case MICROARRAY_1COLOUR_MRNA_DIFFERENTIAL:
case MICROARRAY_2COLOUR_MRNA_DIFFERENTIAL:
case MICROARRAY_1COLOUR_MICRORNA_DIFFERENTIAL:
arrayExpressAndOtherExternalResourcesLinks.addAll(microarrayExperimentExternallyAvailableContentService.list(
(MicroarrayExperiment) experiment, contentType));
otherExternalResourceLinks.addAll(externalResourceType.equals("geo") ?
microarrayExperimentExternallyAvailableContentServiceGeo.list(
(MicroarrayExperiment) experiment, contentType) :
externalResourceType.equals("ega") ?
microarrayExperimentExternallyAvailableContentServiceEga.list(
(MicroarrayExperiment) experiment, contentType) :
microarrayExperimentExternallyAvailableContentServiceEna.list(
(MicroarrayExperiment) experiment, contentType));
arrayExpressAndOtherExternalResourcesLinks.addAll(otherExternalResourceLinks.build());
externalResourcesLinks.addAll(microarrayExperimentExternallyAvailableContentService.list((MicroarrayExperiment) experiment, contentType));
otherExternalResourceLinks = externalResourceLinks(experiment);
externalResourcesLinks.addAll(otherExternalResourceLinks.build());
break;
default:
throw new IllegalArgumentException(experiment.getType() + ": experiment type not supported.");
}

return arrayExpressAndOtherExternalResourcesLinks.build();
if (experimentAccession.matches("E-MTAB.*|E-ERAD.*|E-GEUV.*")) {
externalResourcesLinks.addAll(linkToArrayExpress.get(experiment));
}

return externalResourcesLinks.build();
}

private String externalResourceLinksPriority(Experiment<?> experiment) {
var geoAccessions = experiment.getSecondaryAccessions().stream()
.filter(accession -> accession.matches("GSE.*"))
.collect(toImmutableList());
var egaAccessions = experiment.getSecondaryAccessions().stream()
.filter(accession -> accession.matches("EGA.*"))
.collect(toImmutableList());
private ImmutableList.Builder<ExternallyAvailableContent> externalResourceLinks(Experiment<?> experiment) {
ImmutableList.Builder<ExternallyAvailableContent> otherExternalResourceLinks = ImmutableList.builder();

return geoAccessions.isEmpty() ? egaAccessions.isEmpty() ? "ena" : "ega" : "geo";
Map<String, List<String>> resourceList = experiment.getSecondaryAccessions().stream()
.collect(Collectors.groupingBy(accession -> {
if (accession.matches("GSE.*")) return "GEO";
if (accession.matches("EGA.*")) return "EGA";
if (accession.matches("PDX.*")) return "PRIDE";
if (accession.matches("ERP.*|SRP.*|DRP.*|PRJEB.*|PRJNA.*|PRJDB.*")) return "ENA";
return "OTHER";
}));

resourceList.entrySet().removeIf(entry -> {
String resource = entry.getKey();
var accessions = entry.getValue().stream()
.collect(Collectors.collectingAndThen(Collectors.toList(), ImmutableList::copyOf));

switch (resource) {
case "GEO":
otherExternalResourceLinks.addAll(linkToGeo.get(experiment));
break;
case "EGA":
otherExternalResourceLinks.addAll(linkToEga.get(experiment));
break;
case "ENA":
otherExternalResourceLinks.addAll(linkToEna.get(experiment));
break;
case "PRIDE":
otherExternalResourceLinks.addAll(linkToPride.get(experiment));
break;
case "OTHER":
// Remove this entry by returning true
return true;
}

// Update the entry's value
entry.setValue(accessions);
return false;
});

return otherExternalResourceLinks;
}

}
2 changes: 1 addition & 1 deletion atlas-web-core
Submodule atlas-web-core updated 9 files
+20 −37 src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToArrayExpress.java
+2 −18 src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToEga.java
+2 −22 src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToEna.java
+2 −18 src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToGeo.java
+4 −4 src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToPride.java
+5 −28 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToArrayExpressIT.java
+6 −60 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToEgaIT.java
+6 −57 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToEnaIT.java
+6 −61 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToGeoIT.java

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