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[Feature] Improve Anndata experiment page appearance #397

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May 9, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -57,4 +57,9 @@ public Experiment getExperiment(String experimentAccession) {
idfParser.parse(experimentDto.getExperimentAccession()),
sdrfParser.parseSingleCellTechnologyType(experimentDto.getExperimentAccession()));
}

@Override
public String getExperimentType(String experimentAccession) {
return experimentCrudDao.getExperimentType(experimentAccession);
}
}
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt" %>

<div id="experimentDescription" class="row column expanded">
<div class="media-object stack-for-small">
<div class="media-object stack-for-small ${fn:startsWith(experimentAccession, 'E-ANND-') ? 'anndata' : ''}">
<c:if test="${fn:startsWith(experimentAccession, 'E-EHCA-')}">
<div class="media-object-section middle paddin-right-medium">
<a class="clear padding-right-xlarge" href="https://preview.data.humancellatlas.org/">
Expand Down Expand Up @@ -99,5 +99,12 @@
</div>
</c:if>
</div>
<c:if test="${fn:startsWith(experimentAccession, 'E-ANND-')}">
<div class="experiment-type-icon">
<img src="${pageContext.request.contextPath}/resources/images/experiment-type/anndata.png"
alt="Experiment with annotated data from external source"
style="height: 100px;">
</div>
</c:if>
</div>
</div>
11 changes: 11 additions & 0 deletions app/src/main/webapp/resources/css/atlas.css
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,17 @@
padding-right: 0;
}

.media-object.stack-for-small.anndata {
background: lightyellow;
display: flex;
}

.experiment-type-icon {
margin-left: auto;
margin-right: 10px;
margin-top: 10px;
}

a.clear {
border-bottom: none;
}
Expand Down
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2 changes: 1 addition & 1 deletion atlas-web-core
Submodule atlas-web-core updated 58 files
+0 −3 build.gradle
+17 −0 src/main/java/uk/ac/ebi/atlas/experimentimport/ExperimentCrudDao.java
+3 −2 src/main/java/uk/ac/ebi/atlas/experimentpage/ExternallyAvailableContentService.java
+31 −8 src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToPride.java
+9 −81 src/main/java/uk/ac/ebi/atlas/model/experiment/Experiment.java
+2 −11 src/main/java/uk/ac/ebi/atlas/model/experiment/ExperimentDesign.java
+101 −0 src/main/java/uk/ac/ebi/atlas/model/experiment/ExperimentDesignTable.java
+15 −20 src/main/java/uk/ac/ebi/atlas/model/experiment/ExperimentType.java
+9 −0 src/main/java/uk/ac/ebi/atlas/model/experiment/baseline/BaselineExperiment.java
+0 −7 src/main/java/uk/ac/ebi/atlas/model/experiment/differential/microarray/MicroarrayExperiment.java
+0 −6 src/main/java/uk/ac/ebi/atlas/model/experiment/sdrf/SampleCharacteristics.java
+6 −7 src/main/java/uk/ac/ebi/atlas/model/experiment/summary/AssayGroupSummaryBuilder.java
+13 −19 src/main/java/uk/ac/ebi/atlas/model/experiment/summary/ContrastSummaryBuilder.java
+1 −1 src/main/java/uk/ac/ebi/atlas/model/resource/XmlFile.java
+11 −0 src/main/java/uk/ac/ebi/atlas/model/resource/XmlFileConfigurationException.java
+1 −1 src/main/java/uk/ac/ebi/atlas/solr/cloud/collections/BulkAnalyticsCollectionProxy.java
+10 −0 src/main/java/uk/ac/ebi/atlas/testutils/JdbcUtils.java
+0 −78 src/main/java/uk/ac/ebi/atlas/testutils/TestExperiment.java
+0 −87 src/main/java/uk/ac/ebi/atlas/trader/ExperimentDesignDao.java
+0 −14 src/main/java/uk/ac/ebi/atlas/trader/ExperimentDesignData.java
+3 −0 src/main/java/uk/ac/ebi/atlas/trader/ExperimentRepository.java
+4 −0 src/main/java/uk/ac/ebi/atlas/trader/ExperimentTrader.java
+50 −23 src/main/java/uk/ac/ebi/atlas/trader/factory/BaselineExperimentFactory.java
+12 −1 src/test/java/uk/ac/ebi/atlas/configuration/TestConfig.java
+25 −0 src/test/java/uk/ac/ebi/atlas/experimentimport/ExperimentCrudDaoIT.java
+2 −2 src/test/java/uk/ac/ebi/atlas/experimentimport/analyticsindex/AnalyticsIndexerManagerTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/experimentimport/analyticsindex/DifferentialExperimentDataPointTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/experimentimport/analyticsindex/stream/BaselineExperimentDataPointTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/experimentimport/analyticsindex/stream/MicroarrayExperimentDataPointTest.java
+0 −1 src/test/java/uk/ac/ebi/atlas/experimentpage/ExternallyAvailableContentServiceTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToArrayExpressIT.java
+1 −1 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToEgaIT.java
+1 −1 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToEnaIT.java
+1 −1 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToGeoIT.java
+43 −3 src/test/java/uk/ac/ebi/atlas/experimentpage/link/LinkToPrideIT.java
+4 −4 src/test/java/uk/ac/ebi/atlas/experiments/ExperimentJsonSerializerTest.java
+26 −26 src/test/java/uk/ac/ebi/atlas/model/experiment/ExperimentBuilder.java
+71 −3 src/test/java/uk/ac/ebi/atlas/model/experiment/ExperimentTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/model/experiment/baseline/BaselineExperimentTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/model/experiment/differential/DifferentialExperimentTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/model/experiment/singlecell/SingleCellBaselineExperimentTest.java
+0 −59 src/test/java/uk/ac/ebi/atlas/model/experiment/summary/AssayGroupSummaryBuilderTest.java
+0 −50 src/test/java/uk/ac/ebi/atlas/model/experiment/summary/ContrastPropertyTest.java
+0 −89 src/test/java/uk/ac/ebi/atlas/model/experiment/summary/ContrastSummaryBuilderTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/profiles/ProfileStreamFilterTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/profiles/differential/microarray/MicroarrayProfileStreamFactoryTest.java
+1 −1 .../java/uk/ac/ebi/atlas/profiles/stream/BulkDifferentialProfileStreamFactoryPickUpExpressionsByIndexTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/profiles/stream/MicroarrayProfileStreamFactoryReadValuesTest.java
+1 −1 src/test/java/uk/ac/ebi/atlas/profiles/stream/RnaSeqProfileStreamFactoryTest.java
+2 −0 src/test/java/uk/ac/ebi/atlas/solr/analytics/query/AnalyticsQueryClientIT.java
+0 −89 src/test/java/uk/ac/ebi/atlas/trader/ExperimentDesignDaoIT.java
+28 −1 src/test/java/uk/ac/ebi/atlas/trader/ExperimentTraderTest.java
+72 −34 src/test/java/uk/ac/ebi/atlas/trader/factory/BaselineExperimentFactoryTest.java
+0 −9 src/test/java/uk/ac/ebi/atlas/trader/factory/SingleCellBaselineExperimentFactoryTest.java
+0 −1 src/test/resources/fixtures/scxa/scxa_exp_design-delete.sql
+0 −300 src/test/resources/fixtures/scxa/scxa_exp_design.sql
+0 −1 src/test/resources/fixtures/scxa/scxa_exp_design_column-delete.sql
+0 −15 src/test/resources/fixtures/scxa/scxa_exp_design_column.sql
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