From 9b69e8dd6f7ca1dcd17cbf2c6d84c2586db6af51 Mon Sep 17 00:00:00 2001
From: jnizet <jb@ninja-squad.com>
Date: Fri, 19 Nov 2021 09:28:29 +0100
Subject: [PATCH] feat: display germplasm PUI in germplasm card
---
.../faidare/web/germplasm/GermplasmModel.java | 49 ++++++++++---------
.../main/resources/templates/germplasm.html | 15 ++++++
.../germplasm/GermplasmControllerTest.java | 2 +-
3 files changed, 43 insertions(+), 23 deletions(-)
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java
index ffa24336..da82e809 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java
@@ -11,7 +11,7 @@ import fr.inra.urgi.faidare.domain.data.germplasm.SiteVO;
import fr.inra.urgi.faidare.domain.datadiscovery.data.DataSource;
import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
import fr.inra.urgi.faidare.web.site.MapLocation;
-import org.apache.logging.log4j.util.Strings;
+import org.springframework.util.StringUtils;
/**
* The model used by the germplasm page
@@ -57,13 +57,13 @@ public final class GermplasmModel {
}
public String getTaxon() {
- if (Strings.isNotBlank(this.germplasm.getGenusSpeciesSubtaxa())) {
+ if (StringUtils.hasText(this.germplasm.getGenusSpeciesSubtaxa())) {
return this.germplasm.getGenusSpeciesSubtaxa();
- } else if (Strings.isNotBlank(this.germplasm.getGenusSpecies())) {
+ } else if (StringUtils.hasText(this.germplasm.getGenusSpecies())) {
return this.germplasm.getGenusSpecies();
- } else if (Strings.isNotBlank(this.germplasm.getSubtaxa())) {
+ } else if (StringUtils.hasText(this.germplasm.getSubtaxa())) {
return this.germplasm.getGenus() + " " + this.germplasm.getSpecies() + " " + this.germplasm.getSubtaxa();
- } else if (Strings.isNotBlank(this.germplasm.getSpecies())) {
+ } else if (StringUtils.hasText(this.germplasm.getSpecies())) {
return this.germplasm.getGenus() + " " + this.germplasm.getSpecies();
} else {
return this.germplasm.getGenus();
@@ -71,13 +71,13 @@ public final class GermplasmModel {
}
public String getTaxonAuthor() {
- if (Strings.isNotBlank(this.germplasm.getGenusSpeciesSubtaxa())) {
+ if (StringUtils.hasText(this.germplasm.getGenusSpeciesSubtaxa())) {
return this.germplasm.getSubtaxaAuthority();
- } else if (Strings.isNotBlank(this.germplasm.getGenusSpecies())) {
+ } else if (StringUtils.hasText(this.germplasm.getGenusSpecies())) {
return this.germplasm.getSpeciesAuthority();
- } else if (Strings.isNotBlank(this.germplasm.getSubtaxa())) {
+ } else if (StringUtils.hasText(this.germplasm.getSubtaxa())) {
return this.germplasm.getSubtaxaAuthority();
- } else if (Strings.isNotBlank(this.germplasm.getSpecies())) {
+ } else if (StringUtils.hasText(this.germplasm.getSpecies())) {
return this.germplasm.getSpeciesAuthority();
} else {
return null;
@@ -91,34 +91,34 @@ public final class GermplasmModel {
}
private boolean isCollectingSitePresent() {
- return this.germplasm.getCollectingSite() != null && Strings.isNotBlank(this.germplasm.getCollectingSite().getSiteName());
+ return this.germplasm.getCollectingSite() != null && StringUtils.hasText(this.germplasm.getCollectingSite().getSiteName());
}
private boolean isCollectorInstitutePresent() {
return this.germplasm.getCollector() != null &&
this.germplasm.getCollector().getInstitute() != null &&
- Strings.isNotBlank(this.germplasm.getCollector().getInstitute().getInstituteName());
+ StringUtils.hasText(this.germplasm.getCollector().getInstitute().getInstituteName());
}
private boolean isCollectorIntituteFieldPresent() {
GermplasmInstituteVO collector = this.germplasm.getCollector();
return (collector != null) &&
- (Strings.isNotBlank(collector.getAccessionNumber())
+ (StringUtils.hasText(collector.getAccessionNumber())
|| collector.getAccessionCreationDate() != null
- || Strings.isNotBlank(collector.getMaterialType())
- || Strings.isNotBlank(collector.getCollectors())
+ || StringUtils.hasText(collector.getMaterialType())
+ || StringUtils.hasText(collector.getCollectors())
|| collector.getRegistrationYear() != null
|| collector.getDeregistrationYear() != null
- || Strings.isNotBlank(collector.getDistributionStatus())
+ || StringUtils.hasText(collector.getDistributionStatus())
);
}
public boolean isBreeding() {
GermplasmInstituteVO breeder = this.germplasm.getBreeder();
return breeder != null &&
- ((breeder.getInstitute() != null && Strings.isNotBlank(breeder.getInstitute().getInstituteName())) ||
+ ((breeder.getInstitute() != null && StringUtils.hasText(breeder.getInstitute().getInstituteName())) ||
breeder.getAccessionCreationDate() != null ||
- Strings.isNotBlank(breeder.getAccessionNumber()) ||
+ StringUtils.hasText(breeder.getAccessionNumber()) ||
breeder.getRegistrationYear() != null ||
breeder.getDeregistrationYear() != null);
}
@@ -133,11 +133,11 @@ public final class GermplasmModel {
private boolean isPedigreePresent() {
return this.pedigree != null &&
- (Strings.isNotBlank(this.pedigree.getParent1Name())
- || Strings.isNotBlank(this.pedigree.getParent2Name())
- || Strings.isNotBlank(this.pedigree.getCrossingPlan())
- || Strings.isNotBlank(this.pedigree.getCrossingYear())
- || Strings.isNotBlank(this.pedigree.getFamilyCode()));
+ (StringUtils.hasText(this.pedigree.getParent1Name())
+ || StringUtils.hasText(this.pedigree.getParent2Name())
+ || StringUtils.hasText(this.pedigree.getCrossingPlan())
+ || StringUtils.hasText(this.pedigree.getCrossingYear())
+ || StringUtils.hasText(this.pedigree.getFamilyCode()));
}
public List<MapLocation> getMapLocations() {
@@ -154,4 +154,9 @@ public final class GermplasmModel {
return MapLocation.sitesToDisplayableMapLocations(sites);
}
+
+ public boolean isPuiDisplayedAsLink() {
+ String pui = this.germplasm.getGermplasmPUI();
+ return pui != null && (pui.startsWith("https://doi.org") || pui.startsWith("http://doi.org"));
+ }
}
diff --git a/backend/src/main/resources/templates/germplasm.html b/backend/src/main/resources/templates/germplasm.html
index 79742fba..9de8fa5e 100644
--- a/backend/src/main/resources/templates/germplasm.html
+++ b/backend/src/main/resources/templates/germplasm.html
@@ -90,6 +90,21 @@
<div
th:replace="fragments/row::text-row(label='Accession number', text=${model.germplasm.accessionNumber})"
></div>
+ <div
+ th:replace="fragments/row::row(label='Germplasm PUI', content=~{::#germplasm-pui})"
+ >
+ <th:block id="germplasm-pui">
+ <a
+ th:if="${model.puiDisplayedAsLink}"
+ th:href="${model.germplasm.germplasmPUI}"
+ th:text="${model.germplasm.germplasmPUI}"
+ ></a>
+ <span
+ th:unless="${model.puiDisplayedAsLink}"
+ th:text="${model.germplasm.germplasmPUI}"
+ ></span>
+ </th:block>
+ </div>
<div
th:replace="fragments/source::source(source=${model.source}, url=${model.germplasm.url}, entityType='germplasm')"
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/web/germplasm/GermplasmControllerTest.java b/backend/src/test/java/fr/inra/urgi/faidare/web/germplasm/GermplasmControllerTest.java
index bb25798d..ab1ff169 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/web/germplasm/GermplasmControllerTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/web/germplasm/GermplasmControllerTest.java
@@ -215,7 +215,7 @@ public class GermplasmControllerTest {
}
@Test
- void shouldExporPlantMaterials() throws Exception {
+ void shouldExportPlantMaterials() throws Exception {
List<GermplasmVO> germplasms = Arrays.asList(
Fixtures.createGermplasm(),
Fixtures.createGermplasm()
--
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