Refactor experiment's external resource handling

src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToArrayExpress.java

@@ -1,19 +1,13 @@
 package uk.ac.ebi.atlas.experimentpage.link;
 
 import org.apache.commons.lang3.tuple.Pair;
-import org.jetbrains.annotations.NotNull;
 import org.springframework.stereotype.Component;
-import org.springframework.web.reactive.function.client.WebClient;
 import org.springframework.web.util.DefaultUriBuilderFactory;
 import org.springframework.web.util.UriBuilder;
 import uk.ac.ebi.atlas.model.download.ExternallyAvailableContent;
 import uk.ac.ebi.atlas.model.experiment.Experiment;
-import uk.ac.ebi.atlas.model.experiment.baseline.BaselineExperiment;
-import uk.ac.ebi.atlas.model.experiment.differential.DifferentialExperiment;
 import uk.ac.ebi.atlas.model.experiment.differential.microarray.MicroarrayExperiment;
-import uk.ac.ebi.atlas.model.experiment.singlecell.SingleCellBaselineExperiment;
 
-import java.net.URI;
 import java.text.MessageFormat;
 import java.util.Collection;
 import java.util.function.Function;
@@ -23,44 +17,31 @@
 
 @Component
 public class LinkToArrayExpress {
-    // You’ll get a 302 if the last slash is missing!
+
+    private final ResourceLinkGenerator resourceLinkGenerator;
+
+    public LinkToArrayExpress(ResourceLinkGenerator resourceLinkGenerator) {
+        this.resourceLinkGenerator = resourceLinkGenerator;
+    }
+
     private static final UriBuilder BIOSTUDIES_API_URI_BUILDER =
             new DefaultUriBuilderFactory().builder()
                     .scheme("https")
                     .host("www.ebi.ac.uk")
                     .pathSegment("biostudies")
-                    .pathSegment("api")
-                    .pathSegment("v1")
-                    .pathSegment("studies")
-                    .pathSegment("{0}");
-    // You’ll get a 302 if the last slash is missing!
-    private static final UriBuilder EXPERIMENTS_URI_BUILDER =
-            new DefaultUriBuilderFactory().builder()
-                    .scheme("https")
-                    .host("www.ebi.ac.uk")
-                    .pathSegment("arrayexpress")
-                    .pathSegment("experiments")
-                    .pathSegment("{0}")
-                    .path("/");
-    private static final UriBuilder ARRAYS_URI_BUILDER =
-            new DefaultUriBuilderFactory().builder()
-                    .scheme("https")
-                    .host("www.ebi.ac.uk")
                     .pathSegment("arrayexpress")
-                    .pathSegment("arrays")
                     .pathSegment("{0}")
-                    .path("/");
-    private static final WebClient webClient = WebClient.create();
+                    .pathSegment("{1}");
 
-    private static final Function<Experiment, String> formatLabelToExperiment =
+    private static final Function<Experiment<?>, String> formatLabelToExperiment =
             e -> MessageFormat.format("ArrayExpress: experiment {0}", e.getAccession());
     private static final Function<String, String> formatLabelToArray =
             arrayAccession -> MessageFormat.format("ArrayExpress: array design {0}", arrayAccession);
 
     private static final Function<String, ExternallyAvailableContent.Description> createIcon =
             label -> ExternallyAvailableContent.Description.create("icon-ae", label);
 
-    private static final Function<Experiment, ExternallyAvailableContent.Description> createIconForExperiment =
+    private static final Function<Experiment<?>, ExternallyAvailableContent.Description> createIconForExperiment =
             formatLabelToExperiment.andThen(createIcon);
     private static final Function<String, ExternallyAvailableContent.Description> createIconForArray =
             formatLabelToArray.andThen(createIcon);
@@ -69,21 +50,21 @@ public ExternallyAvailableContent.ContentType contentType() {
         return ExternallyAvailableContent.ContentType.SUPPLEMENTARY_INFORMATION;
     }
 
-    public Collection<ExternallyAvailableContent> get(Experiment experiment) {
+    public Collection<ExternallyAvailableContent> get(Experiment<?> experiment) {
+
         var externalLinkFromExperiment = Stream.of(experiment.getAccession())
-                .map(accession -> Pair.of(EXPERIMENTS_URI_BUILDER.build(accession), BIOSTUDIES_API_URI_BUILDER.build(accession)))
-                .filter(pairOfLinks -> LinkToArrayExpress.isUriValid(pairOfLinks.getRight()))
-                .map(Pair::getLeft)
+                .map(accession -> BIOSTUDIES_API_URI_BUILDER.build("studies", accession))
+                .filter(resourceLinkGenerator::isUriValid)
                 .map(uri -> new ExternallyAvailableContent(
                         uri.toString(),
                         createIconForExperiment.apply(experiment)));
-        if(experiment.getType().isMicroarray()) {
+        if (experiment.getType().isMicroarray()) {
             return Stream.concat(
                             externalLinkFromExperiment,
                             ((MicroarrayExperiment) experiment).getArrayDesignAccessions().stream()
                                     .parallel()
-                                    .map(accession -> Pair.of(ARRAYS_URI_BUILDER.build(accession), accession))
-                                    .filter(uriAccession -> isUriValid(uriAccession.getLeft()))
+                                    .map(accession -> Pair.of(BIOSTUDIES_API_URI_BUILDER.build("arrays", accession), accession))
+                                    .filter(uriAccession -> resourceLinkGenerator.isUriValid(uriAccession.getLeft()))
                                     .map(uriAccession -> new ExternallyAvailableContent(
                                             uriAccession.getLeft().toString(),
                                             createIconForArray.apply(uriAccession.getRight()))))
@@ -92,18 +73,4 @@ public Collection<ExternallyAvailableContent> get(Experiment experiment) {
 
          return externalLinkFromExperiment.collect(toImmutableList());
     }
-
-    private static boolean isUriValid(@NotNull URI uri) {
-        try {
-            return !webClient
-                    .get()
-                    .uri(uri)
-                    .exchange()
-                    .block()
-                    .statusCode()
-                    .isError();
-        } catch (Exception e) {
-            return false;
-        }
-    }
 }

src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToEga.java

@@ -8,17 +8,24 @@
 
 import java.text.MessageFormat;
 import java.util.Collection;
+import java.util.Map;
 import java.util.function.Function;
 
+import static java.util.Map.entry;
+
 @Component
 public class LinkToEga {
     private static final UriBuilder EGA_URI_BUILDER =
             new DefaultUriBuilderFactory().builder()
                     .scheme("https")
                     .host("www.ebi.ac.uk")
                     .pathSegment("ega")
-                    .pathSegment("studies")
-                    .pathSegment("{0}");
+                    .pathSegment("{0}")
+                    .pathSegment("{1}");
+    private static final Map<String, String> EGA_RESOURCE_TYPE_MAPPING = Map.ofEntries(
+            entry("EGAD.*", "datasets"),
+            entry("EGAS.*", "studies")
+    );
 
     private static final Function<String, String> formatLabelToEga =
             arrayAccession -> MessageFormat.format("EGA: {0}", arrayAccession);
@@ -33,8 +40,7 @@ public ExternallyAvailableContent.ContentType contentType() {
         return ExternallyAvailableContent.ContentType.SUPPLEMENTARY_INFORMATION;
     }
 
-    public Collection<ExternallyAvailableContent> get(Experiment experiment) {
-        return GenerateResourceLinks.getLinks(experiment, "EGA.*", EGA_URI_BUILDER, createIconForEga);
+    public Collection<ExternallyAvailableContent> get(Experiment<?> experiment) {
+        return new ResourceLinkGenerator().getLinks(experiment, EGA_RESOURCE_TYPE_MAPPING, EGA_URI_BUILDER, createIconForEga);
     }
-
 }

src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToEna.java

@@ -8,18 +8,24 @@
 
 import java.text.MessageFormat;
 import java.util.Collection;
+import java.util.Map;
 import java.util.function.Function;
 
+import static java.util.Map.entry;
+
 @Component
 public class LinkToEna {
     private static final UriBuilder ENA_URI_BUILDER =
             new DefaultUriBuilderFactory().builder()
                     .scheme("https")
                     .host("www.ebi.ac.uk")
                     .pathSegment("ena")
-                    .pathSegment("data")
-                    .pathSegment("view")
-                    .pathSegment("{0}");
+                    .pathSegment("browser")
+                    .pathSegment("{0}")
+                    .pathSegment("{1}");
+    private static final Map<String, String> ENA_RESOURCE_TYPE_MAPPING = Map.ofEntries(
+            entry("[DES]RP.*", "view")
+    );
 
     private static final Function<String, String> formatLabelToEna =
             arrayAccession -> MessageFormat.format("ENA: {0}", arrayAccession);
@@ -34,8 +40,7 @@ public ExternallyAvailableContent.ContentType contentType() {
         return ExternallyAvailableContent.ContentType.SUPPLEMENTARY_INFORMATION;
     }
 
-    public Collection<ExternallyAvailableContent> get(Experiment experiment) {
-        return GenerateResourceLinks.getLinks(experiment, "[^G]*", ENA_URI_BUILDER, createIconForEna);
+    public Collection<ExternallyAvailableContent> get(Experiment<?> experiment) {
+        return new ResourceLinkGenerator().getLinks(experiment, ENA_RESOURCE_TYPE_MAPPING, ENA_URI_BUILDER, createIconForEna);
     }
-
 }

src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToGeo.java

@@ -5,15 +5,15 @@
 import org.springframework.web.util.UriBuilder;
 import uk.ac.ebi.atlas.model.download.ExternallyAvailableContent;
 import uk.ac.ebi.atlas.model.experiment.Experiment;
-import uk.ac.ebi.atlas.model.experiment.baseline.BaselineExperiment;
-import uk.ac.ebi.atlas.model.experiment.differential.DifferentialExperiment;
-import uk.ac.ebi.atlas.model.experiment.differential.microarray.MicroarrayExperiment;
-import uk.ac.ebi.atlas.model.experiment.singlecell.SingleCellBaselineExperiment;
+import uk.ac.ebi.atlas.model.experiment.sample.ReportsGeneExpression;
 
 import java.text.MessageFormat;
 import java.util.Collection;
+import java.util.Map;
 import java.util.function.Function;
 
+import static java.util.Map.entry;
+
 @Component
 public class LinkToGeo {
     private static final UriBuilder GEO_URI_BUILDER =
@@ -22,8 +22,11 @@ public class LinkToGeo {
                     .host("www.ncbi.nlm.nih.gov")
                     .pathSegment("geo")
                     .pathSegment("query")
-                    .pathSegment("acc.cgi")
-                    .queryParam("acc", "{0}");
+                    .pathSegment("{0}")
+                    .queryParam("acc", "{1}");
+    private static final Map<String, String> GEO_RESOURCE_TYPE_MAPPING = Map.ofEntries(
+            entry(".*G(SE|DS).*", "acc.cgi")
+    );
 
     private static final Function<String, String> formatLabelToGeo =
             arrayAccession -> MessageFormat.format("GEO: {0}", arrayAccession);
@@ -38,8 +41,8 @@ public ExternallyAvailableContent.ContentType contentType() {
         return ExternallyAvailableContent.ContentType.SUPPLEMENTARY_INFORMATION;
     }
 
-    public Collection<ExternallyAvailableContent> get(Experiment experiment) {
-        return GenerateResourceLinks.getLinks(experiment, "GSE.*", GEO_URI_BUILDER, createIconForGeo);
+    public Collection<ExternallyAvailableContent> get(Experiment<? extends ReportsGeneExpression> experiment) {
+        return new ResourceLinkGenerator().getLinks(experiment, GEO_RESOURCE_TYPE_MAPPING, GEO_URI_BUILDER, createIconForGeo);
     }
 
 }

src/main/java/uk/ac/ebi/atlas/experimentpage/link/LinkToPride.java

@@ -1,16 +1,14 @@
 package uk.ac.ebi.atlas.experimentpage.link;
 
 import com.google.common.collect.ImmutableSet;
+import org.jetbrains.annotations.NotNull;
 import org.springframework.stereotype.Component;
 import uk.ac.ebi.atlas.model.download.ExternallyAvailableContent;
 import uk.ac.ebi.atlas.model.experiment.Experiment;
-import uk.ac.ebi.atlas.model.experiment.baseline.BaselineExperiment;
 
 import java.text.MessageFormat;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
-import org.jetbrains.annotations.NotNull;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
@@ -24,15 +22,20 @@ public class LinkToPride {
     private static final Function<String, ExternallyAvailableContent.Description> createIcon =
             formatLabel.andThen(label -> ExternallyAvailableContent.Description.create("icon-pride", label));
 
-    public Collection<ExternallyAvailableContent> get(Experiment experiment) {
-        ImmutableSet<String> secondaryAccessions = experiment.getSecondaryAccessions();
+    public List<ExternallyAvailableContent> get(Experiment<?> experiment) {
+        var secondaryAccessions = experiment.getSecondaryAccessions();
 
-        if (!secondaryAccessions.isEmpty()) {
+        if (noSecondaryAccession(secondaryAccessions)) {
             return getExternallyAvailableContents(secondaryAccessions);
         } else {
             return emptyContent();
         }
     }
+
+    private boolean noSecondaryAccession(ImmutableSet<String> secondaryAccessions) {
+        return secondaryAccessions != null && !secondaryAccessions.isEmpty();
+    }
+
     @NotNull
     private static List<ExternallyAvailableContent> emptyContent() {
         return Collections.emptyList();

src/main/java/uk/ac/ebi/atlas/experimentpage/link/ResourceLinkGenerator.java

@@ -0,0 +1,63 @@
+package uk.ac.ebi.atlas.experimentpage.link;
+
+import com.google.common.collect.ImmutableList;
+import org.springframework.stereotype.Component;
+import org.springframework.web.reactive.function.client.WebClient;
+import org.springframework.web.util.UriBuilder;
+import uk.ac.ebi.atlas.model.download.ExternallyAvailableContent;
+import uk.ac.ebi.atlas.model.experiment.Experiment;
+
+import java.net.URI;
+import java.util.Map;
+import java.util.Objects;
+import java.util.function.Function;
+
+@Component
+public class ResourceLinkGenerator {
+    private static final WebClient webClient = WebClient.create();
+
+    public ImmutableList<ExternallyAvailableContent> getLinks(Experiment<?> experiment,
+                                                                     Map<String, String> resourceTypeMapping,
+                                                                     UriBuilder uriBuilder,
+                                                                     Function<String, ExternallyAvailableContent.Description> createIcon) {
+        if (noSecondaryAccession(experiment)) {
+            return ImmutableList.of();
+        }
+
+        return experiment.getSecondaryAccessions().stream()
+                .map(accession -> getResourceLink(resourceTypeMapping, uriBuilder, createIcon, accession))
+                .filter(Objects::nonNull)
+                .collect(ImmutableList.toImmutableList());
+    }
+
+    private ExternallyAvailableContent getResourceLink(Map<String, String> resourceTypeMapping,
+                                                              UriBuilder uriBuilder,
+                                                              Function<String, ExternallyAvailableContent.Description> createIcon,
+                                                              String accession) {
+        var link = uriBuilder.build(getPathSegment(resourceTypeMapping, accession), accession);
+        return isUriValid(link) ?
+                new ExternallyAvailableContent(link.toString(), createIcon.apply(accession)) :
+                null;
+    }
+
+    private boolean noSecondaryAccession(Experiment<?> experiment) {
+        return experiment.getSecondaryAccessions() == null || experiment.getSecondaryAccessions().isEmpty();
+    }
+
+    private String getPathSegment(Map<String, String> resourceTypeMapping, String accession) {
+        return resourceTypeMapping.entrySet().stream()
+                .filter(entry -> accession.matches(entry.getKey()))
+                .findFirst()
+                .map(Map.Entry::getValue)
+                .orElse("");
+    }
+
+    public boolean isUriValid(URI uri) {
+        var response = webClient
+                .get()
+                .uri(uri)
+                .exchange()
+                .block();
+        return response != null && !response.statusCode().isError();
+    }
+}