Add url decoder for cell type heatmap search (#355)

* Add url decoder for cell type heatmap search * Cover the case when cell type contains a forward slash * Fix the test for checking the empty payload and improve the naming of the test methods --------- Co-authored-by: Karoly Erdos <[email protected]>
ebi-gene-expression-group · Oct 4, 2023 · 4839fdb · 4839fdb
1 parent a994341
commit 4839fdb
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Showing 2 changed files with 30 additions and 6 deletions.
diff --git a/...ava/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesController.java b/...ava/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesController.java
@@ -9,6 +9,8 @@
 import uk.ac.ebi.atlas.controllers.JsonExceptionHandlingController;
 import uk.ac.ebi.atlas.experimentpage.markergenes.HighchartsHeatmapAdapter;
 
+import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
 import java.util.Collection;
 
 import static uk.ac.ebi.atlas.utils.GsonProvider.GSON;
@@ -33,8 +35,10 @@ public String getCellTypeMarkerGenes(
         return GSON.toJson(
                 highchartsHeatmapAdapter.getMarkerGeneHeatmapDataSortedLexicographically(
                         experimentAccessions == null ?
-                                multiexperimentCellTypeMarkerGenesService.getCellTypeMarkerGeneProfile(cellType) :
                                 multiexperimentCellTypeMarkerGenesService.getCellTypeMarkerGeneProfile(
-                                        ImmutableSet.copyOf(experimentAccessions), cellType)));
+                                        URLDecoder.decode(cellType, StandardCharsets.UTF_8)) :
+                                multiexperimentCellTypeMarkerGenesService.getCellTypeMarkerGeneProfile(
+                                        ImmutableSet.copyOf(experimentAccessions),
+                                        URLDecoder.decode(cellType, StandardCharsets.UTF_8))));
     }
 }
diff --git a/.../uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesControllerWIT.java b/.../uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesControllerWIT.java
@@ -14,6 +14,11 @@
 import org.springframework.web.context.WebApplicationContext;
 import uk.ac.ebi.atlas.configuration.TestConfig;
 
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
+
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.isA;
 import static org.springframework.test.context.jdbc.Sql.ExecutionPhase.AFTER_TEST_METHOD;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
@@ -56,9 +61,22 @@ void setUp() {
     }
 
     @Test
-    void returnsAValidJsonPayloadForAValidCellType() throws Exception {
+    void shouldReturnAValidJsonPayloadForAValidCellType() throws Exception {
         this.mockMvc.perform(get("/json/cell-type-marker-genes/{cellType}", "cell cycle S phase")
-                .param("experimentAccession", "E-ENAD-53"))
+                        .param("experimentAccession", "E-ENAD-53"))
+                .andExpect(status().isOk())
+                .andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+                .andExpect(jsonPath("$[0].cellGroupValue", isA(String.class)))
+                .andExpect(jsonPath("$[0].value", isA(Number.class)))
+                .andExpect(jsonPath("$[0].cellGroupValueWhereMarker", isA(String.class)))
+                .andExpect(jsonPath("$[0].pValue", isA(Number.class)));
+    }
+
+    @Test
+    void shouldReturnAValidJsonPayloadForACellTypeContainingAForwardSlash() throws Exception {
+        final String encodedCellType = URLEncoder.encode("cell cycle G2/M phase", StandardCharsets.UTF_8);
+        this.mockMvc.perform(get("/json/cell-type-marker-genes/{cellType}", encodedCellType)
+                        .param("experimentAccession", "E-ENAD-53"))
                 .andExpect(status().isOk())
                 .andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
                 .andExpect(jsonPath("$[0].cellGroupValue", isA(String.class)))
@@ -68,9 +86,11 @@ void returnsAValidJsonPayloadForAValidCellType() throws Exception {
     }
 
     @Test
-    void returnsEmptyPayloadForAnInvalidCellType() throws Exception {
+    void shouldReturnEmptyPayloadForAnInvalidCellType() throws Exception {
         this.mockMvc.perform(get("/json/cell-type-marker-genes/{cellType}", "fooBar")
                 .param("experimentAccession", "E-CURD-4"))
-                .andExpect(status().isOk());
+                .andExpect(status().isOk())
+                .andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+                .andExpect(jsonPath("$", is(empty())));
     }
 }