Bugfix/make the inferred cell type options dynamic shown or disabled in marker gene heatmap dropdown menu

app/src/main/java/uk/ac/ebi/atlas/experimentpage/markergenes/MarkerGeneService.java

@@ -1,6 +1,5 @@
 package uk.ac.ebi.atlas.experimentpage.markergenes;
 
-import com.google.common.collect.ImmutableCollection;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableSet;
 import org.springframework.stereotype.Service;
@@ -64,6 +63,7 @@ public ImmutableList<MarkerGene> getCellTypeMarkerGeneHeatmapData(String experim
                 .filter(markerGene -> !markerGene.cellGroupValueWhereMarker().equalsIgnoreCase("Not available"))
                 .collect(toImmutableList());
     }
+
     /**
      * @param experimentAccession - Id of the experiment
      * @param k                   - no of clusters
@@ -73,4 +73,9 @@ public ImmutableList<MarkerGene> getCellTypeMarkerGeneHeatmapData(String experim
     public ImmutableList<MarkerGene> getMarkerGenesPerCluster(String experimentAccession, String k) {
         return ImmutableList.copyOf(markerGenesDao.getMarkerGenesWithAveragesPerCluster(experimentAccession, k));
     }
+
+    public Integer isMarkerGenesAvailableForTheInferredCellTypes(String experimentAccession, String cellGroupType) {
+        return markerGenesDao.getMarkerGenesForTheInferredCellTypes(experimentAccession, cellGroupType);
+    }
+
 }

app/src/main/java/uk/ac/ebi/atlas/experimentpage/markergenes/MarkerGenesDao.java

@@ -9,14 +9,8 @@
 
 @Repository
 public class MarkerGenesDao {
-    private final NamedParameterJdbcTemplate namedParameterJdbcTemplate;
     static final String CELL_TYPE_ONTOLOGY_LABELS = "inferred cell type - ontology labels";
     static final String CELL_TYPE_AUTHOR_LABELS = "inferred cell type - authors labels";
-
-    public MarkerGenesDao(NamedParameterJdbcTemplate namedParameterJdbcTemplate) {
-        this.namedParameterJdbcTemplate = namedParameterJdbcTemplate;
-    }
-
     private static final String SELECT_MARKER_GENES_WITH_AVERAGES_PER_CLUSTER =
             "SELECT " +
                     "g.experiment_accession, " +
@@ -46,41 +40,13 @@ public MarkerGenesDao(NamedParameterJdbcTemplate namedParameterJdbcTemplate) {
             "ORDER BY " +
                     "m.marker_probability";
 
-    public List<MarkerGene> getMarkerGenesWithAveragesPerCluster(String experimentAccession, String k) {
-        var namedParameters =
-                ImmutableMap.of(
-                        "experiment_accession", experimentAccession,
-                        "k", k);
-
-        return namedParameterJdbcTemplate.query(
-                SELECT_MARKER_GENES_WITH_AVERAGES_PER_CLUSTER,
-                namedParameters,
-                (resultSet, rowNumber) -> MarkerGene.create(
-                        resultSet.getString("gene_id"),
-                        resultSet.getString("k_where_marker"),
-                        resultSet.getString("cluster_id_where_marker"),
-                        resultSet.getDouble("marker_p_value"),
-                        resultSet.getString("cluster_id"),
-                        resultSet.getDouble("median_expression"),
-                        resultSet.getDouble("mean_expression"),
-                        resultSet.getString("expression_unit")));
-    }
-
     private static final String SELECT_DISTINCT_KS_WITH_MARKER_GENES =
             "SELECT DISTINCT h.variable as k_where_marker " +
                     "FROM scxa_cell_group_marker_genes m, scxa_cell_group h " +
                     "WHERE m.cell_group_id = h.id AND " +
                     "h.experiment_accession = :experiment_accession AND m.marker_probability < 0.05 " +
                     "ORDER BY k_where_marker ASC";
 
-    public List<String> getKsWithMarkerGenes(String experimentAccession) {
-        var namedParameters = ImmutableMap.of("experiment_accession", experimentAccession);
-        return namedParameterJdbcTemplate.queryForList(
-                SELECT_DISTINCT_KS_WITH_MARKER_GENES,
-                namedParameters,
-                String.class);
-    }
-
     private static final String SELECT_MARKER_GENES_WITH_AVERAGES_PER_CELL_GROUP =
             "SELECT " +
                     "g.experiment_accession, " +
@@ -111,6 +77,81 @@ public List<String> getKsWithMarkerGenes(String experimentAccession) {
             "ORDER BY " +
                     "m.marker_probability ";
 
+    private static final String SELECT_MARKER_GENES_WITH_AVERAGES_PER_CELL_GROUP_ALL =
+            "SELECT " +
+                    "g.experiment_accession, " +
+                    "m.gene_id, " +
+                    "g.variable AS cell_group_type, " +
+                    "h.value AS cell_group_value_where_marker, " +
+                    "g.value AS cell_group_value, " +
+                    "m.marker_probability AS marker_p_value, " +
+                    "s.mean_expression, " +
+                    "s.median_expression, " +
+                    "e.expression_unit " +
+            "FROM " +
+                    "scxa_cell_group_marker_gene_stats s, " +
+                    "scxa_cell_group_marker_genes m, " +
+                    "scxa_cell_group g, " +
+                    "scxa_cell_group h, " +
+                    "experiment e " +
+            "WHERE " +
+                    "s.cell_group_id = g.id AND " +
+                    "s.marker_id = m.id AND " +
+                    "m.cell_group_id = h.id AND " +
+                    "g.experiment_accession = :experiment_accession AND " +
+                    "m.marker_probability < 0.05 AND " +
+                    "g.variable = :variable AND " +
+                    "s.expression_type = 0 AND " +
+                    "e.accession = g.experiment_accession " +
+            "ORDER BY " +
+                    "m.marker_probability ";
+
+    private static final String SELECT_MARKER_GENES_FOR_INFERRED_CELL_TYPES =
+            "SELECT count(m.gene_id) as marker_genes " +
+            "FROM " +
+                    "scxa_cell_group_marker_genes m, " +
+                    "scxa_cell_group h " +
+            "WHERE " +
+                    "m.cell_group_id = h.id AND " +
+                    "h.experiment_accession = :experiment_accession AND " +
+                    "m.marker_probability < 0.05 AND " +
+                    "h.variable= :variable " +
+            "LIMIT  1";
+
+    private final NamedParameterJdbcTemplate namedParameterJdbcTemplate;
+
+    public MarkerGenesDao(NamedParameterJdbcTemplate namedParameterJdbcTemplate) {
+        this.namedParameterJdbcTemplate = namedParameterJdbcTemplate;
+    }
+
+    public List<MarkerGene> getMarkerGenesWithAveragesPerCluster(String experimentAccession, String k) {
+        var namedParameters =
+                ImmutableMap.of(
+                        "experiment_accession", experimentAccession,
+                        "k", k);
+
+        return namedParameterJdbcTemplate.query(
+                SELECT_MARKER_GENES_WITH_AVERAGES_PER_CLUSTER,
+                namedParameters,
+                (resultSet, rowNumber) -> MarkerGene.create(
+                        resultSet.getString("gene_id"),
+                        resultSet.getString("k_where_marker"),
+                        resultSet.getString("cluster_id_where_marker"),
+                        resultSet.getDouble("marker_p_value"),
+                        resultSet.getString("cluster_id"),
+                        resultSet.getDouble("median_expression"),
+                        resultSet.getDouble("mean_expression"),
+                        resultSet.getString("expression_unit")));
+    }
+
+    public List<String> getKsWithMarkerGenes(String experimentAccession) {
+        var namedParameters = ImmutableMap.of("experiment_accession", experimentAccession);
+        return namedParameterJdbcTemplate.queryForList(
+                SELECT_DISTINCT_KS_WITH_MARKER_GENES,
+                namedParameters,
+                String.class);
+    }
+
     public List<MarkerGene> getCellTypeMarkerGenesOntologyLabels(String experimentAccession,
                                                                  ImmutableCollection<String> cellGroupValues) {
         return getCellTypeMarkerGenes(experimentAccession, CELL_TYPE_ONTOLOGY_LABELS, cellGroupValues);
@@ -148,34 +189,6 @@ public List<MarkerGene> getCellTypeMarkerGenes(String experiment_accession,
                         resultSet.getString("expression_unit")));
     }
 
-    private static final String SELECT_MARKER_GENES_WITH_AVERAGES_PER_CELL_GROUP_ALL =
-            "SELECT " +
-                    "g.experiment_accession, " +
-                    "m.gene_id, " +
-                    "g.variable AS cell_group_type, " +
-                    "h.value AS cell_group_value_where_marker, " +
-                    "g.value AS cell_group_value, " +
-                    "m.marker_probability AS marker_p_value, " +
-                    "s.mean_expression, " +
-                    "s.median_expression, " +
-                    "e.expression_unit " +
-            "FROM " +
-                    "scxa_cell_group_marker_gene_stats s, " +
-                    "scxa_cell_group_marker_genes m, " +
-                    "scxa_cell_group g, " +
-                    "scxa_cell_group h, " +
-                    "experiment e " +
-            "WHERE " +
-                    "s.cell_group_id = g.id AND " +
-                    "s.marker_id = m.id AND " +
-                    "m.cell_group_id = h.id AND " +
-                    "g.experiment_accession = :experiment_accession AND " +
-                    "m.marker_probability < 0.05 AND " +
-                    "g.variable = :variable AND " +
-                    "s.expression_type = 0 AND " +
-                    "e.accession = g.experiment_accession " +
-            "ORDER BY " +
-                    "m.marker_probability ";
     public List<MarkerGene> getCellTypeMarkerGenes(String experiment_accession,
                                                    String cellTypeVariable) {
         var namedParameters =
@@ -196,4 +209,17 @@ public List<MarkerGene> getCellTypeMarkerGenes(String experiment_accession,
                         resultSet.getDouble("mean_expression"),
                         resultSet.getString("expression_unit")));
     }
+
+    public Integer getMarkerGenesForTheInferredCellTypes(String experimentAccession, String cellGroupType) {
+        var namedParameters =
+                ImmutableMap.of(
+                        "experiment_accession", experimentAccession,
+                        "variable", cellGroupType);
+
+        return namedParameterJdbcTemplate.queryForObject(
+                SELECT_MARKER_GENES_FOR_INFERRED_CELL_TYPES,
+                namedParameters,
+                Integer.class);
+
+    }
 }

app/src/main/java/uk/ac/ebi/atlas/experimentpage/tabs/ExperimentPageContentService.java

@@ -7,12 +7,15 @@
 import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonPrimitive;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Service;
 import uk.ac.ebi.atlas.commons.readers.TsvStreamer;
 import uk.ac.ebi.atlas.download.ExperimentFileLocationService;
 import uk.ac.ebi.atlas.download.ExperimentFileType;
 import uk.ac.ebi.atlas.experimentpage.ExternallyAvailableContentService;
 import uk.ac.ebi.atlas.experimentpage.cellplot.CellPlotService;
+import uk.ac.ebi.atlas.experimentpage.markergenes.MarkerGeneService;
 import uk.ac.ebi.atlas.experimentpage.metadata.CellMetadataService;
 import uk.ac.ebi.atlas.experimentpage.tsneplot.TSnePlotSettingsService;
 import uk.ac.ebi.atlas.model.download.ExternallyAvailableContent;
@@ -29,40 +32,52 @@
 
 @Service
 public class ExperimentPageContentService {
+    private static final String INFERRED_CELL_TYPE_ONTOLOGY_LABELS_FROM_DB = "inferred cell type - ontology labels";
+    private static final String INFERRED_CELL_TYPE_AUTHORS_LABELS_FROM_DB = "Inferred cell type - authors labels";
+    private static final Logger LOGGER = LoggerFactory.getLogger(ExperimentPageContentService.class);
+    private static final ImmutableSet<String> EXPERIMENTS_WITH_NO_ANATOMOGRAM = ImmutableSet.of(
+            "E-CURD-10", "E-CURD-11", "E-CURD-126", "E-CURD-135",
+            "E-GEOD-86618", "E-GEOD-114530", "E-GEOD-130473",
+            "E-HCAD-8", "E-HCAD-10",
+            "E-MTAB-6308", "E-MTAB-6653", "E-MTAB-7407", "E-MTAB-9067", "E-MTAB-10662",
+            "E-ANND-1", "E-ANND-2", "E-ANND-3", "E-ANND-4", "E-ANND-5");
+    private static final String EXPERIMENT_TECHNOLOGY_TYPE_PREFIX = "smart-";
+    private static final String INFERRED_CELL_TYPE_ONTOLOGY_LABELS_FROM_SOLR = "inferred_cell_type_-_ontology_labels";
+    private static final String INFERRED_CELL_TYPE_AUTHORS_LABELS_FROM_SOLR = "inferred_cell_type_-_authors_labels";
     private final ExperimentFileLocationService experimentFileLocationService;
     private final DataFileHub dataFileHub;
     private final TSnePlotSettingsService tsnePlotSettingsService;
     private final CellMetadataService cellMetadataService;
     private final OntologyAccessionsSearchService ontologyAccessionsSearchService;
     private final ExperimentTrader experimentTrader;
     private final CellPlotService cellPlotService;
-
-    final static ImmutableSet<String> EXPERIMENTS_WITH_NO_ANATOMOGRAM = ImmutableSet.of(
-            "E-CURD-10", "E-CURD-11", "E-CURD-126", "E-CURD-135",
-            "E-GEOD-86618", "E-GEOD-114530", "E-GEOD-130473",
-            "E-HCAD-8", "E-HCAD-10",
-            "E-MTAB-6308", "E-MTAB-6653", "E-MTAB-7407", "E-MTAB-9067", "E-MTAB-10662",
-            "E-ANND-1", "E-ANND-2", "E-ANND-3", "E-ANND-4", "E-ANND-5");
+    private final MarkerGeneService markerGeneService;
 
     public ExperimentPageContentService(ExperimentFileLocationService experimentFileLocationService,
                                         DataFileHub dataFileHub,
                                         TSnePlotSettingsService tsnePlotSettingsService,
                                         CellMetadataService cellMetadataService,
                                         OntologyAccessionsSearchService ontologyAccessionsSearchService,
                                         ExperimentTrader experimentTrader,
-                                        CellPlotService cellPlotService) {
+                                        CellPlotService cellPlotService, MarkerGeneService markerGeneService) {
         this.experimentFileLocationService = experimentFileLocationService;
         this.dataFileHub = dataFileHub;
         this.tsnePlotSettingsService = tsnePlotSettingsService;
         this.cellMetadataService = cellMetadataService;
         this.ontologyAccessionsSearchService = ontologyAccessionsSearchService;
         this.experimentTrader = experimentTrader;
         this.cellPlotService = cellPlotService;
+        this.markerGeneService = markerGeneService;
+    }
+
+
+    private static boolean isSmartExperiment(Collection<String> technologyType) {
+        return technologyType.stream()
+                .anyMatch(type -> type.toLowerCase().startsWith(EXPERIMENT_TECHNOLOGY_TYPE_PREFIX));
     }
 
     public JsonObject getTsnePlotData(String experimentAccession) {
         var result = new JsonObject();
-
         result.add(
                 "ks",
                 GSON.toJsonTree(tsnePlotSettingsService.getAvailableKs(experimentAccession)));
@@ -82,6 +97,8 @@ public JsonObject getTsnePlotData(String experimentAccession) {
 
         result.add("metadata", getMetadata(experimentAccession));
 
+        result.add("markerGeneMetadata", getMarkerGeneMetadata(getMetadata(experimentAccession), experimentAccession));
+
         var units = new JsonArray();
         units.add("CPM");
         result.add("units", units);
@@ -164,12 +181,6 @@ public JsonArray getAnalysisMethods(String experimentAccession) {
         return result;
     }
 
-    public JsonArray getPerplexities(String experimentAccession) {
-        var perplexityArray = new JsonArray();
-        tsnePlotSettingsService.getAvailablePerplexities(experimentAccession).forEach(perplexityArray::add);
-        return perplexityArray;
-    }
-
     public JsonArray getMetadata(String experimentAccession) {
         var metadataArray = new JsonArray();
         cellMetadataService
@@ -184,7 +195,6 @@ public JsonArray getMetadata(String experimentAccession) {
                 .map(x -> ImmutableMap.of("value", x, "label", StringUtil.snakeCaseToDisplayName(x)))
                 .collect(Collectors.toSet())
                 .forEach(metadata -> metadataArray.add(GSON.toJsonTree(metadata)));
-
         return metadataArray;
     }
 
@@ -235,13 +245,56 @@ private JsonObject customContentTab(String tabType, String name, JsonObject prop
         return result;
     }
 
-    // Smart-Seq-like experiments will contain the substring “smart” in their technology types
-    private static boolean isSmartExperiment(Collection<String> technologyType) {
-        return technologyType.stream()
-                .anyMatch(type -> type.toLowerCase().matches("smart" + "-(?:.*)"));
+    public ImmutableMap fetchDefaultPlotMethodAndParameterisation(String experimentAccession) {
+        return cellPlotService.fetchDefaultPlotMethodWithParameterisation(experimentAccession);
     }
 
-    public ImmutableMap fetchDefaultPlotMethodAndParameterisation(String experimentAccession){
-        return cellPlotService.fetchDefaultPlotMethodWithParameterisation(experimentAccession);
+    public JsonArray getMarkerGeneMetadata(JsonArray metadata, String experimentAccession) {
+        JsonArray markerGenesArray = new JsonArray();
+
+        metadata.forEach(metadataObject -> {
+            JsonObject metaDataObject = getAsJsonObject(metadataObject);
+
+            if (metaDataObject != null) {
+                String value = getValueAsString(metaDataObject);
+
+                if (INFERRED_CELL_TYPE_ONTOLOGY_LABELS_FROM_SOLR.equals(value)) {
+                    markerGenesArray.add(processMarkerGene(metaDataObject, experimentAccession,
+                            INFERRED_CELL_TYPE_ONTOLOGY_LABELS_FROM_DB));
+                } else if (INFERRED_CELL_TYPE_AUTHORS_LABELS_FROM_SOLR.equals(value)) {
+                    markerGenesArray.add(processMarkerGene(metaDataObject, experimentAccession,
+                            INFERRED_CELL_TYPE_AUTHORS_LABELS_FROM_DB));
+                } else {
+                    metaDataObject.addProperty("status", "false");
+                    markerGenesArray.add(metaDataObject);
+                }
+            }
+        });
+        return markerGenesArray;
+    }
+
+    private JsonObject processMarkerGene(JsonObject jsonObject, String experimentAccession, String dbLabel) {
+        boolean isAvailable = markerGeneService.isMarkerGenesAvailableForTheInferredCellTypes(
+                experimentAccession, dbLabel) > 0;
+        jsonObject.addProperty("status", isAvailable);
+        return jsonObject;
+    }
+
+    private JsonObject getAsJsonObject(Object metadataItem) {
+        try {
+            return (JsonObject) metadataItem;
+        } catch (ClassCastException e) {
+            LOGGER.debug("Invalid metadata item: " + metadataItem);
+            return null;
+        }
+    }
+
+    private String getValueAsString(JsonObject jsonObject) {
+        try {
+            return jsonObject.has("value") ? jsonObject.get("value").getAsString() : "";
+        } catch (Exception e) {
+            LOGGER.debug("Error extracting value from JsonObject: " + jsonObject);
+            return "";
+        }
     }
 }