Added pathway summation in neo4j

src/main/java/org/reactome/server/export/tasks/HumanPathwaysWithDiagrams.java

@@ -0,0 +1,130 @@
+package org.reactome.server.export.tasks;
+
+import org.reactome.server.export.annotations.DataExport;
+import org.reactome.server.export.tasks.common.DataExportAbstract;
+
+import java.io.IOException;
+import java.nio.file.*;
+import java.util.*;
+import java.util.stream.Collectors;
+
+// JSON parsing imports (Jackson, for example)
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+/**
+ * Export Pathway Summation Mapping from Neo4j
+ */
+@DataExport
+public class HumanPathwaysWithDiagrams extends DataExportAbstract {
+
+    private static final String DIAGRAM_DIRECTORY = "/data/diagrams";
+
+    private static final Set<String> EXCLUDED_RENDERABLE_CLASSES = new HashSet<>(
+    Arrays.asList(
+        "EncapsulatedNode",
+        "ProcessNode"
+    )
+);
+
+
+    @Override
+    public String getName() {
+        return "humanPathwaysWithDiagrams";
+    }
+
+    @Override
+    public String getQuery() {
+        return "MATCH (p:Pathway)-[:species]->(:Species {dbId: 48887})\n" +
+               "OPTIONAL MATCH (p)-[:disease]->(d:Disease)\n" +
+               "WITH p, d IS NOT NULL AS isDisease\n" +
+               "RETURN DISTINCT p.stId AS pathwayId, p.displayName AS pathwayName, isDisease\n";
+    }
+
+    @Override
+    public void printResult(Collection<Map<String, Object>> result, Path path) throws IOException {
+        // 1) Collect valid pathway IDs from the directory
+        Set<String> validPathwayIds = getValidPathwayIds();
+
+        // 2) Filter the Neo4j results to include only matching IDs
+        List<Map<String, Object>> filteredResults = result.stream()
+                .filter(row -> validPathwayIds.contains(row.get("pathwayId")))
+                .collect(Collectors.toList());
+
+        // // 3) Transform the filtered results by removing "R-HSA-" prefix in a new mutable map
+        // List<Map<String, Object>> transformedResults = filteredResults.stream().map(unmodifiableRow -> {
+        //     // Create a new HashMap from the unmodifiable row
+        //     Map<String, Object> modifiableRow = new HashMap<>(unmodifiableRow);
+
+        //     // Remove prefix if needed
+        //     String pId = (String) modifiableRow.get("pathwayId");
+        //     if (pId != null && pId.startsWith("R-HSA-")) {
+        //         modifiableRow.put("pathwayId", pId.substring("R-HSA-".length()));
+        //     }
+
+        //     return modifiableRow;
+        // }).collect(Collectors.toList());
+
+        // 4) Print (using parent's print method) the final transformed list
+        print(filteredResults, path, "pathwayId", "pathwayName", "isDisease");
+    }
+
+
+    /**
+     * Retrieves a set of valid pathway IDs from the JSON filenames in the target directory,
+     * excluding those where all nodes have renderableClass from the exclusion list.
+     */
+    private Set<String> getValidPathwayIds() {
+        Set<String> pathwayIds = new HashSet<>();
+
+        try (DirectoryStream<Path> stream = Files.newDirectoryStream(Paths.get(DIAGRAM_DIRECTORY))) {
+            for (Path entry : stream) {
+                if (Files.isRegularFile(entry) && entry.toString().endsWith(".json")) {
+                    String filename = entry.getFileName().toString();
+                    String pathwayId = filename.replace(".json", "");
+
+                    // Exclude this JSON file if it consists only of "ProcessNode" renderableClasses
+                    if (!isAllExcludedClasses(entry)) {
+                        pathwayIds.add(pathwayId);
+                    }
+                }
+            }
+        } catch (IOException e) {
+            System.err.println("Error reading directory: " + e.getMessage());
+        }
+
+        return pathwayIds;
+    }
+
+    /**
+     * Checks if the diagram JSON file has ONLY "ProcessNode" items in its "nodes" array.
+     * If it does, we return true (meaning it should be excluded).
+     */
+    private boolean isAllExcludedClasses(Path jsonFilePath) {
+        ObjectMapper mapper = new ObjectMapper();
+        try {
+            JsonNode root = mapper.readTree(jsonFilePath.toFile());
+            JsonNode nodes = root.get("nodes");
+
+            // If nodes is null, not an array, or empty, it's not "all ProcessNode"
+            if (nodes == null || !nodes.isArray() || nodes.size() == 0) {
+                return false;
+            }
+
+            // If ANY node is not from the excluded list, return false
+            for (JsonNode node : nodes) {
+                JsonNode renderableClass = node.get("renderableClass");
+                if (renderableClass == null || !EXCLUDED_RENDERABLE_CLASSES.contains(renderableClass.asText())) {
+                    return false;
+                }
+            }
+            // Every node was in the excluded list
+            return true;
+
+        } catch (IOException e) {
+            // If JSON can't be parsed, treat it as not exclusively in the exlcuded list
+            System.err.println("Error parsing JSON file " + jsonFilePath + ": " + e.getMessage());
+            return false;
+        }
+    }
+}

src/main/java/org/reactome/server/export/tasks/PathwaySummationMapping.java

@@ -0,0 +1,36 @@
+package org.reactome.server.export.tasks;
+
+import org.reactome.server.export.annotations.DataExport;
+import org.reactome.server.export.tasks.common.DataExportAbstract;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.Collection;
+import java.util.Map;
+
+/**
+ * Export Pathway Summation Mapping from Neo4j
+ */
+@DataExport
+public class PathwaySummationMapping extends DataExportAbstract {
+
+    @Override
+    public String getName() {
+        return "pathway2summation";
+    }
+
+    @Override
+    public String getQuery() {
+        return "MATCH (p:Pathway {speciesName: 'Homo sapiens'})-[:summation]->(s:Summation)\n" +
+               "RETURN\n" +
+               "p.stId AS Identifier,\n" +
+               "p.displayName AS Name,\n" +
+               "replace(replace(s.text, '\n', ' '), '\r', ' ') AS Summation\n" +
+               "ORDER BY Name";
+    }
+
+    @Override
+    public void printResult(Collection<Map<String, Object>> result, Path path) throws IOException {
+        print(result, path, "Identifier", "Name", "Summation");
+    }
+}