Added support for moving to debris

ctlab · Jul 31, 2023 · b7902da · b7902da
1 parent 5d37da5
commit b7902da
Show file tree

Hide file tree

Showing 5 changed files with 104 additions and 4 deletions.
diff --git a/src/main/java/ru/itmo/ctlab/hict/hict_library/chunkedfile/ScaffoldingOperations.java b/src/main/java/ru/itmo/ctlab/hict/hict_library/chunkedfile/ScaffoldingOperations.java
@@ -141,6 +141,47 @@ public void unscaffoldRegion(final long startIncl, final long endExcl, final @No
     }
   }
 
+  public void moveRegionToDebris(final long startIncl, final long endExcl, final @NotNull ResolutionDescriptor resolutionDescriptor, final @NotNull QueryLengthUnit units) {
+    assert (startIncl < endExcl) : "Unscaffolding: start >= end??";
+
+    final var contigTree = this.chunkedFile.getContigTree();
+    final var scaffoldTree = this.chunkedFile.getScaffoldTree();
+
+    try {
+      contigTree.getRootLock().writeLock().lock();
+      scaffoldTree.getRootLock().writeLock().lock();
+
+      final long startBp = this.chunkedFile.convertUnits(
+        startIncl,
+        resolutionDescriptor,
+        units,
+        ResolutionDescriptor.fromResolutionOrder(0),
+        QueryLengthUnit.BASE_PAIRS
+      );
+      final long endBp = this.chunkedFile.convertUnits(
+        endExcl,
+        resolutionDescriptor,
+        units,
+        ResolutionDescriptor.fromResolutionOrder(0),
+        QueryLengthUnit.BASE_PAIRS
+      );
+
+      final var leftScaffoldBorders = scaffoldTree.getScaffoldBordersAtBp(startBp);
+      final var rightScaffoldBorders = scaffoldTree.getScaffoldBordersAtBp(endBp - 1);
+
+      final var trueStartBpIncl = leftScaffoldBorders.endBP();
+      final var trueEndBpExcl = rightScaffoldBorders.startBP();
+
+      if (trueStartBpIncl < trueEndBpExcl) {
+        scaffoldRegion(trueStartBpIncl, trueEndBpExcl, ResolutionDescriptor.fromResolutionOrder(0), QueryLengthUnit.BASE_PAIRS, id -> new ScaffoldDescriptor(id, String.format("scaffold_debris_%d", id), 1000));
+        moveSelectionRangeBp(trueStartBpIncl, trueEndBpExcl, this.chunkedFile.getMatrixSizeBins()[0]);
+      }
+    } finally {
+      scaffoldTree.getRootLock().writeLock().unlock();
+      contigTree.getRootLock().writeLock().unlock();
+    }
+  }
+
   public void splitContigAtBin(final long splitPosition, final @NotNull @NonNull ResolutionDescriptor resolutionDescriptor, final @NotNull @NonNull QueryLengthUnit units) {
     assert !QueryLengthUnit.BASE_PAIRS.equals(units) || (resolutionDescriptor.getResolutionOrderInArray() == 0) : "In bp query resolution should be set to 0";
 

diff --git a/src/main/java/ru/itmo/ctlab/hict/hict_library/trees/ScaffoldTree.java b/src/main/java/ru/itmo/ctlab/hict/hict_library/trees/ScaffoldTree.java
@@ -115,6 +115,24 @@ public void commitExposedSegment(final @NotNull Node.ExposedSegment exposedSegme
     }
   }
 
+  public @NotNull ScaffoldDescriptor.ScaffoldBordersBP getScaffoldBordersAtBp(final long queriedBp) {
+    try {
+      var leftBp = queriedBp;
+      var rightBp = queriedBp;
+      this.rootLock.readLock().lock();
+
+      final var es = Node.expose(this.root, leftBp, 1 + rightBp);
+      final var sg = es.segment();
+      if ((sg != null) && sg.scaffoldDescriptor != null) {
+        leftBp = Optional.ofNullable(es.less()).map(n -> n.subtreeLengthBp).orElse(0L);
+        rightBp = leftBp + sg.subtreeLengthBp;
+      }
+      return new ScaffoldDescriptor.ScaffoldBordersBP(leftBp, rightBp);
+    } finally {
+      this.rootLock.readLock().unlock();
+    }
+  }
+
   /**
    * @param startBp           Starting BP of new scaffold.
    * @param endBp             Last (exclusive) BP of new scaffold.
@@ -329,7 +347,7 @@ public static Node.SplitResult splitNodeBp(final Node t, final long expectedLeft
             final var rightPartLengthBp = newTree.subtreeLengthBp - t1.subtreeLengthBp;
             final Node t2;
             if (rightPartLengthBp > 0) {
-              t2 = newTree.cloneBuilder().nodeLengthBp(rightPartLengthBp).left(null).yPriority(rnd.nextLong(Long.min(1L+newTree.yPriority, Long.MAX_VALUE-1), Long.MAX_VALUE)).build().updateSizes();
+              t2 = newTree.cloneBuilder().nodeLengthBp(rightPartLengthBp).left(null).yPriority(rnd.nextLong(Long.min(1L + newTree.yPriority, Long.MAX_VALUE - 1), Long.MAX_VALUE)).build().updateSizes();
             } else {
               t2 = newTree.right;
             }

diff --git a/.../itmo/ctlab/hict/hict_server/dto/request/scaffolding/MoveSelectionToDebrisRequestDTO.java b/.../itmo/ctlab/hict/hict_server/dto/request/scaffolding/MoveSelectionToDebrisRequestDTO.java
@@ -0,0 +1,17 @@
+package ru.itmo.ctlab.hict.hict_server.dto.request.scaffolding;
+
+import io.vertx.core.json.JsonObject;
+import org.jetbrains.annotations.NotNull;
+
+public record MoveSelectionToDebrisRequestDTO(
+  long startBP,
+  long endBP
+) {
+
+  public static @NotNull MoveSelectionToDebrisRequestDTO fromJSONObject(final @NotNull JsonObject json) {
+    return new MoveSelectionToDebrisRequestDTO(
+      json.getLong("startBP"),
+      json.getLong("endBP")
+    );
+  }
+}
diff --git a/.../java/ru/itmo/ctlab/hict/hict_server/handlers/operations/ScaffoldingOpHandlersHolder.java b/.../java/ru/itmo/ctlab/hict/hict_server/handlers/operations/ScaffoldingOpHandlersHolder.java
@@ -119,6 +119,26 @@ public void addHandlersToRouter(final @NotNull Router router) {
 
       chunkedFile.scaffoldingOperations().unscaffoldRegion(request.startBP(), request.endBP(), ResolutionDescriptor.fromResolutionOrder(0), QueryLengthUnit.BASE_PAIRS);
 
+      ctx.response().end(Json.encode(AssemblyInfoDTO.generateFromChunkedFile(chunkedFile)));
+    });
+    router.post("/move_selection_to_debris").blockingHandler(ctx -> {
+      final @NotNull var requestBody = ctx.body();
+      final @NotNull var requestJSON = requestBody.asJsonObject();
+
+      final @NotNull @NonNull var request = MoveSelectionToDebrisRequestDTO.fromJSONObject(requestJSON);
+
+      final var map = vertx.sharedData().getLocalMap("hict_server");
+      log.debug("Got map");
+      final var chunkedFileWrapper = ((ShareableWrappers.ChunkedFileWrapper) (map.get("chunkedFile")));
+      if (chunkedFileWrapper == null) {
+        ctx.fail(new RuntimeException("Chunked file is not present in the local map, maybe the file is not yet opened?"));
+        return;
+      }
+      final var chunkedFile = chunkedFileWrapper.getChunkedFile();
+      log.debug("Got ChunkedFile from map");
+
+      chunkedFile.scaffoldingOperations().moveRegionToDebris(request.startBP(), request.endBP(), ResolutionDescriptor.fromResolutionOrder(0), QueryLengthUnit.BASE_PAIRS);
+
       ctx.response().end(Json.encode(AssemblyInfoDTO.generateFromChunkedFile(chunkedFile)));
     });
   }

diff --git a/src/main/java/ru/itmo/ctlab/hict/hict_server/handlers/tiles/TileHandlersHolder.java b/src/main/java/ru/itmo/ctlab/hict/hict_server/handlers/tiles/TileHandlersHolder.java
@@ -153,11 +153,15 @@ public void addHandlersToRouter(final @NotNull Router router) {
         return;
       }
 
-      final var currentVersion = stats.versionCounter().get();
-      if ((version < currentVersion) || ((version > currentVersion) && !stats.versionCounter().compareAndSet(currentVersion, version))) {
-        ctx.response().setStatusCode(204).end(String.format("Current version is %d and request version is %d", currentVersion, version));
+      var currentVersion = stats.versionCounter().get();
+      if (version < currentVersion) {
+        log.debug(String.format("Current version is %d and request version is %d", currentVersion, version));
+        ctx.response().setStatusCode(204).putHeader("Content-Type", "text/plain").end(String.format("Current version is %d and request version is %d", currentVersion, version));
         return;
       }
+      do {
+        currentVersion = stats.versionCounter().get();
+      } while ((currentVersion < version) && !stats.versionCounter().compareAndSet(currentVersion, version));
 
       final long startRowPx, startColPx, endRowPx, endColPx;
       if (format == TileFormat.PNG_BY_PIXELS) {