From 36b84fd1f6ea8016ca5ea160dd6ba8bae72ff88e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Petrovi=C4=8D?= <mifo.petrovic@gmail.com>
Date: Tue, 12 Mar 2024 01:40:07 +0100
Subject: [PATCH] pagination and lazy load sequences
---
.../analyse/cpg/CpgController.java | 47 ++++++++++++++++++-
.../dnaAnalyser/analyse/cpg/CpgMapper.java | 21 +++++++++
.../dnaAnalyser/analyse/cpg/CpgService.java | 28 +++++++++--
3 files changed, 91 insertions(+), 5 deletions(-)
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgController.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgController.java
index b32d3d0..f29228e 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgController.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgController.java
@@ -3,8 +3,11 @@ package cz.mendelu.dnaAnalyser.analyse.cpg;
import cz.mendelu.dnaAnalyser.analyse.zdna.ZdnaAnalyseResult;
import cz.mendelu.dnaAnalyser.jwt.JwtAuthenticationUtils;
import cz.mendelu.dnaAnalyser.jwt.JwtTokenService;
+import cz.mendelu.dnaAnalyser.sequence.Sequence;
import cz.mendelu.dnaAnalyser.sequence.SequenceService;
import cz.mendelu.dnaAnalyser.exporter.ExporterService;
+import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
+import cz.mendelu.dnaAnalyser.sequence.data.SequenceDataRepository;
import cz.mendelu.dnaAnalyser.utils.analyse.service.heatmap.Heatmap;
import cz.mendelu.dnaAnalyser.utils.controller.DeleteMapping;
import cz.mendelu.dnaAnalyser.utils.controller.GetMapping;
@@ -77,6 +80,9 @@ public class CpgController {
@Autowired
private JwtTokenService jwtTokenService;
+ @Autowired
+ private SequenceDataRepository sequenceDataRepository;
+
@Autowired
private CpgService cpgService;
@@ -100,6 +106,38 @@ public class CpgController {
return Response.response(cpg);
}
+ @GetMapping("/{id}/substring")
+ @ResponseStatus(HttpStatus.OK)
+ @PreAuthorize("isAuthenticated()")
+ @ApiOperation("Get a substring of the sequence by ID, start, and end positions.")
+ public ResponseEntity<String> getSequenceSubstring(
+ @PathVariable UUID id,
+ @RequestParam("start") Integer start,
+ @RequestParam("end") Integer end) {
+
+ // Fetch the sequence using the provided ID. You might need to adjust this code
+ // based on how your SequenceService is implemented and how sequences are stored.
+ Sequence sequence = sequenceService.findOne(id);
+ if (sequence == null) {
+ return new ResponseEntity<>("Sequence not found", HttpStatus.NOT_FOUND);
+ }
+
+
+ String sequence_string = sequenceDataRepository.load(sequence).toPlain();
+
+ // Check if start and end positions are within the sequence length
+ if (start < 0 || end > sequence_string.length() || start >= end) {
+ return new ResponseEntity<>("Invalid start or end position", HttpStatus.BAD_REQUEST);
+ }
+
+ // Extract the substring based on the provided start and end positions
+ String substring = sequence_string.substring(start, end);
+
+ // Return the substring
+ return new ResponseEntity<>(substring, HttpStatus.OK);
+ }
+
+
@GetMapping("/{id}/analysis")
@ResponseStatus(HttpStatus.OK)
@PreAuthorize("isAuthenticated()")
@@ -115,8 +153,13 @@ public class CpgController {
@ResponseStatus(HttpStatus.OK)
@PreAuthorize("isAuthenticated()")
@ApiOperation("Get CpG islands analysis by ID.")
- public ResponsePage<CpgAnalyseResult> getCpgList(@PathVariable UUID id) {
- Page<CpgAnalyseResult> cpgPage = cpgService.returnCpgAnalysis(id);
+ public ResponsePage<CpgAnalyseResult> getCpgList(@PathVariable UUID id,
+ Integer sequenceStart,
+ Integer sequenceLength,
+ PaginationParam paginationParam,
+ SortParam sortParam) {
+ Pageable pageable = paginationParam.toPageable(sortParam.toSort());
+ Page<CpgAnalyseResult> cpgPage = cpgService.returnCpgAnalysis(id, sequenceStart, sequenceLength, pageable);
return ResponsePage.responsePage(cpgPage);
}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgMapper.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgMapper.java
index 66cca01..30ce4e7 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgMapper.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgMapper.java
@@ -25,6 +25,11 @@ public interface CpgMapper extends DataLocalisedMapper<CpgAnalyseResult> {
@Select("SELECT count(*) FROM CPG")
int countAll();
+ @Select("SELECT count(*) FROM CPG WHERE POSITION >= #{startPosition} AND POSITION < #{endPosition}")
+ int countAllBetweenPosition(
+ @Param("startPosition") int startPosition,
+ @Param("endPosition") int endPosition);
+
@Select("SELECT * FROM CPG")
@Results(value = {
@Result(property = "id", column = "ID"),
@@ -99,6 +104,22 @@ public interface CpgMapper extends DataLocalisedMapper<CpgAnalyseResult> {
@Param("orderName") String orderName,
RowBounds rowBounds);
+ @Select("SELECT * FROM CPG WHERE POSITION >= #{startPosition} AND POSITION < #{endPosition} ORDER BY ${orderName} DESC")
+ @Results(value = {
+ @Result(property = "id", column = "ID"),
+ @Result(property = "position", column = "position"),
+ @Result(property = "end", column = "end"),
+ @Result(property = "sequence", column = "sequence"),
+ @Result(property = "gcPerc", column = "gcPerc"),
+ @Result(property = "observedToExpectedCpG", column = "observedToExpectedCpG"),
+ @Result(property = "length", column = "length")
+ })
+ List<CpgAnalyseResult> getAllBetweenPositionOrderDesc(
+ @Param("startPosition") int startPosition,
+ @Param("endPosition") int endPosition,
+ @Param("orderName") String orderName,
+ RowBounds rowBounds);
+
@Delete("DELETE from CPG WHERE ID = #{id}")
void delete(int id);
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgService.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgService.java
index 895d24c..6c012e8 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgService.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgService.java
@@ -87,15 +87,37 @@ public class CpgService extends ModelService<Cpg> {
return cpg;
}
- public Page<CpgAnalyseResult> returnCpgAnalysis(UUID id) {
+ public Page<CpgAnalyseResult> returnCpgAnalysis(UUID id, Integer sequenceStart, Integer sequenceLength, Pageable pageable) {
Cpg analysis = findOne(id);
+
+ int start = (sequenceStart == null) ? 0 : sequenceStart;
+ int end = start + ((sequenceLength == null) ? analysis.getSequence().getLength() : sequenceLength);
+
try (SqlSession sqlSession = cpgDataSessionService.openDataSession(analysis)) {
CpgMapper cpgMapper = sqlSession.getMapper(CpgMapper.class);
- Page<CpgAnalyseResult> cpgPage = new PageImpl<>(cpgMapper.getAll());
- return cpgPage;
+
+ RowBounds rowBounds = new RowBounds((int) pageable.getOffset(), pageable.getPageSize());
+ String orderName = "POSITION";
+ Sort.Direction orderDirection = Sort.Direction.ASC;
+ Sort.Order order = getSortOrderOrNull(pageable);
+ if (order != null) {
+ orderName = order.getProperty().toUpperCase();
+ orderDirection = order.getDirection();
+ }
+
+ List<CpgAnalyseResult> list;
+ if (orderDirection == Sort.Direction.ASC) {
+ list = cpgMapper.getAllBetweenPositionOrderAsc(start, end, orderName, rowBounds);
+ } else {
+ list = cpgMapper.getAllBetweenPositionOrderDesc(start, end, orderName, rowBounds);
+ }
+ int total = cpgMapper.countAllBetweenPosition(start, end);
+
+ return new PageImpl<>(list, pageable, total);
}
}
+
public Heatmap getHeatmap(UUID id, Integer segmentsCount, Integer from, Integer to) {
Cpg analysis = findOne(id);
return cpgDataSessionService.heatmap(CpgMapper.class, analysis, segmentsCount, from, to);
--
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