Spectrum search engine implementation

nomad-nmr-old · Feb 27, 2018 · ffcf939 · ffcf939
1 parent c17972d
commit ffcf939
Show file tree

Hide file tree

Showing 10 changed files with 242 additions and 18 deletions.
diff --git a/peaks/README.md b/peaks/README.md
@@ -1,5 +1,7 @@
 # NMR Spectrum Search Engine
 
+This component is currently under development.
+
 ## Installation
 
 ### Dependencies

diff --git a/peaks/peaks.iml b/peaks/peaks.iml
@@ -88,8 +88,10 @@
     <orderEntry type="library" name="Maven: org.springframework.boot:spring-boot-devtools:1.5.10.RELEASE" level="project" />
     <orderEntry type="library" name="Maven: org.springframework.boot:spring-boot:1.5.10.RELEASE" level="project" />
     <orderEntry type="library" name="Maven: org.springframework.boot:spring-boot-autoconfigure:1.5.10.RELEASE" level="project" />
+    <orderEntry type="library" name="Maven: org.webjars:jquery:3.3.1" level="project" />
     <orderEntry type="library" name="Maven: org.webjars:bootstrap:3.3.7" level="project" />
-    <orderEntry type="library" name="Maven: org.webjars:jquery:1.11.1" level="project" />
+    <orderEntry type="library" name="Maven: org.webjars:bootstrap-select:1.12.4" level="project" />
+    <orderEntry type="library" name="Maven: org.webjars.bower:font-awesome:4.7.0" level="project" />
     <orderEntry type="library" name="Maven: mysql:mysql-connector-java:8.0.8-dmr" level="project" />
     <orderEntry type="library" name="Maven: com.google.guava:guava:24.0-jre" level="project" />
     <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />

diff --git a/peaks/pom.xml b/peaks/pom.xml
@@ -46,12 +46,26 @@
             <optional>true</optional>
         </dependency>
 
-        <!-- Optional, for bootstrap -->
+        <dependency>
+            <groupId>org.webjars</groupId>
+            <artifactId>jquery</artifactId>
+            <version>3.3.1</version>
+        </dependency>
         <dependency>
             <groupId>org.webjars</groupId>
             <artifactId>bootstrap</artifactId>
             <version>3.3.7</version>
         </dependency>
+        <dependency>
+            <groupId>org.webjars</groupId>
+            <artifactId>bootstrap-select</artifactId>
+            <version>1.12.4</version>
+        </dependency>
+        <dependency>
+            <groupId>org.webjars.bower</groupId>
+            <artifactId>font-awesome</artifactId>
+            <version>4.7.0</version>
+        </dependency>
 
         <!-- https://mvnrepository.com/artifact/mysql/mysql-connector-java -->
         <dependency>

diff --git a/peaks/src/main/java/com/mp236/controllers/SearchEngineController.java b/peaks/src/main/java/com/mp236/controllers/SearchEngineController.java
@@ -1,22 +1,67 @@
 package com.mp236.controllers;
 
-import java.util.Map;
+import java.util.*;
+import java.util.stream.Collectors;
 
+import com.mp236.entities.Peak;
+import com.mp236.entities.PeakRepository;
+import com.mp236.entities.Spectrum;
 import com.mp236.entities.SpectrumRepository;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
 
 @Controller
 public class SearchEngineController {
 
     @Autowired
     private SpectrumRepository spectrumRepository;
 
+    @Autowired
+    private PeakRepository peakRepository;
+
     @RequestMapping("/")
-    public String welcome(Map<String, Object> model) {
+    public String welcome(
+            @RequestParam(value = "shift[]", defaultValue = "") double[] shifts,
+            @RequestParam(value = "multiplicity[]", defaultValue = "") String[] multiplicities,
+            @RequestParam(value = "deviation[]", defaultValue = "") double[] deviations,
+            Map<String, Object> model
+    ) {
+
+        Map<Spectrum, Integer> spectrumHash = new HashMap<>();
+        for(int i=0;i<shifts.length;i++) {
+            List<Double> peaks = peakRepository.findInRange(shifts[i] - deviations[i], shifts[i] + deviations[i])
+                    .stream()
+                    .map(Peak::getPeak)
+                    .collect(Collectors.toList());
+            List<Spectrum> spectrums = spectrumRepository.findInPeakList(peaks);
+
+            for(Spectrum s: spectrums) {
+                int times = 0;
+                if(spectrumHash.containsKey(s)) {
+                    times = spectrumHash.get(s);
+                }
+                spectrumHash.put(s, times + 1);
+            }
+        }
+
+        Map<Integer, List<Spectrum>> spectrumMap = new TreeMap<>((o1, o2) -> o2 - o1);
+        spectrumHash.forEach((spectrum, times) -> {
+            if(!spectrumMap.containsKey(times)) {
+                spectrumMap.put(times, new ArrayList<>());
+            }
+            spectrumMap.get(times).add(spectrum);
+        });
+
+        List<List<Spectrum>> spectrums = new ArrayList<>();
+        spectrumMap.values().forEach(spectrums::add);
+        model.put("spectrums", spectrums);
+
+        model.put("shifts", shifts);
+        model.put("multiplicities", multiplicities);
+        model.put("deviations", deviations);
 
-        model.put("spectrums", spectrumRepository.findAll());
         return "welcome";
     }
 

diff --git a/...c/main/java/com/mp236/entities/Peaks.java → ...rc/main/java/com/mp236/entities/Peak.java b/...c/main/java/com/mp236/entities/Peaks.java → ...rc/main/java/com/mp236/entities/Peak.java
@@ -4,7 +4,7 @@
 
 @Entity
 @Table(name = "peaks")
-public class Peaks {
+public class Peak {
 
     @Id
     @GeneratedValue(strategy = GenerationType.AUTO)
@@ -44,4 +44,5 @@ public void setSpectrumId(Integer spectrumId) {
     public String toString() {
         return Double.toString(peak);
     }
+
 }
diff --git a/peaks/src/main/java/com/mp236/entities/PeakRepository.java b/peaks/src/main/java/com/mp236/entities/PeakRepository.java
@@ -0,0 +1,13 @@
+package com.mp236.entities;
+
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.CrudRepository;
+import org.springframework.data.repository.query.Param;
+
+import java.util.List;
+
+public interface PeakRepository extends CrudRepository<Peak, Long>{
+
+    @Query("SELECT p FROM Peak p WHERE p.peak BETWEEN :start AND :stop")
+    List<Peak> findInRange(@Param("start") double start, @Param("stop") double stop);
+}
diff --git a/peaks/src/main/java/com/mp236/entities/Spectrum.java b/peaks/src/main/java/com/mp236/entities/Spectrum.java
@@ -3,8 +3,9 @@
 import com.google.common.base.Joiner;
 
 import javax.persistence.*;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
 
 @Entity
 @Table(name = "spectrum")
@@ -16,7 +17,10 @@ public class Spectrum {
 
     @OneToMany
     @JoinColumn(name = "spectrum_id")
-    private Set<Peaks> peaks = new HashSet<>();
+    private List<Peak> peaks = new ArrayList<>();
+
+    @Column(name = "date")
+    private Date date;
 
     public Integer getId() {
         return id;
@@ -30,7 +34,15 @@ public String getPeaks() {
         return Joiner.on(" ").skipNulls().join(peaks);
     }
 
-    public void setPeaks(Set<Peaks> peaks) {
+    public void setPeaks(ArrayList<Peak> peaks) {
         this.peaks = peaks;
     }
+
+    public Date getDate() {
+        return date;
+    }
+
+    public void setDate(Date date) {
+        this.date = date;
+    }
 }
diff --git a/peaks/src/main/java/com/mp236/entities/SpectrumRepository.java b/peaks/src/main/java/com/mp236/entities/SpectrumRepository.java
@@ -1,6 +1,14 @@
 package com.mp236.entities;
 
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
+import org.springframework.data.repository.query.Param;
+
+import java.util.List;
 
 public interface SpectrumRepository extends CrudRepository<Spectrum, Long> {
+
+    @Query("SELECT s FROM Spectrum s JOIN s.peaks p WHERE p.peak IN :peaks ORDER BY s.date DESC")
+    List<Spectrum> findInPeakList(@Param("peaks") List<Double> peaks);
+
 }
diff --git a/peaks/src/main/resources/static/main.css → peaks/src/main/resources/static/css/main.css b/peaks/src/main/resources/static/main.css → peaks/src/main/resources/static/css/main.css
diff --git a/peaks/src/main/resources/templates/welcome.html b/peaks/src/main/resources/templates/welcome.html
@@ -5,33 +5,160 @@
     <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
 
     <link rel="stylesheet" type="text/css" href="webjars/bootstrap/3.3.7/css/bootstrap.min.css" />
-
-    <link rel="stylesheet" type="text/css" th:href="@{/css/main.css}" href="../../css/main.css" />
+    <link rel="stylesheet" type="text/css" href="webjars/bootstrap-select/1.12.4/css/bootstrap-select.min.css" />
+    <link rel="stylesheet" type="text/css" href="webjars/font-awesome/4.7.0/css/font-awesome.min.css" />
+    <link rel="stylesheet" type="text/css" th:href="@{/css/main.css}" href="../static/css/main.css" />
 
 </head>
 <body>
 
 <div class="container">
+    <h2 class="page-header"><strong>Chemical Shifts</strong></h2>
+    <form th:action="@{/}" target="_self" method="get">
+        <div class="row">
+            <div class="col-md-offset-1 col-md-10">
+                <table class="table table-striped table-condensed">
+                    <thead>
+                    <tr>
+                        <th class="col-md-1 text-center"><strong>Line number</strong></th>
+                        <th class="col-md-3 text-center"><strong>Chemical Shift (ppm)</strong></th>
+                        <th class="col-md-4 text-center"><strong>Multiplicity</strong></th>
+                        <th class="col-md-3 text-center"><strong>Deviation (ppm)</strong></th>
+                        <th class="col-md-1 text-center"><strong>Remove</strong></th>
+                    </tr>
+                    </thead>
+                    <tbody id="tableBody">
+                        <tr th:each="shift,iter: ${shifts}">
+                            <td class="text-center"><p class="text-center form-control-static" th:text="${iter.index + 1}"></p></td>
+                            <td class="text-center"><input class="form-control" type="number" name="shift[]" step="0.01" th:value="${shift}"/></td>
+                            <td class="text-center">
+                                <select class="selectpicker" name="multiplicity[]">
+                                    <option value="m">m</option>
+                                    <option value="s">s</option>
+                                    <option value="d">d</option>
+                                    <option value="t">t</option>
+                                    <option value="q">q</option>
+                                    <option value="p">p</option>
+                                    <option value="h">h</option>
+                                    <option value="hept">hept</option>
+                                    <option value="dd">dd</option>
+                                    <option value="td">td</option>
+                                    <option value="ddt">ddt</option>
+                                    <option value="ddd">ddd</option>
+                                </select>
+                            </td>
+                            <td class="text-center"><input class="form-control" type="number" name="deviation[]" step="0.01" th:value="${deviations[iter.index]}"/></td>
+                            <td class="text-center"><button type="button" class="btn btn-danger btn-sm" onclick="remove(this)"><span class="fa fa-times"></span></button></td>
+                        </tr>
+                    </tbody>
+                </table>
+            </div>
+            <div class="col-md-offset-4 col-md-4">
+                <button type="button" class="btn btn-success btn-block" onclick="add()">Add Chemical Shift</button>
+            </div>
+        </div>
+        <div class="help-block"></div>
+        <div class="row">
+            <div class="text-center col-md-offset-1 col-md-10">
+                <button type="submit" class="btn btn-success">Submit</button>
+            </div>
+        </div>
+    </form>
+
     <div th:unless="${#lists.isEmpty(spectrums)}">
+        <br/>
         <div class="table-responsive">
             <table class="table table-hover table-condensed table-striped">
                 <thead>
                 <tr>
-                    <th>Peaks</th>
-                    <th>Options</th>
+                    <th class="col-md-9 text-center">Peaks</th>
+                    <th class="col-md-2 text-center">Last Updated</th>
+                    <th class="col-md-1 text-center">Options</th>
                 </tr>
                 </thead>
                 <tbody>
-                <tr th:each="spectrum: ${spectrums}">
-                    <td th:text="${{spectrum.getPeaks()}}">Peaks</td>
-                    <td>Empty</td>
-                </tr>
+                <th:block th:each="spectrumList: ${spectrums}">
+                    <tr th:each="spectrum: ${spectrumList}">
+                        <td th:text="${{spectrum.getPeaks()}}">Peaks</td>
+                        <td class="text-center" th:text="${#dates.format(spectrum.getDate(), 'dd-MM-yyyy hh:mm:ss')}">Date</td>
+                        <td class="text-center"></td>
+                    </tr>
+                    <tr>
+                        <td colspan="3"></td>
+                    </tr>
+                </th:block>
                 </tbody>
             </table>
         </div>
     </div>
 </div>
 
+<script type="text/javascript" src="webjars/jquery/3.3.1/jquery.min.js"></script>
 <script type="text/javascript" src="webjars/bootstrap/3.3.7/js/bootstrap.min.js"></script>
+<script type="text/javascript" src="webjars/bootstrap-select/1.12.4/js/bootstrap-select.min.js"></script>
+
+<script th:inline="javascript">
+    /*<![CDATA[*/
+    var lineNumber = /*[[${#lists.size(shifts) + 1}]]*/ 1;
+    /*]]>*/
+</script>
+
+<script type="text/javascript">
+    function add() {
+        $('#tableBody').append(
+            '<tr>' +
+            '<td class="text-center"><p class="text-center form-control-static">'+lineNumber+'</p></td>' +
+            '<td class="text-center"><input class="form-control" type="number" name="shift[]" step="0.01"/></td>' +
+            '<td class="text-center">' +
+                '<select class="selectpicker" name="multiplicity[]">' +
+                    '<option value="m">m</option>' +
+                    '<option value="s">s</option>' +
+                    '<option value="d">d</option>' +
+                    '<option value="t">t</option>' +
+                    '<option value="q">q</option>' +
+                    '<option value="p">p</option>' +
+                    '<option value="h">h</option>' +
+                    '<option value="hept">hept</option>' +
+                    '<option value="dd">dd</option>' +
+                    '<option value="td">td</option>' +
+                    '<option value="ddt">ddt</option>' +
+                    '<option value="ddd">ddd</option>' +
+                '</select>' +
+            '</td>' +
+            '<td class="text-center"><input class="form-control" type="number" name="deviation[]" step="0.01"/></td>' +
+            '<td class="text-center"><button type="button" class="btn btn-danger btn-sm" onclick="remove(this)"><span class="fa fa-times"></span></button></td>' +
+            '</tr>'
+        );
+        lineNumber++;
+        $('.selectpicker').selectpicker();
+    }
+
+    function remove(el) {
+        var row = $(el).parent().parent();
+
+        recalculateLineNumbers(row.next());
+        row.remove();
+        lineNumber--;
+    }
+
+    function recalculateLineNumbers(el) {
+        while(el[0]) {
+            var child = el.children(":first").children(":first");
+            child.html(parseInt(child.html()) - 1);
+
+            el = el.next();
+        }
+    }
+
+
+    $(function () {
+        $('.selectpicker').selectpicker();
+        if(lineNumber === 1) {
+            add();
+        } else {
+            $('.selectpicker').selectpicker();
+        }
+    });
+</script>
 </body>
 </html>