feat: add lab data profiles

src/main/kotlin/dev/pcvolkmer/onco/grzmetadataprocessor/data/LabData.kt

@@ -1,6 +1,7 @@
 package dev.pcvolkmer.onco.grzmetadataprocessor.data
 
 import org.springframework.data.annotation.Id
+import org.springframework.data.annotation.Transient
 import org.springframework.data.relational.core.mapping.Table
 import org.springframework.data.repository.CrudRepository
 
@@ -15,6 +16,7 @@ data class LabData(
     val sequenceType: SequenceType? = null,
     val sequenceSubtype: SequenceSubtype? = null,
     val fragmentationMethod: FragmentationMethod? = null,
+    val profile: Long? = null,
     val libraryType: LibraryType? = null,
     val libraryPrepKit: String = "",
     val libraryPrepKitManufacturer: String = "",
@@ -30,7 +32,10 @@ data class LabData(
     val bioinformaticsPipelineName: String = "",
     val bioinformaticsPipelineVersion: String = "",
     val referenceGenome: ReferenceGenome? = null,
-)
+) {
+    @Transient
+    var profileData: LabDataProfile? = null
+}
 
 enum class SampleConservation(val value: String) {
     FRESH_TISSUE("fresh-tissue"),

src/main/kotlin/dev/pcvolkmer/onco/grzmetadataprocessor/data/LabDataProfile.kt

@@ -0,0 +1,22 @@
+package dev.pcvolkmer.onco.grzmetadataprocessor.data
+
+import org.springframework.data.annotation.Id
+import org.springframework.data.relational.core.mapping.Table
+import org.springframework.data.repository.CrudRepository
+
+@Table("tbl_lab_data_profile")
+data class LabDataProfile(
+    @Id val id: Long? = null,
+    val profileName: String = "",
+    val libraryType: LibraryType? = null,
+    val libraryPrepKit: String = "",
+    val libraryPrepKitManufacturer: String = "",
+    val sequencerModel: String = "",
+    val sequencerManufacturer: String = "",
+    val kitName: String = "",
+    val kitManufacturer: String = "",
+    val enrichmentKit: String = "",
+    val enrichmentKitManufacturer: EnrichmentKitManufacturer? = null
+)
+
+interface LabDataProfileRepository : CrudRepository<LabDataProfile, Long>

src/main/kotlin/dev/pcvolkmer/onco/grzmetadataprocessor/web/LabDataController.kt

@@ -1,6 +1,7 @@
 package dev.pcvolkmer.onco.grzmetadataprocessor.web
 
 import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabData
+import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataProfileRepository
 import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataRepository
 import org.springframework.stereotype.Controller
 import org.springframework.ui.Model
@@ -9,34 +10,44 @@ import org.springframework.web.bind.annotation.*
 @Controller
 @RequestMapping("/donors/{donorId}/labdatas")
 class LabDataController(
-    private val repository: LabDataRepository
+    private val labDataRepository: LabDataRepository,
+    private val labDataProfileRepository: LabDataProfileRepository
 ) {
 
     @GetMapping
     fun getAllLabData(@PathVariable donorId: Long, model: Model): String {
-        model.addAttribute("labdatas", repository.findByDonorId(donorId))
+        model.addAttribute("labdatas", allLabDatasByDonorId(donorId))
+        model.addAttribute("labdataprofiles", labDataProfileRepository.findAll())
         return "labdatas"
     }
 
     @PostMapping
     fun postLabData(@PathVariable donorId: Long, model: Model): String {
-        repository.save(LabData(donorId = donorId))
+        labDataRepository.save(LabData(donorId = donorId))
-        model.addAttribute("labdatas", repository.findByDonorId(donorId))
+        model.addAttribute("labdatas", allLabDatasByDonorId(donorId))
+        model.addAttribute("labdataprofiles", labDataProfileRepository.findAll())
         return "labdatas"
     }
 
     @PutMapping(path = ["{labdataId}"])
     fun putLabData(@PathVariable donorId: Long, labData: LabData, model: Model): String {
-        repository.save(labData)
+        labDataRepository.save(labData)
-        model.addAttribute("labdatas", repository.findByDonorId(donorId))
+        model.addAttribute("labdatas", allLabDatasByDonorId(donorId))
+        model.addAttribute("labdataprofiles", labDataProfileRepository.findAll())
         return "labdatas"
     }
 
     @DeleteMapping(path = ["{labdataId}"])
     fun deleteLabData(@PathVariable donorId: Long, @PathVariable labdataId: Long, model: Model): String {
-        repository.deleteById(labdataId)
+        labDataRepository.deleteById(labdataId)
-        model.addAttribute("labdatas", repository.findByDonorId(donorId))
+        model.addAttribute("labdatas", allLabDatasByDonorId(donorId))
+        model.addAttribute("labdataprofiles", labDataProfileRepository.findAll())
         return "labdatas"
     }
 
+    private fun allLabDatasByDonorId(donorId: Long): List<LabData> {
+        return labDataRepository.findByDonorId(donorId)
+            .map { it.apply { labDataProfileRepository.findById(this.profile ?: 0).ifPresent { profileData = it } } }
+    }
+
 }

src/main/kotlin/dev/pcvolkmer/onco/grzmetadataprocessor/web/LabDataProfileController.kt

@@ -0,0 +1,43 @@
+package dev.pcvolkmer.onco.grzmetadataprocessor.web
+
+import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataProfile
+import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataProfileRepository
+import org.springframework.stereotype.Controller
+import org.springframework.ui.Model
+import org.springframework.web.bind.annotation.*
+
+@Controller
+@RequestMapping("/labdataprofiles")
+class LabDataProfileController(
+    private val repository: LabDataProfileRepository
+) {
+
+    @GetMapping
+    fun getAllLabDataProfiles(model: Model): String {
+        println(repository.findAll().sortedByDescending { it.id })
+        model.addAttribute("labdataprofiles", repository.findAll().sortedByDescending { it.id })
+        return "labdataprofiles"
+    }
+
+    @PostMapping
+    fun postLabDataProfile(model: Model): String {
+        repository.save(LabDataProfile(profileName = "Neues Sequenzierprofil"))
+        model.addAttribute("labdataprofiles", repository.findAll().sortedByDescending { it.id })
+        return "labdataprofiles"
+    }
+
+    @PutMapping(path = ["{labdataProfileId}"])
+    fun putLabData(@PathVariable labdataProfileId: Long, labDataProfile: LabDataProfile, model: Model): String {
+        repository.save(labDataProfile)
+        model.addAttribute("labdataprofiles", repository.findAll().sortedByDescending { it.id })
+        return "labdataprofiles"
+    }
+
+    @DeleteMapping(path = ["{labdataProfileId}"])
+    fun deleteLabData(@PathVariable labdataProfileId: Long, model: Model): String {
+        repository.deleteById(labdataProfileId)
+        model.addAttribute("labdataprofiles", repository.findAll().sortedByDescending { it.id })
+        return "labdataprofiles"
+    }
+
+}

src/main/resources/db/migrations/mariadb/V0_1_0_1__SeqProfiles.sql

@@ -0,0 +1,16 @@
+CREATE TABLE IF NOT EXISTS tbl_lab_data_profile
+(
+    id                              int auto_increment primary key,
+    profile_name                    varchar(255),
+    library_type                    varchar(255),
+    library_prep_kit                varchar(255) not null,
+    library_prep_kit_manufacturer   varchar(255) not null,
+    sequencer_model                 varchar(255) not null,
+    sequencer_manufacturer          varchar(255) not null,
+    kit_name                        varchar(255) not null,
+    kit_manufacturer                varchar(255) not null,
+    enrichment_kit                  varchar(255) not null,
+    enrichment_kit_manufacturer     varchar(255)
+);
+
+ALTER TABLE tbl_lab_data ADD COLUMN profile int;

src/main/resources/templates/casemenu.html

@@ -1,6 +1,7 @@
 <div class="title">GRZ-Metadaten</div>
 
 <nav>
+    <b>Falldaten</b>
     <ul>
         <li>
             <a th:href="@{/}">
@@ -21,5 +22,13 @@
             </a>
         </li>
     </ul>
+    <b>Profile</b>
+    <ul>
+        <li>
+            <a th:href="@{/labdataprofiles}">
+                <span>Sequenzierprofile</span>
+            </a>
+        </li>
+    </ul>
 </nav>
 

src/main/resources/templates/labdataprofiles.html

@@ -0,0 +1,126 @@
+<!DOCTYPE html>
+<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
+<head>
+    <meta charset="UTF-8">
+    <title>Title</title>
+    <link th:href="@{/main.css}" rel="stylesheet" />
+</head>
+<body>
+
+    <aside th:hx-get="@{/cases/menu}" hx-trigger="load"></aside>
+
+    <main>
+        <div>
+            <div th:if="${labdataprofiles.isEmpty()}">
+                <h3>Probe</h3>
+                <form class="lab-data" th:hx-post="@{/labdataprofiles}">
+                    <div>Keine Sequenzierprofile gefunden</div>
+                    <button>Neues Sequenzierprofil hinzufügen</button>
+                </form>
+            </div>
+
+            <div th:each="profile : ${labdataprofiles}">
+                <h3>
+                    Sequenzierprofil
+                    <tt>"[[ ${ profile.profileName } ]]"</tt>
+                </h3>
+
+                <form class="lab-data">
+                    <input type="hidden" name="id" th:value="${profile.id}" />
+
+                    <div>
+                        <label>
+                           Profilname
+                            <input type="text" name="profileName" th:value="${profile.profileName}" />
+                        </label>
+                    </div>
+
+                    <div>
+                        <label>
+                            Library Type
+                            <select name="libraryType">
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'panel'}" value="PANEL">panel</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'panel_lr'}" value="PANEL_LR">panel_lr</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wes'}" value="WES">wes</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wes_lr'}" value="WES_LR">wes_lr</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wgs'}" value="WGS">wgs</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wgs_lr'}" value="WGS_LR">wgs_lr</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wxs'}" value="WXS">wxs</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wxs_lr'}" value="WXS_LR">wxs_lr</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'other'}" value="OTHER">other</option>
+                                <option th:selected="${profile.libraryType != null and profile.libraryType.value == 'unknown'}" value="UNKNOWN">unknown</option>
+                            </select>
+                        </label>
+                    </div>
+
+                    <div>
+                        <label>
+                            Preparation Kit - Name
+                            <input type="text" name="libraryPrepKit" th:value="${profile.libraryPrepKit}" />
+                        </label>
+
+                        <label>
+                            Hersteller
+                            <input type="text" name="libraryPrepKitManufacturer" th:value="${profile.libraryPrepKitManufacturer}" />
+                        </label>
+                    </div>
+
+                    <div>
+                        <label>
+                            Sequencer - Modell
+                            <input type="text" name="sequencerModel" th:value="${profile.sequencerModel}" />
+                        </label>
+
+                        <label>
+                            Hersteller
+                            <input type="text" name="sequencerManufacturer" th:value="${profile.sequencerManufacturer}" />
+                        </label>
+                    </div>
+
+                    <div>
+                        <label>
+                            Kit - Name/Version
+                            <input type="text" name="kitName" th:value="${profile.kitName}" />
+                        </label>
+
+                        <label>
+                            Hersteller
+                            <input type="text" name="kitManufacturer" th:value="${profile.kitManufacturer}" />
+                        </label>
+                    </div>
+
+                    <div>
+                        <label>
+                            Enrichment Kit - Name und Version
+                            <input type="text" name="enrichmentKit" th:value="${profile.enrichmentKit}" />
+                        </label>
+
+                        <label>
+                            Hersteller
+                            <select name="enrichmentKitManufacturer">
+                                <option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'Illumuna'}" value="ILLUMINA">Illumina</option>
+                                <option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'Agilent'}" value="AGILENT">Agilent</option>
+                                <option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'Twist'}" value="TIST">Twist</option>
+                                <option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'NEB'}" value="NEB">NEB</option>
+                                <option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'other'}" value="OTHER">other</option>
+                                <option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'unknown'}" value="UNKNOWN">unknown</option>
+                                <option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'none'}" value="NONE">none</option>
+                            </select>
+                        </label>
+                    </div>
+
+                    <div>
+                        <button class="save" th:hx-put="@{/labdataprofiles/{profileId}(profileId=${profile.id})}" hx-target="body">Änderungen übernehmen</button>
+                        <button class="new" th:hx-post="@{/labdataprofiles}" hx-target="body">Neu</button>
+                        <button class="delete" th:hx-delete="@{/labdataprofiles/{profileId}(profileId=${profile.id})}" hx-target="body">Löschen</button>
+                    </div>
+
+                </form>
+            </div>
+
+        </div>
+    </main>
+
+    <script th:src="@{/main.js}"></script>
+</body>
+</html>