mirror of
https://github.com/pcvolkmer/grz-metadata-processor.git
synced 2025-07-01 20:12:54 +00:00
feat: instant replace kit data
This commit is contained in:
@ -108,6 +108,7 @@ enum class ReferenceGenome(val value: String) {
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}
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interface LabDataRepository : CrudRepository<LabData, Long> {
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fun getById(id: Long): LabData?
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fun findByDonorId(donorId: Long): MutableList<LabData>
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fun countLabDataByDonorIdIsNull(): Long
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fun findByEinsendenummer(einsendenummer: String): LabData
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@ -18,7 +18,13 @@ class LabDataController(
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fun getAllLabData(@PathVariable donorId: Long, model: Model): String {
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model.addAttribute("labdatas", allLabDatasByDonorId(donorId))
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model.addAttribute("labdataprofiles", labDataProfileRepository.findAll())
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return "labdatas"
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return "labdatas/index"
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}
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@GetMapping(path = ["{labdataId}/kits"])
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fun getLabDataKits(@PathVariable labdataId: Long, model: Model): String {
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model.addAttribute("labdata", labDataRepository.getById(labdataId))
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return "labdatas/kits"
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}
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@PostMapping
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@ -26,7 +32,7 @@ class LabDataController(
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labDataRepository.save(LabData(donorId = donorId))
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model.addAttribute("labdatas", allLabDatasByDonorId(donorId))
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model.addAttribute("labdataprofiles", labDataProfileRepository.findAll())
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return "labdatas"
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return "labdatas/index"
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}
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@PutMapping(path = ["{labdataId}"])
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@ -34,7 +40,7 @@ class LabDataController(
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labDataRepository.save(labData)
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model.addAttribute("labdatas", allLabDatasByDonorId(donorId))
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model.addAttribute("labdataprofiles", labDataProfileRepository.findAll())
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return "labdatas"
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return "labdatas/index"
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}
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@DeleteMapping(path = ["{labdataId}"])
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@ -42,7 +48,7 @@ class LabDataController(
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labDataRepository.deleteById(labdataId)
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model.addAttribute("labdatas", allLabDatasByDonorId(donorId))
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model.addAttribute("labdataprofiles", labDataProfileRepository.findAll())
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return "labdatas"
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return "labdatas/index"
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}
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private fun allLabDatasByDonorId(donorId: Long): List<LabData> {
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@ -2,6 +2,7 @@ package dev.pcvolkmer.onco.grzmetadataprocessor.web
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import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataProfile
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import dev.pcvolkmer.onco.grzmetadataprocessor.data.LabDataProfileRepository
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import org.springframework.data.repository.findByIdOrNull
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import org.springframework.stereotype.Controller
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import org.springframework.ui.Model
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import org.springframework.web.bind.annotation.*
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@ -14,7 +15,6 @@ class LabDataProfileController(
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@GetMapping
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fun getAllLabDataProfiles(model: Model): String {
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println(repository.findAll().sortedByDescending { it.id })
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model.addAttribute("labdataprofiles", repository.findAll().sortedByDescending { it.id })
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return "labdataprofiles"
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}
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@ -26,15 +26,21 @@ class LabDataProfileController(
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return "labdataprofiles"
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}
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@GetMapping(path = ["{labdataProfileId}"])
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fun getLabDataProfile(@PathVariable labdataProfileId: Long, model: Model): String {
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model.addAttribute("profile", repository.findByIdOrNull(labdataProfileId))
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return "labdataprofile"
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}
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@PutMapping(path = ["{labdataProfileId}"])
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fun putLabData(@PathVariable labdataProfileId: Long, labDataProfile: LabDataProfile, model: Model): String {
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fun putLabDataProfile(@PathVariable labdataProfileId: Long, labDataProfile: LabDataProfile, model: Model): String {
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repository.save(labDataProfile)
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model.addAttribute("labdataprofiles", repository.findAll().sortedByDescending { it.id })
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return "labdataprofiles"
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}
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@DeleteMapping(path = ["{labdataProfileId}"])
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fun deleteLabData(@PathVariable labdataProfileId: Long, model: Model): String {
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fun deleteLabDataProfile(@PathVariable labdataProfileId: Long, model: Model): String {
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repository.deleteById(labdataProfileId)
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model.addAttribute("labdataprofiles", repository.findAll().sortedByDescending { it.id })
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return "labdataprofiles"
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@ -2,7 +2,7 @@
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<nav>
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<b>Falldaten</b>
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<ul>
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<ul class="datamenu">
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<li>
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<a th:href="@{/}">
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<span>Fallübersicht</span>
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@ -23,7 +23,7 @@
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</li>
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</ul>
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<b>Profile</b>
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<ul>
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<ul class="settingsmenu">
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<li>
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<a th:href="@{/labdataprofiles}">
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<span>Sequenzierprofile</span>
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82
src/main/resources/templates/labdataprofile.html
Normal file
82
src/main/resources/templates/labdataprofile.html
Normal file
@ -0,0 +1,82 @@
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<!DOCTYPE html>
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<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
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<head>
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<meta charset="UTF-8">
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<title>Title</title>
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</head>
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<body>
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<div>
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<label class="disabled">
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Library Type
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<select name="libraryType" disabled>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'panel'}" value="PANEL">panel</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'panel_lr'}" value="PANEL_LR">panel_lr</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wes'}" value="WES">wes</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wes_lr'}" value="WES_LR">wes_lr</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wgs'}" value="WGS">wgs</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wgs_lr'}" value="WGS_LR">wgs_lr</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wxs'}" value="WXS">wxs</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'wxs_lr'}" value="WXS_LR">wxs_lr</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'other'}" value="OTHER">other</option>
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<option th:selected="${profile.libraryType != null and profile.libraryType.value == 'unknown'}" value="UNKNOWN">unknown</option>
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</select>
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</label>
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</div>
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<div>
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<label class="disabled">
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Preparation Kit - Name
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<input type="text" name="libraryPrepKit" th:value="${profile.libraryPrepKit}" disabled />
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</label>
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<label class="disabled">
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Hersteller
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<input type="text" name="libraryPrepKitManufacturer" th:value="${profile.libraryPrepKitManufacturer}" disabled />
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</label>
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</div>
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<div>
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<label class="disabled">
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Sequencer - Modell
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<input type="text" name="sequencerModel" th:value="${profile.sequencerModel}" disabled />
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</label>
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<label class="disabled">
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Hersteller
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<input type="text" name="sequencerManufacturer" th:value="${profile.sequencerManufacturer}" disabled />
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</label>
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</div>
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<div>
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<label class="disabled">
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Kit - Name/Version
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<input type="text" name="kitName" th:value="${profile.kitName}" disabled />
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</label>
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<label class="disabled">
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Hersteller
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<input type="text" name="kitManufacturer" th:value="${profile.kitManufacturer}" disabled />
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</label>
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</div>
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<div>
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<label class="disabled">
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Enrichment Kit - Name und Version
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<input type="text" name="enrichmentKit" th:value="${profile.enrichmentKit}" disabled />
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</label>
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<label class="disabled">
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Hersteller
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<select name="enrichmentKitManufacturer" disabled>
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<option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'Illumuna'}" value="ILLUMINA">Illumina</option>
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<option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'Agilent'}" value="AGILENT">Agilent</option>
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<option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'Twist'}" value="TIST">Twist</option>
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<option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'NEB'}" value="NEB">NEB</option>
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<option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'other'}" value="OTHER">other</option>
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<option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'unknown'}" value="UNKNOWN">unknown</option>
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<option th:selected="${profile.enrichmentKitManufacturer != null and profile.enrichmentKitManufacturer.value == 'none'}" value="NONE">none</option>
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</select>
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</label>
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</div>
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</body>
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</html>
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@ -93,14 +93,18 @@
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<div>
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<label class="optional">
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Sequenzierprofil (Optionale Angabe)
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<select name="profile">
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<option value="">Kein Sequenzierprofil</option>
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<option th:each="labdataprofile : ${labdataprofiles}" th:selected="${labdataprofile.id == labdata.profile}" th:value="${labdataprofile.id}" th:text="${labdataprofile.profileName}"></option>
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<select name="profile" th:hx-target="${'#labdata_' + labdata.id + '_sequencerprofile'}">
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<option value="" th:hx-get="@{/donors/{donorId}/labdatas/{labdataId}/kits(donorId=${donorId},labdataId=${labdata.id})}">Kein Sequenzierprofil</option>
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<option th:each="labdataprofile : ${labdataprofiles}"
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th:selected="${labdataprofile.id == labdata.profile}"
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th:hx-get="@{/labdataprofiles/{labdataprofileId}(labdataprofileId=${labdataprofile.id})}"
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th:value="${labdataprofile.id}"
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th:text="${labdataprofile.profileName}"></option>
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</select>
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</label>
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</div>
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<th:block th:if="${labdata.profileData == null}">
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<div th:if="${labdata.profileData == null}" th:id="${'labdata_' + labdata.id + '_sequencerprofile'}">
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<div>
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<label>
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Library Type
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@ -174,11 +178,11 @@
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</select>
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</label>
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</div>
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</th:block>
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</div>
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<th:block th:if="${labdata.profileData != null}">
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<div th:if="${labdata.profileData != null}" th:id="${'labdata_' + labdata.id + '_sequencerprofile'}">
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<div>
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<label class="optional">
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<label class="disabled">
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Library Type
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<select name="libraryType" disabled>
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<option th:selected="${labdata.profileData.libraryType != null and labdata.profileData.libraryType.value == 'panel'}" value="PANEL">panel</option>
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@ -196,48 +200,48 @@
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</div>
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<div>
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<label class="optional">
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<label class="disabled">
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Preparation Kit - Name
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<input type="text" name="libraryPrepKit" th:value="${labdata.profileData.libraryPrepKit}" disabled/>
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</label>
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<label class="optional">
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<label class="disabled">
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Hersteller
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<input type="text" name="libraryPrepKitManufacturer" th:value="${labdata.profileData.libraryPrepKitManufacturer}" disabled/>
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</label>
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</div>
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<div>
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<label class="optional">
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<label class="disabled">
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Sequencer - Modell
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<input type="text" name="sequencerModel" th:value="${labdata.profileData.sequencerModel}" disabled/>
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</label>
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<label class="optional">
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<label class="disabled">
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Hersteller
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<input type="text" name="sequencerManufacturer" th:value="${labdata.profileData.sequencerManufacturer}" disabled/>
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</label>
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</div>
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<div>
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<label class="optional">
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<label class="disabled">
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Kit - Name/Version
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<input type="text" name="kitName" th:value="${labdata.profileData.kitName}" disabled/>
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</label>
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<label class="optional">
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<label class="disabled">
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Hersteller
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<input type="text" name="kitManufacturer" th:value="${labdata.profileData.kitManufacturer}" disabled/>
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</label>
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</div>
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<div>
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<label class="optional">
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<label class="disabled">
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Enrichment Kit - Name und Version
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<input type="text" name="enrichmentKit" th:value="${labdata.profileData.enrichmentKit}" disabled />
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</label>
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<label class="optional">
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<label class="disabled">
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Hersteller
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<select name="enrichmentKitManufacturer" disabled>
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<option th:selected="${labdata.profileData.enrichmentKitManufacturer != null and labdata.profileData.enrichmentKitManufacturer.value == 'Illumina'}" value="ILLUMINA">Illumina</option>
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@ -250,7 +254,7 @@
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</select>
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</label>
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</div>
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</th:block>
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</div>
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<div>
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<label>
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82
src/main/resources/templates/labdatas/kits.html
Normal file
82
src/main/resources/templates/labdatas/kits.html
Normal file
@ -0,0 +1,82 @@
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<!DOCTYPE html>
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<html lang="de" xmlns="http://www.w3.org/1999/html" xmlns:th="http://www.thymeleaf.org">
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<head>
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<meta charset="UTF-8">
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<title>Title</title>
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</head>
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<body>
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<div>
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<label>
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Library Type
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<select name="libraryType">
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'panel'}" value="PANEL">panel</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'panel_lr'}" value="PANEL_LR">panel_lr</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'wes'}" value="WES">wes</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'wes_lr'}" value="WES_LR">wes_lr</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'wgs'}" value="WGS">wgs</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'wgs_lr'}" value="WGS_LR">wgs_lr</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'wxs'}" value="WXS">wxs</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'wxs_lr'}" value="WXS_LR">wxs_lr</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'other'}" value="OTHER">other</option>
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<option th:selected="${labdata.libraryType != null and labdata.libraryType.value == 'unknown'}" value="UNKNOWN">unknown</option>
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</select>
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</label>
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</div>
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<div>
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<label>
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Preparation Kit - Name
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<input type="text" name="libraryPrepKit" th:value="${labdata.libraryPrepKit}" />
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</label>
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<label>
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Hersteller
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<input type="text" name="libraryPrepKitManufacturer" th:value="${labdata.libraryPrepKitManufacturer}" />
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</label>
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</div>
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<div>
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<label>
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Sequencer - Modell
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<input type="text" name="sequencerModel" th:value="${labdata.sequencerModel}" />
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</label>
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<label>
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Hersteller
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<input type="text" name="sequencerManufacturer" th:value="${labdata.sequencerManufacturer}" />
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</label>
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</div>
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<div>
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<label>
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Kit - Name/Version
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<input type="text" name="kitName" th:value="${labdata.kitName}" />
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</label>
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<label>
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Hersteller
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<input type="text" name="kitManufacturer" th:value="${labdata.kitManufacturer}" />
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</label>
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</div>
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<div>
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<label>
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Enrichment Kit - Name und Version
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<input type="text" name="enrichmentKit" th:value="${labdata.enrichmentKit}" />
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</label>
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<label>
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Hersteller
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<select name="enrichmentKitManufacturer">
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<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'Illumuna'}" value="ILLUMINA">Illumina</option>
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<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'Agilent'}" value="AGILENT">Agilent</option>
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<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'Twist'}" value="TIST">Twist</option>
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<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'NEB'}" value="NEB">NEB</option>
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<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'other'}" value="OTHER">other</option>
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<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'unknown'}" value="UNKNOWN">unknown</option>
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<option th:selected="${labdata.enrichmentKitManufacturer != null and labdata.enrichmentKitManufacturer.value == 'none'}" value="NONE">none</option>
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</select>
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</label>
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</div>
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||||
</body>
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||||
</html>
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@ -9,7 +9,7 @@ aside {
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||||
}
|
||||
|
||||
aside > .title {
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||||
@apply m-2 text-2xl font-bold
|
||||
@apply my-2 text-2xl font-bold
|
||||
}
|
||||
|
||||
aside > nav {
|
||||
@ -17,10 +17,10 @@ aside > nav {
|
||||
}
|
||||
|
||||
aside > nav ul {
|
||||
@apply m-2
|
||||
@apply my-2
|
||||
}
|
||||
|
||||
aside > nav a:before {
|
||||
aside > nav ul.datamenu a:before {
|
||||
content: '🗎';
|
||||
margin-right: 4px;
|
||||
opacity: 0.8;
|
||||
@ -28,6 +28,14 @@ aside > nav a:before {
|
||||
text-align: center;
|
||||
}
|
||||
|
||||
aside > nav ul.settingsmenu a:before {
|
||||
content: '⚙';
|
||||
margin-right: 4px;
|
||||
opacity: 0.8;
|
||||
width: 1.2em;
|
||||
text-align: center;
|
||||
}
|
||||
|
||||
aside > nav a:hover:before {
|
||||
opacity: 1;
|
||||
}
|
||||
@ -94,6 +102,13 @@ label.optional select {
|
||||
background: repeating-linear-gradient(135deg, var(--color-white), var(--color-white) 4px, transparent 4px, transparent 8px)
|
||||
}
|
||||
|
||||
label.disabled input,
|
||||
label.disabled select {
|
||||
@apply text-gray-600;
|
||||
font-style: normal;
|
||||
background: repeating-linear-gradient(135deg, var(--color-white), var(--color-white) 4px, transparent 4px, transparent 8px)
|
||||
}
|
||||
|
||||
input[type=text],
|
||||
input[type=date],
|
||||
input[type=number],
|
||||
|
||||
Reference in New Issue
Block a user