Merge branch 'main' into adapt-export-ui

src/api/BoreholeGeometry/AzIncFormat.cs

@@ -14,14 +14,14 @@ internal sealed class AzIncFormat : IBoreholeGeometryFormat
 
     public string Name => "Azimuth Inclination";
 
-    private Lazy<string> expectedCsvHeader = new(Helper.GetCSVHeader<Geometry>);
+    private Lazy<string> expectedCsvHeader = new(CsvConfigHelper.GetCsvHeader<Geometry>);
 
     public string CsvHeader => expectedCsvHeader.Value;
 
     public IList<BoreholeGeometryElement> ReadCsv(IFormFile file, int boreholeId)
     {
         using var reader = new StreamReader(file.OpenReadStream());
-        using var csv = new CsvReader(reader, Helper.CsvConfig);
+        using var csv = new CsvReader(reader, CsvConfigHelper.CsvConfig);
 
         var data = csv.GetRecords<Geometry>().ToList();
 

src/api/BoreholeGeometry/CsvConfigHelper.cs

@@ -0,0 +1,38 @@
+using BDMS.Models;
+using CsvHelper;
+using CsvHelper.Configuration;
+using Humanizer;
+using NetTopologySuite.Mathematics;
+using NetTopologySuite.Utilities;
+using System.Globalization;
+
+namespace BDMS.BoreholeGeometry;
+
+public static class CsvConfigHelper
+{
+    internal static readonly CsvConfiguration CsvConfig = new(new CultureInfo("de-CH"))
+    {
+        Delimiter = ";",
+        IgnoreReferences = true,
+        PrepareHeaderForMatch = args => args.Header.Humanize(LetterCasing.Title),
+        MissingFieldFound = null,
+    };
+
+    /// <summary>
+    /// Get the CSV header <see cref="CsvHelper"/> for a class of type <typeparamref name="T"/>.
+    /// Uses the map generated by <see cref="CsvHelper.CsvContext.AutoMap{T}()"/>.
+    /// If a property has multiple possible column names only the first is considered.
+    /// </summary>
+    /// <typeparam name="T">The class to get the header for.</typeparam>
+    internal static string GetCsvHeader<T>()
+    {
+        var context = new CsvContext(CsvConfig);
+        var map = context.AutoMap<T>();
+        return string.Join("; ", map.MemberMaps
+            .Select(m =>
+            {
+                var name = m.Data.Names.FirstOrDefault(m.Data.Member.Name);
+                return m.Data.IsOptional ? $"[{name}]" : name;
+            }));
+    }
+}

src/api/BoreholeGeometry/PitchRollFormat.cs

@@ -14,14 +14,14 @@ internal sealed class PitchRollFormat : IBoreholeGeometryFormat
 
     public string Name => "Pitch Roll";
 
-    private Lazy<string> expectedCsvHeader = new(Helper.GetCSVHeader<Geometry>);
+    private Lazy<string> expectedCsvHeader = new(CsvConfigHelper.GetCsvHeader<Geometry>);
 
     public string CsvHeader => expectedCsvHeader.Value;
 
     public IList<BoreholeGeometryElement> ReadCsv(IFormFile file, int boreholeId)
     {
         using var reader = new StreamReader(file.OpenReadStream());
-        using var csv = new CsvReader(reader, Helper.CsvConfig);
+        using var csv = new CsvReader(reader, CsvConfigHelper.CsvConfig);
 
         var data = csv.GetRecords<Geometry>().ToList();
 

src/api/BoreholeGeometry/XYZFormat.cs

@@ -13,14 +13,14 @@ internal sealed class XYZFormat : IBoreholeGeometryFormat
 
     public string Name => "X Y Z";
 
-    private Lazy<string> expectedCsvHeader = new(Helper.GetCSVHeader<Geometry>);
+    private Lazy<string> expectedCsvHeader = new(CsvConfigHelper.GetCsvHeader<Geometry>);
 
     public string CsvHeader => expectedCsvHeader.Value;
 
     public IList<BoreholeGeometryElement> ReadCsv(IFormFile file, int boreholeId)
     {
         using var reader = new StreamReader(file.OpenReadStream());
-        using var csv = new CsvReader(reader, Helper.CsvConfig);
+        using var csv = new CsvReader(reader, CsvConfigHelper.CsvConfig);
 
         var data = csv.GetRecords<Geometry>();
         return ToBoreholeGeometry(data, boreholeId);

src/api/BoreholeGeometry/Helper.cs → src/api/BoreholeGeometryExtensions.cs

@@ -1,42 +1,41 @@
 using BDMS.Models;
-using CsvHelper;
-using CsvHelper.Configuration;
-using Humanizer;
 using NetTopologySuite.Mathematics;
 using NetTopologySuite.Utilities;
-using System.Globalization;
 
-namespace BDMS.BoreholeGeometry;
+namespace BDMS;
 
-public static class Helper
+public static class BoreholeGeometryExtensions
 {
-    internal static readonly CsvConfiguration CsvConfig = new(new CultureInfo("de-CH"))
-    {
-        Delimiter = ";",
-        IgnoreReferences = true,
-        PrepareHeaderForMatch = args => args.Header.Humanize(LetterCasing.Title),
-        MissingFieldFound = null,
-    };
-
     /// <summary>
-    /// Get the CSV header <see cref="CsvHelper"/> expects to read a class <typeparamref name="T"/>.
-    /// Uses the map generated by <see cref="CsvHelper.CsvContext.AutoMap{T}()"/>.
-    /// If a property has multiple possible column names only the first is considered.
+    /// Get the TVD of <paramref name="depthMD"/> according to the <paramref name="geometry"/> if the geometry exists.
     /// </summary>
-    /// <typeparam name="T">The class to get the header for.</typeparam>
-    internal static string GetCSVHeader<T>()
+    /// <param name="geometry">The list of <see cref="BoreholeGeometryElement"/> representing the borehole's path geometry.</param>
+    /// <param name="depthMD">The measured depth (MD) at which to calculate the TVD.</param>
+    /// <returns>The TVD at <paramref name="depthMD"/> if the geometry exists; otherwise <see langword="null"/>.</returns>
+    internal static double? GetTVDIfGeometryExists(this List<BoreholeGeometryElement> geometry, double? depthMD)
     {
-        var context = new CsvContext(CsvConfig);
-        var map = context.AutoMap<T>();
-        return string.Join("; ", map.MemberMaps
-            .Select(m =>
+        if (geometry == null || geometry.Count < 2)
+        {
+            if (depthMD != null && depthMD >= 0)
             {
-                var name = m.Data.Names.FirstOrDefault(m.Data.Member.Name);
-                return m.Data.IsOptional ? $"[{name}]" : name;
-            }));
-    }
+                // Return the depthMD unchanged as if the borehole is perfectly vertical and infinitely long.
+                return depthMD;
+            }
+        }
+        else if (depthMD != null)
+        {
+            try
+            {
+                return geometry.GetDepthTVD(depthMD.Value);
+            }
+            catch (ArgumentOutOfRangeException)
+            {
+                // Exception is ignored so that the method returns null in case the input was invalid.
+            }
+        }
 
-    private static readonly IComparer<BoreholeGeometryElement> geometryMDComparer = Comparer<BoreholeGeometryElement>.Create((a, b) => a.MD.CompareTo(b.MD));
+        return null;
+    }
 
     /// <summary>
     /// Get the TVD of <paramref name="depthMD"/> according to the <paramref name="geometry"/>.
@@ -130,6 +129,8 @@ private static double InterpolateDepthTVD(List<BoreholeGeometryElement> geometry
         }
     }
 
+    private static readonly IComparer<BoreholeGeometryElement> geometryMDComparer = Comparer<BoreholeGeometryElement>.Create((a, b) => a.MD.CompareTo(b.MD));
+
     internal static Vector3D ToVector3D(this BoreholeGeometryElement element)
         => new Vector3D(element.X, element.Y, element.Z);
 

src/api/Controllers/BoreholeGeometryController.cs

@@ -118,28 +118,13 @@ public async Task<IActionResult> GetDepthTVD([FromQuery] int boreholeId, [FromQu
     {
         var geometry = await GetBoreholeGeometry(boreholeId).ConfigureAwait(false);
 
-        if (geometry.Count < 2)
+        var tvd = geometry.GetTVDIfGeometryExists(depthMD);
+        if (tvd == null)
         {
-            if (depthMD >= 0)
-            {
-                // Return the depthMD unchanged as if the borehole is perfectly vertical and infinitely long.
-                return Ok(depthMD);
-            }
-        }
-        else
-        {
-            try
-            {
-                return Ok(geometry.GetDepthTVD(depthMD));
-            }
-            catch (ArgumentOutOfRangeException)
-            {
-             // Exception is ignored so that the action returns an empty response in case the input was invalid.
-            }
+            logger?.LogInformation($"Invalid input, could not calculate true vertical depth from measured depth of {depthMD}");
         }
 
-        logger?.LogInformation($"Invalid input, could not calculate true vertical depth from measured depth of {depthMD}");
-        return Ok();
+        return Ok(tvd);
     }
 
     private async Task<List<BoreholeGeometryElement>> GetBoreholeGeometry(int boreholeId)

src/api/Controllers/UploadController.cs → src/api/Controllers/ImportController.cs

@@ -14,7 +14,7 @@ namespace BDMS.Controllers;
 
 [ApiController]
 [Route("api/v{version:apiVersion}/[controller]")]
-public class UploadController : ControllerBase
+public class ImportController : ControllerBase
 {
     private const int MaxFileSize = 210_000_000; // 1024 x 1024 x 200 = 209715200 bytes
     private readonly BdmsContext context;
@@ -35,7 +35,7 @@ public class UploadController : ControllerBase
 
     private static readonly JsonSerializerOptions jsonImportOptions = new() { PropertyNameCaseInsensitive = true };
 
-    public UploadController(BdmsContext context, ILogger<UploadController> logger, LocationService locationService, CoordinateService coordinateService, BoreholeFileCloudService boreholeFileCloudService)
+    public ImportController(BdmsContext context, ILogger<ImportController> logger, LocationService locationService, CoordinateService coordinateService, BoreholeFileCloudService boreholeFileCloudService)
     {
         this.context = context;
         this.logger = logger;

src/client/cypress/e2e/helpers/testHelpers.js

@@ -109,6 +109,8 @@ export const interceptApiCalls = () => {
   cy.intercept("dataextraction/api/V1/extract_data").as("extract-data");
 
   cy.intercept("https://api3.geo.admin.ch/rest/services/height*").as("height");
+
+  cy.intercept("/api/v2/import*").as("borehole-upload");
 };
 
 /**

src/client/cypress/e2e/mainPage/import.cy.js

@@ -42,9 +42,6 @@ describe("Test for importing boreholes.", () => {
       });
     });
 
-    // Intercept upload request
-    cy.intercept("/api/v2/upload?workgroupId=1").as("borehole-upload");
-
     // Import boreholes and attachments
     cy.get('[data-cy="import-button"]').click();
     cy.wait("@borehole-upload");
@@ -75,9 +72,6 @@ describe("Test for importing boreholes.", () => {
           });
         });
       });
-
-    cy.intercept("/api/v2/upload?workgroupId=1").as("borehole-upload");
-
     cy.get('[data-cy="import-button"]').click();
 
     cy.wait("@borehole-upload");

src/client/cypress/fixtures/import/boreholes-missing-fields-and-duplicates.csv

@@ -1,4 +1,4 @@
-alternate_name;original_name;location_x;location_y
+name;original_name;location_x;location_y
 BH-1001;Wellington 1;
 BH-1002;Wellington 2;
 BH-1003;Wellington 3;2189456;1334567

src/client/cypress/fixtures/import/boreholes-multiple-valid.csv

@@ -1,4 +1,4 @@
-alternate_name;original_name;location_x;location_y;attachments;
+name;original_name;location_x;location_y;attachments;
 BH-1001;Wellington 1;2156784;1154321;borehole_attachment_1.pdf,borehole_attachment_2.zip;
 BH-1002;Wellington 2;2367999;1276543;
 BH-1003;Wellington 3;2189456;1334567;

src/client/cypress/fixtures/import/data-sets/invalid-lithology/borehole-valid.csv

@@ -1,5 +1,5 @@
-import_id;alternate_name;original_name;location_x;location_y;
-344;BH-1001;Wellington 1;2156784;1154321;
-33;BH-1002;Wellington 2;2367999;1276543;
-2;BH-1003;Wellington 3;2189456;1334567;
-55;BH-1004;Wellington 4;2312345;1200987;
+name;original_name;location_x;location_y;
+BH-1001;Wellington 1;2156784;1154321;
+BH-1002;Wellington 2;2367999;1276543;
+BH-1003;Wellington 3;2189456;1334567;
+BH-1004;Wellington 4;2312345;1200987;

src/client/src/api/borehole.ts

@@ -73,7 +73,7 @@ export const updateBorehole = async (borehole: BoreholeV2) => {
 
 /* eslint-disable  @typescript-eslint/no-explicit-any */
 export const importBoreholes = async (workgroupId: string, combinedFormData: any) => {
-  return await upload(`upload?workgroupId=${workgroupId}`, "POST", combinedFormData);
+  return await upload(`import?workgroupId=${workgroupId}`, "POST", combinedFormData);
 };
 
 export const copyBorehole = async (boreholeId: GridRowSelectionModel, workgroupId: string | null) => {

tests/api/Controllers/BoreholeControllerTest.cs

@@ -643,23 +643,23 @@ public async Task CopyInvalidBoreholeId()
     [TestMethod]
     public async Task CopyInvalidWorkgroupId()
     {
-        boreholeId = GetBoreholeIdToCopy();
+        boreholeId = testBoreholeId;
         var result = await controller.CopyAsync(boreholeId, workgroupId: 0).ConfigureAwait(false);
         ActionResultAssert.IsUnauthorized(result.Result);
     }
 
     [TestMethod]
     public async Task CopyMissingWorkgroupPermission()
     {
-        boreholeId = GetBoreholeIdToCopy();
+        boreholeId = testBoreholeId;
         var result = await controller.CopyAsync(boreholeId, workgroupId: 2).ConfigureAwait(false);
         ActionResultAssert.IsUnauthorized(result.Result);
     }
 
     [TestMethod]
     public async Task CopyWithUnknownUser()
     {
-        boreholeId = GetBoreholeIdToCopy();
+        boreholeId = testBoreholeId;
         controller.HttpContext.SetClaimsPrincipal("NON-EXISTENT-NAME", PolicyNames.Admin);
         var result = await controller.CopyAsync(boreholeId, workgroupId: DefaultWorkgroupId).ConfigureAwait(false);
         ActionResultAssert.IsUnauthorized(result.Result);
@@ -668,7 +668,7 @@ public async Task CopyWithUnknownUser()
     [TestMethod]
     public async Task CopyWithUserNotSet()
     {
-        boreholeId = GetBoreholeIdToCopy();
+        boreholeId = testBoreholeId;
         controller.ControllerContext.HttpContext.User = null;
         await Assert.ThrowsExceptionAsync<InvalidOperationException>(async () =>
         {
@@ -679,7 +679,7 @@ await Assert.ThrowsExceptionAsync<InvalidOperationException>(async () =>
     [TestMethod]
     public async Task CopyWithNonAdminUser()
     {
-        boreholeId = GetBoreholeIdToCopy();
+        boreholeId = testBoreholeId;
         controller.HttpContext.SetClaimsPrincipal("sub_editor", PolicyNames.Viewer);
         var result = await controller.CopyAsync(boreholeId, workgroupId: DefaultWorkgroupId).ConfigureAwait(false);
         ActionResultAssert.IsOk(result.Result);
@@ -701,7 +701,7 @@ public async Task DownloadCsvWithValidIdsReturnsFileResultWithMax100Boreholes()
         var csvData = Encoding.UTF8.GetString(result.FileContents);
         var fileLength = csvData.Split('\n').Length;
         var recordCount = fileLength - 2; // Remove header and last line break
-        Assert.IsTrue(recordCount <= 100);
+        Assert.AreEqual(100, recordCount);
     }
 
     [TestMethod]

tests/api/Controllers/UploadControllerTest.cs → tests/api/Controllers/ImportControllerTest.cs

@@ -16,16 +16,16 @@ namespace BDMS.Controllers;
 
 [DeploymentItem("TestData")]
 [TestClass]
-public class UploadControllerTest
+public class ImportControllerTest
 {
     private const int MaxBoreholeSeedId = 1002999;
     private const int MaxStratigraphySeedId = 6002999;
     private const int MaxLayerSeedId = 7029999;
 
     private BdmsContext context;
-    private UploadController controller;
+    private ImportController controller;
     private Mock<IHttpClientFactory> httpClientFactoryMock;
-    private Mock<ILogger<UploadController>> loggerMock;
+    private Mock<ILogger<ImportController>> loggerMock;
     private Mock<ILogger<LocationService>> loggerLocationServiceMock;
     private Mock<ILogger<CoordinateService>> loggerCoordinateServiceMock;
 
@@ -36,7 +36,7 @@ public void TestInitialize()
 
         context = ContextFactory.CreateContext();
         httpClientFactoryMock = new Mock<IHttpClientFactory>(MockBehavior.Strict);
-        loggerMock = new Mock<ILogger<UploadController>>();
+        loggerMock = new Mock<ILogger<ImportController>>();
 
         loggerLocationServiceMock = new Mock<ILogger<LocationService>>(MockBehavior.Strict);
         var locationService = new LocationService(loggerLocationServiceMock.Object, httpClientFactoryMock.Object);
@@ -56,7 +56,7 @@ public void TestInitialize()
         contextAccessorMock.Object.HttpContext.User = new ClaimsPrincipal(new ClaimsIdentity(new[] { new Claim(ClaimTypes.NameIdentifier, context.Users.FirstOrDefault().SubjectId) }));
         var boreholeFileCloudService = new BoreholeFileCloudService(context, configuration, loggerBoreholeFileCloudService.Object, contextAccessorMock.Object, s3ClientMock);
 
-        controller = new UploadController(context, loggerMock.Object, locationService, coordinateService, boreholeFileCloudService) { ControllerContext = GetControllerContextAdmin() };
+        controller = new ImportController(context, loggerMock.Object, locationService, coordinateService, boreholeFileCloudService) { ControllerContext = GetControllerContextAdmin() };
     }
 
     [TestCleanup]
@@ -1137,13 +1137,13 @@ public async Task UploadWithMaxValidationErrorsExceededShouldReturnError()
     [TestMethod]
     public void CompareValueWithTolerance()
     {
-        Assert.AreEqual(true, UploadController.CompareValuesWithTolerance(null, null, 0));
-        Assert.AreEqual(true, UploadController.CompareValuesWithTolerance(2100000, 2099998, 2));
-        Assert.AreEqual(false, UploadController.CompareValuesWithTolerance(2100000, 2000098, 1.99));
-        Assert.AreEqual(false, UploadController.CompareValuesWithTolerance(2100002, 2000000, 1.99));
-        Assert.AreEqual(false, UploadController.CompareValuesWithTolerance(21000020, 2000000, 20));
-        Assert.AreEqual(false, UploadController.CompareValuesWithTolerance(null, 2000000, 0));
-        Assert.AreEqual(false, UploadController.CompareValuesWithTolerance(2000000, null, 2));
+        Assert.AreEqual(true, ImportController.CompareValuesWithTolerance(null, null, 0));
+        Assert.AreEqual(true, ImportController.CompareValuesWithTolerance(2100000, 2099998, 2));
+        Assert.AreEqual(false, ImportController.CompareValuesWithTolerance(2100000, 2000098, 1.99));
+        Assert.AreEqual(false, ImportController.CompareValuesWithTolerance(2100002, 2000000, 1.99));
+        Assert.AreEqual(false, ImportController.CompareValuesWithTolerance(21000020, 2000000, 20));
+        Assert.AreEqual(false, ImportController.CompareValuesWithTolerance(null, 2000000, 0));
+        Assert.AreEqual(false, ImportController.CompareValuesWithTolerance(2000000, null, 2));
     }
 
     [TestMethod]