Merge pull request #7 from nbollis/PsmBulkAddition

Psm bulk addition
smith-chem-wisc · Dec 5, 2023 · d3ab48f · d3ab48f
2 parents da69a3c + cc5da43
commit d3ab48f
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Showing 10 changed files with 629 additions and 10 deletions.
diff --git a/MetaPAL/Controllers/SpectrumMatchesController.cs b/MetaPAL/Controllers/SpectrumMatchesController.cs
@@ -6,8 +6,10 @@
 using Microsoft.AspNetCore.Mvc.Rendering;
 using Microsoft.EntityFrameworkCore;
 using MetaPAL.Data;
+using MetaPAL.DataOperations;
 using MetaPAL.Models;
 using Microsoft.AspNetCore.Authorization;
+using Readers;
 
 namespace MetaPAL.Controllers
 {
@@ -23,11 +25,45 @@ public SpectrumMatchesController(ApplicationDbContext context)
         // GET: SpectrumMatches
         public async Task<IActionResult> Index()
         {
-              return _context.SpectrumMatch != null ? 
-                          View(await _context.SpectrumMatch.ToListAsync()) :
-                          Problem("Entity set 'ApplicationDbContext.SpectrumMatch'  is null.");
+            // TEMPORARY: remove all spectrum matches from database
+            //await Task.Run(() => DataOperations.DataOperations.RemoveAll<SpectrumMatch>(_context));
+
+            if (_context.SpectrumMatch == null)
+                return Problem("Entity set 'ApplicationDbContext.SpectrumMatch'  is null.");
+            return View(await _context.SpectrumMatch.ToListAsync());
         }
 
+        // GET: UploadSpectralMatchesForm
+        public async Task<IActionResult> UploadSpectralMatchesForm()
+        {
+            return _context.SpectrumMatch != null ?
+                View() :
+                Problem("Entity set 'ApplicationDbContext.SpectrumMatch'  is null.");
+        }
+
+        // GET: UploadSpectrumMatches
+        public async Task<IActionResult> UploadSpectralMatches(string PsmPath)
+        {
+            if (_context.SpectrumMatch == null)
+                return Problem("Entity set 'ApplicationDbContext.SpectrumMatch'  is null.");
+            try
+            {
+                foreach (var psm in SpectrumMatchTsvReader.ReadTsv(PsmPath, out _))
+                {
+                    _context.Add(SpectrumMatch.FromSpectrumMatchTsv(psm));
+                }
+
+                await _context.SaveChangesAsync();
+            }
+            catch (Exception e)
+            {
+                return Problem(e.Message);
+            }
+
+            return RedirectToAction(nameof(Index));
+        }
+
+
         // GET: ShowSearchForm
         public async Task<IActionResult> ShowSearchForm()
         {

diff --git a/MetaPAL/Data/ApplicationDbContext.cs b/MetaPAL/Data/ApplicationDbContext.cs
@@ -20,6 +20,20 @@ protected override void OnModelCreating(ModelBuilder builder)
                 .Ignore("ChildScanMatchedIons");
             builder.Entity<SpectrumMatch>()
                 .Ignore("VariantCrossingIons");
+            builder.Entity<SpectrumMatch>()
+                .Property(p => p.IdentifiedSequenceVariations)
+                .IsRequired(false);
+            builder.Entity<SpectrumMatch>()
+                .Property(p => p.IntersectingSequenceVariations)
+                .IsRequired(false);
+            builder.Entity<SpectrumMatch>()
+                .Property(p => p.PEP)
+                .HasConversion(v => double.IsNaN(v) ? -1 : v,
+                    v => v);
+            builder.Entity<SpectrumMatch>()
+                .Property(p => p.PEP_QValue)
+                .HasConversion(v => double.IsNaN(v) ? -1 : v,
+                                       v => v);
 
             base.OnModelCreating(builder);
         }