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Decoupling spectral match model from PsmFromTsv #12

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merged 4 commits into from
Jan 3, 2024
Merged

Decoupling spectral match model from PsmFromTsv #12

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9564973
Created separate spectummatch model
nbollis Jan 3, 2024
8987a9f
Ensured all worked correctly with upload
nbollis Jan 3, 2024
8bfed94
Added comment
nbollis Jan 3, 2024
2b76487
Sped up upload with linq statement
nbollis Jan 3, 2024
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10 changes: 6 additions & 4 deletions MetaPAL/Controllers/SpectrumMatchesController.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -26,15 +26,16 @@
public async Task<IActionResult> Index()
{
// TEMPORARY: remove all spectrum matches from database
//await Task.Run(() => DataOperations.DataOperations.RemoveAll<SpectrumMatch>(_context));
//Task.Run(() => DataOperations.DataOperations.RemoveAll<SpectrumMatch>(_context)).Wait();


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()

Check warning on line 38 in MetaPAL/Controllers/SpectrumMatchesController.cs

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GitHub Actions / build 

This async method lacks 'await' operators and will run synchronously. Consider using the 'await' operator to await non-blocking API calls, or 'await Task.Run(...)' to do CPU-bound work on a background thread.
{
return _context.SpectrumMatch != null ?
View() :
Expand All @@ -48,9 +49,10 @@
return Problem("Entity set 'ApplicationDbContext.SpectrumMatch' is null.");
try
{
foreach (var psm in SpectrumMatchTsvReader.ReadTsv(PsmPath, out _))
foreach (var psm in SpectrumMatchTsvReader.ReadTsv(PsmPath, out _)
.Select(SpectrumMatch.FromSpectrumMatchTsv))
{
_context.Add(SpectrumMatch.FromSpectrumMatchTsv(psm));
_context.Add(psm);
}

await _context.SaveChangesAsync();
Expand All @@ -65,7 +67,7 @@


// GET: ShowSearchForm
public async Task<IActionResult> ShowSearchForm()

Check warning on line 70 in MetaPAL/Controllers/SpectrumMatchesController.cs

View workflow job for this annotation

GitHub Actions / build 

This async method lacks 'await' operators and will run synchronously. Consider using the 'await' operator to await non-blocking API calls, or 'await Task.Run(...)' to do CPU-bound work on a background thread.
{
return _context.SpectrumMatch != null ?
View() :
Expand All @@ -76,7 +78,7 @@
public async Task<IActionResult> ShowSearchResults(string SearchPhrase)
{
return _context.SpectrumMatch != null ?
View(await _context.SpectrumMatch.Where(b=>b.BaseSeq.Contains(SearchPhrase)).ToListAsync()) :
View(await _context.SpectrumMatch.Where(b=>b.BaseSequence.Contains(SearchPhrase)).ToListAsync()) :
Problem("Entity set 'ApplicationDbContext.SpectrumMatch' is null.");
}
// GET: SpectrumMatches/Details/5
Expand Down
21 changes: 0 additions & 21 deletions MetaPAL/Data/ApplicationDbContext.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -14,27 +14,6 @@ public ApplicationDbContext(DbContextOptions<ApplicationDbContext> options)

protected override void OnModelCreating(ModelBuilder builder)
{
builder.Entity<SpectrumMatch>()
.Ignore("MatchedIons");
builder.Entity<SpectrumMatch>()
.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);
}

Expand Down
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