Initital construct

MetaPAL/Controllers/ExperimentsController.cs

@@ -0,0 +1,83 @@
+using Microsoft.AspNetCore.Http;
+using Microsoft.AspNetCore.Mvc;
+
+namespace MetaPAL.Controllers
+{
+    public class ExperimentsController : Controller
+    {
+        // GET: Experiments
+        public ActionResult Index()
+        {
+            return View();
+        }
+
+        // GET: Experiments/Details/5
+        public ActionResult Details(int id)
+        {
+            return View();
+        }
+
+        // GET: Experiments/Create
+        public ActionResult Create()
+        {
+            return View();
+        }
+
+        // POST: Experiments/Create
+        [HttpPost]
+        [ValidateAntiForgeryToken]
+        public ActionResult Create(IFormCollection collection)
+        {
+            try
+            {
+                return RedirectToAction(nameof(Index));
+            }
+            catch
+            {
+                return View();
+            }
+        }
+
+        // GET: Experiments/Edit/5
+        public ActionResult Edit(int id)
+        {
+            return View();
+        }
+
+        // POST: Experiments/Edit/5
+        [HttpPost]
+        [ValidateAntiForgeryToken]
+        public ActionResult Edit(int id, IFormCollection collection)
+        {
+            try
+            {
+                return RedirectToAction(nameof(Index));
+            }
+            catch
+            {
+                return View();
+            }
+        }
+
+        // GET: Experiments/Delete/5
+        public ActionResult Delete(int id)
+        {
+            return View();
+        }
+
+        // POST: Experiments/Delete/5
+        [HttpPost]
+        [ValidateAntiForgeryToken]
+        public ActionResult Delete(int id, IFormCollection collection)
+        {
+            try
+            {
+                return RedirectToAction(nameof(Index));
+            }
+            catch
+            {
+                return View();
+            }
+        }
+    }
+}

MetaPAL/Controllers/ReposController.cs

@@ -0,0 +1,167 @@
+using MetaPAL.Data;
+using MetaPAL.Models;
+using Microsoft.AspNetCore.Http;
+using Microsoft.AspNetCore.Mvc;
+using Microsoft.AspNetCore.Mvc.Rendering;
+using Microsoft.EntityFrameworkCore;
+
+namespace MetaPAL.Controllers
+{
+    public class ReposController : Controller
+    {
+        private readonly ApplicationDbContext _context;
+
+        public ReposController(ApplicationDbContext context)
+        {
+            _context = context;
+        }
+
+        // GET: ReposController
+        public async Task<IActionResult> Index()
+        {
+            List<SelectListItem> selectListItems = new List<SelectListItem>()
+            {
+                new SelectListItem("Title", "Title"),
+                new SelectListItem("Description", "Description"),
+                new SelectListItem("HostingRepositoryURL", "HostingRepositoryURL"),
+                new SelectListItem("DatasetFtpLocation", "DatasetFtpLocation"),
+            };
+
+            ViewBag.RepoFeatures = selectListItems;
+            if (_context.Repos == null)
+                return Problem("Entity set 'ApplicationDbContext.Repos'  is null.");
+            return View(await _context.Repos.ToListAsync());
+        }
+
+        // GET: ReposController/Details/5
+        public ActionResult Details(int id)
+        {
+            return View();
+        }
+
+        // GET: Repos/Create
+        public IActionResult Create()
+        {
+            List<SelectListItem> selectListItems = new List<SelectListItem>()
+            {
+                new SelectListItem("Select Repo Features", ""),
+                new SelectListItem("Title", "Title"),
+                new SelectListItem("Description", "Description"),
+                new SelectListItem("HostingRepositoryURL", "HostingRepositoryURL"),
+                new SelectListItem("DatasetFtpLocation", "DatasetFtpLocation"),
+            };
+
+            ViewBag.RepoFeatures = selectListItems;
+            return View();
+        }
+
+        // POST: Repo/Create
+        // To protect from overposting attacks, enable the specific properties you want to bind to.
+        // For more details, see http://go.microsoft.com/fwlink/?LinkId=317598.
+        [HttpPost]
+        //[ValidateAntiForgeryToken]
+        public async Task<IActionResult> Create([Bind("Id,Title,Description,HostingRepositoryURL,DatasetFtpLocation")] Repo repo)
+        {
+            if (ModelState.IsValid)
+            {
+                _context.Add(repo);
+                await _context.SaveChangesAsync();
+                return RedirectToAction(nameof(Index));
+            }
+            return View(repo);
+        }
+
+        // GET: Repo/Edit/5
+        public async Task<IActionResult> Edit(int? id)
+        {
+            if (id == null || _context.Repos == null)
+            {
+                return NotFound();
+            }
+
+            var repo = await _context.Repos.FindAsync(id);
+            if (repo == null)
+            {
+                return NotFound();
+            }
+            return View(repo);
+        }
+
+        // POST: Repos/Edit/5
+        // To protect from overposting attacks, enable the specific properties you want to bind to.
+        // For more details, see http://go.microsoft.com/fwlink/?LinkId=317598.
+        [HttpPost]
+        //[ValidateAntiForgeryToken]
+        public async Task<IActionResult> Edit(int id, [Bind("Id,Title,Description,HostingRepositoryURL,DatasetFtpLocation")] Repo repo)
+        {
+            if (id != repo.Id)
+            {
+                return NotFound();
+            }
+
+            if (ModelState.IsValid)
+            {
+                try
+                {
+                    _context.Update(repo);
+                    await _context.SaveChangesAsync();
+                }
+                catch (DbUpdateConcurrencyException)
+                {
+                    if (!RepoExists(repo.Id))
+                    {
+                        return NotFound();
+                    }
+                    else
+                    {
+                        throw;
+                    }
+                }
+                return RedirectToAction(nameof(Index));
+            }
+            return View(repo);
+        }
+
+        // GET: Repos/Delete/5
+        public async Task<IActionResult> Delete(int? id)
+        {
+            if (id == null || _context.Repos == null)
+            {
+                return NotFound();
+            }
+
+            var repo = await _context.Repos
+                .FirstOrDefaultAsync(m => m.Id == id);
+            if (repo == null)
+            {
+                return NotFound();
+            }
+
+            return View(repo);
+        }
+
+        // POST: Repos/Delete/5
+        [HttpPost, ActionName("Delete")]
+        //[ValidateAntiForgeryToken]
+        public async Task<IActionResult> DeleteConfirmed(int id)
+        {
+            if (_context.Repos == null)
+            {
+                return Problem("Entity set 'ApplicationDbContext.Repo'  is null.");
+            }
+            var repo = await _context.Repos.FindAsync(id);
+            if (repo != null)
+            {
+                _context.Repos.Remove(repo);
+            }
+
+            await _context.SaveChangesAsync();
+            return RedirectToAction(nameof(Index));
+        }
+
+        private bool RepoExists(int id)
+        {
+            return (_context.Repos?.Any(e => e.Id == id)).GetValueOrDefault();
+        }
+    }
+}

MetaPAL/Controllers/SampleMetaDataController.cs

@@ -0,0 +1,83 @@
+using Microsoft.AspNetCore.Http;
+using Microsoft.AspNetCore.Mvc;
+
+namespace MetaPAL.Controllers
+{
+    public class SampleMetaDataController : Controller
+    {
+        // GET: SampleMetaDataController
+        public ActionResult Index()
+        {
+            return View();
+        }
+
+        // GET: SampleMetaDataController/Details/5
+        public ActionResult Details(int id)
+        {
+            return View();
+        }
+
+        // GET: SampleMetaDataController/Create
+        public ActionResult Create()
+        {
+            return View();
+        }
+
+        // POST: SampleMetaDataController/Create
+        [HttpPost]
+        [ValidateAntiForgeryToken]
+        public ActionResult Create(IFormCollection collection)
+        {
+            try
+            {
+                return RedirectToAction(nameof(Index));
+            }
+            catch
+            {
+                return View();
+            }
+        }
+
+        // GET: SampleMetaDataController/Edit/5
+        public ActionResult Edit(int id)
+        {
+            return View();
+        }
+
+        // POST: SampleMetaDataController/Edit/5
+        [HttpPost]
+        [ValidateAntiForgeryToken]
+        public ActionResult Edit(int id, IFormCollection collection)
+        {
+            try
+            {
+                return RedirectToAction(nameof(Index));
+            }
+            catch
+            {
+                return View();
+            }
+        }
+
+        // GET: SampleMetaDataController/Delete/5
+        public ActionResult Delete(int id)
+        {
+            return View();
+        }
+
+        // POST: SampleMetaDataController/Delete/5
+        [HttpPost]
+        [ValidateAntiForgeryToken]
+        public ActionResult Delete(int id, IFormCollection collection)
+        {
+            try
+            {
+                return RedirectToAction(nameof(Index));
+            }
+            catch
+            {
+                return View();
+            }
+        }
+    }
+}

MetaPAL/Controllers/SpectrumMatchesController.cs

@@ -25,17 +25,22 @@
         // GET: SpectrumMatches
         public async Task<IActionResult> Index()
         {
-            // TEMPORARY: remove all spectrum matches from database
-            //Task.Run(() => DataOperations.DataOperations.RemoveAll<SpectrumMatch>(_context)).Wait();
-
+            List<SelectListItem> selectListItems = new List<SelectListItem>()
+            {
+                new SelectListItem("Select Spectrum Match Features", ""),
+                new SelectListItem("Base Sequence", "BaseSequence"),
+                new SelectListItem("Full Sequence", "FullSequence"),
+                new SelectListItem("Accession", "Accession"),
+            };
 
+            ViewBag.SpectrumMatchFeatures = selectListItems;
             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() :
@@ -67,7 +72,7 @@
 
 
         // GET: ShowSearchForm
         public async Task<IActionResult> ShowSearchForm()
         {
             return _context.SpectrumMatch != null ?
                 View() :
@@ -100,9 +105,17 @@
         }
 
         // GET: SpectrumMatches/Create
-        [Authorize]
         public IActionResult Create()
         {
+            List<SelectListItem> selectListItems = new List<SelectListItem>()
+            {
+                new SelectListItem("Select Spectrum Match Features", ""),
+                new SelectListItem("Base Sequence", "BaseSequence"),
+                new SelectListItem("Full Sequence", "FullSequence"),
+                new SelectListItem("Accession", "Accession"),
+            };
+
+            ViewBag.SpectrumMatchFeatures = selectListItems;
             return View();
         }
 

MetaPAL/Data/ApplicationDbContext.cs

@@ -4,6 +4,7 @@
 using Microsoft.Data.Sqlite;
 using Microsoft.EntityFrameworkCore;
 using Omics.Fragmentation;
+using Proteomics;
 
 namespace MetaPAL.Data
 {
@@ -18,14 +19,11 @@ protected override void OnModelCreating(ModelBuilder builder)
         {
             base.OnModelCreating(builder);
         }
-
+        public DbSet<Repo>? Repos { get; set; }
         public DbSet<SpectrumMatch>? SpectrumMatch { get; set; }
 
-        public DbSet<MsDataScanModel> MsDataScans { get; set; }
-
-        public DbSet<DataFile> MsDataFiles { get; set; }
         public DbSet<Experiment> Experiments { get; set; }
-        public DbSet<MetaData> MetaData { get; set; }
+        public DbSet<SampleMetaData> MetaData { get; set; }
     }