smith-chem-wisc
diff --git a/‎mzLib/PredictionClients/Koina/AbstractClasses/CollisionalCrossSectionModel.cs‎
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+using Omics.SequenceConversion;
+using PredictionClients.Koina.Client;
+using PredictionClients.Koina.Interfaces;
+using PredictionClients.Koina.Util;
+using System.ComponentModel;
+using MzLibUtil;
+using Easy.Common.Extensions;
+
+namespace PredictionClients.Koina.AbstractClasses
+{
+    /// <summary>
+    /// Represents a collisional cross section prediction result for a single peptide.
+    /// </summary>
+    public record PeptideCCSPrediction(
+        string FullSequence,
+        string ValidatedFullSequence,
+        int PrecursorCharge,
+        double? PredictedCCS,
+        WarningException? Warning = null
+    );
+
+    /// <summary>
+    /// Input parameters for CCS prediction models.
+    /// </summary>
+    public record CCSPredictionInput(
+        string FullSequence,
+        int PrecursorCharge
+    )
+    {
+        public string? ValidatedFullSequence { get; set; }
+        public WarningException? SequenceWarning { get; set; }
+        public WarningException? ParameterWarning { get; set; }
+    }
+
+    /// <summary>
+    /// Abstract base class for collisional cross section (CCS) prediction models using the Koina API.
+    ///
+    /// Thread safety: instances are NOT thread-safe. Predict and related methods
+    /// mutate instance state (ModelInputs, ValidInputsMask, Predictions); callers must not invoke
+    /// these methods concurrently on the same instance, nor read Predictions while a call is in flight.
+    /// Use one instance per concurrent caller (or serialize externally) when sharing across pipelines.
+    /// </summary>
+    public abstract class CollisionalCrossSectionModel : KoinaModelBase<CCSPredictionInput, PeptideCCSPrediction>, IPredictor<CCSPredictionInput, PeptideCCSPrediction>
+    {
+        protected CollisionalCrossSectionModel(ISequenceConverter sequenceConverter)
+            : base(sequenceConverter)
+        {
+        }
+
+        public virtual HashSet<int>? AllowedPrecursorCharges => new() { 1, 2, 3, 4, 5, 6 };
+        public override IReadOnlySet<int> AllowedUnimodIds => new HashSet<int>();
+        public override abstract SequenceConversionHandlingMode ModHandlingMode { get; init; }
+        public virtual IncompatibleParameterHandlingMode ParameterHandlingMode { get; init; }
+
+        public List<CCSPredictionInput> ModelInputs { get; protected set; } = new();
+        public bool[] ValidInputsMask { get; protected set; } = Array.Empty<bool>();
+        public List<PeptideCCSPrediction> Predictions { get; protected set; } = new();
+
+        protected virtual async Task<List<PeptideCCSPrediction>> AsyncThrottledPredictor(List<CCSPredictionInput> modelInputs)
+        {
+            if (modelInputs.IsNullOrEmpty())
+            {
+                Predictions = new List<PeptideCCSPrediction>();
+                return Predictions;
+            }
+
+            ModelInputs = modelInputs;
+            ValidInputsMask = new bool[ModelInputs.Count];
+            var validInputs = new List<CCSPredictionInput>();
+
+            for (int i = 0; i < ModelInputs.Count; i++)
+            {
+                var cleanedSequence = TryCleanSequence(ModelInputs[i].FullSequence, out var apiSequence, out var modHandlingWarning);
+                var validModelParams = ValidateModelSpecificInputs(ModelInputs[i], out var parameterWarning);
+                if (cleanedSequence != null && apiSequence != null && validModelParams)
+                {
+                    ModelInputs[i] = ModelInputs[i] with { ValidatedFullSequence = apiSequence, SequenceWarning = modHandlingWarning, ParameterWarning = parameterWarning };
+                    ValidInputsMask[i] = true;
+                    validInputs.Add(ModelInputs[i]);
+                }
+                else
+                {
+                    ModelInputs[i] = ModelInputs[i] with { ValidatedFullSequence = null, SequenceWarning = modHandlingWarning, ParameterWarning = parameterWarning };
+                    ValidInputsMask[i] = false;
+                }
+            }
+
+            var predictions = new List<PeptideCCSPrediction>();
+            if (validInputs.Count > 0)
+            {
+                var batchedRequests = ToBatchedRequests(validInputs);
+                var batchChunks = batchedRequests.Chunk(MaxNumberOfBatchesPerRequest).ToList();
+                int sessionTimeoutInMinutes = (int)Math.Ceiling((batchedRequests.Count * 2 * BenchmarkedTimeForOneMaxBatchSizeInMilliseconds + ThrottlingDelayInMilliseconds * batchChunks.Count) / 6e4);
+                sessionTimeoutInMinutes = Math.Max(sessionTimeoutInMinutes, 1);
+
+                var responses = new List<string>();
+                using var cts = new CancellationTokenSource(TimeSpan.FromMinutes(sessionTimeoutInMinutes));
+
+                for (int i = 0; i < batchChunks.Count; i++)
+                {
+                    var batchChunk = batchChunks[i];
+                    var responseChunk = await Task.WhenAll(batchChunk.Select(request => SendInferenceRequestAsync(ModelName, request, cts.Token)));
+                    responses.AddRange(responseChunk);
+
+                    if (i < batchChunks.Count - 1)
+                    {
+                        await Task.Delay(ThrottlingDelayInMilliseconds);
+                    }
+                }
+
+                predictions = ResponseToPredictions(responses, validInputs);
+            }
+
+            var realignedPredictions = new List<PeptideCCSPrediction>();
+            int predictionIndex = 0;
+            for (int i = 0; i < ValidInputsMask.Length; i++)
+            {
+                if (ValidInputsMask[i])
+                {
+                    realignedPredictions.Add(predictions[predictionIndex]);
+                    predictionIndex++;
+                }
+                else
+                {
+                    realignedPredictions.Add(new PeptideCCSPrediction(
+                        FullSequence: ModelInputs[i].FullSequence,
+                        ValidatedFullSequence: null,
+                        PrecursorCharge: ModelInputs[i].PrecursorCharge,
+                        PredictedCCS: null,
+                        Warning: ModelInputs[i].ParameterWarning ?? ModelInputs[i].SequenceWarning ?? new WarningException("Input was invalid and skipped during prediction.")
+                    ));
+                }
+            }
+
+            Predictions = realignedPredictions;
+            return Predictions;
+        }
+
+        private readonly object _predictLock = new();
+
+        public List<PeptideCCSPrediction> Predict(List<CCSPredictionInput> modelInputs)
+        {
+            // Offload to Task.Run so the awaited continuations inside AsyncThrottledPredictor run on
+            // the ThreadPool (no SynchronizationContext) rather than trying to resume on a blocked
+            // caller thread. Calling .GetAwaiter().GetResult() directly would deadlock under a
+            // single-threaded SynchronizationContext (WinForms/WPF/ASP.NET non-Core). The lock
+            // serializes concurrent callers against the shared instance state. See
+            // FragmentIntensityModel.Predict for the full rationale (stopgap Option A).
+            lock (_predictLock)
+            {
+                return Task.Run(() => AsyncThrottledPredictor(modelInputs)).GetAwaiter().GetResult();
+            }
+        }
+
+        protected virtual bool ValidateModelSpecificInputs(CCSPredictionInput input, out WarningException? warning)
+        {
+            warning = null;
+
+            // Always reject non-physical charges (< 1) regardless of AllowedPrecursorCharges.
+            if (input.PrecursorCharge < 1)
+            {
+                string message = $"Precursor charge {input.PrecursorCharge} is not a valid physical charge. Charge must be positive.";
+                switch (ParameterHandlingMode)
+                {
+                    case IncompatibleParameterHandlingMode.ThrowException:
+                        throw new ArgumentException(message);
+                    case IncompatibleParameterHandlingMode.ReturnNull:
+                        warning = new WarningException(message);
+                        return false;
+                    default:
+                        throw new ArgumentException($"Unhandled ParameterHandlingMode: {ParameterHandlingMode}");
+                }
+            }
+
+            // null = not applicable (skip), empty = any charge, populated = restrict to listed.
+            if (AllowedPrecursorCharges != null && !AllowedPrecursorCharges.IsNullOrEmpty() && !AllowedPrecursorCharges.Contains(input.PrecursorCharge))
+            {
+                string exceptionMessage = $"Precursor charge {input.PrecursorCharge} is not supported by this model. Allowed precursor charges: {string.Join(", ", AllowedPrecursorCharges)}.";
+                switch (ParameterHandlingMode)
+                {
+                    case IncompatibleParameterHandlingMode.ThrowException:
+                        throw new ArgumentException(exceptionMessage);
+
+                    case IncompatibleParameterHandlingMode.ReturnNull:
+                        warning = new WarningException(exceptionMessage);
+                        return false;
+                    default:
+                        throw new ArgumentException($"Unhandled ParameterHandlingMode: {ParameterHandlingMode}");
+                }
+            }
+
+            return true;
+        }
+
+        protected virtual List<PeptideCCSPrediction> ResponseToPredictions(
+            IReadOnlyList<string> responses,
+            List<CCSPredictionInput> requestInputs)
+        {
+            var predictions = new List<PeptideCCSPrediction>();
+            if (requestInputs.IsNullOrEmpty())
+            {
+                return predictions;
+            }
+
+            var deserializedResponses = responses.Select(r => Newtonsoft.Json.JsonConvert.DeserializeObject<ResponseJSONStruct>(r)).ToList();
+            if (deserializedResponses.IsNullOrEmpty() || deserializedResponses.Any(r => r == null))
+            {
+                throw new Exception("Something went wrong during deserialization of responses.");
+            }
+
+            var ccsOutputs = deserializedResponses.SelectMany(r =>
+            {
+                var output = r!.Outputs.FirstOrDefault(o => o.Name == "ccs")
+                    ?? throw new Exception($"API response is missing expected output 'ccs'. Found: {string.Join(", ", r.Outputs.Select(o => o.Name))}.");
+                return output.Data.Select(d => Convert.ToDouble(d));
+            }).ToList();
+
+            if (ccsOutputs.Count != requestInputs.Count)
+            {
+                throw new Exception("The number of CCS predictions does not match the number of input peptides.");
+            }
+
+            for (int i = 0; i < requestInputs.Count; i++)
+            {
+                predictions.Add(new PeptideCCSPrediction(
+                    FullSequence: requestInputs[i].FullSequence,
+                    ValidatedFullSequence: requestInputs[i].ValidatedFullSequence,
+                    PrecursorCharge: requestInputs[i].PrecursorCharge,
+                    PredictedCCS: ccsOutputs[i],
+                    Warning: requestInputs[i].SequenceWarning
+                ));
+            }
+
+            return predictions;
+        }
+    }
+}