Waters connect implementation

pwiz_tools/Shared/CommonMsData/CommonMsData.csproj

@@ -54,9 +54,8 @@
     <Reference Include="IdentityModel">
       <HintPath>..\Lib\IdentityModel.dll</HintPath>
     </Reference>
-    <Reference Include="Newtonsoft.Json, Version=13.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed, processorArchitecture=MSIL">
-      <SpecificVersion>False</SpecificVersion>
-      <HintPath>..\..\..\pwiz_tools\Shared\Lib\Newtonsoft.Json.dll</HintPath>
+    <Reference Include="Newtonsoft.Json">
+      <HintPath>..\Lib\Newtonsoft.Json.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
@@ -119,6 +118,7 @@
     <Compile Include="RemoteApi\Unifi\UnifiSession.cs" />
     <Compile Include="RemoteApi\Unifi\UnifiUrl.cs" />
     <Compile Include="RemoteApi\WatersConnect\WatersConnectAccount.cs" />
+    <Compile Include="RemoteApi\WatersConnect\WatersConnectAcquisitionMethodUrl.cs" />
     <Compile Include="RemoteApi\WatersConnect\WatersConnectFileObject.cs" />
     <Compile Include="RemoteApi\WatersConnect\WatersConnectFolderObject.cs" />
     <Compile Include="RemoteApi\WatersConnect\WatersConnectObject.cs" />
@@ -128,19 +128,25 @@
       <DesignTime>True</DesignTime>
     </Compile>
     <Compile Include="RemoteApi\WatersConnect\WatersConnectSession.cs" />
+    <Compile Include="RemoteApi\WatersConnect\WatersConnectSessionAcquisitionMethod.cs" />
     <Compile Include="RemoteApi\WatersConnect\WatersConnectUrl.cs" />
     <Compile Include="CommonMsDataResources.Designer.cs">
       <AutoGen>True</AutoGen>
       <DesignTime>True</DesignTime>
       <DependentUpon>CommonMsDataResources.resx</DependentUpon>
     </Compile>
+    <Compile Include="RemoteApi\WatersConnect\WatersConnectWatersConnectAcquisitionMethodObjectMethodObject.cs" />
     <Compile Include="SampleHelp.cs" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\CommonUtil\CommonUtil.csproj">
       <Project>{13bf2ffb-50a1-4ab1-83a4-5733e36905ce}</Project>
       <Name>CommonUtil</Name>
     </ProjectReference>
+    <ProjectReference Include="..\Common\Common.csproj">
+      <Project>{a5527be9-4a62-458f-ae47-f0f9204a5cf9}</Project>
+      <Name>Common</Name>
+    </ProjectReference>
     <ProjectReference Include="..\ProteowizardWrapper\ProteowizardWrapper.csproj">
       <Project>{dacee7d5-5a6a-4001-9602-fab1a9a2de59}</Project>
       <Name>ProteowizardWrapper</Name>

pwiz_tools/Shared/CommonMsData/DataSourceUtil.cs

@@ -1,4 +1,4 @@
-/*
+/*
  * Original author: Vagisha Sharma <vsharma .at. u.washington.edu>,
  *                  MacCoss Lab, Department of Genome Sciences, UW
  *
@@ -63,6 +63,8 @@ public static class DataSourceUtil
         public const string FOLDER_TYPE = "File Folder";
         public const string SAMPLE_SET_TYPE = "Sample Set";
         public const string UNKNOWN_TYPE = "unknown";
+        public const string EDIT_ACCOUNT = "edit account";
+        public const string TYPE_WATERS_ACQUISITION_METHOD = "Waters Acquisition Method";
         // ReSharper restore LocalizableElement
 
         public static bool IsDataSource(string path)
@@ -183,6 +185,11 @@ public static bool IsFolderType(string type)
             return Equals(type, FOLDER_TYPE);
         }
 
+        public static bool IsEditAccount(string type)
+        {
+            return Equals(type, EDIT_ACCOUNT);
+        }
+
         public static bool IsSampleSetType(string type)
         {
             return Equals(type, SAMPLE_SET_TYPE);

pwiz_tools/Shared/CommonMsData/MsDataFilePath.cs

@@ -1,4 +1,4 @@
-/*
+/*
  * Original author: Nick Shulman <nicksh .at. u.washington.edu>,
  *                  MacCoss Lab, Department of Genome Sciences, UW
  *

pwiz_tools/Shared/CommonMsData/RemoteApi/RemoteAccount.cs

@@ -32,12 +32,27 @@ private enum ATTR
         {
             username,
             password,
-            server_url
+            server_url,
+            alias
         }
 
         public abstract RemoteSession CreateSession();
         public abstract RemoteUrl GetRootUrl();
 
+        private string _accountAlias;
+        public string AccountAlias {
+            get
+            {
+                if (string.IsNullOrEmpty(_accountAlias))
+                    return ServerUrl;
+                return _accountAlias;
+            }
+            set
+            {
+                _accountAlias = value;
+            }
+        } 
+        public bool HasAlias => !string.IsNullOrEmpty(_accountAlias);
         public bool CanHandleUrl(RemoteUrl remoteUrl)
         {
             if (remoteUrl.AccountType != AccountType)
@@ -105,12 +120,14 @@ protected virtual void ReadXElement(XElement xElement)
             }
 
             ServerUrl = (string) xElement.Attribute(ATTR.server_url.ToString());
+            AccountAlias = (string)xElement.Attribute(ATTR.alias.ToString()) ?? string.Empty;
         }
 
         public virtual void WriteXml(XmlWriter writer)
         {
             writer.WriteAttributeIfString2(ATTR.server_url, ServerUrl);
             writer.WriteAttributeIfString2(ATTR.username, Username);
+            writer.WriteAttributeIfString2(ATTR.alias, AccountAlias);
             if (!string.IsNullOrEmpty(Password))
             {
                 writer.WriteAttributeString2(ATTR.password, CommonTextUtil.EncryptString(Password));

pwiz_tools/Shared/CommonMsData/RemoteApi/RemoteAccountType.cs

@@ -98,7 +98,7 @@ public override string Name
 
             public override RemoteAccount GetEmptyAccount()
             {
-                return new WatersConnectAccount(@"https://devconnect.waters.com:48444", null, null);
+                return WatersConnectAccount.DEFAULT;
             }
         }
     }

pwiz_tools/Shared/CommonMsData/RemoteApi/RemoteApiResources.resx

@@ -127,4 +127,10 @@
     <value>waters_connect</value>
     <comment>Lower case is intentional branding.</comment>
   </data>
+  <data name="Unifi_GroupBox_Label" xml:space="preserve">
+    <value>Advanced Unifi settings</value>
+  </data>
+  <data name="Waters_Connect_GroupBox_Label" xml:space="preserve">
+    <value>Advanced waters_connect settings</value>
+  </data>
 </root>

pwiz_tools/Shared/CommonMsData/RemoteApi/RemoteItem.cs

@@ -20,15 +20,23 @@
 
 namespace pwiz.CommonMsData.RemoteApi
 {
+    public enum AccessType
+    {
+        unknown,
+        no_access,
+        read,
+        read_write
+    }
     public class RemoteItem
     {
-        public RemoteItem(MsDataFileUri msDataFileUri, string label, string type, DateTime? lastModified, long fileSizeBytes, bool hasChildren = false)
+        public RemoteItem(MsDataFileUri msDataFileUri, string label, string type, DateTime? lastModified, long fileSizeBytes, bool hasChildren = false, AccessType access = AccessType.unknown)
         {
             MsDataFileUri = msDataFileUri;
             Label = label;
             Type = type;
             LastModified = lastModified;
             FileSize = (ulong) fileSizeBytes;
+            Access = access;
             HasChildren = hasChildren;
         }
 
@@ -37,6 +45,8 @@ public RemoteItem(MsDataFileUri msDataFileUri, string label, string type, DateTi
         public string Type { get; private set; }
         public DateTime? LastModified { get; private set; }
         public ulong FileSize { get; private set; }
+        public object Data { get; private set; }
+        public AccessType Access { get; private set; }
         public bool HasChildren { get; }
     }
 }

pwiz_tools/Shared/CommonMsData/RemoteApi/RemoteSession.cs

@@ -128,9 +128,20 @@ protected void RetryFetch<T>(Uri requestUri, Func<Uri, T> fetcher)
 
                 if (_fetchRequests.Contains(key))
                 {
-                    return;
+                    if (_responses.TryGetValue(key, out var response))
+                    {
+                        if (response.Exception == null)
+                        {
+                            // Already have the response data.
+                            return;
+                        }
+                        else
+                            _responses.Remove(key);
+                    }
+                    else 
+                        return; // The request is already in progress.
                 }
-                _responses.Remove(key);
+                _fetchRequests.Remove(key);
                 AsyncFetch(requestUri, fetcher, out _);
             }
 
@@ -221,6 +232,11 @@ protected bool TryGetData<T>(Uri requestUri, out T data)
                     data = default(T);
                     return false;
                 }
+                if (remoteResponse.Exception != null)
+                {
+                    data = default(T);
+                    return false;
+                }
                 data = (T) remoteResponse.Data;
                 return true;
             }
@@ -282,4 +298,9 @@ public override int GetHashCode()
             }
         }
     }
+
+    public class ProgressableStreamContents
+    {
+
+    }
 }

pwiz_tools/Shared/CommonMsData/RemoteApi/RemoteUrl.cs

@@ -38,7 +38,7 @@ public interface IRemoteAccountStorage
     public abstract class RemoteUrl : MsDataFileUri
     {
         public static readonly RemoteUrl EMPTY = new Empty();
-        private enum Attr
+        public enum Attr
         {
             centroid_ms1,   // Legacy
             centroid_ms2,   // Legacy
@@ -50,6 +50,7 @@ private enum Attr
             username,
             modified_time,
         }
+        public const string PATH_SEPARATOR = "/";
 
         public abstract RemoteAccountType AccountType { get; }
 
@@ -96,6 +97,31 @@ public override MsDataFileUri ChangeLockMassParameters(LockMassParameters lockMa
         public string Username { get; private set; }
         public DateTime? ModifiedTime { get; private set; }
 
+        public bool BelongsToAccount(RemoteAccount account)
+        {
+            if (account == null)
+            {
+                return false;
+            }
+            if (account.AccountType != AccountType)
+            {
+                return false;
+            }
+            return account.ServerUrl == ServerUrl && account.Username == Username;
+        }
+        public bool SameAccountAs(RemoteUrl url)
+        {
+            if (url == null)
+            {
+                return false;
+            }
+            if (url.AccountType != AccountType)
+            {
+                return false;
+            }
+            return url.ServerUrl == ServerUrl && url.Username == Username;
+        }
+
         public RemoteUrl ChangeModifiedTime(DateTime? modifiedTime)
         {
             return ChangeProp(ImClone(this), im => im.ModifiedTime = modifiedTime);
@@ -168,6 +194,12 @@ public override string ToString()
             return AccountType.Name + @":" + GetParameters();
         }
 
+        public virtual string FormattedString()
+        {
+            var nameValuePairs = GetParameters();
+            return string.Join("\n", nameValuePairs.GetEnumerable().Select(pair => pair.Key + ":\t" + pair.Value));
+        }
+
         public override int GetSampleIndex()
         {
             return -1;
@@ -196,6 +228,12 @@ public virtual RemoteUrl ChangePathParts(IEnumerable<string> parts)
                 im => im.EncodedPath = parts == null ? null : string.Join(@"/", parts.Select(Uri.EscapeDataString)));
         }
 
+        public RemoteUrl ChangePathPartsOnly(IEnumerable<string> parts)
+        {
+            return ChangeProp(ImClone(this),
+                im => im.EncodedPath = parts == null ? null : string.Join(@"/", parts.Select(Uri.EscapeDataString)));
+        }
+
         public IEnumerable<string> GetPathParts()
         {
             if (EncodedPath == null)