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nielshulstaertnielshulstaert
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fix packages.config
removed BOM prefix in indexedMzML (issue 109)
1 parent f51d523 commit 6dff3e7

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+285774
-233061
lines changed

‎ThermoRawFileParser.csproj‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -60,20 +60,20 @@
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<StartupObject>ThermoRawFileParser.MainClass</StartupObject>
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</PropertyGroup>
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<ItemGroup>
63-
<Reference Include="AWS.Logger.Core, Version=2.0.1.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
64-
<HintPath>packages\AWS.Logger.Core.2.0.1\lib\net45\AWS.Logger.Core.dll</HintPath>
63+
<Reference Include="AWS.Logger.Core, Version=1.4.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
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<HintPath>packages\AWS.Logger.Core.1.4.0\lib\net45\AWS.Logger.Core.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="AWSSDK.CloudWatchLogs, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
68-
<HintPath>packages\AWSSDK.CloudWatchLogs.3.5.0.24\lib\net45\AWSSDK.CloudWatchLogs.dll</HintPath>
68+
<HintPath>packages\AWSSDK.CloudWatchLogs.3.3.101.14\lib\net45\AWSSDK.CloudWatchLogs.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="AWSSDK.Core, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
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<HintPath>packages\AWSSDK.Core.3.5.3.2\lib\net45\AWSSDK.Core.dll</HintPath>
72+
<HintPath>packages\AWSSDK.Core.3.3.103.30\lib\net45\AWSSDK.Core.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="AWSSDK.S3, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
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<HintPath>packages\AWSSDK.S3.3.5.8.8\lib\net45\AWSSDK.S3.dll</HintPath>
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<HintPath>packages\AWSSDK.S3.3.3.104.18\lib\net45\AWSSDK.S3.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="IronSnappy, Version=1.3.0.0, Culture=neutral, PublicKeyToken=b1d4b1dc83bdcf31">
@@ -98,12 +98,12 @@
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<HintPath>packages\Namotion.Reflection.1.0.18\lib\net45\Namotion.Reflection.dll</HintPath>
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<Private>True</Private>
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</Reference>
101-
<Reference Include="Newtonsoft.Json, Version=12.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed">
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<HintPath>packages\Newtonsoft.Json.12.0.3\lib\net45\Newtonsoft.Json.dll</HintPath>
101+
<Reference Include="Newtonsoft.Json, Version=13.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed">
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<HintPath>packages\Newtonsoft.Json.13.0.1\lib\net45\Newtonsoft.Json.dll</HintPath>
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<Private>True</Private>
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</Reference>
105-
<Reference Include="NJsonSchema, Version=10.3.8.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
106-
<HintPath>packages\NJsonSchema.10.3.8\lib\net45\NJsonSchema.dll</HintPath>
105+
<Reference Include="NJsonSchema, Version=10.4.0.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
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<HintPath>packages\NJsonSchema.10.4.0\lib\net45\NJsonSchema.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="nunit.framework, Version=3.13.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb">
@@ -226,8 +226,8 @@
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<Content Include="Writer\MzML\mzML1.1.1_idx.xsd" />
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</ItemGroup>
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<ItemGroup>
229-
<Analyzer Include="packages\AWSSDK.CloudWatchLogs.3.5.0.24\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
230-
<Analyzer Include="packages\AWSSDK.S3.3.5.8.8\analyzers\dotnet\cs\AWSSDK.S3.CodeAnalysis.dll" />
229+
<Analyzer Include="packages\AWSSDK.CloudWatchLogs.3.3.101.14\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
230+
<Analyzer Include="packages\AWSSDK.S3.3.3.104.18\analyzers\dotnet\cs\AWSSDK.S3.CodeAnalysis.dll" />
231231
</ItemGroup>
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<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
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<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">

‎ThermoRawFileParserTest/ThermoRawFileParserTest.csproj‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -35,16 +35,16 @@
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<WarningLevel>4</WarningLevel>
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</PropertyGroup>
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<ItemGroup>
38-
<Reference Include="AWS.Logger.Core, Version=2.0.1.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
39-
<HintPath>..\packages\AWS.Logger.Core.2.0.1\lib\net45\AWS.Logger.Core.dll</HintPath>
38+
<Reference Include="AWS.Logger.Core, Version=1.4.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
39+
<HintPath>..\packages\AWS.Logger.Core.1.4.0\lib\net45\AWS.Logger.Core.dll</HintPath>
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<Private>True</Private>
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</Reference>
4242
<Reference Include="AWSSDK.CloudWatchLogs, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
43-
<HintPath>..\packages\AWSSDK.CloudWatchLogs.3.5.0.24\lib\net45\AWSSDK.CloudWatchLogs.dll</HintPath>
43+
<HintPath>..\packages\AWSSDK.CloudWatchLogs.3.3.101.14\lib\net45\AWSSDK.CloudWatchLogs.dll</HintPath>
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<Private>True</Private>
4545
</Reference>
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<Reference Include="AWSSDK.Core, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
47-
<HintPath>..\packages\AWSSDK.Core.3.5.3.2\lib\net45\AWSSDK.Core.dll</HintPath>
47+
<HintPath>..\packages\AWSSDK.Core.3.3.103.30\lib\net45\AWSSDK.Core.dll</HintPath>
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<Private>True</Private>
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</Reference>
5050
<Reference Include="BayesianEstimation, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">
@@ -100,12 +100,12 @@
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<HintPath>..\packages\Namotion.Reflection.1.0.18\lib\net45\Namotion.Reflection.dll</HintPath>
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<Private>True</Private>
102102
</Reference>
103-
<Reference Include="Newtonsoft.Json, Version=12.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed">
104-
<HintPath>..\packages\Newtonsoft.Json.12.0.3\lib\net45\Newtonsoft.Json.dll</HintPath>
103+
<Reference Include="Newtonsoft.Json, Version=13.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed">
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<HintPath>..\packages\Newtonsoft.Json.13.0.1\lib\net45\Newtonsoft.Json.dll</HintPath>
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<Private>True</Private>
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</Reference>
107-
<Reference Include="NJsonSchema, Version=10.3.8.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
108-
<HintPath>..\packages\NJsonSchema.10.3.8\lib\net45\NJsonSchema.dll</HintPath>
107+
<Reference Include="NJsonSchema, Version=10.4.0.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
108+
<HintPath>..\packages\NJsonSchema.10.4.0\lib\net45\NJsonSchema.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="nunit.framework, Version=3.13.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb">
@@ -208,7 +208,7 @@
208208
</Content>
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</ItemGroup>
210210
<ItemGroup>
211-
<Analyzer Include="..\packages\AWSSDK.CloudWatchLogs.3.5.0.24\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
211+
<Analyzer Include="..\packages\AWSSDK.CloudWatchLogs.3.3.101.14\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
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</ItemGroup>
213213
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
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<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">

‎ThermoRawFileParserTest/packages.config‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,16 @@
11
<?xml version="1.0" encoding="utf-8"?>
22
<packages>
3-
<package id="AWS.Logger.Core" version="2.0.1" targetFramework="net472" />
4-
<package id="AWSSDK.CloudWatchLogs" version="3.5.0.24" targetFramework="net472" />
5-
<package id="AWSSDK.Core" version="3.5.3.2" targetFramework="net472" />
3+
<package id="AWS.Logger.Core" version="1.4.0" targetFramework="net472" />
4+
<package id="AWSSDK.CloudWatchLogs" version="3.3.101.14" targetFramework="net472" />
5+
<package id="AWSSDK.Core" version="3.3.103.30" targetFramework="net472" />
66
<package id="DotLiquid" version="2.0.385" targetFramework="net472" />
77
<package id="DotNetZip" version="1.15.0" targetFramework="net472" />
88
<package id="log4net" version="2.0.12" targetFramework="net472" />
99
<package id="MathNet.Numerics" version="4.15.0" targetFramework="net472" />
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<package id="mzLib" version="1.0.450" targetFramework="net472" />
1111
<package id="Namotion.Reflection" version="1.0.18" targetFramework="net472" />
12-
<package id="Newtonsoft.Json" version="12.0.3" targetFramework="net472" />
13-
<package id="NJsonSchema" version="10.3.8" targetFramework="net472" />
12+
<package id="Newtonsoft.Json" version="13.0.1" targetFramework="net472" />
13+
<package id="NJsonSchema" version="10.4.0" targetFramework="net472" />
1414
<package id="NUnit" version="3.13.1" targetFramework="net472" />
1515
<package id="PSI_Interface" version="2.3.2" targetFramework="net472" />
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<package id="zlib.net" version="1.0.4.0" targetFramework="net471" />

‎Writer/MetadataWriter.cs‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,6 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
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$"Scan start time=[MS, MS:1000016, scan start time, {startTime:F2}]",
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$"Time range={startTime:F2};{endTime:F2}",
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$"Mass range={rawFile.RunHeaderEx.LowMass:F4};{rawFile.RunHeaderEx.HighMass:F4}",
65-
"",
6665
"#Sample information",
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"Sample name=" + rawFile.SampleInformation.SampleName,
6867
"Sample id=" + rawFile.SampleInformation.SampleId,

‎Writer/MzMlSpectrumWriter.cs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -81,7 +81,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
8181
ConfigureWriter(".mzML");
8282

8383
XmlSerializer serializer;
84-
var settings = new XmlWriterSettings {Indent = true, Encoding = Encoding.UTF8};
84+
var settings = new XmlWriterSettings {Indent = true, Encoding = new UTF8Encoding()};
8585
var sha1 = SHA1.Create();
8686
CryptoStream cryptoStream = null;
8787
if (_doIndexing)

‎packages.config‎

Lines changed: 6 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,9 @@
11
<?xml version="1.0" encoding="utf-8"?>
22
<packages>
3-
<<<<<<< HEAD
4-
<package id="AWS.Logger.Core" version="2.0.1" targetFramework="net472" />
5-
<package id="AWSSDK.CloudWatchLogs" version="3.5.0.24" targetFramework="net472" />
6-
<package id="AWSSDK.Core" version="3.5.3.2" targetFramework="net472" />
7-
<package id="AWSSDK.S3" version="3.5.8.8" targetFramework="net472" />
3+
<package id="AWS.Logger.Core" version="1.4.0" targetFramework="net472" />
4+
<package id="AWSSDK.CloudWatchLogs" version="3.3.101.14" targetFramework="net472" />
5+
<package id="AWSSDK.Core" version="3.3.103.30" targetFramework="net472" />
6+
<package id="AWSSDK.S3" version="3.3.104.18" targetFramework="net472" />
87
<package id="Parquet.Net" version="2.0.0" targetFramework="net472" />
98
<package id="IronSnappy" version="1.3.0" targetFramework="net472" />
109
<package id="System.Buffers" version="4.5.1" targetFramework="net472" />
@@ -15,8 +14,8 @@
1514
<package id="MathNet.Numerics" version="4.15.0" targetFramework="net472" />
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<package id="Mono.Options" version="6.6.0.161" targetFramework="net472" />
1716
<package id="Namotion.Reflection" version="1.0.18" targetFramework="net472" />
18-
<package id="Newtonsoft.Json" version="12.0.3" targetFramework="net472" />
19-
<package id="NJsonSchema" version="10.3.8" targetFramework="net472" />
17+
<package id="Newtonsoft.Json" version="13.0.1" targetFramework="net472" />
18+
<package id="NJsonSchema" version="10.4.0" targetFramework="net472" />
2019
<package id="NUnit" version="3.13.1" targetFramework="net472" />
2120
<package id="OpenMcdf" version="2.2.1.9" targetFramework="net472" />
2221
<package id="OpenMcdf.Extensions" version="2.2.1.4" targetFramework="net472" />
@@ -25,22 +24,6 @@
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<package id="System.Security.AccessControl" version="5.0.0" targetFramework="net472" />
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<package id="System.Security.Principal.Windows" version="5.0.0" targetFramework="net472" />
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<package id="System.Text.Encoding.CodePages" version="5.0.0" targetFramework="net472" />
28-
=======
29-
<package id="AWS.Logger.Core" version="1.4.0" targetFramework="net472" />
30-
<package id="AWSSDK.CloudWatchLogs" version="3.3.101.14" targetFramework="net472" />
31-
<package id="AWSSDK.Core" version="3.3.103.30" targetFramework="net472" />
32-
<package id="AWSSDK.S3" version="3.3.104.18" targetFramework="net472" />
33-
<package id="log4net" version="2.0.10" targetFramework="net471" />
34-
<package id="MathNet.Numerics" version="4.8.1" targetFramework="net472" />
35-
<package id="Mono.Options" version="5.3.0.1" targetFramework="net471" />
36-
<package id="Namotion.Reflection" version="1.0.8" targetFramework="net472" />
37-
<package id="Newtonsoft.Json" version="12.0.2" targetFramework="net472" />
38-
<package id="NJsonSchema" version="10.1.5" targetFramework="net472" />
39-
<package id="NUnit" version="3.12.0" targetFramework="net472" />
40-
<package id="Parquet.Net" version="2.0.0" targetFramework="net471" />
41-
<package id="System.Runtime.CompilerServices.Unsafe" version="4.5.2" targetFramework="net472" />
42-
<package id="System.Text.Encoding.CodePages" version="4.5.1" targetFramework="net472" />
43-
>>>>>>> 3d302d32dd87d4c7cc1288226b705f19da415274
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<package id="System.ValueTuple" version="4.5.0" targetFramework="net472" />
4528
<package id="ThermoFisher.CommonCore.Data" version="5.0.0.71" targetFramework="net472" />
4629
<package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.71" targetFramework="net472" />

packages/AWS.Logger.Core.2.0.1/.signature.p7s renamed to packages/AWS.Logger.Core.1.4.0/.signature.p7s

9.24 KB
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‎packages/AWS.Logger.Core.1.4.0/AWS.Logger.Core.1.4.0.nupkg‎

79.3 KB
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‎packages/AWS.Logger.Core.1.4.0/lib/net45/AWS.Logger.Core.dll‎

32.4 KB
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‎packages/AWS.Logger.Core.1.4.0/lib/net45/AWS.Logger.Core.pdb‎

5.26 KB
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