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Merge branch 'master' into Issue98
metadata finishing synchronizing between json and txt
2 parents d960f0b + 6dff3e7 commit 9260458

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‎ThermoRawFileParser.csproj‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -60,20 +60,20 @@
6060
<StartupObject>ThermoRawFileParser.MainClass</StartupObject>
6161
</PropertyGroup>
6262
<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">
64+
<HintPath>packages\AWS.Logger.Core.1.4.0\lib\net45\AWS.Logger.Core.dll</HintPath>
6565
<Private>True</Private>
6666
</Reference>
6767
<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>
6969
<Private>True</Private>
7070
</Reference>
7171
<Reference Include="AWSSDK.Core, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
72-
<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>
7373
<Private>True</Private>
7474
</Reference>
7575
<Reference Include="AWSSDK.S3, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
76-
<HintPath>packages\AWSSDK.S3.3.5.8.8\lib\net45\AWSSDK.S3.dll</HintPath>
76+
<HintPath>packages\AWSSDK.S3.3.3.104.18\lib\net45\AWSSDK.S3.dll</HintPath>
7777
<Private>True</Private>
7878
</Reference>
7979
<Reference Include="IronSnappy, Version=1.3.0.0, Culture=neutral, PublicKeyToken=b1d4b1dc83bdcf31">
@@ -98,12 +98,12 @@
9898
<HintPath>packages\Namotion.Reflection.1.0.18\lib\net45\Namotion.Reflection.dll</HintPath>
9999
<Private>True</Private>
100100
</Reference>
101-
<Reference Include="Newtonsoft.Json, Version=12.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed">
102-
<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">
102+
<HintPath>packages\Newtonsoft.Json.13.0.1\lib\net45\Newtonsoft.Json.dll</HintPath>
103103
<Private>True</Private>
104104
</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">
106+
<HintPath>packages\NJsonSchema.10.4.0\lib\net45\NJsonSchema.dll</HintPath>
107107
<Private>True</Private>
108108
</Reference>
109109
<Reference Include="nunit.framework, Version=3.13.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb">
@@ -232,8 +232,8 @@
232232
<Content Include="Writer\MzML\mzML1.1.1_idx.xsd" />
233233
</ItemGroup>
234234
<ItemGroup>
235-
<Analyzer Include="packages\AWSSDK.CloudWatchLogs.3.5.0.24\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
236-
<Analyzer Include="packages\AWSSDK.S3.3.5.8.8\analyzers\dotnet\cs\AWSSDK.S3.CodeAnalysis.dll" />
235+
<Analyzer Include="packages\AWSSDK.CloudWatchLogs.3.3.101.14\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
236+
<Analyzer Include="packages\AWSSDK.S3.3.3.104.18\analyzers\dotnet\cs\AWSSDK.S3.CodeAnalysis.dll" />
237237
</ItemGroup>
238238
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
239239
<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 @@
3535
<WarningLevel>4</WarningLevel>
3636
</PropertyGroup>
3737
<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>
4040
<Private>True</Private>
4141
</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>
4444
<Private>True</Private>
4545
</Reference>
4646
<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>
4848
<Private>True</Private>
4949
</Reference>
5050
<Reference Include="BayesianEstimation, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">
@@ -100,12 +100,12 @@
100100
<HintPath>..\packages\Namotion.Reflection.1.0.18\lib\net45\Namotion.Reflection.dll</HintPath>
101101
<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">
104+
<HintPath>..\packages\Newtonsoft.Json.13.0.1\lib\net45\Newtonsoft.Json.dll</HintPath>
105105
<Private>True</Private>
106106
</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>
109109
<Private>True</Private>
110110
</Reference>
111111
<Reference Include="nunit.framework, Version=3.13.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb">
@@ -208,7 +208,7 @@
208208
</Content>
209209
</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" />
212212
</ItemGroup>
213213
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
214214
<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" />
1010
<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" />
1616
<package id="zlib.net" version="1.0.4.0" targetFramework="net471" />

‎Writer/Metadata.cs‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,9 +31,9 @@ public Metadata(List<CVTerm> fileProperties,
3131

3232
public List<CVTerm> MsData { get; } = new List<CVTerm>();
3333

34-
public List<CVTerm> SampleData { get; } = new List<CVTerm>();
35-
3634
public List<CVTerm> ScanSettings { get; } = new List<CVTerm>();
35+
36+
public List<CVTerm> SampleData { get; } = new List<CVTerm>();
3737

3838
/**
3939
* Add a File property to the fileProperties

‎Writer/MetadataWriter.cs‎

Lines changed: 44 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -156,25 +156,11 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
156156
rawFile.FileHeader.Revision.ToString()));
157157
metadata.addFileProperty(new CVTerm("NCIT:C69199", "NCIT", "Content Creation Date",
158158
rawFile.FileHeader.CreationDate.ToString()));
159-
metadata.addFileProperty(new CVTerm("NCIT:C25365", "NCIT", "Description",
160-
rawFile.FileHeader.FileDescription));
161-
162-
// Scan Settings
163-
metadata.addScanSetting(new CVTerm("MS:1000016", "MS", "scan start time",
164-
startTime.ToString(CultureInfo.InvariantCulture)));
165-
metadata.addScanSetting(new CVTerm("MS:1000011", "MS", "mass resolution",
166-
rawFile.RunHeaderEx.MassResolution.ToString(CultureInfo.InvariantCulture)));
167-
metadata.addScanSetting(new CVTerm("UO:0000002", "MS", "mass unit",
168-
rawFile.GetInstrumentData().Units.ToString()));
169-
metadata.addScanSetting(new CVTerm("PRIDE:0000478", "PRIDE", "Number of scans",
170-
rawFile.RunHeaderEx.SpectraCount.ToString()));
171-
metadata.addScanSetting(new CVTerm("PRIDE:0000479", "PRIDE", "MS scan range",
172-
firstScanNumber + ":" + lastScanNumber));
173-
metadata.addScanSetting(new CVTerm("PRIDE:0000484", "PRIDE", "Retention time range",
174-
startTime + ":" + endTime));
175-
metadata.addScanSetting(new CVTerm("PRIDE:0000485", "PRIDE", "Mz range",
176-
rawFile.RunHeaderEx.LowMass + ":" + rawFile.RunHeaderEx.HighMass));
177-
metadata.addScanSetting(fragmentationTypes);
159+
if (!rawFile.FileHeader.FileDescription.IsNullOrEmpty())
160+
{
161+
metadata.addFileProperty(new CVTerm("NCIT:C25365", "NCIT", "Description",
162+
rawFile.FileHeader.FileDescription));
163+
}
178164

179165
// Instrument Properties
180166
metadata.addInstrumentProperty(new CVTerm("MS:1000494", "MS", "Thermo Scientific instrument model",
@@ -185,8 +171,11 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
185171
rawFile.GetInstrumentData().SerialNumber));
186172
metadata.addInstrumentProperty(new CVTerm("NCIT:C111093", "NCIT", "Software Version",
187173
rawFile.GetInstrumentData().SoftwareVersion));
188-
metadata.addInstrumentProperty(new CVTerm("AFR:0001259", "AFO", "firmware version",
189-
rawFile.GetInstrumentData().HardwareVersion));
174+
if (!rawFile.GetInstrumentData().HardwareVersion.IsNullOrEmpty())
175+
{
176+
metadata.addInstrumentProperty(new CVTerm("AFR:0001259", "AFO", "firmware version",
177+
rawFile.GetInstrumentData().HardwareVersion));
178+
}
190179

191180
// MS Data
192181
foreach (KeyValuePair<string, int> entry in msTypes)
@@ -217,6 +206,23 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
217206
metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS max MZ",
218207
maxMz.ToString(CultureInfo.InvariantCulture)));
219208

209+
// Scan Settings
210+
metadata.addScanSetting(new CVTerm("MS:1000016", "MS", "scan start time",
211+
startTime.ToString(CultureInfo.InvariantCulture)));
212+
metadata.addScanSetting(new CVTerm("MS:1000011", "MS", "mass resolution",
213+
rawFile.RunHeaderEx.MassResolution.ToString(CultureInfo.InvariantCulture)));
214+
metadata.addScanSetting(new CVTerm("UO:0000002", "MS", "mass unit",
215+
rawFile.GetInstrumentData().Units.ToString()));
216+
metadata.addScanSetting(new CVTerm("PRIDE:0000478", "PRIDE", "Number of scans",
217+
rawFile.RunHeaderEx.SpectraCount.ToString()));
218+
metadata.addScanSetting(new CVTerm("PRIDE:0000479", "PRIDE", "MS scan range",
219+
firstScanNumber + ":" + lastScanNumber));
220+
metadata.addScanSetting(new CVTerm("PRIDE:0000484", "PRIDE", "Retention time range",
221+
startTime + ":" + endTime));
222+
metadata.addScanSetting(new CVTerm("PRIDE:0000485", "PRIDE", "Mz range",
223+
rawFile.RunHeaderEx.LowMass + ":" + rawFile.RunHeaderEx.HighMass));
224+
metadata.addScanSetting(fragmentationTypes);
225+
220226
// Sample Data
221227
if (!rawFile.SampleInformation.SampleName.IsNullOrEmpty())
222228
{
@@ -299,9 +305,12 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
299305
"#FileProperties",
300306
"RAW file path=" + rawFile.FileName,
301307
"RAW file version=" + rawFile.FileHeader.Revision,
302-
"Creation date=" + rawFile.FileHeader.CreationDate,
303-
"Description=" + rawFile.FileHeader.FileDescription
308+
"Creation date=" + rawFile.FileHeader.CreationDate
304309
};
310+
if (!rawFile.FileHeader.FileDescription.IsNullOrEmpty())
311+
{
312+
output.Add("Description=" + rawFile.FileHeader.FileDescription);
313+
}
305314

306315
// Instrument Properties
307316
output.Add("#InstrumentProperties");
@@ -311,9 +320,12 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
311320
"Instrument name=" + rawFile.GetInstrumentData().Name,
312321
$"Instrument serial number=[MS, MS:1000529, instrument serial number, {rawFile.GetInstrumentData().SerialNumber}]",
313322
$"Software version=[NCIT, NCIT:C111093, Software Version, {rawFile.GetInstrumentData().SoftwareVersion}]",
314-
"Firmware version=" + rawFile.GetInstrumentData().HardwareVersion,
315323
}
316324
);
325+
if (!rawFile.GetInstrumentData().HardwareVersion.IsNullOrEmpty())
326+
{
327+
output.Add("Firmware version=" + rawFile.GetInstrumentData().HardwareVersion);
328+
}
317329

318330
// MS Data
319331
output.Add("#MsData");
@@ -331,24 +343,24 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
331343
{
332344
"MS min charge=" + minCharge.ToString(CultureInfo.InvariantCulture),
333345
"MS max charge=" + maxCharge.ToString(CultureInfo.InvariantCulture),
334-
$"MS min RT={minTime:F2}",
335-
$"MS max RT={maxTime:F2}",
336-
$"MS min MZ={minMz:F4}",
337-
$"MS max MZ={maxMz:F4}"
346+
$"MS min RT={minTime.ToString(CultureInfo.InvariantCulture)}",
347+
$"MS max RT={maxTime.ToString(CultureInfo.InvariantCulture)}",
348+
$"MS min MZ={minMz.ToString(CultureInfo.InvariantCulture)}",
349+
$"MS max MZ={maxMz.ToString(CultureInfo.InvariantCulture)}"
338350
}
339351
);
340352

341353
// Scan Settings
342354
output.AddRange(new List<string>
343355
{
344356
"#ScanSettings",
345-
$"Scan start time={startTime:F2}",
346-
$"Mass resolution=[MS, MS:1000011, mass resolution, {rawFile.RunHeaderEx.MassResolution:F3}]",
357+
$"Scan start time={startTime.ToString(CultureInfo.InvariantCulture)}",
358+
$"Mass resolution=[MS, MS:1000011, mass resolution, {rawFile.RunHeaderEx.MassResolution.ToString(CultureInfo.InvariantCulture)}]",
347359
"Units=" + rawFile.GetInstrumentData().Units,
348360
$"Number of scans={rawFile.RunHeaderEx.SpectraCount}",
349361
$"Scan range={firstScanNumber};{lastScanNumber}",
350-
$"Time range={startTime:F2};{endTime:F2}",
351-
$"Mass range={rawFile.RunHeaderEx.LowMass:F4};{rawFile.RunHeaderEx.HighMass:F4}",
362+
$"Time range={startTime.ToString(CultureInfo.InvariantCulture)};{endTime.ToString(CultureInfo.InvariantCulture)}",
363+
$"Mass range={rawFile.RunHeaderEx.LowMass.ToString(CultureInfo.InvariantCulture)};{rawFile.RunHeaderEx.HighMass.ToString(CultureInfo.InvariantCulture)}",
352364
"Fragmentation types=" + String.Join(", ", fragmentationTypes.Select(f => f.value))
353365
}
354366
);

‎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 & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
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="3.5.0.72" targetFramework="net472" />
5-
<package id="AWSSDK.Core" version="3.5.3.2" targetFramework="net472" />
6-
<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" />
77
<package id="Parquet.Net" version="2.0.0" targetFramework="net472" />
88
<package id="IronSnappy" version="1.3.0" targetFramework="net472" />
99
<package id="System.Buffers" version="4.5.1" targetFramework="net472" />
@@ -14,8 +14,8 @@
1414
<package id="MathNet.Numerics" version="4.15.0" targetFramework="net472" />
1515
<package id="Mono.Options" version="6.6.0.161" targetFramework="net472" />
1616
<package id="Namotion.Reflection" version="1.0.18" targetFramework="net472" />
17-
<package id="Newtonsoft.Json" version="12.0.3" targetFramework="net472" />
18-
<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" />
1919
<package id="NUnit" version="3.13.1" targetFramework="net472" />
2020
<package id="OpenMcdf" version="2.2.1.9" targetFramework="net472" />
2121
<package id="OpenMcdf.Extensions" version="2.2.1.4" 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
Binary file not shown.

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

79.3 KB
Binary file not shown.

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

32.4 KB
Binary file not shown.

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