daniel/zaaReloaded2
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Add importer for clinic system.

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- Neu: Laborwerte, die vom Ambulanzsystem ausgegeben wurden, können jetzt auch verarbeitet werden.
This commit is contained in:
daniel
2017-09-17 13:28:12 +02:00
parent 6a7508bca0
commit cf765c4c40
18 changed files with 1091 additions and 104 deletions
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55
Tests/Importer/ClinicImporter/ClinicImporterTest.cs Executable file
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@ -0,0 +1,55 @@
/* ClinicImporterTest.cs
* part of zaaReloaded2
*
* Copyright 2017 Daniel Kraus
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.IO;
using zaa = zaaReloaded2.Importer.ClinicImporter;
using NUnit.Framework;
namespace Tests.Importer.ClinicImporter
{
[TestFixture]
class ClinicImporterTest
{
/// <summary>
/// Parses the demo-output.txt file that is built into the assembly.
/// Note that this demo text contains seven time points, only six of
/// which are distinct. Thus, the two time points with identical time
/// stamps should be merged in the <see cref="Laboratory"/>.
/// </summary>
[Test]
public void ParseTimePoints()
{
zaa.ClinicImporter importer = TestHelpers.ClinicImporterFromResource();
// Only 6 distinct time points (see method documentation above).
Assert.AreEqual(5, importer.Laboratory.TimePoints.Count);
}
[Test]
public void ParseInvalidInput()
{
zaa.ClinicImporter importer = new zaa.ClinicImporter();
importer.Import("some arbitrary text\r\nthat does not represent\r\na valid lab");
Assert.IsFalse(importer.Success);
importer.Import("(03.03.1930 13:30:00)\r\n\tNatrium 135 [135 - 145] mmol/l;");
Assert.IsTrue(importer.Success);
}
}
}

56
Tests/Importer/ClinicImporter/ClinicItemTest.cs Executable file
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@ -0,0 +1,56 @@
/* LaurisItemTest.cs
* part of zaaReloaded2
*
* Copyright 2017 Daniel Kraus
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using NUnit.Framework;
using zaaReloaded2.LabModel;
using zaaReloaded2.Importer.ZaaImporter;
namespace Tests.Importer.ClinicImporter
{
/// <summary>
/// The ClinicItemTest really just tests the zaaReloaded2.Importer.ZaaImporter.LaurisItem
/// class with text formatted by the outpatient clinic system to make sure LaurisItem works
/// with clinic-formatted lab data as well.
/// </summary>
[TestFixture]
class ClinicItemTest
{
[Test]
[TestCase(" Natrium: 137 [135 - 145] mmol/l", "Natrium", 137, "mmol/l", 135, 145, true)]
public void ParseClinicWithBothLimits(
string laurisString, string name, double value,
string unit, double lowerLimit, double upperLimit, bool isNormal)
{
LaurisItem i = new LaurisItem(laurisString);
Assert.AreEqual(name, i.Name, "Name");
Assert.AreEqual(unit, i.Unit, "Unit");
Assert.IsFalse(i.IsExtreme, "IsExtreme");
Assert.IsTrue(i.IsNumerical, "IsNumerical");
Assert.AreEqual(value, i.NumericalValue, "NumericalValue");
Assert.AreEqual(lowerLimit, i.LowerLimit, "Lower limit");
Assert.AreEqual(upperLimit, i.UpperLimit, "Upper limit");
Assert.AreEqual(isNormal, i.IsNormal, "IsNormal");
Assert.IsTrue(i.HasLimits, "HasLimits");
Assert.IsTrue(i.HasLowerLimit, "HasLowerLimit");
Assert.IsTrue(i.HasUpperLimit, "HasUpperLimit");
}
}
}

45
Tests/Importer/ClinicImporter/ClinicLineTest.cs Executable file
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@ -0,0 +1,45 @@
/* ClinicLineTest.cs
* part of zaaReloaded2
*
* Copyright 2017 Daniel Kraus
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
using NUnit.Framework;
using zaaReloaded2.LabModel;
using zaaReloaded2.Importer.ClinicImporter;
namespace Tests.Importer.ClinicImporter
{
[TestFixture]
class ClinicLineTest
{
[Test]
public void ParseLine()
{
string demo = "\tNatrium:\t137\t[135 - 145]\tmmol/l";
ClinicLine line = new ClinicLine(demo);
Assert.IsTrue(line.IsClinicLine);
Assert.AreEqual(137, line.Item.NumericalValue);
}
[Test]
public void ParseInvalidLine()
{
// Missing leading tab
string demo = "Natrium:\t137\t[135 - 145]\tmmol/l";
ClinicLine line = new ClinicLine(demo);
Assert.IsFalse(line.IsClinicLine);
}
}
}

67
Tests/Importer/ClinicImporter/TimePointTest.cs Executable file
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@ -0,0 +1,67 @@
/* TimePointTest.cs
* part of zaaReloaded2
*
* Copyright 2017 Daniel Kraus
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using NUnit.Framework;
using zaaReloaded2.LabModel;
using zaaReloaded2.Importer.ClinicImporter;
namespace Tests.Importer.ClinicImporter
{
[TestFixture]
class ClinicTimePointTest
{
[Test]
public void ParseValidClinicTimePoint()
{
ClinicTimePoint tp = new ClinicTimePoint(
"(06.09.2017 09:45:00)" + Environment.NewLine +
"\tKalium:\t4.6\t[3.5 - 5]\tmmol/l");
Assert.IsTrue(tp.IsValidTimePoint);
}
[Test]
public void ParseInvalidClinicTimePoints()
{
ClinicTimePoint tp = new ClinicTimePoint("Mit freundlichen Grüßen");
Assert.IsFalse(tp.IsValidTimePoint,
"Bogus paragraph should be invalid LaurisTimePoint");
tp.ClinicText = "(22.10.2013 12:30:00)";
Assert.IsFalse(tp.IsValidTimePoint,
"LaurisTimePoint should be invalid if it consists of time stamp only.");
}
[Test]
public void ParseClinicTimePointWithDuplicateItems()
{
ClinicTimePoint tp = new ClinicTimePoint(
"(22.10.2013 12:30:00)" + Environment.NewLine +
"\tNatrium:\t137\t[135 - 145]\tmmol/l" + Environment.NewLine +
"\tNatrium:\t140\t[135 - 145]\tmmol/l"
);
Assert.IsTrue(tp.Items.ContainsKey("Natrium"),
"LaurisTimePoint should contain 'Natrium' item.");
Assert.AreEqual(140, tp.Items["Natrium"].NumericalValue,
"LaurisTimePoint does not use last occurrence of 'Natrium'.");
}
}
}

14
Tests/TestHelpers.cs
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@ -21,6 +21,7 @@ using System.IO;
using System.Linq;
using System.Text;
using zaaReloaded2.Importer.ZaaImporter;
using zaaReloaded2.Importer.ClinicImporter;
namespace Tests
{
@ -38,5 +39,18 @@ namespace Tests
importer.Import(r.ReadToEnd());
return importer;
}
/// <summary>
/// Creates a ClinicImporter object and imports demo-output-clinic.txt.
/// </summary>
/// <returns></returns>
public static ClinicImporter ClinicImporterFromResource()
{
Stream s = typeof(TestHelpers).Assembly.GetManifestResourceStream("Tests.demo-output-clinic.txt");
StreamReader r = new StreamReader(s);
ClinicImporter importer = new ClinicImporter();
importer.Import(r.ReadToEnd());
return importer;
}
}
}

8
Tests/Tests.csproj
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@ -91,6 +91,10 @@
<Compile Include="Controller\Comments\CommentPoolTest.cs" />
<Compile Include="Controller\Comments\ItemCommentTest.cs" />
<Compile Include="Controller\Elements\CloneTest.cs" />
<Compile Include="Importer\ClinicImporter\ClinicItemTest.cs" />
<Compile Include="Importer\ClinicImporter\ClinicLineTest.cs" />
<Compile Include="Importer\ClinicImporter\TimePointTest.cs" />
<Compile Include="Importer\ClinicImporter\ClinicImporterTest.cs" />
<Compile Include="Medication\ImporterTest.cs" />
<Compile Include="Medication\PrescriptionTest.cs" />
<Compile Include="SerializationTest.cs" />
@ -144,6 +148,10 @@
<ItemGroup>
<EmbeddedResource Include="Formatter\FormatterTest-all.txt" />
</ItemGroup>
<ItemGroup>
<EmbeddedResource Include="demo-output-clinic.txt" />
</ItemGroup>
<ItemGroup />
<Choose>
<When Condition="'$(VisualStudioVersion)' == '10.0' And '$(IsCodedUITest)' == 'True'">
<ItemGroup>

90
Tests/demo-output-clinic.txt Executable file
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@ -0,0 +1,90 @@
# This file contains 5 distinct time points.
# This leading text should be ignored.
# DO NOT CHANGE THE FOLLOWING TEXT, LEST THE TESTS WILL FAIL!
(06.09.2017 09:54:00)
Gesamt-Eiweiss (PU): 54 [<= 120] mg/l
Gesamt-Eiweiss/Creatinin (PU): 59 [<= 70] mg/g Crea
Albumin (PU): 4 [<= 30] mg/l
Albumin/Creatinin (PU): 4.4 [<= 30] mg/g Crea
Creatinin (PU): 91.1 [29 - 226] mg/dl
(06.09.2017 09:54:00)
Erythrozyten (U): negativ [negativ]
Leukozyten (U): + [negativ]
Nitrit (U): negativ [negativ]
Protein (U): negativ [negativ]
Glucose (U): negativ [negativ]
Ketonkörper (U): + [negativ]
Bilirubin (U): negativ [negativ]
Urobilinogen (U): negativ [negativ]
pH (U): 6.500 [4.8 - 7.4]
spezifisches Gewicht (U): 1.015 [1.00 - 1.04] g/ml
Erythrozyten (U): 3 [<= 25] Ery/µl
Leukozyten (U): 4 [<= 20] Leu/µl
Bakterien (U): 193 Bak/µl
Plattenepithelien (U): 25 Epi/µl
Übergangsepithelien (U): 0 Uge/µl
hyaline Zylinder (U): 0 Zyh/µl
(06.09.2017 09:52:00)
Gesamt-Eiweiss (SU): < 40 [<= 120] mg/l
Albumin (SU): < 3 mg/l
a1-Microglobulin (SU): < 5 mg/l
Immunglobulin G (SU): < 4 mg/l
Sammelzeit (U): 24 h
Sammelmenge (U): 3200 ml
Calcium (SU): 0.26 mmol/l
Calcium (SU)/die: 0.83 [2.5 - 8] mmol/d
Creatinin (SU): 30.2 mg/dl
Harnstoff (SU): 674 [900 - 3000] mg/dl
Harnstoff (SU)/die: 21.6 [<= 35] g/d
Kalium (SU): 45.4 [20 - 80] mmol/l
Kalium (SU)/die: 145.28 [25 - 125] mmol/d
Natrium (SU): 28.9 [54 - 150] mmol/l
Natrium (SU)/die: 92.5 [40 - 220] mmol/d
(06.09.2017 09:50:00)
Cystatin C (Latex Gen. 2): 1.04 [0.61 - 0.95] mg/l
(06.09.2017 09:45:00)
Natrium: 137 [135 - 145] mmol/l
Kalium: 4.6 [3.5 - 5] mmol/l
Calcium: 2.4 [2.0 - 2.7] mmol/l
anorg. Phosphat: 1.29 [0.87 - 1.45] mmol/l
Calcium-Phosphat-Produkt: 3.10 [<= 4.4] mmol²/l²
glomerul. Filtrationsr. CKD-EP: 62 ml/min /1,73qm
glomerul. Filtrationsr. (MDRD): 59 ml/min /1,73qm
Creatinin: 1.06 [0 - 0.95] mg/dl
Harnstoff: 52.1 [10 - 50] mg/dl
Lactat Dehydrogenase: 175 [<= 250] U/l
Cholesterin: 180 [130 - 220] mg/dl
Triglyceride: 51 [74 - 172] mg/dl
LDL - Cholesterin: 91 [0 - 150] mg/dl
HDL - Cholesterin: 79 [>= 35] mg/dl
Albumin: 4.5 [3.5 - 5.5] g/dl
Leukozyten: 4.7 [5 - 10] n*1000/µl
Erythrozyten: 4.09 [4 - 5] n*10E6/µl
Hämoglobin: 11.9 [12 - 16] g/dl
Hämatokrit: 36.6 [35 - 47] %
MCV: 89.5 [82 - 96] fl
MCH (HbE): 29.1 [27 - 33] pg
MCHC: 32.5 [32 - 36] g/dl
Thrombozyten: 302 [150 - 450] n*1000/µl
Mittleres Plättchenvolumen: 11.3 [9.6 - 12.0] fl
Neutrophile: 2.60 [1.8 - 7.2] n*1000/µl
Lymphozyten: 1.35 [1 - 4.05] n*1000/µl
Monozyten: 0.47 [0.08 - 0.8] n*1000/µl
Eosinophile: 0.2 [0.04 - 0.36] n*1000/µl
Basophile: 0.1 [0 - 0.08] n*1000/µl
% Neutrophile: 55.1 [41 - 70] %
% Lymphozyten: 28.7 [25 - 40] %
% Monozyten: 10.0 [2 - 8] %
% Eosinophile: 4.7 [0.8 - 6.2] %
% Basophile: 1.3 [0 - 1] %
Unreife Granulozyten: 0.01 n*1000/µl
% Unreife Granulozyten: 0.2 %
C-reaktives Protein: 0.02 [0 - 0.5] mg/dl
(06.09.2017 09:15:00)
TSH: 1.30 [0.3 - 4.0] mIU/l
PTH intakt: 106.0 [12 - 65] ng/l