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Integration tests for patient details (#229)
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* Added specflow steps and some test data

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Basic tests working but not clearing down workflow instances

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Fixed the deleting after test run task

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Fixed other tests that broke

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Added longer timeout for task status step

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Increased timeout on task check

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Added dev changes

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* .gitignore fix

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Changes to dicom metadata including dev changes to parse date correctly

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Removed uneeded variables in constructor

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Reset build.sh back to the same as develop

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Fixed int and unit tests that broke from dev work

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>

* Unit tests changes

Signed-off-by: Joss Sparkes <joss.sparkes@gmail.com>
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@RemakingEden
RemakingEden committed Jul 15, 2022
1 parent 030c171 commit 8c54e21
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Showing 33 changed files with 946 additions and 2,984 deletions.
11 changes: 6 additions & 5 deletions src/Monai.Deploy.WorkflowManager.Storage/Services/DicomService.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@
using Monai.Deploy.WorkflowManager.Storage.Constants;
using Newtonsoft.Json;
using Monai.Deploy.Storage.API;

using System.Globalization;

namespace Monai.Deploy.WorkflowManager.Storage.Services
{
public class DicomService : IDicomService
Expand Down Expand Up @@ -37,11 +38,11 @@ public async Task<PatientDetails> GetPayloadPatientDetailsAsync(string payloadId
PatientSex = await GetFirstValueAsync(items, payloadId, bucketName, DicomTagConstants.PatientSexTag),
PatientAge = await GetFirstValueAsync(items, payloadId, bucketName, DicomTagConstants.PatientAgeTag),
PatientHospitalId = await GetFirstValueAsync(items, payloadId, bucketName, DicomTagConstants.PatientHospitalIdTag)
};

};

var dob = await GetFirstValueAsync(items, payloadId, bucketName, DicomTagConstants.PatientDateOfBirthTag);

if (DateTime.TryParse(dob, out var dateOfBirth))
if (DateTime.TryParseExact(dob, "yyyyMMdd", CultureInfo.InvariantCulture, DateTimeStyles.None, out var dateOfBirth))
{
patientDetails.PatientDob = dateOfBirth;
}
Expand Down Expand Up @@ -116,7 +117,7 @@ public async Task<string> GetAnyValueAsync(string keyId, string payloadId, strin
Guard.Against.NullOrWhiteSpace(payloadId);
Guard.Against.NullOrWhiteSpace(bucketId);

var path = $"{payloadId}\\dcm";
var path = $"{payloadId}/dcm";
var listOfFiles = await _storageService.ListObjectsAsync(bucketId, path, true);
var listOfJsonFiles = listOfFiles.Where(file => file.Filename.EndsWith(".json")).ToList();
var fileCount = listOfJsonFiles.Count;
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1 change: 0 additions & 1 deletion ...xecutor.IntegrationTests/DICOMs/dcm/series2/07051db3-3c1d-4bf2-8764-ba45dc918e74.dcm.json
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0 .../07051db3-3c1d-4bf2-8764-ba45dc918e74.dcm → .../07051db3-3c1d-4bf2-8764-ba45dc918e74.dcm
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212 changes: 212 additions & 0 deletions ...ationTests/DICOMs/full_patient_metadata/dcm/07051db3-3c1d-4bf2-8764-ba45dc918e74.dcm.json
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@@ -0,0 +1,212 @@
{
"00080008": {
"vr": "CS",
"Value": [
"DERIVED",
"SECONDARY"
]
},
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"vr": "UI",
"Value": [
"1.2.840.10008.5.1.4.1.1.2"
]
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]
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"165227.888340"
]
},
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},
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"vr": "CS",
"Value": [
"CT"
]
},
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"vr": "CS",
"Value": [
"DV"
]
},
"00080090": {
"vr": "PN"
},
"0008103E": {
"vr": "LO",
"Value": [
"Processed by Clara"
]
},
"00100010": {
"vr": "PN",
"Value": [
"Patient_Full_Patient"
]
},
"00100020": {
"vr": "LO",
"Value": [
"1"
]
},
"00100030": {
"vr": "DA",
"Value": [
"20000101"
]
},
"00100040": {
"vr": "CS",
"Value": [
"male"
]
},
"00101010": {
"vr": "AS",
"Value": [
"21"
]
},
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"vr": "LO",
"Value": [
"123"
]
},
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"vr": "UI",
"Value": [
"1.2.826.0.1.3680043.2.1125.1.64854732231592794220757963127858480"
]
},
"0020000E": {
"vr": "UI",
"Value": [
"1.2.826.0.1.3680043.2.1125.1.88346615283577664091166302060792432"
]
},
"00200010": {
"vr": "SH"
},
"00200011": {
"vr": "IS"
},
"00200013": {
"vr": "IS"
},
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0,
0,
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]
},
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"vr": "DS",
"Value": [
1,
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0
]
},
"00200052": {
"vr": "UI",
"Value": [
"1.2.826.0.1.3680043.2.1125.1.72833472134103137404323077718880857"
]
},
"00280002": {
"vr": "US",
"Value": [
1
]
},
"00280004": {
"vr": "CS",
"Value": [
"MONOCHROME2"
]
},
"00280010": {
"vr": "US",
"Value": [
512
]
},
"00280011": {
"vr": "US",
"Value": [
512
]
},
"00280030": {
"vr": "DS",
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0.66796875,
0.66796875
]
},
"00280100": {
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},
"00280101": {
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"00280102": {
"vr": "US",
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"00280103": {
"vr": "US",
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},
"00281052": {
"vr": "DS",
"Value": [
0
]
},
"00281053": {
"vr": "DS",
"Value": [
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]
},
"00281054": {
"vr": "LO",
"Value": [
"US"
]
}
}
0 .../07051db3-3c1d-4bf2-8764-ba45dc918e74.dcm → .../07051db3-3c1d-4bf2-8764-ba45dc918e74.dcm
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