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Merged
merged 7 commits into from
Feb 20, 2025
Merged

update schema to latest version #28

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5b755c2
update schema, bump version
ptahmose Feb 20, 2025
872a92d
Update MegaLinter workflow and action versions
ptahmose Feb 20, 2025
1642d44
fix link
ptahmose Feb 20, 2025
0fa44bb
update version info in "expected results"
ptahmose Feb 20, 2025
478d060
fix
ptahmose Feb 20, 2025
cea4cfc
fix expected-results
ptahmose Feb 20, 2025
21f94bb
trigger rebuild
ptahmose Feb 20, 2025
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6 changes: 3 additions & 3 deletions .github/workflows/mega-linter.yml
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Expand Up @@ -22,14 +22,14 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout Code
uses: actions/checkout@v3
uses: actions/checkout@v4

# MegaLinter
- name: MegaLinter
id: ml
# You can override MegaLinter flavor used to have faster performances
# More info at https://megalinter.io/flavors/
uses: oxsecurity/megalinter/flavors/dotnet@v6
uses: oxsecurity/megalinter/flavors/dotnet@v7
env:
# All available variables are described in documentation
# https://megalinter.io/configuration/
Expand All @@ -38,7 +38,7 @@ jobs:
# Upload MegaLinter artifacts
- name: Archive production artifacts
if: ${{ success() || failure() }}
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: MegaLinter reports
path: |
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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Expand Up @@ -5,7 +5,7 @@
cmake_minimum_required(VERSION 3.15)

project(CZICheck
VERSION 0.6.0
VERSION 0.6.1
HOMEPAGE_URL "https://github.com/ZEISS/czicheck"
DESCRIPTION "CZICheck is a validator for CZI-documents")

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20,694 changes: 10,920 additions & 9,774 deletions CZICheck/checkers/schema/ZEN/flatten/ImageMetadata.xsd
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2 changes: 1 addition & 1 deletion Test/CZICheckSamples/differentpixeltypeinchannel.txt.json
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Expand Up @@ -112,6 +112,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml
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Expand Up @@ -99,6 +99,6 @@
<AggregatedResult>WARN</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/duplicate_coordinates.txt.json
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Expand Up @@ -112,6 +112,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/duplicate_coordinates.txt.xml
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Expand Up @@ -99,6 +99,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
4 changes: 2 additions & 2 deletions Test/CZICheckSamples/edf-missing-texture.txt
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Expand Up @@ -11,8 +11,8 @@ Test "Basic semantic checks of the XML-metadata" : OK
Test "validate the XML-metadata against XSD-schema" :
(101,22): no declaration found for element 'RotationCenter'
(105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'
(112,21): no declaration found for element 'LookupTables'
<3 more findings omitted>
(188,29): attribute 'Id' is not declared for element 'Scaling'
<1 more finding omitted>
FAIL
Test "check if subblocks at pyramid-layer 0 of different scenes are overlapping" : OK
Test "SubBlock-Segments in SubBlockDirectory are valid and valid content" : OK
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12 changes: 1 addition & 11 deletions Test/CZICheckSamples/edf-missing-texture.txt.json
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Expand Up @@ -76,16 +76,6 @@
"description": "(105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'",
"details": ""
},
{
"severity": "FATAL",
"description": "(112,21): no declaration found for element 'LookupTables'",
"details": ""
},
{
"severity": "FATAL",
"description": "(113,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'",
"details": ""
},
{
"severity": "FATAL",
"description": "(188,29): attribute 'Id' is not declared for element 'Scaling'",
Expand Down Expand Up @@ -125,6 +115,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
12 changes: 1 addition & 11 deletions Test/CZICheckSamples/edf-missing-texture.txt.xml
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Expand Up @@ -65,16 +65,6 @@
<Description>(105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'</Description>
<Details></Details>
</Finding>
<Finding>
<Severity>FATAL</Severity>
<Description>(112,21): no declaration found for element 'LookupTables'</Description>
<Details></Details>
</Finding>
<Finding>
<Severity>FATAL</Severity>
<Description>(113,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'</Description>
<Details></Details>
</Finding>
<Finding>
<Severity>FATAL</Severity>
<Description>(188,29): attribute 'Id' is not declared for element 'Scaling'</Description>
Expand Down Expand Up @@ -112,6 +102,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json
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Expand Up @@ -136,6 +136,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml
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Expand Up @@ -123,6 +123,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
4 changes: 2 additions & 2 deletions Test/CZICheckSamples/edf-superfluous.txt
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Expand Up @@ -11,8 +11,8 @@ Test "Basic semantic checks of the XML-metadata" : OK
Test "validate the XML-metadata against XSD-schema" :
(121,22): no declaration found for element 'RotationCenter'
(125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'
(139,21): no declaration found for element 'LookupTables'
<3 more findings omitted>
(222,29): attribute 'Id' is not declared for element 'Scaling'
<1 more finding omitted>
FAIL
Test "check if subblocks at pyramid-layer 0 of different scenes are overlapping" : OK
Test "SubBlock-Segments in SubBlockDirectory are valid and valid content" : OK
Expand Down
12 changes: 1 addition & 11 deletions Test/CZICheckSamples/edf-superfluous.txt.json
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Expand Up @@ -76,16 +76,6 @@
"description": "(125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'",
"details": ""
},
{
"severity": "FATAL",
"description": "(139,21): no declaration found for element 'LookupTables'",
"details": ""
},
{
"severity": "FATAL",
"description": "(140,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'",
"details": ""
},
{
"severity": "FATAL",
"description": "(222,29): attribute 'Id' is not declared for element 'Scaling'",
Expand Down Expand Up @@ -125,6 +115,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
12 changes: 1 addition & 11 deletions Test/CZICheckSamples/edf-superfluous.txt.xml
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Expand Up @@ -65,16 +65,6 @@
<Description>(125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'</Description>
<Details></Details>
</Finding>
<Finding>
<Severity>FATAL</Severity>
<Description>(139,21): no declaration found for element 'LookupTables'</Description>
<Details></Details>
</Finding>
<Finding>
<Severity>FATAL</Severity>
<Description>(140,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'</Description>
<Details></Details>
</Finding>
<Finding>
<Severity>FATAL</Severity>
<Description>(222,29): attribute 'Id' is not declared for element 'Scaling'</Description>
Expand Down Expand Up @@ -112,6 +102,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/inconsistent_coordinates.txt.json
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Expand Up @@ -112,6 +112,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/inconsistent_coordinates.txt.xml
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Expand Up @@ -99,6 +99,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/invalid_componentbitcount.txt.json
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Expand Up @@ -94,6 +94,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/invalid_componentbitcount.txt.xml
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Expand Up @@ -81,6 +81,6 @@
<AggregatedResult>WARN</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json
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Expand Up @@ -100,6 +100,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml
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Expand Up @@ -87,6 +87,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json
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Expand Up @@ -100,6 +100,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml
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Expand Up @@ -87,6 +87,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json
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Expand Up @@ -100,6 +100,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml
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Expand Up @@ -87,6 +87,6 @@
<AggregatedResult>WARN</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/negative_plane_start_index.txt.json
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Expand Up @@ -105,6 +105,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/negative_plane_start_index.txt.xml
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Expand Up @@ -92,6 +92,6 @@
<AggregatedResult>WARN</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/overlapping_scenes.txt.json
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Expand Up @@ -136,6 +136,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/overlapping_scenes.txt.xml
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Expand Up @@ -123,6 +123,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json
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Expand Up @@ -181,6 +181,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml
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Expand Up @@ -168,6 +168,6 @@
<AggregatedResult>FAIL</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/positive_plane_start_index.txt.json
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Expand Up @@ -105,6 +105,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/positive_plane_start_index.txt.xml
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Expand Up @@ -92,6 +92,6 @@
<AggregatedResult>WARN</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/sparse_planes.txt.json
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Expand Up @@ -105,6 +105,6 @@
],
"output_version": {
"command": "CZICheck",
"version": "0.6.0"
"version": "0.6.1"
}
}
2 changes: 1 addition & 1 deletion Test/CZICheckSamples/sparse_planes.txt.xml
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Expand Up @@ -92,6 +92,6 @@
<AggregatedResult>WARN</AggregatedResult>
<OutputVersion>
<Command>CZICheck</Command>
<Version>0.6.0</Version>
<Version>0.6.1</Version>
</OutputVersion>
</TestResults>
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