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Schemas v0.1 v0.2 #76

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merged 18 commits into from
Dec 13, 2021
Merged

Schemas v0.1 v0.2 #76

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2018d3a
Remove v0.2 support from 0.3/schemas/json_schema/image.schema
will-moore Dec 1, 2021
2eaf0c8
Add validation tests and schemas for 0.1 and 0.2
will-moore Dec 1, 2021
880c650
Add plate schema and examples for v0.1
will-moore Dec 1, 2021
e9b5560
Test for SHOULD rules
will-moore Dec 1, 2021
df8962e
multiscales 'name' is not required
will-moore Dec 1, 2021
20481ca
version is not required property 0.1, 0.2, 0.3
will-moore Dec 1, 2021
145b0ad
v0.1. images SHOULD contain 'type' but not 'omero'
will-moore Dec 1, 2021
f392500
Remove unused 'multiscales' from strict_image.schema
will-moore Dec 1, 2021
8449821
Remove non-essential 'version' and 'name' from v0.3 image.json
will-moore Dec 1, 2021
4f2bf33
Use allOf in strict_image.schema to add SHOULD rules to image.schema
will-moore Dec 2, 2021
c3283d1
Remove unused merge()
will-moore Dec 2, 2021
c2c1394
Manually cache image.schema instead of load via URL resolver
will-moore Dec 3, 2021
7513ddc
Subclass RefResolver to load local files
will-moore Dec 3, 2021
37c56dd
Add 'name' to strict_image.schema. multiscales SHOULD have name
will-moore Dec 3, 2021
e4865a6
Improve LocalRefResolver - overwrite resolve_remove()
will-moore Dec 3, 2021
78c658f
Fix omero.version numbers in 0.1 samples
will-moore Dec 9, 2021
7ec782c
remove json_schema/ directory from each version
will-moore Dec 10, 2021
4aeb82b
Remove .DS_Store
will-moore Dec 10, 2021
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2 changes: 2 additions & 0 deletions .github/workflows/validation.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@ jobs:
strategy:
matrix:
ngff:
- '0.1'
- '0.2'
- '0.3'
runs-on: ubuntu-20.04
steps:
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2 changes: 2 additions & 0 deletions .gitignore
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@@ -0,0 +1,2 @@
*/.DS_Store
**/__pycache__/*
31 changes: 31 additions & 0 deletions 0.1/examples/image/invalid/invalid_channels_color.json
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@@ -0,0 +1,31 @@
{
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.1",
"name": "example",
"datasets": [
{
"path": "path/to/0"
}
]
}
],
"omero": {
"channels": [
{
"active": true,
"coefficient": 1.0,
"color": 255,
"family": "linear",
"label": "1234",
"window": {
"end": 1765.0,
"max": 2555.0,
"min": 5.0,
"start": 0.0
}
}
]
}
}
31 changes: 31 additions & 0 deletions 0.1/examples/image/invalid/invalid_channels_window.json
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@@ -0,0 +1,31 @@
{
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.2",
"name": "example",
"datasets": [
{
"path": "path/to/0"
}
]
}
],
"omero": {
"channels": [
{
"active": true,
"coefficient": 1.0,
"color": "ff0000",
"family": "linear",
"label": "1234",
"window": {
"end": "100",
"max": 2555.0,
"min": 5.0,
"start": 0.0
}
}
]
}
}
17 changes: 17 additions & 0 deletions 0.1/examples/image/invalid/invalid_path.json
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@@ -0,0 +1,17 @@
{
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.1",
"name": "example",
"datasets": [
{
"path": "path/to/0"
},
{
"path": 0
}
]
}
]
}
9 changes: 9 additions & 0 deletions 0.1/examples/image/invalid/missing_datasets.json
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@@ -0,0 +1,9 @@
{
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.1",
"name": "example"
}
]
}
28 changes: 28 additions & 0 deletions 0.1/examples/image/invalid/missing_name.json
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@@ -0,0 +1,28 @@
{
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.1",
"datasets": [
{
"path": "path/to/0"
},
{
"path": 0
}
],
"type": "gaussian",
"metadata": {
"method": "skimage.transform.pyramid_gaussian",
"version": "0.16.1",
"args": [
"true",
"false"
],
"kwargs": {
"multichannel": true
}
}
}
]
}
17 changes: 17 additions & 0 deletions 0.1/examples/image/invalid/missing_path.json
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@@ -0,0 +1,17 @@
{
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.1",
"name": "example",
"datasets": [
{
"foo": "path/to/0"
},
{
"path": "1"
}
]
}
]
}
3 changes: 1 addition & 2 deletions 0.3/examples/valid/image_v0.2.json → ...amples/image/invalid/missing_version.json
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Expand Up @@ -2,7 +2,6 @@
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.2",
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This was dropped from v0.3?

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Fixed to "0.1"

"name": "example",
"datasets": [
{
Expand All @@ -11,4 +10,4 @@
]
}
]
}
}
15 changes: 15 additions & 0 deletions 0.1/examples/image/invalid/no_datasets.json
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@@ -0,0 +1,15 @@
{
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.1",
"name": "example",
"datasets": [],
"axes": [
"z",
"y",
"x"
]
}
]
}
4 changes: 4 additions & 0 deletions 0.1/examples/image/invalid/no_multiscales.json
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@@ -0,0 +1,4 @@
{
"@type": "ngff:Image",
"multiscales": []
}
14 changes: 14 additions & 0 deletions 0.1/examples/image/valid/image.json
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@@ -0,0 +1,14 @@
{
"@type": "ngff:Image",
"multiscales": [
{
"version": "0.1",
"name": "example",
"datasets": [
{"path": "path/to/0"},
{"path": "1"},
{"path": "2"}
]
}
]
}
28 changes: 28 additions & 0 deletions 0.1/examples/image/valid/image_metadata.json
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@@ -0,0 +1,28 @@
{
"@id": "top",
"@type": "ngff:Image",
"multiscales": [
{
"@id": "inner",
"version": "0.1",
"name": "example",
"datasets": [
{
"path": "path/to/0"
}
],
"type": "gaussian",
"metadata": {
"method": "skimage.transform.pyramid_gaussian",
"version": "0.16.1",
"args": [
"true",
"false"
],
"kwargs": {
"multichannel": true
}
}
}
]
}
58 changes: 58 additions & 0 deletions 0.1/examples/image/valid/image_omero.json
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@@ -0,0 +1,58 @@
{
"@id": "#my-image",
"@type": "ngff:Image",
"multiscales": [
{
"@id": "#my-pyramid",
"version": "0.1",
"name": "example",
"datasets": [
{
"path": "path/to/0"
},
{
"path": "1"
},
{
"path": "2"
}
],
"type": "gaussian",
"metadata": {
"method": "skimage.transform.pyramid_gaussian",
"version": "0.16.1",
"args": [
"true",
"false"
],
"kwargs": {
"multichannel": true
}
}
}
],
"omero": {
"id": 1,
"version": "0.2",
"channels": [
{
"active": true,
"color": "0000FF",
"family": "linear",
"inverted": false,
"label": "1234",
"window": {
"end": 1765.0,
"max": 2555.0,
"min": 5.0,
"start": 0.0
}
}
],
"rdefs": {
"defaultZ": 0,
"defaultT": 0,
"model": "color"
}
}
}
16 changes: 16 additions & 0 deletions 0.1/examples/plate/invalid/empty_wells.json
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@@ -0,0 +1,16 @@
{
"plate": {
"columns": [
{
"name": "1"
}
],
"rows": [
{
"name": "A"
}
],
"version": "0.1",
"wells": []
}
}
31 changes: 31 additions & 0 deletions 0.1/examples/plate/invalid/invalid_fieldcount.json
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@@ -0,0 +1,31 @@
{
"plate": {
"columns": [
{
"name": "1"
}
],
"field_count": 1,
"name": "plate name",
"rows": [
{
"name": "A"
}
],
"version": "0.1",
"wells": [
{
"path": "A/3"
}
],
"acquisitions": [
{
"id": 1,
"maximumfieldcount": "2"
},
{
"id": 2
}
]
}
}
35 changes: 35 additions & 0 deletions 0.1/examples/plate/invalid/missing_acquisition_id.json
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@@ -0,0 +1,35 @@
{
"plate": {
"columns": [
{
"name": "1"
}
],
"field_count": 1,
"name": "plate name",
"rows": [
{
"name": "A"
}
],
"version": "0.1",
"wells": [
{
"path": "A/3"
}
],
"acquisitions": [
{
"maximumfieldcount": 2,
"name": "Meas_01(2012-07-31_10-41-12)",
"starttime": 1343731272000
},
{
"id": 2,
"maximumfieldcount": 2,
"name": "Meas_02(201207-31_11-56-41)",
"starttime": 1343735801000
}
]
}
}
18 changes: 18 additions & 0 deletions 0.1/examples/plate/invalid/missing_column_name.json
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@@ -0,0 +1,18 @@
{
"plate": {
"columns": [
{}
],
"rows": [
{
"name": "A"
}
],
"version": "0.1",
"wells": [
{
"path": "A/3"
}
]
}
}
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