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Fixed minor issues found with TopQuadrant validator
1 parent 98ab6cb commit cecc69c

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24 files changed

+141
-85
lines changed

24 files changed

+141
-85
lines changed

‎build.sbt

Lines changed: 48 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,29 @@
1+
/*
2+
scalafmt: {
3+
style = defaultWithAlign
4+
maxColumn = 150
5+
align.tokens = [
6+
{ code = "=>", owner = "Case" }
7+
{ code = "?", owner = "Case" }
8+
{ code = "extends", owner = "Defn.(Class|Trait|Object)" }
9+
{ code = "//", owner = ".*" }
10+
{ code = "{", owner = "Template" }
11+
{ code = "}", owner = "Template" }
12+
{ code = ":=", owner = "Term.ApplyInfix" }
13+
{ code = "++=", owner = "Term.ApplyInfix" }
14+
{ code = "+=", owner = "Term.ApplyInfix" }
15+
{ code = "%", owner = "Term.ApplyInfix" }
16+
{ code = "%%", owner = "Term.ApplyInfix" }
17+
{ code = "%%%", owner = "Term.ApplyInfix" }
18+
{ code = "->", owner = "Term.ApplyInfix" }
19+
{ code = "?", owner = "Term.ApplyInfix" }
20+
{ code = "<-", owner = "Enumerator.Generator" }
21+
{ code = "?", owner = "Enumerator.Generator" }
22+
{ code = "=", owner = "(Enumerator.Val|Defn.(Va(l|r)|Def|Type))" }
23+
]
24+
}
25+
*/
26+
127
val commonsVersion = "0.7.6"
228
val provVersion = "1.1.1"
329
val kgVersion = "0.9.4"
@@ -6,16 +32,15 @@ lazy val prov = "ch.epfl.bluebrain.nexus" %% "nexus-prov" % provV
632
lazy val commonsSchemas = "ch.epfl.bluebrain.nexus" %% "commons-schemas" % commonsVersion
733
lazy val kgSchemas = "ch.epfl.bluebrain.nexus" %% "kg-schemas" % kgVersion
834

9-
1035
lazy val core = project
1136
.in(file("modules/core"))
1237
.enablePlugins(WorkbenchPlugin)
1338
.disablePlugins(ScapegoatSbtPlugin, DocumentationPlugin)
1439
.dependsOn(nsgcommons)
1540
.settings(common)
1641
.settings(
17-
name := "nsg-core-schemas",
18-
moduleName := "nsg-core-schemas"
42+
name := "nsg-core-schemas",
43+
moduleName := "nsg-core-schemas"
1944
)
2045

2146
lazy val nexusschema = project
@@ -52,8 +77,8 @@ lazy val nsgcommons = project
5277
.dependsOn(nexusschema)
5378
.settings(common)
5479
.settings(
55-
name := "nsg-commons-schemas",
56-
moduleName := "nsg-commons-schemas",
80+
name := "nsg-commons-schemas",
81+
moduleName := "nsg-commons-schemas",
5782
libraryDependencies += prov
5883
)
5984

@@ -105,22 +130,30 @@ lazy val root = project
105130
.in(file("."))
106131
.settings(name := "nsg-schemas", moduleName := "nsg-schemas")
107132
.settings(common, noPublish)
108-
.aggregate(core, experiment, atlas, morphology, electrophysiology, simulation, nexusschema,nsgcommons)
133+
.aggregate(core, experiment, atlas, morphology, electrophysiology, simulation, nexusschema, nsgcommons)
109134

110135
lazy val common = Seq(
111136
scalacOptions in (Compile, console) ~= (_ filterNot (_ == "-Xfatal-warnings")),
112-
autoScalaLibrary := false,
113-
workbenchVersion := "0.2.2",
114-
bintrayOmitLicense := true,
115-
homepage := Some(url("https://github.com/INCF/neuroshapes")),
116-
licenses := Seq("CC-4.0" -> url("https://github.com/INCF/neuroshapes/blob/master/LICENSE")),
117-
scmInfo := Some(
118-
ScmInfo(url("https://github.com/INCF/neuroshapes"), "scm:git:git@https://github.com/INCF/neuroshapes.git"))
137+
autoScalaLibrary := false,
138+
workbenchVersion := "0.2.2"
119139
)
120140

141+
inThisBuild(
142+
Seq(
143+
homepage := Some(new URL("https://github.com/INCF/neuroshapes")),
144+
licenses := Seq("CC-4.0" -> url("https://github.com/INCF/neuroshapes/blob/master/LICENSE")),
145+
scmInfo := Some(ScmInfo(url("https://github.com/INCF/neuroshapes"), "scm:git:git@https://github.com/INCF/neuroshapes.git")),
146+
bintrayOmitLicense := true,
147+
developers := List(
148+
Developer("MFSY", "Mohameth François SY", "[email protected]", url("https://bluebrain.epfl.ch/")),
149+
Developer("annakristinkaufmann", "anna-Kristin Kaufmann", "[email protected]", url("https://bluebrain.epfl.ch/")),
150+
Developer("huanxiang", "Huanxiang", "[email protected]", url("https://bluebrain.epfl.ch/"))
151+
)
152+
)
153+
)
121154

122-
123-
lazy val noPublish = Seq(publishLocal := {}, publish := {})
155+
lazy val noPublish =
156+
Seq(publishLocal := {}, publish := {}, publishArtifact := false)
124157

125158
addCommandAlias("review", ";clean;test")
126159
addCommandAlias("rel", ";release with-defaults skip-tests")

‎modules/atlas/src/main/resources/schemas/neurosciencegraph/atlas/imagestack/v0.1.0.json

Lines changed: 25 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@
3535
"path": "nsg:sliceDirection",
3636
"name": "Slice Direction",
3737
"description": "Slice direction of the image stack",
38-
"sh:in": [
38+
"in": [
3939
"Sagittal",
4040
"Axial",
4141
"Coronal"
@@ -100,15 +100,29 @@
100100
"path": "nsg:widthResolution",
101101
"name": "Width resolution",
102102
"description": "Slice resolution in width",
103-
"datatype": "xsd:float",
103+
"or" : [
104+
{
105+
"datatype": "xsd:float"
106+
},
107+
{
108+
"datatype": "xsd:double"
109+
}
110+
],
104111
"minCount": 1,
105112
"maxCount": 1
106113
},
107114
{
108115
"path": "nsg:heightResolution",
109116
"name": "Height resolution",
110117
"description": "Slice height",
111-
"datatype": "xsd:float",
118+
"or" : [
119+
{
120+
"datatype": "xsd:float"
121+
},
122+
{
123+
"datatype": "xsd:double"
124+
}
125+
],
112126
"minCount": 1,
113127
"maxCount": 1
114128
}
@@ -129,7 +143,14 @@
129143
"path": "nsg:sliceIntervalValue",
130144
"name": "Slice interval value",
131145
"description": "Slice interval value",
132-
"datatype": "xsd:float",
146+
"or" : [
147+
{
148+
"datatype": "xsd:float"
149+
},
150+
{
151+
"datatype": "xsd:double"
152+
}
153+
],
133154
"minCount": 1,
134155
"maxCount": 1
135156
}

‎modules/atlas/src/main/resources/schemas/neurosciencegraph/atlas/imagestack/v0.2.0.json

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -35,11 +35,11 @@
3535
"path": "nsg:sliceDirection",
3636
"name": "Slice Direction",
3737
"description": "Slice direction of the image stack",
38-
"sh:in": [
39-
"Sagittal",
40-
"Axial",
41-
"Coronal"
42-
],
38+
"in": [
39+
"Sagittal",
40+
"Axial",
41+
"Coronal"
42+
],
4343
"minCount": 1,
4444
"maxCount": 1
4545
},
@@ -90,7 +90,7 @@
9090
{
9191
"@id": "this:SliceResolutionShape",
9292
"@type": "sh:NodeShape",
93-
"and" : [
93+
"and": [
9494
{
9595
"node": "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.2/QuantitativeValueShape"
9696
},
@@ -119,7 +119,7 @@
119119
{
120120
"@id": "this:SliceIntervalShape",
121121
"@type": "sh:NodeShape",
122-
"and" : [
122+
"and": [
123123
{
124124
"node": "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.2/QuantitativeValueShape"
125125
},

‎modules/commons/src/main/resources/contexts/neurosciencegraph/core/data/v0.1.0.json

Lines changed: 10 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -197,7 +197,12 @@
197197
"@id": "nsg:reconstructionRequester"
198198
},
199199
"reconstructionSentDate": {
200-
"@id": "nsg:reconstructionSentDate"
200+
"@id": "nsg:reconstructionSentDate",
201+
"@type": "xsd:dateTime"
202+
},
203+
"atTime": {
204+
"@id": "prov:atTime",
205+
"@type": "xsd:dateTime"
201206
},
202207
"reconstructionDate": {
203208
"@id": "nsg:reconstructionDate"
@@ -259,7 +264,8 @@
259264
"@type": "@id"
260265
},
261266
"releaseDate": {
262-
"@id": "nsg:releaseDate"
267+
"@id": "nsg:releaseDate",
268+
"@type": "xsd:date"
263269
},
264270
"radius": {
265271
"@id": "nsg:radius",
@@ -373,7 +379,8 @@
373379
"@type": "@id"
374380
},
375381
"retrievalDate": {
376-
"@id": "nsg:retrievalDate"
382+
"@id": "nsg:retrievalDate",
383+
"@type": "xsd:dateTime"
377384
},
378385
"timeStep": {
379386
"@id": "nsg:timeStep",

‎modules/commons/src/main/resources/schemas/neurosciencegraph/commons/brainlocation/v0.1.0.json

Lines changed: 12 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -11,13 +11,13 @@
1111
"{{base}}/schemas/neurosciencegraph/commons/labeledontologyentity/v0.1.0"
1212
],
1313
"@type": "nxv:Schema",
14-
"owl:deprecated":true,
14+
"owl:deprecated": true,
1515
"shapes": [
1616
{
1717
"@id": "this:BrainLocationShape",
1818
"@type": "sh:NodeShape",
1919
"label": "Brain location shape definition",
20-
"owl:deprecated":true,
20+
"owl:deprecated": true,
2121
"property": [
2222
{
2323
"path": "nsg:brainRegion",
@@ -50,23 +50,19 @@
5050
"path": "nsg:positionInLayer",
5151
"name": "Position in layer",
5252
"description": "Position in layer (deep / superficial)",
53-
"sh:in": {
54-
"@list": [
55-
"Deep",
56-
"Superficial"
57-
]
58-
},
53+
"in": [
54+
"Deep",
55+
"Superficial"
56+
],
5957
"maxCount": 1
6058
},
6159
{
6260
"path": "nsg:longitudinalAxis",
6361
"name": "Longitudinal axis (dorsal / ventral)",
64-
"sh:in": {
65-
"@list": [
66-
"Dorsal",
67-
"Ventral"
68-
]
69-
},
62+
"in": [
63+
"Dorsal",
64+
"Ventral"
65+
],
7066
"maxCount": 1
7167
},
7268
{
@@ -92,7 +88,7 @@
9288
"@id": "this:CoordinatesInSliceShape",
9389
"@type": "sh:NodeShape",
9490
"label": "Coordinates in slice shape definition",
95-
"owl:deprecated":true,
91+
"owl:deprecated": true,
9692
"property": [
9793
{
9894
"path": "nsg:valueX",
@@ -130,7 +126,7 @@
130126
"@id": "this:DistanceToBoundaryShape",
131127
"@type": "sh:NodeShape",
132128
"label": "Distance to boundary shape definition",
133-
"owl:deprecated":true,
129+
"owl:deprecated": true,
134130
"property": [
135131
{
136132
"path": "nsg:boundary",

‎modules/commons/src/main/resources/schemas/neurosciencegraph/commons/brainlocation/v0.1.1.json

Lines changed: 8 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -48,23 +48,19 @@
4848
"path": "nsg:positionInLayer",
4949
"name": "Position in layer",
5050
"description": "Position in layer (deep / superficial)",
51-
"sh:in": {
52-
"@list": [
53-
"Deep",
54-
"Superficial"
55-
]
56-
},
51+
"in": [
52+
"Deep",
53+
"Superficial"
54+
],
5755
"maxCount": 1
5856
},
5957
{
6058
"path": "nsg:longitudinalAxis",
6159
"name": "Longitudinal axis (dorsal / ventral)",
62-
"sh:in": {
63-
"@list": [
64-
"Dorsal",
65-
"Ventral"
66-
]
67-
},
60+
"in": [
61+
"Dorsal",
62+
"Ventral"
63+
],
6864
"maxCount": 1
6965
},
7066
{

‎modules/electrophysiology/src/test/resources/data/neurosciencegraph/electrophysiology/trace/v0.1.0/all-fields.json

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -10,14 +10,14 @@
1010
"name": "654363",
1111
"providerId": "654363",
1212
"description": "Stimulation trace",
13-
"channel": "0",
13+
"channel": 0,
1414
"citation": "https://doi.org/10.1093/cercor/bhh092",
1515
"projectName": "Somatosensory cortex project",
1616
"retrievalDate": "2016-10-15T00:00:00",
1717
"dataUnit": "pA",
1818
"timeStep": {
1919
"unitText": "seconds",
20-
"value": "0.00005"
20+
"value": 0.00005
2121
},
2222
"qualifiedGeneration": {
2323
"@id": "{{base}}/data/neurosciencegraph/experiment/tracegeneration/v0.1.0/cc4ed155-fb9c-4611-815f-cfe304cba128",

‎modules/electrophysiology/src/test/resources/data/neurosciencegraph/electrophysiology/trace/v0.1.0/min-fields.json

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
"nsg:StimulationTrace"
99
],
1010
"name": "654363",
11-
"channel": "0",
11+
"channel": 0,
1212
"qualifiedGeneration": {
1313
"@id": "{{base}}/data/neurosciencegraph/experiment/tracegeneration/v0.1.0/cc4ed155-fb9c-4611-815f-cfe304cba128",
1414
"@type": "nsg:TraceGeneration"

‎modules/electrophysiology/src/test/resources/data/neurosciencegraph/electrophysiology/trace/v0.1.0/neobase_example.json

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
"nsg:StimulationTrace"
99
],
1010
"name": "654363",
11-
"channel": "0",
11+
"channel": 0,
1212
"qualifiedGeneration": {
1313
"@id": "{{base}}/data/neurosciencegraph/experiment/tracegeneration/v0.1.0/cc4ed155-fb9c-4611-815f-cfe304cba128",
1414
"@type": "nsg:TraceGeneration"

‎modules/electrophysiology/src/test/resources/data/neurosciencegraph/electrophysiology/trace/v1.0.0/all-fields.json

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -10,14 +10,14 @@
1010
"name": "654363",
1111
"providerId": "654363",
1212
"description": "Stimulation trace",
13-
"channel": "0",
13+
"channel": 0,
1414
"citation": "https://doi.org/10.1093/cercor/bhh092",
1515
"projectName": "Somatosensory cortex project",
1616
"retrievalDate": "2016-10-15T00:00:00",
1717
"dataUnit": "pA",
1818
"timeStep": {
1919
"unitText": "seconds",
20-
"value": "0.00005"
20+
"value": 0.00005
2121
},
2222
"qualifiedGeneration": {
2323
"@id": "{{base}}/data/neurosciencegraph/experiment/tracegeneration/v0.1.0/cc4ed155-fb9c-4611-815f-cfe304cba128",

‎modules/electrophysiology/src/test/resources/data/neurosciencegraph/electrophysiology/trace/v1.0.0/min-fields.json

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
"nsg:StimulationTrace"
99
],
1010
"name": "654363",
11-
"channel": "0",
11+
"channel": 0,
1212
"qualifiedGeneration": {
1313
"@id": "{{base}}/data/neurosciencegraph/experiment/tracegeneration/v0.1.0/cc4ed155-fb9c-4611-815f-cfe304cba128",
1414
"@type": "nsg:TraceGeneration"

‎modules/electrophysiology/src/test/resources/data/neurosciencegraph/electrophysiology/trace/v1.0.0/neobase_example.json

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
"nsg:StimulationTrace"
99
],
1010
"name": "654363",
11-
"channel": "0",
11+
"channel": 0,
1212
"qualifiedGeneration": {
1313
"@id": "{{base}}/data/neurosciencegraph/experiment/tracegeneration/v0.1.0/cc4ed155-fb9c-4611-815f-cfe304cba128",
1414
"@type": "nsg:TraceGeneration"

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