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Validate DataSources more strictly when reading from disk #8894
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Validate DataSources more strictly when reading from disk
fm3 29bc4f9
check valid dataLayerNames, also validate datasource in reserveManual…
fm3 17b5d97
changelog
fm3 f79da6c
lint
fm3 692976c
Merge branch 'reserve-manual' into datasource-validation
fm3 ad54a6f
Merge branch 'reserve-manual' into datasource-validation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| ### Changed | ||
| - DataSources are now more strictly validated when reading them from disk or when reserving manual uploads. |
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64 changes: 64 additions & 0 deletions
64
...-datastore/app/com/scalableminds/webknossos/datastore/services/DataSourceValidation.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| package com.scalableminds.webknossos.datastore.services | ||
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| import com.scalableminds.util.tools.{Box, Full, ParamFailure} | ||
| import com.scalableminds.webknossos.datastore.models.datasource.{ElementClass, UsableDataSource} | ||
| import play.api.libs.json.Json | ||
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| trait DataSourceValidation { | ||
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| protected def assertValidateDataSource(dataSource: UsableDataSource): Box[Unit] = { | ||
| val errors = validateDataSourceGetErrors(dataSource) | ||
| if (errors.isEmpty) { | ||
| Full(()) | ||
| } else { | ||
| ParamFailure("DataSource is invalid", Json.toJson(errors.map(e => Json.obj("error" -> e)))) | ||
| } | ||
| } | ||
|
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| protected def validateDataSourceGetErrors(dataSource: UsableDataSource): Seq[String] = { | ||
| def check(expression: Boolean, msg: String): Option[String] = if (!expression) Some(msg) else None | ||
|
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| // Check that when mags are sorted by max dimension, all dimensions are sorted. | ||
| // This means each dimension increases monotonically. | ||
| val magsSorted = dataSource.dataLayers.map(_.resolutions.sortBy(_.maxDim)) | ||
| val magsXIsSorted = magsSorted.map(_.map(_.x)) == magsSorted.map(_.map(_.x).sorted) | ||
| val magsYIsSorted = magsSorted.map(_.map(_.y)) == magsSorted.map(_.map(_.y).sorted) | ||
| val magsZIsSorted = magsSorted.map(_.map(_.z)) == magsSorted.map(_.map(_.z).sorted) | ||
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| val errors = List( | ||
| check(dataSource.scale.factor.isStrictlyPositive, "Voxel size (scale) is negative in at least one dimension."), | ||
| check(magsXIsSorted && magsYIsSorted && magsZIsSorted, "Mags do not monotonically increase in all dimensions."), | ||
| check(magsSorted.forall(magsOfLayer => magsOfLayer.length == magsOfLayer.distinct.length), | ||
| "There are duplicate mags in a layer."), | ||
| check(dataSource.dataLayers.nonEmpty, "No layers."), | ||
| check(dataSource.dataLayers.forall(!_.boundingBox.isEmpty), "Empty bounding box in a layer."), | ||
| check( | ||
| dataSource.segmentationLayers.forall { layer => | ||
| ElementClass.segmentationElementClasses.contains(layer.elementClass) | ||
| }, | ||
| s"Invalid element class for a segmentation layer." | ||
| ), | ||
| check( | ||
| dataSource.segmentationLayers.forall { layer => | ||
| ElementClass.largestSegmentIdIsInRange(layer.largestSegmentId, layer.elementClass) | ||
| }, | ||
| "Largest segment id exceeds range (must be nonnegative, within element class range, and < 2^53)." | ||
| ), | ||
| check( | ||
| dataSource.dataLayers.map(_.name).distinct.length == dataSource.dataLayers.length, | ||
| "Layer names must be unique. At least two layers have the same name." | ||
| ), | ||
| check( | ||
| dataSource.dataLayers.map(_.name).forall(!_.contains("/")), | ||
| "Layer names must not contain forward slash." | ||
| ), | ||
| check( | ||
| dataSource.dataLayers.map(_.name).forall(!_.startsWith(".")), | ||
| "Layer names must not start with dot." | ||
| ) | ||
| ).flatten | ||
|
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| errors | ||
| } | ||
|
|
||
| } |
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Why did you add this change? Is there a possible scenario where the datasource cannot be retrieved from the cache but exists on disk / in dir?
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Yes, the cache only handles usable datasources. If the existing datasource is unusable due to an error, the cache will just return a Failure. However, in this context, we want to re-read the one from disk in this case, re-validate it, and sent it to webknossos if it is now usable. Only after that, it will also be available through the cache. So this part is actually the bugfix for the reload button in the dashboard (for non-virtual datasets). Does that make sense?