@vitessce/constants-internal 3.3.5 → 3.3.7

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (19) hide show
  1. package/dist/index.js +76 -7
  2. package/dist-tsc/constant-relationships.d.ts +5 -0
  3. package/dist-tsc/constant-relationships.d.ts.map +1 -1
  4. package/dist-tsc/constant-relationships.js +48 -0
  5. package/dist-tsc/constants.d.ts +19 -0
  6. package/dist-tsc/constants.d.ts.map +1 -1
  7. package/dist-tsc/constants.js +21 -0
  8. package/dist-tsc/coordination.d.ts.map +1 -1
  9. package/dist-tsc/coordination.js +2 -0
  10. package/dist-tsc/index.d.ts +1 -1
  11. package/dist-tsc/index.d.ts.map +1 -1
  12. package/dist-tsc/index.js +1 -1
  13. package/dist-tsc/version.json +3 -3
  14. package/package.json +1 -1
  15. package/src/constant-relationships.ts +49 -0
  16. package/src/constants.ts +21 -0
  17. package/src/coordination.ts +2 -0
  18. package/src/index.ts +5 -1
  19. package/src/version.json +3 -3
package/dist/index.js CHANGED
@@ -27,11 +27,14 @@ const DataType = {
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  GENOMIC_PROFILES: "genomic-profiles",
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  OBS_SPOTS: "obsSpots",
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  OBS_POINTS: "obsPoints",
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- OBS_LOCATIONS: "obsLocations"
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+ OBS_LOCATIONS: "obsLocations",
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+ SAMPLE_SETS: "sampleSets",
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+ SAMPLE_EDGES: "sampleEdges"
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  };
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  const FileType = {
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  // Joint file types
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  ANNDATA_ZARR: "anndata.zarr",
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+ ANNDATA_ZARR_ZIP: "anndata.zarr.zip",
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  SPATIALDATA_ZARR: "spatialdata.zarr",
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  // Atomic file types
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  OBS_EMBEDDING_CSV: "obsEmbedding.csv",
@@ -44,6 +47,7 @@ const FileType = {
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  OBS_SEGMENTATIONS_JSON: "obsSegmentations.json",
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  OBS_SETS_CSV: "obsSets.csv",
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  OBS_SETS_JSON: "obsSets.json",
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+ SAMPLE_SETS_CSV: "sampleSets.csv",
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  // OME-Zarr
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  IMAGE_OME_ZARR: "image.ome-zarr",
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  OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
@@ -58,6 +62,19 @@ const FileType = {
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  OBS_SEGMENTATIONS_ANNDATA_ZARR: "obsSegmentations.anndata.zarr",
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  OBS_LABELS_ANNDATA_ZARR: "obsLabels.anndata.zarr",
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  FEATURE_LABELS_ANNDATA_ZARR: "featureLabels.anndata.zarr",
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+ SAMPLE_EDGES_ANNDATA_ZARR: "sampleEdges.anndata.zarr",
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+ // AnnData - zipped
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+ OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: "obsFeatureMatrix.anndata.zarr.zip",
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+ OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: "obsFeatureColumns.anndata.zarr.zip",
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+ OBS_SETS_ANNDATA_ZARR_ZIP: "obsSets.anndata.zarr.zip",
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+ OBS_EMBEDDING_ANNDATA_ZARR_ZIP: "obsEmbedding.anndata.zarr.zip",
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+ OBS_SPOTS_ANNDATA_ZARR_ZIP: "obsSpots.anndata.zarr.zip",
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+ OBS_POINTS_ANNDATA_ZARR_ZIP: "obsPoints.anndata.zarr.zip",
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+ OBS_LOCATIONS_ANNDATA_ZARR_ZIP: "obsLocations.anndata.zarr.zip",
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+ OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP: "obsSegmentations.anndata.zarr.zip",
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+ OBS_LABELS_ANNDATA_ZARR_ZIP: "obsLabels.anndata.zarr.zip",
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+ FEATURE_LABELS_ANNDATA_ZARR_ZIP: "featureLabels.anndata.zarr.zip",
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+ SAMPLE_EDGES_ANNDATA_ZARR_ZIP: "sampleEdges.anndata.zarr.zip",
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  // SpatialData
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  IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
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  LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -65,6 +82,7 @@ const FileType = {
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  OBS_FEATURE_MATRIX_SPATIALDATA_ZARR: "obsFeatureMatrix.spatialdata.zarr",
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  OBS_SETS_SPATIALDATA_ZARR: "obsSets.spatialdata.zarr",
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  OBS_SPOTS_SPATIALDATA_ZARR: "obsSpots.spatialdata.zarr",
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+ FEATURE_LABELS_SPATIALDATA_ZARR: "featureLabels.spatialdata.zarr",
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  // TODO:
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  // OBS_POINTS_SPATIALDATA_ZARR: 'obsPoints.spatialdata.zarr',
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  // OBS_LOCATIONS_SPATIALDATA_ZARR: 'obsLocations.spatialdata.zarr',
@@ -226,7 +244,10 @@ const CoordinationType = {
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  LEGEND_VISIBLE: "legendVisible",
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  SPATIAL_CHANNEL_LABELS_VISIBLE: "spatialChannelLabelsVisible",
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  SPATIAL_CHANNEL_LABELS_ORIENTATION: "spatialChannelLabelsOrientation",
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- SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize"
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+ SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize",
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+ // Multi-sample / comparative
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+ SAMPLE_TYPE: "sampleType",
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+ SAMPLE_SET_SELECTION: "sampleSetSelection"
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  };
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  const STATUS = {
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  LOADING: "loading",
@@ -241,6 +262,7 @@ const FILE_TYPE_DATA_TYPE_MAPPING = {
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  [FileType.OBS_LOCATIONS_CSV]: DataType.OBS_LOCATIONS,
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  [FileType.OBS_LABELS_CSV]: DataType.OBS_LABELS,
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  [FileType.FEATURE_LABELS_CSV]: DataType.FEATURE_LABELS,
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+ [FileType.SAMPLE_SETS_CSV]: DataType.SAMPLE_SETS,
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  [FileType.OBS_FEATURE_MATRIX_CSV]: DataType.OBS_FEATURE_MATRIX,
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  [FileType.OBS_SEGMENTATIONS_JSON]: DataType.OBS_SEGMENTATIONS,
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  [FileType.OBS_SETS_CSV]: DataType.OBS_SETS,
@@ -257,6 +279,7 @@ const FILE_TYPE_DATA_TYPE_MAPPING = {
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  [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: DataType.OBS_SEGMENTATIONS,
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  [FileType.OBS_LABELS_ANNDATA_ZARR]: DataType.OBS_LABELS,
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  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
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+ [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
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  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
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  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
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  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -274,6 +297,7 @@ const FILE_TYPE_DATA_TYPE_MAPPING = {
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  [FileType.OBS_SPOTS_SPATIALDATA_ZARR]: DataType.OBS_SPOTS,
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  [FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
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  [FileType.OBS_SETS_SPATIALDATA_ZARR]: DataType.OBS_SETS,
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+ [FileType.FEATURE_LABELS_SPATIALDATA_ZARR]: DataType.FEATURE_LABELS,
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  // For new file types to support old file types
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  [FileType.OBS_EMBEDDING_CELLS_JSON]: DataType.OBS_EMBEDDING,
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  [FileType.OBS_LOCATIONS_CELLS_JSON]: DataType.OBS_LOCATIONS,
@@ -328,7 +352,49 @@ const DATA_TYPE_COORDINATION_VALUE_USAGE = {
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  [DataType.IMAGE]: [
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  CoordinationType.FILE_UID
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  ],
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- [DataType.NEIGHBORHOODS]: []
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+ [DataType.NEIGHBORHOODS]: [],
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+ [DataType.SAMPLE_SETS]: [
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+ CoordinationType.SAMPLE_TYPE
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+ ],
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+ [DataType.SAMPLE_EDGES]: [
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+ CoordinationType.OBS_TYPE,
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+ CoordinationType.SAMPLE_TYPE
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+ ]
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+ };
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+ const ALT_ZARR_STORE_TYPES = {
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+ [FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.OBS_SETS_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_SETS_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.OBS_EMBEDDING_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_EMBEDDING_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.OBS_SPOTS_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_SPOTS_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.OBS_POINTS_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_POINTS_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.OBS_LOCATIONS_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_LOCATIONS_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.OBS_LABELS_ANNDATA_ZARR]: {
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+ zip: FileType.OBS_LABELS_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.FEATURE_LABELS_ANNDATA_ZARR]: {
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+ zip: FileType.FEATURE_LABELS_ANNDATA_ZARR_ZIP
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+ },
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+ [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: {
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+ zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP
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+ }
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  };
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  const AUTO_INDEPENDENT_COORDINATION_TYPES = [
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  CoordinationType.HEATMAP_ZOOM_X,
@@ -591,7 +657,9 @@ const COMPONENT_COORDINATION_TYPES = {
591
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  CoordinationType.OBS_SET_SELECTION,
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  CoordinationType.OBS_SET_HIGHLIGHT,
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  CoordinationType.OBS_SET_COLOR,
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- CoordinationType.ADDITIONAL_OBS_SETS
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+ CoordinationType.ADDITIONAL_OBS_SETS,
661
+ CoordinationType.SAMPLE_TYPE,
662
+ CoordinationType.SAMPLE_SET_SELECTION
595
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  ],
596
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  [ViewType.FEATURE_VALUE_HISTOGRAM]: [
597
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  CoordinationType.DATASET,
@@ -716,10 +784,10 @@ const COMPONENT_COORDINATION_TYPES = {
716
784
  ]
717
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  };
718
786
  const note = "This file is autogenerated by .changeset/post-changelog.mjs.";
719
- const version = "3.3.5";
720
- const date = "2024-02-21";
787
+ const version = "3.3.7";
788
+ const date = "2024-03-04";
721
789
  const branch = "changeset-release/main";
722
- const hash = "effc2322";
790
+ const hash = "c82b4395";
723
791
  const version$1 = {
724
792
  note,
725
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  version,
@@ -728,6 +796,7 @@ const version$1 = {
728
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  hash
729
797
  };
730
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  export {
799
+ ALT_ZARR_STORE_TYPES,
731
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  AUTO_INDEPENDENT_COORDINATION_TYPES,
732
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  COMPONENT_COORDINATION_TYPES,
733
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  CoordinationType,
package/dist-tsc/constant-relationships.d.ts CHANGED
@@ -14,4 +14,9 @@ export declare const FILE_TYPE_DATA_TYPE_MAPPING: {
14
14
  export declare const DATA_TYPE_COORDINATION_VALUE_USAGE: {
15
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  [x: string]: string[];
16
16
  };
17
+ export declare const ALT_ZARR_STORE_TYPES: {
18
+ [x: string]: {
19
+ zip: string;
20
+ };
21
+ };
17
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  //# sourceMappingURL=constant-relationships.d.ts.map
package/dist-tsc/constant-relationships.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"constant-relationships.d.ts","sourceRoot":"","sources":["../src/constant-relationships.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,eAAO,MAAM,2BAA2B;;CA2DvC,CAAC;AAEF;;;;GAIG;AACH,eAAO,MAAM,kCAAkC;;CAsC9C,CAAC"}
1
+ {"version":3,"file":"constant-relationships.d.ts","sourceRoot":"","sources":["../src/constant-relationships.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,eAAO,MAAM,2BAA2B;;CA8DvC,CAAC;AAEF;;;;GAIG;AACH,eAAO,MAAM,kCAAkC;;CA6C9C,CAAC;AAKF,eAAO,MAAM,oBAAoB;;;;CAkChC,CAAC"}
package/dist-tsc/constant-relationships.js CHANGED
@@ -12,6 +12,7 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
12
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  [FileType.OBS_LOCATIONS_CSV]: DataType.OBS_LOCATIONS,
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  [FileType.OBS_LABELS_CSV]: DataType.OBS_LABELS,
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  [FileType.FEATURE_LABELS_CSV]: DataType.FEATURE_LABELS,
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+ [FileType.SAMPLE_SETS_CSV]: DataType.SAMPLE_SETS,
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  [FileType.OBS_FEATURE_MATRIX_CSV]: DataType.OBS_FEATURE_MATRIX,
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  [FileType.OBS_SEGMENTATIONS_JSON]: DataType.OBS_SEGMENTATIONS,
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  [FileType.OBS_SETS_CSV]: DataType.OBS_SETS,
@@ -28,6 +29,7 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
28
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  [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: DataType.OBS_SEGMENTATIONS,
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  [FileType.OBS_LABELS_ANNDATA_ZARR]: DataType.OBS_LABELS,
30
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  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
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+ [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
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  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
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  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
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  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -45,6 +47,7 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
45
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  [FileType.OBS_SPOTS_SPATIALDATA_ZARR]: DataType.OBS_SPOTS,
46
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  [FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
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  [FileType.OBS_SETS_SPATIALDATA_ZARR]: DataType.OBS_SETS,
50
+ [FileType.FEATURE_LABELS_SPATIALDATA_ZARR]: DataType.FEATURE_LABELS,
48
51
  // For new file types to support old file types
49
52
  [FileType.OBS_EMBEDDING_CELLS_JSON]: DataType.OBS_EMBEDDING,
50
53
  [FileType.OBS_LOCATIONS_CELLS_JSON]: DataType.OBS_LOCATIONS,
@@ -105,4 +108,49 @@ export const DATA_TYPE_COORDINATION_VALUE_USAGE = {
105
108
  CoordinationType.FILE_UID,
106
109
  ],
107
110
  [DataType.NEIGHBORHOODS]: [],
111
+ [DataType.SAMPLE_SETS]: [
112
+ CoordinationType.SAMPLE_TYPE,
113
+ ],
114
+ [DataType.SAMPLE_EDGES]: [
115
+ CoordinationType.OBS_TYPE,
116
+ CoordinationType.SAMPLE_TYPE,
117
+ ],
118
+ };
119
+ // For Zarr-based file types, we keep a mapping to file types
120
+ // corresponding to alternative store implementations,
121
+ // to avoid having to rely on file extensions.
122
+ export const ALT_ZARR_STORE_TYPES = {
123
+ [FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: {
124
+ zip: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP,
125
+ },
126
+ [FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR]: {
127
+ zip: FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP,
128
+ },
129
+ [FileType.OBS_SETS_ANNDATA_ZARR]: {
130
+ zip: FileType.OBS_SETS_ANNDATA_ZARR_ZIP,
131
+ },
132
+ [FileType.OBS_EMBEDDING_ANNDATA_ZARR]: {
133
+ zip: FileType.OBS_EMBEDDING_ANNDATA_ZARR_ZIP,
134
+ },
135
+ [FileType.OBS_SPOTS_ANNDATA_ZARR]: {
136
+ zip: FileType.OBS_SPOTS_ANNDATA_ZARR_ZIP,
137
+ },
138
+ [FileType.OBS_POINTS_ANNDATA_ZARR]: {
139
+ zip: FileType.OBS_POINTS_ANNDATA_ZARR_ZIP,
140
+ },
141
+ [FileType.OBS_LOCATIONS_ANNDATA_ZARR]: {
142
+ zip: FileType.OBS_LOCATIONS_ANNDATA_ZARR_ZIP,
143
+ },
144
+ [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: {
145
+ zip: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP,
146
+ },
147
+ [FileType.OBS_LABELS_ANNDATA_ZARR]: {
148
+ zip: FileType.OBS_LABELS_ANNDATA_ZARR_ZIP,
149
+ },
150
+ [FileType.FEATURE_LABELS_ANNDATA_ZARR]: {
151
+ zip: FileType.FEATURE_LABELS_ANNDATA_ZARR_ZIP,
152
+ },
153
+ [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: {
154
+ zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
155
+ },
108
156
  };
package/dist-tsc/constants.d.ts CHANGED
@@ -33,9 +33,12 @@ export declare const DataType: {
33
33
  OBS_SPOTS: string;
34
34
  OBS_POINTS: string;
35
35
  OBS_LOCATIONS: string;
36
+ SAMPLE_SETS: string;
37
+ SAMPLE_EDGES: string;
36
38
  };
37
39
  export declare const FileType: {
38
40
  ANNDATA_ZARR: string;
41
+ ANNDATA_ZARR_ZIP: string;
39
42
  SPATIALDATA_ZARR: string;
40
43
  OBS_EMBEDDING_CSV: string;
41
44
  OBS_SPOTS_CSV: string;
@@ -47,6 +50,7 @@ export declare const FileType: {
47
50
  OBS_SEGMENTATIONS_JSON: string;
48
51
  OBS_SETS_CSV: string;
49
52
  OBS_SETS_JSON: string;
53
+ SAMPLE_SETS_CSV: string;
50
54
  IMAGE_OME_ZARR: string;
51
55
  OBS_SEGMENTATIONS_OME_ZARR: string;
52
56
  OBS_FEATURE_MATRIX_ANNDATA_ZARR: string;
@@ -59,12 +63,25 @@ export declare const FileType: {
59
63
  OBS_SEGMENTATIONS_ANNDATA_ZARR: string;
60
64
  OBS_LABELS_ANNDATA_ZARR: string;
61
65
  FEATURE_LABELS_ANNDATA_ZARR: string;
66
+ SAMPLE_EDGES_ANNDATA_ZARR: string;
67
+ OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: string;
68
+ OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: string;
69
+ OBS_SETS_ANNDATA_ZARR_ZIP: string;
70
+ OBS_EMBEDDING_ANNDATA_ZARR_ZIP: string;
71
+ OBS_SPOTS_ANNDATA_ZARR_ZIP: string;
72
+ OBS_POINTS_ANNDATA_ZARR_ZIP: string;
73
+ OBS_LOCATIONS_ANNDATA_ZARR_ZIP: string;
74
+ OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP: string;
75
+ OBS_LABELS_ANNDATA_ZARR_ZIP: string;
76
+ FEATURE_LABELS_ANNDATA_ZARR_ZIP: string;
77
+ SAMPLE_EDGES_ANNDATA_ZARR_ZIP: string;
62
78
  IMAGE_SPATIALDATA_ZARR: string;
63
79
  LABELS_SPATIALDATA_ZARR: string;
64
80
  SHAPES_SPATIALDATA_ZARR: string;
65
81
  OBS_FEATURE_MATRIX_SPATIALDATA_ZARR: string;
66
82
  OBS_SETS_SPATIALDATA_ZARR: string;
67
83
  OBS_SPOTS_SPATIALDATA_ZARR: string;
84
+ FEATURE_LABELS_SPATIALDATA_ZARR: string;
68
85
  OBS_FEATURE_MATRIX_MUDATA_ZARR: string;
69
86
  OBS_SETS_MUDATA_ZARR: string;
70
87
  OBS_EMBEDDING_MUDATA_ZARR: string;
@@ -206,6 +223,8 @@ export declare const CoordinationType: {
206
223
  SPATIAL_CHANNEL_LABELS_VISIBLE: string;
207
224
  SPATIAL_CHANNEL_LABELS_ORIENTATION: string;
208
225
  SPATIAL_CHANNEL_LABEL_SIZE: string;
226
+ SAMPLE_TYPE: string;
227
+ SAMPLE_SET_SELECTION: string;
209
228
  };
210
229
  export declare const STATUS: {
211
230
  LOADING: string;
package/dist-tsc/constants.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;CAgBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;CAapB,CAAC;AAGF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAsFpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA0G5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC"}
1
+ {"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;CAgBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;CAepB,CAAC;AAGF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAsGpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA6G5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC"}
package/dist-tsc/constants.js CHANGED
@@ -33,10 +33,13 @@ export const DataType = {
33
33
  OBS_SPOTS: 'obsSpots',
34
34
  OBS_POINTS: 'obsPoints',
35
35
  OBS_LOCATIONS: 'obsLocations',
36
+ SAMPLE_SETS: 'sampleSets',
37
+ SAMPLE_EDGES: 'sampleEdges',
36
38
  };
37
39
  export const FileType = {
38
40
  // Joint file types
39
41
  ANNDATA_ZARR: 'anndata.zarr',
42
+ ANNDATA_ZARR_ZIP: 'anndata.zarr.zip',
40
43
  SPATIALDATA_ZARR: 'spatialdata.zarr',
41
44
  // Atomic file types
42
45
  OBS_EMBEDDING_CSV: 'obsEmbedding.csv',
@@ -49,6 +52,7 @@ export const FileType = {
49
52
  OBS_SEGMENTATIONS_JSON: 'obsSegmentations.json',
50
53
  OBS_SETS_CSV: 'obsSets.csv',
51
54
  OBS_SETS_JSON: 'obsSets.json',
55
+ SAMPLE_SETS_CSV: 'sampleSets.csv',
52
56
  // OME-Zarr
53
57
  IMAGE_OME_ZARR: 'image.ome-zarr',
54
58
  OBS_SEGMENTATIONS_OME_ZARR: 'obsSegmentations.ome-zarr',
@@ -63,6 +67,19 @@ export const FileType = {
63
67
  OBS_SEGMENTATIONS_ANNDATA_ZARR: 'obsSegmentations.anndata.zarr',
64
68
  OBS_LABELS_ANNDATA_ZARR: 'obsLabels.anndata.zarr',
65
69
  FEATURE_LABELS_ANNDATA_ZARR: 'featureLabels.anndata.zarr',
70
+ SAMPLE_EDGES_ANNDATA_ZARR: 'sampleEdges.anndata.zarr',
71
+ // AnnData - zipped
72
+ OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: 'obsFeatureMatrix.anndata.zarr.zip',
73
+ OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: 'obsFeatureColumns.anndata.zarr.zip',
74
+ OBS_SETS_ANNDATA_ZARR_ZIP: 'obsSets.anndata.zarr.zip',
75
+ OBS_EMBEDDING_ANNDATA_ZARR_ZIP: 'obsEmbedding.anndata.zarr.zip',
76
+ OBS_SPOTS_ANNDATA_ZARR_ZIP: 'obsSpots.anndata.zarr.zip',
77
+ OBS_POINTS_ANNDATA_ZARR_ZIP: 'obsPoints.anndata.zarr.zip',
78
+ OBS_LOCATIONS_ANNDATA_ZARR_ZIP: 'obsLocations.anndata.zarr.zip',
79
+ OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP: 'obsSegmentations.anndata.zarr.zip',
80
+ OBS_LABELS_ANNDATA_ZARR_ZIP: 'obsLabels.anndata.zarr.zip',
81
+ FEATURE_LABELS_ANNDATA_ZARR_ZIP: 'featureLabels.anndata.zarr.zip',
82
+ SAMPLE_EDGES_ANNDATA_ZARR_ZIP: 'sampleEdges.anndata.zarr.zip',
66
83
  // SpatialData
67
84
  IMAGE_SPATIALDATA_ZARR: 'image.spatialdata.zarr',
68
85
  LABELS_SPATIALDATA_ZARR: 'labels.spatialdata.zarr',
@@ -70,6 +87,7 @@ export const FileType = {
70
87
  OBS_FEATURE_MATRIX_SPATIALDATA_ZARR: 'obsFeatureMatrix.spatialdata.zarr',
71
88
  OBS_SETS_SPATIALDATA_ZARR: 'obsSets.spatialdata.zarr',
72
89
  OBS_SPOTS_SPATIALDATA_ZARR: 'obsSpots.spatialdata.zarr',
90
+ FEATURE_LABELS_SPATIALDATA_ZARR: 'featureLabels.spatialdata.zarr',
73
91
  // TODO:
74
92
  // OBS_POINTS_SPATIALDATA_ZARR: 'obsPoints.spatialdata.zarr',
75
93
  // OBS_LOCATIONS_SPATIALDATA_ZARR: 'obsLocations.spatialdata.zarr',
@@ -231,6 +249,9 @@ export const CoordinationType = {
231
249
  SPATIAL_CHANNEL_LABELS_VISIBLE: 'spatialChannelLabelsVisible',
232
250
  SPATIAL_CHANNEL_LABELS_ORIENTATION: 'spatialChannelLabelsOrientation',
233
251
  SPATIAL_CHANNEL_LABEL_SIZE: 'spatialChannelLabelSize',
252
+ // Multi-sample / comparative
253
+ SAMPLE_TYPE: 'sampleType',
254
+ SAMPLE_SET_SELECTION: 'sampleSetSelection',
234
255
  };
235
256
  export const STATUS = {
236
257
  LOADING: 'loading',
package/dist-tsc/coordination.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.ts"],"names":[],"mappings":"AASA,eAAO,MAAM,mCAAmC,UAc/C,CAAC;AAEF;;;;;;;KAOK;AACL,eAAO,MAAM,4BAA4B;;;CAiXxC,CAAC"}
1
+ {"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.ts"],"names":[],"mappings":"AASA,eAAO,MAAM,mCAAmC,UAc/C,CAAC;AAEF;;;;;;;KAOK;AACL,eAAO,MAAM,4BAA4B;;;CAmXxC,CAAC"}
package/dist-tsc/coordination.js CHANGED
@@ -276,6 +276,8 @@ export const COMPONENT_COORDINATION_TYPES = {
276
276
  CoordinationType.OBS_SET_HIGHLIGHT,
277
277
  CoordinationType.OBS_SET_COLOR,
278
278
  CoordinationType.ADDITIONAL_OBS_SETS,
279
+ CoordinationType.SAMPLE_TYPE,
280
+ CoordinationType.SAMPLE_SET_SELECTION,
279
281
  ],
280
282
  [ViewType.FEATURE_VALUE_HISTOGRAM]: [
281
283
  CoordinationType.DATASET,
package/dist-tsc/index.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  export { ViewType, DataType, FileType, CoordinationType, STATUS, } from './constants.js';
2
- export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE } from './constant-relationships.js';
2
+ export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE, ALT_ZARR_STORE_TYPES, } from './constant-relationships.js';
3
3
  export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
4
4
  export { default as META_VERSION } from './version.json';
5
5
  //# sourceMappingURL=index.d.ts.map
package/dist-tsc/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,GACvD,MAAM,gBAAgB,CAAC;AACxB,OAAO,EAAE,2BAA2B,EAAE,kCAAkC,EAAE,MAAM,6BAA6B,CAAC;AAC9G,OAAO,EAAE,mCAAmC,EAAE,4BAA4B,EAAE,MAAM,mBAAmB,CAAC;AACtG,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,GACvD,MAAM,gBAAgB,CAAC;AACxB,OAAO,EACL,2BAA2B,EAC3B,kCAAkC,EAClC,oBAAoB,GACrB,MAAM,6BAA6B,CAAC;AACrC,OAAO,EAAE,mCAAmC,EAAE,4BAA4B,EAAE,MAAM,mBAAmB,CAAC;AACtG,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAC"}
package/dist-tsc/index.js CHANGED
@@ -1,4 +1,4 @@
1
1
  export { ViewType, DataType, FileType, CoordinationType, STATUS, } from './constants.js';
2
- export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE } from './constant-relationships.js';
2
+ export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE, ALT_ZARR_STORE_TYPES, } from './constant-relationships.js';
3
3
  export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
4
4
  export { default as META_VERSION } from './version.json';
package/dist-tsc/version.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
3
- "version": "3.3.5",
4
- "date": "2024-02-21",
3
+ "version": "3.3.7",
4
+ "date": "2024-03-04",
5
5
  "branch": "changeset-release/main",
6
- "hash": "effc2322"
6
+ "hash": "c82b4395"
7
7
  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@vitessce/constants-internal",
3
- "version": "3.3.5",
3
+ "version": "3.3.7",
4
4
  "author": "Gehlenborg Lab",
5
5
  "homepage": "http://vitessce.io",
6
6
  "repository": {
package/src/constant-relationships.ts CHANGED
@@ -13,6 +13,7 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
13
13
  [FileType.OBS_LOCATIONS_CSV]: DataType.OBS_LOCATIONS,
14
14
  [FileType.OBS_LABELS_CSV]: DataType.OBS_LABELS,
15
15
  [FileType.FEATURE_LABELS_CSV]: DataType.FEATURE_LABELS,
16
+ [FileType.SAMPLE_SETS_CSV]: DataType.SAMPLE_SETS,
16
17
  [FileType.OBS_FEATURE_MATRIX_CSV]: DataType.OBS_FEATURE_MATRIX,
17
18
  [FileType.OBS_SEGMENTATIONS_JSON]: DataType.OBS_SEGMENTATIONS,
18
19
  [FileType.OBS_SETS_CSV]: DataType.OBS_SETS,
@@ -29,6 +30,7 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
29
30
  [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: DataType.OBS_SEGMENTATIONS,
30
31
  [FileType.OBS_LABELS_ANNDATA_ZARR]: DataType.OBS_LABELS,
31
32
  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
33
+ [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
32
34
  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
33
35
  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
34
36
  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -47,6 +49,7 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
47
49
  [FileType.OBS_SPOTS_SPATIALDATA_ZARR]: DataType.OBS_SPOTS,
48
50
  [FileType.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
49
51
  [FileType.OBS_SETS_SPATIALDATA_ZARR]: DataType.OBS_SETS,
52
+ [FileType.FEATURE_LABELS_SPATIALDATA_ZARR]: DataType.FEATURE_LABELS,
50
53
 
51
54
  // For new file types to support old file types
52
55
  [FileType.OBS_EMBEDDING_CELLS_JSON]: DataType.OBS_EMBEDDING,
@@ -109,4 +112,50 @@ export const DATA_TYPE_COORDINATION_VALUE_USAGE = {
109
112
  CoordinationType.FILE_UID,
110
113
  ],
111
114
  [DataType.NEIGHBORHOODS]: [],
115
+ [DataType.SAMPLE_SETS]: [
116
+ CoordinationType.SAMPLE_TYPE,
117
+ ],
118
+ [DataType.SAMPLE_EDGES]: [
119
+ CoordinationType.OBS_TYPE,
120
+ CoordinationType.SAMPLE_TYPE,
121
+ ],
122
+ };
123
+
124
+ // For Zarr-based file types, we keep a mapping to file types
125
+ // corresponding to alternative store implementations,
126
+ // to avoid having to rely on file extensions.
127
+ export const ALT_ZARR_STORE_TYPES = {
128
+ [FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: {
129
+ zip: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP,
130
+ },
131
+ [FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR]: {
132
+ zip: FileType.OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP,
133
+ },
134
+ [FileType.OBS_SETS_ANNDATA_ZARR]: {
135
+ zip: FileType.OBS_SETS_ANNDATA_ZARR_ZIP,
136
+ },
137
+ [FileType.OBS_EMBEDDING_ANNDATA_ZARR]: {
138
+ zip: FileType.OBS_EMBEDDING_ANNDATA_ZARR_ZIP,
139
+ },
140
+ [FileType.OBS_SPOTS_ANNDATA_ZARR]: {
141
+ zip: FileType.OBS_SPOTS_ANNDATA_ZARR_ZIP,
142
+ },
143
+ [FileType.OBS_POINTS_ANNDATA_ZARR]: {
144
+ zip: FileType.OBS_POINTS_ANNDATA_ZARR_ZIP,
145
+ },
146
+ [FileType.OBS_LOCATIONS_ANNDATA_ZARR]: {
147
+ zip: FileType.OBS_LOCATIONS_ANNDATA_ZARR_ZIP,
148
+ },
149
+ [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: {
150
+ zip: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP,
151
+ },
152
+ [FileType.OBS_LABELS_ANNDATA_ZARR]: {
153
+ zip: FileType.OBS_LABELS_ANNDATA_ZARR_ZIP,
154
+ },
155
+ [FileType.FEATURE_LABELS_ANNDATA_ZARR]: {
156
+ zip: FileType.FEATURE_LABELS_ANNDATA_ZARR_ZIP,
157
+ },
158
+ [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: {
159
+ zip: FileType.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
160
+ },
112
161
  };
package/src/constants.ts CHANGED
@@ -34,12 +34,15 @@ export const DataType = {
34
34
  OBS_SPOTS: 'obsSpots',
35
35
  OBS_POINTS: 'obsPoints',
36
36
  OBS_LOCATIONS: 'obsLocations',
37
+ SAMPLE_SETS: 'sampleSets',
38
+ SAMPLE_EDGES: 'sampleEdges',
37
39
  };
38
40
 
39
41
 
40
42
  export const FileType = {
41
43
  // Joint file types
42
44
  ANNDATA_ZARR: 'anndata.zarr',
45
+ ANNDATA_ZARR_ZIP: 'anndata.zarr.zip',
43
46
  SPATIALDATA_ZARR: 'spatialdata.zarr',
44
47
  // Atomic file types
45
48
  OBS_EMBEDDING_CSV: 'obsEmbedding.csv',
@@ -52,6 +55,7 @@ export const FileType = {
52
55
  OBS_SEGMENTATIONS_JSON: 'obsSegmentations.json',
53
56
  OBS_SETS_CSV: 'obsSets.csv',
54
57
  OBS_SETS_JSON: 'obsSets.json',
58
+ SAMPLE_SETS_CSV: 'sampleSets.csv',
55
59
  // OME-Zarr
56
60
  IMAGE_OME_ZARR: 'image.ome-zarr',
57
61
  OBS_SEGMENTATIONS_OME_ZARR: 'obsSegmentations.ome-zarr',
@@ -66,6 +70,19 @@ export const FileType = {
66
70
  OBS_SEGMENTATIONS_ANNDATA_ZARR: 'obsSegmentations.anndata.zarr',
67
71
  OBS_LABELS_ANNDATA_ZARR: 'obsLabels.anndata.zarr',
68
72
  FEATURE_LABELS_ANNDATA_ZARR: 'featureLabels.anndata.zarr',
73
+ SAMPLE_EDGES_ANNDATA_ZARR: 'sampleEdges.anndata.zarr',
74
+ // AnnData - zipped
75
+ OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: 'obsFeatureMatrix.anndata.zarr.zip',
76
+ OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: 'obsFeatureColumns.anndata.zarr.zip',
77
+ OBS_SETS_ANNDATA_ZARR_ZIP: 'obsSets.anndata.zarr.zip',
78
+ OBS_EMBEDDING_ANNDATA_ZARR_ZIP: 'obsEmbedding.anndata.zarr.zip',
79
+ OBS_SPOTS_ANNDATA_ZARR_ZIP: 'obsSpots.anndata.zarr.zip',
80
+ OBS_POINTS_ANNDATA_ZARR_ZIP: 'obsPoints.anndata.zarr.zip',
81
+ OBS_LOCATIONS_ANNDATA_ZARR_ZIP: 'obsLocations.anndata.zarr.zip',
82
+ OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP: 'obsSegmentations.anndata.zarr.zip',
83
+ OBS_LABELS_ANNDATA_ZARR_ZIP: 'obsLabels.anndata.zarr.zip',
84
+ FEATURE_LABELS_ANNDATA_ZARR_ZIP: 'featureLabels.anndata.zarr.zip',
85
+ SAMPLE_EDGES_ANNDATA_ZARR_ZIP: 'sampleEdges.anndata.zarr.zip',
69
86
  // SpatialData
70
87
  IMAGE_SPATIALDATA_ZARR: 'image.spatialdata.zarr',
71
88
  LABELS_SPATIALDATA_ZARR: 'labels.spatialdata.zarr',
@@ -73,6 +90,7 @@ export const FileType = {
73
90
  OBS_FEATURE_MATRIX_SPATIALDATA_ZARR: 'obsFeatureMatrix.spatialdata.zarr',
74
91
  OBS_SETS_SPATIALDATA_ZARR: 'obsSets.spatialdata.zarr',
75
92
  OBS_SPOTS_SPATIALDATA_ZARR: 'obsSpots.spatialdata.zarr',
93
+ FEATURE_LABELS_SPATIALDATA_ZARR: 'featureLabels.spatialdata.zarr',
76
94
  // TODO:
77
95
  // OBS_POINTS_SPATIALDATA_ZARR: 'obsPoints.spatialdata.zarr',
78
96
  // OBS_LOCATIONS_SPATIALDATA_ZARR: 'obsLocations.spatialdata.zarr',
@@ -235,6 +253,9 @@ export const CoordinationType = {
235
253
  SPATIAL_CHANNEL_LABELS_VISIBLE: 'spatialChannelLabelsVisible',
236
254
  SPATIAL_CHANNEL_LABELS_ORIENTATION: 'spatialChannelLabelsOrientation',
237
255
  SPATIAL_CHANNEL_LABEL_SIZE: 'spatialChannelLabelSize',
256
+ // Multi-sample / comparative
257
+ SAMPLE_TYPE: 'sampleType',
258
+ SAMPLE_SET_SELECTION: 'sampleSetSelection',
238
259
  };
239
260
 
240
261
  export const STATUS = {
package/src/coordination.ts CHANGED
@@ -278,6 +278,8 @@ export const COMPONENT_COORDINATION_TYPES = {
278
278
  CoordinationType.OBS_SET_HIGHLIGHT,
279
279
  CoordinationType.OBS_SET_COLOR,
280
280
  CoordinationType.ADDITIONAL_OBS_SETS,
281
+ CoordinationType.SAMPLE_TYPE,
282
+ CoordinationType.SAMPLE_SET_SELECTION,
281
283
  ],
282
284
  [ViewType.FEATURE_VALUE_HISTOGRAM]: [
283
285
  CoordinationType.DATASET,
package/src/index.ts CHANGED
@@ -1,6 +1,10 @@
1
1
  export {
2
2
  ViewType, DataType, FileType, CoordinationType, STATUS,
3
3
  } from './constants.js';
4
- export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE } from './constant-relationships.js';
4
+ export {
5
+ FILE_TYPE_DATA_TYPE_MAPPING,
6
+ DATA_TYPE_COORDINATION_VALUE_USAGE,
7
+ ALT_ZARR_STORE_TYPES,
8
+ } from './constant-relationships.js';
5
9
  export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
6
10
  export { default as META_VERSION } from './version.json';
package/src/version.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
3
- "version": "3.3.5",
4
- "date": "2024-02-21",
3
+ "version": "3.3.7",
4
+ "date": "2024-03-04",
5
5
  "branch": "changeset-release/main",
6
- "hash": "effc2322"
6
+ "hash": "c82b4395"
7
7
  }