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Merge pull request #9 from NFDI4BIOIMAGE/dev
Tests and test data
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,4 +1,5 @@ | ||
| build | ||
| .omero | ||
| node_modules | ||
| aurelia-webpack/aurelia_example/static | ||
| backbone-grunt/backbone_example/static | ||
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| #! /usr/bin/env bash | ||
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| source /infra/utils | ||
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| set -e | ||
| set -u | ||
| set -x | ||
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| cd $TARGET | ||
| DIR=$(setup_dir) | ||
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| # TBD: unify on test or tests | ||
| # TBD: needs setup.py infra | ||
| # python setup.py test -t test* -i ${OMERO_DIST}/etc/ice.config -v | ||
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| # Import test data | ||
| ./.omeroci/test-data | ||
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| set +u | ||
| export DJANGO_SETTINGS_MODULE=omeroweb.settings | ||
| export OMERODIR=/opt/omero/web/OMERO.web | ||
| export ICE_CONFIG=${OMERO_DIST}/etc/ice.config | ||
| pytest -vv |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,40 @@ | ||
| #! /usr/bin/env bash | ||
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| export DATA_DIR=$TARGET"/test/data/MB266" | ||
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| export PATH=$PATH:${OMERO_DIST}/bin | ||
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| ## Set up group and user for testing | ||
| omero login root@omero -w omero | ||
| omero group add TestGroup --type=read-annotate | ||
| omero user add test_user Test User --group-name=TestGroup --userpassword=password | ||
| omero logout | ||
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| # Add test data | ||
| omero login test_user@omero -w password -g TestGroup | ||
| DATASET=$(omero obj new Dataset name=TestDataset) # dataset:1 | ||
| PROJECT=$(omero obj new Project name=TestProject) # project:1 | ||
| omero obj new ProjectDatasetLink parent=$PROJECT child=$DATASET | ||
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| DAPI_IMAGE=$(omero import --output=ids "$DATA_DIR/MB266-DAPI.tiff" -T Dataset:id:1) # image:1 | ||
| CELL_IMAGE=$(omero import --output=ids "$DATA_DIR/MB266-CELLS.png" -T Dataset:id:1) # image:2 | ||
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| CELL_FILE=$(omero upload "$DATA_DIR/cells.csv") | ||
| CELL_ATTACH=$(omero obj new FileAnnotation file=$CELL_FILE) # fileAnnotation:1 | ||
| omero obj new DatasetAnnotationLink parent=$DATASET child=$CELL_ATTACH | ||
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| EMBEDDING_FILE=$(omero upload "$DATA_DIR/embeddings.csv") | ||
| EMBEDDING_ATTACH=$(omero obj new FileAnnotation file=$EMBEDDING_FILE) # fileAnnotation:2 | ||
| omero obj new DatasetAnnotationLink parent=$DATASET child=$EMBEDDING_ATTACH | ||
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| TRANSCRIPT_FILE=$(omero upload "$DATA_DIR/transcripts.csv") | ||
| TRANSCRIPT_ATTACH=$(omero obj new FileAnnotation file=$TRANSCRIPT_FILE) # fileAnnotation:3 | ||
| omero obj new DatasetAnnotationLink parent=$DATASET child=$TRANSCRIPT_ATTACH | ||
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| EXPRESSION_FILE=$(omero upload "$DATA_DIR/feature_matrix.csv") | ||
| EXPRESSION_ATTACH=$(omero obj new FileAnnotation file=$EXPRESSION_FILE) # fileAnnotation:4 | ||
| omero obj new DatasetAnnotationLink parent=$DATASET child=$EXPRESSION_ATTACH | ||
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| CONFIG_FILE=$(omero upload "$DATA_DIR/VitessceConfig.json") | ||
| CONFIG_ATTACH=$(omero obj new FileAnnotation file=$CONFIG_FILE) # fileAnnotation:5 | ||
| omero obj new DatasetAnnotationLink parent=$DATASET child=$CONFIG_ATTACH |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,239 @@ | ||
| { | ||
| "version": "1.0.16", | ||
| "name": "TestDataset", | ||
| "description": "Generated with omero-vitessce", | ||
| "datasets": [ | ||
| { | ||
| "uid": "A", | ||
| "name": "", | ||
| "files": [ | ||
| { | ||
| "fileType": "obsSets.csv", | ||
| "url": "http://localhost:4080/webclient/annotation/1", | ||
| "options": { | ||
| "obsIndex": "cell_id", | ||
| "obsSets": [ | ||
| { | ||
| "name": "Clustering", | ||
| "column": "label" | ||
| } | ||
| ] | ||
| }, | ||
| "coordinationValues": { | ||
| "obsType": "cell" | ||
| } | ||
| }, | ||
| { | ||
| "fileType": "obsFeatureMatrix.csv", | ||
| "url": "http://localhost:4080/webclient/annotation/4" | ||
| }, | ||
| { | ||
| "fileType": "obsEmbedding.csv", | ||
| "url": "http://localhost:4080/webclient/annotation/2", | ||
| "options": { | ||
| "obsIndex": "cell_id", | ||
| "obsEmbedding": [ | ||
| "UMAP_1", | ||
| "UMAP_2" | ||
| ] | ||
| }, | ||
| "coordinationValues": { | ||
| "obsType": "cell", | ||
| "embeddingType": "cell" | ||
| } | ||
| }, | ||
| { | ||
| "fileType": "obsLocations.csv", | ||
| "url": "http://localhost:4080/webclient/annotation/3", | ||
| "options": { | ||
| "obsIndex": "id", | ||
| "obsLocations": [ | ||
| "x", | ||
| "y" | ||
| ] | ||
| }, | ||
| "coordinationValues": { | ||
| "obsType": "molecule" | ||
| } | ||
| }, | ||
| { | ||
| "fileType": "obsLabels.csv", | ||
| "url": "http://localhost:4080/webclient/annotation/3", | ||
| "options": { | ||
| "obsIndex": "id", | ||
| "obsLabels": "gene" | ||
| }, | ||
| "coordinationValues": { | ||
| "obsType": "molecule" | ||
| } | ||
| }, | ||
| { | ||
| "fileType": "raster.json", | ||
| "options": { | ||
| "schemaVersion": "0.0.2", | ||
| "usePhysicalSizeScaling": true, | ||
| "images": [ | ||
| { | ||
| "name": "Image 0", | ||
| "type": "ome-zarr", | ||
| "url": "http://localhost:4080/zarr/v0.4/image/1.zarr" | ||
| }, | ||
| { | ||
| "name": "Segmentation", | ||
| "type": "ome-zarr", | ||
| "url": "http://localhost:4080/zarr/v0.4/image/2.zarr", | ||
| "metadata": { | ||
| "isBitmask": true | ||
| } | ||
| } | ||
| ], | ||
| "renderLayers": [ | ||
| "Image 0", | ||
| "Segmentation" | ||
| ] | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "coordinationSpace": { | ||
| "dataset": { | ||
| "A": "A" | ||
| }, | ||
| "embeddingType": { | ||
| "A": "cell" | ||
| }, | ||
| "spatialPointLayer": { | ||
| "A": { | ||
| "opacity": 1, | ||
| "radius": 2, | ||
| "visible": true | ||
| } | ||
| }, | ||
| "spatialZoom": { | ||
| "A": 2 | ||
| }, | ||
| "spatialTargetX": { | ||
| "A": 0 | ||
| }, | ||
| "spatialTargetY": { | ||
| "A": 0 | ||
| } | ||
| }, | ||
| "layout": [ | ||
| { | ||
| "component": "spatial", | ||
| "coordinationScopes": { | ||
| "dataset": "A", | ||
| "spatialPointLayer": "A" | ||
| }, | ||
| "x": 0.0, | ||
| "y": 0.0, | ||
| "w": 4.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "layerController", | ||
| "coordinationScopes": { | ||
| "dataset": "A", | ||
| "spatialPointLayer": "A" | ||
| }, | ||
| "x": 3.0, | ||
| "y": 6.0, | ||
| "w": 1.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "obsSets", | ||
| "coordinationScopes": { | ||
| "dataset": "A" | ||
| }, | ||
| "x": 4.0, | ||
| "y": 6.0, | ||
| "w": 1.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "featureList", | ||
| "coordinationScopes": { | ||
| "dataset": "A" | ||
| }, | ||
| "x": 5.0, | ||
| "y": 6.0, | ||
| "w": 1.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "scatterplot", | ||
| "coordinationScopes": { | ||
| "dataset": "A", | ||
| "embeddingType": "A" | ||
| }, | ||
| "x": 4.0, | ||
| "y": 0.0, | ||
| "w": 4.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "featureValueHistogram", | ||
| "coordinationScopes": { | ||
| "dataset": "A" | ||
| }, | ||
| "x": 6.0, | ||
| "y": 6.0, | ||
| "w": 2.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "obsSetSizes", | ||
| "coordinationScopes": { | ||
| "dataset": "A" | ||
| }, | ||
| "x": 8.0, | ||
| "y": 6.0, | ||
| "w": 2.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "obsSetFeatureValueDistribution", | ||
| "coordinationScopes": { | ||
| "dataset": "A" | ||
| }, | ||
| "x": 10.0, | ||
| "y": 6.0, | ||
| "w": 2.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "heatmap", | ||
| "coordinationScopes": { | ||
| "dataset": "A" | ||
| }, | ||
| "x": 8.0, | ||
| "y": 0.0, | ||
| "w": 4.0, | ||
| "h": 6.0 | ||
| }, | ||
| { | ||
| "component": "description", | ||
| "coordinationScopes": { | ||
| "dataset": "A" | ||
| }, | ||
| "x": 0.0, | ||
| "y": 6.0, | ||
| "w": 3.0, | ||
| "h": 3.0 | ||
| }, | ||
| { | ||
| "component": "status", | ||
| "coordinationScopes": { | ||
| "dataset": "A" | ||
| }, | ||
| "x": 0.0, | ||
| "y": 9.0, | ||
| "w": 3.0, | ||
| "h": 3.0 | ||
| } | ||
| ], | ||
| "initStrategy": "auto" | ||
| } |
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