Change echo output of example 01, to be used in fractal-containers

fractal-analytics-platform · Oct 5, 2023 · 943cd68 · 943cd68
1 parent 1939dae
commit 943cd68
Showing 1 changed file with 22 additions and 21 deletions.
diff --git a/examples/01_cardio_tiny_dataset/run_example.sh b/examples/01_cardio_tiny_dataset/run_example.sh
@@ -13,10 +13,10 @@ OUTPUT_PATH=`pwd`/output_${LABEL}
 cp ../00_user_setup/.fractal.env .fractal.env
 
 # Set useful variables
-PRJ_NAME="proj-$LABEL"
+PROJECT_NAME="proj-$LABEL"
 DS_IN_NAME="input-ds-$LABEL"
 DS_OUT_NAME="output-ds-$LABEL"
-WF_NAME="Workflow $LABEL"
+WORKFLOW_NAME="Workflow $LABEL"
 
 # Set cache path and remove any previous file from there
 export FRACTAL_CACHE_PATH=`pwd`/".cache"
@@ -25,26 +25,26 @@ rm -rv ${FRACTAL_CACHE_PATH}  2> /dev/null
 ###############################################################################
 
 # Create project
-OUTPUT=`fractal --batch project new $PRJ_NAME`
-PRJ_ID=`echo $OUTPUT | cut -d ' ' -f1`
+OUTPUT=`fractal --batch project new $PROJECT_NAME`
+PROJECT_ID=`echo $OUTPUT | cut -d ' ' -f1`
 DS_IN_ID=`echo $OUTPUT | cut -d ' ' -f2`
-echo "PRJ_ID: $PRJ_ID"
-echo "DS_IN_ID: $DS_IN_ID"
+echo "PROJECT_ID=$PROJECT_ID"  # Do not remove this line, it's used in fractal-containers
+echo "DS_IN_ID=$DS_IN_ID"
 
 # Update dataset name/type, and add a resource
-fractal dataset edit --new-name "$DS_IN_NAME" --new-type image --make-read-only $PRJ_ID $DS_IN_ID
-fractal dataset add-resource $PRJ_ID $DS_IN_ID $INPUT_PATH
+fractal dataset edit --new-name "$DS_IN_NAME" --new-type image --make-read-only $PROJECT_ID $DS_IN_ID
+fractal dataset add-resource $PROJECT_ID $DS_IN_ID $INPUT_PATH
 
 # Add output dataset, and add a resource to it
-DS_OUT_ID=`fractal --batch project add-dataset $PRJ_ID "$DS_OUT_NAME"`
-echo "DS_OUT_ID: $DS_OUT_ID"
+DS_OUT_ID=`fractal --batch project add-dataset $PROJECT_ID "$DS_OUT_NAME"`
+echo "DS_OUT_ID=$DS_OUT_ID"
 
-fractal dataset edit --new-type zarr --remove-read-only $PRJ_ID $DS_OUT_ID
-fractal dataset add-resource $PRJ_ID $DS_OUT_ID $OUTPUT_PATH
+fractal dataset edit --new-type zarr --remove-read-only $PROJECT_ID $DS_OUT_ID
+fractal dataset add-resource $PROJECT_ID $DS_OUT_ID $OUTPUT_PATH
 
 # Create workflow
-WF_ID=`fractal --batch workflow new "$WF_NAME" $PRJ_ID`
-echo "WF_ID: $WF_ID"
+WORKFLOW_ID=`fractal --batch workflow new "$WORKFLOW_NAME" $PROJECT_ID`
+echo "WORKFLOW_ID=$WORKFLOW_ID"
 
 ###############################################################################
 
@@ -68,12 +68,13 @@ echo "{
 ###############################################################################
 
 # Add tasks to workflow
-fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Create OME-Zarr structure" --args-file Parameters/args_create_ome_zarr.json --meta-file Parameters/example_meta.json
-fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Convert Yokogawa to OME-Zarr"
-fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Copy OME-Zarr structure" --args-file Parameters/copy_ome_zarr.json
-fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Maximum Intensity Projection"
-fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Cellpose Segmentation" --args-file Parameters/args_cellpose_segmentation.json #--meta-file Parameters/cellpose_meta.json
-fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Napari workflows wrapper" --args-file Parameters/args_measurement.json --meta-file Parameters/example_meta.json
+fractal --batch workflow add-task $PROJECT_ID $WORKFLOW_ID --task-name "Create OME-Zarr structure" --args-file Parameters/args_create_ome_zarr.json --meta-file Parameters/example_meta.json
+fractal --batch workflow add-task $PROJECT_ID $WORKFLOW_ID --task-name "Convert Yokogawa to OME-Zarr"
+fractal --batch workflow add-task $PROJECT_ID $WORKFLOW_ID --task-name "Copy OME-Zarr structure" --args-file Parameters/copy_ome_zarr.json
+fractal --batch workflow add-task $PROJECT_ID $WORKFLOW_ID --task-name "Maximum Intensity Projection"
+fractal --batch workflow add-task $PROJECT_ID $WORKFLOW_ID --task-name "Cellpose Segmentation" --args-file Parameters/args_cellpose_segmentation.json #--meta-file Parameters/cellpose_meta.json
+fractal --batch workflow add-task $PROJECT_ID $WORKFLOW_ID --task-name "Napari workflows wrapper" --args-file Parameters/args_measurement.json --meta-file Parameters/example_meta.json
 
 # Apply workflow
-fractal --batch workflow apply $PRJ_ID $WF_ID $DS_IN_ID $DS_OUT_ID
+JOB_ID=`fractal --batch workflow apply $PROJECT_ID $WORKFLOW_ID $DS_IN_ID $DS_OUT_ID`
+echo "JOB_ID=$JOB_ID"  # Do not remove this line, it's used in fractal-containers