Merge pull request #63 from fractal-analytics-platform/62-create-01_c…

…ardio_tiny_dataset_with_partial_execution

New example: cardio tiny dataset with partial execution

examples/00_user_setup/install_client.sh

@@ -1,4 +1,4 @@
-VERSION="1.3.2"
+VERSION="1.3.3"
 
 ENVNAME=fractal-client-$VERSION
 conda deactivate

examples/01_cardio_tiny_dataset/.gitignore

@@ -3,3 +3,4 @@ output*
 task_list
 .fractal.env
 proj*
+workflow.json

examples/01_cardio_tiny_dataset/README.md

@@ -9,9 +9,19 @@ This needs to be done in each example folder you're running
 2. Get the example data: `pip install zenodo_get`, then run `. ./fetch_test_data_from_zenodo.sh`
 3. One can then either go through the project creation, dataset creation, workflow creation & submission one by one. Or run it all at once by running: `. ./run_example.sh`
 
-This should complete fairly quickly (submitting the script to it being finished took 30s on my machine). One can check the status with `fractal job show ID` (where the ID is the job ID of the submitted workflow, 1 for the first workflow submitted. This is shown when submitting the workflow)
+This should complete fairly quickly (submitting the script to it being finished took 30s on my machine). One can check the status with `fractal job show ID` (where the ID is the job ID of the submitted workflow: 1 for the first workflow submitted. This is shown when submitting the workflow)
+
+## Running partial workflows
+You can use the run_example_with_partial_execution.sh as an example of how to run only parts of workflows.
+Modify its last lines if you don't want to automatically run the second part of the workflow after a short wait.
+
+
+## Import a workflow, then run it
+1. Create a project & add a workflow to it that is downloaded by running `prepare_and_export_workflow.sh`
+2. Create a second project, import the workflow and apply it by running `import_and_run_workflow.sh`
+
 
 Check the client documentation for details on using the Fractal Client: https://fractal-analytics-platform.github.io/fractal/install.html
 Check the Fractal Tasks Core documentation for details on the individual tasks of this example workflow: https://fractal-analytics-platform.github.io/fractal-tasks-core/
 
-Successfully run with `fractal-server==1.3.0a5`, `fractal-client==1.3.0a3` and `fractal-tasks-core==0.10.0a4`
+Successfully run with `fractal-server==1.3.4`, `fractal-client==1.3.3` and `fractal-tasks-core==0.10.0`

examples/01_cardio_tiny_dataset/run_example_with_partial_execution.sh

@@ -0,0 +1,81 @@
+LABEL="cardiac-test-partial-1"
+
+###############################################################################
+# IMPORTANT: This defines the location of input & output data
+INPUT_PATH=`pwd`/../images/10.5281_zenodo.7059515/
+OUTPUT_PATH=`pwd`/output_${LABEL}
+###############################################################################
+
+# Get the credentials: If you followed the instructions, they can be copied 
+# from the .fractal.env file in ../00_user_setup. Alternatively, you can write
+# a .fractal.env file yourself or add --user & --password entries to all fractal
+# commands below
+cp ../00_user_setup/.fractal.env .fractal.env
+
+# Set useful variables
+PRJ_NAME="proj-$LABEL"
+DS_IN_NAME="input-ds-$LABEL"
+DS_OUT_NAME="output-ds-$LABEL"
+WF_NAME="Workflow $LABEL"
+
+# Set cache path and remove any previous file from there
+export FRACTAL_CACHE_PATH=`pwd`/".cache"
+rm -rv ${FRACTAL_CACHE_PATH}  2> /dev/null
+
+###############################################################################
+
+# Create project
+OUTPUT=`fractal --batch project new $PRJ_NAME`
+PRJ_ID=`echo $OUTPUT | cut -d ' ' -f1`
+DS_IN_ID=`echo $OUTPUT | cut -d ' ' -f2`
+echo "PRJ_ID: $PRJ_ID"
+echo "DS_IN_ID: $DS_IN_ID"
+
+# Update dataset name/type, and add a resource
+fractal dataset edit --new-name "$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
+
+# 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"
+
+fractal dataset edit --new-type zarr --remove-read-only $PRJ_ID $DS_OUT_ID
+fractal dataset add-resource $PRJ_ID $DS_OUT_ID $OUTPUT_PATH
+
+# Create workflow
+WF_ID=`fractal --batch workflow new "$WF_NAME" $PRJ_ID`
+echo "WF_ID: $WF_ID"
+
+###############################################################################
+
+# Prepare some JSON files for task arguments (note: this has to happen here,
+# because we need to include the path of the current directory)
+CURRENT_FOLDER=`pwd`
+echo "{
+  \"level\": 0,
+  \"input_ROI_table\": \"well_ROI_table\",
+  \"workflow_file\": \"$CURRENT_FOLDER/regionprops_from_existing_labels_feature.yaml\",
+  \"input_specs\": {
+    \"dapi_img\": { \"type\": \"image\", \"channel\":{ \"wavelength_id\": \"A01_C01\" } },
+    \"label_img\": { \"type\": \"label\", \"label_name\": \"nuclei\" }
+  },
+  \"output_specs\": {
+    \"regionprops_DAPI\": { \"type\": \"dataframe\", \"table_name\": \"nuclei\" }
+  }
+}
+" > Parameters/args_measurement.json
+
+###############################################################################
+
+# 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"
+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
+
+# Apply workflow
+fractal workflow apply $PRJ_ID $WF_ID $DS_IN_ID $DS_OUT_ID --end 1
+sleep 90
+fractal workflow apply $PRJ_ID $WF_ID $DS_OUT_ID $DS_OUT_ID --start 2

examples/server/install_script.sh

@@ -1,4 +1,4 @@
-VERSION="1.3.3"
+VERSION="1.3.4"
 
 ENVNAME=fractal-server-$VERSION
 conda deactivate