diff --git a/workers/test_worker/Dockerfile b/workers/test_worker/Dockerfile new file mode 100644 index 0000000..2cbbb52 --- /dev/null +++ b/workers/test_worker/Dockerfile @@ -0,0 +1,43 @@ +FROM ubuntu:jammy as base +LABEL isUPennContrastWorker=True + +RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -qy tzdata && \ + apt-get install -qy software-properties-common python3-software-properties && \ + apt-get update && apt-get install -qy \ + build-essential \ + wget \ + python3 \ + r-base \ + libffi-dev \ + libssl-dev \ + libjpeg-dev \ + zlib1g-dev \ + r-base \ + git \ + libpython3-dev && \ + apt-get clean && rm -rf /var/lib/apt/lists/* + +ENV PATH="/root/miniforge3/bin:$PATH" +ARG PATH="/root/miniforge3/bin:$PATH" + +RUN wget \ + https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \ + && mkdir /root/.conda \ + && bash Miniforge3-Linux-x86_64.sh -b \ + && rm -f Miniforge3-Linux-x86_64.sh + +FROM base as build + +COPY ./environment.yml / +RUN conda env create --file /environment.yml +SHELL ["conda", "run", "-n", "worker", "/bin/bash", "-c"] + +RUN git clone https://github.com/Kitware/UPennContrast/ +WORKDIR /UPennContrast + +RUN pip install -r devops/girder/annotation_client/requirements.txt +RUN pip install -e devops/girder/annotation_client/ + +COPY ./entrypoint.py / + +ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "worker", "python3", "/entrypoint.py"] \ No newline at end of file diff --git a/workers/test_worker/LICENSE b/workers/test_worker/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/workers/test_worker/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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The client is available in UPennContrast/devops/girder/annotation_client. + +It is mandatory to specify an entrypoint in the Dockerfile. Anything else is optional though python is recommended for now as it allow usage of the annotation client. + +The following arguments are passed to the entrypoint: + +* `--apiUrl`: the url to the girder API +* `--token`: authentication token for girder +* `--datasetId`: the id of the dataset to process +* `--request`: the request, can be `compute`, `interface`, `preview` +* `--parameters`: json-formatted string containing configuration information related to the property diff --git a/workers/test_worker/entrypoint.py b/workers/test_worker/entrypoint.py new file mode 100644 index 0000000..280dc33 --- /dev/null +++ b/workers/test_worker/entrypoint.py @@ -0,0 +1,106 @@ +import argparse +import json +import sys + +import annotation_client.workers as workers + + +def compute(datasetId, apiUrl, token, params): + """ + In this function: + Annotation workers create new annotations + Property workers compute annotation properties + """ + print(datasetId) + print(apiUrl) + print(token) + print(params) + + # The values retrieved using the worker interface are always in a dict: params['workerInterface'] + + # WARNING: accessing value was done using params['workerInterface']['My property']['value'], + # it is now done using params['workerInterface']['My property'] as the typescript type of + # params['workerInterface'] is IWorkerInterfaceValues + print(params['workerInterface']) + + +def interface(image, apiUrl, token): + """ + Send parameters required by compute() to the frontend + See WorkerInterfaceValues.vue and the type IWorkerInterface in model.ts to be updated on what can be requested + """ + workerInterface = { + 'My number property': { + 'type': 'number', + 'min': -1, + 'max': 5, + 'default': 3.14, + }, + 'My text property': { + 'type': 'text', + 'default': 'Hello, world!', + }, + 'My tags property': { + 'type': 'tags', + 'default': ['cell', 'nuclei'], + }, + 'My layer property': { + 'type': 'layers', + 'default': 0, + }, + 'My select property': { + 'type': 'select', + 'default': 'blue', + 'items': ['orange', 'blue', 'green'], + }, + 'My channel property': { + 'type': 'channel', + 'default': 3, + }, + } + # Send the interface object to the server + client = workers.UPennContrastWorkerPreviewClient(apiUrl=apiUrl, token=token) + client.setWorkerImageInterface(image, workerInterface) + + +def preview(): + # TODO: I don't know what preview should do + pass + + +if __name__ == '__main__': + # Define the command-line interface for the entry point + parser = argparse.ArgumentParser( + description='Compute average intensity values in a circle around point annotations') + + parser.add_argument('--datasetId', type=str, required=False, action='store') + parser.add_argument('--apiUrl', type=str, required=True, action='store') + parser.add_argument('--token', type=str, required=True, action='store') + parser.add_argument('--request', type=str, required=True, action='store') + parser.add_argument('--parameters', type=str, + required=True, action='store') + + args = parser.parse_args(sys.argv[1:]) + + # Params is: + # - for request 'compute': + # see 'computeAnnotationWithWorker' of AnnotationsAPI.ts for annotation workers + # see 'computeProperty' of PropertiesAPI.ts for property workers + # - for request 'interface': + # params is { 'image': image } + # - for request 'preview': + # see 'requestWorkerPreview' of PropertiesAPI.ts + params = json.loads(args.parameters) + datasetId = args.datasetId + apiUrl = args.apiUrl + token = args.token + + # As jammy is the base docker image, python version is >= 3.10.4 + # We can use match/case + match args.request: + case 'compute': + compute(datasetId, apiUrl, token, params) + case 'interface': + interface(params['image'], apiUrl, token) + case 'preview': + preview() diff --git a/workers/test_worker/environment.yml b/workers/test_worker/environment.yml new file mode 100644 index 0000000..ba9ceb1 --- /dev/null +++ b/workers/test_worker/environment.yml @@ -0,0 +1,7 @@ +name: worker +dependencies: +- python +- pip +- imageio +# - pip: +# - \ No newline at end of file