Idr download

utils/idr-download-tool/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0-dev0
+commit = True
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:src/polus/images/utils/idr_download/__init__.py]

utils/idr-download-tool/Dockerfile

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+FROM continuumio/miniconda3
+
+# environment variables defined in polusai/bfio
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
+
+ARG conda_env=myidrenv
+
+# Work directory defined in the base container
+WORKDIR ${EXEC_DIR}
+
+COPY pyproject.toml ${EXEC_DIR}
+COPY environment.yml ${EXEC_DIR}
+COPY VERSION ${EXEC_DIR}
+COPY README.md ${EXEC_DIR}
+COPY src ${EXEC_DIR}/src
+
+RUN conda env create -f environment.yml
+
+ENV PATH /opt/conda/envs/myidrenv/bin:$PATH
+RUN /bin/bash -c "source activate myidrenv"
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+ENTRYPOINT ["python3", "-m", "polus.images.utils.idr_download"]
+CMD ["--help"]

utils/idr-download-tool/README.md

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+# Idr Download (v0.1.0-dev0)
+
+This tool enables the retrieval of data from the [idr](https://idr.openmicroscopy.org/) using the IDR web API.
+
+## Note
+In order to retrieve data from the IDR web server, users need to establish a VPN connection
+
+
+Conda is employed to install all dependencies because one of the critical packages, `omero-py`, encountered installation issues with pip
+
+Currently, the supported object types in a tool include:  `project`, `dataset`, `screen`, `plate`, `well`
+
+
+## Building
+
+To build the Docker image for the download plugin, run
+`bash build-docker.sh`.
+
+## Run the Docker image
+
+To execute the built docker image for the download plugin, run
+`bash run-plugin.sh`.
+
+## Options
+
+This plugin takes 4 input arguments and
+1 output argument:
+
+| Name            | Description                                                  | I/O    | Type        |
+| --------------- | ------------------------------------------------------------ | ------ | ----------- |
+| `--dataType`      | Object types to be retreived from Idr Server                    | Input  | String      |
+| `--name  `      | Name of an object                   | Input  | String      |
+| `--objectId  `      |  Identification of an object of an object                 | Input  | Integer      |
+| `--outDir`      | Directory to store the downloaded data                  | Output | genericData |
+| `--preview`      | Generate a JSON file with outputs                  | Output | JSON |
+
+
+
+## Sample docker command:
+```bash
+docker run -v /home/ec2-user/data/:/home/ec2-user/data/ polusai/idr-download-tool:0.1.0-dev0 --dataType="plate" --name='plate1_1_013' --outDir=/home/ec2-user/data/output```

utils/idr-download-tool/VERSION

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+0.1.0-dev0

utils/idr-download-tool/build-docker.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/idr-download-tool:${version}

utils/idr-download-tool/environment.yml

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+name: myidrenv
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - python==3.9.18
+  - numpy==1.21.0
+  - bfio=*
+  - ome:omero-py
+  - pydantic=*
+  - pip
+  - pip:
+    - preadator==0.4.0-dev2

utils/idr-download-tool/ict.yml

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+author:
+- Hamdah Shafqat
+contact: hamdahshafqat.abbasi@nih.gov
+container: polusai/idr-download-tool:0.1.0-dev0
+description: This plugin allows to retrieve the microscopy image data from the https://idr.openmicroscopy.org.
+entrypoint: python3 -m polus.images.utils.idr_download
+inputs:
+- description: The supported object types to be retreived.
+  format:
+  - dataType
+  name: dataType
+  required: true
+  type: string
+- description: Name of the object to be downloaded.
+  format:
+  - name
+  name: name
+  required: false
+  type: string
+- description: Identifier of the object to be downloaded.
+  format:
+  - objectId
+  name: objectId
+  required: false
+  type: number
+- description: Generate an output preview.
+  format:
+  - preview
+  name: preview
+  required: false
+  type: boolean
+name: polusai/IdrDownload
+outputs:
+- description: Output collection.
+  format:
+  - outDir
+  name: outDir
+  required: true
+  type: path
+repository: https://github.com/PolusAI/image-tools
+specVersion: 1.0.0
+title: Idr Download
+ui:
+- description: The supported object types to be retreived.
+  fields:
+  - project
+  - dataset
+  - screen
+  - plate
+  - well
+  - default
+  key: inputs.dataType
+  title: dataType
+  type: select
+- description: Name of the object to be downloaded.
+  key: inputs.name
+  title: name
+  type: text
+- description: Identifier of the object to be downloaded.
+  key: inputs.objectId
+  title: objectId
+  type: number
+- description: Generate an output preview.
+  key: inputs.preview
+  title: Preview example output of this plugin
+  type: checkbox
+version: 0.1.0-dev0

utils/idr-download-tool/idrdownload.cwl

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+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  dataType:
+    inputBinding:
+      prefix: --dataType
+    type: string
+  name:
+    inputBinding:
+      prefix: --name
+    type: string?
+  objectId:
+    inputBinding:
+      prefix: --objectId
+    type: double?
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+  preview:
+    inputBinding:
+      prefix: --preview
+    type: boolean?
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/idr-download-tool:0.1.0-dev0
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}

utils/idr-download-tool/plugin.json

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+{
+  "name": "Idr Download",
+  "version": "0.1.0-dev0",
+  "containerId": "polusai/idr-download-tool:0.1.0-dev0",
+  "title": "Omero Download",
+  "description": "This plugin allows to retrieve the microscopy image data from the https://idr.openmicroscopy.org.",
+  "author": "Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",
+  "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
+  "repository": "https://github.com/PolusAI/image-tools",
+  "website": "https://ncats.nih.gov/preclinical/core/informatics",
+  "citation": "",
+  "baseCommand": [
+    "python3",
+    "-m",
+    "polus.images.utils.idr_download"
+  ],
+  "inputs": [
+    {
+      "name": "dataType",
+      "type": "enum",
+      "title": "dataType",
+      "description": "The supported object types to be retreived.",
+      "default": "default",
+      "options": {
+        "values": [
+          "project",
+          "dataset",
+          "screen",
+          "plate",
+          "well",
+          "default"
+        ]
+      },
+      "required": true
+    },
+    {
+      "name": "name",
+      "type": "string",
+      "title": "name",
+      "description": "Name of the object to be downloaded.",
+      "required": "False"
+    },
+    {
+      "name": "objectId",
+      "type": "integer",
+      "title": "objectId",
+      "description": "Identifier of the object to be downloaded.",
+      "required": "False"
+    },
+    {
+      "name": "preview",
+      "type": "boolean",
+      "title": "Preview",
+      "description": "Generate an output preview.",
+      "required": "False"
+    }
+  ],
+  "outputs": [
+    {
+      "name": "outDir",
+      "type": "genericData",
+      "description": "Output collection."
+    }
+  ],
+  "ui": [
+    {
+      "key": "inputs.dataType",
+      "type": "enum",
+      "title": "dataType",
+      "description": "The supported object types to be retreived.",
+      "default": "dataset",
+      "required": "True"
+    },
+    {
+      "key": "inputs.name",
+      "type": "string",
+      "title": "name",
+      "description": "Name of the object to be downloaded.",
+      "required": "False"
+    },
+    {
+      "key": "inputs.objectId",
+      "type": "integer",
+      "title": "objectId",
+      "description": "Identifier of the object to be downloaded.",
+      "required": "False"
+    },
+    {
+      "key": "inputs.preview",
+      "type": "boolean",
+      "title": "Preview example output of this plugin",
+      "description": "Generate an output preview.",
+      "required": "False"
+    }
+  ]
+}

utils/idr-download-tool/pyproject.toml

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+[tool.poetry]
+name = "polus-images-utils-idr-download"
+version = "0.1.0-dev0"
+description = "Retrieve the microscopy image data from the idr server"
+authors = [
+           "Hamdah Shafqat abbasi <hamdahshafqat.abbasi@nih.gov>"
+           ]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = "3.9.18"
+bfio = {version = "^2.3.6", extras = ["all"]}
+typer = "^0.7.0"
+pydantic = "^2.5.3"
+pandas = "2.2.2"
+preadator = "0.4.0-dev2"
+tqdm = "^4.66.2"
+
+[[tool.poetry.source]]
+name = "test"
+url = "https://test.pypi.org/simple/"
+default = false
+secondary = true
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+flake8 = "^6.0.0"
+pre-commit = "^3.2.1"
+flake8-docstrings = "^1.7.0"
+black = "^23.3.0"
+mypy = "^1.1.1"
+pytest = "^7.2.2"
+ruff = "^0.0.270"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]

utils/idr-download-tool/run-plugin.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+datapath=$(readlink --canonicalize data)
+echo ${datapath}
+
+# Inputs
+out_dir=${datapath}/out
+data_type="plate"
+object_id=3139
+
+
+# #Show the help options
+# #docker run polusai/polusai/idr_download-tool:${version}
+
+docker run -v ${datapath}:${datapath} \
+            polusai/idr_download-tool:${version} \
+            --dataType ${data_type} \
+            --name ${name} \
+            --objectId ${object_id} \
+            --outDir ${out_dir}

utils/idr-download-tool/src/polus/images/utils/idr_download/__init__.py

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+"""Idr Download Package."""
+
+__version__ = "0.1.0-dev0"