Upgrade Bbbc download plugin

.gitignore

@@ -168,6 +168,11 @@ cython_debug/
 # test data directory
 data
 
+# local manifests
+src/polus/plugins/_plugins/manifests/*
+# allow python scripts insied manifests dir
+!src/polus/plugins/_plugins/manifests/*.py
+uv.lock
 
 #macOS
 *.DS_Store

utils/bbbc-download-plugin/.bumpversion.cfg

@@ -0,0 +1,27 @@
+[bumpversion]
+current_version = 0.1.1-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/plugins/utils/bbbc_download/__init__.py]

utils/bbbc-download-plugin/Dockerfile

@@ -0,0 +1,21 @@
+FROM python:3.13-slim
+
+# 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"
+
+# Work directory defined in the base container
+WORKDIR ${EXEC_DIR}
+
+# When building from repo root: -f utils/bbbc-download-plugin/Dockerfile .
+COPY utils/bbbc-download-plugin/pyproject.toml ${EXEC_DIR}
+COPY utils/bbbc-download-plugin/VERSION ${EXEC_DIR}
+COPY utils/bbbc-download-plugin/README.md ${EXEC_DIR}
+COPY utils/bbbc-download-plugin/src ${EXEC_DIR}/src
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+ENTRYPOINT ["python3", "-m", "polus.plugins.utils.bbbc_download"]
+CMD ["--help"]

utils/bbbc-download-plugin/README.md

@@ -0,0 +1,41 @@
+# BBBC Download (0.1.0-dev1)
+
+This plugin is designed to download the necessary datasets from the Broad Bioimage Benchmark Collection(BBBC) website.
+
+For information on the BBBC dataset, visit
+[BBBC dataset information](https://bbbc.broadinstitute.org/image_sets/).
+The tables on this webpage classify datasets by their biological application. Each dataset has a webpage that contains links to the data and describes information about the dataset. Almost every dataset has image data and ground truth data. There are a few datasets that have metadata rather than ground truth data.
+
+## 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 1 input arguments and
+1 output argument:
+
+| Name            | Description                                                  | I/O    | Type        |
+| --------------- | ------------------------------------------------------------ | ------ | ----------- |
+| `--name  `      | The name of the datasets to be downloaded                    | Input  | String      |
+| `--outDir`      | Directory to store the downloaded datasets                   | Output | genericData |
+
+The following are valid names for datasets:
+`"All"`- To download all the datasets from the bbbc website
+`"IDAndSegmentation"`- To download the datasets from the Identification and segmentation table
+`"PhenotypeClassification"`- To download the datasets from the Phenotype classification table
+`"ImageBasedProfiling"`- To download the datasets from the Image-based Profiling table
+
+To download specific datasets from the website, give the name of each dataset in the input argument seperated by a comma. example: `--name="BBBC001,BBBC002,BBBC003"`
+
+### NOTE
+BBBC046 dataset download is not supported by this plugin.
+
+## Sample docker command:
+```docker run -v /home/ec2-user/data/:/home/ec2-user/data/ polusai/bbbc-download-plugin:0.1.0-dev0 --name="BBBC001" --outDir=/home/ec2-user/data/output```

utils/bbbc-download-plugin/VERSION

@@ -0,0 +1 @@
+0.1.1-dev0

utils/bbbc-download-plugin/build-docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/bbbc-download-plugin:${version}

utils/bbbc-download-plugin/plugin.json

@@ -0,0 +1,39 @@
+{
+  "name": "BBBC Download",
+  "version": "0.1.1-dev0",
+  "title": "BBBC Download",
+  "description": "Downloads the datasets on the Broad Bioimage Benchmark Collection website",
+  "author": "Saket Prem(saket.prem@axleinfo.com), Matthew McIntyre(Matthew.McIntyre@axleinfo.com)",
+  "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
+  "repository": "https://github.com/PolusAI/polus-plugins",
+  "website": "https://ncats.nih.gov/preclinical/core/informatics",
+  "citation": "",
+  "containerId": "polusai/bbbc-download-plugin:0.1.1-dev0",
+  "baseCommand": [
+    "python3",
+    "-m",
+    "polus.plugins.utils.bbbc_download"
+  ],
+  "inputs": [
+    {
+      "name": "name",
+      "type": "string",
+      "description": "The name of the datasets to be downloaded(spereate the datasets with a comma. eg: BBBC001,BBBC002,BBBC003 )",
+      "required": true
+    }
+  ],
+  "outputs": [
+    {
+      "name": "outDir",
+      "type": "genericData",
+      "description": "Output collection"
+    }
+  ],
+  "ui": [
+    {
+      "key": "inputs.name",
+      "title": "Input name of datasets as string",
+      "description": "Input the name of the datasets to be downloaded."
+    }
+  ]
+}

utils/bbbc-download-plugin/pyproject.toml

@@ -0,0 +1,33 @@
+[tool.poetry]
+name = "polus-plugins-utils-bbbc-download-plugin"
+version = "0.1.1-dev0"
+description = ""
+authors = [
+    "Saket Prem <saket.prem@axleinfo.com>", 
+    "Matthew McIntyre <Matthew.McIntyre@axleinfo.com>"
+    ]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.12"
+typer = ">=0.24.0"
+pyarrow = ">=23.0.0"
+scikit-image = ">=0.25.0"
+bfio = ">=2.5.0"
+beautifulsoup4 = ">=4.14.3"
+numpy = ">=1.26.0"
+pandas = ">=2.2.3"
+requests = ">=2.32.5"
+pydantic = ">=2.12.5"
+bump2version = "1.0.1"
+mypy = ">=1.19.1"
+tqdm = ">=4.67.0"
+pytest = ">=9.0.0"
+xmlschema = ">=4.3.1"
+lxml = ">=6.0.2"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

utils/bbbc-download-plugin/run-plugin.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+version=$(<VERSION)
+datapath=$(readlink --canonicalize data)
+mkdir ${datapath}
+# Inputs
+name="BBBC001"
+
+# # Output paths
+outDir=${datapath}
+
+# # Show the help options
+# docker run polusai/bbbc-download-plugin:${version}
+
+
+# # Run the plugin
+docker run -v ${datapath}:${datapath} \
+            polusai/bbbc-download-plugin:${version} \
+            --name ${name} \
+            --outDir ${outDir}