fix microjson dependencies

visualization/microjson-to-ome-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.5
+current_version = 0.1.5-dev1
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

visualization/microjson-to-ome-tool/CHANGELOG.md

@@ -5,3 +5,6 @@
 Fixing property attribute for loading microjson file
 Modifying docker container name
 updating bfio filepattern and microjson to latest
+
+## 0.1.5-dev1
+Updated microjson package, base container image, renamed title in plugin manifest

visualization/microjson-to-ome-tool/Dockerfile

@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.3.3
+FROM polusai/bfio:2.4.2
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"

visualization/microjson-to-ome-tool/README.md

@@ -1,4 +1,4 @@
-# Microjson To Ome(v0.1.5)
+# Microjson To Ome(v0.1.5-dev1)
 
 This plugin reconstructs binary image from polygon coordinates reserved in microjson file format
 
@@ -45,7 +45,7 @@ This plugin can take four input arguments and one output argument:
 ### Run the Docker Container
 
 ```bash
-docker run -v /data:/data polusai/microjson-to-ome-plugin:0.1.2-dev \
+docker run -v /data:/data polusai/microjson-to-ome-tool:0.1.5-dev1 \
   --inpDir /data/input \
   --filePattern ".*.json" \
   --outDir /data/output \

visualization/microjson-to-ome-tool/VERSION

@@ -1 +1 @@
-0.1.5
+0.1.5-dev1

visualization/microjson-to-ome-tool/ict.yaml

@@ -1,51 +1,52 @@
 author:
-- Hamdah Shafqat
+  - Hamdah Shafqat
 contact: [email protected]
-container: polusai/microjson-to-ome-tool:0.1.5-dev0
-description: This plugin reconstruct binary images using polygon coordinates (rectangle,
+container: polusai/microjson-to-ome-tool:0.1.5-dev1
+description:
+  This plugin reconstruct binary images using polygon coordinates (rectangle,
   encodings) of objects from microjson file.
 entrypoint: python3 -m polus.images.visualization.microjson_to_ome
 inputs:
-- description: Input image collection to be processed by this plugin.
-  format:
-  - genericData
-  name: inpDir
-  required: true
-  type: path
-- description: Filename pattern used to separate data.
-  format:
-  - string
-  name: filePattern
-  required: false
-  type: string
-- description: Generate an output preview.
-  format:
-  - boolean
-  name: preview
-  required: false
-  type: boolean
-name: polusai/Reconstructbinaryimageusingpolygoncoordinatesofobjects
+  - description: Input image collection to be processed by this plugin.
+    format:
+      - genericData
+    name: inpDir
+    required: true
+    type: path
+  - description: Filename pattern used to separate data.
+    format:
+      - string
+    name: filePattern
+    required: false
+    type: string
+  - description: Generate an output preview.
+    format:
+      - boolean
+    name: preview
+    required: false
+    type: boolean
+name: polusai/microjsontoome.cwl
 outputs:
-- description: Output collection.
-  format:
-  - collection
-  name: outDir
-  required: true
-  type: path
-repository: https://github.com/labshare/polus-plugins
+  - description: Output collection.
+    format:
+      - collection
+    name: outDir
+    required: true
+    type: path
+repository: https://github.com/polusai/image-tools
 specVersion: 1.0.0
 title: Reconstruct binary image using polygon coordinates of objects
 ui:
-- description: Input image collection to be processed by this plugin.
-  key: inputs.inpDir
-  title: Input collection
-  type: path
-- description: Filename pattern used to separate data.
-  key: inputs.filePattern
-  title: Filename pattern
-  type: text
-- description: Generate an output preview.
-  key: inputs.preview
-  title: Preview example output of this plugin
-  type: checkbox
-version: 0.1.5-dev0
+  - description: Input image collection to be processed by this plugin.
+    key: inputs.inpDir
+    title: Input collection
+    type: path
+  - description: Filename pattern used to separate data.
+    key: inputs.filePattern
+    title: Filename pattern
+    type: text
+  - description: Generate an output preview.
+    key: inputs.preview
+    title: Preview example output of this plugin
+    type: checkbox
+version: 0.1.5-dev1

visualization/microjson-to-ome-tool/reconstructbinaryimageusingpolygoncoordinatesofobjects.cwl → visualization/microjson-to-ome-tool/microjsontoome.cwl

@@ -24,7 +24,7 @@ outputs:
     type: Directory
 requirements:
   DockerRequirement:
-    dockerPull: polusai/microjson-to-ome-tool:0.1.5-dev0
+    dockerPull: polusai/microjson-to-ome-tool:0.1.5-dev1
   InitialWorkDirRequirement:
     listing:
     - entry: $(inputs.outDir)

visualization/microjson-to-ome-tool/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "Microjson To Ome",
-  "version": "0.1.5",
+  "version": "0.1.5-dev1",
   "title": "Reconstruct binary image using polygon coordinates of objects",
   "description": "This plugin reconstruct binary images using polygon coordinates (rectangle, encodings) of objects from microjson file.",
   "author": "Hamdah Shafqat abbasi  ([email protected])",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
-  "repository": "https://github.com/labshare/polus-plugins",
+  "repository": "https://github.com/polusai/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/microjson-to-ome-tool:0.1.5",
+  "containerId": "polusai/microjson-to-ome-tool:0.1.5-dev1",
   "baseCommand": [
     "python3",
     "-m",

visualization/microjson-to-ome-tool/pyproject.toml

@@ -1,23 +1,21 @@
 [tool.poetry]
 name = "polus-images-visualization-microjson-to-ome"
-version = "0.1.5"
+version = "0.1.5-dev1"
 description = "This plugin reconstructs binary images from polygon coordinates"
 authors = ["Hamdah Shafqat abbasi  <[email protected]>"]
 readme = "README.md"
 packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = ">=3.9.15,<3.12"
-bfio = {version = "2.3.3", extras = ["all"]}
-ome-types="0.4.2"
-xmlschema = "^2.4.0"
+bfio = {version = "2.3.6", extras = ["all"]}
 typer = "^0.7.0"
 scipy = ">=1.8,<1.9.2"
 filepattern = "^2.0.4"
 tqdm = "^4.65.0"
-microjson = "^0.1.9"
+microjson = "0.1.11"
 scikit-image = "0.20.0"
-pydantic = "^2.5.2"
+pydantic = "^2.3.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

visualization/microjson-to-ome-tool/run-plugin.sh

@@ -12,7 +12,7 @@ out_dir=${datapath}/output
 # docker run polusai/microjson-to-ome-plugin:${version}
 
 docker run -v ${datapath}:${datapath} \
-            polusai/microjson-to-ome-plugin:${version} \
+            polusai/microjson-to-ome-tool:${version} \
             --inpDir ${inp_dir} \
             --filePattern ${file_pattern} \
             --outDir ${out_dir}

visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/__init__.py

@@ -1,2 +1,3 @@
 """Micojson to Ome."""
-__version__ = "0.1.5"
+
+__version__ = "0.1.5-dev1"

visualization/microjson-to-ome-tool/tests/conftest.py

@@ -54,13 +54,13 @@
 @pytest.fixture()
 def inp_dir() -> Union[str, Path]:
     """Create directory for saving json data."""
-    return Path(tempfile.mkdtemp(dir=Path.cwd()))
+    return Path(tempfile.mkdtemp())
 
 
 @pytest.fixture()
 def output_directory() -> Union[str, Path]:
     """Create output directory."""
-    return Path(tempfile.mkdtemp(dir=Path.cwd()))
+    return Path(tempfile.mkdtemp())
 
 
 @pytest.fixture(