Build branch openpipeline_spatial/v0.1 with version v0.1.1 to openpipeline_spatial on branch v0.1 (2baba3f)

Build pipeline: openpipelines-bio.openpipeline-spatial.0.1.1-5jtw5

Source commit: 2baba3fff0

Source message: merge main

target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_xenium_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -97,6 +97,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -198,7 +200,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -217,6 +219,10 @@ engines:
       nelse:  exit(1)\")"
     upgrade: true
   test_setup:
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   - type: "python"
     user: false
     packages:
@@ -233,11 +239,11 @@ build_info:
   output: "target/executable/convert/from_xenium_to_h5mu"
   executable: "target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -257,7 +263,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_xenium_to_h5mu v0.1.0
+# from_xenium_to_h5mu v0.1.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_h5mu"
-LABEL org.opencontainers.image.created="2025-08-25T12:22:56Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:37:00Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_xenium_to_h5mu v0.1.0"
+  echo "from_xenium_to_h5mu v0.1.1"
   echo ""
   echo "Converts the output from Xenium to a single .h5mu file, where the count matrix"
   echo "is written to the \`rna\` modality."
@@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_xenium_to_h5mu v0.1.0"
+            echo "from_xenium_to_h5mu v0.1.1"
             exit
             ;;
         --input)
@@ -839,7 +839,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_h5mu:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_h5mu:v0.1.1'
   fi
 
   # print dockerfile
@@ -1154,7 +1154,9 @@ from pathlib import Path
 import scanpy as sc
 import pandas as pd
 import mudata as mu
+import zipfile
 import json
+import os
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -1194,21 +1196,46 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
 
 logger = setup_logger()
 
-# Expected folder structure (showing only relevant files):
-# ├── cell_feature_matrix.h5
-# ├── cells.parquet
-# ├── experiment.xenium
-# └── metrics_summary.csv
-input_dir = Path(par["input"])
-input_data = {
-    "count_matrix": input_dir / "cell_feature_matrix.h5",
-    "cells_metadata": input_dir / "cells.parquet",
-    "experiment": input_dir / "experiment.xenium",
-    "metrics_summary": input_dir / "metrics_summary.csv",
-}
+
+def _retrieve_input_data(xenium_output_bundle):
+    # Expected folder structure (showing only relevant files):
+    # ├── cell_feature_matrix.h5
+    # ├── cells.parquet
+    # ├── experiment.xenium
+    # └── metrics_summary.csv
+
+    required_file_patterns = {
+        "count_matrix": "**/cell_feature_matrix.h5",
+        "cells_metadata": "**/cells.parquet",
+        "experiment": "**/experiment.xenium",
+        "metrics_summary": "**/metrics_summary.csv",
+    }
+
+    if zipfile.is_zipfile(xenium_output_bundle):
+        xenium_output_bundle = extract_selected_files_from_zip(
+            xenium_output_bundle,
+            members=[pattern for pattern in required_file_patterns.values()],
+        )
+    else:
+        xenium_output_bundle = Path(xenium_output_bundle)
+
+    assert os.path.isdir(xenium_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(xenium_output_bundle.glob(pattern))
+        assert len(file) == 1, (
+            f"Expected exactly one file matching pattern {pattern}, found {len(file)}."
+        )
+        input_data[key] = file[0]
+
+    return input_data
 
 
 def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
@@ -1221,9 +1248,7 @@ def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
 # Read data from Xenium output bundle
 logger.info("Reading input data...")
 
-assert all([file.exists() for file in input_data.values()]), (
-    f"Not all required input files are found. Make sure that {par['input']} contains {input_data.values()}."
-)
+input_data = _retrieve_input_data(par["input"])
 
 adata = sc.read_10x_h5(input_data["count_matrix"])
 metadata = pd.read_parquet(input_data["cells_metadata"], engine="pyarrow")

target/executable/convert/from_xenium_to_h5mu/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir