Build branch allow-compressed-output-bundles with version allow-compressed-output-bundles (2cc934c)

Build pipeline: openpipelines-bio.openpipeline-spatial.allow-compressed-ou59m5k

Source commit: 2cc934cef9

Source message: wip

target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml

@@ -173,6 +173,8 @@ 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"
@@ -303,6 +305,10 @@ engines:
     github:
     - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
     upgrade: true
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   entrypoint: []
   cmd: null
 - type: "native"
@@ -314,7 +320,7 @@ build_info:
   output: "target/nextflow/convert/from_xenium_to_spatialdata"
   executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
+  git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/nextflow/convert/from_xenium_to_spatialdata/main.nf

@@ -3251,6 +3251,10 @@ meta = [
       "type" : "file",
       "path" : "/src/utils/setup_logger.py"
     },
+    {
+      "type" : "file",
+      "path" : "/src/utils/unzip_archived_folder.py"
+    },
     {
       "type" : "file",
       "path" : "/src/workflows/utils/labels.config",
@@ -3411,6 +3415,13 @@ meta = [
             "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
           ],
           "upgrade" : true
+        },
+        {
+          "type" : "apt",
+          "packages" : [
+            "zip"
+          ],
+          "interactive" : false
         }
       ]
     },
@@ -3425,7 +3436,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
+    "git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3477,6 +3488,7 @@ tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 import sys
 from spatialdata_io import xenium
+import zipfile
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -3523,10 +3535,14 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import unzip_archived_folder
 
 logger = setup_logger()
 
 logger.info("Reading in Xenium data...")
+if zipfile.is_zipfile(par["input"]):
+    par["input"] = unzip_archived_folder(par["input"])
+
 sdata = xenium(
     par["input"],
     cells_boundaries=par["cells_boundaries"],

target/nextflow/convert/from_xenium_to_spatialdata/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
+
+
+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