feat(scripts): add scripts to work with cope binary

install/cope/README.md

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+
+# COPE scripts
+
+## EIP extraction
+
+The script `eip_prepare_for_cope.py` extracts EIP files in a source directory to a target directory. It renames a specific subdirectory (`CaptureOne/Settings153` to `CaptureOne/Settings131`) and moves the EIP files into the `_raw` image directory.
+
+## Usage
+
+```
+usage: eip_prepare_for_cope.py [-h] -s SOURCE -t TARGET
+
+options:
+  -h, --help            show this help message and exit
+  -s SOURCE, --source SOURCE
+                        Source directory
+  -t TARGET, --target TARGET
+                        Target directory
+```
+
+in Goobi workflow this can be integrated in a script step like this:
+
+```shell
+/opt/digiverso/goobi/scripts/eip_prepare_for_cope.py -s {origpath} -t {origpath}
+```
+
+## COPE conversion
+
+The script `cope_folder.py` converts IIQ files from the source directory and uses COPE to convert them to tiff files located in the target directory. Optionally the given resolution value will be used.
+
+## Usage
+
+```
+usage: cope_folder.py [-h] -s SOURCE -t TARGET [-r RESOLUTION]
+
+options:
+  -h, --help            show this help message and exit
+  -s SOURCE, --source SOURCE
+  -t TARGET, --target TARGET
+  -r RESOLUTION, --resolution RESOLUTION
+```
+
+The path to the cope binary can be given by an environment variable named `COPE_PATH`.
+
+In Goobi workflow a script step in the external queue can be used to run the script on a Windows workernode like this:
+
+```CMD
+C:\Windows\py.exe D:\intranda\cope_folder.py -s "//mediaSMB-isilonArchive/GoobiMetadata/{s3_origpath}" -t "//mediaSMB-isilonArchive/GoobiMetadata/{s3_origpath}" -r "{process.File Resolution}"
+```
+

install/cope/cope_folder.py

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+#!/usr/bin/env python3
+
+import logging
+import os
+import shutil
+import subprocess
+from argparse import ArgumentParser
+from pathlib import Path
+
+loglevel = (os.environ.get('PYTHON_LOGLEVEL') or "DEBUG").upper()
+numeric_level = getattr(logging, loglevel.upper(), None)
+logging.basicConfig(
+    format='%(asctime)s %(levelname)-8s %(message)s', level=numeric_level)
+
+file_name_pattern = "*.IIQ"
+path_cope = (os.environ.get('COPE_PATH') or Path(
+    "C:/cope.Win.13.1.15-name_cope131/COPE/Bin/COPE.exe"))
+
+cope_options = ["-bits=8"]
+
+
+def find_files(root_dir: Path, file_name_pattern: str) -> list[list]:
+    """find files matching file_name_pattern in direct subdirectories of root_dir
+
+    Args:
+        root_dir (Path): top level directory to perform search in
+        file_name_pattern (str): globbing expression to match for
+
+    Returns:
+        list[list]: a list of lists with the filename and the parent directory basename of matching files
+    """
+    found_files = []
+    for file in Path(root_dir).glob("*/"+file_name_pattern):
+        found_files.append([file, file.parent.stem])
+    return (found_files)
+
+
+def get_parser():
+    """provides argument parser"""
+    parser = ArgumentParser()
+    parser.add_argument("-s", "--source", dest="source",
+                        required=True, type=str)
+    parser.add_argument("-t", "--target", dest="target",
+                        required=True, type=str)
+    parser.add_argument("-r", "--resolution", dest="resolution",
+                        required=False, type=int)
+    return parser
+
+
+if __name__ == "__main__":
+    parser = get_parser()
+    args = parser.parse_args()
+
+    sourcedir = Path(args.source)
+    targetdir = Path(args.target)
+    resolution = args.resolution
+
+    logging.debug(f"path to cope: {path_cope}")
+    logging.debug(f"source directory: {sourcedir}")
+    logging.debug(f"target directory: {targetdir}")
+
+    if resolution:
+        logging.debug(f"resolution: {resolution}")
+        cope_options.append(f"-resolution={resolution}")
+
+    if not os.path.isdir(sourcedir):
+        logging.error("source directory does not exist")
+        exit(1)
+
+    if not os.path.isdir(targetdir):
+        os.mkdir(targetdir)
+        logging.info("target directory created, as it did not exist")
+
+    logging.info("start processing...")
+    files = find_files(sourcedir, file_name_pattern)
+
+    if not files:
+        logging.info("no matching files found in source directory")
+
+    for file, base in files:
+        target = Path(targetdir) / (base + ".tif")
+        logging.info(f"processing {file}")
+
+        cope_command = [Path(path_cope), file, target] + cope_options
+
+        logging.debug(f"running {cope_command}")
+
+        # execute cope
+        try:
+            subprocess.run(cope_command, check=True)
+        except FileNotFoundError:
+            logging.error(f"cope executable was not found: {path_cope}")
+            exit(1)
+        except Exception as err:
+            logging.error(f"Unexpected {err=}, {type(err)=}")
+            raise
+
+        # cope does not appear to make much use of exit codes, thus we check the existence of the expected tiff file here
+        if not target.is_file():
+            logging.error(f"tiff file expected but not found: {target}")
+            exit(1)
+        else:
+            logging.debug(f"removing source package {target.with_suffix('')}")
+            shutil.rmtree(target.with_suffix(''))

install/cope/eip_prepare_for_cope.py

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+#!/usr/bin/env python3
+
+# This script extracts eip files in a source directory to a target directory, renames a specific subdirectory and moves the original eip files
+
+import os
+import shutil
+from argparse import ArgumentParser
+from pathlib import Path
+
+
+def extract_and_rename_eip(source_dir, target_dir):
+    # Check if source directory exists
+    if not os.path.isdir(source_dir):
+        print("Source directory does not exist")
+        exit(1)
+
+    # Create target directory if it does not exist
+    os.makedirs(target_dir, exist_ok=True)
+
+    if source_dir.name.endswith("_master"):
+        raw_directory = Path.joinpath(
+            source_dir.parent, source_dir.name.replace("_master", "_raw"))
+        os.makedirs(raw_directory, exist_ok=True)
+
+    for filename in os.listdir(source_dir):
+        if filename.endswith(".eip"):
+            file_path = os.path.join(source_dir, filename)
+            if os.path.isfile(file_path):
+                # Unzip eip to target directory
+                unzip_dir = os.path.join(
+                    target_dir, os.path.splitext(filename)[0])
+                shutil.unpack_archive(filename=file_path,
+                                      extract_dir=unzip_dir, format="zip")
+
+                capture_one_dir = os.path.join(unzip_dir, "CaptureOne")
+                settings_old = os.path.join(capture_one_dir, "Settings153")
+                settings_new = os.path.join(capture_one_dir, "Settings131")
+
+                # Check if CaptureOne directory exists
+                if not os.path.isdir(capture_one_dir):
+                    print(f"{capture_one_dir} does not exist")
+                    exit(1)
+
+                # Rename setting directory to matching version for cope
+                if os.path.isdir(settings_old):
+                    os.rename(settings_old, settings_new)
+
+            os.rename(file_path, Path.joinpath(raw_directory, filename))
+
+
+def get_parser():
+    """provides argument parser"""
+    parser = ArgumentParser()
+    parser.add_argument("-s", "--source", dest="source",
+                        required=True, type=str, help="Source directory")
+    parser.add_argument("-t", "--target", dest="target",
+                        required=True, type=str, help="Target directory")
+    return parser
+
+
+if __name__ == "__main__":
+    parser = get_parser()
+    args = parser.parse_args()
+
+    extract_and_rename_eip(Path(args.source), Path(args.target))