adds a --metadata-only option to pack (#72)

* adds a --server option to pack

* removed black autoformatting

* fix too many blank lines

* changes cli option to avoid collision

* line length

* adds store_true to add_argument

* rename tests

* changes cli argument to

* fix line lengths

* removes

* wrong valuerror test

* line length (sorry)

* fix readme (doc was on the wrong section)

* update .omero, some test failing

* remove spurious merge chars, without ruff formating

* merge chores

* restore wrongly deleted lines

* making sure submodule is still there

---------

Co-authored-by: Erick Martins Ratamero <[email protected]>

.omeroci/cli-build

@@ -22,4 +22,5 @@ conda activate omero
 
 export OMERO_DIST=${OMERO_DIST:-/opt/omero/server/OMERO.server}
 omero $PLUGIN -h
+
 python setup.py test -t test -i ${OMERO_DIST}/etc/ice.config -vs

README.md

@@ -63,6 +63,12 @@ about the files (name, mimetype).
 
 `--plugin` allows you to export omero data to a desired format by using an external plugin. See for example the [arc plugin](https://github.com/cmohl2013/omero-arc), which exports omero
 projects to ARC repositories.
+`--binaries` allows to specify whether to archive binary data
+(e.g images, ROIs, FileAnnotations) or only create the transfer.xml.
+Default is `all` and will create the archive. With `none`, only the `transfer.xml`
+file is created, in which case the last cli argument is the path where
+the `transfer.xml` file will be written.
+
 
 Examples:
 ```
@@ -71,6 +77,8 @@ omero transfer pack --zip Image:123 transfer_pack.zip
 omero transfer pack Dataset:1111 /home/user/new_folder/new_pack.tar
 omero transfer pack 999 tarfile.tar  # equivalent to Project:999
 omero transfer pack --plugin arc Project:999 path/to/my/arc/repo
+omero transfer pack --binaries none Dataset:1111 /home/user/new_folder/
+omero transfer pack --binaries all Dataset:1111 /home/user/new_folder/new_pack.tar
 ```
 
 ## `omero transfer unpack`

src/omero_cli_transfer.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+# !/usr/bin/env python
 # -*- coding: utf-8 -*-
 # Copyright (C) 2022 The Jackson Laboratory
 # All rights reserved.
@@ -85,12 +85,21 @@
 orig_group`), other options are `none`, `img_id`, `timestamp`, `software`,
 `version`, `md5`, `hostname`, `db_id`, `orig_user`, `orig_group`.
 
+--binaries allows to specify whether to archive binary data
+(e.g images, ROIs, FileAnnotations) or only create the transfer.xml.
+Default is `all` and will create the archive.
+With `none`, only the `transfer.xml` file is created, in which case
+the last cli argument is the path where the `transfer.xml` file
+will be written.
+
 Examples:
 omero transfer pack Image:123 transfer_pack.tar
 omero transfer pack --zip Image:123 transfer_pack.zip
 omero transfer pack Dataset:1111 /home/user/new_folder/new_pack.tar
 omero transfer pack 999 tarfile.tar  # equivalent to Project:999
 omero transfer pack 1 transfer_pack.tar --metadata img_id version db_id
+omero transfer pack --binaries none Dataset:1111 /home/user/new_folder/
+omero transfer pack --binaries all Dataset:1111 /home/user/new_folder/pack.tar
 """)
 
 UNPACK_HELP = ("""Unpacks a transfer packet into an OMERO hierarchy.
@@ -224,6 +233,14 @@ def _configure(self, parser):
                 "--plugin", help="Use external plugin for packing.",
                 type=str)
         pack.add_argument("filepath", type=str, help=file_help)
+        pack.add_argument(
+            "--binaries",
+            choices=["all", "none"],
+            default="all",
+            help="With `--binaries none`, only generate the metadata file "
+                 "(transfer.xml or ro-crate-metadata.json). "
+                 "With `--binaries all` (the default), both pixel data "
+                 "and annotation are saved.")
 
         file_help = ("Path to where the zip file is saved")
         unpack.add_argument("filepath", type=str, help=file_help)
@@ -396,6 +413,11 @@ def __pack(self, args):
             if args.simple:
                 raise ValueError("Single plate or screen cannot be "
                                  "packaged in human-readable format")
+
+        if (args.binaries == "none") and args.simple:
+            raise ValueError("The `--binaries none` and `--simple` options "
+                             "are  incompatible")
+
         if isinstance(args.object, Image):
             src_datatype, src_dataid = "Image", args.object.id
         elif isinstance(args.object, Dataset):
@@ -422,7 +444,12 @@ def __pack(self, args):
                              " permissions for current user.")
         print("Populating xml...")
         tar_path = Path(args.filepath)
-        folder = str(tar_path) + "_folder"
+        if args.binaries == "all":
+            folder = str(tar_path) + "_folder"
+        else:
+            folder = os.path.splitext(tar_path)[0]
+            print(f"Output will be written to {folder}")
+
         os.makedirs(folder, mode=DIR_PERM, exist_ok=True)
         if args.barchive:
             md_fp = str(Path(folder) / "submission.tsv")
@@ -436,8 +463,11 @@ def __pack(self, args):
                                          args.barchive, args.simple,
                                          args.figure,
                                          self.metadata)
-        print("Starting file copy...")
-        self._copy_files(path_id_dict, folder, self.gateway)
+
+        if args.binaries == "all":
+            print("Starting file copy...")
+            self._copy_files(path_id_dict, folder, self.gateway)
+
         if args.simple:
             self._fix_pixels_image_simple(ome, folder, md_fp)
         if args.barchive:
@@ -477,11 +507,11 @@ def __pack(self, args):
                     tmp_path=Path(folder),
                     image_filenames_mapping=path_id_dict,
                     conn=self.gateway)
-        else:
+        elif args.binaries == "all":
             self._package_files(os.path.splitext(tar_path)[0], args.zip,
                                 folder)
-        print("Cleaning up...")
-        shutil.rmtree(folder)
+            print("Cleaning up...")
+            shutil.rmtree(folder)
         return
 
     def __unpack(self, args):

test/integration/test_transfer.py

@@ -188,6 +188,26 @@ def test_pack_special(self, target_name, tmpdir):
                 assert len(f.getmembers()) == 6
         self.delete_all()
 
+    @pytest.mark.parametrize('target_name', sorted(SUPPORTED))
+    def test_pack_metadata_only(self, target_name, tmpdir):
+        if target_name == "datasetid" or target_name == "projectid" or\
+           target_name == "idonly" or target_name == "imageid":
+            self.create_image(target_name=target_name)
+        elif target_name == "plateid" or target_name == "screenid":
+            self.create_plate(target_name=target_name)
+        target = getattr(self, target_name)
+        args = self.args + ["pack", target, "--binaries", "none",
+                            str(tmpdir)]
+        self.cli.invoke(args, strict=True)
+        assert os.path.exists(str(tmpdir / 'transfer.xml'))
+        assert os.path.getsize(str(tmpdir / 'transfer.xml')) > 0
+
+        args = self.args + ["pack", target, "--binaries", "none", "--simple",
+                            str(tmpdir)]
+        with pytest.raises(ValueError):
+            self.cli.invoke(args, strict=True)
+        self.delete_all()
+
     @pytest.mark.parametrize('folder_name', TEST_FOLDERS)
     def test_unpack_folder(self, folder_name):
         self.args += ["unpack", "--folder", folder_name]