From 581996c21e3591c866759adaffa60284908167a3 Mon Sep 17 00:00:00 2001
From: Erick Martins Ratamero <erickmartins@gmx.net>
Date: Thu, 3 Aug 2023 13:29:31 -0400
Subject: [PATCH] Add `--merge` option to `unpack` (#57)

* bump to new ome-types

* updating things for ome_types=0.4.0

* first try at merge projects, stubs for others

* only missing find_dataset

* first pass at merge, find_dataset needs reviewing

* now resolving dataset refs to actual datasets

* basic merge functionality working

* added basic prepare metadata

* doing clever image matching (again?) considering annotations

* tests passing - made `conn` optional on `make_image_map`

* merge tests passing, some extra minor fixes

- merging orphaned datasets
- using `isInstance` instead of `type`

* updated readme and setup.py
---
 .gitignore                        |   3 +
 README.md                         |   4 +
 requirements.txt                  |   2 +-
 setup.py                          |   4 +-
 src/generate_omero_objects.py     | 144 +++++++++++++++++++++++++-----
 src/generate_xml.py               |  61 +++++++++----
 src/omero_cli_transfer.py         |  40 +++++++--
 test/data/simple_screen.zip       | Bin 23808 -> 24334 bytes
 test/integration/test_prepare.py  |  28 +++---
 test/integration/test_transfer.py |  34 +++++++
 test/unit/test_set.py             |   2 +-
 11 files changed, 255 insertions(+), 67 deletions(-)

diff --git a/.gitignore b/.gitignore
index e6f8fb2..05792f8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -131,3 +131,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# vs code settings
+.vscode/
diff --git a/README.md b/README.md
index 3b17f24..93e1952 100644
--- a/README.md
+++ b/README.md
@@ -73,6 +73,10 @@ Note that unpack needs to be able to identify the images it imports inequivocall
 
 `--folder` allows the user to point to a previously-unpacked folder rather than a single file.
 
+`--merge` will use existing Projects, Datasets and Screens if the current user
+already owns entities with the same name as ones defined in `transfer.xml`,
+effectively merging the "new" unpacked entities with existing ones.
+
 Examples:
 ```
 omero transfer unpack transfer_pack.zip
diff --git a/requirements.txt b/requirements.txt
index 47a5a57..cc188e9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
 ezomero>=2.0.0
-ome-types>=0.3.4
+ome-types>=0.4.0
 setuptools>=58.0.0
\ No newline at end of file
diff --git a/setup.py b/setup.py
index c24dd83..d8df849 100644
--- a/setup.py
+++ b/setup.py
@@ -84,7 +84,7 @@ def read(fname):
     packages=['', 'omero.plugins'],
     package_dir={"": "src"},
     name="omero-cli-transfer",
-    version='0.6.0',
+    version='0.7.0',
     maintainer="Erick Ratamero",
     maintainer_email="erick.ratamero@jax.org",
     description=("A set of utilities for exporting a transfer"
@@ -96,7 +96,7 @@ def read(fname):
     url="https://github.com/TheJacksonLaboratory/omero-cli-transfer",
     install_requires=[
         'ezomero==2.0.0',
-        'ome-types==0.3.4'
+        'ome-types==0.4.0'
     ],
     extras_require={
         "rocrate": ["rocrate==0.7.0"],
diff --git a/src/generate_omero_objects.py b/src/generate_omero_objects.py
index de40c86..3bd0e47 100644
--- a/src/generate_omero_objects.py
+++ b/src/generate_omero_objects.py
@@ -25,6 +25,20 @@
 import copy
 
 
+def create_or_set_projects(pjs: List[Project], conn: BlitzGateway,
+                           merge: bool) -> dict:
+    pj_map = {}
+    if not merge:
+        pj_map = create_projects(pjs, conn)
+    else:
+        for pj in pjs:
+            pj_id = find_project(pj, conn)
+            if not pj_id:
+                pj_id = ezomero.post_project(conn, pj.name, pj.description)
+            pj_map[pj.id] = pj_id
+    return pj_map
+
+
 def create_projects(pjs: List[Project], conn: BlitzGateway) -> dict:
     pj_map = {}
     for pj in pjs:
@@ -33,6 +47,29 @@ def create_projects(pjs: List[Project], conn: BlitzGateway) -> dict:
     return pj_map
 
 
+def find_project(pj: Project, conn: BlitzGateway) -> int:
+    id = 0
+    my_exp_id = conn.getUser().getId()
+    for p in conn.getObjects("Project", opts={'owner': my_exp_id}):
+        if p.getName() == pj.name:
+            id = p.getId()
+    return id
+
+
+def create_or_set_screens(scrs: List[Screen], conn: BlitzGateway, merge: bool
+                          ) -> dict:
+    scr_map = {}
+    if not merge:
+        scr_map = create_screens(scrs, conn)
+    else:
+        for scr in scrs:
+            scr_id = find_screen(scr, conn)
+            if not scr_id:
+                scr_id = ezomero.post_screen(conn, scr.name, scr.description)
+            scr_map[scr.id] = scr_id
+    return scr_map
+
+
 def create_screens(scrs: List[Screen], conn: BlitzGateway) -> dict:
     scr_map = {}
     for scr in scrs:
@@ -41,6 +78,34 @@ def create_screens(scrs: List[Screen], conn: BlitzGateway) -> dict:
     return scr_map
 
 
+def find_screen(sc: Screen, conn: BlitzGateway) -> int:
+    id = 0
+    my_exp_id = conn.getUser().getId()
+    for s in conn.getObjects("Screen", opts={'owner': my_exp_id}):
+        if s.getName() == sc.name:
+            id = s.getId()
+    return id
+
+
+def create_or_set_datasets(dss: List[Dataset], pjs: List[Project],
+                           conn: BlitzGateway, merge: bool) -> dict:
+    ds_map = {}
+    if not merge:
+        ds_map = create_datasets(dss, conn)
+    else:
+        for ds in dss:
+            ds_id = find_dataset(ds, pjs, conn)
+            if not ds_id:
+                dataset = DatasetWrapper(conn, DatasetI())
+                dataset.setName(ds.name)
+                if ds.description is not None:
+                    dataset.setDescription(ds.description)
+                dataset.save()
+                ds_id = dataset.getId()
+            ds_map[ds.id] = ds_id
+    return ds_map
+
+
 def create_datasets(dss: List[Dataset], conn: BlitzGateway) -> dict:
     """
     Currently doing it the non-ezomero way because ezomero always
@@ -58,6 +123,31 @@ def create_datasets(dss: List[Dataset], conn: BlitzGateway) -> dict:
     return ds_map
 
 
+def find_dataset(ds: Dataset, pjs: List[Project], conn: BlitzGateway) -> int:
+    id = 0
+    my_exp_id = conn.getUser().getId()
+    orphan = True
+    for pj in pjs:
+        for dsref in pj.dataset_refs:
+            if dsref.id == ds.id:
+                orphan = False
+    if not orphan:
+        for pj in pjs:
+            for p in conn.getObjects("Project", opts={'owner': my_exp_id}):
+                if p.getName() == pj.name:
+                    for dsref in pj.dataset_refs:
+                        if dsref.id == ds.id:
+                            for ds_rem in p.listChildren():
+                                if ds.name == ds_rem.getName():
+                                    id = ds_rem.getId()
+    else:
+        for d in conn.getObjects("Dataset", opts={'owner': my_exp_id,
+                                                  'orphaned': True}):
+            if d.getName() == ds.name:
+                id = d.getId()
+    return id
+
+
 def create_annotations(ans: List[Annotation], conn: BlitzGateway, hash: str,
                        folder: str, metadata: List[str]) -> dict:
     ann_map = {}
@@ -73,7 +163,7 @@ def create_annotations(ans: List[Annotation], conn: BlitzGateway, hash: str,
             namespace = an.namespace
             map_ann.setNs(namespace)
             key_value_data = []
-            for v in an.value.m:
+            for v in an.value.ms:
                 if int(an.id.split(":")[-1]) < 0:
                     if not metadata:
                         key_value_data.append(['empty_metadata', "True"])
@@ -131,7 +221,7 @@ def create_original_file(ann: FileAnnotation, ans: List[Annotation],
                          conn: BlitzGateway, folder: str
                          ) -> OriginalFileWrapper:
     curr_folder = str(Path('.').resolve())
-    for an in ann.annotation_ref:
+    for an in ann.annotation_refs:
         clean_id = int(an.id.split(":")[-1])
         if clean_id < 0:
             cmnt_id = an.id
@@ -149,7 +239,7 @@ def create_plate_map(ome: OME, img_map: dict, conn: BlitzGateway
     plate_map = {}
     map_ref_ids = []
     for plate in ome.plates:
-        ann_ids = [i.id for i in plate.annotation_ref]
+        ann_ids = [i.id for i in plate.annotation_refs]
         file_path = ""
         for ann in ome.structured_annotations:
             if (ann.id in ann_ids and
@@ -201,9 +291,9 @@ def create_plate_map(ome: OME, img_map: dict, conn: BlitzGateway
             plate_id = create_plate_from_images(plate, img_map, conn)
         plate_map[plate.id] = plate_id
     for p in newome.plates:
-        for ref in p.annotation_ref:
+        for ref in p.annotation_refs:
             if ref.id in map_ref_ids:
-                p.annotation_ref.remove(ref)
+                p.annotation_refs.remove(ref)
     return plate_map, newome
 
 
@@ -342,7 +432,7 @@ def _int_to_rgba(omero_val: int) -> Tuple[int, int, int, int]:
 def create_rois(rois: List[ROI], imgs: List[Image], img_map: dict,
                 conn: BlitzGateway):
     for img in imgs:
-        for roiref in img.roi_ref:
+        for roiref in img.roi_refs:
             roi = next(filter(lambda x: x.id == roiref.id, rois))
             shapes = create_shapes(roi)
             img_id_dest = img_map[img.id]
@@ -354,10 +444,15 @@ def create_rois(rois: List[ROI], imgs: List[Image], img_map: dict,
 def link_datasets(ome: OME, proj_map: dict, ds_map: dict, conn: BlitzGateway):
     for proj in ome.projects:
         proj_id = proj_map[proj.id]
+        proj_obj = conn.getObject("Project", proj_id)
+        existing_ds = []
+        for dataset in proj_obj.listChildren():
+            existing_ds.append(dataset.getId())
         ds_ids = []
-        for ds in proj.dataset_ref:
+        for ds in proj.dataset_refs:
             ds_id = ds_map[ds.id]
-            ds_ids.append(ds_id)
+            if ds_id not in existing_ds:
+                ds_ids.append(ds_id)
         ezomero.link_datasets_to_project(conn, ds_ids, proj_id)
     return
 
@@ -366,10 +461,15 @@ def link_plates(ome: OME, screen_map: dict, plate_map: dict,
                 conn: BlitzGateway):
     for screen in ome.screens:
         screen_id = screen_map[screen.id]
+        scr_obj = conn.getObject("Screen", screen_id)
+        existing_pl = []
+        for pl in scr_obj.listChildren():
+            existing_pl.append(pl.getId())
         pl_ids = []
-        for pl in screen.plate_ref:
+        for pl in screen.plate_refs:
             pl_id = plate_map[pl.id]
-            pl_ids.append(pl_id)
+            if pl_id not in existing_pl:
+                pl_ids.append(pl_id)
         ezomero.link_plates_to_screen(conn, pl_ids, screen_id)
     return
 
@@ -378,7 +478,7 @@ def link_images(ome: OME, ds_map: dict, img_map: dict, conn: BlitzGateway):
     for ds in ome.datasets:
         ds_id = ds_map[ds.id]
         img_ids = []
-        for img in ds.image_ref:
+        for img in ds.image_refs:
             try:
                 img_id = img_map[img.id]
                 img_ids.append(img_id)
@@ -395,14 +495,14 @@ def link_annotations(ome: OME, proj_map: dict, ds_map: dict, img_map: dict,
         proj_id = proj_map[proj.id]
         proj_obj = conn.getObject("Project", proj_id)
         anns = ome.structured_annotations
-        for annref in proj.annotation_ref:
+        for annref in proj.annotation_refs:
             ann = next(filter(lambda x: x.id == annref.id, anns))
             link_one_annotation(proj_obj, ann, ann_map, conn)
     for ds in ome.datasets:
         ds_id = ds_map[ds.id]
         ds_obj = conn.getObject("Dataset", ds_id)
         anns = ome.structured_annotations
-        for annref in ds.annotation_ref:
+        for annref in ds.annotation_refs:
             ann = next(filter(lambda x: x.id == annref.id, anns))
             link_one_annotation(ds_obj, ann, ann_map, conn)
     for img in ome.images:
@@ -410,7 +510,7 @@ def link_annotations(ome: OME, proj_map: dict, ds_map: dict, img_map: dict,
             img_id = img_map[img.id]
             img_obj = conn.getObject("Image", img_id)
             anns = ome.structured_annotations
-            for annref in img.annotation_ref:
+            for annref in img.annotation_refs:
                 ann = next(filter(lambda x: x.id == annref.id, anns))
                 link_one_annotation(img_obj, ann, ann_map, conn)
         except KeyError:
@@ -419,23 +519,23 @@ def link_annotations(ome: OME, proj_map: dict, ds_map: dict, img_map: dict,
         scr_id = scr_map[scr.id]
         scr_obj = conn.getObject("Screen", scr_id)
         anns = ome.structured_annotations
-        for annref in scr.annotation_ref:
+        for annref in scr.annotation_refs:
             ann = next(filter(lambda x: x.id == annref.id, anns))
             link_one_annotation(scr_obj, ann, ann_map, conn)
     for pl in ome.plates:
         pl_id = pl_map[pl.id]
         pl_obj = conn.getObject("Plate", pl_id)
         anns = ome.structured_annotations
-        for annref in pl.annotation_ref:
+        for annref in pl.annotation_refs:
             ann = next(filter(lambda x: x.id == annref.id, anns))
             link_one_annotation(pl_obj, ann, ann_map, conn)
         anns = ome.structured_annotations
         for well in pl.wells:
-            if len(well.annotation_ref) > 0:
+            if len(well.annotation_refs) > 0:
                 row, col = well.row, well.column
                 well_id = ezomero.get_well_id(conn, pl_id, row, col)
                 well_obj = conn.getObject("Well", well_id)
-                for annref in well.annotation_ref:
+                for annref in well.annotation_refs:
                     ann = next(filter(lambda x: x.id == annref.id, anns))
                     link_one_annotation(well_obj, ann, ann_map, conn)
     return
@@ -485,13 +585,13 @@ def rename_plates(pls: List[Plate], pl_map: dict, conn: BlitzGateway):
 
 
 def populate_omero(ome: OME, img_map: dict, conn: BlitzGateway, hash: str,
-                   folder: str, metadata: List[str]):
+                   folder: str, metadata: List[str], merge: bool):
     plate_map, ome = create_plate_map(ome, img_map, conn)
     rename_images(ome.images, img_map, conn)
     rename_plates(ome.plates, plate_map, conn)
-    proj_map = create_projects(ome.projects, conn)
-    ds_map = create_datasets(ome.datasets, conn)
-    screen_map = create_screens(ome.screens, conn)
+    proj_map = create_or_set_projects(ome.projects, conn, merge)
+    ds_map = create_or_set_datasets(ome.datasets, ome.projects, conn, merge)
+    screen_map = create_or_set_screens(ome.screens, conn, merge)
     ann_map = create_annotations(ome.structured_annotations, conn,
                                  hash, folder, metadata)
     create_rois(ome.rois, ome.images, img_map, conn)
diff --git a/src/generate_xml.py b/src/generate_xml.py
index 672c2b3..161e84d 100644
--- a/src/generate_xml.py
+++ b/src/generate_xml.py
@@ -459,7 +459,7 @@ def create_provenance_metadata(conn: BlitzGateway, img_id: int,
             mmap.append(M(k=_key, value=''))
     kv, ref = create_kv_and_ref(id=id,
                                 namespace=ns,
-                                value=Map(m=mmap))
+                                value=Map(ms=mmap))
     return kv, ref
 
 
@@ -527,7 +527,7 @@ def parse_files_import(text):
 
 
 def parse_showinf(text, counter_imgs, counter_plates, target):
-    ome = from_xml(text, parser='xmlschema')
+    ome = from_xml(text)
     images = []
     plates = []
     annotations = []
@@ -552,7 +552,10 @@ def parse_showinf(text, counter_imgs, counter_plates, target):
                                )
         annotations.append(an)
         anref = AnnotationRef(id=an.id)
-        img.annotation_ref.append(anref)
+        img.annotation_refs.append(anref)
+        an, anref = create_prepare_metadata()
+        annotations.append(an)
+        img.annotation_refs.append(anref)
         images.append(img)
     for plate in ome.plates:
         pl_id_str = f"Plate:{str(pl_id)}"
@@ -568,11 +571,33 @@ def parse_showinf(text, counter_imgs, counter_plates, target):
                                )
         annotations.append(an)
         anref = AnnotationRef(id=an.id)
-        pl.annotation_ref.append(anref)
+        pl.annotation_refs.append(anref)
         plates.append(pl)
     return images, plates, annotations
 
 
+def create_prepare_metadata():
+    software = "omero-cli-transfer"
+    version = pkg_resources.get_distribution(software).version
+    date_time = datetime.now().strftime("%d/%m/%Y, %H:%M:%S")
+    ns = 'openmicroscopy.org/cli/transfer/prepare'
+    id = (-1) * uuid4().int
+    md_dict: Dict[str, Any] = {}
+    md_dict['software'] = software
+    md_dict['version'] = version
+    md_dict['packing_timestamp'] = date_time
+    mmap = []
+    for _key, _value in md_dict.items():
+        if _value:
+            mmap.append(M(k=_key, value=str(_value)))
+        else:
+            mmap.append(M(k=_key, value=''))
+    kv, ref = create_kv_and_ref(id=id,
+                                namespace=ns,
+                                value=Map(ms=mmap))
+    return kv, ref
+
+
 def create_empty_pixels(image, id):
     pix_id = f"Pixels:{str(id)}"
     pixels = Pixels(
@@ -630,11 +655,11 @@ def populate_image(obj: ImageI, ome: OME, conn: BlitzGateway, hostname: str,
         if kv_id not in [i.id for i in ome.structured_annotations]:
             ome.structured_annotations.append(kv)
         if ref:
-            img.annotation_ref.append(ref)
+            img.annotation_refs.append(ref)
     filepath_anns, refs = create_filepath_annotations(img_id, conn)
     for i in range(len(filepath_anns)):
         ome.structured_annotations.append(filepath_anns[i])
-        img.annotation_ref.append(refs[i])
+        img.annotation_refs.append(refs[i])
     roi_service = conn.getRoiService()
     rois = roi_service.findByImage(id, None).rois
     for roi in rois:
@@ -668,7 +693,7 @@ def populate_dataset(obj: DatasetI, ome: OME, conn: BlitzGateway,
     for img in obj.listChildren():
         img_obj = conn.getObject('Image', img.getId())
         img_ref = populate_image(img_obj, ome, conn, hostname, metadata)
-        ds.image_ref.append(img_ref)
+        ds.image_refs.append(img_ref)
     ds_id = f"Dataset:{str(ds.id)}"
     if ds_id not in [i.id for i in ome.datasets]:
         ome.datasets.append(ds)
@@ -686,7 +711,7 @@ def populate_project(obj: ProjectI, ome: OME, conn: BlitzGateway,
     for ds in obj.listChildren():
         ds_obj = conn.getObject('Dataset', ds.getId())
         ds_ref = populate_dataset(ds_obj, ome, conn, hostname, metadata)
-        proj.dataset_ref.append(ds_ref)
+        proj.dataset_refs.append(ds_ref)
     ome.projects.append(proj)
 
 
@@ -701,7 +726,7 @@ def populate_screen(obj: ScreenI, ome: OME, conn: BlitzGateway,
     for pl in obj.listChildren():
         pl_obj = conn.getObject('Plate', pl.getId())
         pl_ref = populate_plate(pl_obj, ome, conn, hostname, metadata)
-        scr.plate_ref.append(pl_ref)
+        scr.plate_refs.append(pl_ref)
     ome.screens.append(scr)
 
 
@@ -720,23 +745,23 @@ def populate_plate(obj: PlateI, ome: OME, conn: BlitzGateway,
         if kv_id not in [i.id for i in ome.structured_annotations]:
             ome.structured_annotations.append(kv)
         if ref:
-            pl.annotation_ref.append(ref)
+            pl.annotation_refs.append(ref)
     for well in obj.listChildren():
         well_obj = conn.getObject('Well', well.getId())
         well_ref = populate_well(well_obj, ome, conn, hostname, metadata)
         pl.wells.append(well_ref)
-    last_image_anns = ome.images[-1].annotation_ref
+    last_image_anns = ome.images[-1].annotation_refs
     last_image_anns_ids = [i.id for i in last_image_anns]
     for ann in ome.structured_annotations:
         if (ann.id in last_image_anns_ids and
-                type(ann) == CommentAnnotation and
+                isinstance(ann, CommentAnnotation) and
                 int(ann.id.split(":")[-1]) < 0):
             plate_path = ann.value
     filepath_anns, refs = create_filepath_annotations(pl.id, conn,
                                                       plate_path=plate_path)
     for i in range(len(filepath_anns)):
         ome.structured_annotations.append(filepath_anns[i])
-        pl.annotation_ref.append(refs[i])
+        pl.annotation_refs.append(refs[i])
     pl_id = f"Plate:{str(pl.id)}"
     if pl_id not in [i.id for i in ome.plates]:
         ome.plates.append(pl)
@@ -784,7 +809,7 @@ def add_annotation(obj: Union[Project, Dataset, Image, Plate, Screen,
         kv, ref = create_kv_and_ref(id=ann.getId(),
                                     namespace=ann.getNs(),
                                     value=Map(
-                                    m=mmap))
+                                    ms=mmap))
         if kv.id not in [i.id for i in ome.structured_annotations]:
             ome.structured_annotations.append(kv)
         obj.annotation_ref.append(ref)
@@ -934,10 +959,10 @@ def generate_columns(ome: OME, ids: dict) -> List[str]:
                 columns.append("comment")
     anns = ome.structured_annotations
     for i in ome.images:
-        for ann_ref in i.annotation_ref:
+        for ann_ref in i.annotation_refs:
             ann = next(filter(lambda x: x.id == ann_ref.id, anns))
             if isinstance(ann, MapAnnotation):
-                for v in ann.value.m:
+                for v in ann.value.ms:
                     if v.k not in columns:
                         columns.append(v.k)
     return columns
@@ -969,7 +994,7 @@ def list_files(ome: OME, ids: dict, top_level: str) -> List[str]:
 def find_dataset(id: str, ome: OME) -> Union[str, None]:
     for d in ome.datasets:
         def lfunc(x): return x.id == id
-        if any(filter(lfunc, d.image_ref)):
+        if any(filter(lfunc, d.image_refs)):
             return d.name
     return None
 
@@ -1029,7 +1054,7 @@ def generate_lines_and_move(img: Image, ome: OME, ids: dict, folder: str,
 
 def get_annotation_vals(cols: List[str], img: Image, ome: OME) -> List[str]:
     anns = []
-    for annref in img.annotation_ref:
+    for annref in img.annotation_refs:
         a = next(filter(lambda x: x.id == annref.id,
                  ome.structured_annotations))
         anns.append(a)
diff --git a/src/omero_cli_transfer.py b/src/omero_cli_transfer.py
index 798b0ed..d9524a6 100644
--- a/src/omero_cli_transfer.py
+++ b/src/omero_cli_transfer.py
@@ -95,6 +95,10 @@
 --folder allows the user to point to a previously-unpacked folder rather than
 a single file.
 
+--merge will use existing Projects, Datasets and Screens if the current user
+already owns entities with the same name as ones defined in `transfer.xml`,
+effectively merging the "new" unpacked entities with existing ones.
+
 --metadata allows you to specify which transfer metadata will be used from
 `transfer.xml` as MapAnnotation values to the images. Fields that do not
 exist on `transfer.xml` will be ignored. Default is `all` (equivalent to
@@ -198,6 +202,9 @@ def _configure(self, parser):
         unpack.add_argument(
                 "--ln_s_import", help="Use in-place import",
                 action="store_true")
+        unpack.add_argument(
+                "--merge", help="Use existing entities if possible",
+                action="store_true")
         unpack.add_argument(
                 "--folder", help="Pass path to a folder rather than a pack",
                 action="store_true")
@@ -384,7 +391,7 @@ def __unpack(self, args):
                                                      args.output)
         else:
             folder = Path(args.filepath)
-            ome = from_xml(folder / "transfer.xml", parser='xmlschema')
+            ome = from_xml(folder / "transfer.xml")
             hash = "imported from folder"
         print("Generating Image mapping and import filelist...")
         ome, src_img_map, filelist = self._create_image_map(ome)
@@ -397,10 +404,10 @@ def __unpack(self, args):
                                           ln_s, args.skip, self.gateway)
         self._delete_all_rois(dest_img_map, self.gateway)
         print("Matching source and destination images...")
-        img_map = self._make_image_map(src_img_map, dest_img_map)
+        img_map = self._make_image_map(src_img_map, dest_img_map, self.gateway)
         print("Creating and linking OMERO objects...")
         populate_omero(ome, img_map, self.gateway,
-                       hash, folder, self.metadata)
+                       hash, folder, self.metadata, args.merge)
         return
 
     def _load_from_pack(self, filepath: str, output: Optional[str] = None
@@ -433,7 +440,7 @@ def _load_from_pack(self, filepath: str, output: Optional[str] = None
                 raise ValueError("File is not a zip or tar file")
         else:
             raise FileNotFoundError("filepath is not a zip file")
-        ome = from_xml(folder / "transfer.xml", parser='xmlschema')
+        ome = from_xml(folder / "transfer.xml")
         return hash, ome, folder
 
     def _create_image_map(self, ome: OME
@@ -458,9 +465,9 @@ def _create_image_map(self, ome: OME
                         filelist.append(ann.value)
                     newome.structured_annotations.remove(ann)
         for i in newome.images:
-            for ref in i.annotation_ref:
+            for ref in i.annotation_refs:
                 if ref.id in map_ref_ids:
-                    i.annotation_ref.remove(ref)
+                    i.annotation_refs.remove(ref)
         filelist = list(set(filelist))
         img_map = DefaultDict(list, {x: sorted(img_map[x])
                               for x in img_map.keys()})
@@ -532,7 +539,8 @@ def _get_image_ids(self, file_path: str, conn: BlitzGateway) -> List[str]:
                     image_ids.append(img_id)
         return image_ids
 
-    def _make_image_map(self, source_map: dict, dest_map: dict) -> dict:
+    def _make_image_map(self, source_map: dict, dest_map: dict,
+                        conn: Optional[BlitzGateway] = None) -> dict:
         # using both source and destination file-to-image-id maps,
         # map image IDs between source and destination
         src_dict = DefaultDict(list)
@@ -555,10 +563,24 @@ def _make_image_map(self, source_map: dict, dest_map: dict) -> dict:
             src_v = src_dict[src_k]
             if src_k in dest_dict.keys():
                 dest_v = dest_dict[src_k]
-                if len(src_v) == len(dest_v):
+                clean_dest = []
+                if not conn:
+                    clean_dest = dest_v
+                else:
+                    for i in dest_v:
+                        img_obj = conn.getObject("Image", i)
+                        anns = 0
+                        for j in img_obj.listAnnotations():
+                            ns = j.getNs()
+                            if ns.startswith(
+                                    "openmicroscopy.org/cli/transfer"):
+                                anns += 1
+                        if not anns:
+                            clean_dest.append(i)
+                if len(src_v) == len(clean_dest):
                     for count in range(len(src_v)):
                         map_key = f"Image:{src_v[count]}"
-                        imgmap[map_key] = dest_v[count]
+                        imgmap[map_key] = clean_dest[count]
         return imgmap
 
     def __prepare(self, args):
diff --git a/test/data/simple_screen.zip b/test/data/simple_screen.zip
index 01530e7d10d64c02380afc2f11ee237aa58a4106..52d41dad5b013641182d09aaf39dcd68b88b434d 100644
GIT binary patch
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diff --git a/test/integration/test_prepare.py b/test/integration/test_prepare.py
index 21c8ae4..c3eb80e 100644
--- a/test/integration/test_prepare.py
+++ b/test/integration/test_prepare.py
@@ -168,8 +168,8 @@ def run_asserts_edited(self):
             elif img_name == "edited image name":
                 kvs = ezomero.get_map_annotation_ids(self.gw, "Image",
                                                      img.getId())
-                assert len(kvs) == 1
-                kv = ezomero.get_map_annotation(self.gw, kvs[0])
+                assert len(kvs) == 2
+                kv = ezomero.get_map_annotation(self.gw, kvs[-1])
                 assert len(kv) == 2
                 assert kv['key1'] == "value1"
                 assert kv['key2'] == "2"
@@ -179,7 +179,7 @@ def run_asserts_edited(self):
                 shapes = ezomero.get_shape_ids(self.gw, rois[0])
                 assert len(shapes) == 1
                 shape = ezomero.get_shape(self.gw, shapes[0])
-                assert type(shape) == ezomero.rois.Rectangle
+                assert type(shape) is ezomero.rois.Rectangle
                 assert shape.x == 1
                 assert shape.y == 2
                 assert shape.width == 3
@@ -195,12 +195,12 @@ def run_asserts_edited(self):
         assert len(pl_ids) == 1
 
     def edit_xml(self, filename):
-        ome = from_xml(filename, parser='xmlschema')
+        ome = from_xml(filename)
         new_proj = Project(id="Project:1", name="edited project")
         new_ds = Dataset(id="Dataset:1", name="edited dataset")
         newtag1 = TagAnnotation(id="Annotation:1", value="tag for proj")
         newtag2 = TagAnnotation(id="Annotation:2", value="tag for img")
-        new_proj.annotation_ref.append(AnnotationRef(id=newtag1.id))
+        new_proj.annotation_refs.append(AnnotationRef(id=newtag1.id))
         md_dict = {"key1": "value1", "key2": 2}
         mmap = []
         for _key, _value in md_dict.items():
@@ -208,31 +208,31 @@ def edit_xml(self, filename):
                 mmap.append(M(k=_key, value=str(_value)))
             else:
                 mmap.append(M(k=_key, value=''))
-        mapann = MapAnnotation(id="Annotation:3", value=Map(m=mmap))
+        mapann = MapAnnotation(id="Annotation:3", value=Map(ms=mmap))
         rect = Rectangle(id="Shape:1", x=1, y=2, width=3, height=4)
         roi = ROI(id="ROI:1", union=[rect])
         ome.rois.append(roi)
         ome.structured_annotations.extend([newtag1, newtag2, mapann])
         for img in ome.images:
             if img.name == "test_pyramid.tiff":
-                img.annotation_ref.append(AnnotationRef(id=newtag2.id))
+                img.annotation_refs.append(AnnotationRef(id=newtag2.id))
                 imref = ImageRef(id=img.id)
-                new_ds.image_ref.append(imref)
+                new_ds.image_refs.append(imref)
             elif img.name == "vsi-ets-test-jpg2k.vsi [001 C405, C488]":
                 img.name = "edited image name"
-                img.annotation_ref.append(AnnotationRef(id=mapann.id))
+                img.annotation_refs.append(AnnotationRef(id=mapann.id))
                 imref = ImageRef(id=img.id)
-                new_ds.image_ref.append(imref)
+                new_ds.image_refs.append(imref)
             elif img.name == "vsi-ets-test-jpg2k.vsi [macro image]":
-                img.roi_ref.append(ROIRef(id=roi.id))
+                img.roi_refs.append(ROIRef(id=roi.id))
                 imref = ImageRef(id=img.id)
-                new_ds.image_ref.append(imref)
+                new_ds.image_refs.append(imref)
         dsref = DatasetRef(id=new_ds.id)
-        new_proj.dataset_ref.append(dsref)
+        new_proj.dataset_refs.append(dsref)
         ome.projects.append(new_proj)
         ome.datasets.append(new_ds)
         new_scr = Screen(id="Screen:1", name="edited screen")
-        new_scr.plate_ref.append(PlateRef(id=ome.plates[0].id))
+        new_scr.plate_refs.append(PlateRef(id=ome.plates[0].id))
         ome.screens.append(new_scr)
         with open(filename, 'w') as fp:
             print(to_xml(ome), file=fp)
diff --git a/test/integration/test_transfer.py b/test/integration/test_transfer.py
index 51f12cb..1e047db 100644
--- a/test/integration/test_transfer.py
+++ b/test/integration/test_transfer.py
@@ -317,6 +317,40 @@ def test_unpack_skip(self):
         assert img.getName() == 'combined_result.tiff'
         self.delete_all()
 
+    def test_unpack_merge(self):
+        proj_args = self.args + ["unpack",
+                                 "test/data/valid_single_project.zip"]
+        self.cli.invoke(proj_args, strict=True)
+        proj_args += ['--merge']
+        self.cli.invoke(proj_args, strict=True)
+        pj_ids = ezomero.get_project_ids(self.gw)
+        assert len(pj_ids) == 1
+        ds_ids = ezomero.get_dataset_ids(self.gw, pj_ids[0])
+        assert len(ds_ids) == 2
+        ds_args = self.args + ['unpack', "test/data/valid_single_dataset.zip"]
+        print(ds_args)
+        self.cli.invoke(ds_args, strict=True)
+        orphan = ezomero.get_dataset_ids(self.gw)
+        assert len(orphan) == 1
+        ds_args += ['--merge']
+        self.cli.invoke(ds_args, strict=True)
+        orphan = ezomero.get_dataset_ids(self.gw)
+        assert len(orphan) == 1
+        scr_args = self.args + ['unpack', "test/data/simple_screen.zip"]
+        self.cli.invoke(scr_args, strict=True)
+        scr_args += ['--merge']
+        self.cli.invoke(scr_args, strict=True)
+        scr_ids = []
+        for screen in self.gw.getObjects("Screen"):
+            scr_ids.append(screen.getId())
+        assert len(scr_ids) == 1
+        pl_ids = []
+        screen = self.gw.getObject("Screen", scr_ids[0])
+        for plate in screen.listChildren():
+            pl_ids.append(plate.getId())
+        assert len(pl_ids) == 4
+        self.delete_all()
+
     @pytest.mark.parametrize('target_name', sorted(SUPPORTED))
     def test_pack_unpack(self, target_name, tmpdir):
         if target_name == "datasetid" or target_name == "projectid" or\
diff --git a/test/unit/test_set.py b/test/unit/test_set.py
index 282b54e..726ec21 100644
--- a/test/unit/test_set.py
+++ b/test/unit/test_set.py
@@ -88,7 +88,7 @@ def test_non_existing_file(self):
                                           'data/output_folder')
 
     def test_src_img_map(self):
-        ome = from_xml('test/data/transfer.xml', parser='xmlschema')
+        ome = from_xml('test/data/transfer.xml')
         _, src_img_map, filelist = self.transfer._create_image_map(ome)
         correct_map = {"root_0/2022-01/14/"
                        "18-30-55.264/combined_result.tiff": [1678, 1679]}