Merge pull request #577 from chris-allan/archive-status

Refactors #555 to allow for backward compatibility

omeroweb/webclient/tree.py

@@ -531,7 +531,6 @@ def _marshal_image(
     """Given an Image row (list) marshals it into a dictionary.  Order
     and type of columns in row is:
       * id (rlong)
-      * archived (boolean)
       * name (rstring)
       * details.owner.id (rlong)
       * details.permissions (dict)
@@ -550,22 +549,74 @@ def _marshal_image(
     @param row_pixels The Image row pixels data to marshal
     @type row_pixels L{list}
     """
-    image_id, archived, name, owner_id, permissions, fileset_id = row
+    image_id, name, owner_id, permissions, fileset_id = row
+    data = {
+        "id": image_id,
+        "name": name,
+        "ownerId": owner_id,
+        "image_details_permissions": permissions,
+        "filesetId": fileset_id,
+    }
+    if row_pixels:
+        sizeX, sizeY, sizeZ, sizeT = row_pixels
+        data["sizeX"] = sizeX
+        data["sizeY"] = sizeY
+        data["sizeZ"] = sizeZ
+        data["sizeT"] = sizeT
+    return _marshal_image_map(
+        conn,
+        data,
+        share_id=share_id,
+        date=date,
+        acqDate=acqDate,
+        thumbVersion=thumbVersion,
+    )
+
+
+def _marshal_image_map(
+    conn,
+    data,
+    share_id=None,
+    date=None,
+    acqDate=None,
+    thumbVersion=None,
+):
+    """Given an Image data dictionary marshals it into a dictionary.  Suppored keys are:
+      * id (rlong)
+      * archived (boolean; optional)
+      * name (rstring)
+      * ownerId (rlong)
+      * image_details_permissions (dict)
+      * filesetId (rlong)
+      * sizeX (rlong; optional)
+      * sizeY (rlong; optional)
+      * sizeZ (rlong; optional)
+      * sizeT (rlong; optional)
+
+    @param conn OMERO gateway.
+    @type conn L{omero.gateway.BlitzGateway}
+    @param data The data to marshal
+    @type row L{dict}
+    """
     image = dict()
-    image["id"] = unwrap(image_id)
-    image["archived"] = unwrap(archived) is True
-    image["name"] = unwrap_to_str(name)
-    image["ownerId"] = unwrap(owner_id)
-    image["permsCss"] = parse_permissions_css(permissions, unwrap(owner_id), conn)
-    fileset_id_val = unwrap(fileset_id)
+    image["id"] = unwrap(data["id"])
+    image["archived"] = unwrap(data.get("archived")) is True
+    image["name"] = unwrap_to_str(data["name"])
+    image["ownerId"] = unwrap(data["ownerId"])
+    image["permsCss"] = parse_permissions_css(
+        data["image_details_permissions"], unwrap(data["ownerId"]), conn
+    )
+    fileset_id_val = unwrap(data["filesetId"])
     if fileset_id_val is not None:
         image["filesetId"] = fileset_id_val
-    if row_pixels:
-        sizeX, sizeY, sizeZ, sizeT = row_pixels
-        image["sizeX"] = unwrap(sizeX)
-        image["sizeY"] = unwrap(sizeY)
-        image["sizeZ"] = unwrap(sizeZ)
-        image["sizeT"] = unwrap(sizeT)
+    if "sizeX" in data:
+        image["sizeX"] = unwrap(data["sizeX"])
+    if "sizeY" in data:
+        image["sizeY"] = unwrap(data["sizeY"])
+    if "sizeZ" in data:
+        image["sizeZ"] = unwrap(data["sizeZ"])
+    if "sizeT" in data:
+        image["sizeT"] = unwrap(data["sizeT"])
     if share_id is not None:
         image["shareId"] = share_id
     if date is not None:
@@ -753,31 +804,20 @@ def marshal_images(
     )
 
     for e in qs.projection(q, params, service_opts):
-        e = unwrap(e)[0]
-        d = [
-            e["id"],
-            e["archived"],
-            e["name"],
-            e["ownerId"],
-            e["image_details_permissions"],
-            e["filesetId"],
-        ]
-        kwargs = {"conn": conn, "row": d[0:6]}
-        if load_pixels:
-            d = [e["sizeX"], e["sizeY"], e["sizeZ"], e["sizeT"]]
-            kwargs["row_pixels"] = d
+        data = unwrap(e)[0]
+        kwargs = {}
         if date:
-            kwargs["acqDate"] = e["acqDate"]
-            kwargs["date"] = e["date"]
+            kwargs["acqDate"] = data["acqDate"]
+            kwargs["date"] = data["date"]
 
         # While marshalling the images, determine if there are any
         # images mentioned in shares that are not in the results
         # because they have been deleted
-        if share_id is not None and image_rids and e["id"] in image_rids:
-            image_rids.remove(e["id"])
+        if share_id is not None and image_rids and data["id"] in image_rids:
+            image_rids.remove(data["id"])
             kwargs["share_id"] = share_id
 
-        images.append(_marshal_image(**kwargs))
+        images.append(_marshal_image_map(conn, data, **kwargs))
 
     # Load thumbnails separately
     # We want version of most recent thumbnail (max thumbId) owned by user
@@ -1536,23 +1576,12 @@ def marshal_tagged(
 
     images = []
     for e in qs.projection(q, params, service_opts):
-        e = unwrap(e)
-        row = [
-            e[0]["id"],
-            e[0]["archived"],
-            e[0]["name"],
-            e[0]["ownerId"],
-            e[0]["image_details_permissions"],
-            e[0]["filesetId"],
-        ]
+        data = unwrap(e)[0]
         kwargs = {}
-        if load_pixels:
-            d = [e[0]["sizeX"], e[0]["sizeY"], e[0]["sizeZ"], e[0]["sizeT"]]
-            kwargs["row_pixels"] = d
         if date:
-            kwargs["acqDate"] = e[0]["acqDate"]
-            kwargs["date"] = e[0]["date"]
-        images.append(_marshal_image(conn, row, **kwargs))
+            kwargs["acqDate"] = data["acqDate"]
+            kwargs["date"] = data["date"]
+        images.append(_marshal_image_map(conn, data, **kwargs))
     tagged["images"] = images
 
     # Screens

test/unit/test_tree.py

@@ -23,10 +23,13 @@
 
 import pytest
 
-from omero.rtypes import rlong, rstring, rtime
+from omero.rtypes import rlong, rstring, rtime, unwrap
 from omeroweb.webclient.tree import (
     _marshal_plate_acquisition,
     _marshal_dataset,
+    _marshal_date,
+    _marshal_image,
+    _marshal_image_map,
     _marshal_plate,
     parse_permissions_css,
 )
@@ -68,6 +71,43 @@ def end_time():
     return rtime(1399545510 * 1000)
 
 
+@pytest.fixture(scope="module")
+def image_row(owner_permissions):
+    return [rlong(1), rstring("name"), rlong(10), owner_permissions, rlong(100)]
+
+
+@pytest.fixture(scope="module")
+def pixels_row():
+    return [rlong(1), rlong(2), rlong(3), rlong(4)]
+
+
+@pytest.fixture()
+def image_data(image_row):
+    image_id, name, owner_id, permissions, fileset_id = image_row
+    return {
+        "id": image_id,
+        "archived": False,
+        "name": name,
+        "ownerId": owner_id,
+        "image_details_permissions": permissions,
+        "filesetId": fileset_id,
+    }
+
+
+@pytest.fixture()
+def image_data_with_pixels(image_data, pixels_row):
+    sizeX, sizeY, sizeZ, sizeT = pixels_row
+    image_data.update(
+        {
+            "sizeX": sizeX,
+            "sizeY": sizeY,
+            "sizeZ": sizeZ,
+            "sizeT": sizeT,
+        }
+    )
+    return image_data
+
+
 class TestTree(object):
     """
     Tests to ensure that OMERO.web "tree" infrastructure is working
@@ -213,8 +253,104 @@ def test_marshal_plate_not_owner(self, mock_conn, owner_permissions):
         }
 
         marshaled = _marshal_plate(mock_conn, row)
-        print(marshaled)
-        print(expected)
         assert marshaled == expected
 
+    def assert_image(
+        self,
+        marshaled,
+        with_pixels=False,
+        with_share=False,
+        date=None,
+        acqDate=None,
+        with_thumbVersion=False,
+        is_archived=False,
+    ):
+        expected = {
+            "id": 1,
+            "archived": is_archived,
+            "ownerId": 10,
+            "name": "name",
+            "permsCss": "canEdit canAnnotate canLink canDelete canChgrp",
+            "filesetId": 100,
+        }
+        if with_pixels:
+            expected.update(
+                {
+                    "sizeX": 1,
+                    "sizeY": 2,
+                    "sizeZ": 3,
+                    "sizeT": 4,
+                }
+            )
+        if with_share:
+            expected.update({"shareId": 1})
+        if date:
+            # Cannot be static, will include local timezone
+            expected.update({"date": _marshal_date(unwrap(date))})
+        if acqDate:
+            # Cannot be static, will include local timezone
+            expected.update({"acqDate": _marshal_date(unwrap(acqDate))})
+        if with_thumbVersion:
+            expected.update({"thumbVersion": 1})
+        assert marshaled == expected
+
+    def test_marshal_image(self, mock_conn, image_row):
+        marshaled = _marshal_image(mock_conn, image_row)
+        self.assert_image(marshaled)
+
+    def test_marshal_image_with_pixels(self, mock_conn, image_row, pixels_row):
+        marshaled = _marshal_image(mock_conn, image_row, pixels_row)
+        self.assert_image(marshaled, with_pixels=True)
+
+    def test_marshal_image_with_share(self, mock_conn, image_row):
+        marshaled = _marshal_image(mock_conn, image_row, share_id=1)
+        self.assert_image(marshaled, with_share=True)
+
+    def test_marshal_image_with_date(self, mock_conn, image_row, end_time):
+        marshaled = _marshal_image(mock_conn, image_row, date=end_time)
+        self.assert_image(marshaled, date=end_time)
+
+    def test_marshal_image_with_acquisition_date(
+        self, mock_conn, image_row, start_time
+    ):
+        marshaled = _marshal_image(mock_conn, image_row, acqDate=start_time)
+        self.assert_image(marshaled, acqDate=start_time)
+
+    def test_marshal_image_with_thumb_version(self, mock_conn, image_row, start_time):
+        marshaled = _marshal_image(mock_conn, image_row, thumbVersion=1)
+        self.assert_image(marshaled, with_thumbVersion=True)
+
+    def test_marshal_image_map(self, mock_conn, image_data):
+        marshaled = _marshal_image_map(mock_conn, image_data)
+        self.assert_image(marshaled)
+
+    def test_marshal_image_map_archived(self, mock_conn, image_data):
+        image_data["archived"] = True
+        marshaled = _marshal_image_map(mock_conn, image_data)
+        self.assert_image(marshaled, is_archived=True)
+
+    def test_marshal_image_map_with_pixels(self, mock_conn, image_data_with_pixels):
+        marshaled = _marshal_image_map(mock_conn, image_data_with_pixels)
+        self.assert_image(marshaled, with_pixels=True)
+
+    def test_marshal_image_map_with_share(self, mock_conn, image_data):
+        marshaled = _marshal_image_map(mock_conn, image_data, share_id=1)
+        self.assert_image(marshaled, with_share=True)
+
+    def test_marshal_image_map_with_date(self, mock_conn, image_data, end_time):
+        marshaled = _marshal_image_map(mock_conn, image_data, date=end_time)
+        self.assert_image(marshaled, date=end_time)
+
+    def test_marshal_image_map_with_acquisition_date(
+        self, mock_conn, image_data, start_time
+    ):
+        marshaled = _marshal_image_map(mock_conn, image_data, acqDate=start_time)
+        self.assert_image(marshaled, acqDate=start_time)
+
+    def test_marshal_image_map_with_thumb_version(
+        self, mock_conn, image_data, start_time
+    ):
+        marshaled = _marshal_image_map(mock_conn, image_data, thumbVersion=1)
+        self.assert_image(marshaled, with_thumbVersion=True)
+
     # Add a lot of tests