ome · will-moore · Jan 26, 2024 · Jan 26, 2024 · Jan 26, 2024 · Jan 26, 2024
diff --git a/README.rst b/README.rst
@@ -29,6 +29,7 @@ Install with::
     $ pip install -e .
 
 Configuration
+-------------
 
 ::
 
@@ -67,6 +68,28 @@ In the webclient UI you can use the context menu to `Open With > Vizarr`, or use
 
     [omero-server]/zarr/vizarr/?source=[omero-server]/zarr/v0.4/image/[ID].zarr
 
+Viewing s3 data
+---------------
+
+If you have imported OME-Zarr images into OMERO and the data is publicly accessible, e.g. hosted
+on s3, then you can use this app to view that s3 data directly (instead of using the OMERO server).
+This relies on the public data source being set as the `clientPath` location (shown in the webclient
+as "Imported From"). At least 1 `clientPath` for an Image or Plate should be in the form:
+`http....zarr/.zattrs`.
+For data that matches this criteria, we can replace the image-viewer with `vizarr`` (images that do not
+have such a clientPath will default to using iviewer):
+
+::
+
+    $ omero config set omero.web.viewer.view omero_web_zarr.views.vizarr_or_iviewer
+
+If you want to remove the Preview panel
+
+::
+
+    $ omero config set omero.web.ui.right_plugins '[["Acquisition", "webclient/data/includes/right_plugin.acquisition.js.html", "metadata_tab"]]'
+
+
 Testing
 -------
 
@@ -84,5 +107,5 @@ The application is released under the AGPL.
 Copyright
 ---------
 
-2022-2023, The Open Microscopy Environment
+2022-2024, The Open Microscopy Environment
 
diff --git a/omero_web_zarr/static/omero_web_zarr/vizarr/blosc-5eba38ca.js b/omero_web_zarr/static/omero_web_zarr/vizarr/blosc-5eba38ca.js
diff --git a/omero_web_zarr/static/omero_web_zarr/vizarr/favicon.ico b/omero_web_zarr/static/omero_web_zarr/vizarr/favicon.ico
diff --git a/omero_web_zarr/static/omero_web_zarr/vizarr/index-99be1c79.js b/omero_web_zarr/static/omero_web_zarr/vizarr/index-99be1c79.js
diff --git a/omero_web_zarr/static/omero_web_zarr/vizarr/index.html b/omero_web_zarr/static/omero_web_zarr/vizarr/index.html
@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <link
+      rel="icon"
+      href="data:image/svg+xml,<svg xmlns=%22http://www.w3.org/2000/svg%22 viewBox=%220 0 100 100%22><text y=%22.9em%22 font-size=%2290%22>🔬</text></svg>"
+    />
+    <link rel="alternate icon" href="./favicon.ico" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="description" content="A minimal, purely client-side program for viewing Zarr-based images." />
+    <title>vizarr</title>
+    <script type="module" crossorigin src="./index-99be1c79.js"></script>
+    <link rel="modulepreload" crossorigin href="./vizarr-09ae863b.js">
+  </head>
+  <body>
+    <div id="root"></div>
+    <noscript>You need to enable JavaScript to run this app.</noscript>
+
+    <style>
+      html {
+        background-color: black;
+      }
+    </style>
+  </body>
+</html>
diff --git a/omero_web_zarr/static/omero_web_zarr/vizarr/vizarr-09ae863b.js b/omero_web_zarr/static/omero_web_zarr/vizarr/vizarr-09ae863b.js
diff --git a/omero_web_zarr/utils.py b/omero_web_zarr/utils.py
@@ -17,6 +17,8 @@
 #
 
 from django.http import Http404
+from omero.sys import ParametersI
+from omero.rtypes import rstring
 
 
 def marshal_pixel_sizes(image):
@@ -96,3 +98,57 @@ def generate_coordinate_transformations(shapes):
             transformations.append([{"type": "scale", "scale": scale}])
 
         return transformations
+
+
+def get_clientpath_by_endswith(conn, image_id, pathending):
+    query_service = conn.getQueryService()
+    params = ParametersI()
+    params.addId(image_id)
+    params.add("zarr", rstring("%%%s" % pathending))
+    query = """ select u.clientPath from Fileset fs
+        join fs.usedFiles u
+        left outer join fs.images as image
+        where image.id=:id
+        and u.clientPath like :zarr"""
+    result = query_service.projection(query, params, conn.SERVICE_OPTS)
+    if len(result) == 0:
+        return None
+    return result[0][0].val
+
+
+def get_zarr_s3_path(conn, image_id):
+    """
+    Check Fileset clientPaths for path ending zarr/.zattrs
+
+    If Image is in a Plate/Well, add eg. /A/1/0/ to path.
+    """
+    client_path = get_clientpath_by_endswith(conn, image_id, "zarr/.zattrs")
+    if client_path is None:
+        return None
+
+    # We also need clientPath to be a publicly-accessible URL
+    zarr_path = client_path.replace("/.zattrs", "")
+
+    # Check if Image is in a Well - need to add /row/col/field/ e.g. /A/1/0
+    query_service = conn.getQueryService()
+    wsparams = ParametersI()
+    wsparams.addId(image_id)
+    wsquery = """select well.plate.id, well.row, well.column, index(ws) from Well well
+        join well.wellSamples ws where ws.image.id=:id"""
+    ws = query_service.projection(wsquery, wsparams, conn.SERVICE_OPTS)
+    if len(ws) > 0:
+        plate_id = ws[0][0].val
+        plate = conn.getObject("Plate", plate_id)
+        row = plate.getRowLabels()[ws[0][1].val]
+        column = plate.getColumnLabels()[ws[0][2].val]
+        ws_index = ws[0][3].val
+        row_col_field = f"/{row}/{column}/{ws_index}/"
+        zarr_path += row_col_field
+    else:
+        # Check whether this is a bioformats2raw image
+        metadata_path = get_clientpath_by_endswith(conn, image_id,
+                                                   "OME/METADATA.ome.xml")
+        if metadata_path is not None:
+            zarr_path += "/0/"
+
+    return zarr_path
diff --git a/omero_web_zarr/views.py b/omero_web_zarr/views.py
@@ -26,8 +26,9 @@
 from django.http import HttpResponse, JsonResponse
 from django.urls import reverse
 from django.shortcuts import redirect
+from django.templatetags.static import static
 
-from .utils import marshal_axes, marshal_axes_v3
+from .utils import marshal_axes, marshal_axes_v3, get_zarr_s3_path
 from .utils import generate_coordinate_transformations
 
 from omero.model.enums import PixelsTypeint8, PixelsTypeuint8, PixelsTypeint16
@@ -312,3 +313,25 @@ def apps(request, app, url):
         rsp['content-type'] = "application/javascript"
 
     return rsp
+
+
+@login_required()
+def vizarr_or_iviewer(request, iid=None, conn=None, **kwargs):
+
+    s3_url = get_zarr_s3_path(conn, iid)
+
+    local_vizarr_url = static("omero_web_zarr/vizarr/index.html")
+
+    if s3_url is not None:
+        url = f"{local_vizarr_url}?source={s3_url}"
+        return redirect(url)
+
+    else:
+        try:
+            # Default to iviewer (if installed)...
+            from omero_iviewer.views import index as iviewer_index
+            return iviewer_index(request, iid, **kwargs)
+        except ImportError:
+            # ...otherwise revert to original image viewer
+            from omeroweb.webclient.views import image_viewer
+            return image_viewer(request, iid, **kwargs)