Display bulk annotations in web image viewer, new webgateway API calls

components/tools/OmeroWeb/omeroweb/webgateway/marshal.py

@@ -65,14 +65,20 @@ def imageMarshal (image, key=None):
     image.loadRenderOptions()
     pr = image.getProject()
     ds = None
+    wellsample = None
+    well = None
     try:
         # Replicating the functionality of the deprecated
         # ImageWrapper.getDataset() with shares in mind.
         # -- Tue Sep  6 10:48:47 BST 2011 (See #6660)
         parents = image.listParents()
-        if parents is not None and len(parents) == 1 \
-           and parents[0].OMERO_CLASS == 'Dataset':
-            ds = parents[0]
+        if parents is not None and len(parents) == 1:
+            if parents[0].OMERO_CLASS == 'Dataset':
+                ds = parents[0]
+            elif parents[0].OMERO_CLASS == 'WellSample':
+                wellsample = parents[0]
+                if wellsample.well is not None:
+                    well = wellsample.well
     except omero.SecurityViolation, e:
         # We're in a share so the Image's parent Dataset cannot be loaded
         # or some other permissions related issue has tripped us up.
@@ -90,6 +96,8 @@ def imageMarshal (image, key=None):
                      'datasetName': ds and ds.name or 'Multiple',
                      'datasetId': ds and ds.id or '',
                      'datasetDescription': ds and ds.description or '',
+                     'wellSampleId': wellsample and wellsample.id or '',
+                     'wellId': well and well.id.val or '',
                      'imageTimestamp': time.mktime(image.getDate().timetuple()),
                      'imageId': image.id,},
             }

components/tools/OmeroWeb/omeroweb/webgateway/templates/webgateway/viewport/omero_image.html

@@ -243,6 +243,35 @@
     $('#wblitz-image-pub').html(tmp.projectName);
     $('#wblitz-image-pubid').html(tmp.projectId);
     $('#wblitz-image-timestamp').html(tmp.imageTimestamp);
+
+    $("#bulk-annotations").hide();
+    $("#bulk-annotations").next().hide();
+    if (tmp.wellId) {
+        // Load bulk annotations for plate
+        var onAnnotations = function(result) {
+            if (result.data && result.data.rows) {
+                var table = $("#bulk-annotations").show().next().show().children("table");
+                table.find("tr").remove();
+                for (var col in result.data.columns) {
+                    var label = result.data.columns[col];
+                    var value = '';
+                    for (var row in result.data.rows) {
+                        value += result.data.rows[row][col] + '<br />';
+                    }
+                    var row = $('<tr><td class="title"></td><td></td></tr>');
+                    row.addClass(col % 2 == 1 ? 'odd' : 'even');
+                    $('td:first-child', row).html(label + ":&nbsp;");
+                    $('td:last-child', row).html(value);
+                    table.append(row);
+                }
+            }
+        };
+        $.getJSON('{% url webgateway_object_table_query 'Plate.wells' 999 %}'.replace('999', tmp.wellId) +
+            '?query=Well-' + tmp.wellId +
+            '&callback=?',
+             onAnnotations);
+    }
+
     {% block xtra_metadata %}{% endblock %}
 
     /*$('#wblitz-shortname').attr('title', tmp.imageName).html(gs_text_trim(tmp.imageName, 15, true));*/
@@ -947,6 +976,13 @@ <h3 class="can-collapse"> Dimensions </h3>
           </tr>
         </table>
       </div>
+
+      <h3 class="can-collapse" id="bulk-annotations" style="display: none;">Bulk Annotations</h3>
+      <div style="display: none;">
+		<table cellspacing="0">
+		</table>
+      </div>
+
       <!--<h3 class="can-collapse defclose"> Legend </h3>
       <div id="wblitz-image-description"><span id="wblitz-image-description-content"></span></div>-->
     </div>

components/tools/OmeroWeb/omeroweb/webgateway/urls.py

@@ -18,6 +18,23 @@
 Returns a main prefix
 """
 
+annotations = url(r'^annotations/(?P<objtype>[\w.]+)/(?P<objid>\d+)/$', 'webgateway.views.annotations', name="webgateway_annotations")
+"""
+Retrieve annotations for object specified by object type and identifier,
+optionally traversing object model graph.
+"""
+
+table_query = url(r'^table/(?P<fileid>\d+)/query/$', 'webgateway.views.table_query', name="webgateway_table_query")
+"""
+Query a table specified by fileid
+"""
+
+object_table_query = url(r'^table/(?P<objtype>[\w.]+)/(?P<objid>\d+)/query/$', 'webgateway.views.object_table_query', name="webgateway_object_table_query")
+"""
+Query bulk annotations table attached to an object specified by
+object type and identifier, optionally traversing object model graph.
+"""
+
 render_image = (r'^render_image/(?P<iid>[^/]+)/(?:(?P<z>[^/]+)/)?(?:(?P<t>[^/]+)/)?$', 'webgateway.views.render_image')
 """
 Returns a jpeg of the OMERO image. See L{views.render_image}. Rendering settings can be specified
@@ -196,7 +213,7 @@
     - key:  Optional key of selected attributes to return. E.g. meta, pixel_range, rdefs, split_channel, size etc
 """
 
-wellData_json = (r'^wellData/(?P<wid>[^/]+)/$', 'webgateway.views.wellData_json')
+wellData_json = url(r'^wellData/(?P<wid>[^/]+)/$', 'webgateway.views.wellData_json', name='webgateway_wellData_json')
 """
 json method: returns details of specified Well. See L{views.wellData_json}.
     - webgateway/wellData/<wid>/ params are:
@@ -304,7 +321,11 @@
     copy_image_rdef_json,
     # switch user
     webgateway_su,
-
+    # bulk annotations
+    annotations,
+    table_query,
+    object_table_query,
+
     # Debug stuff
 
 )

components/tools/OmeroWeb/omeroweb/webgateway/views.py

@@ -15,15 +15,17 @@
 
 import omero
 import omero.clients
-from django.http import HttpResponse, HttpResponseServerError, HttpResponseRedirect, Http404
+from django.http import HttpResponse, HttpResponseServerError, HttpResponseRedirect, Http404, HttpResponseNotFound
 from django.utils import simplejson
 from django.utils.encoding import smart_str
 from django.utils.http import urlquote
+from django.views.decorators.http import require_POST
 from django.core import template_loader
 from django.core.urlresolvers import reverse
 from django.conf import settings
 from django.template import RequestContext as Context
 from omero.rtypes import rlong, unwrap
+from omero.constants.namespaces import NSBULKANNOTATIONS
 from marshal import imageMarshal, shapeMarshal
 
 try:
@@ -1679,3 +1681,156 @@ def su (request, user, conn=None, **kwargs):
     conn.revertGroupForSession()
     conn.seppuku()
     return True
+
+
+def _annotations(request, objtype, objid, conn=None, **kwargs):
+    """
+    Retrieve annotations for object specified by object type and identifier,
+    optionally traversing object model graph.
+    Returns dictionary containing annotations in NSBULKANNOTATIONS namespace
+    if successful, error information otherwise
+
+    Example:  /annotations/Plate/1/
+              retrieves annotations for plate with identifier 1
+    Example:  /annotations/Plate.wells/1/
+              retrieves annotations for plate that contains well with
+              identifier 1
+
+    @param request:     http request.
+    @param objtype:     Type of target object, or type of target object followed
+                        by a slash-separated list of properties to resolve
+    @param objid:       Identifier of target object, or identifier of object
+                        reached by resolving given properties
+    @param conn:        L{omero.gateway.BlitzGateway}
+    @param **kwargs:    unused
+    @return:            A dictionary with key 'error' with an error message or
+                        with key 'data' containing an array of dictionaries
+                        with keys 'id' and 'file' of the retrieved annotations
+    """
+    q = conn.getQueryService()
+    # If more than one objtype is specified, use all in query to
+    # traverse object model graph
+    # Example: /annotations/Plate/wells/1/
+    #          retrieves annotations from Plate that contains Well 1
+    objtype = objtype.split('.')
+
+    query = "select obj0 from %s obj0\n" % objtype[0]
+    for i, t in enumerate(objtype[1:]):
+        query += "join fetch obj%d.%s obj%d\n" % (i, t, i+1)
+    query += """
+        left outer join fetch obj0.annotationLinks links
+        left outer join fetch links.child
+        where obj%d.id=:id""" % (len(objtype) - 1)
+
+    try:
+        obj = q.findByQuery(query, omero.sys.ParametersI().addId(objid),
+                            conn.createServiceOptsDict())
+    except omero.QueryException, ex:
+        return HttpResponseNotFound('%s cannot be queried' % objtype)
+
+    if not obj:
+        return HttpResponseNotFound('%s with id %s not found' % (objtype, objid))
+
+    return dict(data=[
+        dict(id=annotation.id.val,
+             file=annotation.file.id.val)
+        for annotation in obj.linkedAnnotationList()
+        if unwrap(annotation.getNs()) == NSBULKANNOTATIONS
+        ])
+
+annotations = login_required()(jsonp(_annotations))
+
+
+def _table_query(request, fileid, conn=None, **kwargs):
+    """
+    Query a table specified by fileid
+    Returns a dictionary with query result if successful, error information
+    otherwise
+
+    @param request:     http request; querystring must contain key 'query'
+                        with query to be executed, or '*' to retrieve all rows.
+                        If query is in the format word-number, e.g. "Well-7",
+                        if will be run as (word==number), e.g. "(Well==7)".
+                        This is supported to allow more readable query strings.
+    @param fileid:      Numeric identifier of file containing the table
+    @param conn:        L{omero.gateway.BlitzGateway}
+    @param **kwargs:    unused
+    @return:            A dictionary with key 'error' with an error message
+                        or with key 'data' containing a dictionary with keys
+                        'columns' (an array of column names) and 'rows'
+                        (an array of rows, each an array of values)
+    """
+    query = request.GET.get('query')
+    if not query:
+        return dict(error='Must specify query parameter, use * to retrieve all')
+
+    r = conn.getSharedResources()
+    t = r.openTable(omero.model.OriginalFileI(fileid),
+                    conn.createServiceOptsDict())
+    if not t:
+        return dict(error="Table %s not found" % fileid)
+
+    cols = t.getHeaders()
+    rows = t.getNumberOfRows()
+
+    if query == '*':
+        hits = range(rows)
+    else:
+        match = re.match(r'^(\w+)-(\d+)', query)
+        if match:
+            query = '(%s==%s)' % (match.group(1), match.group(2))
+        try:
+            hits = t.getWhereList(query, None, 0, rows, 1)
+        except Exception, e:
+            return dict(error='Error executing query: %s' % query)
+
+    return dict(data=dict(
+        columns=[col.name for col in cols],
+        rows=[
+            [col.values[0] for col in t.read(range(len(cols)), hit, hit+1).columns]
+            for hit in hits
+        ],
+        )
+    )
+
+table_query = login_required()(jsonp(_table_query))
+
+
+@login_required()
+@jsonp
+def object_table_query(request, objtype, objid, conn=None, **kwargs):
+    """
+    Query bulk annotations table attached to an object specified by
+    object type and identifier, optionally traversing object model graph.
+    Returns a dictionary with query result if successful, error information
+    otherwise
+
+    Example:  /table/Plate/1/query/?query=*
+              queries bulk annotations table for plate with identifier 1
+    Example:  /table/Plate.wells/1/query/?query=*
+              queries bulk annotations table for plate that contains well with
+              identifier 1
+
+    @param request:     http request.
+    @param objtype:     Type of target object, or type of target object followed
+                        by a slash-separated list of properties to resolve
+    @param objid:       Identifier of target object, or identifier of object
+                        reached by resolving given properties
+    @param conn:        L{omero.gateway.BlitzGateway}
+    @param **kwargs:    unused
+    @return:            A dictionary with key 'error' with an error message
+                        or with key 'data' containing a dictionary with keys
+                        'columns' (an array of column names) and 'rows'
+                        (an array of rows, each an array of values)
+    """
+    a = _annotations(request, objtype, objid, conn, **kwargs)
+    if isinstance(a, HttpResponse) or a.has_key('error'):
+        return a
+
+    if len(a['data']) != 1:
+        return dict(error='Could not retrieve single bulk annotations table')
+
+    # multiple bulk annotations files could be attached, use the most recent
+    # one (= the one with the highest identifier)
+    fileId = max(annotation['file'] for annotation in a['data'])
+    return _table_query(request, fileId, conn, **kwargs)