Merge pull request #6 from German-BioImaging/well_support

Added support for Well objects and owner name
German-BioImaging · Nov 11, 2023 · 9f85cbb · 9f85cbb
2 parents 86f8b06 + f5327a0
commit 9f85cbb
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Showing 6 changed files with 62 additions and 45 deletions.
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-4.0.1
+4.1.0
diff --git a/omero_tagsearch/static/tagsearch/css/webtagging_search.css b/omero_tagsearch/static/tagsearch/css/webtagging_search.css
@@ -62,12 +62,17 @@
   background: url('../image/run16.png') no-repeat;
 }
 
+.tagnav-well .tagnav-icon {
+  background: url('../image/well16.png') no-repeat;
+}
+
 .tagnav-image .tagnav-icon {
   background: url('../image/image16.png') no-repeat;
 }
 
 .tagnav-project, .tagnav-dataset, .tagnav-screen,
-.tagnav-plate, .tagnav-acquisition, .tagnav-image {
+.tagnav-plate, .tagnav-acquisition, .tagnav-well,
+.tagnav-image {
     color: hsl(210,10%,50%);
     font-size: 1.2em;
     text-shadow: 0 1px 0 white;

diff --git a/omero_tagsearch/static/tagsearch/image/well16.png b/omero_tagsearch/static/tagsearch/image/well16.png
diff --git a/omero_tagsearch/templates/omero_tagsearch/search_details.html b/omero_tagsearch/templates/omero_tagsearch/search_details.html
@@ -90,6 +90,7 @@
                     <th class="table_images">{% trans "Object" %}</th>
                     <th class="table_desc">{% trans "Name" %}</th>
                     <th class="table_date">{% trans "Import Date" %}</th>
+                    <th>{% trans "Owner" %}</th>
                     <th>{% trans "Group" %}</th>
                     <th>{% trans "Link" %}</th>
                 </tr>
@@ -111,6 +112,7 @@
                         <a>{{ c.name|truncatebefor:"65" }}</a>
                     </td>
                     <td class="date">{{ c.creationEventDate }}</td>
+                    <td class="owner">{{ c.getOwnerFullName }}</td>
                     <td class="group">{{ c.getDetails.group.name.val }}</td>
                     <td><a href="{% url 'webindex' %}?show={{ byId.otype }}-{{ c.id }}" title="{% trans 'Show in hierarchy view' %}">
                         {% trans "Browse" %}
@@ -125,6 +127,7 @@
                     </td>
                     <td class="desc"><a>{{ c.name|truncatebefor:"65" }}</a></td>
                     <td class="date">{{ c.creationEventDate }}</td>
+                    <td class="owner">{{ c.getOwnerFullName }}</td>
                     <td class="group">{{ c.getDetails.group.name.val }}</td>
                     <td><a href="{% url 'webindex' %}?show=project-{{ c.id }}" title="{% trans 'Show in hierarchy view' %}">
                         {% trans "Browse" %}
@@ -138,6 +141,7 @@
                     </td>
                     <td class="desc"><a>{{ c.name|truncatebefor:"65" }}</a></td>
                     <td class="date">{{ c.creationEventDate }}</td>
+                    <td class="owner">{{ c.getOwnerFullName }}</td>
                     <td class="group">{{ c.getDetails.group.name.val }}</td>
                     <td><a href="{% url 'webindex' %}?show=screen-{{ c.id }}" title="{% trans 'Show in hierarchy view' %}">
                         {% trans "Browse" %}
@@ -151,6 +155,7 @@
                     </td>
                     <td class="desc"><a>{{ c.name|truncatebefor:"65" }}</a></td>
                     <td class="date">{{ c.creationEventDate }}</td>
+                    <td class="owner">{{ c.getOwnerFullName }}</td>
                     <td class="group">{{ c.getDetails.group.name.val }}</td>
                     <td><a href="{% url 'webindex' %}?show=dataset-{{ c.id }}" title="{% trans 'Show in hierarchy view' %}">
                         {% trans "Browse" %}
@@ -164,6 +169,7 @@
                     </td>
                     <td class="desc"><a>{{ c.name|truncatebefor:"65" }}</a></td>
                     <td class="date">{{ c.creationEventDate }}</td>
+                    <td class="owner">{{ c.getOwnerFullName }}</td>
                     <td class="group">{{ c.getDetails.group.name.val }}</td>
                     <td><a href="{% url 'webindex' %}?show=plate-{{ c.id }}" title="{% trans 'Show in hierarchy view' %}">
                         {% trans "Browse" %}
@@ -177,19 +183,35 @@
                     </td>
                     <td class="desc"><a>{{ c.name|truncatebefor:"65" }}</a></td>
                     <td class="date">{{ c.creationEventDate }}</td>
+                    <td class="owner">{{ c.getOwnerFullName }}</td>
                     <td class="group">{{ c.getDetails.group.name.val }}</td>
                     <td><a href="{% url 'webindex' %}?show=acquisition-{{ c.id }}" title="{% trans 'Show in hierarchy view' %}">
                         {% trans "Browse" %}
                     </a></td>
                 </tr>
             {% endfor %}
+            {% for c in manager.containers.well %}
+                <tr id="well-{{ c.id }}" class="{{ c.getPermsCss }}">
+                    <td class="image">
+                        <img id="{{ c.id }}" src="{% static "webclient/image/well16.png" %}" alt="well" title="{{ c.name }}"/>
+                    </td>
+                    <td class="desc"><a>{{ c.name|truncatebefor:"65" }}</a></td>
+                    <td class="date">{{ c.creationEventDate }}</td>
+                    <td class="owner">{{ c.getOwnerFullName }}</td>
+                    <td class="group">{{ c.getDetails.group.name.val }}</td>
+                    <td><a href="{% url 'webindex' %}?show=well-{{ c.id }}" title="{% trans 'Show in hierarchy view' %}">
+                        {% trans "Browse" %}
+                    </a></td>
+                </tr>
+            {% endfor %}
             {% for c in manager.containers.image %}
                 <tr id="image-{{ c.id }}" class="{{ c.getPermsCss }}">
                     <td class="image">
                         <img class="search_thumb" id="{{ c.id }}" src="{% url 'render_thumbnail_resize' 96 c.id  %}" alt="image" title="{{ c.name }}"/>
                     </td>
                     <td class="desc"><a>{{ c.name|truncatebefor:"65" }}</a></td>
                     <td class="date">{{ c.creationEventDate }}</td>
+                    <td class="owner">{{ c.getOwnerFullName }}</td>
                     <td class="group">{{ c.getDetails.group.name.val }}</td>
                     <td><a href="{% url 'webindex' %}?show=image-{{ c.id }}" title="{% trans 'Show in hierarchy view' %}">
                         {% trans "Browse" %}

diff --git a/omero_tagsearch/templates/omero_tagsearch/tagnav.html b/omero_tagsearch/templates/omero_tagsearch/tagnav.html
@@ -72,48 +72,20 @@
                   success: function(data) {
                     $("div#content_details").html(data.html);
 
-                      if (data.project_count > 0) {
-                        $("#tagnav-project span").html(data.project_count);
-                      } else {
-                          $("#tagnav-project span").html('0');
-                      }
-
-                      if (data.dataset_count > 0) {
-                        $(".tagnav-dataset span").html(data.dataset_count);
-                      } else {
-                        $(".tagnav-dataset span").html('0');
-                      }
-
-                      if (data.screen_count > 0) {
-                        $(".tagnav-screen span").html(data.screen_count);
-                      } else {
-                        $(".tagnav-screen span").html('0');
-                      }
-
-                      if (data.plate_count > 0) {
-                        $(".tagnav-plate span").html(data.plate_count);
-                      } else {
-                        $(".tagnav-plate span").html('0');
-                      }
-
-                      if (data.acquisition_count > 0) {
-                        $(".tagnav-acquisition span").html(data.acquisition_count);
-                      } else {
-                        $(".tagnav-acquisition span").html('0');
-                      }
-
-                      if (data.image_count > 0) {
-                        $(".tagnav-image span").html(data.image_count);
-                      } else {
-                        $(".tagnav-image span").html('0');
-                      }
-
-                      if (data.preview) {
-                        $("#filtersearch").removeClass('hidden');
-                        OME.table_selection_changed();
-                      } else {
-                        $("#filtersearch").addClass('hidden');
-                      }
+                    $(".tagnav-project span").html(data.project_count);
+                    $(".tagnav-dataset span").html(data.dataset_count);
+                    $(".tagnav-screen span").html(data.screen_count);
+                    $(".tagnav-plate span").html(data.plate_count);
+                    $(".tagnav-acquisition span").html(data.acquisition_count);
+                    $(".tagnav-well span").html(data.well_count);
+                    $(".tagnav-image span").html(data.image_count);
+
+                    if (data.preview) {
+                      $("#filtersearch").removeClass('hidden');
+                      OME.table_selection_changed();
+                    } else {
+                      $("#filtersearch").addClass('hidden');
+                    }
 
 
                     // Hide any options that are no longer possible and
@@ -221,6 +193,7 @@ <h2>Results</h2>
                   <li class="tagnav-screen"><div class="tagnav-icon">&nbsp;</div>Screen:&nbsp;<span>0</span></li>
                   <li class="tagnav-plate"><div class="tagnav-icon">&nbsp;</div>Plate:&nbsp;<span>0</span></li>
                   <li class="tagnav-acquisition"><div class="tagnav-icon">&nbsp;</div>Plate Acquisition/Run:&nbsp;<span>0</span></li>
+                  <li class="tagnav-well"><div class="tagnav-icon">&nbsp;</div>Well:&nbsp;<span>0</span></li>
                   <li class="tagnav-image"><div class="tagnav-icon">&nbsp;</div>Image:&nbsp;<span>0</span></li>
               </ul>
 

diff --git a/omero_tagsearch/views.py b/omero_tagsearch/views.py
@@ -33,7 +33,7 @@ def index(request, conn=None, **kwargs):
     # path=project=51|dataset=502|image=607 (select the image)
     path = request.GET.get("path", "")
     i = path.split("|")[-1]
-    if i.split("=")[0] in ("project", "dataset", "image", "screen", "plate", "tag"):
+    if i.split("=")[0] in ("project", "dataset", "image", "screen", "plate", "tag", "acquisition", "run", "well"):
         init["initially_select"].append(str(i).replace("=", "-"))
 
     # Now we support show=image-607|image-123  (multi-objects selected)
@@ -207,6 +207,7 @@ def get_tags(obj):
     tags.update(get_tags("Plate"))
     tags.update(get_tags("PlateAcquisition"))
     tags.update(get_tags("Screen"))
+    tags.update(get_tags("Well"))
 
     # Convert back to an ordered list and sort
     tags = list(tags)
@@ -280,6 +281,7 @@ def getObjectsWithAllAnnotations(obj_type, annids):
         screen_count = 0
         plate_count = 0
         acquisition_count = 0
+        well_count = 0
         image_count = 0
 
         if selected_tags:
@@ -303,6 +305,10 @@ def getObjectsWithAllAnnotations(obj_type, annids):
             context["plate_count"] = len(plate_ids)
             plate_count = len(plate_ids)
 
+            well_ids = getObjectsWithAllAnnotations("Well", selected_tags)
+            context["well_count"] = len(well_ids)
+            well_count = len(well_ids)
+
             acquisition_ids = getObjectsWithAllAnnotations(
                 "PlateAcquisition", selected_tags
             )
@@ -330,6 +336,13 @@ def getObjectsWithAllAnnotations(obj_type, annids):
                     plates = conn.getObjects("Plate", ids=plate_ids)
                     manager["containers"]["plate"] = list(plates)
 
+                if well_ids:
+                    wells = []
+                    for well in  conn.getObjects("Well", ids=well_ids):
+                        well.name = well.getParent().name + f" - {well.getWellPos()}"
+                        wells.append(well)
+                    manager["containers"]["well"] = wells
+
                 if acquisition_ids:
                     acquisitions = conn.getObjects(
                         "PlateAcquisition", ids=acquisition_ids
@@ -342,6 +355,7 @@ def getObjectsWithAllAnnotations(obj_type, annids):
                     + len(project_ids)
                     + len(screen_ids)
                     + len(plate_ids)
+                    + len(well_ids)
                     + len(acquisition_ids)
                 )
                 if manager["c_size"] > 0:
@@ -392,6 +406,8 @@ def getAnnotationsForObjects(obj_type, oids):
                 remaining.update(getAnnotationsForObjects("Dataset", dataset_ids))
             if project_ids:
                 remaining.update(getAnnotationsForObjects("Project", project_ids))
+            if well_ids:
+                remaining.update(getAnnotationsForObjects("Well", well_ids))
             if acquisition_ids:
                 remaining.update(
                     getAnnotationsForObjects("PlateAcquisition", acquisition_ids)
@@ -419,6 +435,7 @@ def getAnnotationsForObjects(obj_type, oids):
                     "screen_count": screen_count,
                     "plate_count": plate_count,
                     "acquisition_count": acquisition_count,
+                    "well_count": well_count,
                     "image_count": image_count,
                     "html": html_response,
                 }