Bugs web sprint2 2

components/tools/OmeroPy/src/omero/gateway/__init__.py

@@ -43,10 +43,10 @@
 logger = logging.getLogger(__name__)
 
 try:
-    import Image, ImageDraw, ImageFont
+    from PIL import Image, ImageDraw, ImageFont     # see ticket:2597
 except: #pragma: nocover
     try:
-        from PIL import Image, ImageDraw, ImageFont
+        import Image, ImageDraw, ImageFont          # see ticket:2597
     except:
         logger.error('No PIL installed, line plots and split channel will fail!')
 from cStringIO import StringIO

components/tools/OmeroPy/src/omero/util/script_utils.py

@@ -766,9 +766,9 @@ def split_image(client, imageId, dir, unformattedImageName = "tubulin_P037_T%05d
     pixelsService = session.getPixelsService()
 
     try:
-        from PIL import Image
+        from PIL import Image   # see ticket:2597
     except:
-        import Image
+        import Image        # see ticket:2597
 
     query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%s'" % imageId
     pixels = queryService.findByQuery(query_string, None)

components/tools/OmeroPy/test/integration/bigImages.py

@@ -12,6 +12,14 @@
 import integration.library as lib
 from omero.rtypes import *
 
+try:
+    from PIL import Image, ImageDraw, ImageFont     # see ticket:2597
+except: #pragma: nocover
+    try:
+        import Image, ImageDraw, ImageFont          # see ticket:2597
+    except:
+        logger.error('No PIL installed')
+
 try:
     import hashlib
     hash_sha1 = hashlib.sha1
@@ -77,7 +85,6 @@ def testRenderRegion(self):
         planeDef.z = long(0)
         planeDef.t = long(0)
 
-        from PIL import Image
         import StringIO
 
         # First, get the full rendered plane...

components/tools/OmeroWeb/omeroweb/webclient/static/webclient/javascript/ome.webclient.actions.js

@@ -53,12 +53,14 @@ var handle_tree_selection = function(data) {
         }
         selected.each(function(){
             var oid = $(this).attr('id');
-            // after copy & paste, node will have id E.g. copy_dataset-123
-            if (oid.substring(0,5) == "copy_") oid = oid.substring(5, oid.length);
-            var selected_obj = {"id":oid, "rel":$(this).attr('rel')}
-            selected_obj["class"] = $(this).attr('class');
-            if (share_id) selected_obj["share"] = share_id;
-            selected_objs.push(selected_obj);
+            if (typeof oid !== "undefined") {
+                // after copy & paste, node will have id E.g. copy_dataset-123
+                if (oid.substring(0,5) == "copy_") oid = oid.substring(5, oid.length);
+                var selected_obj = {"id":oid, "rel":$(this).attr('rel')}
+                selected_obj["class"] = $(this).attr('class');
+                if (share_id) selected_obj["share"] = share_id;
+                selected_objs.push(selected_obj);
+            };
         });
     }
     $("body")

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/activities/activitiesContent.html

@@ -48,7 +48,7 @@
             {% for j in jobs %}
                 <!-- Chgrp jobs -->
                 {% ifequal j.job_type "chgrp" %}
-                    <tr id="{{ j.id }}" {% if j.new %}class="new_result"{% endif %}>
+                    <tr id="{{ j.id }}" class="{% if j.new %}new_result{% endif %}{% ifequal j.status 'in progress' %} in_progress{% endifequal %}" >
                         <td width="25px">
                             {% ifequal j.status "in progress" %}<img class="icon" src="{% static "webgateway/img/spinner.gif" %}" />
                             {% else %} <img class="icon" src="{% static "webgateway/img/success.png" %}" />
@@ -85,7 +85,7 @@
 
                 <!-- Delete jobs -->
                 {% ifequal j.job_type "delete" %}
-                    <tr id="{{ j.id }}" {% if j.new %}class="new_result"{% endif %}>
+                    <tr id="{{ j.id }}" class="{% if j.new %}new_result{% endif %}{% ifequal j.status 'in progress' %} in_progress{% endifequal %}">
                         <td class="activities_state">
                             {% ifequal j.status "in progress" %}
                                 <img alt="Deleting" src="{% static "webgateway/img/spinner.gif" %}" />
@@ -138,7 +138,7 @@
 
                 <!-- Status -->
                 {% ifequal j.job_type "script" %}
-                    <tr class="script{% if j.new %} new_result{% endif %}" id="{{ j.id }}">
+                    <tr id="{{ j.id }}" class="script{% if j.new %} new_result{% endif %}{% ifequal j.status 'in progress' %} in_progress{% endifequal %}">
 
 						<!-- State -->
                         <td class="activities_state">
@@ -219,7 +219,7 @@
 
 													<!-- Download -->
                                                     <li class="btn_download">
-														<a href="#" onClick="window.location.href='{% url download_annotation 'download' v.id %}'" title="Download File">Download</a>
+														<a href="{% url download_annotation v.id %}" title="Download File">Download</a>
 													</li>
 
 													{% if v.fileId %}

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/annotations/fileann.html

@@ -32,7 +32,7 @@
 
 {% if fileann.getFileName %}
 <li class="file_ann_wrapper" id="file_ann-{{ fileann.id }}">
-    <a class='tooltip' href="#" onClick="document.location.href='{% url download_annotation "download" fileann.id %}';">
+    <a class='tooltip' href="{% url download_annotation fileann.id %}">
         {{ fileann.getFileName|shortening:40 }}
 		<span>{% if fileann.getFileSize %}({{ fileann.getFileSize|default:0|filesizeformat }}){% endif %}</span>
     </a>

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/annotations/metadata_acquisition.html

@@ -88,7 +88,7 @@ <h1 class="can-collapse defclose">{% trans "Companion Files" %}</h1>
                 <div>
                     {% for fileann in manager.companion_files %}
                     <p>
-                        <a href="#" onClick="document.location.href='{% url download_annotation "download" fileann.id %}';">
+                        <a href="{% url download_annotation fileann.id %}">
                             {{ fileann.getFileName|shortening:40 }}
                         </a>
                         ({{ fileann.getFileSize|default:0|filesizeformat }})
@@ -101,7 +101,7 @@ <h1 class="can-collapse defclose">{% trans "Companion Files" %}</h1>
             <h1 class="can-collapse defclose">{% trans "Original Metadata" %}</h1>
                 <div>
                     <input type="button" value="Download" style="padding: 1px 15px; position:absolute; right:3px"
-                        onClick="document.location.href='{% url download_annotation "download" manager.original_metadata.id %}';"/>
+                        onClick="document.location.href='{% url download_annotation manager.original_metadata.id %}';"/>
                     {% if manager.global_metadata %}
                     <h1>Global Metadata</h1>
                     <div style="height:250px; overflow:auto">

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/base/includes/activities_info.html

@@ -143,7 +143,7 @@
 
         $("#clear_activities").click(function() {
             $.post("{% url activities_update action='clean' %}");
-            $("#activities_content").empty();
+            $("#jobsTable>tbody>tr").filter(":not(.in_progress)").remove();
         });
 
         // close panels on 'ESCAPE'

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/data/includes/center_plugin.thumbs.js.html

@@ -31,7 +31,8 @@
     var syncPanels = function(get_selected) {
         $("#content_details .ui-selectee").removeClass('ui-selected');    // clear selection
         get_selected.each(function(i) {
-            var dtype = $(this).attr("rel").replace("-locked", "");
+            var dtype = $(this).attr("rel");
+            dtype = dtype && dtype.replace("-locked", "");
             if (dtype == "image") {
                 var imgId = $(this).attr("id").split("-")[1];
                 $("#image_icon-"+imgId).addClass('ui-selected');

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/login.html

@@ -63,6 +63,7 @@
 
 
 <div id="login">
+    {% block login %}
     <form class="standard_form inlined" action="{% url weblogin %}{% if url %}?{{url}}{% endif %}" method="post">
 
 
@@ -122,6 +123,7 @@
 
         	<input type="submit" value="Login" />
     </form>
+    {% endblock %}
 </div>
 
 <div id="login-footer">

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/public/public.html

@@ -47,7 +47,8 @@
                 var buttonsShowHide = function(selected) { 
                     var toolbar_config = new Object();
                     if(selected.length > 0) {
-                        if(selected.attr("rel").indexOf("locked")>=0) {                            
+                        if((typeof selected.attr("rel") === 'undefined') ||
+                                (selected.attr("rel").indexOf("locked")>=0)) {
                             toolbar_config = {"adddiscussion":false, 'removecontent':false};
                         } else {
                             if(selected.attr("id").indexOf("experimenter")>=0) {

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/scripts/script_ui.html

@@ -149,6 +149,26 @@
                 e.preventDefault();
                 return false;
             });
+
+            // If 'Data_Type' changes, clear 'IDs' (but note values to add back)
+            var $Data_Type = $("select[name=Data_Type]"),
+                $IDs = $("input[name=IDs]");
+            var noteIDs = function() {
+                var dt = $Data_Type.val(),
+                    ids = $IDs.val();
+                $Data_Type.data(dt, ids);
+            };
+            noteIDs();                  // note the initial value...
+            $IDs.keyup(noteIDs);                // ...update any changes
+            $Data_Type.change(function() {      // Clear IDs (or add back previous data)
+                var dt = $Data_Type.val(),
+                    ids = $Data_Type.data(dt);
+                if (typeof ids !== "undefined") {
+                    $IDs.val(ids);
+                } else {
+                    $IDs.val("");
+                }
+            });
         });
     </script>
 {% endblock %}

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

@@ -107,15 +107,15 @@
     url( r'^annotate_tags/$', views.annotate_tags, name="annotate_tags" ),
     url( r'^annotate_comment/$', views.annotate_comment, name="annotate_comment" ),
     url( r'^annotate_file/$', views.annotate_file, name="annotate_file" ),
-    url( r'^annotation/(?P<action>[a-zA-Z]+)/(?P<iid>[0-9]+)/$', views.download_annotation, name="download_annotation" ),
+    url( r'^annotation/(?P<annId>[0-9]+)/$', views.download_annotation, name="download_annotation" ),
     url( r'^archived_files/download/(?P<iid>[0-9]+)/$', views.archived_files, name="archived_files" ),
 
     url( r'^load_tags/(?:(?P<o_type>((?i)tag|dataset))/(?P<o_id>[0-9]+)/)?$', views.load_data_by_tag, name="load_data_by_tag" ),
 
     # Open Astex Viewer will try to show file as volume, e.g. mrc.map file. 
     url( r'^open_astex_viewer/(?P<obj_type>((?i)image|image_8bit|file))/(?P<obj_id>[0-9]+)/$', views.open_astex_viewer, name='open_astex_viewer' ),  # 'data_url' to load in REQUEST
-    url( r'^file/(?P<iid>[0-9]+)\.map$', views.download_annotation, {'action':'download'}, name='open_astex_map' ),# download file
-    url( r'^file/(?P<iid>[0-9]+)\.bit$', views.download_annotation, {'action':'download'}, name='open_astex_bit' ),# download file
+    url( r'^file/(?P<annId>[0-9]+)\.map$', views.download_annotation, name='open_astex_map' ),# download file
+    url( r'^file/(?P<annId>[0-9]+)\.bit$', views.download_annotation, name='open_astex_bit' ),# download file
     url( r'^image_as_map/(?P<imageId>[0-9]+)\.map$', views.image_as_map, name='webclient_image_as_map' ), # convert image to map (full size)
     url( r'^image_as_map/(?P<imageId>[0-9]+)/(?P<maxSize>[0-9]+)\.map$', views.image_as_map, name='webclient_image_as_map' ), # image to map of max Size (side length)
     url( r'^image_as_map/8bit/(?P<imageId>[0-9]+)\.map$', views.image_as_map, {'8bit':True}, name='webclient_image_as_map_8bit' ), # convert image to map

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

@@ -1727,11 +1727,11 @@ def archived_files(request, iid, conn=None, **kwargs):
     return rsp
 
 @login_required(doConnectionCleanup=False)
-def download_annotation(request, action, iid, conn=None, **kwargs):
+def download_annotation(request, annId, conn=None, **kwargs):
     """ Returns the file annotation as an http response for download """
-    ann = conn.getObject("Annotation", iid)
+    ann = conn.getObject("Annotation", annId)
     if ann is None:
-        return handlerInternalError(request, "Annotation does not exist (id:%s)." % (iid))
+        return handlerInternalError(request, "Annotation does not exist (id:%s)." % (annId))
 
     rsp = ConnCleaningHttpResponse(ann.getFileInChunks())
     rsp.conn = conn

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

@@ -55,12 +55,12 @@
 logger = logging.getLogger(__name__)
 
 try:
-    import Image
-    import ImageDraw
+    from PIL import Image
+    from PIL import ImageDraw
 except: #pragma: nocover
     try:
-        from PIL import Image
-        from PIL import ImageDraw
+        import Image
+        import ImageDraw
     except:
         logger.error('No PIL installed')
 
@@ -421,8 +421,8 @@ def xyListToBbox(xyList):
 
     bBox = None   # bounding box: (x, y, w, h)
     shape = {}
-    theT = s.getTheT().getValue()
-    theZ = s.getTheZ().getValue()
+    theT = s.getTheT() is not None and s.getTheT().getValue() or 0
+    theZ = s.getTheZ() is not None and s.getTheZ().getValue() or 0
     if type(s) == omero.model.RectI:
         shape['type'] = 'Rectangle'
         shape['x'] = s.getX().getValue()
@@ -583,12 +583,17 @@ def resizeXY(xy):
             return (int((x-newX + left_xs)*factor), int((y-newY + top_xs)*factor))
         resizedXY = [ resizeXY(xy) for xy in shape['xyList'] ]
         #draw.polygon(resizedXY, outline=lineColour)    # doesn't support 'width' of line
+        x2 = y2 = None
         for l in range(1, len(resizedXY)):
             x1, y1 = resizedXY[l-1]
             x2, y2 = resizedXY[l]
             draw.line((x1, y1, x2, y2), fill=lineColour, width=2)
         start_x, start_y = resizedXY[0]
         if shape['type'] != 'PolyLine':
+            if x2 is None:          # Seems possible to have Polygon with only 1 point!
+                x2 = start_x + 1    # This will create a visible dot
+            if y2 is None:
+                y2 = start_y + 1
             draw.line((x2, y2, start_x, start_y), fill=lineColour, width=2)
 
     rv = StringIO()