Flake8 remaining examples Python files

examples/Delete/Callback.py

@@ -26,7 +26,7 @@
                 print "ERROR: Failed to cancel"
 
         reports = deleteHandlePrx.report()
-        r = reports[0] # We only sent one command
+        r = reports[0]  # We only sent one command
         print "Report:error=%s,warning=%s,deleted=%s" % \
             (r.error, r.warning, r.actualDeletes)
 

examples/Delete/FileAnnotationDelete.py

@@ -12,8 +12,9 @@
 c = omero.client()
 ice_config = c.getProperty("Ice.Config")
 
-from omero.rtypes import *
-from omero.model import *
+from omero.rtypes import rstring
+from omero.model import DatasetI, FileAnnotationI, OriginalFileI
+from omero.model import DatasetAnnotationLinkI
 
 try:
     s = c.createSession()

examples/Delete/Options.py

@@ -32,7 +32,7 @@
                 print "ERROR: Failed to cancel"
 
         reports = deleteHandlePrx.report()
-        r = reports[0] # We only sent one command
+        r = reports[0]  # We only sent one command
         print "Report:error=%s,warning=%s,deleted=%s" % \
             (r.error, r.warning, r.actualDeletes)
 

examples/Delete/Subclass.py

@@ -10,6 +10,7 @@
 c = omero.client()
 s = c.createSession()
 
+
 class Subclass(omero.callbacks.DeleteCallbackI):
 
     def finished(self, errors):
@@ -19,8 +20,8 @@ def finished(self, errors):
         try:
             reports = self.handle.report()
             for r in reports:
-                print "Report:error=%s,warning=%s,deleted=%s" % \
-                        (r.error, r.warning, r.actualDeletes)
+                print "Report:error=%s,warning=%s,deleted=%s" % (
+                    r.error, r.warning, r.actualDeletes)
 
         except omero.ServerError:
             print "Something happened to the handle?!?"

examples/OmeroTables/first.py

@@ -1,21 +1,19 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import omero
-import omero_Tables_ice
-import omero_SharedResources_ice
 
 c = omero.client()
 s = c.createSession()
 r = s.sharedResources()
 m = r.repositories()
 i = m.descriptions[0].id.val
 t = r.newTable(i, "/example.h5")
-l = omero.grid.LongColumn('name','desc',None)
+l = omero.grid.LongColumn('name', 'desc', None)
 t.initialize([l])
-l.values = [1,2,3,4]
+l.values = [1, 2, 3, 4]
 t.addData([l])
-ids = t.getWhereList('(name==1)',{},0,0,0)
+ids = t.getWhereList('(name==1)', {}, 0, 0, 0)
 data = t.readCoordinates(ids)
 print data.columns[0].values[0]
-data = t.slice([0],[0])
+data = t.slice([0], [0])
 print data.columns[0].values[0]

examples/OmeroTables/iroi.py

@@ -2,21 +2,18 @@
 # -*- coding: utf-8 -*-
 import omero
 import omero.clients
-import omero_Tables_ice
-import omero_api_IRoi_ice
-import omero_SharedResources_ice
 
-from omero.rtypes import *
+from omero.rtypes import rstring, rtime
 
 c = omero.client()
 s = c.createSession()
 
 # Create a table
-table = s.sharedResources().newTable(1,"iroi.h5")
+table = s.sharedResources().newTable(1, "iroi.h5")
 cols = []
-cols.append( omero.grid.RoiColumn('roi_id','Roi ID', None) )
-cols.append( omero.grid.DoubleColumn('area','Area of ROI', None) )
-cols.append( omero.grid.LongColumn('intensity','Intensity of ROI', None) )
+cols.append(omero.grid.RoiColumn('roi_id', 'Roi ID', None))
+cols.append(omero.grid.DoubleColumn('area', 'Area of ROI', None))
+cols.append(omero.grid.LongColumn('intensity', 'Intensity of ROI', None))
 table.initialize(cols)
 file = table.getOriginalFile()
 
@@ -39,12 +36,10 @@
 plate = s.getUpdateService().saveAndReturnObject(plate)
 image_id = plate.copyWells()[0].copyWellSamples()[0].image.id.val
 
-# http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/slice2html/omero/api/IRoi.html#IRoi
 roi_svc = s.getRoiService()
 roi_meas = roi_svc.getRoiMeasurements(image_id, None)
 
 if len(roi_meas) > 0:
     roi_result = roi_svc.getMeasuredRois(image_id, roi_meas[0].id.val, None)
     table = roi_svc.getTable(roi_meas[0].id.val)
-    print table.slice([0],None) # All of column 1
-
+    print table.slice([0], None)  # All of column 1

examples/RegionsOfInterest/Main.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 import omero
 import omero.clients
-from omero.rtypes import *
+from omero.rtypes import rdouble
 
 roi = omero.model.RoiI()
 ellipse = omero.model.EllipseI()

examples/ScreenPlateWell/imagesperwell.py

@@ -2,17 +2,18 @@
 # -*- coding: utf-8 -*-
 import sys
 import omero
-from omero.rtypes import *
-from omero_sys_ParametersI import ParametersI # Temporary
+from omero.rtypes import rint
+from omero_sys_ParametersI import ParametersI  # Temporary
 
-c = omero.client();
-s = c.createSession();
-q = s.getQueryService();
+c = omero.client()
+s = c.createSession()
+q = s.getQueryService()
 
-LOAD_WELLS = """select w from Well w join fetch w.wellSamples ws
-                join fetch ws.image i join fetch i.pixels p where w.plate.id = :id"""
+LOAD_WELLS = (
+    "select w from Well w join fetch w.wellSamples ws"
+    " join fetch ws.image i join fetch i.pixels p where w.plate.id = :id")
 
-filter = omero.sys.Filter();
+filter = omero.sys.Filter()
 filter.limit = rint(10)
 filter.offset = rint(0)
 
@@ -24,7 +25,8 @@
 else:
     import random
     example_plate = random.choice(plates)
-    print "Loading wells for Plate %s (%s)" % (example_plate.getId().getValue(), example_plate.getName().getValue())
+    print "Loading wells for Plate %s (%s)" % (
+        example_plate.getId().getValue(), example_plate.getName().getValue())
 
 # An example of true paging
 filter.limit = rint(12)
@@ -40,7 +42,7 @@
         break
     else:
         offset += len(wells)
-        params.theFilter.offset = rint( offset )
+        params.theFilter.offset = rint(offset)
 
     for well in wells:
         id = well.getId().getValue()
@@ -54,6 +56,7 @@
             sizeC = pix.sizeC.val
             sizeT = pix.sizeT.val
             sizeZ = pix.sizeZ.val
-            images.append( img.getId().getValue() )
+            images.append(img.getId().getValue())
             planes += sizeZ*sizeT*sizeC
-        print "Well %s (%2sx%2s) contains the images: %s with %s planes" % (id, row, col, images, planes)
+        print ("Well %s (%2sx%2s) contains the images: %s with %s planes"
+               % (id, row, col, images, planes))

examples/ScreenPlateWell/listplates.py

@@ -1,44 +1,46 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import omero
-from omero_sys_ParametersI import ParametersI # Temporary
+from omero_sys_ParametersI import ParametersI  # Temporary
 
-c = omero.client();
-s = c.createSession();
-q = s.getQueryService();
+c = omero.client()
+s = c.createSession()
+q = s.getQueryService()
 
-QUERY = 'select p from Plate p left outer join fetch p.wells w left outer join fetch w.wellSamples s left outer join fetch s.image where p.id = :id';
+QUERY = ("select p from Plate p left outer join fetch p.wells w"
+         " left outer join fetch w.wellSamples s"
+         " left outer join fetch s.image where p.id = :id")
 
-filter = omero.sys.Filter();
-plates = q.findAll('Plate', filter);
+filter = omero.sys.Filter()
+plates = q.findAll('Plate', filter)
 
 
 print 'Plate:'
 for i in range(len(plates)):
-    params = ParametersI();
-    params.addId(plates[i].getId().getValue());
-    plate = q.findByQuery(QUERY, params);
-    print '    %d %s '  % ( i, plate.getName().getValue() )
+    params = ParametersI()
+    params.addId(plates[i].getId().getValue())
+    plate = q.findByQuery(QUERY, params)
+    print '    %d %s ' % (i, plate.getName().getValue())
     wells = {}
 
     for well in plate.copyWells():
         row = well.getRow() and well.getRow().getValue() or -1
         col = well.getColumn() and well.getColumn().getValue() or -1
         if row in wells:
-            row_list = wells[row];
+            row_list = wells[row]
         else:
             row_list = []
-            wells[row] = row_list;
-        row_list.append(col);
+            wells[row] = row_list
+        row_list.append(col)
         row_list.sort()
 
-    rows = list(wells.keys());
+    rows = list(wells.keys())
     rows.sort()
 
     for row in rows:
-        msg = '        ';
-        col_list = list(wells[row]);
+        msg = '        '
+        col_list = list(wells[row])
         col_list.sort()
         for col in col_list:
-            msg += '%2dx%2d ' % (row, col);
+            msg += '%2dx%2d ' % (row, col)
         print msg

examples/ScreenPlateWell/platecodebyimage.py

@@ -1,17 +1,21 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import omero
-from omero.rtypes import *
-from omero_sys_ParametersI import ParametersI # Temporary
+from omero.rtypes import rint
+from omero_sys_ParametersI import ParametersI  # Temporary
 
-c = omero.client();
-s = c.createSession();
-q = s.getQueryService();
+c = omero.client()
+s = c.createSession()
+q = s.getQueryService()
 
-GET_IMAGES_WITH_PLATES = 'select i from Image i join i.wellSamples ws join ws.well w join w.plate p' # Inner joins
-GET_PLATE_FROM_IMAGE_ID = 'select p from Plate p join p.wells w join w.wellSamples ws join ws.image i where i.id = :id'
+GET_IMAGES_WITH_PLATES = (
+    "select i from Image i join i.wellSamples ws join ws.well w"
+    " join w.plate p")  # Inner joins
+GET_PLATE_FROM_IMAGE_ID = (
+    "select p from Plate p join p.wells w join w.wellSamples ws"
+    " join ws.image i where i.id = :id")
 
-filter = omero.sys.Filter();
+filter = omero.sys.Filter()
 filter.limit = rint(100)
 filter.offset = rint(0)
 params = ParametersI()
@@ -22,7 +26,10 @@
 
 for image in images:
 
-    params = ParametersI();
-    params.addId(image.getId().getValue());
-    plate = q.findByQuery(GET_PLATE_FROM_IMAGE_ID, params); # Multiple plates per image will through an exception
-    print 'Image %s belongs to Plate %s (%s)'  % ( image.getId().getValue(), plate.getId().getValue(), plate.getName().getValue() )
+    params = ParametersI()
+    params.addId(image.getId().getValue())
+    # Multiple plates per image will through an exception
+    plate = q.findByQuery(GET_PLATE_FROM_IMAGE_ID, params)
+    print 'Image %s belongs to Plate %s (%s)' % (
+        image.getId().getValue(), plate.getId().getValue(),
+        plate.getName().getValue())

examples/TreeList/AllProjects.py

@@ -1,10 +1,14 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-import omero
-from omero.rtypes import *
+
+from omero.rtypes import rstring
 from omero_sys_ParametersI import ParametersI
 
+
 def getProjects(query_prx, username):
     return query_prx.findAllByQuery(
-            "select p from Project p join fetch p.datasetLinks dil join fetch dil.child where p.details.owner.omeName = :name",
-            ParametersI().add("name", rstring(username)))
+        "select p from Project p"
+        " join fetch p.datasetLinks dil"
+        " join fetch dil.child"
+        " where p.details.owner.omeName = :name",
+        ParametersI().add("name", rstring(username)))

examples/TreeList/Main.py

@@ -2,7 +2,9 @@
 # -*- coding: utf-8 -*-
 import sys
 import omero
-import Usage, AllProjects, PrintProjects
+import Usage
+import AllProjects
+import PrintProjects
 
 if __name__ == "__main__":
     try:
@@ -20,4 +22,3 @@
         PrintProjects.print_(projects)
     finally:
         client.closeSession()
-

examples/TreeList/PrintProjects.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+
+
 def print_(projects):
     for project in projects:
         print project.getName().val

examples/TreeList/Usage.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 import sys
 
+
 def usage():
     print"TreeList.Main host port username password"
     sys.exit(-2)