Merge pull request ome#1 from mpievolbio-scicomp/fixes

Fixes

omero/annotation_scripts/MIF/Key_Val_from_Description.py → omero/annotation_scripts/01-KeyVal_from_Description.py

@@ -28,7 +28,6 @@
 @since 5.3
 
 """
-from __future__ import print_function
 
 import sys, os
 import re
@@ -72,7 +71,7 @@ def RemoveMapAnnotations(conn, dtype, Id ):
         conn.c.waitOnCmd(handle, loops=10, ms=500, failonerror=True,
                      failontimeout=False, closehandle=False)
 
-    except Exception, ex:
+    except Exception as ex:
         print("Failed to delete links: {}".format(ex.message))
     return
 
@@ -102,7 +101,7 @@ def AddKeysToMatchingFiles( conn, Id, global_kv, template, file_keys, spec_kv=No
 
         existing_kv = GetExistingMapAnnotions(image)
         updated_kv  = copy.deepcopy(existing_kv)
-        for key,vals in global_kv.iteritems():
+        for key,vals in global_kv.items():
             if key not in updated_kv: updated_kv[key] = set()
             for val in vals:
                 updated_kv[key].add(val)
@@ -129,19 +128,12 @@ def AddKeysToMatchingFiles( conn, Id, global_kv, template, file_keys, spec_kv=No
                         updated_kv[key].add(val)
 
                 if( spec_kv is not None ):
-                    for key,vals in spec_kv.iteritems():
+                    for key,vals in spec_kv.items():
                         if key not in updated_kv: updated_kv[key] = set()
                         for val in vals:
                             updated_kv[key].add(val)
 
 
-        #print("existing_kv")
-        #for k,v in existing_kv.iteritems():
-        #    print("  {} : {}".format(k,v))
-        #print("updated_kv")
-        #for k,v in updated_kv.iteritems():
-        #    print("  {} : {}".format(k,v))
-        #print("Are they the same?",existing_kv == updated_kv )
         nold_i = sum(map( len, existing_kv.values()))
         nnew_i = sum(map( len, updated_kv.values()))
         nkv_added = nkv_added+(nnew_i+nold_i)
@@ -151,11 +143,11 @@ def AddKeysToMatchingFiles( conn, Id, global_kv, template, file_keys, spec_kv=No
             RemoveMapAnnotations( conn, 'image', image.getId()  )
             map_ann = omero.gateway.MapAnnotationWrapper(conn)
             namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
-            namespace = "openmicroscopy.org/mapr/gene" 
+            # namespace = "openmicroscopy.org/mapr/gene" 
             map_ann.setNs(namespace)
             # convert the ordered dict to a list of lists
             kv_list=[]
-            for k,vset in updated_kv.iteritems():
+            for k,vset in updated_kv.items():
                 for v in vset:
                     kv_list.append( [k,v] )
             map_ann.setValue( kv_list )
@@ -268,21 +260,18 @@ def AddMapAnnotations(conn, dtype, Id ):
                  val = match.group(2)
                  if( key not in spec_kv ): spec_kv[key]=set()
                  spec_kv[key].add(val)
-    #print("Global k-v's")
-    #for k,v in global_kv.iteritems():
-    #    print( k,v)
 
     # now add the key value pairs to the dataset
     existing_kv = GetExistingMapAnnotions(dataset)
     if( existing_kv != global_kv ):
         RemoveMapAnnotations( conn, 'dataset', dataset.getId()  )
         map_ann = omero.gateway.MapAnnotationWrapper(conn)
         namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
-        namespace = "openmicroscopy.org/mapr/gene"
+        # namespace = "openmicroscopy.org/mapr/gene"
         map_ann.setNs(namespace)    
         # convert the ordered dict to a list of lists
         kv_list=[]
-        for k,vset in global_kv.iteritems():
+        for k,vset in global_kv.items():
             for v in vset:
                 kv_list.append( [k,v] )
         map_ann.setValue( kv_list )        
@@ -325,10 +314,10 @@ def AddMapAnnotations(conn, dtype, Id ):
                             updated_kv[key].add(val)
 
             print("existing_kv")
-            for k,v in existing_kv.iteritems():
+            for k,v in existing_kv.items():
                 print("  {} : {}".format(k,v))             
             print("updated_kv")
-            for k,v in updated_kv.iteritems():
+            for k,v in updated_kv.items():
                 print("  {} : {}".format(k,v))    
             print("Are they the same?",existing_kv == updated_kv )
 
@@ -337,13 +326,13 @@ def AddMapAnnotations(conn, dtype, Id ):
                 print("The key-values pairs are different")
                 RemoveMapAnnotations( conn, 'image', image.getId()  )
                 map_ann = omero.gateway.MapAnnotationWrapper(conn)
-                namespace ="openmicroscopy.org/mapr/gene"
+                # namespace ="openmicroscopy.org/mapr/gene"
                 map_ann.setNs(namespace)
                 print("Namespace")
                 print(map_ann)
                 # convert the ordered dict to a list of lists
                 kv_list=[]
-                for k,vset in updated_kv.iteritems():
+                for k,vset in updated_kv.items():
                     for v in vset:
                         kv_list.append( [k,v] )            
                 map_ann.setValue( kv_list )
@@ -454,5 +443,8 @@ def getObjects(conn, scriptParams):
         #                   " details")
         #        # Insight will display the 'Message' parameter
         #client.setOutput("Message", rstring(message))
+    except:
+        pass
+
     finally:
         client.closeSession()

omero/annotation_scripts/MIF/Key_Val_to_csv.py → omero/annotation_scripts/02-KeyVal_to_csv.py

@@ -73,8 +73,8 @@ def attach_csv_file( conn, obj, data ):
     # get the list of  keys and maximum number of occurences
     # A key can appear multiple times, for example multiple dyes can be used
     key_union=OrderedDict()
-    for img_n,img_kv in data.iteritems():
-        for key, vset  in img_kv.iteritems():
+    for img_n,img_kv in data.items():
+        for key, vset  in img_kv.items():
             key_union[key] = max(key_union.get(key,0),len(vset))
     all_keys = key_union.keys()
 
@@ -86,15 +86,15 @@ def to_csv( ll ):
 
     # construct the header of the CSV file
     header = ['filename']
-    for key,count in key_union.iteritems():
+    for key,count in key_union.items():
         header.extend( [key]*count )      # keys can repeat multiple times
     tfile.write( to_csv( header ) )
 
     # write the keys values for each file
-    for filename,kv_dict in data.iteritems():
+    for filename,kv_dict in data.items():
         row    = [""]*len(header)   # empty row 
         row[0] = filename
-        for key,vset, in kv_dict.iteritems():
+        for key,vset, in kv_dict.items():
             n0   = header.index(key)     # first occurence of key in header
             for i,val in enumerate(vset):
                 row[n0+i] = val
@@ -173,7 +173,7 @@ def run_script():
                             conn.c.waitOnCmd(handle, loops=10, ms=500, failonerror=True,
                                          failontimeout=False, closehandle=False)
                             print("Deleted existing csv")
-                        except Exception, ex:
+                        except Exception as ex:
                             print("Failed to delete existing csv: {}".format(ex.message))
                 else:
                     print("No exisiting file")
@@ -191,6 +191,9 @@ def run_script():
             print(mess)
         mess="done" 
         client.setOutput("Message", rstring(mess))
+
+    except:
+        pass
 
     finally:
         client.closeSession()

omero/annotation_scripts/MIF/Key_Val_from_csv.py → omero/annotation_scripts/03-KeyVal_from_csv.py

@@ -82,7 +82,7 @@ def remove_MapAnnotations(conn, dtype, Id ):
         conn.c.waitOnCmd(handle, loops=10, ms=500, failonerror=True,
                      failontimeout=False, closehandle=False)
 
-    except Exception, ex:
+    except Exception as ex:
         print("Failed to delete links: {}".format(ex.message))
     return
 
@@ -162,7 +162,7 @@ def populate_metadata(client, conn, script_params):
                 existing_kv = get_existing_MapAnnotions( img )
                 updated_kv  = copy.deepcopy(existing_kv)
                 print("Existing kv ")
-                for k,vset in existing_kv.iteritems():
+                for k,vset in existing_kv.items():
                     print(type(vset),len(vset))
                     for v in vset:
                         print(k,v)
@@ -187,7 +187,7 @@ def populate_metadata(client, conn, script_params):
                     map_ann.setNs(namespace)
                     # convert the ordered dict to a list of lists
                     kv_list=[]
-                    for k,vset in updated_kv.iteritems():
+                    for k,vset in updated_kv.items():
                         for v in vset:
                             kv_list.append( [k,v] )
                     map_ann.setValue(kv_list)
@@ -234,12 +234,14 @@ def run_script():
 
         # wrap client to use the Blitz Gateway
         conn = BlitzGateway(client_obj=client)
-        message="here I am"
-        print "scaript params"
-        for k,v in script_params.iteritems():
-            print k,v
+        print("script params")
+        for k,v in script_params.items():
+            print(k,v)
         message = populate_metadata(client, conn, script_params)
         client.setOutput("Message", rstring(message))
+
+    except:
+        pass
 
     finally:
         client.closeSession()

omero/annotation_scripts/MIF/Key_Val_remove.py → omero/annotation_scripts/04-Remove_KeyVal.py

@@ -27,8 +27,6 @@
 @since   5.3.3
 
 """
-from __future__ import print_function
-
 
 from omero.gateway import BlitzGateway
 import omero
@@ -55,7 +53,7 @@ def RemoveMapAnnotations(conn, dtype, Id ):
         conn.c.waitOnCmd(handle, loops=10, ms=500, failonerror=True,
                      failontimeout=False, closehandle=False)
         return 0
-    except Exception, ex:
+    except Exception as ex:
         print("Failed to delete links: {} ".format(ex.message) )
         return 1
     return
@@ -163,6 +161,9 @@ def getObjects(conn, scriptParams):
         nobjs = len(objs)
         message = "Key value data deleted from  {} of {} files".format( nobjs-nfailed, nobjs)
         client.setOutput("Message", rstring(message))
+
+    except:
+        pass
 
     finally:
         client.closeSession()

omero/annotation_scripts/MIF/Key_Val_from_FileName.py → omero/annotation_scripts/05-KeyVal_from_Filename.py

@@ -28,7 +28,6 @@
 @since 5.3
 
 """
-from __future__ import print_function
 
 import sys, os
 import re
@@ -70,7 +69,7 @@ def RemoveMapAnnotations(conn, dtype, Id ):
         conn.c.waitOnCmd(handle, loops=10, ms=500, failonerror=True,
                      failontimeout=False, closehandle=False)
 
-    except Exception, ex:
+    except Exception as ex:
         print("Failed to delete links: {}".format(ex.message))
     return
 
@@ -103,7 +102,7 @@ def AddMapAnnotations(conn, dtype, Id ):
 
     for line in description:
         # 1. See if this is a mode string
-        for key,value in modes.iteritems():
+        for key,value in modes.items():
             match = re.search( "^#\s+{}".format(key),line.lower())
             if( match is not None ):
                 mode = value
@@ -140,7 +139,7 @@ def AddMapAnnotations(conn, dtype, Id ):
                  file_keys[i] = match.group(2)
 
     print("Global k-v's")
-    for k,v in global_kv.iteritems():
+    for k,v in global_kv.items():
         print( k,v)
 
     # convert the template to a regexp
@@ -163,7 +162,7 @@ def AddMapAnnotations(conn, dtype, Id ):
         map_ann = omero.gateway.MapAnnotationWrapper(conn)
         namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
         map_ann.setNs(namespace)    
-        map_ann.setValue(  [  [k,v] for k,v in global_kv.iteritems() ] )
+        map_ann.setValue(  [  [k,v] for k,v in global_kv.items() ] )
         map_ann.save()
         dataset.linkAnnotation(map_ann)
 
@@ -187,10 +186,6 @@ def AddMapAnnotations(conn, dtype, Id ):
             filename = path+"/"+name
             match = regexp.search(filename)
 
-            # extract the keys
-            #for i,key in file_keys.iteritems():
-            #    val = match.group(int(i))
-            #    updated_kv[key] =  val
             if( match is not None ):
                 for i,val in enumerate(match.groups()):
                     i1 = i+1
@@ -199,10 +194,10 @@ def AddMapAnnotations(conn, dtype, Id ):
                         updated_kv[key] = val
 
         print("existing_kv")
-        for k,v in existing_kv.iteritems():
+        for k,v in existing_kv.items():
             print("  {} : {}".format(k,v))             
         print("updated_kv")
-        for k,v in updated_kv.iteritems():
+        for k,v in updated_kv.items():
             print("  {} : {}".format(k,v))    
         print("Are they the same?",existing_kv == updated_kv )
 
@@ -214,7 +209,7 @@ def AddMapAnnotations(conn, dtype, Id ):
             namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
             map_ann.setNs(namespace)
             # convert the ordered dict to a list of lists
-            map_ann.setValue([  [k,v] for k,v in updated_kv.iteritems() ] )
+            map_ann.setValue([  [k,v] for k,v in updated_kv.items() ] )
             map_ann.save()
             image.linkAnnotation(map_ann)