Merge pull request #235 from VUIIS/xnatutils_methods_call

changed get_full_object and list_project_assessors to be called from …

bin/Xnat_tools/XnatNDAR

@@ -554,7 +554,7 @@ def get_scan_xnat(options, xnat, directory, subjects):
 
     # list of scans and assessors for the full project
     scan_list = xnat.get_project_scans(options.project)
-    assessor_list = XnatUtils.list_project_assessors(xnat, options.project)
+    assessor_list = xnat.list_project_assessors(options.project)
 
     # filter to keep only the scan we need and keep the assessor that we need
     # for the qc Scans
@@ -629,7 +629,7 @@ def get_processed_data_xnat(options, xnat, directory, subjects):
     scan_info, assessor_info = extract_info(proc_info)
 
     # list of scans and assessors for the full project
-    assessor_list = XnatUtils.list_project_assessors(xnat, options.project)
+    assessor_list = xnat.list_project_assessors(options.project)
     assessor_list = filter_list(subjects, 'subject_label', assessor_list)
 
     # From scan:
@@ -769,7 +769,7 @@ def download_scan_file(xnat, directory, scan, resources, fname):
         if not os.path.exists(res_path):
             os.makedirs(res_path)
         # Select the scan:
-        scan_obj = XnatUtils.get_full_object(xnat, scan)
+        scan_obj = xnat.get_full_object(scan)
         for resource in resources:
             if resource in ['bval', 'bvec']:
                 if scan_obj.resource(resource.lower()).exists():
@@ -817,7 +817,7 @@ def download_assessor_file(xnat, directory, assessor, resources, fname):
     else:
         if not os.path.exists(res_path):
             os.makedirs(res_path)
-        assessor_obj = XnatUtils.get_full_object(xnat, assessor)
+        assessor_obj = xnat.get_full_object(assessor)
         for resource in resources:
             if resource:
                 res_obj = assessor_obj.out_resource(resource)

bin/Xnat_tools/Xnatdl

@@ -186,8 +186,7 @@ download_report.csv if you want to start from scratch."""
             for project in projects_list:
                 self.scans.extend(self.xnat.get_project_scans(project))
                 if XnatUtils.has_dax_datatypes(self.xnat):
-                    self.assessors.extend(XnatUtils.list_project_assessors(
-                        self.xnat, project))
+                    self.assessors.extend(xnat.list_project_assessors(project))
 
             # Filter using the options if they are set only if full project:
             self.filter(args)

bin/Xnat_tools/Xnatinfo

@@ -176,7 +176,7 @@ def report_project(xnat, project, ignore_scans, ignore_unusable, running,
             scans_found[scan_dict['type']] = 1
 
     # assessor loop
-    assessors_list = XnatUtils.list_project_assessors(xnat, project)
+    assessors_list = xnat.list_project_assessors(project)
     assessor_number = len(assessors_list)
     for assessor_dict in assessors_list:
         # add to dictionary of process

bin/Xnat_tools/Xnatsessionupdate

@@ -143,7 +143,7 @@ def change_date_all(xnat, sessions_list):
     :return: None
     """
     for session_dict in sessions_list:
-        session_object = XnatUtils.get_full_object(xnat, session_dict)
+        session_object = xnat.get_full_object(session_dict)
         session_object.attrs.set('xnat:mrSessionData/original', ' ')
         msg = '   ->Session "%s" changed to need update.'
         print(msg % (session_dict['label']))
@@ -157,7 +157,7 @@ def get_xnat_subject_need_inputs(xnat, project):
     :param project: project ID on XNAT
     :return: unique list of sessions labels on XNAT
     """
-    assessors_list = XnatUtils.list_project_assessors(xnat, project)
+    assessors_list = xnat.list_project_assessors(project)
     assessors_list = [x for x in assessors_list
                       if x['procstatus'] == 'NEED_INPUTS']
     return list(set([x['session_label'] for x in assessors_list]))

bin/freesurfer_tools/fs6upload

@@ -129,7 +129,7 @@ if __name__ == '__main__':
         # print('diff aeg result='+str(res))
 
         # Upload the edits - brainmask, wm, aseg, control.dat,...
-        assessor_obj = XnatUtils.get_full_object(xnat, fs)
+        assessor_obj = xnat.get_full_object(fs)
         resource = assessor_obj.out_resource('EDITS')
         curtime = time.strftime("%Y%m%d-%H%M%S")
         brainmask_path = os.path.join(

bin/supplemental_tools/Xnatreport_assessor.py

@@ -19,7 +19,7 @@
 
 xnat = XnatUtils.get_interface()
 
-Assrs = XnatUtils.list_project_assessors(xnat, project)
+Assrs = xnat.list_project_assessors(project)
 
 R = list()
 for assr in Assrs :

bin/supplemental_tools/Xnatreport_assessors.py

@@ -17,7 +17,7 @@
 
 
 xnat = XnatUtils.get_interface()
-Assrs = XnatUtils.list_project_assessors(xnat, args.project)
+Assrs = xnat.list_project_assessors(args.project)
 xnat.disconnect()
 
 timestamp = time.strftime("%Y%m%d%H%M%S")