Solved issue 56. #56

iSkyLIMS_core/templates/iSkyLIMS_core/footer.html

@@ -41,7 +41,7 @@ <h4>Powered by :</h4>
 		</div>
 		<div class="row">
 			<div class="col-md-2 col-md-offset-5">
-				<p>Version 2.0.1</p>
+				<p>Version 2.0.2</p>
 			</div>
 		</div>
 		<!--// end row -->

iSkyLIMS_wetlab/scripts/prepare_part0_machines_migration.py

@@ -8,7 +8,7 @@ def run ():
     '''
     The script migration is needed to copy the sequencer information from the table in
     drylab to core.
-
+    The csv file contains "run_id, sequencer_name"
     '''
 
     run_objs = RunProcess.objects.all()

iSkyLIMS_wetlab/scripts/prepare_part1_project_for_migration_to_many2many_runs.py

@@ -4,6 +4,7 @@
     This file is part of the migration preparation for the version 2.0.0.
     It collect the information for the projects table for having the
     functionality that Project name can be repeated in different runs
+    The csv file contains "project_id, run_id"
 '''
 def run ():
 
@@ -13,7 +14,7 @@ def run ():
         print('There is no projects defined in iSkyLIMS\n')
         print('No upload project script is required to execute')
         return
-    with open ('project_migration_data.csv', 'w') as fh:
+    with open ('part_1_projectID_runID_migration.csv', 'w') as fh:
         for project in projects_to_update :
             fh.write(str(project.pk) + ',' + str(project.runprocess_id.pk) + '\n')
 

iSkyLIMS_wetlab/scripts/prepare_part2_project_mig_many2many.py

@@ -3,6 +3,9 @@
     This file is part of the migration preparation for the version 2.0.0.
     It collect the information for the sampleInProject table for having
     the functionality that Project name can be repeated in different runs
+    Two csv files are generated:
+    - part2_Samples_linked_to_Runs_migration_data.csv having smaple_id, run_id
+    - part2_Samples_linked_to_Users_migration_data.csv having sample_id, user_id
 '''
 
 def run ():
@@ -13,13 +16,13 @@ def run ():
         print('There is no SamplesInProjects defined in iSkyLIMS\n')
         print('No upload SamplesInProject script is required to execute')
         return
-    with open ('part1_sampleInProject_migration_data.csv', 'w') as fh:
+    with open ('part2_SamplesID_RunsID_migration.csv', 'w') as fh:
         for sample in samples_to_update :
             project_obj = sample.project_id
-            run_objs =  project_obj.runProcess.all()
-            fh.write(str(sample.pk) + ',' + str(run_objs[0].pk) + '\n')
+            run_obj =  project_obj.runprocess_id
+            fh.write(str(sample.pk) + ',' + str(run_obj.pk) + '\n')
 
-    with open ('part2_sampleInProject_migration_data.csv', 'w') as fh:
+    with open ('part2_SamplesID_UsersID_migration.csv', 'w') as fh:
         for sample in samples_to_update :
             project_obj = sample.project_id
             user_id =  project_obj.user_id.pk

iSkyLIMS_wetlab/scripts/update_part0_machines_migration.py

@@ -1,6 +1,11 @@
 from iSkyLIMS_wetlab.models import RunProcess
 from iSkyLIMS_core.models import SequencerInLab
 
+'''
+The script migration restore the information collected in the prepare_part0_machines_migration .
+Fetching the run_id and the sequencer name.
+The csv file contains "run_id, sequencer_name"
+'''
 
 def get_list_defined_sequencers ():
     if SequencerInLab.objects.all().exists():

iSkyLIMS_wetlab/scripts/update_part1_project_mig_many2many.py

@@ -1,10 +1,16 @@
 from iSkyLIMS_wetlab.models import SamplesInProject, RunProcess, Projects
 from django.contrib.auth.models import User
 
+'''
+The script migration restore the information collected in the prepare_part1_project_for_migration_to_many_to_many .
+Fetching the run_id and the sequencer name.
+The csv file contains "project_id ,run_id"
+'''
+
 def run ():
     invalids = 0
 
-    with open ('project_migration_data.csv', 'r') as fh:
+    with open ('part_1_projectID_runID_migration.csv', 'r') as fh:
         for line in fh.readlines():
             split_line = line.split(',')
             if len(split_line )!= 2:

iSkyLIMS_wetlab/scripts/update_part2_project_mig_many2many.py

@@ -5,7 +5,7 @@ def run ():
 
     invalids = 0
 
-    with open ('part1_sampleInProject_migration_data.csv', 'r') as fh:
+    with open ('part2_SamplesID_RunsID_migration.csv', 'r') as fh:
         for line in fh.readlines():
             split_line = line.split(',')
             if len(split_line )!= 2:
@@ -28,37 +28,7 @@ def run ():
             s_obj.runProcess_id = (r_obj)
             s_obj.save()
 
-    with open ('part1.1_sampleInProject_migration_data.csv', 'r') as fh:
-        for line in fh.readlines():
-            split_line = line.split(',')
-            if len(split_line )!= 2:
-                print('invalid line :' , line , '\n')
-                continue
-            s_id = split_line[0]
-            p_id = split_line[1]
-            if SamplesInProject.objects.filter(pk__exact = s_id).exists():
-                s_obj = SamplesInProject.objects.get(pk__exact = s_id)
-            else:
-                print('sample in project id ' , s_id , 'does not longer exists in database\n')
-                invalids += 1
-                continue
-            if Projects.objects.filter(pk__exact = r_id).exists():
-                p_obj = Projects.objects.get(pk__exact = p_id)
-            else:
-                print('Project id ' , p_id, 'does not longer exists in database\n')
-                invalids += 1
-                continue
-            s_obj.project_id = (p_obj)
-            s_obj.save()
-
-    if invalids == 0:
-        print( 'All samples have been updated to get relation with run\n')
-    else:
-        print('Unable to migrate all Samples to have runProcess relation ')
-
-    invalids = 0
-
-    with open ('part2_sampleInProject_migration_data.csv', 'r') as fh:
+    with open ('part2_SamplesID_UsersID_migration.csv', 'r') as fh:
         for line in fh.readlines():
             split_line = line.split(',')
             if len(split_line )!= 2: