Merge branch 'feature-s/update_classification_for_fresh_install' into 'dev'

update classifications and configurations

See merge request !931

.gitlab-ci.yml

@@ -408,6 +408,10 @@ test_server_unit:
   artifacts:
     reports:
       junit: server/web2py/applications/vidjil/tests/test/TEST-*.xml
+    when: always
+    expire_in: 1 week
+    paths:
+    - server/web2py/ap‎plications/vidjil‎/tests/
   only:
     - /^feature-.*s.*\/.*$/
     - /^hotfix-.*s.*\/.*$/

server/web2py/applications/vidjil/modules/vidjil_utils.py

@@ -622,24 +622,28 @@ def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_pas
 
         ### Base config classification
         db.classification.insert(
-            name = 'Vidjil-algo',
-            info = 'Vidjil-algo'
+            name = 'Human V(D)J recombinations',
+            info = 'Analysis with vidjil-algo of human TR/IG recombinations'
         )
         db.classification.insert(
-            name = 'Sub groups',
-            info = 'Sub groups'
+            name = 'Other recombinations',
+            info = 'Analysis with vidjil-algo of human non-V(D)J recombinations'
         )
         db.classification.insert(
-            name = 'Other germlines',
-            info = 'Other germlines'
+            name = 'Analysis with/for other software',
+            info = 'Analysis that use other repertoire software or generate with vidjil-algo compatible output formats'
         )
         db.classification.insert(
             name = 'Other species',
-            info = 'Other species'
+            info = 'Analysis with vidjil-algo of V(D)J recombinations for other species. Contact us at support@vidjil.org should you need other species.'
         )
         db.classification.insert(
-            name = 'Experimentals',
-            info = 'Experimentals'
+            name = 'Experimental configs',
+            info = '"Experimental analyses, under development,may evolve without notice.'
+        )
+        db.classification.insert(
+            name = 'Old configs, do not use',
+            info = '"Old configurations. We do not recommend to use them. Should you need something, contact us at  support@vidijl.org'
         )
 
 
@@ -693,6 +697,22 @@ def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_pas
             info = 'IGH, Vh(Dh)Jh',
             classification = 2
         )
+        db.config.insert(
+            name = 'Clonality',
+            program = 'vidjil',
+            command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -2 -w 90 -y all --no-airr',
+            fuse_command = '-t 100 -d lenSeqAverage --overlaps',
+            info = 'incomplete germlines + larger window (90bp), thus 20bp more on each side. This configuration is advised for studies on IGH clonality',
+            classification = 1
+        )
+        db.config.insert(
+            name = 'Export all clones (AIRR)',
+            program = 'vidjil',
+            command = '-c clones -3 -y all -z all -g germline/homo-sapiens.g -e 1 -2 -d -w 50 -r 5 --no-vidjil',
+            fuse_command = '-t 100',
+            info = 'Export all clones in the tabular AIRR format. The results can not be browsed online. See http://www.vidjil.org/doc/vidjil-algo/#airr-tsv-output',
+            classification = 3
+        )
 
         ## permission
         ## system admin have admin/read/create rights on all patients, groups and configs

server/web2py/applications/vidjil/tests/functional/browser_test.rb

@@ -64,4 +64,17 @@ class BrowserTest < MiniTest::Test
     end
   end
 
+  def teardown
+    #Save image if test fails
+    unless passed?
+      #Where to save the image and the file name
+      folder_path = File.expand_path(File.dirname(__FILE__))
+      folder_path.sub! '/functional', ''
+      screenshot_file = folder_path+"/screenshot_teardown_#{Time.now.strftime('%Y%m%d-%H%M%S')}.png"
+
+      #Save the image
+      $b.screenshot.save screenshot_file
+    end
+  end
+
 end

server/web2py/applications/vidjil/tests/functional/server_test.rb

 load 'browser_test.rb'
 class ServerTest < BrowserTest
 
-  def self.test_order
-    :random
-  end
+  ## Comment to allow test to run in writing order; allow to debug error
+  # def self.test_order
+  #   :random
+  # end
 
 end
 

server/web2py/applications/vidjil/tests/functional/test_sample.rb

@@ -360,7 +360,7 @@ class TestSample < ServerTest
     table = go_to_set_by_tag "#set_assoc_0"
 
     config_list = $b.select_list(:id => "choose_config")
-    assert ( config_list.optgroup(:label => "Vidjil-algo").exist? ), "optgroup is present in configlist"
+    assert ( config_list.optgroup(:label => "Human V(D)J recombinations").exist? ), "optgroup is present in configlist"
 
     config_list.select("2")
     Watir::Wait.until(timeout: 30) {$b.execute_script("return jQuery.active") == 0}