From 215efdb11402fcaabce48d7bf0a139f981aefa93 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Wed, 7 Jun 2017 17:43:45 +0200
Subject: [PATCH 1/4] tests: remove outdated documentation

Everything is now under 'doc/dev.org'.
---
 browser/test/QUnit/QUnit-Manual.txt | 33 -----------------------------
 1 file changed, 33 deletions(-)
 delete mode 100644 browser/test/QUnit/QUnit-Manual.txt

diff --git a/browser/test/QUnit/QUnit-Manual.txt b/browser/test/QUnit/QUnit-Manual.txt
deleted file mode 100644
index 74e9cd7ba..000000000
--- a/browser/test/QUnit/QUnit-Manual.txt
+++ /dev/null
@@ -1,33 +0,0 @@
-—
-Redacted by Carette Antonin - the Vidjil Project
-—
-
-
-usage:
-
-    with browser:
-        -> open test_Qunit.html
-    with phantomjs:
-        -> install phantomJS (apt-get phantomjs)
-        -> phantomjs phantom_test.js
-
-
-
-QUnit tests:
-
-    dbscan (dbscan_test.js)
-    model (model.js)
-    ------
-
-    DONE:
-        -> Existing DBSCAN object
-        -> Not null
-        -> Good clustering
-            -> 2 nodes
-            -> multiple nodes
-
-
-        -> Model object
-            -> load/parse json data
-            -> timepoint
-            
-- 
GitLab


From 1da3d51c8ddc614f182ab403a369bb73b163d32b Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Wed, 7 Jun 2017 18:00:03 +0200
Subject: [PATCH 2/4] views/sample_set/*.html: remove references to 'patient'

See #2519.
---
 .../web2py/applications/vidjil/views/sample_set/custom.html | 6 +++---
 .../applications/vidjil/views/sample_set/permission.html    | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/server/web2py/applications/vidjil/views/sample_set/custom.html b/server/web2py/applications/vidjil/views/sample_set/custom.html
index 4ed0c28f6..60cc0d434 100644
--- a/server/web2py/applications/vidjil/views/sample_set/custom.html
+++ b/server/web2py/applications/vidjil/views/sample_set/custom.html
@@ -6,9 +6,9 @@
 <div>
 
 	{{ if request.vars['id']: }}
-		<h3>Compare samples</h3>	
+		<h3>Compare samples from {{=helper.get_type_display()}} {{=helper.get_name(request.vars['id'])}}</h3>
 	{{ else: }}
-    	<h3>Compare samples from different sample_set</h3>
+	        <h3>Compare samples</h3>
     {{pass}}
 
     <p>Select up to 10 samples to be compared.</p>
@@ -50,7 +50,7 @@
     <table class="db_table table_compare" id="table">
         <thead>
             <tr><td class="column5"> </td>
-                <td class="column_200"> patient </td>
+                <td class="column_200"> {{=helper.get_type_display()}} </td>
                 <td class="column_200"> file name </td>
                 <td class="column_100"> sampling date </td>
                 <td> info </td>
diff --git a/server/web2py/applications/vidjil/views/sample_set/permission.html b/server/web2py/applications/vidjil/views/sample_set/permission.html
index ac8d79b04..6bf05eb6b 100644
--- a/server/web2py/applications/vidjil/views/sample_set/permission.html
+++ b/server/web2py/applications/vidjil/views/sample_set/permission.html
@@ -38,5 +38,5 @@
 </div>
 
 {{if not auth.can_modify_patient(request.vars["id"]) :}}
-    <div>you need admin access on this patient if you want to change permission </div>
+    <div>you need admin access on this {{=helper.get_type_display()}} if you want to change permission </div>
 {{pass}}
-- 
GitLab


From f42510196bed7f613581848eb2ab6382711e69b5 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Wed, 7 Jun 2017 18:45:10 +0200
Subject: [PATCH 3/4] controllers/sample_set.py: pass 'helper' to some views

See #2519.
---
 .../web2py/applications/vidjil/controllers/sample_set.py  | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/server/web2py/applications/vidjil/controllers/sample_set.py b/server/web2py/applications/vidjil/controllers/sample_set.py
index aa724c4fc..43b6dcee8 100644
--- a/server/web2py/applications/vidjil/controllers/sample_set.py
+++ b/server/web2py/applications/vidjil/controllers/sample_set.py
@@ -332,7 +332,8 @@ def custom():
         request.vars["custom_list"] = []
     if type(request.vars["custom_list"]) is str :
         request.vars["custom_list"] = [request.vars["custom_list"]]
-        
+
+    factory = ModelFactory()
     myGroupBy = None
     if request.vars["id"] and auth.can_view_sample_set(request.vars["id"]):
         q = ((auth.vidjil_accessible_query(PermissionEnum.read_config.value, db.config))
@@ -343,6 +344,7 @@ def custom():
                 & (db.results_file.data_file != '')
                 & (db.config.id==db.results_file.config_id)
             )
+        helper = factory.get_instance(type=db.sample_set[request.vars["id"]].sample_type)    
         
     else:
         q = ((auth.vidjil_accessible_query(PermissionEnum.read.value, db.patient)
@@ -356,6 +358,7 @@ def custom():
                 & (db.config.id==db.results_file.config_id)
             )
         myGroupBy = db.sequence_file.id|db.patient.id|db.run.id|db.generic.id|db.results_file.config_id
+        helper = factory.get_instance(type=defs.SET_TYPE_GENERIC)    
 
     query = db(q).select(
                 db.patient.id, db.patient.info, db.patient.first_name, db.patient.last_name,
@@ -403,7 +406,8 @@ def custom():
 
     return dict(query=query,
                 config_id=config_id,
-                config=config)
+                config=config,
+                helper=helper)
 
 def confirm():
     if auth.can_modify_sample_set(request.vars["id"]):
-- 
GitLab


From 3b519c025fc54ec4802b8c6d58525b62a0c1c9a0 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Wed, 7 Jun 2017 18:49:17 +0200
Subject: [PATCH 4/4] views/sample_set/custom.html: full name does not work now

See #2519.
---
 server/web2py/applications/vidjil/views/sample_set/custom.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server/web2py/applications/vidjil/views/sample_set/custom.html b/server/web2py/applications/vidjil/views/sample_set/custom.html
index 60cc0d434..f9fd93b97 100644
--- a/server/web2py/applications/vidjil/views/sample_set/custom.html
+++ b/server/web2py/applications/vidjil/views/sample_set/custom.html
@@ -6,7 +6,7 @@
 <div>
 
 	{{ if request.vars['id']: }}
-		<h3>Compare samples from {{=helper.get_type_display()}} {{=helper.get_name(request.vars['id'])}}</h3>
+		<h3>Compare samples from {{=helper.get_type_display()}} {{=request.vars['id']}}</h3>
 	{{ else: }}
 	        <h3>Compare samples</h3>
     {{pass}}
-- 
GitLab