Merge branch 'feature-s/3489-fix-multi-upload-edit' into 'dev'

Feature s/3489 fix multi upload edit

See merge request !300

server/web2py/applications/vidjil/controllers/file.py

@@ -48,7 +48,9 @@ def link_to_sample_sets(seq_file_id, id_dict):
     Create sample set memberships and return a dict of the sample set ids.
     The keys to the dict are thee same as the ones passed in id_dict
     '''
+    log.debug("linking file %d to sets:" % seq_file_id)
     for key in id_dict:
+        log.debug("%s: %s" % (key, str(id_dict[key])))
         arr = [{'sample_set_id': oid, 'sequence_file_id': seq_file_id} for oid in id_dict[key]]
         db.sample_set_membership.bulk_insert(arr)
     db.commit()

server/web2py/applications/vidjil/tests/functional/init_test_db.py

@@ -16,6 +16,7 @@ class DBInitialiser(object):
         self._init_sequence_files()
         self._init_results_files()
         self._init_notifications()
+        self._init_set_association_data()
 
 
     def _needs_init(func):
@@ -135,5 +136,32 @@ class DBInitialiser(object):
             c = db.auth_group.insert(role="test child %d" % i)
             db.group_assoc.insert(first_group_id=parent, second_group_id=c)
 
+    @_needs_init
+    def _init_set_association_data(self):
+        types = [defs.SET_TYPE_PATIENT, defs.SET_TYPE_RUN, defs.SET_TYPE_GENERIC]
+        public_group = db(db.auth_group.role == "public").select().first()
+        for i in range(3):
+            tag_id = db.tag.insert(name="set_assoc_%d" % i)
+            db.group_tag.insert(group_id=public_group.id, tag_id=tag_id)
+            sfid = db.sequence_file.insert(
+                sampling_date="2010-10-10",
+                info="#set_assoc_%d" % i,
+                filename="test_file.fasta",
+                size_file=1024,
+                network=False,
+                data_file="test_sequence_file"
+            )
+            db.tag_ref.insert(tag_id=tag_id, table_name=db.sequence_file, record_id=sfid)
+
+            for t in types:
+                ssid = db.sample_set.insert(sample_type=t)
+                d = self.get_set_dict(t, ssid, i)
+                d['info'] = "set association test #set_assoc_%d" % i
+                sid = db[t].insert(**d)
+                auth.add_permission(public_group.id, PermissionEnum.access.value, db.sample_set, ssid)
+                db.tag_ref.insert(tag_id=tag_id, table_name=t, record_id=sid)
+                db.sample_set_membership.insert(sample_set_id=ssid, sequence_file_id=sfid)
+
+
 initialiser = DBInitialiser()
 initialiser.run()

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

@@ -21,12 +21,17 @@ class TestSample < ServerTest
     go_to_set 0
   end
 
-  def go_to_set(index)
+  def go_to_patient_list
     # load patient list
     $b.a(:class => "button button_token patient_token", :text => "patients").click
     Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
     table = $b.table(:id => "table")
     table.wait_until_present
+    table
+  end
+
+  def go_to_set(index)
+    table = go_to_patient_list
     lines = table.tbody.rows
     lines[index].wait_until_present
     # select first patient
@@ -38,8 +43,18 @@ class TestSample < ServerTest
     table
   end
 
+  def go_to_set_by_tag(tag)
+    table = go_to_patient_list
+
+    table.a(:text => tag).parent.parent.cells[2].click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+    samples_table = $b.table(:id => "table")
+    samples_table.wait_until_present
+    samples_table
+  end
+
   def test_add
-    table = go_to_first_set
+    table = go_to_set_by_tag "#test4"
 
     count = table.tbody.rows.count
 
@@ -84,7 +99,7 @@ class TestSample < ServerTest
   end
 
   def test_edit
-    table = go_to_first_set
+    table = go_to_set_by_tag "#test3"
 
     lines = table.tbody.rows
     lines[0].wait_until_present
@@ -106,8 +121,120 @@ class TestSample < ServerTest
     assert($b.link(:text => "#edited").present?)
   end
 
+  def test_set_association_preservation
+    samples_table = go_to_set_by_tag "#set_assoc_1"
+    samples_table.a(:text => "#set_assoc_1").parent.parent.i(:class => "icon-pencil-2").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+
+    form = $b.form(:id => "upload_form")
+    form.wait_until_present
+
+    assert(form.div(:id => 'set_div').spans.length == 3)
+    sets_text = form.input(:id => "file_set_list").text
+
+    form.text_field(:id => "file_info_0").set("#set_assoc_1 #edited")
+    form.input(:type => "submit").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+
+    samples_table.a(:text => "#set_assoc_1").parent.parent.i(:class => "icon-pencil-2").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+    form = $b.form(:id => "upload_form")
+    form.wait_until_present
+
+    assert(form.div(:id => 'set_div').spans.length == 3)
+    assert(sets_text == form.input(:id => "file_set_list").text)
+  end
+
+  def test_set_association_create
+    $b.a(:class => "button button_token patient_token", :text => "patients").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+    table = $b.table(:id => "table")
+    table.wait_until_present
+
+    patient_id = table.a(:text => "#set_assoc_0").parent.parent.cells[0].text
+
+    $b.a(:class => "button button_token run_token", :text => "runs").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+    table = $b.table(:id => "table")
+    table.wait_until_present
+
+    run_id = table.a(:text => "#set_assoc_0").parent.parent.cells[0].text
+
+    $b.a(:class => "button button_token generic_token", :text => "sets").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+    table = $b.table(:id => "table")
+    table.wait_until_present
+
+    set_id = table.a(:text => "#set_assoc_0").parent.parent.cells[0].text
+
+    samples_table = go_to_set_by_tag "#set_assoc_0"
+    $b.span(:class => "button2", :text => "+ add samples").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+
+    form = $b.form(:id => "upload_form")
+    form.wait_until_present
+
+    $b.input(:id => "source_nfs").click
+
+    jstree = $b.div(:id => "jstree")
+    $b.div(:id => "jstree_field_0").span(:text => "browse").click
+    assert(jstree.visible?)
+    jstree_file = jstree.a(:id => "//Demo-X5.fa_anchor")
+    unless jstree_file.present? and jstree_file.present?
+      jstree.a(:id => "/_anchor").double_click
+    end
+    jstree_file.wait_until_present
+    jstree_file.click
+
+    $b.span(:id => "jstree_button").click
+    assert(!jstree.visible?)
+
+    form.text_field(:id => "file_sampling_date_0").set("2010-10-10")
+    form.text_field(:id => "file_info_0").set("#my_file_add")
+
+    val = ":p 0 (2010-10-10) (#{patient_id})|:r run 0 (#{run_id})|:s generic 0 (#{set_id})"
+    $b.execute_script("return $('#file_set_list').val('#{val}');")
+
+    form.input(:type => "submit").click
+
+    samples_table = $b.table(:id => "table")
+    samples_table.wait_until_present
+    samples_table.a(:text => "#set_assoc_0").parent.parent.i(:class => "icon-pencil-2").click
+
+    form = $b.form(:id => "upload_form")
+    form.wait_until_present
+    set_div = form.div(:id => 'set_div')
+    assert(set_div.spans.length == 3)
+  end
+
+  def test_set_association_update
+    samples_table = go_to_set_by_tag "#set_assoc_2"
+    samples_table.a(:text => "#set_assoc_2").parent.parent.i(:class => "icon-pencil-2").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+
+    form = $b.form(:id => "upload_form")
+    form.wait_until_present
+
+    set_div = form.div(:id => 'set_div')
+    assert(set_div.spans.length == 3)
+
+    set_div.spans[1].i(:class => "icon-cancel").click
+    form.input(:type => "submit").click
+
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+    samples_table = $b.table(:id => "table")
+    samples_table.wait_until_present
+    samples_table.a(:text => "#set_assoc_2").parent.parent.i(:class => "icon-pencil-2").click
+    Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
+
+    form = $b.form(:id => "upload_form")
+    form.wait_until_present
+    set_div = form.div(:id => 'set_div')
+    assert(set_div.spans.length == 2)
+  end
+
   def test_delete
-    table = go_to_set 3
+    table = go_to_set_by_tag "#test2"
 
     count = table.tbody.rows.count
 
@@ -135,12 +262,14 @@ class TestSample < ServerTest
   end
 
   def test_run
-    table = go_to_first_set
+    table = go_to_set_by_tag "#set_assoc_0"
 
     $b.select_list(:id => "choose_config").select_value(2)
     Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}
 
-    lines = table.tbody.rows
+    samples_table = $b.table(:id => "table")
+    samples_table.wait_until_present
+    lines = samples_table.tbody.rows
     lines[0].wait_until_present
     lines[0].i(:class => "icon-cog-2").click
     Watir::Wait.until(30) {$b.execute_script("return jQuery.active") == 0}

server/web2py/applications/vidjil/views/file/form.html

@@ -54,7 +54,7 @@
                 id="file_set_list"
                 name="set_ids"
                 type="text"
-                value="{{=",".join([set['id'] for set in sets])}}">
+                value="{{="|".join([set['id'] for set in sets])}}">
             <div id="set_div" class="token_container" data-min-tokens=1>
                 {{ for set in sets: }}
                     <span class="set_token {{=set['type']}}_token" data-set-id="{{=set['id']}}">