Merge branch 'feature-sc/4219-config-par-groupe' into 'dev'

Resolve "Avoir un classement par groupe des config proposées"

Closes #4219

See merge request !627

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

@@ -18,6 +18,7 @@ def index():
     query = db((auth.vidjil_accessible_query(PermissionEnum.read_config.value, db.config) | auth.vidjil_accessible_query(PermissionEnum.admin_config.value, db.config) ) ).select(orderby=~db.config.name)
     used_query = db(db.results_file.config_id > 0).select(db.results_file.config_id, distinct=True)
     used_configs = [row.config_id for row in used_query]
+    classification = db( (db.classification) ).select()
 
     mes = u"Access config list"
     log.info(mes, extra={'user_id': auth.user.id, 'record_id': -1, 'table_name': 'config'})
@@ -25,12 +26,14 @@ def index():
     return dict(message=T('Configs'),
                query=query,
                used_configs=used_configs,
+               classification=classification,
                isAdmin = auth.is_admin())
 
 
 def add():
     if (auth.can_create_config()):
-        return dict(message=T('Add config'))
+        classification = db( (db.classification) ).select()
+        return dict(message=T('Add config'), classification=classification)
     return error_message(ACCESS_DENIED)
 
 
@@ -45,13 +48,20 @@ def add_form():
         if request.vars[field] == "" :
             error += field+" needed, "
 
+    ## test if classification id exist
+    classification = db(db.classification.id ==  request.vars["config_classification"]).select()
+    if len(classification) == 0:
+        error += "classification id don't exist, "
+
+
     if error=="" :
         
         config_id = db.config.insert(name=request.vars['config_name'],
                         info=request.vars['config_info'],
                         command=request.vars['config_command'],
                         fuse_command=request.vars['config_fuse_command'],
-                        program=request.vars['config_program']
+                        program=request.vars['config_program'],
+                        classification=request.vars['config_classification']
                         )
 
         user_group = None
@@ -83,8 +93,9 @@ def add_form():
 def edit():
     if (auth.can_modify_config(request.vars['id'])):
         mes = u"Load config edit form"
+        classification = db( (db.classification) ).select()
         log.info(mes, extra={'user_id': auth.user.id, 'record_id': request.vars['id'], 'table_name': 'config'})
-        return dict(message=T('edit config'))
+        return dict(message=T('edit config'), classification=classification)
     return error_message(ACCESS_DENIED)
 
 
@@ -98,6 +109,11 @@ def edit_form():
     for field in required_fields:
         if request.vars[field] == "" :
             error += field+" needed, "
+    
+    ## test if classification id exist
+    classification = db(db.classification.id ==  request.vars["config_classification"]).select()
+    if len(classification) == 0:
+        error += "classification id don't exist, "
 
     if error=="" :
 
@@ -105,7 +121,8 @@ def edit_form():
                                              info=request.vars['config_info'],
                                              command=request.vars['config_command'],
                                              fuse_command=request.vars['config_fuse_command'],
-                                             program=request.vars['config_program']
+                                             program=request.vars['config_program'],
+                                             classification=request.vars['config_classification']
                                              )
 
         res = {"redirect": "config/index",

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

@@ -4,6 +4,7 @@ import vidjil_utils
 import time
 import json
 from vidjilparser import VidjilParser
+from collections  import defaultdict
 import operator
 import math
 
@@ -129,7 +130,9 @@ def index():
     pre_process_list = {}
     for row in query_pre_process:
         pre_process_list[row.id] = row.name
-    
+
+    classification   = getConfigsByClassification()
+
     log.info('sample_set (%s)' % request.vars["id"], extra={'user_id': auth.user.id,
         'record_id': request.vars["id"],
         'table_name': "sample_set"})
@@ -148,6 +151,7 @@ def index():
                 analysis_filename = analysis_filename,
                 sample_type = db.sample_set[request.vars["id"]].sample_type,
                 config=config,
+                classification=classification,
                 tag_decorator=tag_decorator)
 
 ## return a list of generic sample_sets
@@ -262,6 +266,8 @@ def stats():
     else:
         result = sorted(result, key = lambda row : row.id, reverse=not reverse)
 
+    classification   = getConfigsByClassification()
+
     result = helper.filter(search, result)
     log.info("%s stat list %s" % (request.vars["type"], search), extra={'user_id': auth.user.id,
         'record_id': None,
@@ -273,6 +279,7 @@ def stats():
                 helper = helper,
                 group_ids = group_ids,
                 isAdmin = isAdmin,
+                classification=classification,
                 reverse = False)
 
 def result_files():
@@ -679,13 +686,34 @@ def custom():
     log.info("load compare list", extra={'user_id': auth.user.id, 'record_id': None, 'table_name': "results_file"})
     log.debug("sample_set/custom (%.3fs) %s" % (time.time()-start, search))
 
+
+    classification   = getConfigsByClassification()
+
     return dict(query=query,
                 config_id=config_id,
                 config=config,
                 helper=helper,
                 tag_decorator=tag_decorator,
+                classification=classification,
                 group_ids=group_ids)
 
+def getConfigsByClassification():
+    """ Return list of available and auth config, classed by classification values """
+    i = 0
+    classification   = defaultdict( lambda: {"info":"", "name":"", "configs":[]} )
+    if auth.can_process_sample_set(request.vars['id']) :
+        for class_elt in db( (db.classification)).select(orderby=db.classification.id):
+            configs = db( (db.config.classification == class_elt.id) & (auth.vidjil_accessible_query(PermissionEnum.read.value, db.config) | auth.vidjil_accessible_query(PermissionEnum.admin.value, db.config) ) ).select(orderby=db.config.id)
+            if len(configs): # don't show empty optgroup
+                classification["%02d_%s" % (i, class_elt)]["name"]    = class_elt.name
+                classification["%02d_%s" % (i, class_elt)]["info"]    = class_elt.info
+                classification["%02d_%s" % (i, class_elt)]["configs"] = configs
+            i += 1
+        classification["%02d_noclass" % i]["name"]    = "–"
+        classification["%02d_noclass" % i]["info"]    = ""
+        classification["%02d_noclass" % i]["configs"] = db( (db.config.classification == None) & (auth.vidjil_accessible_query(PermissionEnum.read.value, db.config) | auth.vidjil_accessible_query(PermissionEnum.admin.value, db.config) ) ).select(orderby=db.config.id)
+    return classification
+
 def getStatHeaders():
     m = StatDecorator()
     s = SetsDecorator()

server/web2py/applications/vidjil/models/db.py

@@ -197,13 +197,18 @@ db.define_table('sequence_file',
 
 
 
+db.define_table('classification',
+                Field('name', 'string'),
+                Field('info','text'))
+
 
 db.define_table('config',
                 Field('name', 'string'),
                 Field('program', 'string'),
                 Field('command', 'string'),
                 Field('fuse_command', 'string'),
-                Field('info','text'))
+                Field('info','text'),
+                Field('classification', 'reference classification', ondelete='SET NULL'))
 
 
 db.define_table('results_file',

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

@@ -619,6 +619,30 @@ def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_pas
         db.auth_membership.insert(user_id=id_first_user, group_id=id_sa_group)
         db.auth_membership.insert(user_id=id_first_user, group_id=id_public_group)
 
+
+        ### Base config classification
+        db.classification.insert(
+            name = 'Vidjil-algo',
+            info = 'Vidjil-algo'
+        )
+        db.classification.insert(
+            name = 'Sub groups',
+            info = 'Sub groups'
+        )
+        db.classification.insert(
+            name = 'Other germlines',
+            info = 'Other germlines'
+        )
+        db.classification.insert(
+            name = 'Other species',
+            info = 'Other species'
+        )
+        db.classification.insert(
+            name = 'Experimentals',
+            info = 'Experimentals'
+        )
+
+
         ## base Vidjil configs
 
         db.config.insert(
@@ -626,42 +650,48 @@ def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_pas
             program = 'vidjil',
             command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -2 -d -w 50 -U ',
             fuse_command = '-t 100',
-            info = 'Same as the default "multi+inc+xxx" (multi-locus, with some incomplete/unusual/unexpected recombinations), and extract analyzed reads in the "out" temporary directory.'
+            info = 'Same as the default "multi+inc+xxx" (multi-locus, with some incomplete/unusual/unexpected recombinations), and extract analyzed reads in the "out" temporary directory.',
+            classification = 1
         )
         db.config.insert(
             name = 'multi+inc+xxx',
             program = 'vidjil',
             command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -2 -d -w 50 ',
             fuse_command = '-t 100',
-            info = 'multi-locus, with some incomplete/unusual/unexpected recombinations'
+            info = 'multi-locus, with some incomplete/unusual/unexpected recombinations',
+            classification = 1
         )
         db.config.insert(
             name = 'multi+inc',
             program = 'vidjil',
             command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -w 50 ',
             fuse_command = '-t 100',
-            info = 'multi-locus, with some incomplete/unusual recombinations'
+            info = 'multi-locus, with some incomplete/unusual recombinations',
+            classification = 1
         )
         db.config.insert(
             name = 'multi',
             program = 'vidjil',
             command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g:IGH,IGK,IGL,TRA,TRB,TRG,TRD -e 1 -d -w 50 ',
             fuse_command = '-t 100',
-            info = 'multi-locus, only complete recombinations'
+            info = 'multi-locus, only complete recombinations',
+            classification = 2
         )
         db.config.insert(
             name = 'TRG',
             program = 'vidjil',
             command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g:TRG ',
             fuse_command = '-t 100',
-            info = 'TRG, VgJg'
+            info = 'TRG, VgJg',
+            classification = 2
         )
         db.config.insert(
             name = 'IGH',
             program = 'vidjil',
             command = '-c clones -w 60 -d -3 -z 100 -r 1 -g germline/homo-sapiens.g:IGH ',
             fuse_command = '-t 100',
-            info = 'IGH, Vh(Dh)Jh'
+            info = 'IGH, Vh(Dh)Jh',
+            classification = 2
         )
 
         ## permission

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

@@ -265,7 +265,10 @@ class TestSample < ServerTest
   def test_run
     table = go_to_set_by_tag "#set_assoc_0"
 
-    $b.select_list(:id => "choose_config").select("2")
+    config_list = $b.select_list(:id => "choose_config")
+    assert ( config_list.optgroup(:label => "Vidjil-algo").exist? ), "optgroup is present in configlist"
+
+    config_list.select("2")
     Watir::Wait.until(timeout: 30) {$b.execute_script("return jQuery.active") == 0}
 
     samples_table = $b.table(:id => "table")

server/web2py/applications/vidjil/tests/unit/controllers/config.py

@@ -61,12 +61,16 @@ class ConfigController(unittest.TestCase):
     
     
     def test2AddForm1(self):
+        # Add a testing classification
+        db.classification.insert(name="test_class", info="test_class_info")
+
         #test valid request
         request.vars['config_name'] = test_config_name
         request.vars['config_info'] = " plop"
         request.vars['config_command'] = " -plop"
         request.vars['config_fuse_command'] = " -plop"
         request.vars['config_program'] = " plop.cpp"
+        request.vars['config_classification'] = 1
         
         resp = add_form()
         self.assertTrue( len(db( db.config.name == test_config_name ).select()) == 1 , "fail to insert a new config") 
@@ -84,6 +88,7 @@ class ConfigController(unittest.TestCase):
         request.vars["id"] = id_config
         request.vars['config_name'] = test_config_name
         request.vars['config_info'] = "plup"
+        request.vars['config_classification'] = 1
         
         resp = edit_form()
         self.assertTrue( db.config[id_config].info == "plup" , "fail to edit config info")

server/web2py/applications/vidjil/views/config/add.html

@@ -8,6 +8,15 @@
                 <td > <input class="string" id="config_name" name="config_name" type="text" value=""> </td> 
                 <td > </td>
             </tr>
+            <tr>
+                <td> <label for="config_classification" id="config_classification__label">classification: </label> </td>
+                <td><select id="config_classification" name="config_classification">
+                        {{for class_elt in classification: }}
+                            <option value="{{=class_elt.id}}" title="{{=class_elt.info}}">{{=class_elt.name}}</option>
+                        {{pass}}
+                    </select></td>
+                <td> </td>
+            </tr>
             <tr>
                 <td> <label for="config_program" id="config_program__label">Program: </label> </td>
                 <td><select id="config_program" name="config_program">

server/web2py/applications/vidjil/views/config/edit.html

@@ -13,6 +13,15 @@ info = db.config[request.vars["id"]]
                 <td > <input class="string" id="config_name" name="config_name" type="text" value="{{=info.name}}"> </td> 
                 <td > </td>
             </tr>
+            <tr>
+                <td> <label for="config_classification" id="config_classification__label">classification: </label> </td>
+                <td><select id="config_classification" name="config_classification">
+                        {{for class_elt in classification: }}
+                            <option value="{{=class_elt.id}}" {{if class_elt.id == info.classification:}}selected="selected"{{pass}} title="{{=class_elt.info}}">{{=class_elt.name}}</option>
+                        {{pass}}
+                    </select></td>
+                <td> </td>
+            </tr>
             <tr>
                 <td> <label for="config_program" id="config_program__label">Program: </label> </td>
                 <td><select id="config_program" name="config_program">

server/web2py/applications/vidjil/views/config/index.html

@@ -3,12 +3,15 @@
 {{('message' in globals())}}
 {{if 'message' in globals():}}
 
+
+
 <h3>{{=message}}</h3>
 
 <div id="db_table_container">
     <table class="db_table" id="table">
         <thead>
             <tr><td class="column_50"></td>
+                <td class="column2"> classification </td>
                 <td class="column2"> name </td>
                 <td class="column1"> program </td>
                 <td> command </td>
@@ -25,6 +28,17 @@
        for row in query :}}
             <tr>
                 <td> {{=row.id }} </td>
+                {{ found = False }}
+                {{for class_elt in classification: }}
+                    {{ if class_elt.id == row.classification: }}
+                        <td title="{{ =class_elt.name}}">{{=class_elt.name}}</td>
+                        {{ found = True }}
+                    {{pass}}
+                {{pass}}
+                {{ if not found: }}
+                    <td title="Not defined">Not defined</td>
+                {{pass}}
+
                 <td> {{=row.name }} </td>
                 <td> {{=row.program }} </td>
                 <td> {{=row.command }} </td>

server/web2py/applications/vidjil/views/sample_set/custom.html

@@ -35,10 +35,15 @@
                                                                   'custom_list' : db.getListInput('custom_result[]'),
                                                                   'id' : '{{='' if request.vars["id"] is None else request.vars["id"]}}' })">
                     <option value="-1" {{if not config :}}selected{{pass}}> --- </option>
-                    {{for row in db((auth.vidjil_accessible_query(PermissionEnum.read_config.value, db.config) | auth.accessible_query(PermissionEnum.admin_config.value, db.config) ) ).select(orderby=~db.config.name) :}}
-                        <option value="{{=row.id }}" {{if row.id==config_id:}}selected{{pass}} >
-                            {{=row.name}}
-                        </option>
+                    {{ for class_name in classification.keys(): }}
+                      {{ class_elt = classification[class_name] }}
+                      <optgroup label="{{ =class_elt['name'] }}"  title="{{ =class_elt['info'] }}">
+                        {{ for row in class_elt['configs']: }}
+                            <option value="{{=row.id }}" {{if row.id==config_id:}}selected{{pass}} title="{{=row.info}}" >
+                              {{=row.name}}
+                            </option>
+                        {{pass}}
+                      </optgroup>
                     {{pass}}
                 </select>
             </span>

server/web2py/applications/vidjil/views/sample_set/index.html

@@ -21,10 +21,15 @@
             <span>
                 <select id="choose_config" name="config" onchange="db.call('sample_set/index', {'id' :'{{=request.vars['id']}}', 'config_id' : this.value})">
                     <option value="-1" {{if not config :}}selected{{pass}}> --- </option>
-                    {{for row in db((auth.vidjil_accessible_query(PermissionEnum.read.value, db.config) | auth.vidjil_accessible_query(PermissionEnum.admin.value, db.config) ) ).select(orderby=~db.config.name) :}}
-                        <option value="{{=row.id }}" {{if row.id==config_id:}}selected{{pass}} title="{{=row.info}}" >
-                            {{=row.name}}
-                        </option>
+                    {{ for class_name in classification.keys(): }}
+                      {{ class_elt = classification[class_name] }}
+                      <optgroup label="{{ =class_elt['name'] }}"  title="{{ =class_elt['info'] }}">
+                        {{ for row in class_elt['configs']: }}
+                            <option value="{{=row.id }}" {{if row.id==config_id:}}selected{{pass}} title="{{=row.info}}" >
+                                {{=row.name}}
+                            </option>
+                        {{pass}}
+                      </optgroup>
                     {{pass}}
                 </select>
             </span>
@@ -34,10 +39,7 @@
 
 </div>
 
-    
-    
-    
-    
+
     
     
     

server/web2py/applications/vidjil/views/sample_set/stats.html

@@ -21,10 +21,15 @@
     <span>
         <select id="choose_config" name="config" onchange="db.updateStatsButton()">
             <option value="-1" selected> --- </option>
-            {{for row in db((auth.vidjil_accessible_query(PermissionEnum.read.value, db.config) | auth.vidjil_accessible_query(PermissionEnum.admin.value, db.config) ) ).select(orderby=~db.config.name) :}}
-                <option value="{{=row.id }}" title="{{=row.info}}" >
-                    {{=row.name}}
-                </option>
+            {{ for class_name in classification.keys(): }}
+              {{ class_elt = classification[class_name] }}
+              <optgroup label="{{ =class_elt['name'] }}"  title="{{ =class_elt['info'] }}">
+                {{ for row in class_elt['configs']: }}
+                    <option value="{{=row.id }}" {{if row.id==config_id:}}selected{{pass}} title="{{=row.info}}" >
+                      {{=row.name}}
+                    </option>
+                {{pass}}
+              </optgroup>
             {{pass}}
         </select>
     </span>