solved issue BU-ISCIII#319 incorrect state set for molecule after fil…

…ling the extraction data
luissian · Sep 27, 2024 · 8abc1dc · 8abc1dc
1 parent 0df6259
commit 8abc1dc
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Showing 6 changed files with 37 additions and 24 deletions.
diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json
@@ -324,21 +324,32 @@
     "model": "core.statesformolecule",
     "pk": 3,
     "fields": {
-        "molecule_state_name": "Defined"
+        "molecule_state_name": "defined",
+        "molecule_state_display": "Defined"
     }
 },
 {
     "model": "core.statesformolecule",
     "pk": 4,
     "fields": {
-        "molecule_state_name": "Assigned Protocol"
+        "molecule_state_name": "assigned_parameters",
+        "molecule_state_display": "Assigned Parameters"
     }
 },
 {
     "model": "core.statesformolecule",
     "pk": 5,
     "fields": {
-        "molecule_state_name": "Completed"
+        "molecule_state_name": "completed",
+        "molecule_state_display": "Completed"
+    }
+},
+{
+    "model": "core.statesformolecule",
+    "pk": 6,
+    "fields": {
+        "molecule_state_name": "sent_external",
+        "molecule_state_display": "Sent to external service"
     }
 },
 {

diff --git a/core/core_config.py b/core/core_config.py
@@ -22,7 +22,7 @@
 ]
 HEADING_FOR_MOLECULE_ADDING_PARAMETERS = [
     "Sample",
-    "Molecule Code ID",
+    "Extraction Code ID",
     "Lot Commercial Kit",
 ]
 
@@ -74,8 +74,8 @@
 
 HEADING_FOR_SELECTING_MOLECULE_USE = [
     "Sample Name",
-    "Molecule CodeID",
-    "Molecule use for",
+    "Extraction CodeID",
+    "Sample continue on",
 ]
 
 # ################ PROTOCOL PARAMETER SETTINGS ##############################

diff --git a/core/models.py b/core/models.py
@@ -372,6 +372,7 @@ def get_id(self):
 
 class StatesForMolecule(models.Model):
     molecule_state_name = models.CharField(max_length=50)
+    molecule_state_display = models.CharField(max_length=80, null=True, blank=True)
 
     class Meta:
         db_table = "core_states_for_molecule"
@@ -1495,7 +1496,7 @@ def create_molecule(self, molecule_data):
             protocol_used=protocol_used_obj,
             sample=molecule_data["sample"],
             molecule_type=molecule_used_obj,
-            state=StatesForMolecule.objects.get(molecule_state_name__exact="Defined"),
+            state=StatesForMolecule.objects.get(molecule_state_name__exact="defined"),
             molecule_code_id=molecule_data["molecule_code_id"],
             molecule_extraction_date=molecule_data["molecule_extraction_date"],
             extraction_type=molecule_data["extraction_type"],

diff --git a/core/utils/samples.py b/core/utils/samples.py
@@ -565,7 +565,7 @@ def add_molecule_protocol_parameters(data, parameters):
                 molecule_parameter_value
             )
 
-        molecule_obj.set_state("Completed")
+        molecule_obj.set_state("assigned_parameters")
         # Update sample state
         sample_obj = molecule_obj.get_sample_obj()
         sample_obj.set_state("Pending for use")
@@ -701,10 +701,10 @@ def create_table_molecule_pending_use(sample_list, app_name):
     use_type = {}
     use_type["data"] = list(
         core.models.MoleculePreparation.objects.filter(
-            molecule_used_for=None, sample__in=sample_list
-        )
-        .exclude(state__molecule_state_name="Completed")
-        .values_list("sample__sample_name", "molecule_code_id", "pk")
+            molecule_used_for=None,
+            sample__in=sample_list,
+            state__molecule_state_name="assigned_parameters",
+        ).values_list("sample__sample_name", "molecule_code_id", "pk")
     )
     if len(use_type["data"]) > 0:
         if core.models.MoleculeUsedFor.objects.filter(

diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/handling_molecules.html
@@ -108,15 +108,15 @@ <h3>Information missing</h3>
                     <div class="col-md">
                         <div class="card ">
                             <div class="card-header">
-                                <h3>Update molecules data with defined parameters</h3>
+                                <h3>Update sample extraction data with defined parameters</h3>
                             </div>
                             <div class="card-body">
                                 <form method="post"
                                       enctype="multipart/form-data"
-                                      name="addMoleculeParameters"
-                                      id="addMoleculeParameters">
+                                      name="addExtractionParameters"
+                                      id="addExtractionParameters">
                                     {% csrf_token %}
-                                    <input type="hidden" name="action" value="addMoleculeParameters" />
+                                    <input type="hidden" name="action" value="addExtractionParameters" />
                                     <input type="hidden" name="protocol_list" value="{{ protocol_list }}" />
                                     {% for prot, value_dict in molecule_parameters.items %}
                                         <input type="hidden"
@@ -147,13 +147,13 @@ <h5>Protocol: {{ prot }}</h5>
                     <div class="col-sm-12">
                         <div class="card ">
                             <div class="card-header text-center">
-                                <h3>Molecules have been updated with required parameters.</h3>
+                                <h3>Samples have been updated with Extraction required parameters.</h3>
                             </div>
                             <div class="row my-3  justify-content-center">
                                 <div class="col-md-3">
                                     <input type="button"
                                            class="btn btn-outline-secondary"
-                                           value="Return to handling molecules"
+                                           value="Return to handling extraction samples"
                                            onclick="location.href ='/wetlab/handlingMolecules' ;" />
                                 </div>
                             </div>
@@ -208,7 +208,7 @@ <h3>Molecules are updated with their use.</h3>
                                         type="button"
                                         role="tab"
                                         aria-controls="n_samples"
-                                        aria-selected="true">New Samples</button>
+                                        aria-selected="true">Recorded Samples</button>
                             </li>
                             <li class="nav-item" role="presentation">
                                 <button class="nav-link"
@@ -218,7 +218,7 @@ <h3>Molecules are updated with their use.</h3>
                                         type="button"
                                         role="tab"
                                         aria-controls="molecule"
-                                        aria-selected="false">Pending molecules</button>
+                                        aria-selected="false">Pending Extraction data</button>
                             </li>
                             <li class="nav-item" role="presentation">
                                 <button class="nav-link"
@@ -228,7 +228,7 @@ <h3>Molecules are updated with their use.</h3>
                                         type="button"
                                         role="tab"
                                         aria-controls="mol_use"
-                                        aria-selected="false">Molecules use specification</button>
+                                        aria-selected="false">Next action after extraction</button>
                             </li>
                         </ul>
                         <div class="tab-content bg-white border-tab p-2" id="nav-tabContent">
@@ -669,13 +669,13 @@ <h4>Not molecule uses have been defined yet</h4>
                     });
 
 
-                    $("#addMoleculeParameters").submit(function (e) {
+                    $("#addExtractionParameters").submit(function (e) {
                         var table_data =  {{ prot }}_data_table.getData()
                         var data_json = JSON.stringify(table_data)
                         $("<input />").attr("type", "hidden")
                             .attr("name", "{{ prot }}")
                             .attr("value", data_json)
-                            .appendTo("#addMoleculeParameters");
+                            .appendTo("#addExtractionParameters");
                         $("#button-submit").attr("disabled", true);
                         return true;
                     });

diff --git a/wetlab/views.py b/wetlab/views.py
@@ -3303,7 +3303,7 @@ def handling_molecules(request):
             },
         )
 
-    elif request.method == "POST" and request.POST["action"] == "addMoleculeParameters":
+    elif request.method == "POST" and request.POST["action"] == "addExtractionParameters":
         protocols = request.POST["protocol_list"].split(";")
         for protocol in protocols:
             heading = core.core_config.HEADING_FOR_MOLECULE_ADDING_PARAMETERS.copy()
@@ -3371,6 +3371,7 @@ def handling_molecules(request):
         molecule_use_defined = core.utils.samples.check_if_molecule_use_defined(
             __package__
         )
+
         return render(
             request,
             "wetlab/handling_molecules.html",