Merge branch 'master' of gitlab.pasteur.fr:ippidb/ippidb-web

ansible/celeryd

@@ -2,7 +2,7 @@ CELERYD_NODES="worker"
 CELERY_BIN="/usr/local/bin/celery"
 CELERY_APP="ippisite"
 CELERYD_CHDIR="/home/ippidb/ippidb-web-{{ http_port }}/ippisite"
-CELERYD_OPTS="--time-limit=3000 --concurrency=1 --max-tasks-per-child=1"
+CELERYD_OPTS="--time-limit=172800 --concurrency=1 --max-tasks-per-child=1"
 CELERYD_LOG_FILE="/var/ippidb-{{ http_port }}-celery/celery%n%I.log"
 CELERYD_PID_FILE="/var/ippidb-{{ http_port }}-celery/celery%n.pid"
 CELERYD_LOG_LEVEL="DEBUG"

ippisite/ippidb/forms.py

@@ -844,7 +844,7 @@ class CompoundActivityResultForm(ModelForm):
     activity_unit = forms.CharField(
         label="Activity unit",
         max_length=5,
-        required=True,
+        required=False,
         widget=widgets.Select(
             choices=(
                 (None, "-----"),
@@ -855,6 +855,7 @@ class CompoundActivityResultForm(ModelForm):
                 ("1e-12", "pmol"),
             ),
         ),
+        help_text="Only required if 'activity type' is not Kd ratio.",
     )
 
     class Meta:
@@ -896,20 +897,27 @@ class CompoundActivityResultForm(ModelForm):
             return cleaned_data
         if cleaned_data["activity_mol"] is None:
             return cleaned_data
-        if cleaned_data["activity_unit"] in (None, ""):
-            self.add_error("activity_unit", "Unit must be provided")
+        if (
+            cleaned_data.get("activity_unit", "") == ""
+            and cleaned_data.get("activity_type", None) != "KdRat"
+        ):
+            self.add_error("activity_unit", "Unit is required if type is not Kd ratio")
             return cleaned_data
         try:
-            d = Decimal(
-                -log10(
-                    Decimal(self.cleaned_data["activity_mol"])
-                    * Decimal(self.cleaned_data["activity_unit"])
+            if self.cleaned_data["activity_type"] != "KdRat":
+                d = Decimal(
+                    -log10(
+                        Decimal(self.cleaned_data["activity_mol"])
+                        * Decimal(self.cleaned_data["activity_unit"])
+                    )
                 )
-            )
-            d = d.quantize(
-                Decimal(10) ** -self.instance._meta.get_field("activity").decimal_places
-            )
-            self.cleaned_data["activity"] = d
+                d = d.quantize(
+                    Decimal(10)
+                    ** -self.instance._meta.get_field("activity").decimal_places
+                )
+                self.cleaned_data["activity"] = d
+            else:
+                self.cleaned_data["activity"] = self.cleaned_data["activity_mol"]
         except Exception as e:
             self.add_error(
                 "activity_mol",
@@ -945,6 +953,7 @@ class CompoundActivityResultBaseInlineNestedFormSet(BaseInlineNestedFormSet):
         ("pEC50", "EC50 (half maximal effective concentration)"),
         ("pKd", "Kd (dissociation constant)"),
         ("pKi", "Ki (inhibition constant)"),
+        ("KdRat", "Kd ratio (Kd w/o ligand / Kd with ligand"),
     ]
 
     def add_fields(self, form, index):

ippisite/ippidb/migrations/0050_auto_20200420_2015.py

+# Generated by Django 2.2.1 on 2020-04-20 20:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ippidb', '0049_auto_20200419_2005'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='compoundactivityresult',
+            name='activity_type',
+            field=models.CharField(choices=[('pIC50', 'pIC50 (half maximal inhibitory concentration, -log10)'), ('pEC50', 'pEC50 (half maximal effective concentration, -log10)'), ('pKd', 'pKd (dissociation constant, -log10)'), ('pKi', 'pKi (inhibition constant, -log10)'), ('KdRat', 'Kd ratio (Kd without/with ligand')], max_length=5, verbose_name='Activity type'),
+        ),
+    ]

ippisite/ippidb/models.py

@@ -1078,6 +1078,7 @@ class CompoundActivityResult(models.Model):
         ("pEC50", "pEC50 (half maximal effective concentration, -log10)"),
         ("pKd", "pKd (dissociation constant, -log10)"),
         ("pKi", "pKi (inhibition constant, -log10)"),
+        ("KdRat", "Kd ratio (Kd without/with ligand"),
     )
     compound = models.ForeignKey(Compound, models.CASCADE)
     test_activity_description = models.ForeignKey(

ippisite/ippidb/templates/compound_form_content.html

@@ -41,7 +41,7 @@
                     {{form.common_name.label}}
                 </label>
             </div>
-            {%if form.show_is_a_ligand != None %}
+            {%if form.ligand_id != None %}
             <div class="input-inline">
                 <input type="text" name="{{form.ligand_id.html_name}}"
                     {%if form.ligand_id.value %}value="{{form.ligand_id.value}}" {%endif%}

ippisite/ippidb/tests/test_simple_heterodimer_208.yaml

@@ -49,9 +49,8 @@ activity_tests:
     cell_line_name: 'Human small-cell lung cancer'
     protein_complex: '1'
     compound_activity_results:
-    - activity_mol: 61
-      activity_type: pIC50
-      activity_unit: 1e-9
+    - activity_mol: 20
+      activity_type: "KdRat"
       compound_name: 'compound 12'
       modulation_type: I
   
\ No newline at end of file

ippisite/ippidb/tests/tests_contribute_e2e.py

@@ -149,10 +149,15 @@ class ContributionE2ETestCase(TestCase):
                     "activity_mol" in compound_activity_results
                     and compound_activity_results["activity_mol"] != ""
                 ):
-                    compound_activity_results["activity"] = -math.log10(
-                        Decimal(str(compound_activity_results["activity_mol"]))
-                        * Decimal(str(compound_activity_results["activity_unit"]))
-                    )
+                    if compound_activity_results["activity_type"] != "KdRat":
+                        compound_activity_results["activity"] = -math.log10(
+                            Decimal(str(compound_activity_results["activity_mol"]))
+                            * Decimal(str(compound_activity_results["activity_unit"]))
+                        )
+                    else:
+                        compound_activity_results["activity"] = Decimal(
+                            str(compound_activity_results["activity_mol"])
+                        )
 
         self._process_contribution_wizard_without_sanity_check(entry_data)
 
@@ -574,15 +579,6 @@ class ContributionE2ETestCase(TestCase):
                 and activity_test["cell_line_name"] != ""
             ):
                 tad_filters["cell_line__name"] = activity_test["cell_line_name"]
-            for tad in models.TestActivityDescription.objects.all():
-                print(
-                    tad.test_type,
-                    tad.test_name,
-                    tad.protein_bound_construct,
-                    tad.test_modulation_type,
-                    tad.nb_active_compounds,
-                    tad.cell_line,
-                )
             test_activity_description = models.TestActivityDescription.objects.get(
                 **tad_filters
             )
@@ -625,4 +621,5 @@ class ContributionE2ETestCase(TestCase):
         """
         with NamedTemporaryFile(delete=False, suffix=".html") as f:
             f.write(response.content)
+            print(response.content)
             return f.name

ippisite/ippidb/views/contribute.py

@@ -395,15 +395,7 @@ class IppiWizard(
                 bibliography.autofill()
                 return bibliography
         if self.steps.current == "ProteinDomainComplexTypeForm":
-            print (
-                "blablabla",
-                self.storage.get_step_data("PDBForm").get("PDBForm-proteins"),
-            )
             protein_ids = self.storage.get_step_data("PDBForm").get("PDBForm-proteins")
-            print (
-                "blablabla",
-                self.storage.get_step_data("PDBForm").get("PDBForm-proteins"),
-            )
             return models.Protein.objects.filter(id__in=protein_ids)
 
     def get_template_names(self):
@@ -583,7 +575,7 @@ def admin_session_view(request, biblio_pk, ppi_pk, contribution_pk=None):
         contribution = get_object_or_404(models.Contribution, pk=contribution_pk)
         bibliography = contribution.bibliography
         ppi = contribution.ppi
-        context["contribution"] = contribution        
+        context["contribution"] = contribution
     else:
         bibliography = None
         ppi = None