From 2af7683b05b1b58684d4b91675819867d2ce8642 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@pasteur.fr>
Date: Thu, 23 Apr 2020 22:29:20 +0200
Subject: [PATCH] remove the need to specify "protein bound construct" in Test
step
the value for the field is:
- automatically deducted if there is only one ProteinDomainBoundComplex
in the PPI
- NULL otherwise
WIP on #204
---
ippisite/ippidb/forms.py | 27 +++----------------
.../migrations/0052_auto_20200423_2019.py | 19 +++++++++++++
ippisite/ippidb/models.py | 2 +-
...tation_and_storage_pIC50_2380_002_e-9.yaml | 1 -
...ation_and_storage_pIC50_4_9846073_e-6.yaml | 1 -
...ation_and_storage_pIC50_639_39406_e-3.yaml | 1 -
...omputation_and_storage_pIC50_6_85_e-0.yaml | 1 -
ippisite/ippidb/tests/test_basic_entry.yaml | 1 -
.../ippidb/tests/test_complex_no_pfam.yaml | 1 -
ippisite/ippidb/tests/test_entry_28.yaml | 1 -
.../ippidb/tests/test_simple_heterodimer.yaml | 1 -
.../tests/test_simple_heterodimer_208.yaml | 2 --
.../test_simple_stabilized_heterodimer.yaml | 1 -
.../ippidb/tests/test_stabilizer_204.yaml | 1 -
.../ippidb/tests/test_with_all_tests.yaml | 1 -
ippisite/ippidb/tests/tests_contribute_e2e.py | 1 -
ippisite/ippidb/views/contribute.py | 8 +++++-
17 files changed, 30 insertions(+), 40 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0052_auto_20200423_2019.py
diff --git a/ippisite/ippidb/forms.py b/ippisite/ippidb/forms.py
index 29892e0b..8b8d64f5 100644
--- a/ippisite/ippidb/forms.py
+++ b/ippisite/ippidb/forms.py
@@ -1053,13 +1053,6 @@ class TestActivityDescriptionForm(forms.ModelForm):
required=False,
)
- protein_complex = forms.ModelChoiceField(
- queryset=models.Protein.objects.none(),
- label=_("protein_domain_bound_complex_label"),
- help_text=_("protein_domain_bound_complex_help_text"),
- required=True,
- )
-
class Meta:
model = models.TestActivityDescription
fields = "__all__"
@@ -1115,13 +1108,6 @@ class TestActivityDescriptionForm(forms.ModelForm):
name=self.cleaned_data["cell_line_name"]
)
self.instance.cell_line = cell_line
- if "protein_complex" in self.cleaned_data:
- try:
- self.instance.protein_domain_bound_complex = self.complexes[
- self.cleaned_data["protein_complex"].pk
- ]
- except KeyError:
- pass
return super().save(commit=commit)
@@ -1148,13 +1134,6 @@ class TestActivityDescriptionBaseModelFormSet(BaseInlineNestedFormSet):
)
form.nested.set_compound_names(self.__compound_names)
form.nested.set_modulation_type(self.__modulation_type)
- form.fields["protein_complex"].queryset = models.Protein.objects.filter(
- id__in=self.__protein_subset_ids
- )
- if models.Protein.objects.filter(id__in=self.__protein_subset_ids).count() == 1:
- form.fields["protein_complex"].initial = models.Protein.objects.filter(
- id__in=self.__protein_subset_ids
- ).first()
def set_compound_names(self, compound_names):
"""
@@ -1173,15 +1152,15 @@ class TestActivityDescriptionBaseModelFormSet(BaseInlineNestedFormSet):
"""
self.__protein_subset_ids = protein_subset_ids
- def set_complexes(self, complexes):
+ def set_complex(self, protein_domain_bound_complex):
"""
- Provided to the form the complexes dictionary received from the wizard
+ Set the protein domain bound complex for all the form instances in the formset
:param complexes:
:return:
"""
for form in self.forms:
- form.complexes = complexes
+ form.instance.protein_domain_bound_complex = protein_domain_bound_complex
def set_compounds(self, compounds):
"""
diff --git a/ippisite/ippidb/migrations/0052_auto_20200423_2019.py b/ippisite/ippidb/migrations/0052_auto_20200423_2019.py
new file mode 100644
index 00000000..e25caeff
--- /dev/null
+++ b/ippisite/ippidb/migrations/0052_auto_20200423_2019.py
@@ -0,0 +1,19 @@
+# Generated by Django 2.2.1 on 2020-04-23 20:19
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0051_remove_testactivitydescription_protein_bound_construct'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='testactivitydescription',
+ name='protein_domain_bound_complex',
+ field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainBoundComplex'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 93733c7b..43e189f8 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -1014,7 +1014,7 @@ class TestActivityDescription(models.Model):
)
biblio = models.ForeignKey(Bibliography, on_delete=models.CASCADE)
protein_domain_bound_complex = models.ForeignKey(
- ProteinDomainBoundComplex, on_delete=models.CASCADE
+ ProteinDomainBoundComplex, on_delete=models.CASCADE, null=True, blank=True
)
ppi = models.ForeignKey(Ppi, models.CASCADE, blank=True, null=True)
test_type = models.CharField(
diff --git a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_2380_002_e-9.yaml b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_2380_002_e-9.yaml
index 61828344..d23e8c9a 100644
--- a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_2380_002_e-9.yaml
+++ b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_2380_002_e-9.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 2
- protein_complex: '2'
test_modulation_type: I
test_name: test
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_4_9846073_e-6.yaml b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_4_9846073_e-6.yaml
index 1206c530..963453ff 100644
--- a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_4_9846073_e-6.yaml
+++ b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_4_9846073_e-6.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 2
- protein_complex: '2'
test_modulation_type: I
test_name: test
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_639_39406_e-3.yaml b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_639_39406_e-3.yaml
index 306f48ab..8dd666a7 100644
--- a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_639_39406_e-3.yaml
+++ b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_639_39406_e-3.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 2
- protein_complex: '2'
test_modulation_type: I
test_name: test
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_6_85_e-0.yaml b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_6_85_e-0.yaml
index eb93af6d..a11ee0b6 100644
--- a/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_6_85_e-0.yaml
+++ b/ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_6_85_e-0.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 2
- protein_complex: '2'
test_modulation_type: I
test_name: test
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_basic_entry.yaml b/ippisite/ippidb/tests/test_basic_entry.yaml
index 6f28b468..af3ac0d2 100644
--- a/ippisite/ippidb/tests/test_basic_entry.yaml
+++ b/ippisite/ippidb/tests/test_basic_entry.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 2
- protein_complex: '2'
test_modulation_type: I
test_name: test
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_complex_no_pfam.yaml b/ippisite/ippidb/tests/test_complex_no_pfam.yaml
index cc7429b4..9ff962bf 100644
--- a/ippisite/ippidb/tests/test_complex_no_pfam.yaml
+++ b/ippisite/ippidb/tests/test_complex_no_pfam.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 2
- protein_complex: '1'
test_modulation_type: I
test_name: test
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_entry_28.yaml b/ippisite/ippidb/tests/test_entry_28.yaml
index 7fddcc4b..5923d952 100644
--- a/ippisite/ippidb/tests/test_entry_28.yaml
+++ b/ippisite/ippidb/tests/test_entry_28.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 1
- protein_complex: '1'
test_modulation_type: B
test_name: biolayer interferometry assay
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_simple_heterodimer.yaml b/ippisite/ippidb/tests/test_simple_heterodimer.yaml
index 72cd7db1..31762772 100644
--- a/ippisite/ippidb/tests/test_simple_heterodimer.yaml
+++ b/ippisite/ippidb/tests/test_simple_heterodimer.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 2
- protein_complex: '1'
test_modulation_type: I
test_name: test
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_simple_heterodimer_208.yaml b/ippisite/ippidb/tests/test_simple_heterodimer_208.yaml
index a3c8e2a8..84608560 100644
--- a/ippisite/ippidb/tests/test_simple_heterodimer_208.yaml
+++ b/ippisite/ippidb/tests/test_simple_heterodimer_208.yaml
@@ -33,7 +33,6 @@ activity_tests:
test_modulation_type: I
nb_active_compounds: 1
cell_line_name: ''
- protein_complex: '1'
compound_activity_results:
- activity_mol: 6
activity_type: pIC50
@@ -46,7 +45,6 @@ activity_tests:
test_modulation_type: I
nb_active_compounds: 1
cell_line_name: 'Human small-cell lung cancer'
- protein_complex: '1'
compound_activity_results:
- activity_mol: 20
activity_type: "KdRat"
diff --git a/ippisite/ippidb/tests/test_simple_stabilized_heterodimer.yaml b/ippisite/ippidb/tests/test_simple_stabilized_heterodimer.yaml
index 57c5b923..3dc5abcd 100644
--- a/ippisite/ippidb/tests/test_simple_stabilized_heterodimer.yaml
+++ b/ippisite/ippidb/tests/test_simple_stabilized_heterodimer.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: S
is_primary: true
nb_active_compounds: 2
- protein_complex: '1'
test_modulation_type: I
test_name: pull down
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/test_stabilizer_204.yaml b/ippisite/ippidb/tests/test_stabilizer_204.yaml
index e7d9d13a..32e3ded6 100644
--- a/ippisite/ippidb/tests/test_stabilizer_204.yaml
+++ b/ippisite/ippidb/tests/test_stabilizer_204.yaml
@@ -30,7 +30,6 @@ activity_tests:
test_name: Fluorescence Polarization
test_modulation_type: B
nb_active_compounds: 1
- protein_complex: '1'
compound_activity_results:
- activity_mol: 20
activity_type: pKd
diff --git a/ippisite/ippidb/tests/test_with_all_tests.yaml b/ippisite/ippidb/tests/test_with_all_tests.yaml
index 26fc81b4..154992d5 100644
--- a/ippisite/ippidb/tests/test_with_all_tests.yaml
+++ b/ippisite/ippidb/tests/test_with_all_tests.yaml
@@ -8,7 +8,6 @@ activity_tests:
modulation_type: I
is_primary: true
nb_active_compounds: 2
- protein_complex: '2'
test_modulation_type: I
test_name: test
test_type: BIOCH
diff --git a/ippisite/ippidb/tests/tests_contribute_e2e.py b/ippisite/ippidb/tests/tests_contribute_e2e.py
index ad6959b0..09c8983f 100644
--- a/ippisite/ippidb/tests/tests_contribute_e2e.py
+++ b/ippisite/ippidb/tests/tests_contribute_e2e.py
@@ -369,7 +369,6 @@ class ContributionE2ETestCase(TestCase):
]
if "cell_line_name" in activity_test:
data[f"{idx}-cell_line_name"] = activity_test["cell_line_name"]
- data[f"{idx}-protein_complex"] = activity_test["protein_complex"]
data[
f"{idx}-compoundactivityresult_set-activity-results-TOTAL_FORMS"
] = 1 # len(activity_test.get("compound_activity_results",[]))
diff --git a/ippisite/ippidb/views/contribute.py b/ippisite/ippidb/views/contribute.py
index 6e88540f..31e28ae6 100644
--- a/ippisite/ippidb/views/contribute.py
+++ b/ippisite/ippidb/views/contribute.py
@@ -489,7 +489,13 @@ class IppiWizard(
# Step 8.1 Activity Tests
# We set the dicts to translates attributes into model
- form_dict["ActivityDescriptionFormSet"].set_complexes(complexes)
+ bound_complexes = [
+ protein_domain_complex
+ for protein_domain_complex in complexes.values()
+ if isinstance(protein_domain_complex, models.ProteinDomainBoundComplex)
+ ]
+ if len(bound_complexes) == 1:
+ form_dict["ActivityDescriptionFormSet"].set_complex(bound_complexes[0])
form_dict["ActivityDescriptionFormSet"].set_compounds(compounds)
# We set the constants attributes among the instances to be created by the modelformset
form_dict["ActivityDescriptionFormSet"].instance = dict(
--
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