From 455f6e7d3f0dea173f02e80d433d589f9ac19099 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@pasteur.fr>
Date: Thu, 30 Apr 2020 22:23:20 +0200
Subject: [PATCH] replace some PK test result values with booleans for
availability
- Area under curve (ng.mL-1.hr)
- Clearance (mL/hr)
- Maximal concentration (ng/mL)
- Volume distribution (Vd)
become availabilities
FIX #215
---
ippisite/ippidb/forms.py | 8 ++--
.../migrations/0058_auto_20200430_1915.py | 47 +++++++++++++++++++
.../migrations/0059_auto_20200430_1926.py | 29 ++++++++++++
ippisite/ippidb/models.py | 26 ++++------
.../ippidb/tests/test_with_all_tests.yaml | 8 ++--
ippisite/ippidb/tests/test_with_pk_test.yaml | 8 ++--
ippisite/ippidb/tests/tests_contribute_e2e.py | 16 +++----
7 files changed, 105 insertions(+), 37 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0058_auto_20200430_1915.py
create mode 100644 ippisite/ippidb/migrations/0059_auto_20200430_1926.py
diff --git a/ippisite/ippidb/forms.py b/ippisite/ippidb/forms.py
index 77c9ce62..0a4fba0c 100644
--- a/ippisite/ippidb/forms.py
+++ b/ippisite/ippidb/forms.py
@@ -1716,15 +1716,15 @@ class TestsForm(forms.Form):
pkRes_tolerated = forms.ChoiceField(
label="Tolerated", widget=forms.TextInput(), required=False
)
- pkRes_auc = forms.IntegerField(label="AUC", initial=1, required=False)
- pkRes_clearance = forms.DecimalField(label="Clearance", required=False)
- pkRes_cmax = forms.DecimalField(label="C max", required=False)
+ pkRes_auc_av = forms.BooleanField(label="AUC available", initial=1, required=False)
+ pkRes_clearance_av = forms.BooleanField(label="Clearance available", required=False)
+ pkRes_cmax_av = forms.BooleanField(label="Maximal concentration available", required=False)
pkRes_oral_bioavailability = forms.IntegerField(
label="Oral bio-availability", initial=1, required=False
)
pkRes_t_demi = forms.IntegerField(label="T 1/2", initial=1, required=False)
pkRes_t_max = forms.IntegerField(label="T max", initial=1, required=False)
- pkRes_voldistribution = forms.DecimalField(label="Voldistribution", required=False)
+ pkRes_voldistribution_av = forms.BooleanField(label="Volume distribution (Vd) available", required=False)
UNIT_CONCENTRATION = (("micro", "µM"), ("nano", "nM"), ("pico", "pM"))
diff --git a/ippisite/ippidb/migrations/0058_auto_20200430_1915.py b/ippisite/ippidb/migrations/0058_auto_20200430_1915.py
new file mode 100644
index 00000000..bab8608b
--- /dev/null
+++ b/ippisite/ippidb/migrations/0058_auto_20200430_1915.py
@@ -0,0 +1,47 @@
+# Generated by Django 2.2.1 on 2020-04-30 19:15
+
+from django.db import migrations, models
+
+def fill_pkresult_avail_values(apps, schema_editor):
+ CompoundPKResult = apps.get_model("ippidb", "CompoundPKResult")
+ for cpr in CompoundPKResult.objects.all():
+ cpr.auc_av = cpr.auc is not None
+ cpr.clearance_av = cpr.clearance is not None
+ cpr.c_max_av = cpr.c_max is not None
+ cpr.voldistribution_av = cpr.voldistribution is not None
+ cpr.save()
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0057_auto_20200430_0740'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='compoundpkresult',
+ name='auc_av',
+ field=models.BooleanField(default=False, verbose_name='Area under curve available'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='compoundpkresult',
+ name='c_max_av',
+ field=models.BooleanField(default=False, verbose_name='Maximal concentration available'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='compoundpkresult',
+ name='clearance_av',
+ field=models.BooleanField(default=False, verbose_name='Clearance available'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='compoundpkresult',
+ name='voldistribution_av',
+ field=models.BooleanField(default=False, verbose_name='Volume distribution (Vd)'),
+ preserve_default=False,
+ ),
+ migrations.RunPython(fill_pkresult_avail_values),
+ ]
diff --git a/ippisite/ippidb/migrations/0059_auto_20200430_1926.py b/ippisite/ippidb/migrations/0059_auto_20200430_1926.py
new file mode 100644
index 00000000..7b4d5920
--- /dev/null
+++ b/ippisite/ippidb/migrations/0059_auto_20200430_1926.py
@@ -0,0 +1,29 @@
+# Generated by Django 2.2.1 on 2020-04-30 19:26
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0058_auto_20200430_1915'),
+ ]
+
+ operations = [
+ migrations.RemoveField(
+ model_name='compoundpkresult',
+ name='auc',
+ ),
+ migrations.RemoveField(
+ model_name='compoundpkresult',
+ name='c_max',
+ ),
+ migrations.RemoveField(
+ model_name='compoundpkresult',
+ name='clearance',
+ ),
+ migrations.RemoveField(
+ model_name='compoundpkresult',
+ name='voldistribution',
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index d2108802..b7722d9b 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -1262,28 +1262,20 @@ class CompoundPKResult(models.Model):
compound = models.ForeignKey(Compound, models.CASCADE)
test_pk_description = models.ForeignKey(TestPKDescription, models.CASCADE)
tolerated = models.NullBooleanField("Tolerated", null=True)
- auc = models.IntegerField("Area under curve (ng.mL-1.hr)", blank=True, null=True)
- clearance = models.DecimalField(
- "Clearance (mL/hr)", max_digits=7, decimal_places=3, blank=True, null=True
- )
- c_max = models.DecimalField(
- "Maximal concentration (ng/mL)",
- max_digits=7,
- decimal_places=3,
- blank=True,
- null=True,
- )
oral_bioavailability = models.IntegerField(
"Oral Bioavailability (%F)", blank=True, null=True
)
t_demi = models.IntegerField("t½ (mn)", blank=True, null=True)
t_max = models.IntegerField("tmax (mn)", blank=True, null=True)
- voldistribution = models.DecimalField(
- "Volume distribution (Vd)",
- max_digits=5,
- decimal_places=2,
- blank=True,
- null=True,
+ auc_av = models.BooleanField("Area under curve available")
+ clearance_av = models.BooleanField(
+ "Clearance available"
+ )
+ c_max_av = models.BooleanField(
+ "Maximal concentration available"
+ )
+ voldistribution_av = models.BooleanField(
+ "Volume distribution (Vd) available"
)
class Meta:
diff --git a/ippisite/ippidb/tests/test_with_all_tests.yaml b/ippisite/ippidb/tests/test_with_all_tests.yaml
index 47145d44..73f7d142 100644
--- a/ippisite/ippidb/tests/test_with_all_tests.yaml
+++ b/ippisite/ippidb/tests/test_with_all_tests.yaml
@@ -52,15 +52,15 @@ pharmacokinetic: true
pharmacokinetic_tests:
- administration_mode: IV
compound_pk_results:
- - auc: '1'
- c_max: '5.2'
- clearance: '1.2'
+ - auc_av: True
+ c_max_av: True
+ clearance_av: True
compound_name: toto
oral_bioavailability: '22'
t_demi: '5'
t_max: '5'
tolerated: 'True'
- voldistribution: '5.5'
+ voldistribution_av: True
concentration: '1.2'
dose: '3.5'
dose_interval: '2'
diff --git a/ippisite/ippidb/tests/test_with_pk_test.yaml b/ippisite/ippidb/tests/test_with_pk_test.yaml
index e6fa88bd..60136f05 100644
--- a/ippisite/ippidb/tests/test_with_pk_test.yaml
+++ b/ippisite/ippidb/tests/test_with_pk_test.yaml
@@ -43,15 +43,15 @@ pharmacokinetic: true
pharmacokinetic_tests:
- administration_mode: IV
compound_pk_results:
- - auc: '1'
- c_max: '5.2'
- clearance: '1.2'
+ - auc_av: False
+ c_max_av: True
+ clearance_av: '1.2'
compound_name: toto
oral_bioavailability: '22'
t_demi: '5'
t_max: '5'
tolerated: 'True'
- voldistribution: '5.5'
+ voldistribution_av: '5.5'
dose: '3.5'
organism: 1
test_name: test
diff --git a/ippisite/ippidb/tests/tests_contribute_e2e.py b/ippisite/ippidb/tests/tests_contribute_e2e.py
index f14b7da0..d5d2877f 100644
--- a/ippisite/ippidb/tests/tests_contribute_e2e.py
+++ b/ippisite/ippidb/tests/tests_contribute_e2e.py
@@ -467,15 +467,15 @@ class ContributionE2ETestCase(TestCase):
data[
f"{idx}-compoundpkresult_set-pk-results-{nidx}-tolerated"
] = result["tolerated"]
- data[f"{idx}-compoundpkresult_set-pk-results-{nidx}-auc"] = result[
- "auc"
+ data[f"{idx}-compoundpkresult_set-pk-results-{nidx}-auc_av"] = result[
+ "auc_av"
]
data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-clearance"
- ] = result["clearance"]
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-clearance_av"
+ ] = result["clearance_av"]
data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-c_max"
- ] = result["c_max"]
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-c_max_av"
+ ] = result["c_max_av"]
data[
f"{idx}-compoundpkresult_set-pk-results-{nidx}-oral_bioavailability"
] = result["oral_bioavailability"]
@@ -486,8 +486,8 @@ class ContributionE2ETestCase(TestCase):
f"{idx}-compoundpkresult_set-pk-results-{nidx}-t_max"
] = result["t_max"]
data[
- f"{idx}-compoundpkresult_set-pk-results-{nidx}-voldistribution"
- ] = result["voldistribution"]
+ f"{idx}-compoundpkresult_set-pk-results-{nidx}-voldistribution_av"
+ ] = result["voldistribution_av"]
data[
f"{idx}-compoundpkresult_set-pk-results-{nidx}-compound_name"
] = result["compound_name"]
--
GitLab