Merge pull request #261 from CanDIG/sonchau/model_3_1

DIG-1782: Add <field>_not_available for all numeric fields
CanDIG · Sep 15, 2024 · 3349786 · 3349786
2 parents 2bedb63 + 321ba56
commit 3349786
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Showing 9 changed files with 592 additions and 18 deletions.
diff --git a/chord_metadata_service/mohpackets/docs/schema.json b/chord_metadata_service/mohpackets/docs/schema.json
diff --git a/chord_metadata_service/mohpackets/docs/schema.md b/chord_metadata_service/mohpackets/docs/schema.md
diff --git a/chord_metadata_service/mohpackets/docs/schema.yml b/chord_metadata_service/mohpackets/docs/schema.yml
diff --git a/chord_metadata_service/mohpackets/docs/schema_version.txt b/chord_metadata_service/mohpackets/docs/schema_version.txt
@@ -1 +1 @@
-4b47c8b9c4ddbb0ac6c97c3f11b2bba675d5abe7
+0416ebdcca7b12b2ed2c9ef3107aad08db10e6aa
diff --git a/chord_metadata_service/mohpackets/migrations/0001_initial.py b/chord_metadata_service/mohpackets/migrations/0001_initial.py
@@ -1,4 +1,4 @@
-# Generated by Django 5.0.6 on 2024-09-06 17:05
+# Generated by Django 5.0.6 on 2024-09-15 19:36
 
 import chord_metadata_service.mohpackets.models
 import django.contrib.postgres.fields
@@ -85,6 +85,7 @@ class Migration(migrations.Migration):
                 ('tobacco_smoking_status', models.CharField(blank=True, max_length=255, null=True)),
                 ('tobacco_type', django.contrib.postgres.fields.ArrayField(base_field=models.CharField(blank=True, max_length=128, null=True), blank=True, null=True, size=None)),
                 ('pack_years_smoked', models.FloatField(blank=True, null=True)),
+                ('pack_years_smoked_not_available', models.BooleanField(default=False)),
                 ('donor_uuid', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='mohpackets.donor')),
                 ('program_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='mohpackets.program')),
             ],
@@ -105,6 +106,7 @@ class Migration(migrations.Migration):
                 ('prior_malignancy', models.CharField(blank=True, max_length=32, null=True)),
                 ('laterality_of_prior_malignancy', models.CharField(blank=True, max_length=64, null=True)),
                 ('age_at_comorbidity_diagnosis', models.IntegerField(blank=True, null=True)),
+                ('age_at_comorbidity_diagnosis_not_available', models.BooleanField(default=False)),
                 ('comorbidity_type_code', models.CharField(blank=True, max_length=64, null=True)),
                 ('comorbidity_treatment_status', models.CharField(blank=True, max_length=32, null=True)),
                 ('comorbidity_treatment', models.CharField(blank=True, max_length=255, null=True)),
@@ -126,8 +128,11 @@ class Migration(migrations.Migration):
                 ('submitter_follow_up_id', models.CharField(blank=True, max_length=64, null=True)),
                 ('test_date', models.JSONField(blank=True, null=True)),
                 ('psa_level', models.IntegerField(blank=True, null=True)),
+                ('psa_level_not_available', models.BooleanField(default=False)),
                 ('ca125', models.IntegerField(blank=True, null=True)),
+                ('ca125_not_available', models.BooleanField(default=False)),
                 ('cea', models.IntegerField(blank=True, null=True)),
+                ('cea_not_available', models.BooleanField(default=False)),
                 ('er_status', models.CharField(blank=True, max_length=64, null=True)),
                 ('er_percent_positive', models.FloatField(blank=True, null=True)),
                 ('pr_status', models.CharField(blank=True, max_length=64, null=True)),
@@ -205,15 +210,19 @@ class Migration(migrations.Migration):
                 ('submitter_treatment_id', models.CharField(max_length=64)),
                 ('systemic_therapy_type', models.CharField(blank=True, max_length=32, null=True)),
                 ('days_per_cycle', models.IntegerField(blank=True, null=True)),
+                ('days_per_cycle_not_available', models.BooleanField(default=False)),
                 ('number_of_cycles', models.IntegerField(blank=True, null=True)),
+                ('number_of_cycles_not_available', models.BooleanField(default=False)),
                 ('start_date', models.JSONField(blank=True, null=True)),
                 ('end_date', models.JSONField(blank=True, null=True)),
                 ('drug_reference_database', models.CharField(blank=True, max_length=64, null=True)),
                 ('drug_name', models.CharField(blank=True, max_length=255, null=True)),
                 ('drug_reference_identifier', models.CharField(blank=True, max_length=64, null=True)),
                 ('drug_dose_units', models.CharField(blank=True, max_length=64, null=True)),
                 ('prescribed_cumulative_drug_dose', models.FloatField(blank=True, null=True)),
+                ('prescribed_cumulative_drug_dose_not_available', models.BooleanField(default=False)),
                 ('actual_cumulative_drug_dose', models.FloatField(blank=True, null=True)),
+                ('actual_cumulative_drug_dose_not_available', models.BooleanField(default=False)),
                 ('donor_uuid', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='mohpackets.donor')),
                 ('program_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='mohpackets.program')),
                 ('treatment_uuid', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='mohpackets.treatment')),
@@ -232,8 +241,11 @@ class Migration(migrations.Migration):
                 ('surgery_site', models.CharField(blank=True, max_length=255, null=True)),
                 ('surgery_location', models.CharField(blank=True, max_length=128, null=True)),
                 ('tumour_length', models.IntegerField(blank=True, null=True)),
+                ('tumour_length_not_available', models.BooleanField(default=False)),
                 ('tumour_width', models.IntegerField(blank=True, null=True)),
+                ('tumour_width_not_available', models.BooleanField(default=False)),
                 ('greatest_dimension_tumour', models.IntegerField(blank=True, null=True)),
+                ('greatest_dimension_tumour_not_available', models.BooleanField(default=False)),
                 ('tumour_focality', models.CharField(blank=True, max_length=64, null=True)),
                 ('residual_tumour_classification', models.CharField(blank=True, max_length=64, null=True)),
                 ('margin_types_involved', django.contrib.postgres.fields.ArrayField(base_field=models.CharField(blank=True, max_length=128, null=True), blank=True, null=True, size=None)),
@@ -260,7 +272,9 @@ class Migration(migrations.Migration):
                 ('radiation_therapy_modality', models.CharField(blank=True, max_length=255, null=True)),
                 ('radiation_therapy_type', models.CharField(blank=True, max_length=64, null=True)),
                 ('radiation_therapy_fractions', models.IntegerField(blank=True, null=True)),
+                ('radiation_therapy_fractions_not_available', models.BooleanField(default=False)),
                 ('radiation_therapy_dosage', models.IntegerField(blank=True, null=True)),
+                ('radiation_therapy_dosage_not_available', models.BooleanField(default=False)),
                 ('anatomical_site_irradiated', models.CharField(blank=True, max_length=255, null=True)),
                 ('radiation_boost', models.CharField(blank=True, max_length=32, null=True)),
                 ('reference_radiation_treatment_id', models.CharField(blank=True, max_length=64, null=True)),

diff --git a/chord_metadata_service/mohpackets/models.py b/chord_metadata_service/mohpackets/models.py
@@ -227,15 +227,19 @@ class SystemicTherapy(models.Model):
     submitter_treatment_id = models.CharField(max_length=64, null=False, blank=False)
     systemic_therapy_type = models.CharField(max_length=32, null=True, blank=True)
     days_per_cycle = models.IntegerField(null=True, blank=True)
+    days_per_cycle_not_available = models.BooleanField(default=False)
     number_of_cycles = models.IntegerField(null=True, blank=True)
+    number_of_cycles_not_available = models.BooleanField(default=False)
     start_date = models.JSONField(null=True, blank=True)
     end_date = models.JSONField(null=True, blank=True)
     drug_reference_database = models.CharField(max_length=64, null=True, blank=True)
     drug_name = models.CharField(max_length=255, null=True, blank=True)
     drug_reference_identifier = models.CharField(max_length=64, null=True, blank=True)
     drug_dose_units = models.CharField(max_length=64, null=True, blank=True)
     prescribed_cumulative_drug_dose = models.FloatField(blank=True, null=True)
+    prescribed_cumulative_drug_dose_not_available = models.BooleanField(default=False)
     actual_cumulative_drug_dose = models.FloatField(blank=True, null=True)
+    actual_cumulative_drug_dose_not_available = models.BooleanField(default=False)
 
     class Meta:
         ordering = ["uuid"]
@@ -260,7 +264,9 @@ class Radiation(models.Model):
     radiation_therapy_modality = models.CharField(max_length=255, null=True, blank=True)
     radiation_therapy_type = models.CharField(max_length=64, null=True, blank=True)
     radiation_therapy_fractions = models.IntegerField(null=True, blank=True)
+    radiation_therapy_fractions_not_available = models.BooleanField(default=False)
     radiation_therapy_dosage = models.IntegerField(null=True, blank=True)
+    radiation_therapy_dosage_not_available = models.BooleanField(default=False)
     anatomical_site_irradiated = models.CharField(max_length=255, null=True, blank=True)
     radiation_boost = models.CharField(max_length=32, blank=True, null=True)
     reference_radiation_treatment_id = models.CharField(
@@ -291,8 +297,11 @@ class Surgery(models.Model):
     surgery_site = models.CharField(max_length=255, null=True, blank=True)
     surgery_location = models.CharField(max_length=128, null=True, blank=True)
     tumour_length = models.IntegerField(null=True, blank=True)
+    tumour_length_not_available = models.BooleanField(default=False)
     tumour_width = models.IntegerField(null=True, blank=True)
+    tumour_width_not_available = models.BooleanField(default=False)
     greatest_dimension_tumour = models.IntegerField(null=True, blank=True)
+    greatest_dimension_tumour_not_available = models.BooleanField(default=False)
     tumour_focality = models.CharField(max_length=64, null=True, blank=True)
     residual_tumour_classification = models.CharField(
         max_length=64, null=True, blank=True
@@ -384,8 +393,11 @@ class Biomarker(models.Model):
     )  # ref field, not true id
     test_date = models.JSONField(null=True, blank=True)
     psa_level = models.IntegerField(null=True, blank=True)
+    psa_level_not_available = models.BooleanField(default=False)
     ca125 = models.IntegerField(null=True, blank=True)
+    ca125_not_available = models.BooleanField(default=False)
     cea = models.IntegerField(null=True, blank=True)
+    cea_not_available = models.BooleanField(default=False)
     er_status = models.CharField(max_length=64, null=True, blank=True)
     er_percent_positive = models.FloatField(null=True, blank=True)
     pr_status = models.CharField(max_length=64, null=True, blank=True)
@@ -419,6 +431,7 @@ class Comorbidity(models.Model):
         max_length=64, null=True, blank=True
     )
     age_at_comorbidity_diagnosis = models.IntegerField(null=True, blank=True)
+    age_at_comorbidity_diagnosis_not_available = models.BooleanField(default=False)
     comorbidity_type_code = models.CharField(max_length=64, null=True, blank=True)
     comorbidity_treatment_status = models.CharField(
         max_length=32, null=True, blank=True
@@ -446,6 +459,7 @@ class Exposure(models.Model):
         models.CharField(max_length=128, null=True, blank=True), null=True, blank=True
     )
     pack_years_smoked = models.FloatField(null=True, blank=True)
+    pack_years_smoked_not_available = models.BooleanField(default=False)
 
     class Meta:
         ordering = ["uuid"]

diff --git a/config/settings/local.py b/config/settings/local.py
@@ -56,17 +56,17 @@
     "user_1": {
         "is_admin": False,
         "write_datasets": [],
-        "read_datasets": ["PROGRAM_01", "PROGRAM_02"],
+        "read_datasets": ["SYNTH_01", "SYNTH_02"],
     },
     "user_2": {
         "is_admin": False,
-        "write_datasets": ["PROGRAM_03", "PROGRAM_04"],
-        "read_datasets": ["PROGRAM_03", "PROGRAM_04"],
+        "write_datasets": ["SYNTH_01"],
+        "read_datasets": ["SYNTH_01", "SYNTH_02"],
     },
     "site_admin": {
         "is_admin": True,
-        "write_datasets": ["PROGRAM_01", "PROGRAM_02", "PROGRAM_03", "PROGRAM_04"],
-        "read_datasets": ["PROGRAM_01", "PROGRAM_02", "PROGRAM_03", "PROGRAM_04"],
+        "write_datasets": ["SYNTH_01", "SYNTH_02"],
+        "read_datasets": ["SYNTH_01", "SYNTH_02"],
     },
 }
 

diff --git a/requirements/base.txt b/requirements/base.txt
@@ -1,4 +1,4 @@
-Django==5.1 # Python web framework
+Django==5.1.1 # Python web framework
 psycopg[binary]==3.2.1 # PostgreSQL driver for Python
 django-cors-headers==4.4.0 # handling the server headers required for CORS
 django-ninja==1.3.0 # API & schema

diff --git a/requirements/local.txt b/requirements/local.txt
@@ -1,7 +1,7 @@
 -r base.txt # inherit from base.txt
 coverage==7.6.1 # measures code coverage
 flake8==7.1.1 # style guide enforcement
-tox==4.18.0 # test command line tool 
+tox==4.18.1 # test command line tool 
 django-debug-toolbar==4.4.6 # display debug information
-factory-boy==3.3.0 # setup test cases
+factory-boy==3.3.1 # setup test cases
 tqdm==4.66.5 # progress bar for data loader script
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		4b47c8b9c4ddbb0ac6c97c3f11b2bba675d5abe7
		0416ebdcca7b12b2ed2c9ef3107aad08db10e6aa