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add na fields for pr/er #268

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merged 5 commits into from
Sep 23, 2024
Merged

add na fields for pr/er #268

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b639bd8
add na fields for pr/er
mshadbolt Sep 23, 2024
4b653ab
Update schemas
mshadbolt Sep 23, 2024
5c91d0a
Update schema version
mshadbolt Sep 23, 2024
fd2be0b
Merge branch 'develop' into mshadbolt/percent-pos-na
mshadbolt Sep 23, 2024
09d95aa
Update schema version
mshadbolt Sep 23, 2024
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2 changes: 1 addition & 1 deletion chord_metadata_service/mohpackets/docs/schema_version.txt
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
3ed28cbab36e7b1fd4c441cd729211035539486a
4b653ab06c520bf1a38751c196ba4b0aaecfe93b
30 changes: 30 additions & 0 deletions chord_metadata_service/mohpackets/docs/schemas/schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4314,6 +4314,11 @@
],
"title": "Er Percent Positive"
},
"er_percent_positive_not_available": {
"default": false,
"title": "Er Percent Positive Not Available",
"type": "boolean"
},
"pr_status": {
"anyOf": [
{
Expand All @@ -4335,6 +4340,11 @@
],
"title": "Pr Percent Positive"
},
"pr_percent_positive_not_available": {
"default": false,
"title": "Pr Percent Positive Not Available",
"type": "boolean"
},
"her2_ihc_status": {
"anyOf": [
{
Expand Down Expand Up @@ -7244,6 +7254,11 @@
],
"title": "Er Percent Positive"
},
"er_percent_positive_not_available": {
"default": false,
"title": "Er Percent Positive Not Available",
"type": "boolean"
},
"pr_status": {
"anyOf": [
{
Expand All @@ -7265,6 +7280,11 @@
],
"title": "Pr Percent Positive"
},
"pr_percent_positive_not_available": {
"default": false,
"title": "Pr Percent Positive Not Available",
"type": "boolean"
},
"her2_ihc_status": {
"anyOf": [
{
Expand Down Expand Up @@ -9635,6 +9655,11 @@
],
"title": "Er Percent Positive"
},
"er_percent_positive_not_available": {
"default": false,
"title": "Er Percent Positive Not Available",
"type": "boolean"
},
"pr_status": {
"anyOf": [
{
Expand All @@ -9656,6 +9681,11 @@
],
"title": "Pr Percent Positive"
},
"pr_percent_positive_not_available": {
"default": false,
"title": "Pr Percent Positive Not Available",
"type": "boolean"
},
"her2_ihc_status": {
"anyOf": [
{
Expand Down
20 changes: 20 additions & 0 deletions chord_metadata_service/mohpackets/docs/schemas/schema.md
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Original file line number Diff line number Diff line change
Expand Up @@ -726,8 +726,10 @@ Retrieves a single donor along with all related clinical data, organized in a ne
"cea_not_available": false,
"er_status": "Cannot be determined",
"er_percent_positive": 0,
"er_percent_positive_not_available": false,
"pr_status": "Cannot be determined",
"pr_percent_positive": 0,
"pr_percent_positive_not_available": false,
"her2_ihc_status": "Cannot be determined",
"her2_ish_status": "Cannot be determined",
"hpv_ihc_status": "Cannot be determined",
Expand Down Expand Up @@ -983,8 +985,10 @@ Retrieves a single donor along with all related clinical data, organized in a ne
"cea_not_available": false,
"er_status": "Cannot be determined",
"er_percent_positive": 0,
"er_percent_positive_not_available": false,
"pr_status": "Cannot be determined",
"pr_percent_positive": 0,
"pr_percent_positive_not_available": false,
"her2_ihc_status": "Cannot be determined",
"her2_ish_status": "Cannot be determined",
"hpv_ihc_status": "Cannot be determined",
Expand Down Expand Up @@ -2261,8 +2265,10 @@ uBooleanEnum
"cea_not_available": false,
"er_status": "Cannot be determined",
"er_percent_positive": 0,
"er_percent_positive_not_available": false,
"pr_status": "Cannot be determined",
"pr_percent_positive": 0,
"pr_percent_positive_not_available": false,
"her2_ihc_status": "Cannot be determined",
"her2_ish_status": "Cannot be determined",
"hpv_ihc_status": "Cannot be determined",
Expand Down Expand Up @@ -2466,6 +2472,7 @@ continued

|Name|Type|Required|Restrictions|Description|
|---|---|---|---|---|
|er_percent_positive_not_available|boolean|false|none|none|
|pr_status|any|false|none|none|

anyOf
Expand Down Expand Up @@ -2502,6 +2509,7 @@ continued

|Name|Type|Required|Restrictions|Description|
|---|---|---|---|---|
|pr_percent_positive_not_available|boolean|false|none|none|
|her2_ihc_status|any|false|none|none|

anyOf
Expand Down Expand Up @@ -7043,8 +7051,10 @@ TreatmentTypeEnum
"cea_not_available": false,
"er_status": "Cannot be determined",
"er_percent_positive": 0,
"er_percent_positive_not_available": false,
"pr_status": "Cannot be determined",
"pr_percent_positive": 0,
"pr_percent_positive_not_available": false,
"her2_ihc_status": "Cannot be determined",
"her2_ish_status": "Cannot be determined",
"hpv_ihc_status": "Cannot be determined",
Expand Down Expand Up @@ -7298,8 +7308,10 @@ continued
"cea_not_available": false,
"er_status": "Cannot be determined",
"er_percent_positive": 0,
"er_percent_positive_not_available": false,
"pr_status": "Cannot be determined",
"pr_percent_positive": 0,
"pr_percent_positive_not_available": false,
"her2_ihc_status": "Cannot be determined",
"her2_ish_status": "Cannot be determined",
"hpv_ihc_status": "Cannot be determined",
Expand Down Expand Up @@ -7500,6 +7512,7 @@ continued

|Name|Type|Required|Restrictions|Description|
|---|---|---|---|---|
|er_percent_positive_not_available|boolean|false|none|none|
|pr_status|any|false|none|none|

anyOf
Expand Down Expand Up @@ -7536,6 +7549,7 @@ continued

|Name|Type|Required|Restrictions|Description|
|---|---|---|---|---|
|pr_percent_positive_not_available|boolean|false|none|none|
|her2_ihc_status|any|false|none|none|

anyOf
Expand Down Expand Up @@ -11572,8 +11586,10 @@ continued
"cea_not_available": false,
"er_status": "Cannot be determined",
"er_percent_positive": 0,
"er_percent_positive_not_available": false,
"pr_status": "Cannot be determined",
"pr_percent_positive": 0,
"pr_percent_positive_not_available": false,
"her2_ihc_status": "Cannot be determined",
"her2_ish_status": "Cannot be determined",
"hpv_ihc_status": "Cannot be determined",
Expand Down Expand Up @@ -11776,6 +11792,7 @@ continued

|Name|Type|Required|Restrictions|Description|
|---|---|---|---|---|
|er_percent_positive_not_available|boolean|false|none|none|
|pr_status|any|false|none|none|

anyOf
Expand Down Expand Up @@ -11812,6 +11829,7 @@ continued

|Name|Type|Required|Restrictions|Description|
|---|---|---|---|---|
|pr_percent_positive_not_available|boolean|false|none|none|
|her2_ihc_status|any|false|none|none|

anyOf
Expand Down Expand Up @@ -11932,8 +11950,10 @@ continued
"cea_not_available": false,
"er_status": "Cannot be determined",
"er_percent_positive": 0,
"er_percent_positive_not_available": false,
"pr_status": "Cannot be determined",
"pr_percent_positive": 0,
"pr_percent_positive_not_available": false,
"her2_ihc_status": "Cannot be determined",
"her2_ish_status": "Cannot be determined",
"hpv_ihc_status": "Cannot be determined",
Expand Down
24 changes: 24 additions & 0 deletions chord_metadata_service/mohpackets/docs/schemas/schema.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -132,6 +132,10 @@ components:
- type: number
- type: 'null'
title: Er Percent Positive
er_percent_positive_not_available:
default: false
title: Er Percent Positive Not Available
type: boolean
er_status:
anyOf:
- $ref: '#/components/schemas/ErPrHpvStatusEnum'
Expand Down Expand Up @@ -164,6 +168,10 @@ components:
- type: number
- type: 'null'
title: Pr Percent Positive
pr_percent_positive_not_available:
default: false
title: Pr Percent Positive Not Available
type: boolean
pr_status:
anyOf:
- $ref: '#/components/schemas/ErPrHpvStatusEnum'
Expand Down Expand Up @@ -246,6 +254,10 @@ components:
- type: number
- type: 'null'
title: Er Percent Positive
er_percent_positive_not_available:
default: false
title: Er Percent Positive Not Available
type: boolean
er_status:
anyOf:
- $ref: '#/components/schemas/ErPrHpvStatusEnum'
Expand Down Expand Up @@ -278,6 +290,10 @@ components:
- type: number
- type: 'null'
title: Pr Percent Positive
pr_percent_positive_not_available:
default: false
title: Pr Percent Positive Not Available
type: boolean
pr_status:
anyOf:
- $ref: '#/components/schemas/ErPrHpvStatusEnum'
Expand Down Expand Up @@ -1360,6 +1376,10 @@ components:
- type: number
- type: 'null'
title: Er Percent Positive
er_percent_positive_not_available:
default: false
title: Er Percent Positive Not Available
type: boolean
er_status:
anyOf:
- $ref: '#/components/schemas/ErPrHpvStatusEnum'
Expand Down Expand Up @@ -1392,6 +1412,10 @@ components:
- type: number
- type: 'null'
title: Pr Percent Positive
pr_percent_positive_not_available:
default: false
title: Pr Percent Positive Not Available
type: boolean
pr_status:
anyOf:
- $ref: '#/components/schemas/ErPrHpvStatusEnum'
Expand Down
4 changes: 3 additions & 1 deletion chord_metadata_service/mohpackets/migrations/0001_initial.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Generated by Django 5.0.6 on 2024-09-15 19:36
# Generated by Django 5.0.6 on 2024-09-23 21:47

import chord_metadata_service.mohpackets.models
import django.contrib.postgres.fields
Expand Down Expand Up @@ -135,8 +135,10 @@ class Migration(migrations.Migration):
('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)),
('er_percent_positive_not_available', models.BooleanField(default=False)),
('pr_status', models.CharField(blank=True, max_length=64, null=True)),
('pr_percent_positive', models.FloatField(blank=True, null=True)),
('pr_percent_positive_not_available', models.BooleanField(default=False)),
('her2_ihc_status', models.CharField(blank=True, max_length=64, null=True)),
('her2_ish_status', models.CharField(blank=True, max_length=64, null=True)),
('hpv_ihc_status', models.CharField(blank=True, max_length=64, null=True)),
Expand Down
2 changes: 2 additions & 0 deletions chord_metadata_service/mohpackets/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -400,8 +400,10 @@ class Biomarker(models.Model):
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)
er_percent_positive_not_available = models.BooleanField(default=False)
pr_status = models.CharField(max_length=64, null=True, blank=True)
pr_percent_positive = models.FloatField(null=True, blank=True)
pr_percent_positive_not_available = models.BooleanField(default=False)
her2_ihc_status = models.CharField(max_length=64, null=True, blank=True)
her2_ish_status = models.CharField(max_length=64, null=True, blank=True)
hpv_ihc_status = models.CharField(max_length=64, null=True, blank=True)
Expand Down