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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 @@
aff7d68b373affb90ad1bb3a0e50a11371181b9d
fd2be0bb1831f72571095a6e231e4b74131e070c
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 @@ -4412,6 +4412,11 @@
],
"title": "Er Percent Positive"
},
"er_percent_positive_not_available": {
"default": false,
"title": "Er Percent Positive Not Available",
"type": "boolean"
},
"pr_status": {
"anyOf": [
{
Expand All @@ -4433,6 +4438,11 @@
],
"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 @@ -7342,6 +7352,11 @@
],
"title": "Er Percent Positive"
},
"er_percent_positive_not_available": {
"default": false,
"title": "Er Percent Positive Not Available",
"type": "boolean"
},
"pr_status": {
"anyOf": [
{
Expand All @@ -7363,6 +7378,11 @@
],
"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 @@ -9986,6 +10006,11 @@
],
"title": "Er Percent Positive"
},
"er_percent_positive_not_available": {
"default": false,
"title": "Er Percent Positive Not Available",
"type": "boolean"
},
"pr_status": {
"anyOf": [
{
Expand All @@ -10007,6 +10032,11 @@
],
"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 @@ -1050,8 +1052,10 @@ Used by the query service to return donors along with their sample IDs, treatmen
"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 @@ -2328,8 +2332,10 @@ 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 @@ -2533,6 +2539,7 @@ 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 @@ -2569,6 +2576,7 @@ 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 @@ -7110,8 +7118,10 @@ 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 @@ -7365,8 +7375,10 @@ 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 @@ -7567,6 +7579,7 @@ 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 @@ -7603,6 +7616,7 @@ 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 @@ -12063,8 +12077,10 @@ 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 @@ -12267,6 +12283,7 @@ 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 @@ -12303,6 +12320,7 @@ 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 @@ -12423,8 +12441,10 @@ 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