From b639bd846393d20222d3d38a758d4b17ff571b6e Mon Sep 17 00:00:00 2001 From: Marion Date: Mon, 23 Sep 2024 14:48:27 -0700 Subject: [PATCH 1/4] add na fields for pr/er --- chord_metadata_service/mohpackets/migrations/0001_initial.py | 4 +++- chord_metadata_service/mohpackets/models.py | 2 ++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/chord_metadata_service/mohpackets/migrations/0001_initial.py b/chord_metadata_service/mohpackets/migrations/0001_initial.py index 33a1c4584..40dc86423 100644 --- 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 2024-09-15 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 @@ -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)), diff --git a/chord_metadata_service/mohpackets/models.py b/chord_metadata_service/mohpackets/models.py index d6c24eea7..2b237b844 100644 --- a/chord_metadata_service/mohpackets/models.py +++ b/chord_metadata_service/mohpackets/models.py @@ -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) From 4b653ab06c520bf1a38751c196ba4b0aaecfe93b Mon Sep 17 00:00:00 2001 From: mshadbolt Date: Mon, 23 Sep 2024 21:49:37 +0000 Subject: [PATCH 2/4] Update schemas --- .../mohpackets/docs/schemas/schema.json | 30 +++++++++++++++++++ .../mohpackets/docs/schemas/schema.md | 20 +++++++++++++ .../mohpackets/docs/schemas/schema.yml | 24 +++++++++++++++ 3 files changed, 74 insertions(+) diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.json b/chord_metadata_service/mohpackets/docs/schemas/schema.json index 43b054b90..7258bb543 100644 --- a/chord_metadata_service/mohpackets/docs/schemas/schema.json +++ b/chord_metadata_service/mohpackets/docs/schemas/schema.json @@ -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": [ { @@ -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": [ { @@ -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": [ { @@ -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": [ { @@ -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": [ { @@ -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": [ { diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.md b/chord_metadata_service/mohpackets/docs/schemas/schema.md index 856037691..9014c6211 100644 --- a/chord_metadata_service/mohpackets/docs/schemas/schema.md +++ b/chord_metadata_service/mohpackets/docs/schemas/schema.md @@ -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", @@ -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", @@ -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", @@ -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 @@ -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 @@ -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", @@ -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", @@ -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 @@ -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 @@ -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", @@ -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 @@ -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 @@ -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", diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.yml b/chord_metadata_service/mohpackets/docs/schemas/schema.yml index 0bbb29933..968c529c5 100644 --- a/chord_metadata_service/mohpackets/docs/schemas/schema.yml +++ b/chord_metadata_service/mohpackets/docs/schemas/schema.yml @@ -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' @@ -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' @@ -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' @@ -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' @@ -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' @@ -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' From 5c91d0a9de1a8b496f41a3e253e9e897ed5b7f51 Mon Sep 17 00:00:00 2001 From: mshadbolt Date: Mon, 23 Sep 2024 21:49:38 +0000 Subject: [PATCH 3/4] Update schema version --- chord_metadata_service/mohpackets/docs/schema_version.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_version.txt b/chord_metadata_service/mohpackets/docs/schema_version.txt index 21736b853..ec1fb73a2 100644 --- a/chord_metadata_service/mohpackets/docs/schema_version.txt +++ b/chord_metadata_service/mohpackets/docs/schema_version.txt @@ -1 +1 @@ -3ed28cbab36e7b1fd4c441cd729211035539486a +4b653ab06c520bf1a38751c196ba4b0aaecfe93b From 09d95aa502279fb23110c8454b3c866b6dbeb78b Mon Sep 17 00:00:00 2001 From: mshadbolt Date: Mon, 23 Sep 2024 22:05:26 +0000 Subject: [PATCH 4/4] Update schema version --- chord_metadata_service/mohpackets/docs/schema_version.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chord_metadata_service/mohpackets/docs/schema_version.txt b/chord_metadata_service/mohpackets/docs/schema_version.txt index ec1fb73a2..818b74da1 100644 --- a/chord_metadata_service/mohpackets/docs/schema_version.txt +++ b/chord_metadata_service/mohpackets/docs/schema_version.txt @@ -1 +1 @@ -4b653ab06c520bf1a38751c196ba4b0aaecfe93b +fd2be0bb1831f72571095a6e231e4b74131e070c