From bdd2d82c4f357b7bcc2ad960b25193c096936caf Mon Sep 17 00:00:00 2001
From: Catherine <bullen@uchicago.edu>
Date: Thu, 29 Aug 2024 12:15:06 -0500
Subject: [PATCH 1/4] okazaki p2 diagnosis updates
---
src/gdcdictionary/schemas/diagnosis.yaml | 21 ++++++++++++++++++---
1 file changed, 18 insertions(+), 3 deletions(-)
diff --git a/src/gdcdictionary/schemas/diagnosis.yaml b/src/gdcdictionary/schemas/diagnosis.yaml
index 112951fb..b18e5ad1 100644
--- a/src/gdcdictionary/schemas/diagnosis.yaml
+++ b/src/gdcdictionary/schemas/diagnosis.yaml
@@ -982,9 +982,6 @@ properties:
T4:
$ref:
- "_terms_enum.yaml#/t4/common"
- T4a:
- $ref:
- - "_terms_enum.yaml#/t4a/common"
T4b:
$ref:
- "_terms_enum.yaml#/t4b/common"
@@ -1025,6 +1022,18 @@ properties:
$ref:
- "_terms_enum.yaml#/not_allowed_to_collect/common"
+ ajcc_serum_tumor_markers:
+ $ref:
+ - "_terms.yaml#/ajcc_serum_tumor_markers/common"
+ enum:
+ - S0
+ - S1
+ - S2
+ - S3
+ - SX
+ - Unknown
+ - Not Reported
+
ajcc_staging_system_edition:
$ref:
- "_terms.yaml#/ajcc_staging_system_edition/common"
@@ -18294,6 +18303,7 @@ properties:
- Groin
- Head, Face or Neck, NOS
- Heart
+ - Hilar Fat
- Inferior Vena Cava
- Kidney, Lower Pole
- Kidney, Middle
@@ -18365,9 +18375,11 @@ properties:
- Prostate
- Rectum
- Renal Vein
+ - Rete testis
- Retroperitoneum
- Salivary gland
- Scalp
+ - Scrotum
- Sigmoid colon
- Sinus
- Skin
@@ -18377,6 +18389,7 @@ properties:
- Skin, Trunk
- Small intestine
- Soft tissue
+ - Spermatic Cord
- Spinal Cord
- Spleen
- Stomach
@@ -18389,6 +18402,8 @@ properties:
- Trachea
- Transplanted kidney
- Transverse colon
+ - Tunica albuginea
+ - Tunica vaginalis
- Upper lobe, lung
- Urethra
- Uterus
From 765a86f8b92a198a5c7cebd2ef971f8ebfb47308 Mon Sep 17 00:00:00 2001
From: Catherine <bullen@uchicago.edu>
Date: Thu, 29 Aug 2024 12:18:14 -0500
Subject: [PATCH 2/4] add ref back in
---
src/gdcdictionary/schemas/diagnosis.yaml | 3 +++
1 file changed, 3 insertions(+)
diff --git a/src/gdcdictionary/schemas/diagnosis.yaml b/src/gdcdictionary/schemas/diagnosis.yaml
index b18e5ad1..ab5daf4e 100644
--- a/src/gdcdictionary/schemas/diagnosis.yaml
+++ b/src/gdcdictionary/schemas/diagnosis.yaml
@@ -982,6 +982,9 @@ properties:
T4:
$ref:
- "_terms_enum.yaml#/t4/common"
+ T4a:
+ $ref:
+ - "_terms_enum.yaml#/t4/common"
T4b:
$ref:
- "_terms_enum.yaml#/t4b/common"
From 693ad899256d089ef05967386f5b508700e6d4f2 Mon Sep 17 00:00:00 2001
From: Catherine <bullen@uchicago.edu>
Date: Thu, 29 Aug 2024 12:51:56 -0500
Subject: [PATCH 3/4] fix typo
---
src/gdcdictionary/schemas/diagnosis.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/gdcdictionary/schemas/diagnosis.yaml b/src/gdcdictionary/schemas/diagnosis.yaml
index ab5daf4e..f9ae3a43 100644
--- a/src/gdcdictionary/schemas/diagnosis.yaml
+++ b/src/gdcdictionary/schemas/diagnosis.yaml
@@ -984,7 +984,7 @@ properties:
- "_terms_enum.yaml#/t4/common"
T4a:
$ref:
- - "_terms_enum.yaml#/t4/common"
+ - "_terms_enum.yaml#/t4a/common"
T4b:
$ref:
- "_terms_enum.yaml#/t4b/common"
From 2d90bbfef861bbabc419dc4e3524baced1a3855b Mon Sep 17 00:00:00 2001
From: Catherine <bullen@uchicago.edu>
Date: Thu, 29 Aug 2024 14:52:16 -0500
Subject: [PATCH 4/4] update case
---
src/gdcdictionary/schemas/diagnosis.yaml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/gdcdictionary/schemas/diagnosis.yaml b/src/gdcdictionary/schemas/diagnosis.yaml
index f9ae3a43..8ac74e8a 100644
--- a/src/gdcdictionary/schemas/diagnosis.yaml
+++ b/src/gdcdictionary/schemas/diagnosis.yaml
@@ -18378,7 +18378,7 @@ properties:
- Prostate
- Rectum
- Renal Vein
- - Rete testis
+ - Rete Testis
- Retroperitoneum
- Salivary gland
- Scalp
@@ -18405,8 +18405,8 @@ properties:
- Trachea
- Transplanted kidney
- Transverse colon
- - Tunica albuginea
- - Tunica vaginalis
+ - Tunica Albuginea
+ - Tunica Vaginalis
- Upper lobe, lung
- Urethra
- Uterus