nci-cidc-api-modules 1.1.4__py3-none-any.whl → 1.1.5__py3-none-any.whl

cidc_api/models/csms_api.py

@@ -126,7 +126,7 @@ def _get_upload_type(samples: Iterable[Dict[str, Any]]) -> str:
 
     for sample in samples:
         processed_type = sample.get("processed_sample_type").lower()
-        if processed_type == "h&e-stained fixed tissue slide specimen":
+        if processed_type == "h&e fixed tissue slide":
             processed_type = "h_and_e"
 
         if processed_type in [
@@ -268,11 +268,11 @@ def _process_csms_sample(csms_sample: dict):
 
     # differences in naming convention
     processed_sample_type_map: Dict[str, str] = {
-        "tissue_slide": "Fixed Slide",
-        "tumor_tissue_dna": "Tissue Scroll",
+        "tissue_slide": "Fixed Tissue Slide",
+        "tumor_tissue_dna": "FFPE Tissue Scroll",
         "plasma": "Plasma",
-        "normal_tissue_dna": "Tissue Scroll",
-        "h_and_e": "H&E-Stained Fixed Tissue Slide Specimen",
+        "normal_tissue_dna": "FFPE Tissue Scroll",
+        "h_and_e": "H&E Fixed Tissue Slide",
         "pbmc": "PBMC",
     }
     if csms_sample["processed_sample_type"] in processed_sample_type_map:

{nci_cidc_api_modules-1.1.4.dist-info → nci_cidc_api_modules-1.1.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nci_cidc_api_modules
-Version: 1.1.4
+Version: 1.1.5
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -91,8 +91,8 @@ In production, the CIDC API connects to a PostgreSQL instance hosted by Google C
 To do so, first install and start PostgreSQL:
 
 ```bash
-brew install postgresql@11
-brew services start postgresql@11 # launches the postgres service whenever your computer launches
+brew install postgresql@16
+brew services start postgresql@16 # launches the postgres service whenever your computer launches
 ```
 
 > The cidc-devops repo creates a Cloud SQL instance using postgresql@9.6 which is disabled through homebrew. The earliest non-deprecated version through homebrew is postgresql@11.
@@ -117,12 +117,12 @@ In that case, use the plist file referenced in the command output to locate wher
 
 ---
 
-Homebrew will install the psql client (psql) under /opt/homebrew/Cellar/postgresql@11/11.20_2/bin/ ; you may want to create a symlink from here to somewhere in your path.
+Homebrew will install the psql client (psql) under /opt/homebrew/Cellar/postgresql@16/16.8/bin/ ; you may want to create a symlink from here to somewhere in your path.
 
 By default, the postgres service listens on port 5432. Next, create the `cidcdev` user, your local `cidc` development database, and a local `cidctest` database that the unit/integration tests will use:
 
 ```bash
-psql postgresec -c "create user cidcdev with password '1234'"
+psql postgres -c "create user cidcdev with password '1234'"
 
 # Database to use for local development
 psql postgres -c "create database cidc"

{nci_cidc_api_modules-1.1.4.dist-info → nci_cidc_api_modules-1.1.5.dist-info}/RECORD

@@ -6,7 +6,7 @@ cidc_api/config/settings.py,sha256=2VHOVWdN4yUCNYMob2gaWgH2-1_4sbuo46JEIVT_PCY,4
 cidc_api/csms/__init__.py,sha256=eJkY6rWNOAUBmSd4G1_U6h7i472druKEtBdVmgFZVPg,20
 cidc_api/csms/auth.py,sha256=25Yma2Kz3KLENAPSeBYacFuSZXng-EDgmgInKBsRyP0,3191
 cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
-cidc_api/models/csms_api.py,sha256=k8QAE-uU6b8PvkFx_dBG-i224J-bUhM4KGwqZSq6Ua8,31630
+cidc_api/models/csms_api.py,sha256=hw5ahcXZgE6huP18S0y0Hjin5rCSefMIUNYPOh1x5n8,31613
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
 cidc_api/models/models.py,sha256=kszT6ApBOIDsRJRHiYQvWo8283Jox_x0nPuetXBeK74,126680
 cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
@@ -19,8 +19,8 @@ cidc_api/shared/emails.py,sha256=TXKrga3A8rvaUKIH68ASmjkg9qMdFCWDf5HHxPvro5M,489
 cidc_api/shared/gcloud_client.py,sha256=7dDs0crLMJKdIp4IDSfrZBMB3h-zvWNieB81azoeLO4,33746
 cidc_api/shared/jose.py,sha256=QO30uIhbYDwzPEWWJXz0PfyV7E1AZHReEZJUVT70UJY,1844
 cidc_api/shared/rest_utils.py,sha256=LMfBpvJRjkfQjCzVXuhTTe4Foz4wlvaKg6QntyR-Hkc,6648
-nci_cidc_api_modules-1.1.4.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.1.4.dist-info/METADATA,sha256=yjWt9akogGeUeMl9aHlL-ZIJ6yUdR3L0_ttodeBFEnY,40807
-nci_cidc_api_modules-1.1.4.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-nci_cidc_api_modules-1.1.4.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.1.4.dist-info/RECORD,,
+nci_cidc_api_modules-1.1.5.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.5.dist-info/METADATA,sha256=uqkkK2Ks9VrPuvKv1ZqmV3nGE_Q2tNbWyQ3lquMf8Dw,40802
+nci_cidc_api_modules-1.1.5.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+nci_cidc_api_modules-1.1.5.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.5.dist-info/RECORD,,