nci-cidc-api-modules 1.0.13__py3-none-any.whl → 1.0.16__py3-none-any.whl

cidc_api/models/files/details.py

@@ -907,6 +907,19 @@ details_dict = {
         "other possible solutions also calculated by ichorCNA",
         "",
     ),
+    "/ctdna/OnPrem.RData": FileDetails(
+        "source",
+        "Rdata file generated by ichorCNA",
+        "",
+    ),
+    "/ctdna/OnPrem.correctedDepth.txt": FileDetails(
+        "source",
+        "Corrected depth file generated by ichorCNA",
+        "",
+    ),
+    "/ctdna/OnPrem.params.txt": FileDetails(
+        "source", "On premise parameters file generated by ichorCNA", ""
+    ),
     # Microbiome Assay
     "/microbiome/forward.fastq.gz": FileDetails(
         "source",

cidc_api/models/files/facets.py

@@ -473,6 +473,9 @@ assay_facets: Facets = {
             ["/ctdna/summary_plots.pdf"],
             "Plots showing Copy Number Alteration (CNA) across the whole genome for each sample for the top 2 solutions generated by ichorCNA.",
         ),
+        "On Premise Corrected Depth": FacetConfig(["/ctdna/OnPrem.correctedDepth.txt"]),
+        "On Premise Parameters": FacetConfig(["/ctdna/OnPrem.params.txt"]),
+        "On Premise Rdata": FacetConfig(["/ctdna/OnPrem.RData"]),
     },
     "Microbiome": {
         "Source": FacetConfig(

{nci_cidc_api_modules-1.0.13.dist-info → nci_cidc_api_modules-1.0.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_api_modules
-Version: 1.0.13
+Version: 1.0.16
 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
@@ -26,7 +26,7 @@ Requires-Dist: pandas ==1.5.3
 Requires-Dist: python-dotenv ==0.10.3
 Requires-Dist: requests ==2.32.3
 Requires-Dist: jinja2 ==3.1.4
-Requires-Dist: nci-cidc-schemas ==0.26.34
+Requires-Dist: nci-cidc-schemas ==0.26.35
 
 # NCI CIDC API <!-- omit in TOC -->
 
@@ -202,15 +202,16 @@ Install the [Cloud SQL Proxy](https://cloud.google.com/sql/docs/mysql/quickstart
 curl -o /usr/local/bin/cloud_sql_proxy https://dl.google.com/cloudsql/cloud_sql_proxy.darwin.amd64
 chmod +x /usr/local/bin/cloud_sql_proxy
 mkdir ~/.cloudsql
+chmod 777 ~/.cloudsql
 ```
 
-Proxy to the staging Cloud SQL instance:
+Proxy to the dev Cloud SQL instance:
 
 ```bash
-cloud_sql_proxy -instances cidc-dfci-staging:us-central1:cidc-postgresql-staging -dir ~/.cloudsql
+cloud-sql-proxy --unix-socket ~/.cloudsql/ nih-nci-cimac-cidc-dev2:us-east4:cidc-postgresql-dev2 &
 ```
 
-In your `.env` file, comment out `POSTGRES_URI` and uncomment all environment variables prefixed with `CLOUD_SQL_`. Restart your local API instance, and it will connect to the staging Cloud SQL instance via the local proxy.
+In your `.env` file, comment out `POSTGRES_URI` and uncomment all environment variables prefixed with `CLOUD_SQL_`. Change CLOUD_SQL_SOCKET_DIR to contain a reference to your home directory. Restart your local API instance, and it will connect to the staging Cloud SQL instance via the local proxy.
 
 If you wish to connect to the staging Cloud SQL instance via the postgres REPL, download and run the CIDC sql proxy tool (a wrapper for `cloud_sql_proxy`):
 

{nci_cidc_api_modules-1.0.13.dist-info → nci_cidc_api_modules-1.0.16.dist-info}/RECORD

@@ -11,15 +11,15 @@ cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ
 cidc_api/models/models.py,sha256=Hjp9sieGdldNbUzneFi-7vRYyo9wwr0D-0m_UbxsDEk,124106
 cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
-cidc_api/models/files/details.py,sha256=eg1u8uZwtxb0m9mFobcTL_mnPBMq1MPZv3NN3KWMGOI,62309
-cidc_api/models/files/facets.py,sha256=5xI5eM1J0Uc97W0-MvAPSRRN-2Hs2xb_AIupliJRMJU,29172
+cidc_api/models/files/details.py,sha256=DimrGmyL216j9eB47ZlX19b5GANf2nrD_crl79RPgqg,62699
+cidc_api/models/files/facets.py,sha256=n2Xi4zaC2pcJQw31gOLFxnF0nwtUBIkvw-5Th21-5uQ,29403
 cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cidc_api/shared/auth.py,sha256=VMd_3QJE2iG16QxuGzHBV9MzJJItOZNn9gcw0_iUBLI,11647
 cidc_api/shared/emails.py,sha256=5dyuKlpcg1M4P_RrAt0ss2hiCqb-Y7p2XXR1d9uBXg8,4868
 cidc_api/shared/gcloud_client.py,sha256=7dDs0crLMJKdIp4IDSfrZBMB3h-zvWNieB81azoeLO4,33746
 cidc_api/shared/rest_utils.py,sha256=LMfBpvJRjkfQjCzVXuhTTe4Foz4wlvaKg6QntyR-Hkc,6648
-nci_cidc_api_modules-1.0.13.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.0.13.dist-info/METADATA,sha256=h7mLp6PwAyxWMxNplQeNczSRoePAVvglgyPsVAIJsxs,40509
-nci_cidc_api_modules-1.0.13.dist-info/WHEEL,sha256=mguMlWGMX-VHnMpKOjjQidIo1ssRlCFu4a4mBpz1s2M,91
-nci_cidc_api_modules-1.0.13.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.0.13.dist-info/RECORD,,
+nci_cidc_api_modules-1.0.16.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.0.16.dist-info/METADATA,sha256=iseyUVZ1hiy6aXTM4bWY99UIapzfgcFWq24QI0dcHSo,40603
+nci_cidc_api_modules-1.0.16.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
+nci_cidc_api_modules-1.0.16.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.0.16.dist-info/RECORD,,

{nci_cidc_api_modules-1.0.13.dist-info → nci_cidc_api_modules-1.0.16.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.1.1)
+Generator: setuptools (71.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any