nci-cidc-api-modules 1.0.13__tar.gz → 1.0.15__tar.gz

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Files changed (35) hide show
  1. {nci_cidc_api_modules-1.0.13/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.0.15}/PKG-INFO +6 -5
  2. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/README.md +4 -3
  3. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/files/facets.py +3 -0
  4. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15/nci_cidc_api_modules.egg-info}/PKG-INFO +6 -5
  5. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/nci_cidc_api_modules.egg-info/requires.txt +1 -1
  6. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/requirements.modules.txt +1 -1
  7. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/LICENSE +0 -0
  8. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/MANIFEST.in +0 -0
  9. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/config/__init__.py +0 -0
  10. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/config/db.py +0 -0
  11. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/config/logging.py +0 -0
  12. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/config/secrets.py +0 -0
  13. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/config/settings.py +0 -0
  14. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/csms/__init__.py +0 -0
  15. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/csms/auth.py +0 -0
  16. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/__init__.py +0 -0
  17. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/csms_api.py +0 -0
  18. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/files/__init__.py +0 -0
  19. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/files/details.py +0 -0
  20. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/migrations.py +0 -0
  21. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/models.py +0 -0
  22. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/schemas.py +0 -0
  23. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/shared/__init__.py +0 -0
  24. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/shared/auth.py +0 -0
  25. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/shared/emails.py +0 -0
  26. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/shared/gcloud_client.py +0 -0
  27. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/shared/rest_utils.py +0 -0
  28. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/nci_cidc_api_modules.egg-info/SOURCES.txt +0 -0
  29. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/nci_cidc_api_modules.egg-info/dependency_links.txt +0 -0
  30. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/nci_cidc_api_modules.egg-info/not-zip-safe +0 -0
  31. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/nci_cidc_api_modules.egg-info/top_level.txt +0 -0
  32. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/pyproject.toml +0 -0
  33. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/setup.cfg +0 -0
  34. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/setup.py +0 -0
  35. {nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/tests/test_api.py +0 -0
{nci_cidc_api_modules-1.0.13/nci_cidc_api_modules.egg-info → nci_cidc_api_modules-1.0.15}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: nci_cidc_api_modules
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- Version: 1.0.13
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+ Version: 1.0.15
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  Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
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  Home-page: https://github.com/NCI-CIDC/cidc-api-gae
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  License: MIT license
@@ -26,7 +26,7 @@ Requires-Dist: pandas==1.5.3
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  Requires-Dist: python-dotenv==0.10.3
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  Requires-Dist: requests==2.32.3
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  Requires-Dist: jinja2==3.1.4
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- Requires-Dist: nci-cidc-schemas==0.26.34
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+ Requires-Dist: nci-cidc-schemas==0.26.35
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  # NCI CIDC API <!-- omit in TOC -->
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@@ -202,15 +202,16 @@ Install the [Cloud SQL Proxy](https://cloud.google.com/sql/docs/mysql/quickstart
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  curl -o /usr/local/bin/cloud_sql_proxy https://dl.google.com/cloudsql/cloud_sql_proxy.darwin.amd64
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  chmod +x /usr/local/bin/cloud_sql_proxy
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  mkdir ~/.cloudsql
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+ chmod 777 ~/.cloudsql
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  ```
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- Proxy to the staging Cloud SQL instance:
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+ Proxy to the dev Cloud SQL instance:
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  ```bash
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- cloud_sql_proxy -instances cidc-dfci-staging:us-central1:cidc-postgresql-staging -dir ~/.cloudsql
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+ cloud-sql-proxy --unix-socket ~/.cloudsql/ nih-nci-cimac-cidc-dev2:us-east4:cidc-postgresql-dev2 &
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  ```
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- 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.
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+ 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.
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  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`):
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{nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/README.md RENAMED
@@ -172,15 +172,16 @@ Install the [Cloud SQL Proxy](https://cloud.google.com/sql/docs/mysql/quickstart
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  curl -o /usr/local/bin/cloud_sql_proxy https://dl.google.com/cloudsql/cloud_sql_proxy.darwin.amd64
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  chmod +x /usr/local/bin/cloud_sql_proxy
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  mkdir ~/.cloudsql
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+ chmod 777 ~/.cloudsql
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  ```
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- Proxy to the staging Cloud SQL instance:
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+ Proxy to the dev Cloud SQL instance:
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  ```bash
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- cloud_sql_proxy -instances cidc-dfci-staging:us-central1:cidc-postgresql-staging -dir ~/.cloudsql
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+ cloud-sql-proxy --unix-socket ~/.cloudsql/ nih-nci-cimac-cidc-dev2:us-east4:cidc-postgresql-dev2 &
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  ```
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- 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.
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+ 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.
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  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`):
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{nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/cidc_api/models/files/facets.py RENAMED
@@ -473,6 +473,9 @@ assay_facets: Facets = {
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  ["/ctdna/summary_plots.pdf"],
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  "Plots showing Copy Number Alteration (CNA) across the whole genome for each sample for the top 2 solutions generated by ichorCNA.",
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  ),
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+ "On Premise Corrected Depth": FacetConfig(["/ctdna/OnPrem.correctedDepth.txt"]),
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+ "On Premise Parameters": FacetConfig(["/ctdna/OnPrem.params.txt"]),
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+ "On Premise Rdata": FacetConfig(["/ctdna/OnPrem.RData"]),
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  },
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  "Microbiome": {
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  "Source": FacetConfig(
{nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15/nci_cidc_api_modules.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: nci_cidc_api_modules
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- Version: 1.0.13
3
+ Version: 1.0.15
4
4
  Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
5
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  Home-page: https://github.com/NCI-CIDC/cidc-api-gae
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  License: MIT license
@@ -26,7 +26,7 @@ Requires-Dist: pandas==1.5.3
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  Requires-Dist: python-dotenv==0.10.3
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  Requires-Dist: requests==2.32.3
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  Requires-Dist: jinja2==3.1.4
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- Requires-Dist: nci-cidc-schemas==0.26.34
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+ Requires-Dist: nci-cidc-schemas==0.26.35
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  # NCI CIDC API <!-- omit in TOC -->
32
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@@ -202,15 +202,16 @@ Install the [Cloud SQL Proxy](https://cloud.google.com/sql/docs/mysql/quickstart
202
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  curl -o /usr/local/bin/cloud_sql_proxy https://dl.google.com/cloudsql/cloud_sql_proxy.darwin.amd64
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  chmod +x /usr/local/bin/cloud_sql_proxy
204
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  mkdir ~/.cloudsql
205
+ chmod 777 ~/.cloudsql
205
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  ```
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207
- Proxy to the staging Cloud SQL instance:
208
+ Proxy to the dev Cloud SQL instance:
208
209
 
209
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  ```bash
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- cloud_sql_proxy -instances cidc-dfci-staging:us-central1:cidc-postgresql-staging -dir ~/.cloudsql
211
+ cloud-sql-proxy --unix-socket ~/.cloudsql/ nih-nci-cimac-cidc-dev2:us-east4:cidc-postgresql-dev2 &
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  ```
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- 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.
214
+ 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.
214
215
 
215
216
  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`):
216
217
 
{nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/nci_cidc_api_modules.egg-info/requires.txt RENAMED
@@ -17,4 +17,4 @@ pandas==1.5.3
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  python-dotenv==0.10.3
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  requests==2.32.3
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  jinja2==3.1.4
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- nci-cidc-schemas==0.26.34
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+ nci-cidc-schemas==0.26.35
{nci_cidc_api_modules-1.0.13 → nci_cidc_api_modules-1.0.15}/requirements.modules.txt RENAMED
@@ -17,4 +17,4 @@ pandas==1.5.3
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  python-dotenv==0.10.3
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  requests==2.32.3
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  jinja2==3.1.4
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- nci-cidc-schemas==0.26.34
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+ nci-cidc-schemas==0.26.35