Merge branch 'develop' of github.com:jhu-bids/TermHub into develop

jhu-bids · Sep 5, 2024 · 6c9ec11 · 6c9ec11
2 parents cb597ab + fea8389
commit 6c9ec11
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diff --git a/.github/workflows/backend_dev.yml b/.github/workflows/backend_dev.yml
@@ -53,9 +53,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 # todo: optional: run tests
 #      - name: Run tests
 #        run: python -m unittest discover -v

diff --git a/.github/workflows/backend_prod.yml b/.github/workflows/backend_prod.yml
@@ -53,9 +53,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 # todo: optional: run tests
 #      - name: Run tests
 #        run: python -m unittest discover -v

diff --git a/.github/workflows/kill_idle_cons.yml b/.github/workflows/kill_idle_cons.yml
@@ -33,9 +33,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 
       # Run the action
       - name: Kill idle connections

diff --git a/.github/workflows/refresh_counts.yml b/.github/workflows/refresh_counts.yml
@@ -40,9 +40,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 
       # Refresh
       - name: Refresh counts

diff --git a/.github/workflows/refresh_db.yml b/.github/workflows/refresh_db.yml
@@ -55,9 +55,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 
       # Refresh
       - name: Refresh db

diff --git a/.github/workflows/refresh_from_datasets.yml b/.github/workflows/refresh_from_datasets.yml
@@ -37,9 +37,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 
       # todo: Do we actually need this here?
       #  i. termhub-vocab: Not needed for this i think

diff --git a/.github/workflows/refresh_voc.yml b/.github/workflows/refresh_voc.yml
@@ -40,9 +40,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 
       # Refresh
       - name: Refresh vocab

diff --git a/.github/workflows/resolve_fetch_failures_0_members.yml b/.github/workflows/resolve_fetch_failures_0_members.yml
@@ -43,9 +43,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 
       - name: Resolve fetch failures
         run: |

diff --git a/.github/workflows/resolve_fetch_failures_excess_items.yml b/.github/workflows/resolve_fetch_failures_excess_items.yml
@@ -40,9 +40,10 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
 
       - name: Resolve fetch failures
         run: |

diff --git a/.github/workflows/test_backend_e2e_and_unit_and_qc.yml b/.github/workflows/test_backend_e2e_and_unit_and_qc.yml
@@ -42,10 +42,9 @@ jobs:
           # python -m pip install --upgrade pip
           # pip install --upgrade wheel
           # pip install --upgrade setuptools
+          # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+          # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
+          # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
           pip install -r requirements.txt
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
-          TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2)
-          python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple"
       - name: Run tests
         run: make test-backend
diff --git a/enclave_wrangler/utils.py b/enclave_wrangler/utils.py
@@ -13,7 +13,10 @@
 from datetime import datetime, timezone, timedelta
 from http.client import HTTPConnection
 from requests import Response
-from vshub_sdk.core.api import UserTokenAuth
+try:
+    from vshub_sdk.core.api import UserTokenAuth
+except ModuleNotFoundError:  # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
+    pass
 
 from enclave_wrangler.config import OUTDIR_OBJECTS, config, TERMHUB_VERSION, CSET_VERSION_MIN_ID
 from backend.utils import dump
@@ -48,7 +51,7 @@ class ActionValidateError(RuntimeError):
     """Wrapper just to handle errors from this module"""
 
 
-def get_headers(personal=False, content_type="application/json", for_curl=False, oauth=True):
+def get_headers(personal=False, content_type="application/json", for_curl=False, oauth=False):
     """Format headers for enclave calls
 
     todo: fix all this -- we've been switching back and forth between service token and personal because some APIs are
@@ -116,7 +119,7 @@ def get_oauth_token() -> str:
     return OAUTH_TOKEN if OAUTH_TOKEN_EXPIRES > datetime.now() else refresh_oauth_token()
 
 
-def get_auth_token(oauth=True) -> str:
+def get_auth_token(oauth=False) -> str:
     """Returns the auth token for the N3C Palantir Foundry data enclave."""
     service_user_token: str = config[TOKEN_KEY]
     return get_oauth_token() if oauth else service_user_token
@@ -237,7 +240,7 @@ def handle_response_error(
         })
 
 
-def enclave_get(url: str, verbose: bool = True, args: Dict = {}, error_dir: str = None, oauth=True) -> Response:
+def enclave_get(url: str, verbose: bool = True, args: Dict = {}, error_dir: str = None, oauth=False) -> Response:
     """Get from the enclave and print curl"""
     if verbose:
         print_curl(url, args=args)
@@ -502,7 +505,7 @@ def process_validate_errors(response: Response, err_type: Exception=None, print_
     return out_errors
 
 
-def enclave_post(url: str, data: Union[List, Dict], raise_validate_error: bool=False, verbose=True, oauth=True) -> Response:
+def enclave_post(url: str, data: Union[List, Dict], raise_validate_error: bool=False, verbose=True, oauth=False) -> Response:
     """Post to the enclave and handle / report on some common issues"""
     if verbose:
         print_curl(url, data)

diff --git a/install-requirements.sh b/install-requirements.sh
diff --git a/requirements-unlocked.txt b/requirements-unlocked.txt
@@ -37,4 +37,4 @@ setuptools
 # non-PyPi packages
 # - For the command to install these, consult: install-requirements.sh
 # foundry-sdk-runtime==1.113.0
-# vshub_sdk==0.1.0
+# vshub_sdk==0.1.0  # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863
diff --git a/requirements.txt b/requirements.txt
@@ -211,7 +211,6 @@ validators==0.20.0
 virtualenv==20.15.1
 virtualenv-clone==0.5.7
 virtualenvwrapper==4.8.4
-# vshub_sdk==0.1.0
 watchdog==3.0.0
 watchfiles==0.15.0
 webcolors==1.12