nci-cidc-api-modules 1.0.17__py3-none-any.whl → 1.0.19__py3-none-any.whl

cidc_api/config/settings.py

@@ -62,7 +62,6 @@ DEV_CFUNCTIONS_SERVER = environ.get("DEV_CFUNCTIONS_SERVER")
 ### Configure Auth0 ###
 AUTH0_DOMAIN = environ.get("AUTH0_DOMAIN")
 AUTH0_CLIENT_ID = environ.get("AUTH0_CLIENT_ID")
-ALGORITHMS = ["RS256"]
 
 ### Configure GCP ###
 GOOGLE_CLOUD_PROJECT = environ["GOOGLE_CLOUD_PROJECT"]

cidc_api/models/files/details.py

@@ -957,24 +957,14 @@ details_dict = {
         "TSV-formatted table containing metadata about the run",
         "",
     ),
-    "/mibi/multichannel_image.ome.tiff": FileDetails(
-        "miscellaneous",
+    "/mibi/.ome.tiff": FileDetails(
+        "source",
         "Analysis-ready multilayer OME-TIFF image file",
         "",
     ),
-    "/mibi/cluster_labels.tif": FileDetails(
-        "miscellaneous",
-        "TIF-formatted whole cell segmentation masks for each multiplexed image",
-        "",
-    ),
-    "/mibi/channel_names.csv": FileDetails(
-        "miscellaneous",
-        "CSV-formatted table of each channel and the corresponding mass",
-        "",
-    ),
-    "/mibi/single_cell_table.csv": FileDetails(
-        "miscellaneous",
-        "Single cell data table containing eg integrated expression values, XY location",
+    "/mibi/he_file.": FileDetails(
+        "source",
+        "H and E file from MIBI analysis",
         "",
     ),
 }

cidc_api/models/files/facets.py

@@ -340,20 +340,12 @@ assay_facets: Facets = {
             "TSV-formatted table containing metadata about the run",
         ),
         "Multichannel OME TIFFs": FacetConfig(
-            ["/mibi/multichannel_image.ome.tiff"],
+            ["/mibi/.ome.tiff"],
             "Analysis-ready multilayer OME-TIFF image file",
         ),
-        "Segmentation Masks": FacetConfig(
-            ["/mibi/cluster_labels.tif"],
-            "TIF-formatted whole cell segmentation masks for each multiplexed image",
-        ),
-        "Channel Names": FacetConfig(
-            ["/mibi/channel_names.csv"],
-            "CSV-formatted table of each channel and the corresponding mass",
-        ),
-        "Single-cell Data": FacetConfig(
-            ["/mibi/single_cell_table.csv"],
-            "Single cell data table containing eg integrated expression values, XY location",
+        "H&E File": FacetConfig(
+            ["/mibi/he_file."],
+            "H and E file from MIBI analysis",
         ),
     },
     "mIF": {

cidc_api/models/models.py

@@ -2194,6 +2194,12 @@ class UploadJobs(CommonColumns):
             return None
         return upload
 
+    @classmethod
+    @with_default_session
+    def find_by_trial_id(cls, trial_id: str, session):
+        uploads = session.query(UploadJobs).filter_by(trial_id=trial_id)
+        return uploads
+
     @with_default_session
     def ingestion_success(
         self, trial, session: Session, commit: bool = False, send_email: bool = False
@@ -2803,6 +2809,30 @@ class DownloadableFiles(CommonColumns):
                 )
         return results
 
+    @classmethod
+    @with_default_session
+    def remove_participants_and_samples_info_files(
+        cls, trial_id: str, session: Session
+    ):
+        """
+        Remove participants info and samples info downloadable files
+        """
+        files_to_delete = (
+            session.query(cls)
+            .filter(cls.trial_id == trial_id)
+            .filter(
+                or_(
+                    cls.upload_type == "participants info",
+                    cls.upload_type == "samples info",
+                )
+            )
+            .all()
+        )
+
+        for file in files_to_delete:
+            file.delete(commit=True)
+        session.execute("REFRESH MATERIALIZED VIEW CONCURRENTLY trial_summaries_mv")
+
     @classmethod
     @with_default_session
     def get_trial_facets_with_permissions(

cidc_api/shared/auth.py

@@ -1,19 +1,18 @@
 from functools import wraps
 from typing import List
 
-import requests
 from packaging import version
-from jose import jwt
+
 from flask import g, request, current_app as app, Flask
 from werkzeug.exceptions import Unauthorized, BadRequest, PreconditionFailed
 
 from ..models import Users, UserSchema
-from ..config.settings import AUTH0_DOMAIN, ALGORITHMS, AUTH0_CLIENT_ID
+
 from ..config.logging import get_logger
 
-logger = get_logger(__name__)
+from ..shared.jose import decode_id_token
 
-TIMEOUT_IN_SECONDS = 20
+logger = get_logger(__name__)
 
 
 ### Main auth utility functions ###
@@ -147,8 +146,7 @@ _user_schema = UserSchema()
 
 def authenticate() -> Users:
     id_token = _extract_token()
-    public_key = _get_issuer_public_key(id_token)
-    token_payload = _decode_id_token(id_token, public_key)
+    token_payload = decode_id_token(id_token)
     profile = {"email": token_payload["email"]}
     return _user_schema.load(profile)
 
@@ -173,87 +171,6 @@ def _extract_token() -> str:
     return id_token
 
 
-def _get_issuer_public_key(token: str) -> dict:
-    """
-    Get the appropriate public key to check this token for authenticity.
-
-    Args:
-        token: an encoded JWT.
-
-    Raises:
-        Unauthorized: if no public key can be found.
-
-    Returns:
-        str: the public key.
-    """
-    try:
-        header = jwt.get_unverified_header(token)
-    except jwt.JWTError as e:
-        raise Unauthorized(str(e)) from e
-
-    # Get public keys from our Auth0 domain
-    jwks_url = f"https://{AUTH0_DOMAIN}/.well-known/jwks.json"
-    jwks = requests.get(jwks_url, timeout=TIMEOUT_IN_SECONDS).json()
-
-    # Obtain the public key used to sign this token
-    public_key = None
-    for key in jwks["keys"]:
-        if key["kid"] == header["kid"]:
-            public_key = key
-
-    # If no matching public key was found, we can't validate the token
-    if not public_key:
-        raise Unauthorized(f"Found no public key with id {header['kid']}")
-
-    return public_key
-
-
-def _decode_id_token(token: str, public_key: dict) -> dict:
-    """
-    Decodes the token and checks it for validity.
-
-    Args:
-        token: the JWT to validate and decode
-        public_key: public_key
-
-    Raises:
-        Unauthorized:
-            - if token is expired
-            - if token has invalid claims
-            - if token signature is invalid in any way
-            - if no `.email` field on token
-
-    Returns:
-        dict: the decoded token as a dictionary.
-    """
-    try:
-        payload = jwt.decode(
-            token,
-            public_key,
-            algorithms=ALGORITHMS,
-            audience=AUTH0_CLIENT_ID,
-            issuer=f"https://{AUTH0_DOMAIN}/",
-            options={"verify_at_hash": False},
-        )
-    except jwt.ExpiredSignatureError as e:
-        raise Unauthorized(
-            f"{e} Token expired. Obtain a new login token from the CIDC Portal, then try logging in again."
-        ) from e
-    except jwt.JWTClaimsError as e:
-        raise Unauthorized(str(e)) from e
-    except jwt.JWTError as e:
-        raise Unauthorized(str(e)) from e
-
-    # Currently, only id_tokens are accepted for authentication.
-    # Going forward, we could also accept access tokens that we
-    # use to query the userinfo endpoint.
-    if "email" not in payload:
-        msg = "An id_token with an 'email' field is required to authenticate"
-        raise Unauthorized(msg)
-
-    return payload
-
-
 ### Authorization logic ###
 def authorize(
     user: Users, allowed_roles: List[str], resource: str, method: str

cidc_api/shared/jose.py

@@ -0,0 +1,72 @@
+# external modules
+import requests
+from joserfc import jwt
+from joserfc.jwk import RSAKey
+from werkzeug.exceptions import Unauthorized
+from cachetools import cached, TTLCache
+
+# loacal modules
+from ..config.settings import AUTH0_DOMAIN, AUTH0_CLIENT_ID
+
+
+ALGORITHMS = ["RS256"]
+TIMEOUT_IN_SECONDS = 20
+PUBLIC_KEYS_CACHE = TTLCache(maxsize=3600, ttl=1024)  # 1 hour, 1 MB
+
+
+@cached(cache=PUBLIC_KEYS_CACHE)
+def get_jwks() -> list:
+    # get jwks from our Auth0 domain
+    return requests.get(
+        f"https://{AUTH0_DOMAIN}/.well-known/jwks.json", timeout=TIMEOUT_IN_SECONDS
+    ).json()
+
+
+def decode_id_token(token: str) -> dict:
+    """
+    Decodes the token and checks it for validity.
+
+    Args:
+        token: the JWT to validate and decode
+
+    Raises:
+        Unauthorized:
+            - if token is expired
+            - if token has invalid claims (email, aud and iss)
+            - if token signature is invalid
+
+    Returns:
+        dict: claims as a dictionary.
+    """
+
+    jwks = get_jwks()["keys"]
+    if not jwks:
+        raise Unauthorized("No public keys found")
+
+    decoded_token = False
+
+    for jwk in jwks:
+        if decoded_token:
+            continue
+        try:
+            key = RSAKey.import_key(jwk)
+            decoded_token = jwt.decode(token, key, ALGORITHMS)
+        except Exception as e:
+            pass
+
+    if decoded_token:
+        claims = decoded_token.claims
+    else:
+        raise Unauthorized("No valid public key found")
+
+    try:
+        claims_requests = jwt.JWTClaimsRegistry(
+            iss={"essential": True, "value": f"https://{AUTH0_DOMAIN}/"},
+            aud={"essential": True, "value": AUTH0_CLIENT_ID},
+            email={"essential": True},
+        )
+        claims_requests.validate(claims)
+    except Exception as e:
+        raise Unauthorized(str(e)) from e
+
+    return claims

{nci_cidc_api_modules-1.0.17.dist-info → nci_cidc_api_modules-1.0.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_api_modules
-Version: 1.0.17
+Version: 1.0.19
 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

{nci_cidc_api_modules-1.0.17.dist-info → nci_cidc_api_modules-1.0.19.dist-info}/RECORD

@@ -2,24 +2,25 @@ cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,1
 cidc_api/config/db.py,sha256=ayeeNV-sV20hGoFyMMTMncI2V-FI9lVN3JV-Lmpr3xI,1981
 cidc_api/config/logging.py,sha256=gJ2TGgQVREng4Hv0phlCCkQai7HhumKYjJxubpxS6Q0,1090
 cidc_api/config/secrets.py,sha256=2DXeew1Pm0lnf2SLuo8wW5c5kOJp2WrhjflxZGsY_Ng,1505
-cidc_api/config/settings.py,sha256=Ua6UpiQu9l1ZD-YlmpaWuQOv9tPyYLxWFLC2DEJdAyQ,4044
+cidc_api/config/settings.py,sha256=2VHOVWdN4yUCNYMob2gaWgH2-1_4sbuo46JEIVT_PCY,4021
 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=Wp4b53vwOqSlOIaoAYGlI1p8ZfXRXmVJ6MLcsvzq0LA,31664
 cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
-cidc_api/models/models.py,sha256=Hjp9sieGdldNbUzneFi-7vRYyo9wwr0D-0m_UbxsDEk,124106
+cidc_api/models/models.py,sha256=SBVbIUbkeUSAA2jl-3IL93HDdR8tRrTHYQ80nH_8gq0,125025
 cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
 cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
-cidc_api/models/files/details.py,sha256=DimrGmyL216j9eB47ZlX19b5GANf2nrD_crl79RPgqg,62699
-cidc_api/models/files/facets.py,sha256=n2Xi4zaC2pcJQw31gOLFxnF0nwtUBIkvw-5Th21-5uQ,29403
+cidc_api/models/files/details.py,sha256=h6R0p_hi-ukHsO7HV-3Wukccp0zRLJ1Oie_JNA_7Pl0,62274
+cidc_api/models/files/facets.py,sha256=0owlp-is2QJ7DemcsJ4VdlnN255NkkV1Cimg0VaXHpY,28967
 cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cidc_api/shared/auth.py,sha256=VMd_3QJE2iG16QxuGzHBV9MzJJItOZNn9gcw0_iUBLI,11647
+cidc_api/shared/auth.py,sha256=EzMpYAR_gN5x985hgFAXTd24xygyctqZ80Yp05Ph_HQ,9104
 cidc_api/shared/emails.py,sha256=5dyuKlpcg1M4P_RrAt0ss2hiCqb-Y7p2XXR1d9uBXg8,4868
 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-1.0.17.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
-nci_cidc_api_modules-1.0.17.dist-info/METADATA,sha256=s-VGHMZCidyAeiQWFl4IP7XjZPgpDZzK2ESu3TmwPUc,40673
-nci_cidc_api_modules-1.0.17.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
-nci_cidc_api_modules-1.0.17.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
-nci_cidc_api_modules-1.0.17.dist-info/RECORD,,
+nci_cidc_api_modules-1.0.19.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.0.19.dist-info/METADATA,sha256=cYPVMMJcy0KeUbdFLmchOSZc4EM16gjepAAgxPtQAXc,40673
+nci_cidc_api_modules-1.0.19.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
+nci_cidc_api_modules-1.0.19.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.0.19.dist-info/RECORD,,

{nci_cidc_api_modules-1.0.17.dist-info → nci_cidc_api_modules-1.0.19.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (71.1.0)
+Generator: setuptools (72.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any