Merge pull request #1349 from microbiomedata/main

Merge `main` into `berkeley-schema-migration`

Author: eecavanna

.env.example

@@ -7,6 +7,11 @@
 # ORCID OAuth Setup
 # NMDC_ORCID_CLIENT_ID=changeme
 # NMDC_ORCID_CLIENT_SECRET=changeme
+#
+# Base URL (without a trailing slash) at which the application can access an instance of ORCID.
+# Note: For the production instance of ORCID, use: "https://orcid.org" (default)
+#       For the sandbox instance of ORCID, use: "https://sandbox.orcid.org"
+# NMDC_ORCID_BASE_URL="https://orcid.org"
 
 # MongoDB Ingest Setup
 # NMDC_MONGO_USER=changeme

docs/development.md

@@ -31,7 +31,7 @@ NMDC_ORCID_CLIENT_SECRET=changeme
 ```bash
 NMDC_SESSION_SECRET_KEY=changeme
 NMDC_API_JWT_SECRET=changeme
-
+```
 ### Production Redirect URIs
 
 These are the set of redirect URIs enabled in ORCiD. We need to file a support ticket with ORCID to modify these.

nmdc_server/api.py

@@ -633,8 +633,10 @@ async def list_submissions(
     db: Session = Depends(get_db),
     user: models.User = Depends(get_current_user),
     pagination: Pagination = Depends(),
+    column_sort: str = "created",
+    sort_order: str = "desc",
 ):
-    query = crud.get_submissions_for_user(db, user)
+    query = crud.get_submissions_for_user(db, user, column_sort, sort_order)
     return pagination.response(query)
 
 
@@ -671,6 +673,8 @@ async def get_submission(
             created=submission.created,
             author=schemas.User(**submission.author.__dict__),
             permission_level=permission_level,
+            templates=submission.templates,
+            study_name=submission.study_name,
         )
         if submission.locked_by is not None:
             submission_metadata_schema.locked_by = schemas.User(**submission.locked_by.__dict__)
@@ -938,8 +942,14 @@ async def submit_metadata(
     db: Session = Depends(get_db),
     user: models.User = Depends(get_current_user),
 ):
-    submission = SubmissionMetadata(**body.dict(), author_orcid=user.orcid)
+    submission = SubmissionMetadata(
+        **body.dict(),
+        author_orcid=user.orcid,
+    )
     submission.author_id = user.id
+    submission.study_name = body.metadata_submission.studyForm.studyName
+    submission.templates = body.metadata_submission.templates
+
     db.add(submission)
     db.commit()
     owner_role = SubmissionRole(

nmdc_server/auth.py

@@ -58,7 +58,7 @@
 )
 
 API_JWT_ALGORITHM = "HS256"
-ORCID_JWT_ISSUER = "https://orcid.org"
+ORCID_JWT_ISSUER = settings.orcid_base_url  # e.g. "https://orcid.org", "https://sandbox.orcid.org"
 
 
 class JwtTypes(str, Enum):

nmdc_server/config.py

@@ -33,11 +33,24 @@ class Settings(BaseSettings):
 
     # for orcid oauth
     session_secret_key: str = "secret"
+    orcid_base_url: str = "https://orcid.org"
     orcid_client_id: str = "oauth client id"
     orcid_client_secret: str = "oauth secret key"
-    orcid_openid_config_url: str = "https://orcid.org/.well-known/openid-configuration"
     orcid_authorize_scope: str = "/authenticate"
 
+    @property
+    def orcid_openid_config_url(self) -> str:
+        r"""
+        Derives the `orcid_openid_config_url` field's value based upon another field's value.
+        Note: This project currently depends upon Pydantic version 1, which does not offer
+              the `@computed_field` decorator offered by Pydantic version 2. So, we implement
+              a "getter" method using Python's built-in `@property` decorator instead.
+              References:
+              - https://docs.python.org/3/library/functions.html#property
+              - https://docs.pydantic.dev/2.7/concepts/fields/#the-computed_field-decorator
+        """
+        return f"{self.orcid_base_url}/.well-known/openid-configuration"
+
     # host name for the ORCID oauth2 redirect and our own JWT issuer
     host: str = "http://127.0.0.1:8000"
 

nmdc_server/crud.py

@@ -629,10 +629,18 @@ def can_edit_entire_submission(db: Session, submission_id: str, user_orcid: str)
     return (role and models.SubmissionEditorRole(role.role) in contributors_edit_roles) is True
 
 
-def get_submissions_for_user(db: Session, user: models.User):
+def get_submissions_for_user(db: Session, user: models.User, column_sort: str, order: str):
     """Return all submissions that a user has permission to view."""
-    all_submissions = db.query(models.SubmissionMetadata).order_by(
-        models.SubmissionMetadata.created.desc()
+    column = (
+        models.User.name
+        if column_sort == "author.name"
+        else getattr(models.SubmissionMetadata, column_sort)
+    )
+
+    all_submissions = (
+        db.query(models.SubmissionMetadata)
+        .join(models.User, models.SubmissionMetadata.author_id == models.User.id)
+        .order_by(column.asc() if order == "asc" else column.desc())
     )
 
     if user.is_admin:

nmdc_server/fakes.py

@@ -345,6 +345,8 @@ class Meta:
     author = SubFactory(UserFactory)
     author_orcid = Faker("pystr")
     status = "In Progress"
+    study_name = Faker("word")
+    templates = Faker("pylist", nb_elements=2, value_types=[str])
     created = datetime.utcnow()
     # TODO specify all fields!
     metadata_submission = {

nmdc_server/migrations/versions/0ff690fb929d_add_study_name_and_template_columns_to_.py

@@ -0,0 +1,65 @@
+"""Add study_name and template columns to submission_metadata
+
+Revision ID: 0ff690fb929d
+Revises: c0b36f8dc4b8
+Create Date: 2024-08-01 16:01:05.023371
+
+"""
+
+from typing import Optional
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "0ff690fb929d"
+down_revision: Optional[str] = "c0b36f8dc4b8"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("submission_metadata", sa.Column("study_name", sa.String(), nullable=True))
+    op.add_column(
+        "submission_metadata",
+        sa.Column("templates", JSONB(astext_type=sa.Text()), nullable=True),  # type:ignore
+    )
+    submission_metadata = table(
+        "submission_metadata",
+        column("id", sa.String),
+        column("metadata_submission", JSONB),
+        column("study_name", sa.String),
+        column("templates", JSONB),
+    )
+
+    connection = op.get_bind()
+    submissions = connection.execute(
+        sa.select([submission_metadata.c.id, submission_metadata.c.metadata_submission])
+    )
+
+    for submission in submissions:
+        study_name = submission.metadata_submission["studyForm"].get("studyName")
+        templates = submission.metadata_submission.get("templates")
+        if study_name:
+            connection.execute(
+                submission_metadata.update()
+                .where(submission_metadata.c.id == submission.id)
+                .values(study_name=study_name)
+            )
+        if templates:
+            connection.execute(
+                submission_metadata.update()
+                .where(submission_metadata.c.id == submission.id)
+                .values(templates=templates)
+            )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("submission_metadata", "templates")
+    op.drop_column("submission_metadata", "study_name")
+    # ### end Alembic commands ###

nmdc_server/models.py

@@ -851,6 +851,8 @@ class SubmissionMetadata(Base):
     status = Column(String, nullable=False, default="in-progress")
     metadata_submission = Column(JSONB, nullable=False)
     author_id = Column(UUID(as_uuid=True), ForeignKey(User.id))
+    study_name = Column(String, nullable=True)
+    templates = Column(JSONB, nullable=True)
 
     # The client which initially created the submission. A null value indicates it was created by
     # an "unregistered" client. This could be legitimate usage, but it should be monitored.

nmdc_server/schemas_submission.py

@@ -111,6 +111,8 @@ class SubmissionMetadataSchema(SubmissionMetadataSchemaCreate):
     created: datetime
     status: str
     author: schemas.User
+    templates: List[str]
+    study_name: Optional[str]
 
     lock_updated: Optional[datetime]
     locked_by: Optional[schemas.User]