WIP project/permission

server/src/scimodom/app.py

@@ -19,6 +19,7 @@
     add_annotation,
     add_assembly,
     add_project,
+    add_user_to_project,
     add_dataset,
     add_all,
     validate_dataset_title,
@@ -113,12 +114,34 @@ def annotation(id):
         "project", epilog="Check docs at https://dieterich-lab.github.io/scimodom/."
     )
     @click.argument("template", type=click.Path(exists=True))
-    def project(template):
+    @click.option(
+        "--skip-add-user",
+        is_flag=True,
+        show_default=True,
+        default=False,
+        help="Do not add user to project.",
+    )
+    def project(template, skip_add_user):
         """Add a new project to the database.
 
         TEMPLATE is the path to a project template (json).
         """
-        add_project(template)
+        add_user = not skip_add_user
+        add_project(template, add_user=add_user)
+
+    @app.cli.command(
+        "permission", epilog="Check docs at https://dieterich-lab.github.io/scimodom/."
+    )
+    @click.argument("username", type=click.STRING)
+    @click.argument("smid", type=click.STRING)
+    def permission(username, smid):
+        """Force add a user to a project.
+
+        \b
+        USERNAME is the user email.
+        SMID is the project ID to which this user is to be associated.
+        """
+        add_user_to_project(username, smid)
 
     @app.cli.command(
         "dataset", epilog="Check docs at https://dieterich-lab.github.io/scimodom/."

server/src/scimodom/plugins/cli.py

@@ -5,10 +5,12 @@
 import traceback
 
 import click
+from sqlalchemy import select
 
 from scimodom.config import Config
 from scimodom.database.database import get_session
 from scimodom.database.models import (
+    Project,
     Dataset,
     Modification,
     DetectionTechnology,
@@ -18,9 +20,10 @@
 import scimodom.database.queries as queries
 from scimodom.services.annotation import AnnotationService
 from scimodom.services.assembly import AssemblyService
-from scimodom.services.project import ProjectService
+from scimodom.services.project import get_project_service
 from scimodom.services.dataset import DataService
 from scimodom.services.setup import get_setup_service
+from scimodom.services.user import get_user_service, NoSuchUser
 import scimodom.utils.utils as utils
 
 
@@ -97,14 +100,15 @@ def add_annotation(annotation_id: int) -> None:
     session.close()
 
 
-def add_project(project_template: str | Path) -> None:
+def add_project(project_template: str | Path, add_user: bool = True) -> None:
     """Provides a CLI function to add a new project.
 
     :param project_template: Path to a json file with
     require fields.
     :type project_template: str or Path
+    :param add_user: Associate user and newly created project
+    :type add_user: bool
     """
-    session = get_session()
     # load project metadata
     project = json.load(open(project_template))
     # add project
@@ -115,13 +119,72 @@ def add_project(project_template: str | Path) -> None:
     c = click.getchar()
     if c not in ["y", "Y"]:
         return
-    service = ProjectService(session, project)
-    service.create_project()
+    project_service = get_project_service()
+    project_service.create_project(project)
     click.secho(
-        f"Successfully created. The SMID for this project is {service.get_smid()}.",
+        f"Successfully created. The SMID for this project is {project_service.get_smid()}.",
         fg="green",
     )
-    session.close()
+    if add_user:
+        username = project["contact_email"]
+        click.secho(f"Adding user {username} to newly created project...", fg="green")
+        click.secho("Continue [y/n]?", fg="green")
+        c = click.getchar()
+        if c not in ["y", "Y"]:
+            return
+        user_service = get_user_service()
+        try:
+            user = user_service.get_user_by_email(username)
+        except NoSuchUser:
+            click.secho(
+                f"Unknown user {username}... Aborting!",
+                fg="red",
+            )
+        else:
+            project_service.associate_project_to_user(user)
+            click.secho(
+                "Successfully added user to project.",
+                fg="green",
+            )
+
+
+def add_user_to_project(username: str, smid: str) -> None:
+    """Provides a CLI function to force add a user to a project.
+
+    :param username: Username (email)
+    :type username: str
+    :param smid: SMID
+    :type smid: str
+    """
+    session = get_session()
+    click.secho(f"Adding user {username} to {smid}...", fg="green")
+    click.secho("Continue [y/n]?", fg="green")
+    c = click.getchar()
+    if c not in ["y", "Y"]:
+        return
+    project_service = get_project_service()
+    user_service = get_user_service()
+    try:
+        user = user_service.get_user_by_email(username)
+    except NoSuchUser:
+        click.secho(
+            f"Unknown user {username}... Aborting!",
+            fg="red",
+        )
+    else:
+        query = select(Project.id)
+        smids = session.execute(query).scalars().all()
+        if smid not in smids:
+            click.secho(
+                f"Unrecognised SMID {smid}... Aborting!",
+                fg="red",
+            )
+            return
+        project_service.associate_project_to_user(user, smid=smid)
+        click.secho(
+            "Successfully added user to project.",
+            fg="green",
+        )
 
 
 def add_dataset(
@@ -210,8 +273,8 @@ def add_all(directory: Path, templates: list[str]) -> None:
         project_title = project["title"]
         click.secho(f"Adding {project_title}...", fg="green")
         try:
-            project_service = ProjectService(session, project)
-            project_service.create_project()
+            project_service = get_project_service()
+            project_service.create_project(project)
             smid = project_service.get_smid()
             metadata = _get_dataset(project, extra_cols["file"])
             for filen, meta in metadata.items():

server/src/scimodom/services/permission.py

@@ -9,7 +9,7 @@
 
 class PermissionService:
     def __init__(self, session: Session):
-        self._db_session = session
+        self._session = session
 
     def may_change_dataset(self, user: User, dataset: Dataset) -> bool:
         query = select(UserProjectAssociation).where(
@@ -18,9 +18,23 @@ def may_change_dataset(self, user: User, dataset: Dataset) -> bool:
                 UserProjectAssociation.project_id == dataset.project_id,
             )
         )
-        results = self._db_session.execute(query).fetchall()
+        results = self._session.execute(query).fetchall()
         return len(results) > 0
 
+    def insert_into_user_project_association(self, user: User, project_id: str) -> None:
+        """Insert values into table.
+
+        :param user: User
+        :type user: User
+        :param project_id: SMID. There is no check
+        on the validity of this value, this must be done
+        before calling this function.
+        :type project_id: str
+        """
+        permission = UserProjectAssociation(user_id=user.id, project_id=project_id)
+        self._session.add(permission)
+        self._session.commit()
+
 
 _cached_permission_service: Optional[PermissionService] = None
 

server/src/scimodom/services/project.py

@@ -4,12 +4,13 @@
 import json
 import logging
 from pathlib import Path
-from typing import ClassVar
+from typing import ClassVar, Optional
 
 from sqlalchemy.orm import Session
 from sqlalchemy import select, func
 
 from scimodom.config import Config
+from scimodom.database.database import get_session
 from scimodom.database.models import (
     Project,
     ProjectSource,
@@ -18,10 +19,12 @@
     DetectionTechnology,
     Organism,
     Selection,
+    User,
 )
 import scimodom.database.queries as queries
 from scimodom.services.annotation import AnnotationService
 from scimodom.services.assembly import AssemblyService
+from scimodom.services.permission import get_permission_service
 import scimodom.utils.specifications as specs
 import scimodom.utils.utils as utils
 
@@ -35,12 +38,10 @@ class DuplicateProjectError(Exception):
 
 
 class ProjectService:
-    """Utility class to create a project.
+    """Utility class to create/manage a project.
 
     :param session: SQLAlchemy ORM session
     :type session: Session
-    :param project: Project description (json template)
-    :type project: dict
     :param SMID_LENGTH: Length of Sci-ModoM ID (SMID)
     :type SMID_LENGTH: int
     :param DATA_PATH: Data path
@@ -54,14 +55,15 @@ class ProjectService:
     DATA_SUB_PATH: ClassVar[str] = "metadata"
     DATA_SUB_PATH_SUB: ClassVar[str] = "project_requests"
 
-    def __init__(self, session: Session, project: dict) -> None:
+    def __init__(self, session: Session) -> None:
         """Initializer method."""
         self._session = session
-        self._project = project
+
+        self._project: dict
         self._smid: str
         self._assemblies: set[tuple[int, str]] = set()
 
-    def __new__(cls, session: Session, project: dict):
+    def __new__(cls, session: Session):
         """Constructor method."""
         if cls.DATA_PATH is None:
             msg = "Missing environment variable: DATA_PATH. Terminating!"
@@ -121,8 +123,16 @@ def create_project_request(project: dict):
             json.dump(project, f, indent="\t")
         return uuid
 
-    def create_project(self, wo_assembly: bool = False) -> None:
-        """Project constructor."""
+    def create_project(self, project: dict, wo_assembly: bool = False) -> None:
+        """Project constructor.
+
+        :param project: Project description (json template)
+        :type project: dict
+        :param wo_assembly: Skip assembly set up
+        :type wo_assembly: bool
+        """
+        self._project = project
+
         self._validate_keys()
         self._validate_entry()
         self._add_selection()
@@ -141,13 +151,39 @@ def create_project(self, wo_assembly: bool = False) -> None:
                     session=self._session, taxa_id=taxid
                 ).create_annotation()
 
+    def associate_project_to_user(self, user: User, smid: str | None = None):
+        """Associate a project to a user.
+        When called after project creation, the SMID is
+        available (default), else nothing is done, unless
+        it is passed as argument.
+
+        :param smid: SMID. There is no check
+        on the validity of this value, this must be done
+        before calling this function.
+        :type smid: str
+        """
+        if not smid:
+            try:
+                smid = self._smid
+            except AttributeError:
+                msg = "Undefined SMID. Nothing will be done."
+                logger.warning(msg)
+                return
+        permission_service = get_permission_service()
+        permission_service.insert_into_user_project_association(user, smid)
+
     def get_smid(self) -> str:
-        """Return newly created SMID.
+        """Return newly created SMID, else
+        raises a ValueError.
 
         :returns: SMID
         :rtype: str
         """
-        return self._smid
+        try:
+            return self._smid
+        except AttributeError:
+            msg = "Undefined SMID. This is only defined when creating a project."
+            raise AttributeError(msg)
 
     def _validate_keys(self) -> None:
         """Validate keys from project description (dictionary)."""
@@ -353,3 +389,18 @@ def _write_metadata(self) -> None:
         parent = Path(self.DATA_PATH, self.DATA_SUB_PATH)
         with open(Path(parent, f"{self._smid}.json"), "w") as f:
             json.dump(self._project, f, indent="\t")
+
+
+_cached_project_service: Optional[ProjectService] = None
+
+
+def get_project_service():
+    """Helper function to set up a ProjectService object by injecting its dependencies.
+
+    :returns: Project service instance
+    :rtype: ProjectService
+    """
+    global _cached_project_service
+    if _cached_project_service is None:
+        _cached_project_service = ProjectService(session=get_session())
+    return _cached_project_service

server/tests/unit/services/test_permission.py

@@ -0,0 +1,45 @@
+from datetime import datetime, timezone
+
+import pytest
+from sqlalchemy import select
+
+from scimodom.services.permission import PermissionService
+from scimodom.database.models import (
+    User,
+    UserState,
+    Project,
+    ProjectContact,
+    UserProjectAssociation,
+)
+
+
+def test_insert_user_project_association(Session):
+    stamp = datetime.now(timezone.utc).replace(microsecond=0)
+    with Session() as session, session.begin():
+        contact = ProjectContact(
+            contact_name="contact_name",
+            contact_institution="contact_institution",
+            contact_email="contact@email",
+        )
+        user = User(email="contact@email", state=UserState.active, password_hash="xxx")
+        session.add_all([contact, user])
+        session.flush()
+        contact_id = contact.id
+        project = Project(
+            id="12345678",
+            title="title",
+            summary="summary",
+            contact_id=contact_id,
+            date_published=datetime.fromisoformat("2024-01-01"),
+            date_added=stamp,
+        )
+        session.add(project)
+        session.flush()
+        smid = project.id
+
+        service = PermissionService(Session())
+        service.insert_into_user_project_association(user, smid)
+
+        records = session.execute(select(UserProjectAssociation)).scalar()
+        assert records.user_id == user.id
+        assert records.project_id == smid