Add missing modules

Copy over missing modules and functions to completely disconnect
gn-auth from GN3.

5 files changed, 245 insertions, 1 deletions

diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py
index 9e55dd8..03b416f 100644
--- a/gn_auth/auth/authorisation/data/views.py
+++ b/gn_auth/auth/authorisation/data/views.py
@@ -11,9 +11,9 @@ from authlib.integrations.flask_oauth2.errors import _HTTPException
 from flask import request, jsonify, Response, Blueprint, current_app as app
 
 import gn_auth.auth.db.mariadb as gn3db
+
 from gn_auth import jobs
 from gn_auth.commands import run_async_cmd
-from gn_auth.db.traits import build_trait_name
 
 from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.db.sqlite3 import with_db_connection
@@ -39,6 +39,34 @@ from gn_auth.auth.authorisation.data.genotypes import (
 
 data = Blueprint("data", __name__)
 
+def build_trait_name(trait_fullname):
+    """
+    Initialises the trait's name, and other values from the search data provided
+
+    This is a copy of `gn3.db.traits.build_trait_name` function.
+    """
+    def dataset_type(dset_name):
+        if dset_name.find('Temp') >= 0:
+            return "Temp"
+        if dset_name.find('Geno') >= 0:
+            return "Geno"
+        if dset_name.find('Publish') >= 0:
+            return "Publish"
+        return "ProbeSet"
+
+    name_parts = trait_fullname.split("::")
+    assert len(name_parts) >= 2, f"Name format error: '{trait_fullname}'"
+    dataset_name = name_parts[0]
+    dataset_type = dataset_type(dataset_name)
+    return {
+        "db": {
+            "dataset_name": dataset_name,
+            "dataset_type": dataset_type},
+        "trait_fullname": trait_fullname,
+        "trait_name": name_parts[1],
+        "cellid": name_parts[2] if len(name_parts) == 3 else ""
+    }
+
 @data.route("species")
 def list_species() -> Response:
     """List all available species information."""
diff --git a/gn_auth/commands.py b/gn_auth/commands.py
new file mode 100644
index 0000000..d6f6f56
--- /dev/null
+++ b/gn_auth/commands.py
@@ -0,0 +1,64 @@
+"""Procedures used to work with the various bio-informatics cli
+commands"""
+import sys
+import json
+import subprocess
+from uuid import uuid4
+from datetime import datetime
+from typing import Dict, Optional, Tuple, Union, Sequence
+
+
+from redis.client import Redis
+
+def queue_cmd(conn: Redis,
+              job_queue: str,
+              cmd: Union[str, Sequence[str]],
+              email: Optional[str] = None,
+              env: Optional[dict] = None) -> str:
+    """Given a command CMD; (optional) EMAIL; and a redis connection CONN, queue
+it in Redis with an initial status of 'queued'.  The following status codes
+are supported:
+
+    queued:  Unprocessed; Still in the queue
+    running: Still running
+    success: Successful completion
+    error:   Erroneous completion
+
+Returns the name of the specific redis hash for the specific task.
+
+    """
+    if not conn.ping():
+        raise RedisConnectionError
+    unique_id = ("cmd::"
+                 f"{datetime.now().strftime('%Y-%m-%d%H-%M%S-%M%S-')}"
+                 f"{str(uuid4())}")
+    conn.rpush(job_queue, unique_id)
+    for key, value in {
+            "cmd": json.dumps(cmd), "result": "", "status": "queued"}.items():
+        conn.hset(name=unique_id, key=key, value=value)
+    if email:
+        conn.hset(name=unique_id, key="email", value=email)
+    if env:
+        conn.hset(name=unique_id, key="env", value=json.dumps(env))
+    return unique_id
+
+def run_cmd(cmd: str, success_codes: Tuple = (0,), env: str = None) -> Dict:
+    """Run CMD and return the CMD's status code and output as a dict"""
+    parsed_cmd = json.loads(cmd)
+    parsed_env = (json.loads(env) if env is not None else None)
+    results = subprocess.run(
+        parsed_cmd, capture_output=True, shell=isinstance(parsed_cmd, str),
+        check=False, env=parsed_env)
+    out = str(results.stdout, 'utf-8')
+    if results.returncode not in success_codes:  # Error!
+        out = str(results.stderr, 'utf-8')
+    return {"code": results.returncode, "output": out}
+
+def run_async_cmd(
+        conn: Redis, job_queue: str, cmd: Union[str, Sequence[str]],
+        email: Optional[str] = None, env: Optional[dict] = None) -> str:
+    """A utility function to call `gn3.commands.queue_cmd` function and run the
+    worker in the `one-shot` mode."""
+    cmd_id = queue_cmd(conn, job_queue, cmd, email, env)
+    subprocess.Popen([f"{sys.executable}", "-m", "sheepdog.worker"]) # pylint: disable=[consider-using-with]
+    return cmd_id
diff --git a/gn_auth/jobs.py b/gn_auth/jobs.py
new file mode 100644
index 0000000..6fc9bba
--- /dev/null
+++ b/gn_auth/jobs.py
@@ -0,0 +1,61 @@
+"""Handle external processes in a consistent manner."""
+import json
+from typing import Any
+from uuid import UUID, uuid4
+from datetime import datetime
+
+from redis import Redis
+from pymonad.either import Left, Right, Either
+
+from gn_auth import json_encoders_decoders as jed
+
+JOBS_NAMESPACE = "GN3_AUTH::JOBS"
+
+class InvalidCommand(Exception):
+    """Raise if the command to run is invalid."""
+
+def job_key(job_id: UUID, namespace_prefix: str = JOBS_NAMESPACE):
+    """Build the namespace key for a specific job."""
+    return f"{namespace_prefix}::{job_id}"
+
+def job(redisconn: Redis, job_id: UUID) -> Either:
+    """Retrive the job details of a job identified by `job_id`."""
+    the_job = redisconn.hgetall(job_key(job_id))
+    if the_job:
+        return Right({
+            key: json.loads(value, object_hook=jed.custom_json_decoder)
+            for key, value in the_job.items()
+        })
+    return Left({
+        "error": "NotFound",
+        "error_description": f"Job '{job_id}' was not found."
+    })
+
+def __command_valid__(job_command: Any) -> Either:
+    if not isinstance(job_command, list):
+        return Left({
+            "error": "InvalidJobCommand",
+            "error_description": "The job command MUST be a list."
+        })
+    if not all((isinstance(val, str) for val in job_command)):
+        return Left({
+            "error": "InvalidJobCommand",
+            "error_description": "All parts of the command MUST be strings."
+        })
+    return Right(job_command)
+
+def create_job(redisconn: Redis, job_details: dict[str, Any]) -> UUID:
+    """Create a new job and put it on Redis."""
+    def __create__(_job_command):
+        job_id = job_details.get("job_id", uuid4())
+        redisconn.hset(job_key(job_id), mapping={
+            key: json.dumps(value, cls=jed.CustomJSONEncoder) for key, value in {
+                **job_details, "job_id": job_id, "created": datetime.now(),
+                "status": "queued"
+            }.items()
+        })
+        return job_id
+    def __raise__(err):
+        raise InvalidCommand(err["error_description"])
+    return __command_valid__(job_details.get("command")).either(
+        __raise__, __create__)
diff --git a/gn_auth/json_encoders_decoders.py b/gn_auth/json_encoders_decoders.py
new file mode 100644
index 0000000..be15b34
--- /dev/null
+++ b/gn_auth/json_encoders_decoders.py
@@ -0,0 +1,31 @@
+"""Custom json encoders for various purposes."""
+import json
+from uuid import UUID
+from datetime import datetime
+
+__ENCODERS__ = {
+    UUID: lambda obj: {"__type": "UUID", "__value": str(obj)},
+    datetime: lambda obj: {"__type": "DATETIME", "__value": obj.isoformat()}
+}
+
+class CustomJSONEncoder(json.JSONEncoder):
+    """
+    A custom JSON encoder to handle cases where the default encoder fails.
+    """
+    def default(self, obj):# pylint: disable=[arguments-renamed]
+        """Return a serializable object for `obj`."""
+        if type(obj) in __ENCODERS__:
+            return __ENCODERS__[type(obj)](obj)
+        return json.JSONEncoder.default(self, obj)
+
+
+__DECODERS__ = {
+    "UUID": UUID,
+    "DATETIME": datetime.fromisoformat
+}
+
+def custom_json_decoder(obj_dict):
+    """Decode custom types"""
+    if "__type" in obj_dict:
+        return __DECODERS__[obj_dict["__type"]](obj_dict["__value"])
+    return obj_dict
diff --git a/gn_auth/session.py b/gn_auth/session.py
new file mode 100644
index 0000000..7226ac5
--- /dev/null
+++ b/gn_auth/session.py
@@ -0,0 +1,60 @@
+"""Handle any GN3 sessions."""
+from functools import wraps
+from datetime import datetime, timezone, timedelta
+
+from flask import flash, request, session, url_for, redirect
+
+__SESSION_KEY__ = "GN::AUTH::session_details"
+
+def __session_expired__():
+    """Check whether the session has expired."""
+    return datetime.now(tz=timezone.utc) >= session[__SESSION_KEY__]["expires"]
+
+def logged_in(func):
+    """Verify the user is logged in."""
+    @wraps(func)
+    def __logged_in__(*args, **kwargs):
+        if bool(session.get(__SESSION_KEY__)) and not __session_expired__():
+            return func(*args, **kwargs)
+        flash("You need to be logged in to access that page.", "alert-danger")
+        return redirect(url_for(
+            "oauth2.admin.login", next=request.url_rule.endpoint))
+    return __logged_in__
+
+def session_info():
+    """Retrieve the session information."""
+    return session.get(__SESSION_KEY__, False)
+
+def session_user():
+    """Retrieve session user."""
+    info = session_info()
+    return info and info["user"]
+
+def clear_session_info():
+    """Clear any session info."""
+    try:
+        session.pop(__SESSION_KEY__)
+    except KeyError as _keyerr:
+        pass
+
+def session_expired() -> bool:
+    """
+    Check whether the session has expired. Will always return `True` if no
+    session currently exists.
+    """
+    if bool(session.get(__SESSION_KEY__)):
+        now = datetime.now(tz=timezone.utc)
+        return now >= session[__SESSION_KEY__]["expires"]
+    return True
+
+def update_expiry() -> bool:
+    """Update the session expiry and return a boolean indicating success."""
+    if not session_expired():
+        now = datetime.now(tz=timezone.utc)
+        session[__SESSION_KEY__]["expires"] = now + timedelta(minutes=10)
+        return True
+    return False
+
+def update_session_info(**info):
+    """Update the session information."""
+    session[__SESSION_KEY__] = info