From 761634314b6a0597790dfa4c847ae87e661a4302 Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Mon, 21 Oct 2024 18:05:03 +0100
Subject: [PATCH] mega-commit

---
 pyvatti/.pre-commit-config.yaml               |   1 -
 pyvatti/poetry.lock                           | 781 +-----------------
 pyvatti/pyproject.toml                        |  13 +-
 pyvatti/src/pyvatti/__init__.py               |   9 -
 pyvatti/src/pyvatti/config.py                 |  18 +-
 pyvatti/src/pyvatti/helm.py                   |   2 +-
 pyvatti/src/pyvatti/job.py                    |  41 +-
 pyvatti/src/pyvatti/main.py                   | 119 +++
 .../pyvatti/{models.py => messagemodels.py}   |   0
 .../pyvatti/{monitor.py => notifymodels.py}   |  42 +-
 pyvatti/src/pyvatti/render_cli.py             |  10 +
 pyvatti/src/pyvatti/resources.py              |   4 +-
 12 files changed, 249 insertions(+), 791 deletions(-)
 rename pyvatti/src/pyvatti/{models.py => messagemodels.py} (100%)
 rename pyvatti/src/pyvatti/{monitor.py => notifymodels.py} (56%)
 create mode 100644 pyvatti/src/pyvatti/render_cli.py

diff --git a/pyvatti/.pre-commit-config.yaml b/pyvatti/.pre-commit-config.yaml
index 3ca7dc5..ae891ab 100644
--- a/pyvatti/.pre-commit-config.yaml
+++ b/pyvatti/.pre-commit-config.yaml
@@ -9,4 +9,3 @@ repos:
   rev: 'v1.11.2'  # Use the sha / tag you want to point at
   hooks:
     - id: mypy
-      args: [--config-file, mypy.ini]
diff --git a/pyvatti/poetry.lock b/pyvatti/poetry.lock
index 5826579..b972954 100644
--- a/pyvatti/poetry.lock
+++ b/pyvatti/poetry.lock
@@ -53,85 +53,6 @@ files = [
     {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
-[[package]]
-name = "cffi"
-version = "1.17.1"
-description = "Foreign Function Interface for Python calling C code."
-optional = false
-python-versions = ">=3.8"
-files = [
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-]
-
-[package.dependencies]
-pycparser = "*"
-
 [[package]]
 name = "charset-normalizer"
 version = "3.4.0"
@@ -246,20 +167,6 @@ files = [
     {file = "charset_normalizer-3.4.0.tar.gz", hash = "sha256:223217c3d4f82c3ac5e29032b3f1c2eb0fb591b72161f86d93f5719079dae93e"},
 ]
 
-[[package]]
-name = "click"
-version = "8.1.7"
-description = "Composable command line interface toolkit"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
-    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
-]
-
-[package.dependencies]
-colorama = {version = "*", markers = "platform_system == \"Windows\""}
-
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -465,63 +372,15 @@ http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
 trio = ["trio (>=0.22.0,<1.0)"]
 
-[[package]]
-name = "httptools"
-version = "0.6.1"
-description = "A collection of framework independent HTTP protocol utils."
-optional = false
-python-versions = ">=3.8.0"
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-
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 description = "The next generation HTTP client."
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 cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
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 name = "idna"
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+lz4 = ["lz4"]
+snappy = ["python-snappy"]
+zstd = ["zstandard"]
+
 [[package]]
 name = "mypy"
 version = "1.12.0"
@@ -700,27 +513,6 @@ files = [
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-description = "Core tools for working with polygenic scores (PGS) and the PGS Catalog"
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-
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-
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@@ -798,17 +590,6 @@ files = [
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@@ -953,17 +734,6 @@ azure-key-vault = ["azure-identity (>=1.16.0)", "azure-keyvault-secrets (>=4.8.0
 toml = ["tomli (>=2.0.1)"]
 yaml = ["pyyaml (>=6.0.1)"]
 
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 version = "8.3.3"
@@ -1095,6 +865,20 @@ files = [
 [package.dependencies]
 pyasn1 = ">=0.1.3"
 
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+description = "Job scheduling for humans."
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+[package.extras]
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+
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 version = "0.9.2"
@@ -1170,17 +919,6 @@ six = "*"
 diagrams = ["pygraphviz"]
 test = ["pytest"]
 
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-]
-
-[package.dependencies]
-cffi = {version = ">=1.11", markers = "platform_python_implementation == \"PyPy\""}
-
-[package.extras]
-cffi = ["cffi (>=1.11)"]
-
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.12"
-content-hash = "4a82687c1f9ae7630e18f58f833bd12d0a34ecf8994e9f2ac332d8b230b5c975"
+content-hash = "bac38259fd7a8ebdf59a44baa023642cc68f15b4b762e99c52f79542a867c498"
diff --git a/pyvatti/pyproject.toml b/pyvatti/pyproject.toml
index a919b91..fb330c5 100644
--- a/pyvatti/pyproject.toml
+++ b/pyvatti/pyproject.toml
@@ -11,20 +11,19 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.12"
-uvicorn = {extras = ["standard"], version = "^0.29.0"}
-pgscatalog-core = "^0.1.0"
-transitions = "^0.9.0"
+transitions = "^0.9.2"
 google-cloud-storage = "^2.18.2"
 pydantic-settings = "^2.2.1"
-types-pyyaml = "^6.0.12.20240917"
+schedule = "^1.2.2"
+httpx = "^0.27.2"
+pydantic = "^2.9.2"
+pyyaml = "^6.0.2"
+kafka-python-ng = "^2.2.3"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.1.1"
 mypy = "^1.12.0"
 
-[tool.poetry.group.standard.dependencies]
-uvicorn = "^0.29.0"
-
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
diff --git a/pyvatti/src/pyvatti/__init__.py b/pyvatti/src/pyvatti/__init__.py
index 22ad989..3923c22 100644
--- a/pyvatti/src/pyvatti/__init__.py
+++ b/pyvatti/src/pyvatti/__init__.py
@@ -1,14 +1,5 @@
 import logging
-import pathlib
-import tempfile
-
-import httpx
 
 logger = logging.getLogger(__name__)
 log_fmt = "%(name)s: %(asctime)s %(levelname)-8s %(message)s"
 logging.basicConfig(format=log_fmt, datefmt="%Y-%m-%d %H:%M:%S", level=logging.INFO)
-
-CLIENT = httpx.AsyncClient()
-TEMP_DIR = tempfile.mkdtemp()
-SHELF_PATH = str(pathlib.Path(TEMP_DIR) / "shelve.dat")
-logger.info(f"Created temporary shelf file {SHELF_PATH}")
diff --git a/pyvatti/src/pyvatti/config.py b/pyvatti/src/pyvatti/config.py
index cd37f99..1eb32ab 100644
--- a/pyvatti/src/pyvatti/config.py
+++ b/pyvatti/src/pyvatti/config.py
@@ -1,5 +1,7 @@
 import enum
+import pathlib
 import sys
+from tempfile import NamedTemporaryFile
 from typing import Optional
 
 from pydantic import Field, DirectoryPath, AnyHttpUrl
@@ -45,9 +47,23 @@ class Settings(BaseSettings):
         description="Number of seconds to wait before polling Seqera platform API",
     )
     NOTIFY_TOKEN: str = Field(description="Token for backend notifications")
+    SQLITE_DB_PATH: pathlib.Path = Field(
+        description="Path to a sqlite database",
+        default_factory=lambda: NamedTemporaryFile(delete=False).name,
+    )
 
 
 if "pytest" in sys.modules:
-    settings = None
+    settings = Settings(
+        HELM_CHART_PATH="/tmp",
+        TOWER_TOKEN="test",
+        TOWER_WORKSPACE="test",
+        GLOBUS_DOMAIN="https://example.com",
+        GLOBUS_CLIENT_ID="test",
+        GLOBUS_CLIENT_SECRET="test",
+        GLOBUS_SCOPES="test",
+        NOTIFY_URL="https://example.com",
+        NOTIFY_TOKEN="test",
+    )
 else:
     settings = Settings()
diff --git a/pyvatti/src/pyvatti/helm.py b/pyvatti/src/pyvatti/helm.py
index bcc07c3..60445fb 100644
--- a/pyvatti/src/pyvatti/helm.py
+++ b/pyvatti/src/pyvatti/helm.py
@@ -12,7 +12,7 @@
 import yaml
 from pydantic import BaseModel, Field, field_validator
 from pyvatti.config import settings
-from pyvatti.models import JobRequest
+from pyvatti.messagemodels import JobRequest
 
 
 @lru_cache
diff --git a/pyvatti/src/pyvatti/job.py b/pyvatti/src/pyvatti/job.py
index 56a3f67..8a3eeb6 100644
--- a/pyvatti/src/pyvatti/job.py
+++ b/pyvatti/src/pyvatti/job.py
@@ -2,17 +2,23 @@
 """This module contains a state machine that represents job states and their transitions"""
 
 import logging
-from typing import Optional
+from functools import lru_cache
+from typing import Optional, ClassVar
 
+import httpx
 from transitions import Machine, EventData, MachineError
 
+from pyvatti.config import settings
 from pyvatti.jobstates import States
-from pyvatti.models import JobRequest
+from pyvatti.messagemodels import JobRequest
+from pyvatti.notifymodels import SeqeraLog
 
 from pyvatti.resources import GoogleResourceHandler, DummyResourceHandler
 
 logger = logging.getLogger(__name__)
 
+API_ROOT = "https://api.cloud.seqera.io"
+
 
 class PolygenicScoreJob(Machine):
     """A state machine for polygenic score calculation jobs
@@ -108,6 +114,13 @@ class PolygenicScoreJob(Machine):
         },
     ]
 
+    # map from destination states to triggers
+    state_trigger_map: ClassVar[dict] = {
+        States.FAILED: "error",
+        States.SUCCEEDED: "succeed",
+        States.DEPLOYED: "deploy",
+    }
+
     def __init__(self, intp_id, dry_run=False):
         states = [
             # a dummy initial state: /launch got POSTed
@@ -165,5 +178,29 @@ def notify(self, event: Optional[EventData]):
         logger.info(f"Sending state notification: {self.state}")
         # TODO: add kafka
 
+    def get_job_state(self) -> Optional[States]:
+        """Get the state of a job by checking the Seqera Platform API
+
+        Job state matches the state machine triggers"""
+        params = {
+            "workspaceId": settings.TOWER_WORKSPACE,
+            "search": f"{settings.NAMESPACE}-{self.intp_id}",
+        }
+
+        with httpx.Client() as client:
+            response = client.get(
+                f"{API_ROOT}/workflow", headers=get_headers(), params=params
+            )
+
+        return SeqeraLog.from_response(response).get_job_state()
+
     def __repr__(self):
         return f"{self.__class__.__name__}(id={self.intp_id!r})"
+
+
+@lru_cache
+def get_headers():
+    return {
+        "Authorization": f"Bearer {settings.TOWER_TOKEN}",
+        "Accept": "application/json",
+    }
diff --git a/pyvatti/src/pyvatti/main.py b/pyvatti/src/pyvatti/main.py
index 1027d0a..adde27e 100644
--- a/pyvatti/src/pyvatti/main.py
+++ b/pyvatti/src/pyvatti/main.py
@@ -1,5 +1,124 @@
+import json
 import logging
+import signal
+import sys
+import threading
+import time
+from typing import Optional
 
+import pydantic
+import schedule
+
+from pyvatti.config import settings
+from pyvatti.db import SqliteJobDatabase
+
+from kafka import KafkaConsumer
+
+from pyvatti.job import PolygenicScoreJob
+from pyvatti.jobstates import States
+from pyvatti.messagemodels import JobRequest
 
 logger = logging.getLogger()
 logger.setLevel(logging.INFO)
+
+JOB_DATABASE = SqliteJobDatabase(settings.SQLITE_DB_PATH)
+SHUTDOWN_EVENT = threading.Event()
+
+
+def check_job_state() -> None:
+    """Check the state of the job on the Seqera Platform and update active jobs in the database if the state has changed
+
+    Created (resources requested) -> Deployed (running) -> Succeeded / Failed
+    """
+    # active jobs: haven't succeeded or failed
+    jobs: list[PolygenicScoreJob] = JOB_DATABASE.get_active_jobs()
+    logger.info(f"{len(jobs)} active jobs found")
+    for job in jobs:
+        logger.info(f"Checking {job=} state")
+        job_state: Optional[States] = job.get_job_state()
+        if job_state is not None:
+            if job_state != job.state:
+                logger.info(
+                    f"Job state change detected: From {job_state} to {job.state}"
+                )
+                # get the trigger from the destination state enum
+                # e.g. "deploy" -> "succeed" / "error"
+                trigger: str = PolygenicScoreJob.state_trigger_map[job_state]
+                job.trigger(trigger)
+                JOB_DATABASE.update_job(job)
+
+
+def kafka_consumer() -> None:
+    consumer = KafkaConsumer(
+        topic=settings.KAFKA_CONSUMER_TOPIC,
+        bootstrap_servers=settings.KAFKA_BOOTSTRAP_SERVERS,
+        enable_auto_commit=False,
+        value_deserializer=lambda m: json.loads(m.decode("ascii")),
+    )
+
+    # want to avoid partially processing a commit if the thread is terminated
+    try:
+        for message in consumer:
+            if SHUTDOWN_EVENT.is_set():
+                logger.info("Shutdown event received")
+                break
+            process_message(message.value)
+            consumer.commit()
+    finally:
+        logger.info("Closing kafka connection")
+        consumer.close()
+
+
+def process_message(msg_value: dict) -> None:
+    """Each kafka message:
+
+    - Gets validated by the pydantic model JobRequest
+    - Instantiate a PolygenicScoreJob object
+    - Trigger the "create" state where compute resources are provisioned
+    - Adds the job object to the database
+    """
+    try:
+        job_message: JobRequest = JobRequest(**msg_value)
+        job: PolygenicScoreJob = PolygenicScoreJob(
+            intp_id=job_message.pipeline_param.id
+        )
+        PolygenicScoreJob.create(job_model=job_message)
+        JOB_DATABASE.insert_job(job)
+    except pydantic.ValidationError as e:
+        logger.critical("Job request message validation failed")
+        logger.critical(f"{e}")
+
+
+def graceful_shutdown(*args):
+    logger.info("Shutdown signal received")
+    SHUTDOWN_EVENT.set()
+
+
+def main():
+    # handle shutdowns gracefully (partially processing a job request would be bad)
+    signal.signal(signal.SIGINT, graceful_shutdown)
+    signal.signal(signal.SIGTERM, graceful_shutdown)
+
+    # create the job database if it does not exist (if it exists, nothing happens here)
+    JOB_DATABASE.create()
+
+    # consume new kafka messages and insert them into the database in a background thread
+    consumer_thread: threading.Thread = threading.Thread(
+        target=kafka_consumer, daemon=True
+    )
+    consumer_thread.start()
+
+    # check for timed out jobs with schedule
+    schedule.every(15).minutes.do(JOB_DATABASE.timeout_jobs)
+
+    # check if job states have changed and produce new messages
+    schedule.every(1).minutes.do(check_job_state)
+
+    # run scheduled tasks:
+    while True:
+        schedule.run_pending()
+        time.sleep(1)
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/pyvatti/src/pyvatti/models.py b/pyvatti/src/pyvatti/messagemodels.py
similarity index 100%
rename from pyvatti/src/pyvatti/models.py
rename to pyvatti/src/pyvatti/messagemodels.py
diff --git a/pyvatti/src/pyvatti/monitor.py b/pyvatti/src/pyvatti/notifymodels.py
similarity index 56%
rename from pyvatti/src/pyvatti/monitor.py
rename to pyvatti/src/pyvatti/notifymodels.py
index f2f9fbd..14a939f 100644
--- a/pyvatti/src/pyvatti/monitor.py
+++ b/pyvatti/src/pyvatti/notifymodels.py
@@ -1,3 +1,7 @@
+""" This module contains pydantic models that represent responses from the Seqera platform API
+
+The platform API is queried to poll and monitor the state of running jobs
+"""
 import logging
 from datetime import datetime
 import enum
@@ -5,7 +9,7 @@
 from typing import Optional
 
 import httpx
-from pydantic import BaseModel, field_serializer
+from pydantic import BaseModel, PastDatetime
 
 from pyvatti.config import settings
 from pyvatti.jobstates import States
@@ -16,24 +20,24 @@
 logger = logging.getLogger(__name__)
 
 
-@lru_cache
+@lru_cache(maxsize=1)
 def get_headers():
+    """Headers that authorise querying the Seqera platform API"""
     return {
         "Authorization": f"Bearer {settings.TOWER_TOKEN}",
         "Accept": "application/json",
     }
 
 
-class SeqeraJobStatus(enum.Enum):
+class SeqeraJobStatus(str, enum.Enum):
+    """Job states on the Seqera platform"""
+
     SUBMITTED = "SUBMITTED"
     RUNNING = "RUNNING"
     SUCCEEDED = "SUCCEEDED"
     FAILED = "FAILED"
     UNKNOWN = "UNKNOWN"
 
-    def __str__(self):
-        return str(self.value)
-
 
 class SeqeraLog(BaseModel):
     runName: str
@@ -49,28 +53,30 @@ def from_response(cls, response: httpx.Response):
         else:
             return None
 
-    def get_job_state(self):
-        """Get valid state machine trigger strings from states"""
+    def get_job_state(self) -> Optional[States]:
+        """Get valid job states"""
         match self.status:
             case SeqeraJobStatus.SUCCEEDED:
-                state = "succeed"
+                state = States.SUCCEEDED
             case SeqeraJobStatus.FAILED | SeqeraJobStatus.UNKNOWN:
-                state = "error"
+                state = States.FAILED
             case SeqeraJobStatus.RUNNING:
-                state = "deploy"
+                state = States.DEPLOYED
             case _:
                 logger.warning(f"Unknown state: {self.status}")
-                raise Exception
+                state = None
         return state
 
 
 class BackendStatusMessage(BaseModel):
-    """A message updating the backend about job state"""
+    """A message updating the backend about job state
+
+    >>> from datetime import datetime
+    >>> d = {"run_name": "INTP123456", "utc_time": datetime(1999, 12, 31), "event": States.SUCCEEDED}
+    >>> BackendStatusMessage(**d).model_dump_json()
+    '{"run_name":"INTP123456","utc_time":"1999-12-31T00:00:00","event":"succeeded"}'
+    """
 
     run_name: str
-    utc_time: datetime
+    utc_time: PastDatetime
     event: States
-
-    @field_serializer("event")
-    def event_field(self, event):
-        return str(event)
diff --git a/pyvatti/src/pyvatti/render_cli.py b/pyvatti/src/pyvatti/render_cli.py
new file mode 100644
index 0000000..4d463fe
--- /dev/null
+++ b/pyvatti/src/pyvatti/render_cli.py
@@ -0,0 +1,10 @@
+import sys
+
+
+def main():
+    # TODO: build a CLI that renders a helm template from a message for testing
+    pass
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/pyvatti/src/pyvatti/resources.py b/pyvatti/src/pyvatti/resources.py
index bfebcef..3c06c2a 100644
--- a/pyvatti/src/pyvatti/resources.py
+++ b/pyvatti/src/pyvatti/resources.py
@@ -8,7 +8,7 @@
 import yaml
 from google.cloud import storage
 
-from pyvatti.models import JobRequest
+from pyvatti.messagemodels import JobRequest
 from pyvatti.helm import render_template
 from pyvatti.config import settings
 from pyvatti.jobstates import States
@@ -43,7 +43,7 @@ async def destroy_resources(self, state):
 
 
 class DummyResourceHandler(ResourceHandler):
-    """A dummy resource handler for testing"""
+    """A dummy resource handler that doesn't do anything for testing"""
 
     def __init__(self, intp_id: str):
         self.intp_id = intp_id