Merge pull request #177 from StochSS/develop

v1.0.1 - #175 #176 #178

.cloud.dockerfile

@@ -0,0 +1,22 @@
+FROM python:3.11.1-buster
+
+LABEL authors="Ethan Green <egreen4@unca.edu>, Matthew Dippel <mdip226@gmail.com>"
+
+# set up virtual environment inside container
+ENV VIRTUAL_ENV=/opt/venv
+RUN python3 -m venv $VIRTUAL_ENV
+# activate the venv
+ENV PYTHONPATH="$VIRTUAL_ENV:$PYTHONPATH"
+ENV PATH="$VIRTUAL_ENV:$PATH"
+# make the venv a volume
+VOLUME [ "/opt/venv" ]
+
+WORKDIR /usr/src/app
+
+COPY stochss_compute /usr/src/app/stochss_compute
+COPY requirements.txt *.py *.md *.dockerfile *.cfg /usr/src/app/
+RUN pip install '.[AWS]'
+
+EXPOSE 29681
+
+CMD [ "stochss-compute-cluster"]

.github/workflows/docker.yml

@@ -29,5 +29,12 @@ jobs:
         with:
           push: true
           file: .api.dockerfile
-          tags: stochss/stochss-compute:latest, stochss/stochss-compute:cloud
+          tags: stochss/stochss-compute:latest
+      -
+        name: Build and push to stochss org on DockerHub
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          file: .cloud.dockerfile
+          tags: stochss/stochss-compute:cloud
       - run: echo "🍏 This job's status is ${{ job.status }}."

.gitignore

@@ -142,13 +142,14 @@ Thumbs.db #thumbnail cache on Windows
 # profiling data
 .prof
 
-
 ### vscode ###
 .vscode/*
-!.vscode/settings.json
-!.vscode/tasks.json
-!.vscode/launch.json
-!.vscode/extensions.json
 *.code-workspace
 
+# StochSS-Compute
 **/dask-worker-space
+**/cache/
+
+# Development team
+**/.mdip/
+bs*

docs/tutorials/aws/aws.rst

@@ -48,11 +48,11 @@ AWS Configuration
 
 2. In order to make the AWS API calls to your account, you need an AWS access key and access key ID.  
 
-   From the IAM dashboard, click 'Manage access keys'.  
+   From the IAM dashboard, click 'My security credentials'.  
 
-   Then, under the Access keys tab, click 'Create New Access Key'.  
+   Then, under the Access keys tab, click 'Create Access Key'.  
 
-   This file can only be downloaded once, but if something happens you can just make a new one.  
+   Make sure to record the Access and Secrety keys. We recommend you download the CSV file now, as it can only be downloaded once. if you lose these keys you can just make a new ones.  
 
    This file contains the Access Key ID and a Secret Access Key.
 
@@ -75,4 +75,4 @@ AWS Configuration
 .. code-block:: python
 
     from dotenv import load_dotenv
-    load_dotenv() # Loads from a file named .env by default
+    load_dotenv() # Loads from a file named .env by default

stochss_compute/__version__.py

@@ -26,7 +26,7 @@
 # =============================================================================
 
 
-__version__      = '1.0.0'
+__version__      = '1.0.1'
 
 __title__        = "stochss-compute"
 __description__  = "A compute delegation package for the StochSS family of stochastic simulators"

stochss_compute/server/status.py

@@ -22,18 +22,26 @@
 from tornado.web import RequestHandler
 from stochss_compute.core.errors import RemoteSimulationError
 from stochss_compute.core.messages import SimStatus, StatusResponse
-
 from stochss_compute.server.cache import Cache
 
 class StatusHandler(RequestHandler):
     '''
     Endpoint for requesting the status of a simulation.
     '''
-
+    def __init__(self, application, request, **kwargs):
+        self.scheduler_address = None
+        self.cache_dir = None
+        self.task_id = None
+        self.results_id = None
+        super().__init__(application, request, **kwargs)
+
+    def data_received(self, chunk: bytes):
+        raise NotImplementedError()
+
     def initialize(self, scheduler_address, cache_dir):
         '''
         Sets the address to the Dask scheduler and the cache directory.
-        
+
         :param scheduler_address: Scheduler address.
         :type scheduler_address: str
 
@@ -52,30 +60,34 @@ async def get(self, results_id, n_traj, task_id):
 
         :param n_traj: Number of trajectories in the request. Default 1.
         :type n_traj: str
-        
+
         :param task_id: ID of the running simulation. Required.
         :type task_id: str
         '''
         if '' in (results_id, n_traj):
             self.set_status(404, reason=f'Malformed request: {self.request.uri}')
             self.finish()
             raise RemoteSimulationError(f'Malformed request: {self.request.uri}')
+
         self.results_id = results_id
         self.task_id = task_id
         n_traj = int(n_traj)
+
         cache = Cache(self.cache_dir, results_id)
+
         print(f'{datetime.now()} | <{self.request.remote_ip}> | \
-              Status Request | <{results_id}> | Trajectories: {n_traj} | \
-              Task ID: {task_id}' )
-        msg = f'{datetime.now()} | <{results_id}> | <{task_id}> |Status: '
+            Status Request | <{results_id}> | Trajectories: {n_traj} | \
+            Task ID: {task_id}' )
+
+        msg = f'{datetime.now()} | <{results_id}> | <{task_id}> | Status: '
+
         exists = cache.exists()
         if exists:
             empty = cache.is_empty()
             if empty:
                 if self.task_id not in ('', None):
-                    state, err = await self.check_with_scheduler()
-
-                    print(msg+SimStatus.RUNNING.name+f' | Task: {state} | error: {err}')
+                    state, err = await self._check_with_scheduler()
+                    print(msg + SimStatus.RUNNING.name + f' | Task: {state} | Error: {err}')
                     if state == 'erred':
                         self._respond_error(err)
                     else:
@@ -90,7 +102,7 @@ async def get(self, results_id, n_traj, task_id):
                     self._respond_ready()
                 else:
                     if self.task_id not in ('', None):
-                        state, err = await self.check_with_scheduler()
+                        state, err = await self._check_with_scheduler()
                         print(msg+SimStatus.RUNNING.name+f' | Task: {state} | error: {err}')
                         if state == 'erred':
                             self._respond_error(err)
@@ -103,7 +115,6 @@ async def get(self, results_id, n_traj, task_id):
             print(msg+SimStatus.DOES_NOT_EXIST.name)
             self._respond_dne()
 
-
     def _respond_ready(self):
         status_response = StatusResponse(SimStatus.READY)
         self.write(status_response.encode())
@@ -133,14 +144,13 @@ async def _check_with_scheduler(self):
         # define function here so that it is pickle-able
         def scheduler_task_state(task_id, dask_scheduler=None):
             task = dask_scheduler.tasks.get(task_id)
-
             if task is None:
                 return (None, None)
             if task.exception_text == "":
                 return (task.state, None)
             return (task.state, task.exception_text)
+
         # Do not await. Reasons. It returns sync.
         ret = client.run_on_scheduler(scheduler_task_state, self.task_id)
         client.close()
         return ret
-