Mdip226/gillespy2.remote

.gitignore

@@ -70,4 +70,4 @@ __pycache__
 htmlcov
 /build
 .idea
-
+env/

gillespy2/remote/__init__.py

@@ -0,0 +1,23 @@
+'''
+gillespy2.remote
+'''
+# Copyright (C) 2019-2023 GillesPy2 and StochSS developers.
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+from gillespy2.remote.client import *
+from gillespy2.remote.core import *
+from gillespy2.remote.server import *
+from gillespy2.remote.cloud import *

gillespy2/remote/__version__.py

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+# '''
+# gillespy2.remote.__version__
+# '''
+# # StochSS-Compute is a tool for running and caching GillesPy2 simulations remotely.
+# # Copyright (C) 2019-2023 GillesPy2 and StochSS developers.
+
+# # This program is free software: you can redistribute it and/or modify
+# # it under the terms of the GNU General Public License as published by
+# # the Free Software Foundation, either version 3 of the License, or
+# # (at your option) any later version.
+
+# # This program is distributed in the hope that it will be useful,
+# # but WITHOUT ANY WARRANTY; without even the implied warranty of
+# # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# # GNU General Public License for more details.
+
+# # You should have received a copy of the GNU General Public License
+# # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+# # =============================================================================
+# # @file    __version__.py
+# # @brief   stochss-compute version info
+# # @license Please see the file named LICENSE.md in parent directory
+# # @website https://github.com/StochSS/stochss-compute
+# # =============================================================================
+
+
+# __version__      = '1.0.1'
+
+# __title__        = "stochss-compute"
+# __description__  = "A compute delegation package for the StochSS family of stochastic simulators"
+# __url__          = "https://github.com/StochSS/stochss-compute"
+# __download_url__ = "https://pypi.org/project/stochss-compute/#files"
+# __author__       = "See CONTRIBUTORS.md"
+# __email__        = "[email protected]"
+# __license__      = "GPLv3"
+# __copyright__    = "Copyright (C) 2017-2023"

gillespy2/remote/client/__init__.py

@@ -0,0 +1,19 @@
+'''
+gillespy2.remote.client
+'''
+# Copyright (C) 2019-2023 GillesPy2 and StochSS developers.
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from .compute_server import ComputeServer

gillespy2/remote/client/compute_server.py

@@ -0,0 +1,46 @@
+'''
+ComputeServer(Server)
+'''
+# StochSS-Compute is a tool for running and caching GillesPy2 simulations remotely.
+# Copyright (C) 2019-2023 GillesPy2 and StochSS developers.
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from gillespy2.remote.client.server import Server
+
+class ComputeServer(Server):
+    '''
+    Simple object representing a remote instance of StochSS-Compute.
+
+    :param host: Address of the remote server.
+    :type host: str
+
+    :param port: Port on which to connect. Defaults to 29681.
+    :type port: int
+    '''
+    # pylint: disable=super-init-not-called
+    def __init__(self, host: str, port: int = 29681):
+        host = host.replace('http://','')
+        host = host.split(':')[0]
+        self._address = f"http://{host}:{port}"
+    # pylint: enable=super-init-not-called
+
+    @property
+    def address(self) -> str:
+        """
+        The server's IP address and port.
+
+        :returns: "http://{host}:{port}"
+        """
+        return self._address

gillespy2/remote/client/endpoint.py

@@ -0,0 +1,30 @@
+'''
+Endpoint(Enum)
+'''
+# StochSS-Compute is a tool for running and caching GillesPy2 simulations remotely.
+# Copyright (C) 2019-2023 GillesPy2 and StochSS developers.
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from enum import Enum
+
+class Endpoint(Enum):
+    '''
+    API Endpoints.
+    '''
+    SIMULATION_GILLESPY2 = 1
+    CLOUD = 2
+    CACHE = 3
+    DASK = 4
+

gillespy2/remote/client/server.py

@@ -0,0 +1,135 @@
+'''
+Server(ABC)
+'''
+# StochSS-Compute is a tool for running and caching GillesPy2 simulations remotely.
+# Copyright (C) 2019-2023 GillesPy2 and StochSS developers.
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from time import sleep
+from abc import ABC, abstractmethod
+import requests
+from gillespy2.remote.client.endpoint import Endpoint
+from gillespy2.remote.core.messages.base import Request
+
+from gillespy2.remote.core.utils.log_config import init_logging
+log = init_logging(__name__)
+
+class Server(ABC):
+    '''
+    Abstract Server class with hard coded endpoints.
+
+    :raises TypeError: Server cannot be instantiated directly. Must be ComputeServer or Cluster.
+    '''
+
+    _endpoints = {
+        Endpoint.SIMULATION_GILLESPY2: "/api/v3/simulation/gillespy2",
+        Endpoint.CLOUD: "/api/v3/cloud",
+        Endpoint.CACHE: "/api/v3/cache",
+        Endpoint.DASK: '/api/v3/dask',
+    }
+
+    def __init__(self) -> None:
+        raise TypeError('Server cannot be instantiated directly. Must be ComputeServer or Cluster.')
+
+    @property
+    @abstractmethod
+    def address(self):
+        '''
+        NotImplemented
+        '''
+        return NotImplemented
+
+    def get(self, endpoint: Endpoint, sub: str, request: Request = None):
+        '''
+        Send a GET request to endpoint.
+
+        :param endpoint: The API endpoint.
+        :type endpoint: Endpoint
+
+        :param sub: Final part of url string.
+        :type sub: str
+
+        :param request: An object that inherits from Request.
+        :type request: Request
+
+        :returns: The HTTP response.
+        :rtype: requests.Response
+        '''
+        if request is not None:
+            log.debug(request.encode())
+        url = f"{self.address}{self._endpoints[endpoint]}{sub}"
+        log.debug(url)
+        n_try = 1
+        sec = 3
+        while n_try <= 3:
+            try:
+                if request is not None:
+                    return requests.get(url, timeout=30, params=request.encode())
+                return requests.get( url, timeout=30)
+
+            except ConnectionError:
+                print(f"Connection refused by server. Retrying in {sec} seconds....")
+                sleep(sec)
+                n_try += 1
+                sec *= n_try
+            except Exception as err:
+                print(f"Unknown error: {err}. Retrying in {sec} seconds....")
+                sleep(sec)
+                n_try += 1
+                sec *= n_try
+
+    def post(self, endpoint: Endpoint, sub: str, request: Request = None):
+        '''
+        Send a POST request to endpoint.
+
+        :param endpoint: The API endpoint.
+        :type endpoint: Endpoint
+
+        :param sub: Final part of url string.
+        :type sub: str
+
+        :param request: An object that inherits from Request.
+        :type request: Request
+
+        :returns: The HTTP response.
+        :rtype: requests.Response
+        '''
+        log.debug(request.encode())
+
+        if self.address is NotImplemented:
+            raise NotImplementedError
+
+        url = f"{self.address}{self._endpoints[endpoint]}{sub}"
+        log.debug(url)
+        n_try = 1
+        sec = 3
+        while n_try <= 3:
+            try:
+                if request is None:
+                    print(f"[POST] {url}")
+                    return requests.post(url, timeout=30)
+                print(f"[{type(request).__name__}] {url}")
+                return requests.post(url, json=request.encode(), timeout=30)
+
+            except ConnectionError:
+                print(f"Connection refused by server. Retrying in {sec} seconds....")
+                sleep(sec)
+                n_try += 1
+                sec *= n_try
+            except Exception as err:
+                print(f"Unknown error: {err}. Retrying in {sec} seconds....")
+                sleep(sec)
+                n_try += 1
+                sec *= n_try

gillespy2/remote/cloud/__init__.py

@@ -0,0 +1,21 @@
+'''
+gillespy2.remote.cloud
+'''
+# StochSS-Compute is a tool for running and caching GillesPy2 simulations remotely.
+# Copyright (C) 2019-2023 GillesPy2 and StochSS developers.
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from .ec2 import EC2Cluster
+from .ec2_config import EC2LocalConfig, EC2RemoteConfig