fixing hardcoded home dir

.github/workflows/cloud-deploy.yml

@@ -36,18 +36,18 @@ jobs:
         ls -al image.tar*
 
 
-    - name: Prepare SSH Dir
+    - name: Prepare SSH dir
       run: |
         mkdir -pv ~/.ssh/
 
-    - name: Write Key
+    - name: Write key
       env:
         EC2_SSH_KEY: ${{ secrets.EC2_SSH_KEY }}
       run: |
         echo "$EC2_SSH_KEY" > ~/.ssh/actions.key
         chmod 600 ~/.ssh/actions.key
 
-    - name: Write SSH Config
+    - name: Write SSH config
       env:
         EC2_HOST: ${{ secrets.EC2_HOST }}
         EC2_USERNAME: ${{ secrets.EC2_USERNAME }}
@@ -63,21 +63,36 @@ jobs:
         END
 
     - name: Copy Docker image to EC2 instance
+      env:
+        EC2_USERNAME: ${{ secrets.EC2_USERNAME }}
       run: |
-        scp image.tar.gz ec2:/home/ubuntu
+        scp image.tar.gz ec2:/home/$EC2_USERNAME
 
-    - name: Stop Running Container
+    - name: Ensure Docker is installed and running
+      run: |
+        ssh ec2 'sudo snap install docker'
+        ssh ec2 'sudo systemctl start docker'   
+
+    - name: Stop running container
       run: | 
-        ssh ec2 'docker ps -q | xargs --no-run-if-empty docker stop | xargs --no-run-if-empty docker rm'
+        ssh ec2 'sudo docker ps -q | xargs --no-run-if-empty docker stop | xargs --no-run-if-empty docker rm'
 
-    - name: Configure Docker & Load Image
+    - name: Configure Docker & load lmage
+      env:
+        EC2_USERNAME: ${{ secrets.EC2_USERNAME }}
       run: |
-        ssh ec2 "docker load -i /home/ubuntu/image.tar.gz"
+        ssh ec2 "sudo docker load -i /home/$EC2_USERNAME/image.tar.gz"
 
-    - name: Delete Gzipped Image Tarball
+    - name: Delete gzipped image tarball
+      env:
+        EC2_USERNAME: ${{ secrets.EC2_USERNAME }}
       run: |
-        ssh ec2 "rm -f /home/ubuntu/image.tar.gz"
+        ssh ec2 "rm -f /home/$EC2_USERNAME/image.tar.gz"
 
     - name: Run Docker container on EC2 instance
       run: |
-        ssh ec2 "docker run -p 80:80 -d ramanujan-machine-web-portal:latest"
+        ssh ec2 "sudo docker run -p 80:80 -d ramanujan-machine-web-portal:latest"
+
+    - name: Cleanup Docker detritus
+      run: |
+        ssh ec2 "sudo docker system prune -f"

Dockerfile

@@ -17,6 +17,7 @@ RUN apt-get -y install curl gnupg
 RUN apt-get -y install libpq-dev libgmp-dev libgmp3-dev libmpfr-dev libmpc-dev
 RUN apt-get install -y npm
 RUN npm i -g n && n lts && npm i -g npm@latest
+RUN pip install --upgrade protobuf grpcio grpcio-tools --break-system-packages
 
 # React frontend
 COPY react-frontend ./react-frontend
@@ -30,36 +31,39 @@ RUN npm run build
 # create virtual environment for FastAPI web server and install dependencies
 WORKDIR /srv/ramanujan-machine-web-portal
 ENV BKPATH=$PATH
+COPY protos ./protos
 COPY python-backend ./python-backend
 RUN cp -rf react-frontend/build python-backend/build
 WORKDIR /srv/ramanujan-machine-web-portal/python-backend
-RUN --mount=type=secret,id=creds cat /run/secrets/creds >> .env
+COPY .creds .creds
+RUN --mount=type=secret,id=creds cat .creds >> .env
 RUN rm -rf venv
 RUN python3 -m venv venv
+# . is equivalent to source in sh
 RUN . venv/bin/activate
 RUN ./venv/bin/python -m pip install -r /srv/ramanujan-machine-web-portal/python-backend/requirements.txt
+RUN ./venv/bin/python -m pip install --upgrade protobuf grpcio grpcio-tools --break-system-packages
+# generate gRPC code for web server
+RUN ./venv/bin/python -m grpc_tools.protoc --proto_path=/srv/ramanujan-machine-web-portal/protos --python_out=/srv/ramanujan-machine-web-portal/python-backend/ --grpc_python_out=/srv/ramanujan-machine-web-portal/python-backend/ /srv/ramanujan-machine-web-portal/protos/lirec.proto
 ENV PATH=$BKPATH
 RUN unset VIRTUAL_ENV
 
 # create virtual environment for gRPC server and install dependencies
 WORKDIR /srv/ramanujan-machine-web-portal
-COPY protos ./protos
 COPY lirec-grpc-server ./lirec-grpc-server
 WORKDIR /srv/ramanujan-machine-web-portal/lirec-grpc-server
 RUN rm -rf venv
 RUN python3 -m venv venv
+# . is equivalent to source in sh
 RUN . venv/bin/activate
-RUN venv/bin/python -m pip install -r requirements.txt
+RUN ./venv/bin/python -m pip install -r /srv/ramanujan-machine-web-portal/lirec-grpc-server/requirements.txt
+RUN ./venv/bin/python -m pip install --upgrade protobuf grpcio grpcio-tools --break-system-packages
+# generate gRPC code for gRPC server directories
+RUN ./venv/bin/python -m grpc_tools.protoc --proto_path=/srv/ramanujan-machine-web-portal/protos --python_out=/srv/ramanujan-machine-web-portal/lirec-grpc-server/ --grpc_python_out=/srv/ramanujan-machine-web-portal/lirec-grpc-server/ /srv/ramanujan-machine-web-portal/protos/lirec.proto
 ENV PATH=$BKPATH
 RUN unset VIRTUAL_ENV
 
-# generate gRPC code in both client (web server) and gRPC server directories
-WORKDIR /srv/ramanujan-machine-web-portal
-RUN pip install grpcio grpcio-tools --break-system-packages
-WORKDIR /srv/ramanujan-machine-web-portal/python-backend
-RUN python3 -m grpc_tools.protoc --proto_path=/srv/ramanujan-machine-web-portal/protos --python_out=/srv/ramanujan-machine-web-portal/python-backend/ --grpc_python_out=/srv/ramanujan-machine-web-portal/python-backend/ /srv/ramanujan-machine-web-portal/protos/lirec.proto
-WORKDIR /srv/ramanujan-machine-web-portal/lirec-grpc-server
-RUN python3 -m grpc_tools.protoc --proto_path=/srv/ramanujan-machine-web-portal/protos --python_out=/srv/ramanujan-machine-web-portal/lirec-grpc-server/ --grpc_python_out=/srv/ramanujan-machine-web-portal/lirec-grpc-server/ /srv/ramanujan-machine-web-portal/protos/lirec.proto
+
 
 # expose web port
 EXPOSE 80

README.md

@@ -12,6 +12,7 @@ You will need to replace `XXXXXX-XXXXXXXXXX` with a Wolfram App Id, which you ca
 Note that the first port is the port you can access via your web browser, e.g. `http://localhost:80` is where you would be able to interact with the app given the above configuration. You can change `80` to whatever port you wish, and the frontend of the web application runs on port `80` inside the container.
 
 ## Run Frontend and Backend Locally without Docker
+Comprehensive developer documentation is available in a separate [README](./docs/DEVELOPER.md). Short versions of the instructions for each part of the web app can be found in READMEs in each subdirectory:
 - Refer to [React Frontend README](./react-frontend/README.md) to run the web interface locally.
 - Refer to [Python Backend README](./python-backend/README.md) to run the API locally.
 - Refer to [Python gRPC Server README](./lirec-grpc-server/README.md) to run the gRPC server locally.

docker_start.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 
 # Start gRPC server
 cd lirec-grpc-server
@@ -14,7 +14,7 @@ uvicorn main:app --host "0.0.0.0" --port 80 &
 deactivate
 
 # Wait for any process to exit
-wait -n
+wait
 
 # Exit with status of process that exited first
 exit $?

docs/DEVELOPER.md

@@ -8,6 +8,8 @@ The web portal was developed by the [Virtual Institute for Scientific Software](
 
 The repository comprises a complete web application, including web server code, React UI code and an automated deployment in GitHub Actions workflows that builds a Docker container and deploys it to a cloud server, currently AWS EC2.
 
+![architecture.png](architecture.png)
+
 ### 1.2. Technologies Used
 
 The web portal was written primarily in [Typescript](https://www.typescriptlang.org/docs/handbook/2/basic-types.html) and [Python](https://docs.python.org/3/tutorial/index.html). 

lirec-grpc-server/requirements.txt

@@ -1,16 +1,16 @@
-numpy==1.26.4
-setuptools==65.5.1
-packaging==24.0
-logger==1.4
+## The following requirements were added by pip freeze:
 gmpy2==2.2.0a1
-grpcio>=1.64.0
-grpcio-tools>=1.64.0
-LIReC @ git+https://github.com/RamanujanMachine/LIReC.git@main
+grpcio==1.66.1
+grpcio-tools==1.66.1
+LIReC @ git+https://github.com/RamanujanMachine/LIReC.git@ba7d9a9e6ec3c1126cacdcb628b4497a5a51be1c
+logger==1.4
 mpmath==1.3.0
+numpy==1.26.4
 ordered-set==4.1.0
+packaging==24.0
 protobuf==5.26.1
 psycopg2==2.9.9
 PyLaTeX==1.4.2
 SQLAlchemy==2.0.30
 sympy==1.12
-typing_extensions==4.11.0
+typing_extensions==4.11.0

lirec-grpc-server/server.py

@@ -1,7 +1,7 @@
 from concurrent import futures
 
 import grpc
-from LIReC.db.access import db
+from LIReC.db.access import db, PolyPSLQRelation
 
 import constants
 import lirec_pb2
@@ -14,10 +14,12 @@
 class LIReCServicer(lirec_pb2_grpc.LIReCServicer):
     def Identify(self, request: lirec_pb2.IdentifyRequest, context: object) -> lirec_pb2.IdentifyResponse:
         logger.debug(f"Received request: <{type(request)}> {request}")
-        closed_forms = db.identify(values=[request.limit], wide_search=[1], min_prec=constants.DEFAULT_PRECISION)
-        logger.debug(f"Received response: <{type(closed_forms)}> {[str(item) for item in closed_forms]}")
-        return lirec_pb2.IdentifyResponse(closed_forms=[str(item) for item in closed_forms])
-
+        results = db.identify(values=[request.limit], wide_search=[1], min_prec=constants.DEFAULT_PRECISION, see_also=True)
+        logger.debug(f"Received response: <{type(results)}> {[str(item) for item in results]}")
+        if len(results) > 0 and type(results[0]) is list:
+            return lirec_pb2.IdentifyResponse(closed_forms=[str(item) for item in results[0]], see_also=[str(item) for item in results[1]])
+        else:
+            return lirec_pb2.IdentifyResponse(closed_forms=[str(item) for item in results])
 
 def serve() -> None:
     """

protos/lirec.proto

@@ -7,7 +7,6 @@ option objc_class_prefix = "HLW";
 package lirec_rpc;
 
 service LIReC {
-  // Sends a greeting
   rpc Identify(IdentifyRequest) returns (IdentifyResponse) {}
 }
 
@@ -17,4 +16,5 @@ message IdentifyRequest {
 
 message IdentifyResponse {
   repeated string closed_forms = 1;
+  repeated string see_also = 2;
 }

python-backend/call_wrapper.py

@@ -1,56 +1,61 @@
 import logging
-import signal
 
 import grpc
 import lirec_pb2
 import sympy.core.numbers
-from constants import EXTERNAL_PROCESS_TIMEOUT
 import lirec_pb2_grpc
 from ramanujantools.pcf import PCF
+import signal
+from constants import EXTERNAL_PROCESS_TIMEOUT
 
 logger = logging.getLogger('rm_web_app')
 
 
-class TimeoutError(Exception):
+class TimeoutException(Exception):
     pass
 
 
-def timeout_handler(signum: object, frame: object) -> None:
-    """
-    Simple handler when execution of functions exceeds time limit specified as EXTERNAL_PROCESS_TIMEOUT
-    """
-    raise TimeoutError("Function execution timed out")
-
-signal.signal(signal.SIGALRM, timeout_handler)
-signal.alarm(EXTERNAL_PROCESS_TIMEOUT)
+def timeout_handler(signum, frame):
+    raise TimeoutException()
 
 
 def pcf_limit(a, b, n) -> str:
     """
     Invokes ResearchTools limit computation
     """
+    signal.signal(signal.SIGALRM, timeout_handler)
+    signal.alarm(EXTERNAL_PROCESS_TIMEOUT)
+
     try:
         pcf = PCF(a, b)
         lim = pcf.limit(n)
         return lim.as_rounded_number()
-
-    except TimeoutError:
-        logger.error("Function execution timed out after {} seconds".format(EXTERNAL_PROCESS_TIMEOUT))
+    except TimeoutException:
+        print(f"PCF limit query exceeded timeout.")
+        return None
+    except Exception as e:
+        logger.error(f"Exception: {e}")
     finally:
         signal.alarm(0)
 
 
-def lirec_identify(limit) -> list[sympy.core.numbers.Number]:
+def lirec_identify(limit) -> [list[sympy.core.numbers.Number], list[sympy.core.numbers.Number]]:
     """
     Invokes LIReC pslq algorithm
     """
+    signal.signal(signal.SIGALRM, timeout_handler)
+    signal.alarm(EXTERNAL_PROCESS_TIMEOUT)
+
     try:
         with grpc.insecure_channel('localhost:50051') as channel:
             stub = lirec_pb2_grpc.LIReCStub(channel)
             request = lirec_pb2.IdentifyRequest(limit=limit)
             response = stub.Identify(request)
-            return response.closed_forms
-    except TimeoutError:
-        logger.error("Function execution timed out after {} seconds".format(EXTERNAL_PROCESS_TIMEOUT))
+            return [response.closed_forms, response.see_also]
+    except TimeoutException:
+        print(f"PCF limit query exceeded timeout.")
+        return None
+    except Exception as e:
+        logger.error(f"Exception: {e}")
     finally:
         signal.alarm(0)

python-backend/constants.py

@@ -5,6 +5,6 @@
 # evalf allows for verbose output via param universally set to this:
 VERBOSE_EVAL = False
 # when calling ResearchTools, only way this many seconds before throwing a timeout exception
-EXTERNAL_PROCESS_TIMEOUT = 10
+EXTERNAL_PROCESS_TIMEOUT = 30
 # the free Wolfram API limits queries to 200 characters
 WOLFRAM_CHAR_LIMIT = 200