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omoponfhir / omoponfhir-main

Main OMOPonFHIR Settings
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Error 404 on http://localhost:8080/omoponfhir #8

Closed salvolpe closed 3 years ago

salvolpe commented 3 years ago

I just tried setting up an omoponfhir instance on my desktop using the README from this omoponfhir-main and linking it to the smart-postgres SQL database that I forked from the link provided in the README. I can get the Tomcat to open at localhost:8080, but http://localhost:8080/omoponfhir3 throws an Error 404.

Here is what my Dockerfile looks like:

#Build the Maven project
FROM maven:3.6.1-alpine as builder
COPY . /usr/src/app
WORKDIR /usr/src/app
RUN mvn clean install

#Build the Tomcat container
FROM tomcat:alpine
#set environment variables below and uncomment the line. Or, you can manually set your environment on your server.
ENV JDBC_URL=jdbc:postgresql://omopv5fhir-pgsql:5432/smart-postgres?currentSchema=omop_v5 JDBC_USERNAME=smart-postgres JDBC_PASSWORD=i3lworks
RUN apk update
RUN apk add zip postgresql-client

# Copy GT-FHIR war file to webapps.
COPY --from=builder /usr/src/app/omoponfhir-stu3-server/target/omoponfhir-stu3-server.war $CATALINA_HOME/webapps/omoponfhir3.war

EXPOSE 8080

I don't know if I'm not typing something correctly into one of the environment variables or if I have to change things in my docker-compose.yml file. I'm not sure. This is my first time working with Docker containers.

Do you have any thoughts?

myungchoi commented 3 years ago

The URL path is http://localhost:8080/omoponfhir3/ http://localhost:8080/omoponfhir3/

Please try with this link URL. And, if it does not work, please see if you can talk to the database container from FHIR server container. I think omopv5fhir-psql will not be resolvable inside the omoponfhir3 container unless you set up container network in the docker environment.

On Oct 24, 2020, at 3:18 PM, Salvatore Volpe notifications@github.com wrote:

I just tried setting up an omoponfhir instance on my desktop using the README from this omoponfhir-main and linking it to the smart-postgres SQL database that I forked from the link provided in the README https://github.com/omoponfhir/omopv5fhir-pgsql/. I can get the Tomcat to open at localhost:8080, but http://localhost:8080/omoponfhir throws an Error 404.

Here is what my Dockerfile looks like:

Build the Maven project

FROM maven:3.6.1-alpine as builder COPY . /usr/src/app WORKDIR /usr/src/app RUN mvn clean install

Build the Tomcat container

FROM tomcat:alpine

set environment variables below and uncomment the line. Or, you can manually set your environment on your server.

ENV JDBC_URL=jdbc:postgresql://omopv5fhir-pgsql:5432/smart-postgres?currentSchema=omop_v5 JDBC_USERNAME=smart-postgres JDBC_PASSWORD=i3lworks RUN apk update RUN apk add zip postgresql-client

Copy GT-FHIR war file to webapps.

COPY --from=builder /usr/src/app/omoponfhir-stu3-server/target/omoponfhir-stu3-server.war $CATALINA_HOME/webapps/omoponfhir3.war

EXPOSE 8080 I don't know if I'm not typing something correctly into one of the environment variables or if it's something else. This is my first time working with Docker containers.

Do you have any thoughts?

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salvolpe commented 3 years ago

The URL issue was a typo. I actually tried it with http://localhost:8080/omoponfhir3/ and the other prefab URLs and they do not work.

I am completely unfamiliar with Docker. Would you explain in a general sense how I would go about setting up the communication? I have the desktop version and CLI-tools for Docker

myungchoi commented 3 years ago

Please post here the output of “sudo docker ps -a” here. We can see what you have there and status of docker containers. We can go from there.

On Oct 30, 2020, at 2:11 PM, Salvatore Volpe notifications@github.com wrote:

The URL issue was a typo. I actually tried it with http://localhost:8080/omoponfhir3/ and the other prefab URLs and they do not work.

I am completely unfamiliar with Docker. Would you explain in a general sense how I would go about setting up the communication? I have the desktop version and CLI-tools for Docker

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/omoponfhir/omoponfhir-main/issues/8#issuecomment-719715395, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABQRHRWC6P2XARK7VJKKSZTSNL6WPANCNFSM4S5ZB7KA.

salvolpe commented 3 years ago

Sorry to leave you hanging @myungchoi . I tried to resolve the issue by attaching smart-postgres to the omoponfhir-main_default bridge that comes with the installation and that didn't solve the problem. Here is the output of my sudo call:

CONTAINER ID        IMAGE                        COMMAND                  CREATED             STATUS                   PORTS                    NAMES
ad6ca8813ebd        omoponfhir-main_omoponfhir   "catalina.sh run"        13 days ago         Up 44 hours              0.0.0.0:8080->8080/tcp   omoponfhir-main_omoponfhir_1
338cdf426eef        smart-postgres:latest        "docker-entrypoint.s…"   2 weeks ago         Up 10 minutes            0.0.0.0:5432->5432/tcp   smart-postgres
2b9724195181        docker/getting-started       "/docker-entrypoint.…"   2 weeks ago         Exited (0) 13 days ago                            funny_kirch

In case it is helpful, this is the docker inspection results for the omoponfhir-main_default network after I connected smart-postgres to it:

"Name": "omoponfhir-main_default",
        "Id": "bfb4d8ede0422a4bd821eecc25d78a89918814c579607a645623f5d5da180c82",
        "Created": "2020-10-23T16:48:09.591035052Z",
        "Scope": "local",
        "Driver": "bridge",
        "EnableIPv6": false,
        "IPAM": {
            "Driver": "default",
            "Options": null,
            "Config": [
                {
                    "Subnet": "172.19.0.0/16",
                    "Gateway": "172.19.0.1"
                }
            ]
        },
        "Internal": false,
        "Attachable": true,
        "Ingress": false,
        "ConfigFrom": {
            "Network": ""
        },
        "ConfigOnly": false,
        "Containers": {
            "338cdf426eef836e655e3e5284d4052ef457930ca36e52759744bc0006aa4c43": {
                "Name": "smart-postgres",
                "EndpointID": "375b5b9084dab161b5776efef6237567912211afacf456a2dfb7a8de36d9e9f3",
                "MacAddress": "02:42:ac:13:00:03",
                "IPv4Address": "172.19.0.3/16",
                "IPv6Address": ""
            },
            "ad6ca8813ebdf2ab8450ced2915c71a5a40ec1fa6ae9d080cc954aa29dd8af3f": {
                "Name": "omoponfhir-main_omoponfhir_1",
                "EndpointID": "7caaedb082812055540e2425c9b86f3b106ea9cf0ac7231e9671de45eb13fc83",
                "MacAddress": "02:42:ac:13:00:02",
                "IPv4Address": "172.19.0.2/16",
                "IPv6Address": ""
            }
        },
        "Options": {},
        "Labels": {
            "com.docker.compose.network": "default",
            "com.docker.compose.project": "omoponfhir-main",
            "com.docker.compose.version": "1.27.4"
        }
salvolpe commented 3 years ago

@myungchoi Any thoughts on these?

salvolpe commented 3 years ago

This issue has been resolved!

In case anyone else has similar issues with connecting omopv5fhir-pgsql to omoponfhir-main, here is what worked for me:

Modifying variables when using the omopv5fhir-pgsql instructions

Your ENV variables in the Dockerfile for omopfhir-main should be updated as such

ENV JDBC_URL=jdbc:postgresql://smart-postgres:5432/postgres?currentSchema=omop_v5 JDBC_USERNAME=omop_v5 JDBC_PASSWORD=i3lworks