ohdsi / ohdsi-in-a-box Goto Github PK

To save time for anyone wanting to apply an IAM role to the creation here's a json dump of the policy rules required:

{
    "Version": "2012-10-17",
    "Statement": [
        {
            "Sid": "VisualEditor0",
            "Effect": "Allow",
            "Action": [
                "iam:GetRole",
                "iam:PassRole",
                "iam:DetachRolePolicy",
                "iam:DeleteRolePolicy",
                "iam:CreateRole",
                "iam:DeleteRole",
                "iam:AttachRolePolicy",
                "iam:PutRolePolicy",
                "iam:GetRolePolicy"
            ],
            "Resource": "arn:aws:iam::123456789:role/*"
        },
        {
            "Sid": "VisualEditor1",
            "Effect": "Allow",
            "Action": [
                "lambda:CreateFunction",
                "ec2:AuthorizeSecurityGroupIngress",
                "lambda:InvokeFunction",
                "ec2:DescribeVpcs",
                "ec2:CreateSecurityGroup",
                "ec2:CreateTags",
                "lambda:GetFunction",
                "ec2:DeleteSecurityGroup",
                "ec2:DescribeRegions",
                "lambda:DeleteFunction",
                "ec2:DescribeSubnets",
                "ec2:DescribeSecurityGroups"
            ],
            "Resource": "*"
        }
    ]
}

You will need to update arn:aws:iam::123456789:role/* to match the ARN for the role.

These same policies can be added to a user directly if your account has restrictions.

I get the error message ROLLBACK_COMPLETE when I tried to install OHDSI-in-a-boxaccording to the video.

I tried twice and both times I got ROLLBACK_COMPLETE instead of the message CREATE_COMPLETE.

What could be the problem ?

I am trying to setup the ODHSI-in-a-box stack following the video instructions. However at the initial cloudformations screen where it populates the template yaml, I get the following error:
S3 error: Access Denied For more information check http://docs.aws.amazon.com/AmazonS3/latest/API/ErrorResponses.html

Trying to directly access the file via a browser:

<Error>
    <Code>AccessDenied</Code>
    <Message>Access Denied</Message>
    <RequestId>........</RequestId>
    <HostId>..........</HostId>
</Error>

When uploading ohdsi-in-a-box-linux.yaml myself from a git checkout this works fine.
So this looks to be a permissions issue on the S3 side.

Hi All,

I trying to run AchillesWeb. I have changed the datasourcepath, but it still does not work. What else do I need to change?

Thanks!

On starting the instance it is not very responsive on the recommended base instance type for ~30 minutes as it is running unattended-upgrades to apply updates. Rather than people incur unnecessary inflated costs any of the following would be sensible:

1. Update to a current version of the underlying OS with updates (best)
2. Refresh with relevant security updates
3. Uninstall unattended-upgrades (worst)

I realize this is synthetic data, but I was still surprised by the number of records for which visit_concept_id=0 . Perhaps because his If a majority of data have non-standard values, maybe this has been documented somewhere?

set search_path to cmsdesynpuf100kpostgres, public;
select visit_concept_id,count(*) from visit_occurrence
group by 1
order by 1;

Hi,
I am using RStudio version 1.2.1335 with R version 3.5.3 in OHDSI-in-a-Box instance running over x86_64-pc-linux-gnu (64-bit).

I get the following error every time I try to use ggplot() or ts.plot() functions.

Error in RStudioGD() : Shadow graphics device error: r error 4 (R code execution error)

Warning messages:
1: In grDevices:::png("/tmp/RtmpsXd9n8/6f8227ef665849fb83a03d96380b8980.png", ... :
unable to load shared object '/usr/lib/R/library/grDevices/libs//cairo.so':
libjpeg.so.62: cannot open shared object file: No such file or directory
2: In grDevices:::png("/tmp/RtmpsXd9n8/6f8227ef665849fb83a03d96380b8980.png", ... :
failed to load cairo DLL

The ggplot() function works fine in R when run in terminal.

I have installed Cairo package and I do see cairo.so in the folder '/usr/lib/R/library/grDevices/libs//

DOo I need to re-install the RStudio or is there something else I am missing here??

Thanks

This caused some confusion as some of the OHSDI OMOP CMD training specifically asks for details around foreign keys, those are technical go to the database as a source of truth, especially for a listing.

This may apply to all the datasets in the image.

HTTP Status 404 - Not Found
Hello
I need a hand with this, I'm trying to run atlas from the cloud but when the machine finally runs and is perfectly mounted, this inconvenience occurs when opening the browser from the remote desktop.
Any help?

I originally used the OHDSI-in-a-box stack. I was able to access via remote desktop. I am trying to create ETL database. So I followed the instructions in the OHDSI-In-a-box-PostgreSQL-QuickStart-Installation-Guide-v1.05.pdf. I am not able to access S3 bucket to sync.
Please help.

I get the following error message:

C:\Users\Administrator.aws>aws s3 sync s3://ohdsi-installation-preperation/software/ C:\ohdsi\install\software
fatal error: An error occurred (SignatureDoesNotMatch) when calling the ListObjectsV2 operation: The request signature we calculated does not match the signature you provided. Check your key and signing method.

I tried to access S3 bucket using the aboave s3://ohdsi-installation-preperation link. I got the following error message:

Thanks,
Priya

Dear,

I'm trying to follow your 'OHDSI In-a-box Quick Start – Installation Guide' for POSTGRESQL.

I've got an error on this step 'WebAPI Initialization -> 4) Click on the Start Button for the WebAPI service'

When I click the 'Start' button in 'WebAPI' section, I received the following message:

FAIL - Application at context path [/WebAPI] could not be started
FAIL - Encountered exception [org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/WebAPI]]]

Ane, when I launched the atlas, I also received this error message:

application initialization failed
unable to connect to an instance of the webapi.
please contact your administrator to resolve this issue.

*I'm following your guide on VMware station 15.

Hello,

The AWS create stack process for the OHDSI-in-a-box fails. The following message is displayed:

2020-01-13 14:30:00 UTC+0200 | EC2InstancesFunction | CREATE_FAILED | The runtime parameter of nodejs8.10 is no longer supported for creating or updating AWS Lambda functions. We recommend you use the new runtime (nodejs12.x) while creating or updating functions. (Service: AWSLambdaInternal; Status Code: 400; Error Code: InvalidParameterValueException; Request ID: bf31d60c-90da-40e9-ad1b-cddf21e3c201)

Could you please suggest how to progress with OHDSI-in-a-box deployment? Thank you for help.

No matter which option I use, it tries to connect to port 3350 (instead of 3389?) and says login failure. Yes, I carefully read the instructions and I know my password is correct.

Unfortunately, the app does not seem to permit ssh into the instance so that problems could be debugged.

I can't seem to find the AMI image. Is it region locked to a specific region? I am on the Ohio region. Thanks!

Hello
I created an instance on AWS as instructed. However, when connecting to it I get the error:

application initialization failed
unable to connect to an instance of the web API.
please contact your administrator to resolve this issue.
I see the ATLAS menu on the left hand side but nothing can be selected or viewed because of the error.

What could be the issue. Thank you

Hello,

I tried several times to follow the instructions mentionned on this Github. So, I successfully create the OHDSI stack with the associated instances, but, when I c/p the public IPv4 and try to connect with the remote desktop manager of Windows, nothing happens. The connection is simply refused as the server was down. Same for a ping, each paquet is lost.

I do not have any warning or error message, so I really have no idea of what's wrong...

Do you have any idea ?

Thanks in advance,

Nathalie

This appears to be by design, but is there a statement anywhere in the project's documentation that this data would be excluded?

Is there a reason why something like Docker / Docker-Compose isn't used, or is it something that hasn't been explored yet?

I was reading through the Quickstart and it seems like most of the components involved installing dependencies which could be standardized using Dockerfiles, and organized as a network with a docker-compose.yml file, then deployed to AWS using ECR/ECS. This could be a viable alternative or successor methodology

Dear,

I trying to run AchillesWeb. I have changed the datasourcepath, but it still does not work. What else do I need to change?

Thanks!

Hi,

We have problems with AWS in China, is there any possible to pack up all the stuff from the VM and clone them onto the other cloud base platforms?

Thanks

When following steps to add users, all apps are not visible and there is an error when attempting to access files:

After creating the stack and connecting, I am able to see all the applications, connect to the database, etc. However, when I click on the Chrome application it gets stuck waiting for localhost.

I saw in a previous ticket that ATLAS is running on port 80, so to be sure I tried localhost:80 and I got the ATLAS splash screen. However, it still seems to get stuck there. How can I debug it? @JamesSWiggins