Troubleshooting

Some topics (sorry disorganized notes)

Containers
- can't seem to connect
- Complaints about bad certificate
- cannot connect to (minioadmin,graph,sparqlui)
- Minoadmin/Graph/etc seem to be there, but do not connect
glcon/gleaner application
Blazegraph
- journal truncation
updating portainer
OS issues
- Ubuntu docker
- Ubuntu 16. glcon
issue with a repository

can't seem to connect;

are containers running docker ps

can you connect to portainer and traefik

traefik:

https://admin.{HOST}

portainer:

https://portainer.{host}

In traefik, are errors on the https://admin.{host}

Complaints about bad certificate

Initially, we are using letsencypt dev services. THis message will show until you rebuild the base containers with the dev line commented out

But that line is commented out.

need to delete the acme.json and restart the container.

log onto console via portainer, use /bin/sh

/ # ls
acme.json      dev            etc            lib            mnt            proc           run            srv            tmp            var
bin            entrypoint.sh  home           media          opt            root           sbin           sys            usr
/ # cat acme.json 
{
  "httpresolver": {
    "Account": {
      "Email": "dwvalentine@ucsd.edu",
      "Registration": {
        "body": {
          "status": "valid",
          "contact": [
            "mailto:dwvalentine@ucsd.edu"
          ]
        },
        "uri": "https://acme-v02.api.letsencrypt.org/acme/acct/1030461777"

rm acme.json

some docker command also...

cannot connect to (minioadmin,graph,sparqlui)

is the traefik proxy a SCOPE swarm docker network ls
portainerui, networks
is the DNS correct?
need a dig example, since editing host and NS looku
are they running?
docker ps
- do you see portainer stack

Minoadmin/Graph/etc seem to be there, but do not connect

If minioadmin complains that it cannot connect with a 10.0.0.x message, then there may be two

open portainer
select containers
sort by name
look and see if two of the s3 stack are running.
if yes, delete both, and one should restart.

have also seen something similar for graph.

glcon

setup failure

./glcon gleaner setup --cfgName {name}

{"file":"/github/workspace/pkg/gleaner.go:63","func":"github.com/gleanerio/gleaner/pkg.Setup","level":"error","msg":"Connection issue, make sure the minio server is running and accessible.The Access Key Id you provided does not exist in our records.","time":"2022-07-22T19:08:01Z"}

You probably have environment variables set.

ubuntu@geocodes-dev:~/indexing$ env
[snip]
MINIO_SECRET_KEY=MySecretSecretKeyforMinio
MINIO_ACCESS_KEY=MySecretAccessKey
[snip]
ubuntu@geocodes-dev:~/indexing$ unset MINIO_SECRET_KEY
ubuntu@geocodes-dev:~/indexing$ unset MINIO_ACCESS_KEY

Blazegraph journal truncation:

for a container

in newer container, the command is available, but the service needs to be stopped. guess running an container with an exec command in a different container might work.

cd /var/lib/blazegraph ;java -jar /usr/bin/blazegraph.jar com.bigdata.journal.CompactJournalUtility blazegraph.jnl blazegraph.jnl.compact

count quads

SELECT (COUNT(*) as ?Triples) WHERE {graph ?g {?s ?p ?o}}

updating Portainer, or treafik

the latest image needs to be pulled

docker pull portainer/portainer-ce:latest

then ./run_base.sh

OS Issues

place where os issues may be

Ubuntu Docker

If you are running on Ubuntu, you need to remove the provided docker.com version. Official docker package We suggest that for others, confirm that you can run

```shell
docker compose version
Docker Compose version v2.13.0
```

If you cannot run `docker compose` then update to the docker.com version
This is the version we are presently running.

```    
Client: Docker Engine - Community
     Version:           20.10.21
     API version:       1.41
```

Ubuntu 18 and glcon

there appears to be issues with Ubuntu 18 and the latest versions of the golang library viper. If you run on Ubuntu 20.X it works. Solution is to 'do-realse-upgrade' and wait ;)

shell ubuntu@geocodes-dev:~$ uname -a Linux geocodes-dev 4.15.0-194-generic #205-Ubuntu SMP Fri Sep 16 19:49:27 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux ubuntu@geocodes-dev:~$ cd indexing/ ubuntu@geocodes-dev:~/indexing$ ./glcon gleaner batch --cfgName ci version: v3.0.8-ec {"file":"/Users/valentin/development/dev_earthcube/gleanerio/gleaner/pkg/cli/gleaner.go:71","func":"github.com/gleanerio/gleaner/pkg/cli.initGleanerConfig","level":"fatal","msg":"error reading config file While parsing config: yaml: unmarshal errors:\n line 1: cannot unmarshal !!str `\u003c?xml v...` into map[string]interface {}","time":"2023-02-14T15:58:00Z"} ubuntu@geocodes-dev:~/indexing$