I am trying to use config.yml in R. But whenever I load the file using
my config file looks like this
default:
dataconnection:
driver: 'ODBC Driver 11 for SQL Server'
server: 'server'
uid: 'Username'
pwd: 'password'
port: 1433
database: 'Data_Science'
rsconnect:
dataconnection:
driver: 'FreeTDS'
server: 'server'
uid: 'username'
pwd: 'password'
port: 1433
database: 'Data_Science'
Code:
config <- config::get(file = "C:/Users/Samuel.Golomeke/Documents/Data Science/Codes/R codes/SQL_Server_shiny_connect/config")
I keep getting the following warning message:
Warning message:
In readLines(con) :
incomplete final line found on 'C:\Users\Samuel.Golomeke\Documents\Data Science\Codes\R codes\SQL_Server_shiny_connect\config.yaml'"
why is that?
Make sure the last line in the config.yaml file has a blank line with no whitespace (space, tab, etc).
Related
I'm working on the observability part of Opensearch so I'm trying to collect the trace data of a wordpress website and send it to Opensearch.
I'm collecting the trace data using the wordpress plugin Decalog, this later sends the data to Jaeger agent, then from jaeger i'm sending the data to Opentelemetry and then to Data prepper and lastly to Opensearch.
Jaeger agent service in docker-compose :
jaeger-agent:
container_name: jaeger-agent
image: jaegertracing/jaeger-agent:latest
command: [ "--reporter.grpc.host-port=otel-collector:14250" ]
ports:
- "5775:5775/udp"
- "6831:6831/udp"
- "6832:6832/udp"
- "5778:5778/tcp"
networks:
- our-network
The "command" ligne got me this error : Err: connection error: desc = "transport: Error while dialing dial tcp: lookup otel-collector on 127.0.0.11:53: server misbehaving"","system":"grpc","grpc_log":true
So I changed otel-collector to the IP of the otel-collector container.
Otel collector and data prepper are installed using docker-compose.
data-prepper:
restart: unless-stopped
container_name: data-prepper
image: opensearchproject/data-prepper:latest
volumes:
- ./data-prepper/examples/trace_analytics_no_ssl.yml:/usr/share/data-prepper/pipelines.yaml
- ./data-prepper/examples/data-prepper-config.yaml:/usr/share/data-prepper/data-prepper-config.yaml
- ./data-prepper/examples/demo/root-ca.pem:/usr/share/data-prepper/root-ca.pem
ports:
- "21890:21890"
networks:
- our-network
depends_on:
- "opensearch"
otel-collector:
container_name: otel-collector
image: otel/opentelemetry-collector:0.54.0
command: [ "--config=/etc/otel-collector-config.yml" ]
working_dir: "/project"
volumes:
- ${PWD}/:/project
- ./otel-collector-config.yml:/etc/otel-collector-config.yml
- ./data-prepper/examples/demo/demo-data-prepper.crt:/etc/demo-data-prepper.crt
ports:
- "4317:4317"
depends_on:
- data-prepper
networks:
- our-network
The configuration of otel.yaml (to send data from opentelemetry to opensearch):
receivers:
jaeger:
protocols:
grpc:
exporters:
otlp/2:
endpoint: data-prepper:21890
tls:
insecure: true
insecure_skip_verify: true
logging:
service:
pipelines:
traces:
receivers: [jaeger]
exporters: [logging, otlp/2]
The configuration for data prepper pipeline : entry-pipeline:
delay: "100"
source:
otel_trace_source:
ssl: false
sink:
- pipeline:
name: "raw-pipeline"
- pipeline:
name: "service-map-pipeline"
raw-pipeline:
source:
pipeline:
name: "entry-pipeline"
prepper:
- otel_trace_raw_prepper:
sink:
- opensearch:
hosts: [ "http://localhost:9200" ]
cert: "/usr/share/data-prepper/root-ca.pem"
username: "admin"
password: "admin"
trace_analytics_raw: true
service-map-pipeline:
delay: "100"
source:
pipeline:
name: "entry-pipeline"
prepper:
- service_map_stateful:
sink:
- opensearch:
hosts: ["http://localhost:9200"]
cert: "/usr/share/data-prepper/root-ca.pem"
username: "admin"
password: "admin"
trace_analytics_service_map: true
As of now I'm getting the following errors:
Jaeger agent :
Err: connection error: desc = \"transport: Error while dialing dial tcp otel-collector-container-IP:14250: i/o timeout\"","system":"grpc","grpc_log":true}
Open telemetry collector :
2022-08-04T15:31:32.675Z info pipelines/pipelines.go:78 Exporter is starting... {"kind": "exporter", "data_type": "traces", "name": "logging"}
2022-08-04T15:31:32.675Z info pipelines/pipelines.go:82 Exporter started. {"kind": "exporter", "data_type": "traces", "name": "logging"}
2022-08-04T15:31:32.675Z info pipelines/pipelines.go:78 Exporter is starting... {"kind": "exporter", "data_type": "traces", "name": "otlp/2"}
2022-08-04T15:31:32.682Z info pipelines/pipelines.go:82 Exporter started. {"kind": "exporter", "data_type": "traces", "name": "otlp/2"}
2022-08-04T15:31:32.682Z info pipelines/pipelines.go:86 Starting processors...
2022-08-04T15:31:32.682Z info pipelines/pipelines.go:98 Starting receivers...
2022-08-04T15:31:32.682Z info pipelines/pipelines.go:102 Exporter is starting... {"kind": "receiver", "name": "jaeger", "pipeline": "traces"}
2022-08-04T15:31:32.683Z info static/strategy_store.go:203 No sampling strategies provided or URL is unavailable, using defaults {"kind": "receiver", "name": "jaeger", "pipeline": "traces"}
2022-08-04T15:31:32.683Z info pipelines/pipelines.go:106 Exporter started. {"kind": "receiver", "name": "jaeger", "pipeline": "traces"}
2022-08-04T15:31:32.683Z info service/collector.go:220 Starting otelcol... {"Version": "0.54.0", "NumCPU": 2}
2022-08-04T15:31:32.683Z info service/collector.go:128 Everything is ready. Begin running and processing data.
2022-08-04T15:31:32.684Z warn zapgrpc/zapgrpc.go:191 [core] [Channel #1 SubChannel #2] grpc: addrConn.createTransport failed to connect to {
"Addr": "data-prepper:21890",
"ServerName": "data-prepper:21890",
"Attributes": null,
"BalancerAttributes": null,
"Type": 0,
"Metadata": null
}. Err: connection error: desc = "transport: Error while dialing dial tcp data-prepper-container-ip:21890: connect: connection refused" {"grpc_log": true}
Data prepper :
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [com.amazon.dataprepper.DataPrepper]: Constructor threw exception; nested exception is java.lang.RuntimeException: No valid pipeline is available for execution, exiting
Followed by this at the end :
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2022-08-04T15:23:22,803 [main] INFO com.amazon.dataprepper.parser.config.DataPrepperAppConfiguration - Command line args: /usr/share/data-prepper/pipelines.yaml,/usr/share/data-prepper/data-prepper-config.yaml
2022-08-04T15:23:22,806 [main] INFO com.amazon.dataprepper.parser.config.DataPrepperArgs - Using /usr/share/data-prepper/pipelines.yaml configuration file
Opensearch needs a separate tool to support ingestion of Opentelemetry data. It is called DataPrepper and is part of the Opensearch project. There is a nice getting started guide on how to set up trace analytics in Opensearch.
DataPrepper works similar as Fluentd or the Opentelemetry Collector, but has proper support for Opensearch as a data sink. It pre-processes trace data adequately for the Opensearch Dashboards UI tracing plugin. DataPrepper also supports the Opentelemetry metrics format.
Are you still having issues running Data Prepper? The configuration used in this example has been updated since the latest release, and should now be up to date and working (https://github.com/opensearch-project/data-prepper/blob/main/examples/trace_analytics_no_ssl.yml)
Background
I have a YAML file like this on a web server. I am trying to read it and make user accounts in the file with an Ansible playbook.
users:
- number: 20210001
name: Aoki Alice
id: alice
- number: 20210002
name: Bob Bryant
id: bob
- number: 20210003
name: Charlie Cox
id: charlie
What I tried
To confirm how to read a downloaded YAML file dynamically with include_vars, I had written a playbook like this:
- name: Add users from list
hosts: workstation
tasks:
- name: Download yaml
get_url:
url: http://fqdn.of.webserver/path/to/yaml.yml
dest: "/tmp/tmp.yml"
notify:
- Read yaml
- List usernames
handlers:
- name: Read yaml
include_vars:
file: /tmp/tmp.yml
name: userlist
- name: List usernames
debug:
var: "{{ item }}"
loop: "{{ userlist.users }}"
Problem
In the handler Read yaml, I got the following error message. On the target machine (workstation.example.com), /tmp/tmp.yml is downloaded correctly.
RUNNING HANDLER [Read yaml] *****
fatal: [workstation.example.com]: FAILED! => {"ansible facts": {"userlist": []},
"ansible included var files": [], "changed": false, "message": "Could not find o
r access '/tmp/tmp. yml' on the Ansible Controller.\nIf you are using a module a
nd expect the file to exist on the remote, see the remote src option"}
Question
How can I get a YAML file with HTTP and use it as a variable with include_vars?
Another option would be to use the uri module to retrieve the value into an Ansible variable, then the from_yaml filter to parse it.
Something like:
- name: Add users from list
hosts: workstation
tasks:
- name: Download YAML userlist
uri:
url: http://fqdn.of.webserver/path/to/yaml.yml
return_content: yes
register: downloaded_yaml
- name: Decode YAML userlist
set_fact:
userlist: "{{ downloaded_yaml.content | from_yaml }}"
Note that uri works on the Ansible Controller, while get_url works on the target host (or on the host specified in delegate_to); depending on your network configuration, you may need to use different proxy settings or firewall rules to permit the download.
The include_vars task looks for files on the local (control) host, but you've downloaded the file to /tmp/tmp.yml on the remote host. There are a number of ways of getting this to work.
Perhaps the easiest is just running the download task on the control machine instead (note the use of delegate_to):
tasks:
- name: Download yaml
delegate_to: localhost
get_url:
url: http://fqdn.of.webserver/path/to/yaml.yml
dest: "/tmp/tmp.yml"
notify:
- Read yaml
- List usernames
This will download the file to /tmp/tmp.yml on the local system, where it will be available to include_vars. For example, if I run this playbook (which grabs YAML content from an example gist I just created)...
- hosts: target
gather_facts: false
tasks:
- name: Download yaml
delegate_to: localhost
get_url:
url: https://gist.githubusercontent.com/larsks/70d8ac27399cb51fde150902482acf2e/raw/676a1d17bcfc01b1a947f7f87e807125df5910c1/example.yaml
dest: "/tmp/tmp.yml"
notify:
- Read yaml
- List usernames
handlers:
- name: Read yaml
include_vars:
file: /tmp/tmp.yml
name: userlist
- name: List usernames
debug:
var: item
loop: "{{ userlist.users }}"
...it produces the following output:
RUNNING HANDLER [Read yaml] ******************************************************************
ok: [target]
RUNNING HANDLER [List usernames] *************************************************************
ok: [target] => (item=bob) => {
"ansible_loop_var": "item",
"item": "bob"
}
ok: [target] => (item=alice) => {
"ansible_loop_var": "item",
"item": "alice"
}
ok: [target] => (item=mallory) => {
"ansible_loop_var": "item",
"item": "mallory"
}
Side note: based on what I see in your playbook, I'm not sure you want
to be using notify and handlers here. If you run your playbook a
second time, nothing will happen because the file /tmp/tmp.yml
already exists, so the handlers won't get called.
With #Larsks 's answer, I made this playbook that works correctly in my environment:
- name: Download users list
hosts: 127.0.0.1
connection: local
become: no
tasks:
- name: Download yaml
get_url:
url: http://fqdn.of.webserver/path/to/yaml/users.yml
dest: ./users.yml
- name: Add users from list
hosts: workstation
tasks:
- name: Read yaml
include_vars:
file: users.yml
- name: List usernames
debug:
msg: "{{ item.id }}"
loop: "{{ users }}"
Point
Run get_url on the control host
As #Larsks said, you have to run the get_url module on the control host rather than the target host.
Add become: no to the task run on the control host
Without "become: no", you will get the following error message:
TASK [Gathering Facts] ******************************************************
fatal: [127.0.0.1]: FAILED! => {"ansible_facts": {}, "changed": false, "msg":
"The following modules failed to execute: setup\n setup: MODULE FAILURE\nSee
stdout/stderr for the exact error\n"}
Use connection: local rather than local_action
If you use local_action rather than connection: local like this:
- name: test get_url
hosts: workstation
tasks:
- name: Download yaml
local_action:
module: get_url
url: http://fqdn.of.webserver/path/to/yaml/users.yml
dest: ./users.yml
- name: Read yaml
include_vars:
file: users.yml
- name: output remote yaml
debug:
msg: "{{ item.id }}"
loop: "{{ users }}"
You will get the following error message:
TASK [Download yaml] ********************************************************
fatal: [workstation.example.com]: FAILED! => {"changed": false, "module_stde
rr": "sudo: a password is required\n", "module_stdout":"", "msg":"MODULE FAIL
URE\nSee stdout/stderr for the exact error", "rc": 1}
get_url stores a file on the control host
In this situation, the get_url module stores users.yml on the control host (in the current directory). So you have to delete the users.yml if you don't want to leave it.
I have:
a simple Python app ("iss-web") writing JSON log output to stdout
the Python app ("iss-web") is within a Docker Container
the Python app ("iss-web") Container logging driver is set to "fluentd"
a separate Container running "fluent/fluent-bit:1.7" to collect the Python app JSON log output
Loki 2.2.1 deployed via a Container to receive the Python app log output from fluent-bit
Grafana connected to Loki to visualize the log data
The issue is that the "log" field is not filtered/parsed by fluent-bit, therefore in Loki/Grafana the content of the "log" field is not parsed and used as "Detected fields".
"iss-web" docker-compose.yml
version: '3'
services:
iss-web:
build: ./iss-web
image: iss-web
container_name: iss-web
env_file:
- ./iss-web/app.env
ports:
- 46664:46664
logging:
driver: fluentd
options:
tag: iss.web
redis:
image: redis
container_name: redis
ports:
- 6379:6379
logging:
driver: "json-file"
options:
max-file: ${LOG_EXPIRE}
max-size: ${LOG_SEGMENT}
"fluent-bit" docker-compose.yml
version: '3'
services:
fluent-bit:
image: fluent/fluent-bit:1.7
container_name: fluent-bit
environment:
- LOKI_URL=http://135.86.186.75:3100/loki/api/v1/push
user: root
volumes:
- ./fluent-bit.conf:/fluent-bit/etc/fluent-bit.conf
- ./parsers.conf:/fluent-bit/etc/parsers.conf
ports:
- "24224:24224"
- "24224:24224/udp"
fluent-bit.conf
[SERVICE]
Flush 1
Daemon Off
log_level debug
Parsers_File /fluent-bit/etc/parsers.conf
[INPUT]
Name forward
Listen 0.0.0.0
port 24224
[FILTER]
Name parser
Match iss.web
Key_Name log
Parser docker
Reserve_Data On
Preserve_Key On
[OUTPUT]
Name loki
Match *
host 135.86.186.75
port 3100
labels job=fluentbit
[OUTPUT]
Name stdout
Match *
parsers.conf
I've tried with/without Time_Key, Time_Format, Time_Keep
[PARSER]
Name docker
Format json
#Time_Key time
#Time_Format %Y-%m-%dT%H:%M:%S.%L
#Time_Keep On
# Command | Decoder | Field | Optional Action
# =============|==================|=================
#Decode_Field_As escaped_utf8 log do_next
Decode_Field_As json log
fluent-bit log extract
[0] iss.web: [1620640820.000000000, {"log"=>"{'timestamp': '2021:05:10 11:00:20.439513', 'epoch': 1620640820.4395688, 'pid': 1, 'level': 'DEBUG', 'message': '/ping', 'data': {'message': 'PONG', 'timestamp': '1620640820.4394963', 'version': '0.1'}}", "container_id"=>"bffd720e9ac1e8c3992c1120eed37e00c536cd44ec99e9c13cf690d840363f80", "container_name"=>"/iss-web", "source"=>"stdout"}]
Grafana/Loki screen
I would expect the "Detected fields" to contain pid=1, message=/ping etc
I needed a "json.dumps" in my "logger":
def log(message, level="INFO", **extra):
out = {"timestamp": get_now(), "epoch": get_epoch(), "pid": get_pid(), "level": level, "message": message}
if extra: out |= extra
print(json.dumps(out), flush=True)
return True
I was setting up Argo in my k8s cluster in Argo namespace.
I also Installed MinIO as an Artifact repository (https://github.com/argoproj/argo-workflows/blob/master/docs/configure-artifact-repository.md).
I am configuring a workflow which tries to access that Non-Default Artifact Repository as:
apiVersion: argoproj.io/v1alpha1
kind: Workflow
metadata:
generateName: artifact-passing-
spec:
entrypoint: artifact-example
templates:
- name: artifact-example
steps:
- - name: generate-artifact
template: whalesay
- - name: consume-artifact
template: print-message
arguments:
artifacts:
# bind message to the hello-art artifact
# generated by the generate-artifact step
- name: message
from: "{{steps.generate-artifact.outputs.artifacts.hello-art}}"
- name: whalesay
container:
image: docker/whalesay:latest
command: [sh, -c]
args: ["cowsay hello world | tee /tmp/hello_world.txt"]
outputs:
artifacts:
# generate hello-art artifact from /tmp/hello_world.txt
# artifacts can be directories as well as files
- name: hello-art
path: /tmp/hello_world.txt
s3:
endpoint: argo-artifacts-minio.argo:9000
bucket: my-bucket
key: /my-output-artifact.tgz
accessKeySecret:
name: argo-artifacts-minio
key: accesskey
secretKeySecret:
name: argo-artifacts-minio
key: secretkey
- name: print-message
inputs:
artifacts:
# unpack the message input artifact
# and put it at /tmp/message
- name: message
path: /tmp/message
s3:
endpoint: argo-artifacts-minio.argo:9000
bucket: my-bucket
accessKeySecret:
name: argo-artifacts-minio
key: accesskey
secretKeySecret:
name: argo-artifacts-minio
key: secretkey
container:
image: alpine:latest
command: [sh, -c]
args: ["cat /tmp/message"]
I created the workflow in argo namespace by:
argo submit --watch artifact-passing-nondefault-new.yaml -n argo
But the workflow fails with an error:
STEP PODNAME DURATION MESSAGE
✖ artifact-passing-z9g64 child 'artifact-passing-z9g64-150231068' failed
└---⚠ generate-artifact artifact-passing-z9g64-150231068 12s failed to save outputs: Get https://argo-artifacts-minio.argo:9000/my-bucket/?location=: http: server gave HTTP response to HTTPS client
Can someone help me to solve this error?
Since the minio setup runs without TLS configured, the workflow should specify that it should connect to an insecure artifact repository.
Including a field insecure: true in the s3 definition section of the workflow solves the issue.
s3:
endpoint: argo-artifacts-minio.argo:9000
insecure: true
bucket: my-bucket
key: /my-output-artifact.tgz
accessKeySecret:
name: argo-artifacts-minio
key: accesskey
secretKeySecret:
name: argo-artifacts-minio
key: secretkey
I've been working with Symfony 2.7 and the RabbitMQBundle to handle some long processes asynchronously.
After facing the issue where the MySQL connection dies after a few minutes, I discovered rabbitmq-cli-consumer, a small app in Go that takes care of consuming the queue, and gives its content to a command.
In my case, I use it with this command: ./rabbitmq-cli-consumer -c configuration-stock.conf --include -V -e 'php app/console amqp:consume:stock --env=prod -vvv', with this configuration file:
[rabbitmq]
host = HOST
username = USERNAME
password = PASSWORD
vhost=/VHOST
port=PORT
queue=stock
compression=Off
[exchange]
name=exports
type=direct
durable=On
[queuesettings]
routingkey=stock
messagettl=10000
deadLetterExchange=exports.dl
deadLetterroutingkey=stock
priority=10
To handle errors, I intend to use RabbitMQ's x-dead-letter-exchange and x-dead-letter-routing-key configuration, to be able to retry the message later (in case something went temporarly wrong).
My issue is that, when I define my queues in RabbitMQBundle's configuration, rabbitmq-cli-consumer is unable to consume the queue, throwing this error:
2018/04/23 11:35:54 Connecting RabbitMQ...
2018/04/23 11:35:54 Connected.
2018/04/23 11:35:54 Opening channel...
2018/04/23 11:35:54 Done.
2018/04/23 11:35:54 Setting QoS...
2018/04/23 11:35:54 Succeeded setting QoS.
2018/04/23 11:35:54 Declaring queue "stock"...
2018/04/23 11:35:54 Registering consumer...
2018/04/23 11:35:54 failed to register a consumer: Exception (504) Reason: "channel/connection is not open"
Here is the configuration I use for RabbitMQBundle:
old_sound_rabbit_mq:
producers:
exports:
connection: default
exchange_options:
name: 'exports'
type: direct
exports_dl:
connection: default
exchange_options:
name: 'exports.dl'
type: direct
consumers:
stock_dead_letter:
connection: default
exchange_options:
name: exports.dl
type: direct
queue_options:
name: stock.dl
routing_keys:
- stock
arguments:
x-dead-letter-exchange: ['S', 'exports']
x-dead-letter-routing-key: ['S', 'stock']
x-message-ttl: ['I', 60000]
callback: amqp.consumers.exports.stock
multiple_consumers:
exports:
connection: default
exchange_options:
name: 'exports'
type: direct
queues:
stock:
name: stock
callback: amqp.consumers.exports.stock
routing_keys:
- stock
arguments:
x-dead-letter-exchange: ['S', 'exports.dl']
x-dead-letter-routing-key: ['S', 'stock']
Has anyone ever encountered something similar ? And how did you solve it ?