Troubleshooting Common Issues and

Solutions to MongoDB ETL Errors

Sandeep Devarapalli · Mar 29, 2023 · 16 min read

Data Engineering

Troubleshooting
CommonIssues
andSolutionsto
MongoDBETL mongoDB.
Errors

MongoDB is a popular NoSQL document-oriented database that

allows for flexible and scalable data storage, querying and
manipulation. Its JSON-like document format allows for dynamic
schema design and easy representation of complex data
structures. Users may encounter MongoDB ETL errors while using
:
 MongoDB. So, understanding the common MongoDB ETL errors
and implementing best practices can minimize issues and
optimize the MongoDB experience

In this article, we will be exploring the different types of best

practices to set up MongoDB for ETL (extraction, transformation,
and loading errors) and also analytics. Further, we will work on
troubleshooting the common issues of MongoDB ETL errors.

Contents

Setting up MongoDB for ETL

Maximizing MongoDB for Analytics

Common Errors when connecting to MongoDB Atlas

Popular MongoDB ETL Errors

Common Errors when syncing multi-document transactions from

MongoDB

Custom solutions for syncing multi-document transactions from

MongoDB

Conclusion

Setting up MongoDB for ETL

:
 Before diving into the MongoDB ETL issues, let us understand
some of the best practices for setting up MongoDB for ETL.
Depending on your budget, infrastructure requirements, and use
case, there are several ways to set up MongoDB. Some of them
are listed as follows.

Learn how Datazip helped Topmate increase their customer growth

Local Installation

Installing MongoDB on your development environment or local

machine is typically used for development and testing purposes.

Follow the installation instructions for your specific operating

system from the MongoDB documentation:

Windows users

macOS

Linux

Self-Hosted

You can set up MongoDB on your virtual machines or servers in a

cloud environment or data center. This approach provides more
control over the security, infrastructure, and configuration.

You can follow the installation instructions for various

environments and platforms in the MongoDB documentation.

Docker
:
 You can run MongoDB using Docker containers, which simplifies
deployment and ensures consistent environments. You can use
the official MongoDB Docker image to set up a container running
MongoDB.

MongoDB Atlas

MongoDB Atlas is a fully managed, global cloud database service

provided by MongoDB. It allows you to easily deploy, operate, and
scale your MongoDB instances in the cloud. With built-in
automation, security, and monitoring features, Atlas simplifies the
process of managing your databases and ensures optimal
performance. By choosing MongoDB Atlas, you can take
advantage of the benefits of a managed service, including
automatic backups, scaling, and patches, as well as a range of
integrations with other cloud services.

To get started with MongoDB Atlas, sign up for an account and

follow the guided setup to create and configure your cluster. You
can choose from various cloud providers, regions, and instance
sizes to best suit your needs. Once your cluster is up and running,
you can connect your ETL tools and applications using the
provided connection strings and credentials.

Maximizing MongoDB for Analytics

Before deep-diving into detailed solutions on addressing the
MongoDB ETL issues, let’s first cover best practices to set up your
MongoDB cluster in a way that doesn’t impact your operational
:
 database.

For this, we will discuss some of the MongoDB Analytics Setup

Best Practices now.

At the very least, always point your analytics client to a secondary

node instead of your primary node from your analytics application,
so that operational performance is not affected.

Configure a hidden replica set member V This prevents this replica

set member from becoming a primary. A hidden member maintains
a copy of the primary’s data but is invisible to client applications
and can thus be used for read-only analytics purposes. To connect
to a hidden member, use the directConnect option.

Example

mongodb://user:password@192.168.0.1_27017/?
authSource=db&directConnection=True

If you are using MongoDB Atlas with an M10 or larger cluster,

set up an Analytics Node. Analytics Nodes isolate queries on
read-only nodes that do not contend with operational
workloads.

To connect, use a connection string like below:

mongodb+srv://eUSERNAMEg_ePASSWORD>@foo-
q8i1v.mycluster.com/test?
readPreference=secondary&readPreferenceTags=nodeType:
ANALYTICS
:
 Let us now divide these common MongoDB ETL errors and issues
in Atlas based on their category and try to understand some quick
solutions to tackle them.

Common Errors when connecting to MongoDB

Atlas

Connection timeout errors

This comes under one of the MongoDB ETL connector errors and
occurs when the connector takes too long to establish a
connection with the MongoDB Atlas cluster.

Solution: One way around this is to Increase the connection

timeout value in your connector configuration or check your
network connectivity to ensure a stable connection.

Authentication errors

These arise when the connector uses incorrect credentials to

connect to the Atlas cluster.

Solution: Some ways to work around these are to double-check

your Atlas username and password, ensuring that the user has the
correct privileges to access the cluster.

TLS/SSL certiGcate errors

These occur when the connector cannot validate the Atlas

cluster's SSL certificate.
:
 Solution: To tackle this, make sure to include the appropriate CA
kCertificate Authority) certificate in your connector's
configuration. This will enable it to establish a secure connection.

IP access list errors

These happen when your application's IP address is not

whitelisted in the MongoDB Atlas cluster.

Solution: Adding your application's IP address to the Atlas

cluster's IP access list or using a CIDR block to allow a range of IP
addresses might help to handle these errors.

Incorrect connection string

This error occurs when your connector's configuration uses an

incorrect connection string.

Solution: Verify that the connection string in your configuration

matches the one provided in the MongoDB Atlas dashboard. This
ensures that it includes the correct cluster address and replica set
information.

DNS resolution errors

These happen when the connector cannot resolve the domain

name in the connection string.

Solution: Check your DNS settings, and ensure that your system
can resolve the Atlas cluster's domain name.
:
 Exceeded a maximum number of connections

This error occurs when your application attempts to open more

connections than allowed by the Atlas cluster's maximum
connection limit.

Solution: Either Close any unused connections or if applicable,

increase the maximum connection limit in your Atlas cluster's
settings.

Driver compatibility issues

These arise when your connector's driver is incompatible with the

version of MongoDB used in your Atlas cluster.

Solution: Update your connector's driver to the latest version or

one that is compatible with your Atlas cluster's MongoDB version.

Note: Each error's solution may vary depending on the specific

circumstances, and the above solutions serve as a general guide.
Consult the MongoDB Atlas documentation and relevant forums
for more details on troubleshooting and resolving these common
errors.

Most Common MongoDB ETL Errors

:
 MostCommonMongoDB
ETLErrors

"Connectionrefused"error

(2"Invalidcredentials"error

(3]"Unabletofetchcollections"error

4I"SSLcertificateerror"

(5)"Timeouterror"

6"Datatypemismatch"

7"Duplicatekeyerror"

Now, let us discuss some of the various MongoDB ETL errors or

ELT errors that users have reported when trying to use ETL tools.
These include popular platforms like Fivetran, Hevo Data, Talend,
and Airbyte with the MongoDB database. Some of these include
the following.

“Connection refused” error

Occurs when the ETL tool is unable to connect to the MongoDB

server due to network issues or incorrect connection settings
from the user’s end.

"Invalid credentials" error

Usually occurs when the credentials provided to the ETL tool to

:
 authenticate with the MongoDB server are either incorrect or do
not have the required permissions to access the database.

"Unable to fetch collections” error

This error usually occurs when the ETL tool is unable to fetch the
collections from the MongoDB server. This can happen if there are
network issues or the server is down.

"SSL certiGcate error"

This occurs when the ETL tool is unable to verify the SSL
certificate provided by the MongoDB server. This can happen if
the certificate is either invalid or if the ETL tool does not have the
necessary CA certificates installed.

"Timeout error"

Occurs when the ETL tool is unable to connect to the MongoDB

server within the specified timeout period.

This can happen due to any of the following reasons:

Network issues

Server downtime

Incorrect connection settings.

"Data type mismatch"

:
 This shows up when the ETL tool is unable to map the data types
from MongoDB to the target database. This can happen if the data
types in MongoDB and the target database are incompatible.

"Duplicate key error"

This happens when the MongoDB ETL tool is unable to insert a

record into the target database due to a duplicate key violation.
This occurs if the target database already contains a record with
the same key as the record being inserted.

Popular MongoDB ETL Errors

Timed out after 30000 ms while waiting to connect

This error is a connection error where the ETL tool is unable to

establish a connection with the MondoDB server.

Error Message

Client view of cluster state is {type=UNKNOWN,

servers=[{address=<REDACTED_DOMAIN>.mongodb.net:27017,
type=UNKNOWN, state=CONNECTING, exception=
{com.mongodb.MongoSocketException:
<REDACTED_DOMAIN>.mongodb.net}, caused by
{java.net.UnknownHostException:
<REDACTED_DOMAIN>.mongodb.net} }]

Root Cause

The error you're encountering indicates a connection timeout. The

:
 client was unable to connect to the MongoDB cluster after waiting
for 30,000 milliseconds k30 seconds). The root cause of this error
appears to be a DNS resolution issue, as seen from the
java.net.UnknownHostException in the error message.

The client cannot resolve the domain name

(<REDACTED_DOMAIN>.mongodb.net) provided in the
connection string. This issue prevents the client from
establishing a connection with the MongoDB Atlas
cluster.

Possible solutions

Verify the connection string: Double-check the connection string

to ensure it's correct and matches the one provided in the
MongoDB Atlas dashboard. Make sure there are no typographical
errors or missing information in the domain name.

Check your DNS settings: Ensure that your system is properly

configured to resolve domain names. You can test the DNS
resolution using tools like nslookup or dig (on Unix-based
systems) or by trying to access the domain in a web browser.

Use a different DNS resolver: If the issue persists, consider

changing your system's DNS resolver to a public DNS service like
Google's Public DNS k8.8.8.8 and 8.8.4.4r or Cloudflare's DNS
k1.1.1.1 and 1.0.0.1r.

Firewall or network restrictions: Check if there are any firewall

rules or network restrictions in place that could be blocking the
DNS resolution or the connection to the MongoDB Atlas cluster.
:
 Inspect the host's file: In some cases, the issue may arise from
incorrect entries in the system's hosts file (/etc/hosts on Unix-
based systems or C_\Windows\System32\drivers\etc\hosts on
Windows). Check the file to ensure that there are no conflicting or
incorrect entries.

Restart your system or network devices: Sometimes, a simple

restart of your computer, modem, or router can help resolve
temporary connectivity issues.

'Failed to Fetch Schema' Error in MongoDB ETL

The "MongoDB Failed to fetch Schema" error is one of the

MongoDB data integration problems and arises during ETL
kExtract, Transform, Load) processes. This occurs when an ETL
tool or data integration platform cannot accurately determine the
structure of the data within the MongoDB collection.

Root Causes

This error typically arises due to the following reasons:

Dynamic schema: MongoDB is a schema-less, document-

oriented database that allows flexible data storage in BSON
format. Documents within the same collection can have different
structures or varying data types for the same field. This dynamic
schema can make it challenging for ETL tools to accurately map
the data structure.

Insufficient data sampling: When an ETL tool attempts to infer

the schema from a MongoDB collection, it may use sampling
:
 techniques to analyze a subset of documents. If the sample size is
too small or unrepresentative of the overall data, the inferred
schema may not accurately reflect the data's structure, leading to
the error.

Incompatible data types: Some ETL tools may not support all
BSON data types used by MongoDB, such as Decimal128 or
ObjectID. If the source collection contains unsupported data
types, the ETL tool may fail to fetch the schema.

Connectivity issues: If the ETL tool cannot establish a stable

connection with the MongoDB instance, it may fail to fetch the
schema. This can be due to network issues, incorrect connection
parameters, or IP whitelisting problems.

Possible Solutions

To resolve the "MongoDB Failed to fetch Schema" error during

ETL, consider the following solutions:

Manual schema definition: Manually define a JSON schema that

accurately represents the data structure in MongoDB. This
approach requires a deep understanding of the source data and
may need updates if the data structure changes.

Improve data sampling: Increase the sample size or use more

representative samples when inferring the schema, ensuring that
the ETL tool captures the variations in the data structure.

Data type conversions: If the ETL tool does not support specific
BSON data types, convert them to compatible data types before
:
 the ETL process.

Address connectivity issues: Check the connection parameters,

network settings, and IP whitelisting to ensure a stable connection
between the ETL tool and MongoDB instance.

Use a compatible ETL tool: Choose an ETL tool or data integration

platform that offers better support for MongoDB's dynamic
schema and BSON data types.

Learn about Kano Model

The Airbyte MongoDB connector “schema discovery issue”

Airbyte is an open-source data integration platform that simplifies

ETL by using connectors to interact with different data sources
and destinations, including MongoDB. However, the MongoDB
connector faces challenges with schema discovery due to the
dynamic nature of MongoDB's schema. MongoDB's schema-less,
the document-oriented format allows for storing unstructured and
semi-structured data in a flexible BSON format, resulting in
varying structures and data types within the same collection.

Root Cause

The schema discovery issue arises when the Airbyte MongoDB

connector tries to infer the schema from the source MongoDB
collection. Due to the lack of a fixed schema, it can be challenging
for the connector to determine the exact structure of the data,
especially if the collection has a high degree of variability.
:
 Possible Solutions

To address the schema discovery issue with the Airbyte MongoDB

connector, you can consider the following approaches.

Schema inference: The connector can use sampling techniques

to analyze a subset of documents in the MongoDB collection and
infer a schema based on the most common fields and data types.
This approach may not cover all possible variations in the data but
can provide a reasonable approximation.

Schema definition: You can manually define a JSON schema for

the MongoDB source data, ensuring that the schema accurately
represents the data structure. This approach requires a deep
understanding of the source data and may need to be updated if
the data structure evolves over time.

Schema evolution: The connector can be designed to handle

schema changes during the replication process. This involves
updating the schema in the destination whenever new fields or
data types are discovered. However, this approach may require
additional complexity and processing overhead.

Custom transformations: You can implement custom data

transformations before ingesting the data into Airbyte to
normalize the schema or convert semi-structured data (e.g., JSON
or XMLr into a structured format that can be more easily mapped
by the connector.
:
 Common Errors when syncing multi-document
transactions from MongoDB
When syncing multi-document transactions from MongoDB using
ETL tools like Airbyte, Fivetran or Hevo Data, you might encounter
the following error examples:

Unsupported MongoDB version

Example: "Error: MongoDB version not supported for multi-

document transactions."

Multi-document transactions are only supported in MongoDB 4.0

and later for replica sets, and 4.2 and later for sharded clusters.
Ensure that you are using a compatible version of MongoDB
before attempting to sync multi-document transactions.

Connector conGguration error

Example: "Error: Invalid connector configuration for syncing multi-

document transactions."

This error occurs when the connector settings in Airbyte or Hevo

Data are not configured correctly to handle multi-document
transactions. Review the connector settings and ensure they are
correctly set up for multi-document transaction syncing.

Incomplete or partial transaction data

Example: "Error: Incomplete transaction data received."

:
 This error can occur when the source MongoDB database is
experiencing high load, causing the connector to receive
incomplete or partial transaction data. Ensure that the source
MongoDB instance has sufficient resources to handle the
workload, and consider increasing the connector's timeout
settings to allow for more time to receive complete transaction
data.

Unsupported operations in transactions

Example: "Error: Unsupported operation in multi-document

transaction."

Certain operations, such as creating or dropping collections, are

not supported within multi-document transactions. If your
transaction includes unsupported operations, you may encounter
this error. To resolve this issue, remove unsupported operations
from the transaction and perform them outside the transaction
context.

Data type mismatch or schema changes

Example: "Error: Data type mismatch or schema change detected

in multi-document transaction."

This error occurs when the connector encounters a data type

mismatch or schema change during the sync process. Ensure that
the data types and schema in the source MongoDB database are
consistent with the target data store. You might need to adjust the
connector's settings to handle data type conversions or schema
:
 changes correctly.
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Custom solutions for syncing multi-document
transactions from MongoDB
Many off-the-shelf tools may not support the complex nature of
multi-document transactions. However, you can implement a
custom solution that handles these transactions more effectively.
Here's a high-level overview of how you can approach this:

wx Change Data Capture ICDCJK Leverage MongoDB's oplog

(operation log) or Change Streams to capture changes, including
multi-document transactions, in real-time. Oplog is a capped
collection that stores an ordered history of logical write operations
on a MongoDB replica set, while Change Streams provide real-
time data change notifications through MongoDB's aggregation
framework.

yx Data Transformation: Process the captured changes and

transform the data into a format that is compatible with BigQuery.
This may involve normalizing the data, converting data types, and
handling nested structures.

zx Transaction Handling: Ensure your custom ELT solution can

handle multi-document transactions by:

a. Identifying transactions in the oplog or Change Streams.

Transactions are represented as a series of operations with
:
 a unique transaction ID (txnId). Group operations with the
same txnId together to process them as a single unit.

b. Ensuring consistency and atomicity when applying

changes to BigQuery. One approach is to stage the changes
in a temporary table or dataset in BigQuery, and then apply
them as a single transaction using BigQuery's support for
DML transactions.

3. Incremental Updates: Design the custom ELT job to perform

incremental updates, minimizing the data transfer and processing
overhead. This helps in addressing and resolving MongoDB data
migration problems. Keep track of the last processed operation's
timestamp or resume token in the oplog or Change Streams, and use it
to fetch only new changes during the next run.

4. Error Handling and Monitoring: Implement robust error handling and

monitoring to ensure that the custom ELT job is resilient to failures and
provides visibility into the data sync process.

4. Scheduling and Orchestration: Use a scheduling and orchestration

tool like Apache Airflow to automate and manage the custom ELT job's
execution.

Conclusion
MongoDB is a powerful NoSQL database that provides flexible and
scalable data storage and manipulation. However, as with any
technology, it is prone to errors. In this article, we explored the most
:
 common MongoDB ETL errors and issues encountered and provided
solutions to address these issues. By understanding the common errors
and implementing best practices, users can optimize their MongoDB
experience and minimize issues.

Are you interested in unlocking the full potential of your data without
the need for expensive data teams? Look no further than Datazip - the
all-in-one, scalable data platform for organizations.

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