# API and Database

- [API Portal](/api-and-database/api-docs.md)
- [REST](/api-and-database/api-docs/rest.md)
- [REST General Concepts](/api-and-database/api-docs/rest/rest-general-concepts.md)
- [REST Web Services](/api-and-database/api-docs/rest/rest-web-services.md)
- [HTTP Response Codes and Errors](/api-and-database/api-docs/rest/http-response-codes-and-errors.md)
- [XML UTF-8 Character Encoding](/api-and-database/api-docs/rest/xml-utf-8-character-encoding.md)
- [Requesting API Version Information](/api-and-database/api-docs/rest/requesting-api-version-information.md)
- [Viewing Paginated List Resources](/api-and-database/api-docs/rest/viewing-paginated-list-resources.md)
- [Filtering List Resources](/api-and-database/api-docs/rest/filtering-list-resources.md)
- [Working with User-Defined Fields (UDF) and Types (UDT)](/api-and-database/api-docs/rest/working-with-user-defined-fields-udf-and-types-udt.md)
- [Traversing a Genealogy](/api-and-database/api-docs/rest/traversing-a-genealogy.md)
- [Working with Batch Resources](/api-and-database/api-docs/rest/working-with-batch-resources.md)
- [Getting Started with API](/api-and-database/api-docs/getting-started-with-api.md)
- [Understanding API Terminology (LIMS v5 and later)](/api-and-database/api-docs/getting-started-with-api/understanding-api-terminology-lims-v5-and-later.md)
- [API-Based URIs (LIMS v4 and later)](/api-and-database/api-docs/getting-started-with-api/api-based-uris-lims-v4-and-later.md)
- [Development Prerequisites](/api-and-database/api-docs/getting-started-with-api/development-prerequisites.md)
- [Structure of REST Resources](/api-and-database/api-docs/getting-started-with-api/structure-of-rest-resources.md)
- [The Life Cycle of a Sample: Stages Versus Steps](/api-and-database/api-docs/getting-started-with-api/the-life-cycle-of-a-sample-stages-versus-steps.md)
- [Integrating Scripts](/api-and-database/api-docs/getting-started-with-api/integrating-scripts.md)
- [Automation](/api-and-database/api-docs/automation.md)
- [Automation Triggers and Command Line Calls](/api-and-database/api-docs/automation/automation-triggers-and-command-line-calls.md)
- [Automation Execution Environment](/api-and-database/api-docs/automation/automation-execution-environment.md)
- [Supported Command Line Interpreters](/api-and-database/api-docs/automation/supported-command-line-interpreters.md)
- [Automation Channels](/api-and-database/api-docs/automation/automation-channels.md)
- [Error Handling](/api-and-database/api-docs/automation/error-handling.md)
- [Automation Tokens](/api-and-database/api-docs/automation/automation-tokens.md)
- [Derived Sample Automation Tokens](/api-and-database/api-docs/automation/automation-tokens/derived-sample-automation-tokens.md)
- [Step Automation Tokens](/api-and-database/api-docs/automation/automation-tokens/step-automation-tokens.md)
- [Project Automation Tokens](/api-and-database/api-docs/automation/automation-tokens/project-automation-tokens.md)
- [Automation Testing](/api-and-database/api-docs/automation/automation-testing.md)
- [Troubleshooting Automation](/api-and-database/api-docs/automation/troubleshooting-automation.md)
- [Tips and Tricks](/api-and-database/api-docs/tips-and-tricks.md)
- [Accessing Step UDFs from a different Step](/api-and-database/api-docs/tips-and-tricks/accessing-step-udfs-from-a-different-step.md)
- [Obfuscating Sensitive Data in Scripts](/api-and-database/api-docs/tips-and-tricks/obfuscating-sensitive-data-in-scripts.md)
- [Integrating Clarity LIMS with Upstream Sample Accessioning Systems](/api-and-database/api-docs/tips-and-tricks/integrating-clarity-lims-with-upstream-sample-accessioning-systems.md)
- [Creating Samples and Projects via the API](/api-and-database/api-docs/tips-and-tricks/creating-samples-and-projects-via-the-api.md)
- [Displaying Files From an Earlier Step](/api-and-database/api-docs/tips-and-tricks/displaying-files-from-an-earlier-step.md)
- [Transitioning Output Artifacts into the Next Step](/api-and-database/api-docs/tips-and-tricks/transitioning-output-artifacts-into-the-next-step.md)
- [Determining the Workflow(s) to Which a Sample is Assigned](/api-and-database/api-docs/tips-and-tricks/determining-the-workflow-s-to-which-a-sample-is-assigned.md)
- [Standardizing Sample Naming via the API](/api-and-database/api-docs/tips-and-tricks/standardizing-sample-naming-via-the-api.md)
- [Copying UDF Values from Source to Destination](/api-and-database/api-docs/tips-and-tricks/copying-udf-values-from-source-to-destination.md)
- [Updating Preset Value of a Step UDF through API](/api-and-database/api-docs/tips-and-tricks/updating-preset-value-of-a-step-udf-through-api.md)
- [Automating BCL Conversion](/api-and-database/api-docs/tips-and-tricks/automating-bcl-conversion.md)
- [Finding QC Flags in Aggregate QC (Library Validation) via REST API](/api-and-database/api-docs/tips-and-tricks/finding-qc-flags-in-aggregate-qc-library-validation-via-rest-api.md)
- [Setting the Value of a QC Flag on an Artifact](/api-and-database/api-docs/tips-and-tricks/setting-the-value-of-a-qc-flag-on-an-artifact.md)
- [Creating Notifications When Files are Added via LabLink](/api-and-database/api-docs/tips-and-tricks/creating-notifications-when-files-are-added-via-lablink.md)
- [Remote HTTP Filestore Setup](/api-and-database/api-docs/tips-and-tricks/remote-http-filestore-setup.md)
- [Cookbook](/api-and-database/api-docs/cookbook.md)
- [Get Started with the Cookbook](/api-and-database/api-docs/cookbook/get-started-with-the-cookbook.md)
- [Tips and Troubleshooting](/api-and-database/api-docs/cookbook/get-started-with-the-cookbook/tips-and-troubleshooting.md): This article provides hints and tips to help you get the most out of the Cookbook recipes included in this section.
- [Obtain and Use the REST API Utility Classes](/api-and-database/api-docs/cookbook/get-started-with-the-cookbook/obtain-and-use-the-rest-api-utility-classes.md)
- [Work with EPP/Automation and Files](/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files.md)
- [Automation Trigger Configuration](/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files/automation-trigger-configuration.md)
- [Process Execution with EPP/Automation Support](/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files/process-execution-with-epp-automation-support.md)
- [Work with Submitted Samples](/api-and-database/api-docs/cookbook/work-with-submitted-samples.md)
- [Adding Samples to the System](/api-and-database/api-docs/cookbook/work-with-submitted-samples/adding-samples-to-the-system.md)
- [Renaming Samples](/api-and-database/api-docs/cookbook/work-with-submitted-samples/renaming-samples.md)
- [Assigning Samples to Workflows](/api-and-database/api-docs/cookbook/work-with-submitted-samples/assigning-samples-to-workflows.md)
- [Updating Sample Information](/api-and-database/api-docs/cookbook/work-with-submitted-samples/updating-sample-information.md)
- [Show the Relationship Between Samples and Analyte Artifacts (Derived Samples)](/api-and-database/api-docs/cookbook/work-with-submitted-samples/show-the-relationship-between-samples-and-analyte-artifacts-derived-samples.md)
- [Work with Containers](/api-and-database/api-docs/cookbook/work-with-containers.md)
- [Add an Empty Container to the System](/api-and-database/api-docs/cookbook/work-with-containers/add-an-empty-container-to-the-system.md)
- [Find the Contents of a Well Location in a Container](/api-and-database/api-docs/cookbook/work-with-containers/find-the-contents-of-a-well-location-in-a-container.md)
- [Filter Containers by Name](/api-and-database/api-docs/cookbook/work-with-containers/filter-containers-by-name.md)
- [Work with Derived Sample Automations](/api-and-database/api-docs/cookbook/work-with-derived-sample-automations.md)
- [Remove Samples from Workflows](/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/remove-samples-from-workflows.md)
- [Requeue Samples](/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/requeue-samples.md)
- [Rearray Samples](/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/rearray-samples.md)
- [Work with Process/Step Outputs](/api-and-database/api-docs/cookbook/work-with-process-step-outputs.md)
- [Update UDF/Custom Field Values for a Derived Sample Output](/api-and-database/api-docs/cookbook/work-with-process-step-outputs/update-udf-custom-field-values-for-a-derived-sample-output.md)
- [Rename Derived Samples Using the API](/api-and-database/api-docs/cookbook/work-with-process-step-outputs/rename-derived-samples-using-the-api.md)
- [Find the Container Location of a Derived Sample](/api-and-database/api-docs/cookbook/work-with-process-step-outputs/find-the-container-location-of-a-derived-sample.md)
- [Traverse a Pooled and Demultiplexed Sample History/Genealogy](/api-and-database/api-docs/cookbook/work-with-process-step-outputs/traverse-a-pooled-and-demultiplexed-sample-history-genealogy.md)
- [View the Inputs and Outputs of a Process/Step](/api-and-database/api-docs/cookbook/work-with-process-step-outputs/view-the-inputs-and-outputs-of-a-process-step.md)
- [Work with Projects and Accounts](/api-and-database/api-docs/cookbook/work-with-projects-and-accounts.md)
- [Remove Information from a Project](/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/remove-information-from-a-project.md)
- [Add a New Project to the System with UDF/Custom Field Value](/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/add-a-new-project-to-the-system-with-udf-custom-field-value.md)
- [Get a Project Name](/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/get-a-project-name.md)
- [Find an Account Registered in the System](/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/find-an-account-registered-in-the-system.md)
- [Update Contact (User and Client) Information](/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/update-contact-user-and-client-information.md)
- [Work with Multiplexing](/api-and-database/api-docs/cookbook/work-with-multiplexing.md)
- [Find the Index Sequence for a Reagent Label](/api-and-database/api-docs/cookbook/work-with-multiplexing/find-the-index-sequence-for-a-reagent-label.md)
- [Demultiplexing](/api-and-database/api-docs/cookbook/work-with-multiplexing/demultiplexing.md)
- [Pool Samples with Reagent Labels](/api-and-database/api-docs/cookbook/work-with-multiplexing/pool-samples-with-reagent-labels.md)
- [Apply Reagent Labels with REST](/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-with-rest.md)
- [Apply Reagent Labels When Samples are Imported](/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-when-samples-are-imported.md)
- [Apply Reagent Labels by Adding Reagents to Samples](/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-by-adding-reagents-to-samples.md)
- [Working with User Defined Fields/Custom Fields](/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields.md)
- [About UDFs/Custom Fields and UDTs](/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields/about-udfs-custom-fields-and-udts.md)
- [Performing Post-Step Calculations with Custom Fields/UDFs](/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields/performing-post-step-calculations-with-custom-fields-udfs.md)
- [Work with Processes/Steps](/api-and-database/api-docs/cookbook/work-with-processes-steps.md)
- [Filter Processes by Date and Type](/api-and-database/api-docs/cookbook/work-with-processes-steps/filter-processes-by-date-and-type.md)
- [Find Terminal Processes/Steps](/api-and-database/api-docs/cookbook/work-with-processes-steps/find-terminal-processes-steps.md)
- [Run a Process/Step](/api-and-database/api-docs/cookbook/work-with-processes-steps/run-a-process-step.md)
- [Update UDF/Custom Field Information for a Process/Step](/api-and-database/api-docs/cookbook/work-with-processes-steps/update-udf-custom-field-information-for-a-process-step.md)
- [Work with the Steps Pooling Endpoint](/api-and-database/api-docs/cookbook/work-with-processes-steps/work-with-the-steps-pooling-endpoint.md)
- [Work with Batch Resources](/api-and-database/api-docs/cookbook/work-with-batch-resources.md)
- [Introduction to Batch Resources](/api-and-database/api-docs/cookbook/work-with-batch-resources/introduction-to-batch-resources.md)
- [Update UDF/Custom Field Information with Batch Operations](/api-and-database/api-docs/cookbook/work-with-batch-resources/update-udf-custom-field-information-with-batch-operations.md)
- [Retrieve Multiple Entities with a Single API Interaction](/api-and-database/api-docs/cookbook/work-with-batch-resources/page-4.md)
- [Select the Optimal Batch Size](/api-and-database/api-docs/cookbook/work-with-batch-resources/page-3.md)
- [Work with Files](/api-and-database/api-docs/cookbook/page.md)
- [Attach a File with REST and Python](/api-and-database/api-docs/cookbook/page/page-9.md)
- [Attach Files Located Outside the Default File Storage Repository](/api-and-database/api-docs/cookbook/page/attach-files-located-outside-the-default-file-storage-repository.md)
- [Attach a File to a File Placeholder with REST](/api-and-database/api-docs/cookbook/page/attach-a-file-to-a-file-placeholder-with-rest.md)
- [Work with Controls](/api-and-database/api-docs/cookbook/work-with-controls.md)
- [Automated Removal of Controls from a Workflow](/api-and-database/api-docs/cookbook/work-with-controls/automated-removal-of-controls-from-a-workflow.md)
- [Application Examples](/api-and-database/api-docs/application-examples.md)
- [Python API Library (glsapiutil.py) Location](/api-and-database/api-docs/application-examples/page-16.md)
- [Scripts That Help Automate Steps](/api-and-database/api-docs/application-examples/page-15.md)
- [Route Artifacts Based Off a Template File](/api-and-database/api-docs/application-examples/page-15/route-artifacts-based-off-a-template-file.md)
- [Invoking bcl2fastq from BCL Conversion and Demultiplexing Step](/api-and-database/api-docs/application-examples/page-15/invoking-bcl2fastq-from-bcl-conversion-and-demultiplexing-step.md)
- [Email Notifications](/api-and-database/api-docs/application-examples/page-15/email-notifications.md)
- [Finishing the Current Step and Starting the Next](/api-and-database/api-docs/application-examples/page-15/finishing-the-current-step-and-starting-the-next.md)
- [Adding Downstream Samples to Additional Workflows](/api-and-database/api-docs/application-examples/page-15/adding-downstream-samples-to-additional-workflows.md)
- [Advancing/Completing a Protocol Step via the API](/api-and-database/api-docs/application-examples/page-15/advancing-completing-a-protocol-step-via-the-api.md)
- [Setting a Default Next Action](/api-and-database/api-docs/application-examples/page-15/setting-a-default-next-action.md)
- [Automatic Placement of Samples Based on Input Plate Map (Multiple Plates)](/api-and-database/api-docs/application-examples/page-15/automatic-placement-of-samples-based-on-input-plate-map-multiple-plates.md)
- [Automatic Placement of Samples Based on Input Plate Map](/api-and-database/api-docs/application-examples/page-15/automatic-placement-of-samples-based-on-input-plate-map.md)
- [Publishing Files to LabLink](/api-and-database/api-docs/application-examples/page-15/publishing-files-to-lablink.md)
- [Automatic Pooling Based on a Sample UDF/Custom Field](/api-and-database/api-docs/application-examples/page-15/automatic-pooling-based-on-a-sample-udf-custom-field.md)
- [Completing a Step Programmatically](/api-and-database/api-docs/application-examples/page-15/completing-a-step-programmatically.md)
- [Automatic Sample Placement into Existing Containers](/api-and-database/api-docs/application-examples/page-15/automatic-sample-placement-into-existing-containers.md)
- [Routing Output Artifacts to Specific Workflows/Stages](/api-and-database/api-docs/application-examples/page-15/routing-output-artifacts-to-specific-workflows-stages.md)
- [Creating Multiple Containers / Types for Placement](/api-and-database/api-docs/application-examples/page-15/creating-multiple-containers-types-for-placement.md)
- [Starting a Protocol Step via the API](/api-and-database/api-docs/application-examples/page-15/starting-a-protocol-step-via-the-api.md)
- [Setting Quality Control Flags](/api-and-database/api-docs/application-examples/page-15/setting-quality-control-flags.md)
- [Applying Indexing Patterns to Containers Automatically](/api-and-database/api-docs/application-examples/page-15/applying-indexing-patterns-to-containers-automatically.md)
- [Assignment of Sample Next Steps Based On a UDF](/api-and-database/api-docs/application-examples/page-15/assignment-of-sample-next-steps-based-on-a-udf.md)
- [Parsing Metadata into UDFs (BCL Conversion and Demultiplexing)](/api-and-database/api-docs/application-examples/page-15/parsing-metadata-into-udfs-bcl-conversion-and-demultiplexing.md)
- [Scripts That Validate Step Contents](/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents.md)
- [Validating Process/Step Level UDFs](/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/page-14.md)
- [Checking That Containers Are Named Appropriately](/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/checking-that-containers-are-named-appropriately.md)
- [Checking for Index Clashes Based on Index Sequence](/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/checking-for-index-clashes-based-on-index-sequence.md)
- [Validating Illumina TruSeq Index Adapter Combinations](/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/validating-illumina-truseq-index-adapter-combinations.md)
- [Scripts Triggered Outside of Workflows/Steps](/api-and-database/api-docs/application-examples/page-13.md)
- [Repurposing a Process to Upload Indexes](/api-and-database/api-docs/application-examples/page-13/repurposing-a-process-to-upload-indexes.md)
- [Adding Users in Bulk](/api-and-database/api-docs/application-examples/page-13/adding-users-in-bulk.md)
- [Moving Reagent Kits & Lots to New Clarity LIMS Server](/api-and-database/api-docs/application-examples/page-13/moving-reagent-kits-and-lots-to-new-clarity-lims-server.md)
- [Programatically Importing the Sample Submission Excel File](/api-and-database/api-docs/application-examples/page-13/programatically-importing-the-sample-submission-excel-file.md)
- [Generating an MS Excel Sample Submission Spreadsheet](/api-and-database/api-docs/application-examples/page-13/generating-an-ms-excel-sample-submission-spreadsheet.md)
- [Assigning Samples to New Workflows](/api-and-database/api-docs/application-examples/page-13/assigning-samples-to-new-workflows.md)
- [Miscellaneous Scripts](/api-and-database/api-docs/application-examples/page-12.md)
- [Illumina LIMS Integration](/api-and-database/api-docs/application-examples/page-12/illumina-lims-integration.md)
- [Generating a Hierarchical Sample History](/api-and-database/api-docs/application-examples/page-12/generating-a-hierarchical-sample-history.md)
- [Protocol-based Permissions](/api-and-database/api-docs/application-examples/page-12/protocol-based-permissions.md)
- [Self-Incremental Counters](/api-and-database/api-docs/application-examples/page-12/self-incremental-counters.md)
- [Generic CSV Parser Template (Python)](/api-and-database/api-docs/application-examples/page-12/generic-csv-parser-template-python.md)
- [Renaming Samples to Add an Internal ID](/api-and-database/api-docs/application-examples/page-12/renaming-samples-to-add-an-internal-id.md)
- [Creating Custom Sample Sheets](/api-and-database/api-docs/application-examples/page-12/creating-custom-sample-sheets.md)
- [Copying Output UDFs to Submitted Samples](/api-and-database/api-docs/application-examples/page-12/copying-output-udfs-to-submitted-samples.md)
- [Parsing Sequencing Meta-Data into Clarity LIMS](/api-and-database/api-docs/application-examples/page-12/parsing-sequencing-meta-data-into-clarity-lims.md)
- [Submit to a Compute Cluster via PBS](/api-and-database/api-docs/application-examples/page-12/submit-to-a-compute-cluster-via-pbs.md)
- [Downloading a File and PDF Image Extraction](/api-and-database/api-docs/application-examples/page-12/downloading-a-file-and-pdf-image-extraction.md)
- [Resources and References](/api-and-database/api-docs/application-examples/resources-and-references.md)
- [Understanding LIMS ID Prefixes](/api-and-database/api-docs/application-examples/resources-and-references/understanding-lims-id-prefixes.md)
- [Container States](/api-and-database/api-docs/application-examples/resources-and-references/container-states.md)
- [Useful Tools](/api-and-database/api-docs/application-examples/resources-and-references/useful-tools.md)
- [Unsupported Artifact Types](/api-and-database/api-docs/application-examples/resources-and-references/unsupported-artifact-types.md)
- [Unsupported Process Types](/api-and-database/api-docs/application-examples/resources-and-references/unsupported-process-types.md)
- [Suggested Reading](/api-and-database/api-docs/application-examples/resources-and-references/suggested-reading.md)
- [API Training Videos](/api-and-database/api-docs/application-examples/resources-and-references/api-training-videos.md)