zcloud

SCU Upload

  • SCU_upload
    • Creating an SCU Upload Template
    • SCU Upload Template Structure
    • Discovery Rules
      • Pattern Rule Criteria
      • Paired Group Rule Criteria
    • Elements
    • Registering a New SCU Upload Template
    • Examples
      • Omegafold Example
      • RFD Example
      • MPNN Example
      • Bad Behavior Example
  • Tools and Resources
  • Supported SCU Upload Templates
  • Generic Upload Example

Benchling Order Uploader

  • Order Uploader Documentation
    • Overview
    • Quick Start
    • Additional files
    • Usage Scenarios
      • Scenario 1: Well-Formatted CSV Upload
      • Scenario 2: CSV Without Design Names
      • Scenario 3: Conflicting Data Requiring Correction
      • Scenario 4: Handling Typos with Fuzzy Matching
      • Scenario 5: CSV with Score Columns
    • Design Naming Convention
      • Components
      • Examples
      • Fusion Proteins
    • CLI Reference
      • upload_order()
      • Core Parameters
      • Metadata Parameters
      • Advanced Options
    • Required CSV Columns
    • API Reference
      • Core Validation Functions
        • check_program_id()
        • check_target_id()
        • check_binding_site_id()
        • check_fusion_id()
      • Candidate Resolution
        • confirm_single_value_from_user()
        • confirm_set_of_values_from_user()
      • Fuzzy Matching and Error Handling
        • check_metadata_against_oracle_with_fuzzy_find_on_fail()
        • ask_user_to_confirm_fuzzy_match()
      • SCU and Score Column Processing
        • check_scu_against_oracle_with_fuzzy_find_on_fail()
        • check_scu_schema()
      • Design Name Generation
        • pdapply_build_design_names_from_row()
        • check_generated_design_names()
      • Benchling Integration
        • create_benchling_order_folder()
        • register_protein_entities()
        • publish_benchling_entry()
    • Troubleshooting
      • Common Issues and Solutions
      • Environment Setup
      • Tips for Success

API documentation

  • zcloud
    • zcloud package
      • Subpackages
        • zcloud.console_scripts package
        • zcloud.pubsub package
      • Submodules
        • zcloud.avro module
        • zcloud.benchling_order module
        • zcloud.data_enums module
        • zcloud.gcp_services module
        • zcloud.generic_scu_transfer module
        • zcloud.network_requests module
        • zcloud.rapidfuzz module
        • zcloud.scu_enums module
        • zcloud.service_enums module
        • zcloud.util module
      • Module contents
zcloud
  • Search

© Copyright 2024, ZipBio.

Built with Sphinx using a theme provided by Read the Docs.