# UI/UX

NOTE

This documentation is a work in progress and is incomplete.

Please contact developers for more details.

Configuration related to the user interface and user experience in ELLA. Most are defined as default settings for all users, but some settings may be overridden by user group specific settings.

# Configure elements to show

Configure user interface elements for different pages. See /example_config.yml for examples.

# OVERVIEW and INFO page

Define defaults view on OVERVIEW and INFO pages for all users, or per user group.

Default settings for all users (overridden by any group settings) are configured in:

  • File: ella_config.yml (set by ELLA_CONFIG env variable)
  • Key: user.user_config.overview

User group settings are configured in:

  • File: usergroups.json (see user groups)
  • Key: config.overview
Subkey Explanation Values
views Tabs to show on the OVERVIEW page. variants: Variant centered workflow;
analyses-by-findings: Sample centered workflow, grouped by the findings in the analysis;
import: Manual import
show_variant_report Show/hide externally generated variant report on INFO page. true/false

Examples also in /src/vardb/testdata/usergroups.json.

# Priority

Define how to display priority values from pipeline.

  • File: ella_config.yml (set by ELLA_CONFIG env variable)
  • Key: analysis.priority.display
  • Value: Examples: "1": "Normal", "2": "High", ...

Define side bar content for different views in ANALYSES workflows: full, quick, visual, report, list.

  • File: ella_config.yml (set by ELLA_CONFIG env variable)
  • Key: analysis.sidebar.[view]
Subkey Explanation Values
columns Define which columns to show. [Depending on annotation.]
classification_options Define how to group different classifications (existing/current).
comment_type Define which comment field to show. None, analysis, evaluation
shade_multiple_in_gene Apply background shade to variants if there are more than one in the same gene. true / false

# Comment field templates

It is possible to define templates for most comment fields in ELLA, which are available to add for the user in the text format menu. This is a user group specific setting, see /src/vardb/testdata/usergroups.json for examples.

Templates can be defined as pure text or with basic html formatting in:

  • File: usergroups.json (see user groups)
  • Key: config.comment_templates
Subkey Explanation Values
name Provide a name for the template [text]
comment_fields Defines where (which comment fields) the template should be available. classificationAnalysisSpecific,
classificationEvaluation,
classificationAcmg,
classificationReport,
classificationFrequency,
classificationPrediction,
classificationExternal,
classificationReferences,
reportIndications,
reportSummary,
referenceEvaluation,
workLogMessage
template Specifies the template [pure text or basic html]

# IGV in VISUAL

Configuration of IGV in VISUAL mode. See /example_config.yml for examples.

  • File: ella_config.yml (set by ELLA_CONFIG env variable)
  • Key: igv
Subkey Explanation Values
reference Define what to show as reference data.
valid_resource_files Files permitted accessible on /igv/<file> resource, relative to $IGV_DATA env.

# Auto-text in REPORT

Configure text to include automatically for different classifications on the REPORT page. See /example_config.yml for examples.

  • File: ella_config.yml (set by ELLA_CONFIG env variable)
  • Key: report.classification_text
  • Value: "[class]": "[text]"

# Workflows

# Finalize requirements

Define default requirements for finalizing a workflow for all users. Values will be used unless overridden by user group specific settings. See /example_config.yml for examples.

  • File: ella_config.yml (set by ELLA_CONFIG env variable)
  • Key: user.user_config.workflows

Separate settings are given for subkeys allele.finalize_requirements (VARIANTS workflows) and analysis.finalize_requirements (ANALYSES workflows):

Workflow Subkey Explanation Values
allele or analysis workflow_status Workflow statuses allowing finalization. [list of statuses]
analysis allow_not_relevant Allow variants marked as "Not relevant" when finalizing. True / False
analysis allow_technical Allow variants marked as "Technical" when finalizing. True / False
analysis allow_unclassified Allow unclassified variants when finalizing. True / False

# Define references as IGNORED

Certain references retrieved from annotation sources such as ClinVar are generic and do not contain information relevant for any particular variant classification per se (an example is the ACMG guidelines (opens new window)). These references can be set to be automatically IGNORED in the reference evaluation module.

This is a user group specific setting, see /src/vardb/testdata/usergroups.json for examples. PubMed IDs to be ignored should be added in:

  • File: usergroups.json (see user groups)
  • Key: interpretation.autoIgnoreReferencePubmedIds
  • Value: [list of PubMedIDs (integers)]
Last Updated: 4/22/2020, 3:02:50 PM