coyote3

Navigation and Pages

This chapter defines the primary navigation model of Coyote3 and explains what each major page is responsible for.

Navigation model

Coyote3 is organized around a single operational spine:

1. Start in Samples.
2. Open a case into DNA or RNA workflow.
3. Review, classify, and comment.
4. Preview and save report artifacts.
5. Re-open from reported history when needed.

Main entry points

• Samples worklist: /samples
• Dashboard: /dashboard/
• Administration: /admin/
• Public information pages: /public/...
• In-app handbook index: /handbook/

Navbar discovery tools:

• Matrix: /assay-catalog-matrix
• Catalog: /assay-catalog
• Variant Search: /search/tiered_variants

Detailed tool guide:

• Navbar Tools: Matrix, Catalog, and Variant Search
• Application Features Reference
• Flow Diagrams (DNA, RNA, Sample, Admin)

Samples worklist

Supported routes:

• /samples
• /samples/live
• /samples/done
• /samples/<panel_type>/<panel_tech>/<assay_group>
• /samples/<panel_type>/<panel_tech>/<assay_group>/<status>

Primary user actions:

• Search by sample name.
• Switch between live and done scopes.
• Open sample settings.
• Open DNA or RNA case workspace.
• Open report links for previously reported cases.

Live and done semantics

The worklist state is driven by samples.report_num.

• Live: report_num missing or 0.
• Done/reported: report_num > 0.

Operational effect:

• A case remains live until report save is successful.
• After successful save, report metadata is written and the case appears in done/reported scope.

Opening a case

From /samples:

• DNA case route: /dna/sample/<sample_id>
• RNA case route: /rna/sample/<sample_id>K=

sample_id accepts the sample name used by the worklist.

Sample settings workspace

Route:

• /samples/<sample_id>/edit

Purpose:

• Manage ISGL (In Silico Gene List) selection for the case.
• Manage ad-hoc case genes.
• Verify effective genes.
• Compare raw versus filtered variant statistics.

Supporting route handlers used by the page:

• GET /samples/<sample_id>/isgls
• POST /samples/<sample_id>/genes/apply-isgl
• POST /samples/<sample_id>/adhoc_genes
• POST /samples/<sample_id>/adhoc_genes/clear
• GET /samples/<sample_id>/effective-genes/all

DNA workspace

Primary route:

• /dna/sample/<sample_id>

Navigation from DNA list:

• SNV detail: /dna/<sample_id>/var/<var_id>
• CNV detail: /dna/<sample_id>/cnv/<cnv_id>
• Translocation detail: /dna/<sample_id>/transloc/<transloc_id>
• Report preview: /dna/sample/<sample_id>/preview_report
• Report save: /dna/sample/<sample_id>/report/save

RNA workspace

Primary route:

• /rna/sample/<sample_id>K=

Navigation from RNA list:

• Fusion detail: /rna/fusion/<fusion_id>
• Fusion false-positive flag/unflag routes
• Report preview: /rna/sample/preview_report/<sample_id>
• PDF generation: /rna/sample/report/pdf/<sample_id>

Report retrieval

Saved reports are opened through sample-scoped routes:

• View: /samples/<sample_id>/reports/<report_id>
• Download: /samples/<sample_id>/reports/<report_id>/download

If filepath is absent in report metadata, the app reconstructs path from configured report base and assay report folder.

Search and historical review

Interpretation history routes:

• Tiered search: /search/tiered_variants
• Reported occurrence view: /reported_variants/variant/<variant_id>/<tier>

These routes are designed for cross-sample context and report-time traceability.

For complete usage patterns, see:

• Navbar Tools: Matrix, Catalog, and Variant Search

Administration navigation

Administration root:

• /admin/

Managed domains:

• sample management
• users
• roles
• permissions
• schemas
• ASP (Assay Specific Panel)
• ASPC (Assay Specific Panel Config)
• ISGL (In Silico Gene List)
• audit log views

Administration pages govern system behavior; they are not part of day-to-day interpretation workflow.

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