mrugakshi77/omics-registry

How mrugakshi77/omics-registry works

Omics Registry is a genomics metadata and provenance platform whose central workflow is finding samples with all requested assays and exporting the matching cohort as a manifest. Researchers can use either the CLI or REST API to query cohorts and register metadata or analysis results; the service layer applies the business operations over PostgreSQL. The README also documents a real GDC/TCGA metadata path. Source excerpts confirm CLI and service behavior; some API and ingestion details are supported only by the README or source index.

Main entry points: registry.py Registry writes · omics_registry/main.py REST application · cli/main.py CLI · session.py DB sessions

Components 24

Researcher interfaces

REST application src/omics_registry/main.py
Cohort API src/omics_registry/api/cohort.py
Analysis API src/omics_registry/api/analyses.py
Experiment API src/omics_registry/api/experiments.py
Patient API src/omics_registry/api/patients.py
Sample API src/omics_registry/api/samples.py
CLI src/omics_registry/cli/main.py

Registry services

Cohort query src/omics_registry/services/cohort.py
Registry writes src/omics_registry/services/registry.py
Request schemas src/omics_registry/schemas
DB sessions src/omics_registry/db/session.py

Metadata and provenance

PostgreSQL
Patients src/omics_registry/models/patient.py
Samples src/omics_registry/models/sample.py
Experiments src/omics_registry/models/experiment.py
Analyses src/omics_registry/models/analysis.py
Result files src/omics_registry/models/result_file.py
Domain enums src/omics_registry/models/enums.py

GDC metadata

GDC public metadata
Metadata fetch scripts/fetch_gdc_metadata.py
Metadata curation scripts/curate_gdc_metadata.py
Curated snapshot data/gdc_curated.json
Database seeding scripts/seed_data.py

Other components

Researcher

Connections 36

Researcher → CLI: runs commands README.md
Researcher → REST application: uses API README.md
REST application → Cohort API: mounts routes src/omics_registry/main.py
REST application → Analysis API: mounts routes src/omics_registry/main.py
REST application → Experiment API: mounts routes src/omics_registry/main.py
REST application → Patient API: mounts routes src/omics_registry/main.py
REST application → Sample API: mounts routes src/omics_registry/main.py
Cohort API → Cohort query: queries via src/omics_registry/api/cohort.py
Analysis API → Registry writes: registers via src/omics_registry/api/analyses.py
Experiment API → Registry writes: writes via src/omics_registry/api/experiments.py
Patient API → Registry writes: writes via src/omics_registry/api/patients.py
Sample API → Registry writes: writes via src/omics_registry/api/samples.py
CLI → Cohort query: queries via src/omics_registry/cli/main.py
CLI → Registry writes: registers via src/omics_registry/cli/main.py
CLI → DB sessions: opens session src/omics_registry/cli/main.py
CLI → Request schemas: validates inputs src/omics_registry/cli/main.py
Cohort API → DB sessions: gets session src/omics_registry/api/cohort.py
Analysis API → DB sessions: gets session src/omics_registry/api/analyses.py
Registry writes → Request schemas: accepts validated data src/omics_registry/services/registry.py
Registry writes → Patients: creates and reads src/omics_registry/services/registry.py
Registry writes → Samples: creates and reads src/omics_registry/services/registry.py
Registry writes → Experiments: creates and reads src/omics_registry/services/registry.py
Registry writes → Analyses: registers runs src/omics_registry/services/registry.py
Registry writes → Result files: records outputs src/omics_registry/services/registry.py
Registry writes → PostgreSQL: writes records README.md
Cohort query → PostgreSQL: queries assays src/omics_registry/services/cohort.py
DB sessions → PostgreSQL: opens connections src/omics_registry/db/session.py
Patients → Samples: has samples src/omics_registry/models/patient.py
Samples → Experiments: has experiments src/omics_registry/models/sample.py
Experiments → Analyses: has analyses src/omics_registry/models/experiment.py
Analyses → Result files: has outputs src/omics_registry/models/analysis.py
GDC public metadata → Metadata fetch: provides metadata README.md
Metadata fetch → Metadata curation: curates records README.md
Metadata curation → Curated snapshot: produces snapshot README.md
Curated snapshot → Database seeding: loads metadata README.md
Database seeding → PostgreSQL: populates records README.md

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Drawn by GitDiagram on September 30, 2026 from the repository's file tree, README and source files. Read as Markdown ·