Platform

GoliathApp is a database-governed application platform. A specialized application stores its workflow as data: action rows, data types, and a graph. The engine activates nodes, leases ACTION nodes to workers, and continues the graph from result codes. Domain meaning stays in the application that extends the platform.

The repository map is workspace-index.md. Apply order is schema-apply.md. The HTTP contract is contracts/openapi.yaml.

Schemas

Schema	What the SQL in this tree defines
Meta	Class model. Instances are "Meta"."Objs".
RBAC	Users, groups, roles, permissions, scopes, sessions, external identities. Quoted PascalCase identifiers.
portal	Portal functions (portal.sp_*) for workflow definitions, worker enrollment, RBAC administration, studies, and related operator calls.
wf	Workflow definitions, instances, actions, data types, worker registry, leases, and the event plane.
cfg	Sites, pipeline profiles, assay procedures, domain programs, studies, credentials, storage, and reference-asset registry tables.
Contract, Onboarding	Contract and onboarding tables and parity APIs.

cfg.analyte is referenced by repository and portal SQL. cfg_registry_tables.sql does not create that table. portal."Customers", portal."Diseases", portal."NavTree", and portal."Role2Node" are referenced by later functions and are not created by a script in this tree.

There is no separate obj schema. Object identity is "Meta"."Objs".

Processes in this repository

Piece	Where	What it does
REST gateway	workflow_engine/rest/	goliath-gateway / methyl-gateway. Worker enroll, claim, submit, heartbeat, fail, and POST /v1/events.
Local runner	workflow_engine/local/	goliath-workflow-run. Compiles a DomainProgram and can execute the graph in-process.
Compiler	workflow_engine/domain/	Lowers DomainProgram JSON to WorkflowDefinitionSpec.
Config CLI	workflow_engine/cfg/	goliath-cfg. File-backed registry under $METHYL_CFG_STORE or $METHYL_WORK_ROOT/goliath/cfg-store (default /work/goliath/cfg-store).
Claim client	goliath_worker/	HTTP client for the worker routes. No database connection.
Shared storage helpers	goliath_worker/work_share.py, scripts/init_work_layout.sh	Optional /work layout and cross-host permissions.
Contract check	workflow_engine/contract/validate_contract.py	Requires the objects in db_objects.yaml to appear in both SQL trees.
Delphi gateway	workflow_engine/delphi/	Frozen Windows reference. The Python gateway is the middle tier that ships here.

publish-program --deploy-db imports ops.workflow_deploy, which is not in this tree. sync-actions runs workflow_engine/sql_mssql/seed_action_catalog.py, which is not in this tree. sync-library-presets imports methyl_enricher.preset_registry, which is not in this tree.

Gateway and database defaults

BACKEND_DB selects the gateway backend and defaults to mssql. PostgreSQL is postgres, postgresql, or pg.

PostgreSQL connection fields are POSTGRES_HOST (default localhost), POSTGRES_PORT (default 5432), POSTGRES_DB (default methylpipeline), POSTGRES_USER (default postgres), POSTGRES_PASSWORD, and PGSSLMODE (default require). METHYLPIPELINE_DB replaces the built connection string. WF_USE_MANAGED_IDENTITY=1 omits the password so an Entra token can be supplied at connect time. WF_SCHEMA defaults to wf.

Azure SQL uses AZURE_SQL_SERVER, AZURE_SQL_DB, AZURE_SQL_USER, and AZURE_SQL_PASSWORD.

The gateway listens on WF_GATEWAY_HOST or REST_HOST (default 127.0.0.1) and WF_GATEWAY_PORT or REST_PORT (default 8080). Health is GET /, GET /v1, and GET /v1/health. The health body reports service as methyl-workflow-gateway.

The gateway does not load an action catalog and does not resolve study configuration when a worker claims a task. input_json on the claim is whatever the database function returns.

Config CLI

goliath-cfg (alias methyl-cfg) subcommands that call code in this tree:

import-fs, upsert, materialize, publish-program, scaffold-action, verify-workflow, link-site-assets, provision-assets, expand-endpoint, list, get, and the study-group commands (set-study-group, set-study-group-members, list-study-groups, list-study-group-members, materialize-study-lists).

import-fs reads JSON under workflow_engine/domain/ when that layout is present, or under domain/ when the checkout is a flattened runtime bundle. This repository's workflow_engine/domain/ contains the compiler modules and no fixture directory, so an import of this tree records no domain documents.

Kinds accepted by the file store are site, pipeline_profile, assay_procedure, analyte, domain_program, study, credential, storage_endpoint, storage_profile, reference_asset, and enrichment_library_preset. Credential documents stay in the store. materialize does not write them under /work.

Shared storage

scripts/init_work_layout.sh creates a layout under METHYL_WORK_ROOT, or WORK_ROOT, or /work. The mount must already exist. Writable directories (0777, with a default ACL when setfacl works): samples/, projects/, cache/. Directories created mode 0755: genomes/, site/, goliath/. If site/methyl_site.json is absent, the script copies scripts/default_methyl_site.json. An existing site file is left in place.

goliath_worker.work_share treats /work as optional. It also honors METHYL_WORK_ROOT and an existing /lambda/nfs/Work. A workflow that never calls those helpers has no dependency on the mount.

Local workflow run

goliath-workflow-run --program path/to/program.json --compile-only
goliath-workflow-run --program path/to/program.json --stub-external
goliath-workflow-run --workflow path/to/spec.json --dry-run

--compile-only writes WorkflowDefinitionSpec JSON and does not execute. Execution without --stub-external imports methyl_worker handlers. That package is not in this tree. --stub-external sets WORKER_STUB_EXTERNAL=1 and returns a stub payload per action. A checked-in program used by tests is workflow_engine/tests/fixtures/sample_prep.program.json.

finalize_instance_context enriches a run from methyl_utils (project file, site manifest, modality gate). The local engine logs and continues when that import or the project file fails.