pm-illumina-basespace

pm-illumina-basespace

Purpose

Reads and writes documented Illumina BaseSpace v1pre3 REST API resources through the declarative connector engine.

Icon

• id: pm-sample
• asset: icons/pm-sample.svg
• source: polymetrics
• review_status: polymetrics
• review_url: https://github.com/polymetrics-ai/cli

Capabilities

• check=true catalog=true read=true write=true query=false
• Integration type: api

Authentication

• Use pm credentials add with --from-env or --value-stdin for secret fields.

Configuration

• application_id
• appsession_id
• base_url (required)
• biosample_id
• dataset_id
• datasettype_id
• labrequeue_id
• lane_id
• librarypool_id
• name
• page_size
• project_id
• run_id
• trash_id
• user
• user_id
• workgroup_id
• access_token (secret) (required)

ETL Streams

• projects:
  • primary key: id
  • cursor: date_created
  • fields: date_created(string), date_modified(string), href(string), id(string), name(string), total_size(integer), user_owned_by(object)
• runs:
  • primary key: id
  • cursor: date_created
  • fields: date_created(string), date_modified(string), experiment_name(string), href(string), id(string), instrument_name(string), name(string), status(string), total_size(integer)
• samples:
  • primary key: id
  • cursor: date_created
  • fields: date_created(string), href(string), id(string), name(string), num_reads_pf(integer), num_reads_raw(integer), sample_id(string), status(string), total_size(integer)
• appsessions:
  • primary key: id
  • cursor: date_created
  • fields: application(object), date_completed(string), date_created(string), href(string), id(string), name(string), status(string), status_summary(string), total_size(integer)
• datasets:
  • primary key: id
  • cursor: date_created
  • fields: dataset_type(object), date_created(string), href(string), id(string), name(string), project(object), total_size(integer)
• applications:
  • fields: Id(string), id(string)
• application:
  • fields: Id(string), id(string)
• application_qcthresholds:
  • fields: Id(string), id(string)
• application_settings:
  • fields: Id(string), id(string)
• application_workflowdependencies:
  • fields: Id(string), id(string)
• appsessions_all:
  • fields: Id(string), id(string)
• appsession:
  • fields: Id(string), id(string)
• appsession_comments:
  • fields: Id(string), id(string)
• appsessions_logfiles:
  • fields: Id(string), id(string)
• appsession_properties:
  • fields: Id(string), id(string)
• appsession_property:
  • fields: Id(string), id(string)
• appsession_property_items:
  • fields: Id(string), id(string)
• biosamples:
  • fields: Id(string), id(string)
• biosample_labrequeues:
  • fields: Id(string), id(string)
• biosample:
  • fields: Id(string), id(string)
• biosample_libraries:
  • fields: Id(string), id(string)
• biosample_runlane_summaries:
  • fields: Id(string), id(string)
• datasets_all:
  • fields: Id(string), id(string)
• dataset:
  • fields: Id(string), id(string)
• dataset_comments:
  • fields: Id(string), id(string)
• dataset_files:
  • fields: Id(string), id(string)
• datasettype:
  • fields: Id(string), id(string)
• instrumentstatistics:
  • fields: Id(string), id(string)
• labrequeues:
  • fields: Id(string), id(string)
• labrequeue:
  • fields: Id(string), id(string)
• laneqcthresholds:
  • fields: Id(string), id(string)
• lane:
  • fields: Id(string), id(string)
• lane_comments:
  • fields: Id(string), id(string)
• libraries:
  • fields: Id(string), id(string)
• librarypool_libraries:
  • fields: Id(string), id(string)
• project:
  • fields: Id(string), id(string)
• project_datasets:
  • fields: Id(string), id(string)
• run_files:
  • fields: Id(string), id(string)
• trash:
  • fields: Id(string), id(string)
• trash_2:
  • fields: Id(string), id(string)
• current_user:
  • fields: Id(string), id(string)
• current_user_subscription:
  • fields: Id(string), id(string)
• current_user_usage:
  • fields: Id(string), id(string)
• current_user_workgroups:
  • fields: Id(string), id(string)
• user:
  • fields: Id(string), id(string)
• user_settings:
  • fields: Id(string), id(string)
• workgroup:
  • fields: Id(string), id(string)
• configured_user:
  • fields: Id(string), id(string)

Sync Modes

• ETL sync modes: full_refresh_append, full_refresh_overwrite, full_refresh_overwrite_deduped

Reverse ETL Actions

• update_applications_id_qcthresholds:
  • endpoint: PUT /v1pre3/applications/{{ record.application_id }}/qcthresholds
  • required fields: application_id
  • risk: BaseSpace mutation: PUT /v1pre3/applications/{application_id}/qcthresholds.
• update_applications_id_workflowdependencies:
  • endpoint: PUT /v1pre3/applications/{{ record.application_id }}/workflowdependencies
  • required fields: application_id
  • risk: BaseSpace mutation: PUT /v1pre3/applications/{application_id}/workflowdependencies.
• applications_id_workflows:
  • endpoint: POST /v1pre3/applications/{{ record.application_id }}/workflows
  • required fields: application_id
  • risk: BaseSpace mutation: POST /v1pre3/applications/{application_id}/workflows.
• delete_appsessions_id:
  • endpoint: DELETE /v1pre3/appsessions/{{ record.appsession_id }}
  • required fields: appsession_id
  • risk: Destructive BaseSpace mutation: DELETE /v1pre3/appsessions/{appsession_id}.
• appsessions_id:
  • endpoint: POST /v1pre3/appsessions/{{ record.appsession_id }}
  • required fields: appsession_id
  • risk: BaseSpace mutation: POST /v1pre3/appsessions/{appsession_id}.
• appsessions_id_properties:
  • endpoint: POST /v1pre3/appsessions/{{ record.appsession_id }}/properties
  • required fields: appsession_id
  • risk: BaseSpace mutation: POST /v1pre3/appsessions/{appsession_id}/properties.
• delete_appsessions_id_properties_name:
  • endpoint: DELETE /v1pre3/appsessions/{{ record.appsession_id }}/properties/{{ record.name }}
  • required fields: appsession_id, name
  • risk: Destructive BaseSpace mutation: DELETE /v1pre3/appsessions/{appsession_id}/properties/{name}.
• appsessions_id_stop:
  • endpoint: POST /v1pre3/appsessions/{{ record.appsession_id }}/stop
  • required fields: appsession_id
  • risk: Destructive BaseSpace mutation: POST /v1pre3/appsessions/{appsession_id}/stop.
• biosamples_bulkupdate:
  • endpoint: POST /v1pre3/biosamples/bulkupdate
  • risk: BaseSpace mutation: POST /v1pre3/biosamples/bulkupdate.
• biosamples_id:
  • endpoint: POST /v1pre3/biosamples/{{ record.biosample_id }}
  • required fields: biosample_id
  • risk: BaseSpace mutation: POST /v1pre3/biosamples/{biosample_id}.
• datasets_id:
  • endpoint: POST /v1pre3/datasets/{{ record.dataset_id }}
  • required fields: dataset_id
  • risk: BaseSpace mutation: POST /v1pre3/datasets/{dataset_id}.
• update_laneqcthresholds:
  • endpoint: PUT /v1pre3/laneqcthresholds
  • risk: BaseSpace mutation: PUT /v1pre3/laneqcthresholds.
• lanes_id:
  • endpoint: POST /v1pre3/lanes/{{ record.lane_id }}
  • required fields: lane_id
  • risk: BaseSpace mutation: POST /v1pre3/lanes/{lane_id}.
• libraries_libraryid_labrequeues:
  • endpoint: POST /v1pre3/libraries/{{ record.library_id }}/labrequeues
  • required fields: library_id
  • risk: BaseSpace mutation: POST /v1pre3/libraries/{library_id}/labrequeues.
• librarypools_id:
  • endpoint: POST /v1pre3/librarypools/{{ record.librarypool_id }}
  • required fields: librarypool_id
  • risk: BaseSpace mutation: POST /v1pre3/librarypools/{librarypool_id}.
• librarypools_poolid_labrequeues:
  • endpoint: POST /v1pre3/librarypools/{{ record.pool_id }}/labrequeues
  • required fields: pool_id
  • risk: BaseSpace mutation: POST /v1pre3/librarypools/{pool_id}/labrequeues.
• preprequests_preprequestid_labrequeues:
  • endpoint: POST /v1pre3/preprequests/{{ record.preprequest_id }}/labrequeues
  • required fields: preprequest_id
  • risk: BaseSpace mutation: POST /v1pre3/preprequests/{preprequest_id}/labrequeues.
• delete_trash:
  • endpoint: DELETE /v1pre3/trash
  • risk: Destructive BaseSpace mutation: DELETE /v1pre3/trash.
• trash_id_restorefromtrash:
  • endpoint: POST /v1pre3/trash/{{ record.trash_id }}/restorefromtrash
  • required fields: trash_id
  • risk: Destructive BaseSpace mutation: POST /v1pre3/trash/{trash_id}/restorefromtrash.
• users_id_settings:
  • endpoint: POST /v1pre3/users/{{ record.user_id }}/settings
  • required fields: user_id
  • risk: BaseSpace mutation: POST /v1pre3/users/{user_id}/settings.

Security

• read risk: external Illumina BaseSpace API read of documented v1pre3 resources
• write risk: external Illumina BaseSpace API mutations including settings, workflow, threshold, trash, lab requeue, and app session actions
• approval: required for every write action; destructive actions are marked confirm: destructive
• Never pass secret values in chat, shell arguments, logs, docs, or JSON output.

Commands

Inspect as a manual

pm connectors inspect illumina-basespace

Inspect as structured JSON

pm connectors inspect illumina-basespace --json

Agent Rules

• Run pm connectors inspect illumina-basespace before creating credentials or plans.
• Use --json only when the caller needs structured output; use the manual for human-readable guidance.
• Never ask the user to paste secret values into chat.
• For reverse ETL writes, create a plan, show the preview, wait for explicit approval, then run with the approval token.