Retire explicit managed-viewer routes through original lifecycle owners (#519)

docs/validation/viewer-retirement-519-selection95/CHECKPOINT.rst

@@ -0,0 +1,174 @@
+522 selected-member receiving packet: published source checkpoint
+================================================================
+
+Current packet location
+-----------------------
+
+Owned checkout /home/ts/wt/openhcs-ui-workflow-rendering-20261001, directory
+docs/validation/viewer-retirement-519-selection95. RECEIVING.rst contains the
+custody, source relation,64MiB total budget and precise remaining prerequisite;
+PUBLIC.commands contains public argv templates, not an executable batch.
+fixture_522.py and pipeline.py are a NEW tiny engineering declaration/document,
+not scientific inputs or product changes. None has been executed or staged.
+
+Source integration completed
+----------------------------
+
+Only Planck fixture commits7cfcf1713/945b959 were cherry-picked, as499800a2d/
+170370dce. The first context conflict introduced the already-merged524 feature
+test missing from the old522 base; unrelated calibration context was not copied
+by that pick. Normal merge130ef9d36e1856669f2e1920fdeadf7fd127ebc7 then integrates
+parent-reviewed mainb1e9b5ca84b52c4831965421b2e33fd42a4e15ed, including its
+original calibration consumers. No Planck combined-package ancestry imported.
+
+The native point builder retains original ROIArchiveSourceMetadata.feature_metadata
+and derives member keys from NapariStreamLayerItem.ELEMENT_IDENTITY_FEATURE in
+its existing assembly loop. The Shapes owner also retains that original metadata
+projection. No duplicate transport-field exclusion, codec or selection authority.
+The controller/cooperative presentation retention owner remains the reviewed522
+implementation. Root producer/persistence/materialization files were not edited.
+
+Exact byte comparisons against qualified package07 source8168e3aa:
+napari_viewer_server.py and napari_streaming_handlers.py MATCH. The whole
+openhcs production-tree comparison has ONLY the three independently-owned511
+catalog-preparation paths; no other production difference. Those511 paths are
+not borrowed into522. This is byte equivalence, not a new runtime result.
+
+All three migrated test files byte-match Planck945b959 exactly:
+
+* test_napari_streaming_handlers.py:
+  b6466a57ad45ec6e28d5edeb6a645953715daec1a7f71bfea7d80571d457920e
+* test_streaming_service.py:
+  b7ff0978f3ecbeab717621845f79a090284143cddeec377d7aa1b6284cf8e091
+* test_materialization_core.py:
+  6ba9f0636d113954ce993c900265f093b57a356e5e9c7450d5956872937320d5
+
+One stdlib-only syntax/byte check parsed the two integrated production files,
+three fixtures and two new packet Python files: seven parsed, zero errors,
+0.15s. No OpenHCS/scientific import, test, detector rerun, build, install or
+runtime launch. Original installed88+24+3 controls and104-tool/fresh-health
+receipts are READY-PACKAGE07-42.json/PACKAGE07-FAMILY42.rst under engineering494.
+Original40 failures remain. Historical a78 all-nine-path R0/complete AST and
+uncompleted global NRA OOM retain their original pins/limitations; neither is
+renamed as a fresh integrated-head scan. Target07 is immutable; no rebuild.
+
+Precise remaining public prerequisite
+------------------------------------
+
+Parent owns the sole future95 client/native receiving. Saved-archive-only public
+reopening does not yet demonstrate TWO endpoint items in each surviving route:
+record-key producer grouping and declared-domain containment are determining
+contracts, not permissions to fabricate a producer/source receipt. A singleton
+well-coordinate translation is not rematerialization. The conditional grouped
+pipeline is essential to the current proposed3-to2 relation and therefore needs
+parent's decision on the known Root435 main-flow publication risk. No publication
+fix, failed scientific replay, pipeline execution or native selection proof is
+claimed. Source/installed selection controls and old06 public raw-survivor PASS
+remain separate from the new Points-and-Shapes live remount acceptance.
+
+Packet bytes before this checkpoint
+-----------------------------------
+
+Four files28099 apparent bytes/36KiB allocated, before this text receipt:
+
+* RECEIVING.rst SHA256
+  5db0fd3b697695cd81cc086d72fd928909582baf06d6bf0e45dafe4a2aa75ab8
+* PUBLIC.commands SHA256
+  41ecfc50c0ac6f728d232a61d4ec0ca78ec84a43e59c81c4a23a15b24a9c64d0
+* fixture_522.py SHA256
+  f8f05ea40b53d7a4a0cfb1d6cf4744fe6b2d092d270af4788138b9233fcaeba7
+* pipeline.py SHA256
+  08f61ffb266250aad4a93ecf1977d2a2989c290cec028927759bd3d3878552a9
+
+Foreign dirty gitlinks/untracked validation traces and frozen source/archives
+are unchanged. No cleanup, package/skill hot update or scientific author contact.
+
+Root435 current source repair verified; receiving deferred
+--------------------------------------------------------
+
+After parent deferred95 to Dewey's full-volume SCI launch, Singer read current
+PR394 head5af63decedc018a905c33057b47758bf84dc6520 and actual repair
+e8587bd7eb0c4aa283bc300c5eb9f2294f24890f. The production writer compares the
+persisted occurrence against record.filename_address, not the optional scalar
+artifact address, while retaining complete image-metadata equality. This is
+already implemented by Root, not an unowned patch for Singer to recreate.
+
+Current GitHub source blobs byte-identify the original repair:
+function_outputs.py7297a44416dbead154e7950fddfe2fe2737001ad and
+test_collapsed_persisted_occurrence_435.py564af6fce342a9cec9b650285e2fd7afa7cc464e.
+The full383-line fixture covers collapsed SITE, scalar, genuine metadata/address
+conflicts and original real TIFF publication/reopening. Root reports243 local
+controls, not installed original494 acceptance. It does not declare this packet's
+four-plane aggregateZ/two-endpoint Points-and-Shapes journey. No new test run.
+
+Existing Root integration request updated with that actual source progress:
+https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5968788140
+Root retains the writer/shared fixture; request is a link to an existing exact
+aggregate control or a narrow extension through that owner. No competing edit,
+new writer, installed patch or claim that whole394 must meet its optimization
+target before an independently qualified usage repair can ship.
+
+Package07 still excludes Root435; all packet/current target bytes unchanged.
+No95 reservation/process exists here. Parent must provide a fresh custody and
+funding handoff after the SCI lane releases before any native receiving. No
+source or runtime operation is waiting on an UNKNOWN retry, and no old failure
+or untracked/foreign source is overwritten.
+
+Existing152 automatic Point-ROI producer: new installed witness
+--------------------------------------------------------------
+
+Parent requested read-only diagnosis of the original third-H002 v2 execution;
+no scientist contact, live call, replay, image/table/ROI decode or source edit.
+The retained original reply is under
+/home/ts/wt/openhcs-issue-batch-20260929/next-h002-distinct95-20261003/third-h00207/
+H002_THIRD95/author-workspace/output/candidates/v2/execution-failed-viewer.json,
+SHA256a6cc3d758e8101bfd8935d9a3fbb0917a1ee5c238ddcfdebed762f5cf1e32600.
+Job5/fa9c98c9-81d3-4338-96c3-88ee8ac2a3f7 axis completed, but execution FAILED.
+Computational output persistence is not successful viewer settlement.
+
+Original output/runtime/scratch/data/openhcs/logs/napari_detached_port_6015.log
+lines73..124 records the first route error: NapariPointsLayerDisplayHandler.
+geometric_component_values rejects "Fractional-Z point ROI requires a projected
+z_index axis" at installed target07 line2191. The native execution log later
+records the settlement progress request's Resource temporarily unavailable and
+the generic execution failure. Original ManagedViewerLifecycleMixin settlement
+and compiled_plate_execution failure propagation were read; no timeout change.
+The v1 trailing-return ABI error is an independent original author failure.
+
+Saved viewer-state-complete.json has the automatic centre route unmounted with
+empty axes. Saved viewer-state-reopened.json retains that unmounted route while
+the separate manual archive route is mounted with STACK Z1..60. This is a saved
+public-state comparison, not a new reopen, point-coordinate read or biology QA.
+The actual failing automatic request's complete incoming wire operands were not
+retained; do not claim those operands were directly observed.
+
+This is SAME tracked152 witness5962961567, not a new issue or viewer fallback:
+https://github.com/OpenHCSDev/openhcs/issues/152#issuecomment-5962961567
+Planck already released the coherent494 producer family to Root394:
+https://github.com/OpenHCSDev/openhcs/pull/394#issuecomment-5969244906
+Planck has appended this fresh witness to that existing request; no duplicate
+request or competing patch here. Current source checks pin Root5570b7a458ab035c
+and mainba7b26b82717a7bc4de5c9701b413aa64ba13e35. AST queries of both original
+core/options modules show their point writer matches target07 exactly; neither
+contains PointROIOutput or PointROIOptions.stream_source_identities. Both retain
+merged523 ViewerStreamBackendCallKwargs.projected_outputs. Merged531's CP output
+policy changes do not add that point producer family. These targeted AST facts
+are not a new whole-family census or a structural refactor qualification.
+
+The ownership distinction is emitted scalar planes versus the source planes
+represented by one archive (IDEN-1/BOUND-2). Existing MaterializationSpec.
+emitted_source_identities only returns variable-plane writer identities;
+ArtifactStreamSourceMetadataAuthority consumes that result, while the scoped
+component layout removes missing declared axes. Original494 already provides
+PointROIOutput's exact source-plane anchor, PointROIOptions.measurement_payload/
+stream_source_identities, shared FileOutputOptions behavior, and the existing
+MaterializationSpec/ArtifactStreamSourceMetadataAuthority consumer migration.
+
+Shortest coherent closure is Root integrating that released family, preserving
+full archive provenance/calibration, all original source guards and merged523
+projected-output accounting. Do not bulk-copy old494 core, guess Z in the viewer,
+force a display mode, suppress settlement failure, add a pending store or widen
+timeouts. Root owns its tiny new automatic producer/wire/strict-receiver control
+and genuine malformed-domain negatives; parent owns fresh installed/public
+acceptance after an explicit safe handoff. Original job remains FAILED and all
+scientific outputs/journals/negative inputs remain untouched. No native test now.

docs/validation/viewer-retirement-519-selection95/PUBLIC.commands

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+# SOURCE-ONLY, parent retained shell only; NOT an automatic batch.
+# NOT DISPATCH-READY: grouped publication prerequisite/Root435 risk in RECEIVING.rst.
+# Runtime markers are replaced from current public replies, NEVER old handles.
+call openhcs_health_check --arguments '{}' --json
+call openhcs_get_authoring_context --arguments '{"kind":"first_use"}' --json
+call openhcs_get_authoring_context --arguments '{"kind":"headless_execution"}' --json
+call openhcs_get_authoring_context --arguments '{"kind":"viewer_review"}' --json
+tools --contains openhcs_register_custom_function --json
+tools --contains openhcs_create_orchestrator_session_from_pipeline_source --json
+tools --contains openhcs_submit_compile --json
+tools --contains openhcs_submit_pipeline_execution --json
+tools --contains openhcs_get_execution_status --json
+tools --contains openhcs_query_plate_files --json
+tools --contains openhcs_stream_plate_files_to_viewer --json
+tools --contains openhcs_retire_viewer_window_layers --json
+tools --contains openhcs_navigate_viewer_window --json
+tools --contains openhcs_get_viewer_window_payloads --json
+call openhcs_start_owned_runtime --arguments '{"host":"127.0.0.1","port":6014,"transport_mode":"tcp","persistent":true}' --json
+# Observe SAME original returned native handle to READY, no start retry.
+call openhcs_observe_owned_runtime --arguments '{"handle":<COMPLETE_NEW_NATIVE_HANDLE>}' --json
+call openhcs_start_function_catalog_preparation --arguments '{"host":"127.0.0.1","port":6014,"transport_mode":"tcp","persistent":true}' --json
+# Observe original returned catalog preparation, then register actual file bytes.
+call openhcs_register_custom_function --arguments '{"source_code":<JSON_STRING_OF_fixture_522.py_BYTES>,"function_name":"point_shape_volume_fixture_522","storage_dir":<NEW_NATIVE_launch_plan.storage_dir>,"persist":true,"host":"127.0.0.1","port":6014,"transport_mode":"tcp","persistent":true}' --json
+# Describe actual returned canonical ID; stable import must match pipeline.py.
+call openhcs_create_config --arguments '{"config_type":"global","values":{"num_workers":1,"use_threading":true,"microscope":"source_bindings","materialize_runtime_artifacts":true}}' --json
+call openhcs_inspect_pipeline_source_artifact_plan --arguments '{"plate_path":"/home/ts/wt/openhcs-issue-batch-20260929/engineering494/standalone95-selection40/endpoints","pipeline_source":<JSON_STRING_OF_pipeline.py_BYTES>,"global_config_id":<RETURNED_CONFIG_ID>}' --json
+# Reflect current query schema; query source workspace returned by original projector.
+call openhcs_query_plate_files --arguments '{"plate_path":<RETURNED_MIDDLE_WORKSPACE>,"kind":"image","limit":4}' --json
+call openhcs_stream_plate_files_to_viewer --arguments '{"plate_path":<RETURNED_MIDDLE_WORKSPACE>,"file_paths":<EXACT_PUBLIC_A02_IMAGE_PATHS>,"kind":"image","host":"127.0.0.1","port":6015,"transport_mode":"tcp","persistent":true,"fresh_viewer":false}' --json
+viewer-state --port 6015 --host 127.0.0.1 --transport-mode tcp --json
+call openhcs_create_orchestrator_session_from_pipeline_source --arguments '{"plate_path":"/home/ts/wt/openhcs-issue-batch-20260929/engineering494/standalone95-selection40/endpoints","pipeline_source":<JSON_STRING_OF_pipeline.py_BYTES>,"global_config_id":<RETURNED_CONFIG_ID>,"host":"127.0.0.1","port":6014,"transport_mode":"tcp","persistent":true}' --json
+# Compile/execute/observe use original reflected schemas and returned IDs.
+call openhcs_submit_compile --arguments '{"session_id":<RETURNED_SESSION_ID>,"wait":false}' --json
+call openhcs_get_execution_status --arguments '{"job_id":<ORIGINAL_COMPILE_JOB_ID>}' --json
+# Only when that compile is terminal COMPLETE with the original artifact:
+call openhcs_submit_pipeline_execution --arguments '{"session_id":<RETURNED_SESSION_ID>,"compile_artifact_id":<ORIGINAL_COMPILE_ARTIFACT_ID>,"wait":false,"runtime_observation_export_path":"/home/ts/wt/openhcs-issue-batch-20260929/engineering494/standalone95-selection40/runtime/VALUES","runtime_observation_export_scope":"values"}' --json
+call openhcs_get_execution_status --arguments '{"job_id":<ORIGINAL_EXECUTION_JOB_ID>}' --json
+# Observe ONE execution through terminal including automatic viewer settlement.
+# Never dispatch another pipeline on an error/UNKNOWN or fabricate a stream receipt.
+viewer-state --port 6015 --host 127.0.0.1 --transport-mode tcp --json
+call openhcs_get_viewer_window_payloads --arguments '{"host":"127.0.0.1","port":6015,"transport_mode":"tcp","route_key":<CURRENT_POINTS_ROUTE>,"include_array_values":false,"include_shape_payloads":true,"max_shape_payloads":8}' --json
+call openhcs_get_viewer_window_payloads --arguments '{"host":"127.0.0.1","port":6015,"transport_mode":"tcp","route_key":<CURRENT_SHAPES_ROUTE>,"include_array_values":false,"include_shape_payloads":true,"max_shape_payloads":8}' --json
+call openhcs_navigate_viewer_window --arguments '{"host":"127.0.0.1","port":6015,"transport_mode":"tcp","route_key":<CURRENT_POINTS_ROUTE>,"data_index":<ACTUAL_A03_POINT_MEMBER>,"visible":true,"selected":true}' --json
+call openhcs_navigate_viewer_window --arguments '{"host":"127.0.0.1","port":6015,"transport_mode":"tcp","route_key":<CURRENT_SHAPES_ROUTE>,"data_index":<ACTUAL_A03_SHAPE_MEMBER>,"visible":true,"selected":true}' --json
+# Record BOTH selected sets/source association after original earlier work settles.
+# Matched triples before/after use original public visibility/viewport/intensity
+# commands with selected:null/no data_index; exact axes/camera from current replies.
+call openhcs_set_viewer_native_window --arguments '{"host":"127.0.0.1","port":6015,"transport_mode":"tcp","presentation":{}}' --json
+call openhcs_viewer_snapshot_window --arguments '{"host":"127.0.0.1","port":6015,"transport_mode":"tcp","output_dir_path":<NEW_CASE_QA_STAGE>,"capture_scope":"window"}' --json
+# Require BEFORE well extent3 in BOTH geometry survivors and complete member proof.
+call openhcs_retire_viewer_window_layers --arguments '{"host":"127.0.0.1","port":6015,"transport_mode":"tcp","expected_producers":<CURRENT_A02_RAW_ROUTE_TO_COMPLETE_NINE_FIELD_PRODUCERS>}' --json
+# No reselection: read native indices/domain and original source/payloads FIRST.
+viewer-state --port 6015 --host 127.0.0.1 --transport-mode tcp --json
+# Require BOTH extent2 + same source member/group; 12 matched captures total.
+# State/payload/source identity + actual native selected geometry, not indices alone.
+# Stop at first definitive contradiction/UNKNOWN; preserve complete raw journals.
+call openhcs_close_viewer_window --arguments '{"host":"127.0.0.1","port":6015,"transport_mode":"tcp","confirmed":true}' --json
+call openhcs_close_owned_runtime --arguments '{"handle":<COMPLETE_ORIGINAL_NEW_NATIVE_HANDLE>}' --json
+# Verify ACK/process identity+exit/ports gone; normal retained shell terminal.
+exit