421 lines
21 KiB
Org Mode
421 lines
21 KiB
Org Mode
#+TITLE: The System Memory (memory.lisp)
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#+AUTHOR: Amr
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#+FILETAGS: :harness:memory:
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#+STARTUP: content
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* The System Memory (memory.lisp)
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** Architectural Intent: The Single Address Space (Live Memory)
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Yes, the Memory module is the cognitive bedrock of the opencortex. It is not a database; it is the agent's live, active "brain" state.
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Traditional architectures rely on external databases (SQLite, Vector DBs) which introduce I/O latency and structural impedance. The opencortex architecture chooses a different path: the **Single Address Space**. By treating the entire knowledge base as a graph of Lisp pointers, we achieve microsecond recollection and total structural transparency.
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- **Pointer-Based Reasoning:** By loading the entire knowledge graph into a live Common Lisp hash table, we achieve microsecond recollection. The harness doesn't "search a file"; it traverses a memory pointer.
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- **Memory Imaging:** The ability to snapshot the Lisp image allows the agent to resume its entire cognitive state instantly, solving the "Cold Start" problem.
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- **Merkle-Tree Integrity:** Every node in the Memory is cryptographically hashed. By recursively hashing content and children, the root hash provides a single, immutable fingerprint of the entire system state.
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** System Architecture
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#+begin_src mermaid
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flowchart TD
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subgraph LispMachine[Lisp Machine]
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H[Harness Pipeline] --> OS[(Memory)]
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S1[Skill: Architect] --> OS
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S2[Skill: Analyst] --> OS
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S3[Skill: GTD] --> OS
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H -- Pointers --> S1
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H -- Pointers --> S2
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end
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subgraph IPCSlow[External Layer]
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E[Emacs / Actuators] -. communication protocol .-> H
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end
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#+end_src
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** Package Context
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(in-package :opencortex)
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#+end_src
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** The Object Repository
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The `*memory*` is the global hash table that holds every Org element by its unique ID. This is the "live RAM" of the agent's memory.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defvar *memory* (make-hash-table :test 'equal))
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(defvar *history-store* (make-hash-table :test 'equal)
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"Immutable Merkle-Tree versioning store mapping hashes to objects.")
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#+end_src
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** The Data Structure (org-object)
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Every element in the Memex (headlines, paragraphs, etc.) is represented by an `org-object` structure. It contains both semantic metadata (attributes, content) and structural metadata (parent/child pointers, Merkle hashes).
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defstruct org-object
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id type attributes content vector parent-id children version last-sync hash)
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;; Enable serialization via make-load-form (standard CL)
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(defmethod make-load-form ((obj org-object) &optional env)
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(make-load-form-saving-slots obj :environment env))
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#+end_src
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** Merkle Tree Integrity (compute-merkle-hash)
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The `compute-merkle-hash` function ensures the cryptographic integrity of the knowledge graph. A node's hash depends on its own properties and the hashes of all its children. This creates a recursive fingerprint where any change to a single note propagates up to the root hash.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defun compute-merkle-hash (id type attributes content child-hashes)
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"Computes a SHA-256 Merkle hash for a node based on its core properties and children's hashes."
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(let* ((alist (loop for (k v) on attributes by #'cddr collect (cons k v)))
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(sorted-alist (sort alist #'string< :key (lambda (x) (format nil "~a" (car x)))))
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(attr-string (format nil "~s" sorted-alist))
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(children-string (format nil "~{~a~}" child-hashes))
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(data-string (format nil "ID:~a|TYPE:~s|ATTRS:~a|CONTENT:~a|CHILDREN:~a"
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id type attr-string (or content "") children-string))
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(digester (ironclad:make-digest :sha256)))
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(ironclad:update-digest digester (ironclad:ascii-string-to-byte-array data-string))
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(ironclad:byte-array-to-hex-string (ironclad:produce-digest digester))))
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#+end_src
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** Ingesting the AST (ingest-ast)
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The `ingest-ast` function is the primary bridge between the external world (Emacs/JSON) and the internal Lisp machine. It recursively parses an Org-mode Abstract Syntax Tree (AST) into `org-object` structures and registers them in the store.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defun ingest-ast (ast &optional parent-id)
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"Parses an Org AST into the recursive Lisp Memory with Merkle hashing."
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(let* ((type (getf ast :type))
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(props (getf ast :properties))
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(id (or (getf props :ID) (format nil "temp-~a" (get-universal-time))))
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(contents (getf ast :contents))
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(raw-content (when (eq type :HEADLINE)
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(format nil "~a~%~a" (getf props :TITLE) (or (cl:getf ast :raw-content) ""))))
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(should-embed (and raw-content (equal (getf props :EMBED) "t")))
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(child-ids nil)
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(child-hashes nil))
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(dolist (child contents)
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(when (listp child)
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(let ((child-id (ingest-ast child id)))
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(push child-id child-ids)
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(let ((child-id-val child-id))
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(let ((child-obj (lookup-object child-id-val)))
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(when child-obj (push (org-object-hash child-obj) child-hashes)))))))
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(setf child-ids (nreverse child-ids))
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(setf child-hashes (nreverse child-hashes))
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(let* ((hash (compute-merkle-hash id type props raw-content child-hashes))
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(existing-obj (gethash hash *history-store*))
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(obj (or existing-obj
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(make-org-object
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:id id :type type :attributes props :content raw-content
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:vector (when should-embed (get-embedding raw-content))
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:parent-id parent-id :children child-ids
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:version (get-universal-time) :last-sync (get-universal-time)
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:hash hash))))
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(unless existing-obj
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(setf (gethash hash *history-store*) obj))
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(setf (gethash id *memory*) obj)
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id)))
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#+end_src
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** Memory Snapshots (snapshot-memory)
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Because objects are stored immutably in the `*history-store*`, a snapshot is a lightweight shallow copy of the active `*memory*` pointers. The system maintains a rolling buffer of 20 snapshots, allowing for near-instant, zero-cost rollback.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defvar *object-store-snapshots* nil)
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(defun copy-hash-table (hash-table)
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"Creates a shallow copy of a hash table."
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(let ((new-table (make-hash-table :test (hash-table-test hash-table)
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:size (hash-table-size hash-table))))
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(maphash (lambda (k v) (setf (gethash k new-table) v)) hash-table)
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new-table))
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(defun snapshot-memory ()
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"Creates a lightweight, Copy-on-Write snapshot using Merkle-Tree pointers."
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;; To prevent live modification of objects from affecting snapshots,
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;; we must copy the objects themselves when creating the snapshot.
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(let ((snapshot (make-hash-table :test 'equal :size (hash-table-size *memory*))))
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(maphash (lambda (k v)
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(setf (gethash k snapshot) (copy-org-object v)))
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*memory*)
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(push (list :timestamp (get-universal-time) :data snapshot) *object-store-snapshots*)
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(when (> (length *object-store-snapshots*) 20)
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(setf *object-store-snapshots* (subseq *object-store-snapshots* 0 20)))
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(harness-log "MEMORY - CoW Memory snapshot created.")))
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#+end_src
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** Memory Rollback (rollback-memory)
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Restores the state of the Memex from one of the previous snapshots.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defun rollback-memory (&optional (index 0))
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"Restores the Memory to a previously captured snapshot using immutable history pointers."
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(let ((snapshot (nth index *object-store-snapshots*)))
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(if snapshot
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(progn (setf *memory* (copy-hash-table (getf snapshot :data)))
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(harness-log "MEMORY - Memory rolled back to snapshot ~a" index))
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(harness-log "MEMORY ERROR - Snapshot ~a not found." index))))
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#+end_src
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** Disk Persistence (save-memory / load-memory)
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Essential for surviving crashes. Saves the in-memory hash tables to disk and loads them back on restart.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defvar *memory-snapshot-path* nil
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"Path to the memory snapshot file. Set from MEMORY_SNAPSHOT_PATH env or default.")
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(defun ensure-memory-snapshot-path ()
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"Initializes the snapshot path from environment or default location."
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(or *memory-snapshot-path*
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(let ((env-path (uiop:getenv "MEMORY_SNAPSHOT_PATH")))
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(setf *memory-snapshot-path*
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(or env-path
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(uiop:merge-pathnames* "memory.snap" (user-homedir-pathname)))))))
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(defun save-memory-to-disk ()
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"Serializes *memory* and *history-store* to disk for crash recovery.
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Converts hash tables to alists for proper serialization."
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(let ((path (ensure-memory-snapshot-path)))
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(with-open-file (stream path :direction :output :if-exists :supersede :if-does-not-exist :create)
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(format stream ";; OpenCortex Memory Snapshot~%")
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(format stream ";; Created: ~a~%~%" (format nil "~a" (get-universal-time)))
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(let ((memory-alist nil)
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(history-alist nil))
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(maphash (lambda (k v) (push (cons k v) memory-alist)) *memory*)
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(maphash (lambda (k v) (push (cons k v) history-alist)) *history-store*)
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(prin1 (list :memory memory-alist :history-store history-alist) stream)))
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(harness-log "MEMORY - Saved to ~a" path)
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path))
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(defun load-memory-from-disk ()
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"Loads *memory* and *history-store* from disk if the snapshot exists.
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Reconstitutes alists into hash tables."
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(let ((path (ensure-memory-snapshot-path)))
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(when (uiop:file-exists-p path)
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(handler-case
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(with-open-file (stream path :direction :input)
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(let ((data (read stream nil)))
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(when data
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(let ((memory-alist (getf data :memory))
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(history-alist (getf data :history-store)))
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(setf *memory* (make-hash-table :test 'equal :size (length memory-alist)))
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(dolist (kv memory-alist)
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(setf (gethash (car kv) *memory*) (cdr kv)))
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(setf *history-store* (make-hash-table :test 'equal :size (length history-alist)))
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(dolist (kv history-alist)
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(setf (gethash (car kv) *history-store*) (cdr kv)))
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(harness-log "MEMORY - Loaded from ~a (~a objects)" path (hash-table-size *memory*))))))
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(error (c)
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(harness-log "MEMORY WARNING - Failed to load snapshot: ~a" c))))
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t))
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#+end_src
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** Semantic Search (get-embedding, semantic-search)
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Support for vector embeddings via Ollama and semantic search with cosine similarity.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defvar *embedding-cache* (make-hash-table :test 'equal)
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"Cache for embeddings to avoid redundant API calls.")
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(defun get-embedding (text)
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"Generates a vector embedding for the given text via Ollama. Returns nil on failure."
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(when (or (null text) (string= text ""))
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(return-from get-embedding nil))
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(let ((cached (gethash text *embedding-cache*)))
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(when cached (return-from get-embedding cached)))
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(let ((result (funcall (get-cognitive-tool-body :get-ollama-embedding) (list :text text))))
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(when (eq (getf result :status) :success)
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(let ((vec (getf result :vector)))
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(setf (gethash text *embedding-cache*) vec)
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vec))))
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(defun cosine-similarity (vec-a vec-b)
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"Computes cosine similarity between two vectors. Both should be sequences of numbers."
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(when (or (null vec-a) (null vec-b) (zerop (length vec-a)) (zerop (length vec-b)))
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(return-from cosine-similarity 0.0))
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(let ((dot-product (loop for a across vec-a
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for b across vec-b
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sum (* a b)))
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(norm-a (sqrt (loop for a across vec-a sum (* a a))))
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(norm-b (sqrt (loop for b across vec-b sum (* b b)))))
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(if (or (zerop norm-a) (zerop norm-b))
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0.0
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(/ dot-product (* norm-a norm-b)))))
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(defun semantic-search (query &key (limit 10) (min-similarity 0.5))
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"Searches memory for objects semantically similar to the query.
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Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similarity descending."
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(let* ((query-vec (get-embedding query))
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(results nil))
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(unless query-vec
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(harness-log "EMBEDDING: Failed to generate embedding for query: ~a" query)
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(return-from semantic-search nil))
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(maphash (lambda (id obj)
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(let ((obj-vec (org-object-vector obj)))
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(when obj-vec
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(let ((sim (cosine-similarity query-vec obj-vec)))
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(when (>= sim min-similarity)
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(push (list :id id :object obj :similarity sim) results))))))
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*memory*)
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(setf results (sort results #'> :key (lambda (r) (getf r :similarity))))
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(subseq results 0 (min limit (length results)))))
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#+end_src
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** Cognitive Tool: Semantic Search
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(def-cognitive-tool :semantic-search
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"Searches memory for objects semantically similar to a query."
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((:query :type :string :description "The search query.")
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(:limit :type :integer :description "Maximum results to return." :default 10)
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(:min-similarity :type :number :description "Minimum similarity threshold (0-1)." :default 0.5))
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:body (lambda (args)
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(semantic-search (getf args :query)
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:limit (or (getf args :limit) 10)
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:min-similarity (or (getf args :min-similarity) 0.5))))
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#+end_src
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** Cognitive Tool: Generate Embeddings
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(def-cognitive-tool :generate-embeddings
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"Generates vector embeddings for given text via the configured embedding backend (Ollama)."
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((:texts :type :list :description "List of text strings to embed."))
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:body (lambda (args)
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(let ((texts (getf args :texts)))
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(if (not (and texts (listp texts)))
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(list :status :error :message ":texts must be a list of strings.")
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(let ((results nil) (errors nil))
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(dolist (text texts)
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(let ((vec (get-embedding text)))
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(if vec
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(push (list :text text :vector vec) results)
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(push text errors))))
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(list :status (if errors :partial :success)
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:embeddings (nreverse results)
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:failed (when errors (nreverse errors))
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:count (length results)))))))
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#+end_src
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** Lookup Utilities
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Basic functions for retrieving objects by ID or type.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defun org-id-new ()
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"Generates a new UUID string for Org-mode identification."
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(string-downcase (format nil "~a" (uuid:make-v4-uuid))))
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(defun lookup-object (id)
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"Retrieves an object from the store by its unique ID."
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(gethash id *memory*))
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(defun list-objects-by-type (type)
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"Returns a list of all objects matching a specific Org element type."
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(let ((results nil))
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(maphash (lambda (id obj) (declare (ignore id)) (when (eq (org-object-type obj) type) (push obj results))) *memory*)
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results))
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(defun list-objects-with-attribute (attr-name value)
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"Returns a list of all objects where ATTR-NAME matches VALUE."
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(let ((results nil))
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(maphash (lambda (id obj)
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(declare (ignore id))
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(let ((attrs (org-object-attributes obj)))
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(when (equal (getf attrs attr-name) value)
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(push obj results))))
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*memory*)
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results))
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#+end_src
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** Structural Helpers
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Utility functions for AST traversal and path resolution.
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#+begin_src lisp :tangle (expand-file-name "memory.lisp" (or (identity (getenv "INSTALL_DIR")) (file-name-directory (buffer-file-name))))
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(defun find-headline-missing-id (ast)
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"Traverses an AST to find headlines that lack an :ID: property."
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(when (listp ast)
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(if (and (eq (getf ast :type) :HEADLINE) (not (getf (getf ast :properties) :ID)))
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ast
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(cl:some #'find-headline-missing-id (getf ast :contents)))))
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(defun file-name-nondirectory (path)
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"Extracts the filename from a full path string."
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(let ((pos (position #\/ path :from-end t))) (if pos (subseq path (1+ pos)) path)))
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#+end_src
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* Test Suite
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#+begin_src lisp :tangle (expand-file-name "memory-tests.lisp" (concat (or (identity (getenv "INSTALL_DIR")) ".") "/tests"))
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(defpackage :opencortex-memory-tests
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(:use :cl :fiveam :opencortex)
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(:export #:memory-suite))
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(in-package :opencortex-memory-tests)
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(def-suite memory-suite
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:description "Tests for the Merkle-Tree Memory")
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(in-suite memory-suite)
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(test merkle-hash-consistency
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"Verify identical ASTs produce identical Merkle hashes."
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(let* ((ast1 '(:type :HEADLINE :properties (:ID "test-1" :TITLE "Node 1") :contents nil)))
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(clrhash *memory*)
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(let ((id1 (ingest-ast ast1)))
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(let ((hash1 (org-object-hash (lookup-object id1))))
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(clrhash *memory*)
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(let ((id2 (ingest-ast ast1)))
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(let ((hash2 (org-object-hash (lookup-object id2))))
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(is (equal hash1 hash2))))))))
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(test history-store-immutability
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"Verify that *history-store* retains old versions."
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(clrhash *memory*)
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(clrhash *history-store*)
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(let* ((ast-v1 '(:type :HEADLINE :properties (:ID "test-node" :TITLE "Version 1") :contents nil))
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(id-v1 (ingest-ast ast-v1))
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(obj-v1 (lookup-object id-v1))
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(hash-v1 (org-object-hash obj-v1)))
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(let* ((ast-v2 '(:type :HEADLINE :properties (:ID "test-node" :TITLE "Version 2") :contents nil))
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(id-v2 (ingest-ast ast-v2))
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(hash-v2 (org-object-hash (lookup-object id-v2))))
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(is (equal (org-object-hash (lookup-object "test-node")) hash-v2))
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(is (not (null (gethash hash-v1 *history-store*))))
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(is (not (null (gethash hash-v2 *history-store*)))))))
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(test cow-snapshot-and-rollback
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"Verify that lightweight snapshots restore previous pointer states."
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(clrhash *memory*)
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(setf *object-store-snapshots* nil)
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(let* ((ast-v1 '(:type :HEADLINE :properties (:ID "cow-node" :TITLE "State A") :contents nil))
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(id-v1 (ingest-ast ast-v1))
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|
(hash-v1 (org-object-hash (lookup-object id-v1))))
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|
(snapshot-memory)
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|
(let* ((ast-v2 '(:type :HEADLINE :properties (:ID "cow-node" :TITLE "State B") :contents nil))
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|
(id-v2 (ingest-ast ast-v2))
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|
(hash-v2 (org-object-hash (lookup-object id-v2))))
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|
(is (equal (org-object-hash (lookup-object "cow-node")) hash-v2))
|
|
(rollback-memory 0)
|
|
(is (equal (org-object-hash (lookup-object "cow-node")) hash-v1)))))
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|
|
|
(test test-merkle-corruption-rollback
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|
"Tier 2 Chaos: Verify that Merkle hash corruption triggers a Micro-Rollback."
|
|
(clrhash *memory*)
|
|
(setf *object-store-snapshots* nil)
|
|
(let* ((ast '(:type :HEADLINE :properties (:ID "node-1" :TITLE "Original") :contents nil))
|
|
(id (ingest-ast ast)))
|
|
(snapshot-memory)
|
|
;; Manually corrupt the hash in the live memory
|
|
(let ((obj (lookup-object id)))
|
|
(setf (org-object-hash obj) "CORRUPTED-HASH"))
|
|
|
|
;; Simulate a system integrity check that should fail and rollback
|
|
;; We'll use a manual check here since automatic validation is in the Loop
|
|
(let ((obj (lookup-object id)))
|
|
(let ((current-hash (org-object-hash obj))
|
|
(computed-hash (opencortex::compute-merkle-hash (org-object-id obj)
|
|
(org-object-type obj)
|
|
(org-object-attributes obj)
|
|
(org-object-content obj)
|
|
nil)))
|
|
(unless (string= current-hash computed-hash)
|
|
(rollback-memory 0))))
|
|
|
|
;; Verify that the memory was rolled back to the clean snapshot
|
|
(is (string/= "CORRUPTED-HASH" (org-object-hash (lookup-object id))))))
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#+end_src
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