fix(memory): add missing tangle header
This commit is contained in:
@@ -1,3 +1,4 @@
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#+PROPERTY: header-args:lisp :tangle memory.lisp
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#+TITLE: The System Memory (memory.lisp)
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#+AUTHOR: Amr
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#+FILETAGS: :harness:memory:
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@@ -31,24 +32,24 @@ flowchart TD
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#+end_src
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** Package Context
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#+begin_src lisp :tangle (expand-file-name "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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"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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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@@ -60,7 +61,7 @@ Every element in the Memex (headlines, paragraphs, etc.) is represented by an `o
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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@@ -68,7 +69,7 @@ The `compute-merkle-hash` function ensures the cryptographic integrity of the kn
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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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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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@@ -77,7 +78,7 @@ The `compute-merkle-hash` function ensures the cryptographic integrity of the kn
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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@@ -85,8 +86,8 @@ The `ingest-ast` function is the primary bridge between the external world (Emac
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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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(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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@@ -116,7 +117,7 @@ The `ingest-ast` function is the primary bridge between the external world (Emac
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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(defvar *object-store-snapshots* nil)
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(defun copy-hash-table (hash-table)
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@@ -137,13 +138,13 @@ Because objects are stored immutably in the `*history-store*`, a snapshot is a l
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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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(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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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@@ -156,14 +157,14 @@ Restores the state of the Memex from one of the previous snapshots.
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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"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 (getenv "MEMORY_SNAPSHOT_PATH")))
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(let ((env-path (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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@@ -173,7 +174,7 @@ Essential for surviving crashes. Saves the in-memory hash tables to disk and loa
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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 ";; 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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@@ -209,13 +210,13 @@ Reconstitutes alists into hash tables."
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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"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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(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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@@ -258,10 +259,10 @@ Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similar
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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((: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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@@ -271,14 +272,14 @@ Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similar
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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((: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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(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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@@ -294,7 +295,7 @@ Returns up to LIMIT objects with similarity >= MIN-SIMILARITY, sorted by similar
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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@@ -324,7 +325,7 @@ Basic functions for retrieving objects by ID or type.
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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 "harness/memory.lisp" (expand-file-name "harness/"))
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#+begin_src lisp :tangle memory.lisp" )
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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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@@ -339,7 +340,7 @@ Utility functions for AST traversal and path resolution.
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* Test Suite
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#+begin_src lisp :tangle (expand-file-name "harness/memory-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR") ".") "/harness") "/tests"))
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#+begin_src lisp :tangle memory-tests.lisp" (concat (concat (or (getenv "INSTALL_DIR ". "/harness "/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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@@ -347,13 +348,13 @@ Utility functions for AST traversal and path resolution.
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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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: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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(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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@@ -366,14 +367,14 @@ Utility functions for AST traversal and path resolution.
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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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(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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(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 (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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@@ -381,27 +382,27 @@ Utility functions for AST traversal and path resolution.
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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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(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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(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))
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(is (equal (org-object-hash (lookup-object "cow-node) hash-v2))
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(rollback-memory 0)
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(is (equal (org-object-hash (lookup-object "cow-node")) hash-v1)))))
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(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."
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(clrhash *memory*)
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(setf *object-store-snapshots* nil)
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(let* ((ast '(:type :HEADLINE :properties (:ID "node-1" :TITLE "Original") :contents nil))
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(let* ((ast '(:type :HEADLINE :properties (:ID "node-1" :TITLE "Original :contents nil))
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(id (ingest-ast ast)))
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(snapshot-memory)
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;; Manually corrupt the hash in the live memory
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(let ((obj (lookup-object id)))
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(setf (org-object-hash obj) "CORRUPTED-HASH"))
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(setf (org-object-hash obj) "CORRUPTED-HASH)
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;; Simulate a system integrity check that should fail and rollback
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;; We'll use a manual check here since automatic validation is in the Loop
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