Add a command to produce a graph of the indexed notes

CHANGELOG.md

@@ -6,6 +6,7 @@ All notable changes to this project will be documented in this file.
 
 ### Added
 
+* New `zk graph --format json` command which produces a JSON graph of the notes matching the given criteria.
 * New template variables `filename` and `filename-stem` when formatting notes (e.g. with `zk list --format`) and for the [`fzf-line`](docs/tool-fzf.md) config key.
 * Customize how LSP completion items appear in your editor when auto-completing links with the [`[lsp.completion]` configuration section](docs/config-lsp.md).
     ```toml

README.md

@@ -14,9 +14,9 @@
 * [Creating notes from templates](docs/note-creation.md)
 * [Advanced search and filtering capabilities](docs/note-filtering.md) including [tags](docs/tags.md), links and mentions
 * [Integration with your favorite editors](docs/editors-integration.md):
-    * [`zk.nvim`](https://github.com/megalithic/zk.nvim) for Neovim 0.5+, maintained by [Seth Messer](https://github.com/megalithic)
-    * [`zk-vscode`](https://github.com/mickael-menu/zk-vscode) for Visual Studio Code
     * [Any LSP-compatible editor](docs/editors-integration.md)
+    * [`zk-vscode`](https://github.com/mickael-menu/zk-vscode) for Visual Studio Code
+    * (*unmaintained*) [`zk.nvim`](https://github.com/megalithic/zk.nvim) for Neovim 0.5+ by [Seth Messer](https://github.com/megalithic)
 * [Interactive browser](docs/tool-fzf.md), powered by `fzf`
 * [Git-style command aliases](docs/config-alias.md) and [named filters](docs/config-filter.md)
 * [Made with automation in mind](docs/automation.md)

internal/adapter/sqlite/db.go

@@ -196,6 +196,17 @@ func (db *DB) migrate() error {
 				},
 				NeedsReindexing: true,
 			},
+
+			{ // 6
+				SQL: []string{
+					// View of links with the source and target notes metadata, for simpler queries.
+					`CREATE VIEW resolved_links AS
+					 SELECT l.*, s.path AS source_path, s.title AS source_title, t.path AS target_path, t.title AS target_title
+					   FROM links l
+					   LEFT JOIN notes s ON l.source_id = s.id
+					   LEFT JOIN notes t ON l.target_id = t.id`,
+				},
+			},
 		}
 
 		needsReindexing := false

internal/adapter/sqlite/db_test.go

@@ -27,7 +27,7 @@ func TestMigrateFrom0(t *testing.T) {
 		var version int
 		err := tx.QueryRow("PRAGMA user_version").Scan(&version)
 		assert.Nil(t, err)
-		assert.Equal(t, version, 5)
+		assert.Equal(t, version, 6)
 
 		_, err = tx.Exec(`
 			INSERT INTO notes (path, sortable_path, title, body, word_count, checksum)

internal/adapter/sqlite/link_dao.go

@@ -0,0 +1,156 @@
+package sqlite
+
+import (
+	"database/sql"
+	"fmt"
+
+	"github.com/mickael-menu/zk/internal/core"
+	"github.com/mickael-menu/zk/internal/util"
+)
+
+// LinkDAO persists links in the SQLite database.
+type LinkDAO struct {
+	tx     Transaction
+	logger util.Logger
+
+	// Prepared SQL statements
+	addLinkStmt        *LazyStmt
+	setLinksTargetStmt *LazyStmt
+	removeLinksStmt    *LazyStmt
+}
+
+// NewLinkDAO creates a new instance of a DAO working on the given database
+// transaction.
+func NewLinkDAO(tx Transaction, logger util.Logger) *LinkDAO {
+	return &LinkDAO{
+		tx:     tx,
+		logger: logger,
+
+		// Add a new link.
+		addLinkStmt: tx.PrepareLazy(`
+			INSERT INTO links (source_id, target_id, title, href, type, external, rels, snippet, snippet_start, snippet_end)
+			VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+		`),
+
+		// Set links matching a given href and missing a target ID to the given
+		// target ID.
+		setLinksTargetStmt: tx.PrepareLazy(`
+			UPDATE links
+			   SET target_id = ?
+			 WHERE target_id IS NULL AND external = 0 AND ? LIKE href || '%'
+		`),
+
+		// Remove all the outbound links of a note.
+		removeLinksStmt: tx.PrepareLazy(`
+			DELETE FROM links
+			 WHERE source_id = ?
+		`),
+	}
+}
+
+// Add inserts all the outbound links of the given note.
+func (d *LinkDAO) Add(links []core.ResolvedLink) error {
+	for _, link := range links {
+		sourceID := noteIDToSQL(link.SourceID)
+		targetID := noteIDToSQL(link.TargetID)
+
+		_, err := d.addLinkStmt.Exec(sourceID, targetID, link.Title, link.Href, link.Type, link.IsExternal, joinLinkRels(link.Rels), link.Snippet, link.SnippetStart, link.SnippetEnd)
+		if err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+// RemoveAll removes all the outbound links of the given note.
+func (d *LinkDAO) RemoveAll(id core.NoteID) error {
+	_, err := d.removeLinksStmt.Exec(noteIDToSQL(id))
+	return err
+}
+
+// SetTargetID updates the missing target_id for links matching the given href.
+// FIXME: Probably doesn't work for all type of href (partial, wikilinks, etc.)
+func (d *LinkDAO) SetTargetID(href string, id core.NoteID) error {
+	_, err := d.setLinksTargetStmt.Exec(int64(id), href)
+	return err
+}
+
+// joinLinkRels will concatenate a list of rels into a SQLite ready string.
+// Each rel is delimited by \x01 for easy matching in queries.
+func joinLinkRels(rels []core.LinkRelation) string {
+	if len(rels) == 0 {
+		return ""
+	}
+	delimiter := "\x01"
+	res := delimiter
+	for _, rel := range rels {
+		res += string(rel) + delimiter
+	}
+	return res
+}
+
+func (d *LinkDAO) FindBetweenNotes(ids []core.NoteID) ([]core.ResolvedLink, error) {
+	links := make([]core.ResolvedLink, 0)
+
+	idsString := joinNoteIDs(ids, ",")
+	rows, err := d.tx.Query(fmt.Sprintf(`
+		SELECT id, source_id, source_path, target_id, target_path, title, href, type, external, rels, snippet, snippet_start, snippet_end
+		  FROM resolved_links
+		 WHERE source_id IN (%s) AND target_id IN (%s)
+	`, idsString, idsString))
+	if err != nil {
+		return links, err
+	}
+	defer rows.Close()
+
+	for rows.Next() {
+		link, err := d.scanLink(rows)
+		if err != nil {
+			d.logger.Err(err)
+			continue
+		}
+		if link != nil {
+			links = append(links, *link)
+		}
+	}
+
+	return links, nil
+}
+
+func (d *LinkDAO) scanLink(row RowScanner) (*core.ResolvedLink, error) {
+	var (
+		id, sourceID, targetID, snippetStart, snippetEnd       int
+		sourcePath, targetPath, title, href, linkType, snippet string
+		external                                               bool
+		rels                                                   sql.NullString
+	)
+
+	err := row.Scan(
+		&id, &sourceID, &sourcePath, &targetID, &targetPath, &title, &href,
+		&linkType, &external, &rels, &snippet, &snippetStart, &snippetEnd,
+	)
+	switch {
+	case err == sql.ErrNoRows:
+		return nil, nil
+	case err != nil:
+		return nil, err
+	default:
+		return &core.ResolvedLink{
+			SourceID:   core.NoteID(sourceID),
+			SourcePath: sourcePath,
+			TargetID:   core.NoteID(targetID),
+			TargetPath: targetPath,
+			Link: core.Link{
+				Title:        title,
+				Href:         href,
+				Type:         core.LinkType(linkType),
+				IsExternal:   external,
+				Rels:         core.LinkRels(parseListFromNullString(rels)...),
+				Snippet:      snippet,
+				SnippetStart: snippetStart,
+				SnippetEnd:   snippetEnd,
+			},
+		}, nil
+	}
+}

internal/adapter/sqlite/link_dao_test.go

@@ -0,0 +1,53 @@
+package sqlite
+
+import (
+	"fmt"
+	"testing"
+
+	"github.com/mickael-menu/zk/internal/core"
+	"github.com/mickael-menu/zk/internal/util"
+	"github.com/mickael-menu/zk/internal/util/test/assert"
+)
+
+func testLinkDAO(t *testing.T, callback func(tx Transaction, dao *LinkDAO)) {
+	testTransaction(t, func(tx Transaction) {
+		callback(tx, NewLinkDAO(tx, &util.NullLogger))
+	})
+}
+
+type linkRow struct {
+	SourceId                         core.NoteID
+	TargetId                         *core.NoteID
+	Href, Type, Title, Rels, Snippet string
+	SnippetStart, SnippetEnd         int
+	IsExternal                       bool
+}
+
+func queryLinkRows(t *testing.T, q RowQuerier, where string) []linkRow {
+	links := make([]linkRow, 0)
+
+	rows, err := q.Query(fmt.Sprintf(`
+		SELECT source_id, target_id, title, href, type, external, rels, snippet, snippet_start, snippet_end
+		  FROM links
+		 WHERE %v
+		 ORDER BY id
+	`, where))
+	assert.Nil(t, err)
+
+	for rows.Next() {
+		var row linkRow
+		var sourceId int64
+		var targetId *int64
+		err = rows.Scan(&sourceId, &targetId, &row.Title, &row.Href, &row.Type, &row.IsExternal, &row.Rels, &row.Snippet, &row.SnippetStart, &row.SnippetEnd)
+		assert.Nil(t, err)
+		row.SourceId = core.NoteID(sourceId)
+		if targetId != nil {
+			row.TargetId = idPointer(*targetId)
+		}
+		links = append(links, row)
+	}
+	rows.Close()
+	assert.Nil(t, rows.Err())
+
+	return links
+}