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(refactor): org-roam-graph (#490)

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- Consolidate graph build/display commands into org-roam-graph command
  See #450
- Require org-roam-db
  Rather than declaring its functions.
- Move obsolete variable org-roam-graph-node-shape to org-roam-compat
- org-roam-graph--build-connected-component accepts a file argument
  Allows building a graph without having the target file as the current
  buffer
- Eliminate repeating code
- Fix checkdoc warnings
master
N V 6 years ago committed by GitHub
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  1. 20
      doc/installation.md
  2. 10
      org-roam-compat.el
  3. 180
      org-roam-graph.el

20
doc/installation.md
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@ -14,7 +14,7 @@ The recommended method of configuration is to use [use-package][use-package].
```emacs-lisp
(use-package org-roam
:hook
:hook
(after-init . org-roam-mode)
:custom
(org-roam-directory "/path/to/org-files/")
@ -22,7 +22,7 @@ The recommended method of configuration is to use [use-package][use-package].
(("C-c n l" . org-roam)
("C-c n f" . org-roam-find-file)
("C-c n b" . org-roam-switch-to-buffer)
("C-c n g" . org-roam-graph-show))
("C-c n g" . org-roam-graph))
:map org-mode-map
(("C-c n i" . org-roam-insert))))
```
@ -34,7 +34,7 @@ Or without `use-package`:
(define-key org-roam-mode-map (kbd "C-c n l") #'org-roam)
(define-key org-roam-mode-map (kbd "C-c n f") #'org-roam-find-file)
(define-key org-roam-mode-map (kbd "C-c n b") #'org-roam-switch-to-buffer)
(define-key org-roam-mode-map (kbd "C-c n g") #'org-roam-graph-show)
(define-key org-roam-mode-map (kbd "C-c n g") #'org-roam-graph)
(define-key org-mode-map (kbd "C-c n i") #'org-roam-insert)
(org-roam-mode +1)
```
@ -71,7 +71,7 @@ wraps Org-roam. Paste the following into a new file
"arl" 'org-roam
"art" 'org-roam-dailies-today
"arf" 'org-roam-find-file
"arg" 'org-roam-graph-show)
"arg" 'org-roam-graph)
(spacemacs/declare-prefix-for-mode 'org-mode "mr" "org-roam")
(spacemacs/set-leader-keys-for-major-mode 'org-mode
@ -80,7 +80,7 @@ wraps Org-roam. Paste the following into a new file
"rb" 'org-roam-switch-to-buffer
"rf" 'org-roam-find-file
"ri" 'org-roam-insert
"rg" 'org-roam-graph-show))))
"rg" 'org-roam-graph))))
```
Next, append `org-roam` to the `dotspacemacs-configuration-layers`
@ -94,7 +94,7 @@ with that of the ranger layer. You might want to change it to 'aor'
## Doom Emacs
[Doom Emacs][doom] has a `+roam` flag on its `org` module for easy
[Doom Emacs][doom] has a `+roam` flag on its `org` module for easy
installation and configuration. Simply add the flag to the `org` section
of your `~/.doom.d/init.el` and run `~/.emacs.d/bin/doom sync`.
@ -108,12 +108,12 @@ of your `~/.doom.d/init.el` and run `~/.emacs.d/bin/doom sync`.
On Windows, if you follow the installation instructions above, you will likely get the error message: **"No EmacSQL SQLite binary available, aborting"**, and `org-roam` won't start properly.
You need to do some additional steps to get `org-roam` to work.
You need to do some additional steps to get `org-roam` to work.
Essentially, you will need to have a binary file for `emacsql-sqlite` so that your Emacs can work with `sqlite` database -- `org-roam` uses it to track backlinks. The following options have been reported to work by Windows users in the community.
Option 1. **Windows Subsystem for Linux (WSL)**
: This option lets you use Linux on your Windows machine. It's Linux, so you don't need to do anything specific for Windows.
Option 1. **Windows Subsystem for Linux (WSL)**
: This option lets you use Linux on your Windows machine. It's Linux, so you don't need to do anything specific for Windows.
Option 2. **mingw-x64**
: Use mingw-x64. You would spend a bit of time to download it, and get familiar with how it works. You should be able to use Linux tools within your Windows [more contribution welcome].
@ -175,7 +175,7 @@ You will see the process triggered with lots of text automatically scrolling dow
Once compilation is done, check that `emacsql-sqlite.exe` has been added to the directory.
**Step 6.** Relaunch Emacs, use `org-roam`
When you start `org-roam` (e.g. via `org-roam-mode`), now you should no longer see the "No EmacSQL SQLite binary available, aborting" error. You are good to go.

10
org-roam-compat.el
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@ -67,17 +67,25 @@
"org-roam 1.0.0")
(define-obsolete-function-alias 'org-roam-date 'org-roam-dailies-date
"org-roam 1.0.0")
(define-obsolete-function-alias 'org-roam-graph-show 'org-roam-graph
"org-roam 1.0.0")
(define-obsolete-function-alias 'org-roam-graph-build 'org-roam-graph
"org-roam 1.0.0")
;;;; Variables
(define-obsolete-variable-alias 'org-roam-graphviz-extra-options
'org-roam-graph-extra-config "org-roam 1.0.0")
(define-obsolete-variable-alias 'org-roam-grapher-extra-options
'org-roam-graph-extra-config "org-roam 1.0.0")
(make-obsolete-variable 'org-roam-graph-node-shape 'org-roam-graph-node-extra-config "org-roam 1.0.0")
(defcustom org-roam-graph-node-shape "ellipse"
"Shape of graph nodes."
:type 'string
:group 'org-roam)
(define-obsolete-variable-alias 'org-roam--db-connection
'org-roam-db--connection "org-roam 1.0.0")
(define-obsolete-variable-alias 'org-roam--current-buffer
'org-roam-buffer--current "org-roam 1.0.0")
(define-obsolete-variable-alias 'org-roam-date-title-format
'org-roam-dailies-capture-templates "org-roam 1.0.0")
(define-obsolete-variable-alias 'org-roam-date-filename-format

180
org-roam-graph.el
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@ -33,12 +33,10 @@
(require 'xml) ;xml-escape-string
(require 's) ;s-truncate, s-replace
(require 'org-roam-macs)
(require 'org-roam-db)
;;;; Declarations
(defvar org-roam-directory)
(declare-function org-roam-db--ensure-built "org-roam-db")
(declare-function org-roam-db-query "org-roam-db")
(declare-function org-roam-db--connected-component "org-roam-db")
(declare-function org-roam--org-roam-file-p "org-roam")
(declare-function org-roam--path-to-slug "org-roam")
@ -100,27 +98,18 @@ are excluded."
(list :tag "Matchers"))
:group 'org-roam)
(make-obsolete-variable 'org-roam-graph-node-shape 'org-roam-graph-node-extra-config "2020/04/01")
(defcustom org-roam-graph-node-shape "ellipse"
"Shape of graph nodes."
:type 'string
:group 'org-roam)
;;;; Functions
(defun org-roam-graph--expand-matcher (col &optional negate where)
"Return the exclusion regexp from `org-roam-graph-exclude-matcher'.
COL is the symbol to be matched against. if NEGATE, add :not to sql query.
set WHERE to true if WHERE query already exists."
(let ((matchers (cond ((null org-roam-graph-exclude-matcher)
nil)
((stringp org-roam-graph-exclude-matcher)
(cons (concat "%" org-roam-graph-exclude-matcher "%") nil))
((listp org-roam-graph-exclude-matcher)
(mapcar (lambda (m)
(concat "%" m "%"))
org-roam-graph-exclude-matcher))
(t
(error "Invalid org-roam-graph-exclude-matcher"))))
(let ((matchers (pcase org-roam-graph-exclude-matcher
('nil nil)
((pred stringp) `(,(concat "%" org-roam-graph-exclude-matcher "%")))
((pred listp) (mapcar (lambda (m)
(concat "%" m "%"))
org-roam-graph-exclude-matcher))
(_ (error "Invalid org-roam-graph-exclude-matcher"))))
res)
(dolist (match matchers)
(if where
@ -134,8 +123,16 @@ set WHERE to true if WHERE query already exists."
(push match res))
(nreverse res)))
(defun org-roam-graph--build (node-query)
"Build the graphviz string for NODE-QUERY.
(defun org-roam-graph--dot-option (option &optional wrap-key wrap-val)
"Return dot string of form KEY=VAL for OPTION cons.
If WRAP-KEY is non-nil it wraps the KEY.
If WRAP-VAL is non-nil it wraps the VAL."
(concat wrap-key (car option) wrap-key
"="
wrap-val (cdr option) wrap-val))
(defun org-roam-graph--dot (node-query)
"Build the graphviz dot string for NODE-QUERY.
The Org-roam database titles table is read, to obtain the list of titles.
The links table is then read to obtain all directed links, and formatted
into a digraph."
@ -149,115 +146,108 @@ into a digraph."
(edges-cites-query
`[:with selected :as [:select [file] :from ,node-query]
:select :distinct [file from]
:from links :inner :join refs :on (and (= links:to refs:ref) (= links:type "cite"))
:from links :inner :join refs :on (and (= links:to refs:ref)
(= links:type "cite"))
:where (and (in file selected) (in from selected))])
(edges (org-roam-db-query edges-query))
(edges (org-roam-db-query edges-query))
(edges-cites (org-roam-db-query edges-cites-query)))
(insert "digraph \"org-roam\" {\n")
(dolist (option org-roam-graph-extra-config)
(insert (concat " "
(car option)
"="
(cdr option)
";\n")))
(insert (format " node [%s];\n"
(->> org-roam-graph-node-extra-config
(mapcar (lambda (n)
(concat (car n) "=" (cdr n))))
(s-join ","))))
(insert (format " edge [%s];\n"
(->> org-roam-graph-edge-extra-config
(mapcar (lambda (n)
(concat (car n) "=" (cdr n))))
(s-join ","))))
(insert (org-roam-graph--dot-option option) ";\n"))
(dolist (attribute '("node" "edge"))
(insert (format " %s [%s];\n" attribute
(mapconcat #'org-roam-graph--dot-option
(symbol-value
(intern (concat "org-roam-graph-" attribute "-extra-config")))
","))))
(dolist (node nodes)
(let* ((file (xml-escape-string (car node)))
(title (or (caadr node)
(org-roam--path-to-slug file)))
(shortened-title (s-truncate org-roam-graph-max-title-length title))
(node-properties (list (cons "label" (s-replace "\"" "\\\"" shortened-title))
(cons "URL" (concat "org-protocol://roam-file?file="
(url-hexify-string file)))
(cons "tooltip" (xml-escape-string title)))))
(node-properties
`(("label" . ,(s-replace "\"" "\\\"" shortened-title))
("URL" . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
("tooltip" . ,(xml-escape-string title)))))
(insert
(format " \"%s\" [%s];\n"
file
(->> node-properties
(mapcar (lambda (n)
(concat (car n) "=" "\"" (cdr n) "\"")))
(s-join ","))))))
(format " \"%s\" [%s];\n" file
(mapconcat (lambda (n)
(org-roam-graph--dot-option n nil "\""))
node-properties ",")))))
(dolist (edge edges)
(insert (format " \"%s\" -> \"%s\";\n"
(xml-escape-string (car edge))
(xml-escape-string (cadr edge)))))
(insert (apply #'format `(" \"%s\" -> \"%s\";\n"
,@(mapcar #'xml-escape-string edge)))))
(insert (format " edge [%s];\n"
(->> org-roam-graph-edge-cites-extra-config
(mapcar (lambda (n)
(concat (car n) "=" (cdr n))))
(s-join ","))))
(mapconcat #'org-roam-graph--dot-option
org-roam-graph-edge-cites-extra-config ",")))
(dolist (edge edges-cites)
(insert (format " \"%s\" -> \"%s\";\n"
(xml-escape-string (car edge))
(xml-escape-string (cadr edge)))))
(insert (apply #'format `(" \"%s\" -> \"%s\";\n"
,@(mapcar #'xml-escape-string edge)))))
(insert "}")
(buffer-string))))
(defun org-roam-graph-build (&optional node-query)
"Generate a graph showing the relations between nodes in NODE-QUERY.
For building and showing the graph in a single step see `org-roam-graph-show'."
(interactive)
(defun org-roam-graph--build (&optional node-query)
"Generate a graph showing the relations between nodes in NODE-QUERY."
(unless org-roam-graph-executable
(user-error "Can't find %s executable. Please check if it is in your path"
org-roam-graph-executable))
(let* ((node-query (or node-query
`[:select [file titles]
:from titles
,@(org-roam-graph--expand-matcher 'file t)]))
(graph (org-roam-graph--build node-query))
:from titles
,@(org-roam-graph--expand-matcher 'file t)]))
(graph (org-roam-graph--dot node-query))
(temp-dot (make-temp-file "graph." nil ".dot" graph))
(temp-graph (make-temp-file "graph." nil ".svg")))
(call-process org-roam-graph-executable nil 0 nil
temp-dot "-Tsvg" "-o" temp-graph)
temp-graph))
(defun org-roam-graph--open (file)
"Open FILE using `org-roam-graph-viewer', with `view-file' as a fallback."
(if (and org-roam-graph-viewer (executable-find org-roam-graph-viewer))
(call-process org-roam-graph-viewer nil 0 nil file)
(view-file file)))
(defun org-roam-graph-show (&optional node-query)
"Generate and display a graph showing the relations between nodes in NODE-QUERY.
The graph is generated using `org-roam-graph-build' and subsequently displayed
using `org-roam-graph-viewer', if it refers to a valid executable, or using
`view-file' otherwise."
(interactive)
(org-roam-graph--open (org-roam-graph-build node-query)))
(defun org-roam-graph-build-connected-component (&optional max-distance)
"Like `org-roam-graph-build', but only include nodes connected to the current entry.
If MAX-DISTANCE is non-nil, only nodes within the given number of steps are shown."
(interactive "P")
(unless (org-roam--org-roam-file-p)
(user-error "Not in an Org-roam file"))
(let* ((file (file-truename (buffer-file-name)))
(files (or (if (and max-distance (>= (prefix-numeric-value max-distance) 0))
(defun org-roam-graph--build-connected-component (file &optional max-distance)
"Build a graph of nodes connected to FILE.
If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
(let* ((file (file-truename file))
(files (or (if (and max-distance (>= max-distance 0))
(org-roam-db--links-with-max-distance file max-distance)
(org-roam-db--connected-component file))
(list file)))
(query `[:select [file titles]
:from titles
:where (in file [,@files])]))
(org-roam-graph-build query)))
(org-roam-graph--build query)))
(defun org-roam-graph--open (file)
"Open FILE using `org-roam-graph-viewer', with `view-file' as a fallback."
(if (and org-roam-graph-viewer (executable-find org-roam-graph-viewer))
(call-process org-roam-graph-viewer nil 0 nil file)
(view-file file)))
(defun org-roam-graph-show-connected-component (&optional max-distance)
"Like `org-roam-graph-show', but only include nodes connected to the current entry.
If MAX-DISTANCE is non-nil, only nodes within the given number of steps are shown."
;;;; Commands
;;;###autoload
(defun org-roam-graph (&optional arg file node-query)
"Build and possibly display a graph for FILE from NODE-QUERY.
If FILE is nil, default to current buffer's file name.
ARG may be any of the following values:
- nil show the graph.
- `\\[universal-argument]' show the graph for FILE.
- `\\[universal-argument]' N show the graph for FILE limiting nodes to N steps.
- `\\[universal-argument] \\[universal-argument]' build the graph.
- `\\[universal-argument]' - build the graph for FILE.
- `\\[universal-argument]' -N build the graph for FILE limiting nodes to N steps."
(interactive "P")
(org-roam-graph--open (org-roam-graph-build-connected-component max-distance)))
(let ((file (or file (buffer-file-name))))
(unless file
(user-error "Cannot build graph for nil file. Is current buffer visiting a file?"))
(unless (org-roam--org-roam-file-p file)
(user-error "\"%s\" is not an org-roam file" file))
(pcase arg
('nil (org-roam-graph--open (org-roam-graph--build node-query)))
('(4) (org-roam-graph--open (org-roam-graph--build-connected-component file)))
((pred integerp) (let ((graph (org-roam-graph--build-connected-component (buffer-file-name) (abs arg))))
(when (>= arg 0)
(org-roam-graph--open graph))))
('(16) (org-roam-graph--build node-query))
('- (org-roam-graph--build-connected-component file))
(_ (user-error "Unrecognized ARG: %s" arg)))))
(provide 'org-roam-graph)

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