(release): v1.2.3 (#1269)

* (feat): add `org-roam-db-update-method`

Add `org-roam-db-update-method`, which can be one of two choices:

1. `immediate`: the cache is updated upon file changes
2. `idle-timer`: Marks the org-roam database as dirty. If Emacs idles
for some seconds, the Org-roam cache is updated. This is the default,
and current behaviour.

The idle method makes for a smoother editing experience, but some
inconsistencies can be faced.

* org-roam-update-db-idle-seconds -> org-roam-db-update-idle-seconds

.gitignore

@@ -12,4 +12,4 @@
 /doc/mimetype
 /doc/stats/
 /config.mk
-/doc/manual/
+/doc/manual.html

.readthedocs.yml

@@ -1,8 +0,0 @@
-version: 2
-mkdocs:
- configuration: mkdocs.yml
-formats: all
-python:
-  version: 3.7
-  install:
-    - requirements: doc/requirements.txt

CHANGELOG.md

@@ -1,5 +1,71 @@
 # Changelog
 
+## 1.2.3 (13-11-2020)
+
+Primarily a stabilization and bug-fix release.
+
+Org-roam-dailies has also been revamped to include new features, see [this video](https://www.youtube.com/watch?v=1q9x2aZCJJ4) for a quick overview.
+
+### Added
+- [#978](https://github.com/org-roam/org-roam/pull/978) Revamp org-roam-dailies
+- [#1183](https://github.com/org-roam/org-roam/pull/1183) Interactive functions for managing aliases and tags in Org-roam file, namely `org-roam-alias-add`, `org-roam-alias-delete`, `org-roam-tag-add`, and `org-roam-tag-delete`.
+- [#1215](https://github.com/org-roam/org-roam/pull/1215) Multiple `ROAM_KEY` keywords can now be specified in one file. This allows bibliographical entries to share the same note file.
+- [#1238](https://github.com/org-roam/org-roam/pull/1238) Add `org-roam-prefer-id-links` variable to select linking method
+- [#1239](https://github.com/org-roam/org-roam/pull/1239) Allow `org-roam-protocol` to capture the webpage's selection, and add a toggle for storing the links to the pages
+- [#1264](https://github.com/org-roam/org-roam/pull/1264) add `org-roam-db-update-method` to control when the cache is rebuilt.
+
+### Changed
+- [#1264](https://github.com/org-roam/org-roam/pull/1264) renamed `org-roam-update-db-idle-seconds` to `org-roam-db-idle-idle-seconds` 
+
+### Fixed
+- [#1074](https://github.com/org-roam/org-roam/issues/1074) fix `org-roam--extract-links` to handle content boundaries.
+- [#1193](https://github.com/org-roam/org-roam/issues/1193) fix `org-roam-db-build-cache` by not killing temporary buffer in `org-roam--extract-links`.
+- [#1195](https://github.com/org-roam/org-roam/issues/1195) fix ID face showing as invalid if within Org ID files, but not Org-roam's.
+- [#1199](https://github.com/org-roam/org-roam/issues/1199) make Org-roam link insertions respect `org-roam-link-title-format` everywhere.
+- [#1201](https://github.com/org-roam/org-roam/issues/1201) fix `org-roam-db-build-cache` failing in scenarios involving duplicate IDs and deleted files.
+- [#1226](https://github.com/org-roam/org-roam/issues/1226) only update relative path of file links
+- [#1232](https://github.com/org-roam/org-roam/issues/1232) fix incorrect title extractions from narrowed buffers
+- [#1233](https://github.com/org-roam/org-roam/issues/1233) fixes bug where descriptive file links become plain links during update for relative paths
+- [#1252](https://github.com/org-roam/org-roam/issues/1252) respect original link type during automatic replacement
+
+## 1.2.2 (06-10-2020)
+
+In this release we support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`. Completion for these fuzzy links is supported via `completion-at-point`.
+
+Org-roam now does not resolve symlinks. This significantly speeds up cache builds, but may result in some workflows breaking. In particular, Org-roam now cannot figure out if two distinct file paths in the Org-roam directory are the same file, and both files will be processed as if they were different files. This error seems to be unavoidable now that symlinks are not resolved, but this workflow is rare and should not affect most users.
+
+This change requires you to set `org-roam-directory` to the resolved path of a folder. That is:
+
+```elisp
+(setq org-roam-directory (file-truename "/path/to/directory/"))
+```
+
+### Breaking Changes
+
+- [#1164](https://github.com/org-roam/org-roam/pull/1164) Org-roam now stores the database in the user's Emacs directory by default
+- [#910](https://github.com/org-roam/org-roam/pull/910) Deprecate `company-org-roam`, using `completion-at-point` instead. To use this with company, add the `company-capf` backend instead.
+- [#1109](https://github.com/org-roam/org-roam/pull/1109) Org-roam now does not resolve symlinks.
+
+### Features
+
+- [#1163](https://github.com/org-roam/org-roam/pull/1163) Support file-level IDs introduced in Org 9.4
+- [#1093](https://github.com/org-roam/org-roam/pull/1093) Add `vanilla` org-roam-tag-source to extract buffer Org tags
+- [#1079](https://github.com/org-roam/org-roam/pull/1079) Add `org-roam-tag-face` to customize appearance of tags in interactive commands
+- [#1073](https://github.com/org-roam/org-roam/pull/1073) Rename file on title change, when `org-roam-rename-file-on-title-change` is non-nil.
+- [#1071](https://github.com/org-roam/org-roam/pull/1071) Update link descriptions on title changes, and clean-up rename file advice
+- [#1061](https://github.com/org-roam/org-roam/pull/1061) Speed up the extraction of file properties, headlines, and titles
+- [#1046](https://github.com/org-roam/org-roam/pull/1046) New user option to exclude files from Org-roam
+- [#1032](https://github.com/org-roam/org-roam/pull/1032) File changes are now propagated to the database on idle timer. This prevents large wait times during file saves.
+- [#974](https://github.com/org-roam/org-roam/pull/974) Protect region targeted by `org-roam-insert`
+- [#994](https://github.com/org-roam/org-roam/pull/994) Simplify org-roam-store-link
+- [#1062](https://github.com/org-roam/org-roam/pull/1062) Variable `org-roam-completions-everywhere` allows for completions everywhere from word at point
+- [#910](https://github.com/org-roam/org-roam/pull/910), [#1105](https://github.com/org-roam/org-roam/pull/1105) Support fuzzy links of the form [[roam:Title]], [[roam:*Headline]] and [[roam:Title*Headline]]
+
+### Bugfixes
+
+- [#1057](https://github.com/org-roam/org-roam/pull/1057) Improve performance of database builds by preventing generation of LaTeX and image previews.
+- [#1103](https://github.com/org-roam/org-roam/pull/1103) Fix long build-times for Windows on files with URL links
+
 ## 1.2.1 (27-07-2020)
 
 This release consisted of a big deal of refactoring and bug fixes. Notably, we fixed several catastrophic failures on db builds with bad setups (#854), and modularized tag and title extractions.
@@ -10,9 +76,11 @@ We also added some new features that had been a long time coming:
 2. We now support nested captures, which is crucial for `org-roam-protocol` (#966)
 
 ### Breaking Changes
+
 - [#908](https://github.com/org-roam/org-roam/pull/908) Normalized titles in database. May break external packages that rely on unnormalized titles.
 
 ### Features
+
 - [#814](https://github.com/org-roam/org-roam/pull/814) Implement `org-roam-insert-immediate`
 - [#833](https://github.com/org-roam/org-roam/pull/833) Add customization of file titles with `org-roam-title-to-slug-function`.
 - [#839](https://github.com/org-roam/org-roam/pull/839) Return selected file from `org-roam-insert`
@@ -54,6 +122,7 @@ We also add `org-roam-unlinked-references`, which naively finds text that could
 - [#679](https://github.com/org-roam/org-roam/pull/679), [#683](https://github.com/org-roam/org-roam/pull/683) Building of the graph now happens in a separate process
 
 ### Bugfixes
+
 - [#714](https://github.com/org-roam/org-roam/pull/714) No longer print citelinks in backlinks buffer if there is no `ROAM_KEY` property or `org-ref` is not installed
 - [#759](https://github.com/org-roam/org-roam/pull/759), [#760](https://github.com/org-roam/org-roam/pull/760) Tags are only added to the tags table if there are actually tags present
 - [#700](https://github.com/org-roam/org-roam/pull/700), [#733](https://github.com/org-roam/org-roam/pull/733) Allow symlinks within the `org-roam` directory

README.md

@@ -4,6 +4,11 @@
 
 ## Synopsis
 
+> **NOTE:** Org-roam builds upon Emacs and Org-mode, both of which are intricate
+> tools that require time investment for mastery. This makes Org-roam less
+> friendly for beginners, but extremely powerful for those familiar with the
+> ecosystem, or willing to invest effort in it.
+
 Org-roam is a [Roam][roamresearch] replica built on top of the
 all-powerful [Org-mode][org].
 
@@ -58,7 +63,7 @@ Here's a sample configuration with using `use-package`:
       :bind (:map org-roam-mode-map
               (("C-c n l" . org-roam)
                ("C-c n f" . org-roam-find-file)
-               ("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))
               (("C-c n I" . org-roam-insert-immediate))))
@@ -116,7 +121,7 @@ General Public License, Version 3
 [roamresearch]: https://www.roamresearch.com/
 [org]: https://orgmode.org/
 [badge-license]: https://img.shields.io/badge/license-GPL_3-green.svg
-[docs]: https://www.orgroam.com/manual/
+[docs]: https://www.orgroam.com/manual.html
 [discourse]: https://org-roam.discourse.group/
 [slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
 [issues]: https://github.com/org-roam/org-roam/issues

doc/AUTHORS.md

@@ -34,4 +34,4 @@ Contributors
 - Rafael Accácio Nogueira <raccacio@poli.ufrj.br>
 - Roland Coeurjoly <rolandcoeurjoly@gmail.com>
 - Sayan <dit7ya@users.noreply.github.com>
-- Tim Quelch <tim@quelch.name>
+- Tim Quelch <tim@tquelch.com>

doc/Makefile

@@ -28,11 +28,8 @@ dir: org-roam.info
 	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) $<
 
 html-dir:
-	@printf "Generating org-roam/*.html\n"
+	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) org-roam.texi
-	@$(MAKEINFO) --html $(MANUAL_HTML_ARGS) org-roam.texi
+	mv org-roam.html manual.html
-	mv org-roam manual
-	cp -r assets manual
-	cp -r images manual
 
 %.pdf: %.texi
 	@printf "Generating $@\n"

doc/assets/page.css

@@ -1,442 +1,59 @@
-/* Import Inter font */
-/* More info at https://github.com/xz/fonts */
-@import url("https://fonts.xz.style/serve/inter.css");
-
 :root {
-  --nc-font-sans: "Inter", -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto,
+  --border: #526980;
-    Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif,
+  --code: #007;
-    "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
-  --nc-font-mono: "Courier New", Courier, "Ubuntu Mono", "Liberation Mono",
-    monospace;
-  --nc-tx-1: #000000;
-  --nc-tx-2: #1a1a1a;
-  --nc-bg-1: #ffffff;
-  --nc-bg-2: #f6f8fa;
-  --nc-bg-3: #e5e7eb;
-  --nc-lk-1: #0070f3;
-  --nc-lk-2: #0366d6;
-  --nc-lk-tx: #ffffff;
-  --nc-ac-1: #79ffe1;
-  --nc-ac-tx: #0c4047;
-}
-
-@media (prefers-color-scheme: dark) {
-  :root {
-    --nc-tx-1: #ffffff;
-    --nc-tx-2: #eeeeee;
-    --nc-bg-1: #000000;
-    --nc-bg-2: #111111;
-    --nc-bg-3: #222222;
-    --nc-lk-1: #3291ff;
-    --nc-lk-2: #0070f3;
-    --nc-lk-tx: #ffffff;
-    --nc-ac-1: #7928ca;
-    --nc-ac-tx: #ffffff;
-  }
-}
-
-* {
-  /* Reset margins and padding */
-  margin: 0;
-  padding: 0;
-}
-
-address,
-area,
-article,
-aside,
-audio,
-blockquote,
-datalist,
-details,
-dl,
-fieldset,
-figure,
-form,
-input,
-iframe,
-img,
-meter,
-nav,
-ol,
-optgroup,
-option,
-output,
-p,
-pre,
-progress,
-ruby,
-section,
-table,
-textarea,
-ul,
-video {
-  /* Margins for most elements */
-  margin-bottom: 1rem;
-}
-
-html,
-input,
-select,
-button {
-  /* Set body font family and some finicky elements */
-  font-family: var(--nc-font-sans);
 }
 
 body {
-  /* Center body in page */
+    margin: 5ex 10ex;
-  margin: 0 auto;
+    max-width: 80ex;
-  max-width: 750px;
-  padding: 2rem;
-  border-radius: 6px;
-  overflow-x: hidden;
-  background: var(--nc-bg-1);
-
-  /* Main body text */
-  color: var(--nc-tx-2);
-  font-size: 1.03rem;
     line-height: 1.5;
+    font-family: sans-serif;
 }
 
-::selection {
+h1, h2, h3 {
-  /* Set background color for selected text */
+    font-weight: normal;
-  background: var(--nc-ac-1);
-  color: var(--nc-ac-tx);
 }
 
-p {
+pre, code {
-  margin-bottom: 1rem;
+    font-family: x, monospace;
-}
-
-h1,
-h2,
-h3,
-h4,
-h5,
-h6 {
-  line-height: 1;
-  color: var(--nc-tx-1);
-  padding-top: 0.875rem;
-}
-
-h1,
-h2,
-h3 {
-  color: var(--nc-tx-1);
-  padding-bottom: 2px;
-  margin-bottom: 8px;
-  border-bottom: 1px solid var(--nc-bg-2);
-}
-
-h4,
-h5,
-h6 {
-  margin-bottom: 0.3rem;
-}
-
-h1 {
-  font-size: 2.25rem;
-}
-
-h2 {
-  font-size: 1.85rem;
-}
-
-h3 {
-  font-size: 1.55rem;
-}
-
-h4 {
-  font-size: 1.25rem;
-}
-
-h5 {
-  font-size: 1rem;
-}
-
-h6 {
-  font-size: 0.875rem;
-}
-
-a {
-  color: var(--nc-lk-1);
-}
-
-a:hover {
-  color: var(--nc-lk-2);
-}
-
-abbr:hover {
-  /* Set the '?' cursor while hovering an abbreviation */
-  cursor: help;
-}
-
-blockquote {
-  padding: 1.5rem;
-  background: var(--nc-bg-2);
-  border-left: 5px solid var(--nc-bg-3);
-}
-
-abbr {
-  cursor: help;
-}
-
-blockquote *:last-child {
-  padding-bottom: 0;
-  margin-bottom: 0;
-}
-
-header {
-  background: var(--nc-bg-2);
-  border-bottom: 1px solid var(--nc-bg-3);
-  padding: 2rem 1.5rem;
-
-  /* This sets the right and left margins to cancel out the body's margins. It's width is still the same, but the background stretches across the page's width. */
-
-  margin: -2rem calc(0px - (50vw - 50%)) 2rem;
-
-  /* Shorthand for:
-
-	margin-top: -2rem;
-	margin-bottom: 2rem;
-
-	margin-left: calc(0px - (50vw - 50%));
-	margin-right: calc(0px - (50vw - 50%)); */
-
-  padding-left: calc(50vw - 50%);
-  padding-right: calc(50vw - 50%);
-}
-
-header h1,
-header h2,
-header h3 {
-  padding-bottom: 0;
-  border-bottom: 0;
-}
-
-header > *:first-child {
-  margin-top: 0;
-  padding-top: 0;
-}
-
-header > *:last-child {
-  margin-bottom: 0;
-}
-
-.button,
-button,
-input[type="submit"],
-input[type="reset"],
-input[type="button"] {
-  font-size: 1rem;
-  display: inline-block;
-  padding: 6px 12px;
-  text-align: center;
-  text-decoration: none;
-  white-space: nowrap;
-  background: var(--nc-lk-1);
-  color: var(--nc-lk-tx);
-  border: 0;
-  border-radius: 4px;
-  box-sizing: border-box;
-  cursor: pointer;
-  color: var(--nc-lk-tx);
-}
-
-.button[disabled],
-button[disabled],
-input[type="submit"][disabled],
-input[type="reset"][disabled],
-input[type="button"][disabled] {
-  cursor: default;
-  opacity: 0.5;
-
-  /* Set the [X] cursor while hovering a disabled link */
-  cursor: not-allowed;
-}
-
-.button:focus,
-.button:hover,
-button:focus,
-button:hover,
-input[type="submit"]:focus,
-input[type="submit"]:hover,
-input[type="reset"]:focus,
-input[type="reset"]:hover,
-input[type="button"]:focus,
-input[type="button"]:hover {
-  background: var(--nc-lk-2);
-}
-
-code,
-pre,
-kbd,
-samp {
-  /* Set the font family for monospaced elements */
-  font-family: var(--nc-font-mono);
-}
-
-code,
-samp,
-kbd,
-pre {
-  /* The main preformatted style. This is changed slightly across different cases. */
-  background: var(--nc-bg-2);
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-  padding: 3px 6px;
-  font-size: 0.9rem;
-}
-
-kbd {
-  /* Makes the kbd element look like a keyboard key */
-  border-bottom: 3px solid var(--nc-bg-3);
 }
 
 pre {
-  padding: 1rem 1.4rem;
+    padding: 1ex;
-  max-width: 100%;
+    background: #eee;
+    border: solid 1px #ddd;
+    min-width: 0;
+    font-size: 80%;
     overflow: auto;
 }
 
-pre code {
+code {
-  /* When <code> is in a <pre>, reset it's formatting to blend in */
+    color: var(--code);
-  background: inherit;
-  font-size: inherit;
-  color: inherit;
-  border: 0;
-  padding: 0;
-  margin: 0;
-}
-
-code pre {
-  /* When <pre> is in a <code>, reset it's formatting to blend in */
-  display: inline;
-  background: inherit;
-  font-size: inherit;
-  color: inherit;
-  border: 0;
-  padding: 0;
-  margin: 0;
-}
-
-details {
-  /* Make the <details> look more "clickable" */
-  padding: 0.6rem 1rem;
-  background: var(--nc-bg-2);
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-}
-
-summary {
-  /* Makes the <summary> look more like a "clickable" link with the pointer cursor */
-  cursor: pointer;
-  font-weight: bold;
-}
-
-details[open] {
-  /* Adjust the <details> padding while open */
-  padding-bottom: 0.75rem;
-}
-
-details[open] summary {
-  /* Adjust the <details> padding while open */
-  margin-bottom: 6px;
-}
-
-details[open] > *:last-child {
-  /* Resets the bottom margin of the last element in the <details> while <details> is opened. This prevents double margins/paddings. */
-  margin-bottom: 0;
-}
-
-dt {
-  font-weight: bold;
-}
-
-dd::before {
-  /* Add an arrow to data table definitions */
-  content: "→ ";
-}
-
-hr {
-  /* Reset the border of the <hr> separator, then set a better line */
-  border: 0;
-  border-bottom: 1px solid var(--nc-bg-3);
-  margin: 1rem auto;
-}
-
-fieldset {
-  margin-top: 1rem;
-  padding: 2rem;
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-}
-
-legend {
-  padding: auto 0.5rem;
-}
-
-textarea {
-  /* Don't let the <textarea> extend off the screen naturally or when dragged by the user */
-  max-width: 100%;
-}
-
-ol,
-ul {
-  /* Replace the browser default padding */
-  padding-left: 2rem;
-}
-
-li {
-  margin-top: 0.4rem;
-}
-
-ul ul,
-ol ul,
-ul ol,
-ol ol {
-  margin-bottom: 0;
-}
-
-mark {
-  padding: 3px 6px;
-  background: var(--nc-ac-1);
-  color: var(--nc-ac-tx);
-}
-
-textarea,
-select,
-input {
-  padding: 6px 12px;
-  margin-bottom: 0.5rem;
-  background: var(--nc-bg-2);
-  color: var(--nc-tx-2);
-
-  /* Set a border of the same color as the main background. It isn't visible on idle, but prevents the cell from growing in size when a darker border is set on focus. */
-  border: 1px solid var(--nc-bg-2);
-  border-radius: 4px;
-  box-shadow: none;
-  box-sizing: border-box;
-}
-
-textarea:focus,
-select:focus,
-input[type]:focus {
-  border: 1px solid var(--nc-bg-3);
-
-  /* Reset any browser default outlines */
-  outline: 0;
 }
 
 img {
     max-width: 100%;
 }
 
-/* Customizations */
+table {
-.menu-comment {
+  border-collapse: collapse;
-  font-weight: bold;
+  width: 100%;
-  border: 0;
+}
-  margin: 0;
+
-  padding: 0;
+thead {
-  font-size: 1.2rem;
+  border-bottom: 1px solid var(--border);
+}
+
+tfoot {
+  border-top: 1px solid var(--border);
+}
+
+blockquote {
+  margin-left: 1rem;
+  font-style: italic;
+  font-family: serif;
+  border-left: 3px solid;
+  border-left-color: currentcolor;
+  border-color: var(--text-color);
+  padding-left: 1em;
 }

doc/index.html

@@ -93,7 +93,7 @@
         You can find us on Discourse and Slack.
         
         <ul>
-            <li>Read our documentation within Emacs, or on the <a href="https://www.orgroam.com/manual/">Online Manual</a></li>
+            <li>Read our documentation within Emacs, or on the <a href="https://www.orgroam.com/manual.html">Online Manual</a></li>
             <li>Participate in our forum discussions on <a href="https://org-roam.discourse.group">Discourse</a></li>
             <li>Chat with us on <a href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg">Slack</a></li>
           </ul>
@@ -120,13 +120,6 @@
             >org-roam-server</a
           >
         </div>
-        <div class="row">
-          <a
-            class="content footer-links"
-            href="https://github.com/org-roam/company-org-roam"
-            >company-org-roam</a
-          >
-        </div>
       </div>
 
       <div class="col">

makem.sh

@@ -591,6 +591,12 @@ function debug {
         }
     fi
 }
+
+function error_nonblocking {
+    echo_color red "ERROR ($(ts)): $@" >&2
+    ((errors_nonblocking++))
+}
+
 function error {
     echo_color red "ERROR ($(ts)): $@" >&2
     ((errors++))
@@ -763,7 +769,7 @@ function lint-package {
         --funcall package-lint-batch-and-exit \
         "${files_project_feature[@]}" \
         && success "Linting package finished without errors." \
-            || error "Linting package failed."
+            || error_nonblocking "Linting package failed."
 }
 
 function lint-regexps {
@@ -832,6 +838,7 @@ test_files_regexp='^((tests?|t)/)|-test.el$|^test-'
 
 emacs_command=("emacs")
 errors=0
+errors_nonblocking=0
 verbose=0
 compile=true
 arg_batch="--batch"
@@ -1072,9 +1079,9 @@ done
 
 if [[ $errors -gt 0 ]]
 then
-    log_color red "Finished with $errors errors."
+    log_color red "Finished with $errors errors and $errors_nonblocking non-blocking errors."
 else
-    success "Finished without errors."
+    success "Finished with $errors errors and $errors_nonblocking non-blocking errors."
 fi
 
 exit $errors

org-roam-buffer.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,6 +34,8 @@
 (require 'cl-lib)
 (require 'dash)
 (require 's)
+(require 'f)
+(require 'ol)
 
 (defvar org-roam-directory)
 (defvar org-link-frame-setup)
@@ -42,14 +44,18 @@
 (defvar org-roam-last-window)
 (defvar org-ref-cite-types) ;; in org-ref-core.el
 (defvar org-roam-mode)
+(defvar org-roam--org-link-bracket-typed-re)
 
 (declare-function org-roam-db--ensure-built   "org-roam-db")
-(declare-function org-roam--extract-ref       "org-roam")
+(declare-function org-roam--extract-refs      "org-roam")
+(declare-function org-roam--extract-titles    "org-roam")
 (declare-function org-roam--get-title-or-slug "org-roam")
 (declare-function org-roam--get-backlinks     "org-roam")
 (declare-function org-roam-backlinks-mode     "org-roam")
 (declare-function org-roam-mode               "org-roam")
 (declare-function org-roam--find-file         "org-roam")
+(declare-function org-roam-format-link        "org-roam")
+(declare-function org-roam-link-get-path      "org-roam-link")
 
 (defcustom org-roam-buffer-position 'right
   "Position of `org-roam' buffer.
@@ -100,11 +106,13 @@ For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
 
 (defun org-roam-buffer--find-file (file)
   "Open FILE in the window `org-roam' was called from."
-  (if (and org-roam-last-window (window-valid-p org-roam-last-window))
+  (setq file (expand-file-name file))
-      (progn (with-selected-window org-roam-last-window
+  (let ((last-window org-roam-last-window))
+    (if (window-valid-p last-window)
+        (progn (with-selected-window last-window
                  (org-roam--find-file file))
-             (select-window org-roam-last-window))
+               (select-window last-window))
-    (org-roam--find-file file)))
+      (org-roam--find-file file))))
 
 (defun org-roam-buffer--insert-title ()
   "Insert the org-roam-buffer title."
@@ -123,12 +131,29 @@ For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
                                    ,wrong-type))))))
     (concat string (when (> l 1) "s"))))
 
+(defun org-roam-buffer-expand-links (content orig-path)
+  "Crawl CONTENT for relative links and corrects them to be correctly displayed.
+ORIG-PATH is the path where the CONTENT originated."
+  (with-temp-buffer
+    (insert content)
+    (goto-char (point-min))
+    (let (link link-type)
+      (while (re-search-forward org-roam--org-link-bracket-typed-re (point-max) t)
+        (setq link-type (match-string 1)
+              link (match-string 2))
+        (when (and (string-equal link-type "file")
+                   (f-relative-p link))
+          (replace-match (org-roam-link-get-path (expand-file-name link (file-name-directory orig-path)))
+                         nil t nil 2))))
+    (buffer-string)))
+
 (defun org-roam-buffer--insert-ref-links ()
   "Insert ref backlinks for the current buffer."
-  (when-let ((ref (cdr (with-temp-buffer
+  (when-let* ((refs (with-temp-buffer
                       (insert-buffer-substring org-roam-buffer--current)
-                        (org-roam--extract-ref)))))
+                      (org-roam--extract-refs)))
-    (if-let* ((key-backlinks (org-roam--get-backlinks ref))
+              (paths (mapcar #'cdr refs)))
+    (if-let* ((key-backlinks (mapcan #'org-roam--get-backlinks paths))
               (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
         (progn
           (insert (let ((l (length key-backlinks)))
@@ -137,48 +162,58 @@ For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
           (dolist (group grouped-backlinks)
             (let ((file-from (car group))
                   (bls (cdr group)))
-              (insert (format "** [[file:%s][%s]]\n"
+              (insert (format "** %s\n"
-                              file-from
+                              (org-roam-format-link file-from
-                              (org-roam--get-title-or-slug file-from)))
+                                                    (org-roam--get-title-or-slug file-from)
+                                                    "file")))
               (dolist (backlink bls)
                 (pcase-let ((`(,file-from _ ,props) backlink))
-                  (insert (propertize (plist-get props :content)
+                  (insert (if-let ((content (plist-get props :content)))
+                              (propertize (org-roam-buffer-expand-links content file-from)
                                           'help-echo "mouse-1: visit backlinked note"
                                           'file-from file-from
-                           'file-from-point (plist-get props :point)))
+                                          'file-from-point (plist-get props :point))
-                  (insert "\n\n"))))))
+                            "")
+                          "\n\n"))))))
       (insert "\n\n* No ref backlinks!"))))
 
 (defun org-roam-buffer--insert-backlinks ()
   "Insert the org-roam-buffer backlinks string for the current buffer."
+  (let (props file-from)
     (if-let* ((file-path (buffer-file-name org-roam-buffer--current))
-            (backlinks (org-roam--get-backlinks file-path))
+              (titles (with-current-buffer org-roam-buffer--current
+                        (org-roam--extract-titles)))
+              (backlinks (org-roam--get-backlinks (push file-path titles)))
               (grouped-backlinks (--group-by (nth 0 it) backlinks)))
         (progn
           (insert (let ((l (length backlinks)))
                     (format "\n\n* %d %s\n"
                             l (org-roam-buffer--pluralize "Backlink" l))))
           (dolist (group grouped-backlinks)
-          (let ((file-from (car group))
+            (setq file-from (car group))
-                (bls (cdr group)))
+            (setq props (mapcar (lambda (row) (nth 2 row)) (cdr group)))
-            (insert (format "** [[file:%s][%s]]\n"
+            (setq props (seq-sort-by (lambda (p) (plist-get p :point)) #'< props))
-                            file-from
+            (insert (format "** %s\n"
-                            (org-roam--get-title-or-slug file-from)))
+                            (org-roam-format-link file-from
-            (dolist (backlink bls)
+                                                  (org-roam--get-title-or-slug file-from)
-              (pcase-let ((`(,file-from _ ,props) backlink))
+                                                  "file")))
+            (dolist (prop props)
               (insert "*** "
-                        (if-let ((outline (plist-get props :outline)))
+                      (if-let ((outline (plist-get prop :outline)))
-                            (string-join outline " > ")
+                          (-> outline
+                              (string-join " > ")
+                              (org-roam-buffer-expand-links file-from))
                         "Top")
                       "\n"
+                      (if-let ((content (plist-get prop :content)))
                           (propertize
-                         (s-trim (s-replace "\n" " "
+                           (s-trim (s-replace "\n" " " (org-roam-buffer-expand-links content file-from)))
-                                            (plist-get props :content)))
                            'help-echo "mouse-1: visit backlinked note"
                            'file-from file-from
-                         'file-from-point (plist-get props :point))
+                           'file-from-point (plist-get prop :point))
-                        "\n\n"))))))
+                        "")
-    (insert "\n\n* No backlinks!")))
+                      "\n\n"))))
+      (insert "\n\n* No backlinks!"))))
 
 (defun org-roam-buffer-update ()
   "Update the `org-roam-buffer'."
@@ -216,7 +251,7 @@ This needs to be quick or infrequent, because this is run at
     (when (and (or redisplay
                    (not (eq org-roam-buffer--current buffer)))
                (eq 'visible (org-roam-buffer--visibility))
-               (buffer-local-value 'buffer-file-truename buffer))
+               (buffer-file-name buffer))
       (setq org-roam-buffer--current buffer)
       (org-roam-buffer-update))))
 

org-roam-capture.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -31,6 +31,7 @@
 ;;; Code:
 ;;;; Library Requires
 (require 'org-capture)
+(require 'org-roam-macs)
 (require 'dash)
 (require 's)
 (require 'cl-lib)
@@ -40,20 +41,15 @@
 (defvar org-roam-directory)
 (defvar org-roam-mode)
 (defvar org-roam-title-to-slug-function)
+
 (declare-function  org-roam--get-title-path-completions "org-roam")
 (declare-function  org-roam--get-ref-path-completions   "org-roam")
 (declare-function  org-roam--file-path-from-id          "org-roam")
 (declare-function  org-roam--find-file                  "org-roam")
-(declare-function  org-roam--format-link                "org-roam")
+(declare-function  org-roam-format-link                "org-roam")
 (declare-function  org-roam-mode                        "org-roam")
 (declare-function  org-roam-completion--completing-read "org-roam-completion")
 
-(defvar org-roam-capture--file-name-default "%<%Y%m%d%H%M%S>"
-  "The default file name format for Org-roam templates.")
-
-(defvar org-roam-capture--header-default "#+title: ${title}\n"
-  "The default capture header for Org-roam templates.")
-
 (defvar org-roam-capture--file-path nil
   "The file path for the Org-roam capture.
 This variable is set during the Org-roam capture process.")
@@ -79,11 +75,11 @@ note with the given `ref'.")
 (defvar org-roam-capture-additional-template-props nil
   "Additional props to be added to the Org-roam template.")
 
-(defconst org-roam-capture--template-keywords '(:file-name :head)
+(defconst org-roam-capture--template-keywords '(:file-name :head :olp)
   "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
 
 (defcustom org-roam-capture-templates
-  '(("d" "default" plain (function org-roam-capture--get-point)
+  `(("d" "default" plain (function org-roam-capture--get-point)
      "%?"
      :file-name "%<%Y%m%d%H%M%S>-${slug}"
      :head "#+title: ${title}\n"
@@ -102,7 +98,7 @@ The Org-roam capture-templates  builds on the default behaviours of
 
 3. The `:head' key is added, which contains the template that is
    inserted upon the creation of a new file. This is where you
-   should add your note metadata should go.
+   your note metadata should go.
 
 Each template should have the following structure:
 
@@ -223,10 +219,10 @@ Template string   :\n%v")
                  ((const :format "%v " :kill-buffer) (const t))))))
 
 (defcustom org-roam-capture-ref-templates
-  '(("r" "ref" plain (function org-roam-capture--get-point)
+  '(("r" "ref" plain #'org-roam-capture--get-point
      "%?"
      :file-name "${slug}"
-     :head "#+title: ${title}\n#+roam_key: ${ref}\n"
+     :head "#+title: ${title}\n#+roam_key: ${ref}"
      :unnarrowed t))
   "The Org-roam templates used during a capture from the roam-ref protocol.
 Details on how to specify for the template is given in `org-roam-capture-templates'."
@@ -320,8 +316,14 @@ the capture)."
 
 (defun org-roam-capture--finalize ()
   "Finalize the `org-roam-capture' process."
+  (let* ((finalize (org-roam-capture--get :finalize))
+         ;; In case any regions were shielded before, unshield them
+         (region (when-let ((region (org-roam-capture--get :region)))
+                   (org-roam-unshield-region (car region) (cdr region))))
+         (beg (car region))
+         (end (cdr region)))
     (unless org-note-abort
-    (pcase (org-roam-capture--get :finalize)
+      (pcase finalize
         ('find-file
          (when-let ((file-path (org-roam-capture--get :file-path)))
            (org-roam--find-file file-path)
@@ -330,16 +332,20 @@ the capture)."
          (when-let* ((mkr (org-roam-capture--get :insert-at))
                      (buf (marker-buffer mkr)))
            (with-current-buffer buf
-           (when-let ((region (org-roam-capture--get :region))) ;; Remove previously selected text.
+             (when region
                (delete-region (car region) (cdr region)))
              (let ((path (org-roam-capture--get :file-path))
+                   (type (org-roam-capture--get :link-type))
                    (desc (org-roam-capture--get :link-description)))
                (if (eq (point) (marker-position mkr))
-                 (insert (org-roam--format-link path desc))
+                   (insert (org-roam-format-link path desc type))
                  (org-with-point-at mkr
-                 (insert (org-roam--format-link path desc))))))))))
+                   (insert (org-roam-format-link path desc type))))))))))
+    (when region
+      (set-marker beg nil)
+      (set-marker end nil))
     (org-roam-capture--save-file-maybe)
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize))
+    (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
 
 (defun org-roam-capture--install-finalize ()
   "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
@@ -404,27 +410,36 @@ aborted, we do the following:
 the file if the original value of :no-save is not t and
 `org-note-abort' is not t."
   (let* ((name-templ (or (org-roam-capture--get :file-name)
-                         org-roam-capture--file-name-default))
+                         (user-error "Template needs to specify `:file-name'")))
          (new-id (s-trim (org-roam-capture--fill-template
                           name-templ)))
          (file-path (org-roam--file-path-from-id new-id))
          (roam-head (or (org-roam-capture--get :head)
-                        org-roam-capture--header-default))
+                        ""))
          (org-template (org-capture-get :template))
          (roam-template (concat roam-head org-template)))
-    (unless (file-exists-p file-path)
+    (unless (or (file-exists-p file-path)
+                (cl-some (lambda (buffer)
+                           (string= (buffer-file-name buffer)
+                                    file-path))
+                         (buffer-list)))
       (make-directory (file-name-directory file-path) t)
       (org-roam-capture--put :orig-no-save (org-capture-get :no-save)
                              :new-file t)
-      (org-capture-put :template
+      (pcase org-roam-capture--context
-                       ;; Fixes org-capture-place-plain-text throwing 'invalid search bound'
+        ('dailies
-                       ;; when both :unnarowed t and "%?" is missing from the template string;
+         ;; Populate the header of the daily file before capture to prevent it
-                       ;; may become unnecessary when the upstream bug is fixed
+         ;; from appearing in the buffer-restriction
-                       (if (s-contains-p "%?" roam-template)
+         (save-window-excursion
-                           roam-template
+           (find-file file-path)
-                         (concat roam-template "%?"))
+           (insert (substring (org-capture-fill-template (concat roam-head "*"))
-                       :type 'plain
+                              0 -2))
-                       :no-save t))
+           (set-buffer-modified-p nil))
+         (org-capture-put :template org-template))
+        (_
+         (org-capture-put :template roam-template
+           :type 'plain)))
+      (org-capture-put :no-save t))
     file-path))
 
 (defun org-roam-capture--get-point ()
@@ -443,7 +458,7 @@ If there is no file with that ref, a file with that ref is created.
 
 This function is used solely in Org-roam's capture templates: see
 `org-roam-capture-templates'."
-  (let ((file-path (pcase org-roam-capture--context
+  (let* ((file-path (pcase org-roam-capture--context
                       ('capture
                        (or (cdr (assoc 'file org-roam-capture--info))
                            (org-roam-capture--new-file)))
@@ -461,14 +476,35 @@ This function is used solely in Org-roam's capture templates: see
                       (_ (error "Invalid org-roam-capture-context")))))
     (org-capture-put :template
       (org-roam-capture--fill-template (org-capture-get :template)))
-    (org-roam-capture--put :file-path file-path)
+    (org-roam-capture--put :file-path file-path
+                           :finalize (or (org-capture-get :finalize)
+                                         (org-roam-capture--get :finalize)))
     (while org-roam-capture-additional-template-props
       (let ((prop (pop org-roam-capture-additional-template-props))
             (val (pop org-roam-capture-additional-template-props)))
         (org-roam-capture--put prop val)))
     (set-buffer (org-capture-target-buffer file-path))
     (widen)
-    (goto-char (point-max))))
+    (if-let* ((olp (when (eq org-roam-capture--context 'dailies)
+                     (--> (org-roam-capture--get :olp)
+                          (pcase it
+                            ((pred stringp)
+                             (list it))
+                            ((pred listp)
+                             it)
+                            (wrong-type
+                             (signal 'wrong-type-argument
+                                     `((stringp listp)
+                                       ,wrong-type))))))))
+        (condition-case err
+            (when-let ((marker (org-find-olp `(,file-path ,@olp))))
+              (goto-char marker)
+              (set-marker marker nil))
+          (error
+           (when (org-roam-capture--get :new-file)
+             (kill-buffer))
+           (signal (car err) (cdr err))))
+      (goto-char (point-min)))))
 
 (defun org-roam-capture--convert-template (template)
   "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax."
@@ -483,6 +519,9 @@ This function is used solely in Org-roam's capture templates: see
          (let* ((key (pop rest))
                 (val (pop rest))
                 (custom (member key org-roam-capture--template-keywords)))
+           (when (and custom
+                      (not val))
+             (user-error "Invalid capture template format: %s\nkey %s cannot be nil" template key))
            (push val (if custom org-roam-plist options))
            (push key (if custom org-roam-plist options))))
        (append converted options `(:org-roam ,org-roam-plist))))
@@ -506,7 +545,8 @@ GOTO and KEYS argument have the same functionality as
 `org-capture'."
   (let* ((org-capture-templates (mapcar #'org-roam-capture--convert-template org-roam-capture-templates))
          (one-template-p (= (length org-capture-templates) 1))
-         org-capture-templates-contexts)
+         org-capture-templates-contexts
+         (org-capture-link-is-already-stored t))
     (when one-template-p
       (setq keys (caar org-capture-templates)))
     (if (or one-template-p
@@ -515,10 +555,11 @@ GOTO and KEYS argument have the same functionality as
       (funcall-interactively org-roam-capture-function))))
 
 ;;;###autoload
-(defun org-roam-capture ()
+(defun org-roam-capture (&optional goto keys)
   "Launches an `org-capture' process for a new or existing note.
-This uses the templates defined at `org-roam-capture-templates'."
+This uses the templates defined at `org-roam-capture-templates'.
-  (interactive)
+Arguments GOTO and KEYS see `org-capture'."
+  (interactive "P")
   (unless org-roam-mode (org-roam-mode))
   (let* ((completions (org-roam--get-title-path-completions))
          (title-with-keys (org-roam-completion--completing-read "File: "
@@ -531,7 +572,7 @@ This uses the templates defined at `org-roam-capture-templates'."
                                         (cons 'file file-path)))
           (org-roam-capture--context 'capture))
       (condition-case err
-          (org-roam-capture--capture)
+          (org-roam-capture--capture goto keys)
         (error (user-error "%s.  Please adjust `org-roam-capture-templates'"
                            (error-message-string err)))))))
 

org-roam-compat.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -41,8 +41,6 @@
   "org-roam 1.0.0")
 (define-obsolete-function-alias 'org-roam-sql         'org-roam-db-query
   "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--get-db     'org-roam-db--get
-  "org-roam 1.0.0")
 (define-obsolete-function-alias 'org-roam--db-clear   'org-roam-db--clear
   "org-roam 1.0.0")
 (define-obsolete-function-alias 'org-roam-show-graph  'org-roam-graph-show
@@ -81,9 +79,14 @@
   "org-roam 1.1.0")
 (define-obsolete-function-alias 'org-roam-db--clear 'org-roam-db-clear
   "org-roam 1.2.0")
-
+(define-obsolete-function-alias 'org-roam-dailies-today 'org-roam-dailies-find-today
-(when (version< (org-version) "9.3")
+  "org-roam 1.2.2")
-  (defalias 'org-link-make-string 'org-make-link-string))
+(define-obsolete-function-alias 'org-roam-dailies-yesterday 'org-roam-dailies-find-yesterday
+  "org-roam 1.2.2")
+(define-obsolete-function-alias 'org-roam-dailies-tomorrow 'org-roam-dailies-find-tomorrow
+  "org-roam 1.2.2")
+(define-obsolete-function-alias 'org-roam-dailies-date 'org-roam-dailies-find-date
+  "org-roam 1.2.2")
 
 ;;;; Variables
 (define-obsolete-variable-alias 'org-roam-graphviz-extra-options
@@ -100,6 +103,9 @@
   'org-roam-dailies-capture-templates "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam-date-filename-format
   'org-roam-dailies-capture-templates "org-roam 1.0.0")
+(define-obsolete-variable-alias 'org-roam-update-db-idle-seconds
+  'org-roam-db-update-idle-seconds "org-roam 1.2.2")
+
 (make-obsolete-variable 'org-roam-buffer-no-delete-other-windows
   'org-roam-buffer-window-parameters "org-roam 1.1.1")
 

org-roam-completion.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -47,6 +47,11 @@
           (function :tag "Custom function"))
   :group 'org-roam)
 
+(defcustom org-roam-completion-ignore-case t
+  "Whether to ignore case in Org-roam `completion-at-point' completions."
+  :group 'org-roam
+  :type 'boolean)
+
 (defun org-roam-completion--helm-candidate-transformer (candidates _source)
   "Transforms CANDIDATES for Helm-based completing read.
 SOURCE is not used."
@@ -74,6 +79,7 @@ Return user choice."
             (if (fboundp 'ivy-read)
                 (ivy-read prompt choices
                           :initial-input initial-input
+                          :preselect initial-input
                           :require-match require-match
                           :action (prog1 action
                                     (setq action nil))

org-roam-dailies.el

@@ -1,12 +1,14 @@
-;;; org-roam-dailies.el --- Daily notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 Leo Vivier <leo.vivier+dev@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; 	Leo Vivier <leo.vivier+dev@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,7 +29,7 @@
 
 ;;; Commentary:
 ;;
-;; This library provides functionality for creating daily notes. This is a
+;; This library provides functionality for creating daily-notes. This is a
 ;; concept borrowed from Roam Research.
 ;;
 ;;; Code:
@@ -35,31 +37,52 @@
 (require 'org-capture)
 (require 'org-roam-capture)
 (require 'org-roam-macs)
+(require 'f)
+
+;;;; Declarations
+(defvar org-roam-mode)
+(defvar org-roam-directory)
+(declare-function org-roam--org-file-p        "org-roam")
+(declare-function org-roam--file-path-from-id "org-roam")
+(declare-function org-roam--find-file         "org-roam")
+(declare-function org-roam-mode               "org-roam")
+
+;;;; Customizable variables
+(defcustom org-roam-dailies-directory "daily/"
+  "Path to daily-notes."
+  :group 'org-roam
+  :type 'string)
+
+(defcustom org-roam-dailies-find-file-hook nil
+  "Hook that is run right after navigating to a daily-note."
+  :group 'org-roam
+  :type 'hook)
 
 (defcustom org-roam-dailies-capture-templates
-  '(("d" "daily" plain (function org-roam-capture--get-point)
+  '(("d" "default" entry (function org-roam-capture--get-point)
-     ""
+     "* %?"
-     :immediate-finish t
+     :file-name "daily/%<%Y-%m-%d>"
-     :file-name "%<%Y-%m-%d>"
+     :head "#+title: %<%Y-%m-%d>\n"))
-     :head "#+title: %<%Y-%m-%d>"))
+  "Capture templates for daily-notes in Org-roam."
-  "Capture templates for daily notes in Org-roam."
   :group 'org-roam
   ;; Adapted from `org-capture-templates'
   :type
   '(repeat
-    (choice :value ("d" "daily" plain (function org-roam-capture--get-point)
+    (choice :value ("d" "default" plain (function org-roam-capture--get-point)
-                    ""
+                    "%?"
-                    :immediate-finish t
+                    :file-name "daily/%<%Y-%m-%d>"
-                    :file-name "%<%Y-%m-%d>"
+                    :head "#+title: %<%Y-%m-%d>\n"
-                    :head "#+title: %<%Y-%m-%d>")
+                    :unnarrowed t)
       (list :tag "Multikey description"
         (string :tag "Keys       ")
         (string :tag "Description"))
       (list :tag "Template entry"
         (string :tag "Keys              ")
         (string :tag "Description       ")
-                  (const :format "" plain)
+        (choice :tag "Type              "
-                  (const :format "" (function org-roam-capture--get-point))
+         (const :tag "Plain" plain)
+         (const :tag "Entry (for creating headlines)" entry))
+        (const :format "" #'org-roam-capture--get-point)
         (choice :tag "Template          "
           (string :tag "String"
                   :format "String:\n            \
@@ -70,16 +93,20 @@ Template string   :\n%v")
           (list :tag "Function"
             (const :format "" function)
             (function :tag "Template function ")))
-                  (const :format "" :immediate-finish) (const :format "" t)
         (const :format "File name format  :" :file-name)
-                  (string :format " %v" :value "#+title: ${title}\n")
+        (string :format " %v" :value "daily/%<%Y-%m-%d>")
         (const :format "Header format     :" :head)
-                  (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
+        (string :format " %v" :value "#+title: ${title}\n")
         (plist :inline t
                :tag "Options"
           ;; Give the most common options as checkboxes
                :options
-                         (((const :format "%v " :prepend) (const t))
+               (((const :tag "Outline path" :olp)
+                 (repeat :tag "Headings"
+                   (string :tag "Heading")))
+                ((const :format "%v " :unnarrowed) (const t))
+                ((const :format "%v " :prepend) (const t))
+                ((const :format "%v " :immediate-finish) (const t))
                 ((const :format "%v " :jump-to-captured) (const t))
                 ((const :format "%v " :empty-lines) (const 1))
                 ((const :format "%v " :empty-lines-before) (const 1))
@@ -90,48 +117,250 @@ Template string   :\n%v")
                 ((const :format "%v " :time-prompt) (const t))
                 ((const :format "%v " :tree-type) (const week))
                 ((const :format "%v " :table-line-pos) (string))
-                          ((const :format "%v " :kill-buffer) (const t))
+                ((const :format "%v " :kill-buffer) (const t))))))))
-                          ((const :format "%v " :unnarrowed) (const t))))))))
 
-;; Declarations
+;;;; Utilities
-(defvar org-roam-mode)
+(defun org-roam-dailies-directory--get-absolute-path ()
-(declare-function org-roam--file-path-from-id "org-roam")
+  "Get absolute path to `org-roam-dailies-directory'."
-(declare-function org-roam-mode               "org-roam")
+  (-> (concat
+       (file-name-as-directory org-roam-directory)
+       org-roam-dailies-directory)
+      (file-truename)))
 
-(defun org-roam-dailies--file-for-time (time)
+(defun org-roam-dailies-find-directory ()
-  "Create and find file for TIME."
+  "Find and open `org-roam-dailies-directory'."
-  (let ((org-roam-capture-templates org-roam-dailies-capture-templates)
+  (interactive)
+  (org-roam--find-file (org-roam-dailies-directory--get-absolute-path)))
+
+(defun org-roam-dailies--daily-note-p (&optional file)
+  "Return t if FILE is an Org-roam daily-note, nil otherwise.
+
+If FILE is not specified, use the current buffer's file-path."
+  (when-let ((path (or file
+                       (-> (buffer-base-buffer)
+                           (buffer-file-name))))
+             (directory (org-roam-dailies-directory--get-absolute-path)))
+    (setq path (file-truename path))
+    (save-match-data
+      (and
+       (org-roam--org-file-p path)
+       (f-descendant-of-p path directory)))))
+
+(defun org-roam-dailies--capture (time &optional goto)
+  "Capture an entry in a daily-note for TIME, creating it if necessary.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (unless org-roam-mode (org-roam-mode))
+  (let ((org-roam-capture-templates (--> org-roam-dailies-capture-templates
+                                         (if goto (list (car it)) it)))
         (org-roam-capture--info (list (cons 'time time)))
         (org-roam-capture--context 'dailies))
     (setq org-roam-capture-additional-template-props (list :finalize 'find-file))
-    (org-roam--with-template-error 'org-roam-dailies-capture-templates
+    (org-roam-capture--capture (when goto '(4)))))
-      (org-roam-capture--capture))))
 
-(defun org-roam-dailies-today ()
+;;;; Commands
-  "Create and find the daily note for today."
+;;; Today
+(defun org-roam-dailies-capture-today (&optional goto)
+  "Create an entry in the daily-note for today.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "P")
+  (org-roam-dailies--capture (current-time) goto)
+  (when goto
+    (run-hooks 'org-roam-dailies-find-file-hook)
+    (message "Showing daily-note for today")))
+
+(defun org-roam-dailies-find-today ()
+  "Find the daily-note for today, creating it if necessary."
   (interactive)
-  (unless org-roam-mode (org-roam-mode))
+  (org-roam-dailies-capture-today t))
-  (org-roam-dailies--file-for-time (current-time)))
 
-(defun org-roam-dailies-tomorrow (n)
+;;; Tomorrow
-  "Create and find the daily note for tomorrow.
+(defun org-roam-dailies-capture-tomorrow (n &optional goto)
-With numeric argument N, use N days in the future."
+  "Create an entry in the daily-note for tomorrow.
+
+With numeric argument N, use the daily-note N days in the future.
+
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry."
   (interactive "p")
-  (unless org-roam-mode (org-roam-mode))
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
-  (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
 
-(defun org-roam-dailies-yesterday (n)
+(defun org-roam-dailies-find-tomorrow (n)
-  "Create and find the file for yesterday.
+  "Find the daily-note for tomorrow, creating it if necessary.
-With numeric argument N, use N days in the past."
+
+With numeric argument N, use the daily-note N days in the
+future."
   (interactive "p")
-  (unless org-roam-mode (org-roam-mode))
+  (org-roam-dailies-capture-tomorrow n t))
-  (org-roam-dailies-tomorrow (- n)))
 
-(defun org-roam-dailies-date ()
+;;; Yesterday
-  "Create the file for any date using the calendar interface."
+(defun org-roam-dailies-capture-yesterday (n &optional goto)
+  "Create an entry in the daily-note for yesteday.
+
+With numeric argument N, use the daily-note N days in the past.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow (- n) goto))
+
+(defun org-roam-dailies-find-yesterday (n)
+  "Find the daily-note for yesterday, creating it if necessary.
+
+With numeric argument N, use the daily-note N days in the
+future."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow (- n) t))
+
+;;; Calendar
+(defvar org-roam-dailies-calendar-hook (list 'org-roam-dailies-calendar-mark-entries)
+  "Hooks to run when showing the `org-roam-dailies-calendar'.")
+
+(defun org-roam-dailies-calendar--install-hook ()
+  "Install Org-roam-dailies hooks to calendar."
+  (add-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar--run-hook)
+  (add-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar--run-hook))
+
+(defun org-roam-dailies-calendar--run-hook ()
+  "Run Org-roam-dailies hooks to calendar."
+  (run-hooks 'org-roam-dailies-calendar-hook)
+  (remove-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar--run-hook)
+  (remove-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar--run-hook))
+
+(defun org-roam-dailies-calendar--file-to-date (&optional file)
+  "Convert FILE to date.
+
+Return (MONTH DAY YEAR)."
+  (let ((file (or file
+                  (-> (buffer-base-buffer)
+                      (buffer-file-name)))))
+    (cl-destructuring-bind (_ _ _ d m y _ _ _)
+        (-> file
+            (file-name-nondirectory)
+            (file-name-sans-extension)
+            (org-parse-time-string))
+      (list m d y))))
+
+(defun org-roam-dailies-calendar--date-to-time (date)
+  "Convert DATE as returned from the calendar (MONTH DAY YEAR) to a time."
+  (encode-time 0 0 0 (nth 1 date) (nth 0 date) (nth 2 date)))
+
+(defun org-roam-dailies-calendar-mark-entries ()
+  "Mark days in the calendar for which a daily-note is present."
+  (when (file-exists-p (org-roam-dailies-directory--get-absolute-path))
+    (dolist (date (mapcar #'org-roam-dailies-calendar--file-to-date
+                          (org-roam-dailies--list-files)))
+      (when (calendar-date-is-visible-p date)
+        (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
+
+;;; Date
+(defun org-roam-dailies-capture-date (&optional goto prefer-future)
+  "Create an entry in the daily-note for a date using the calendar.
+
+Prefer past dates, unless PREFER-FUTURE is non-nil.
+
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry."
+  (interactive "P")
+  (org-roam-dailies-calendar--install-hook)
+  (let* ((time-str (let ((org-read-date-prefer-future prefer-future))
+                     (org-read-date nil nil nil (if goto
+                                                    "Find daily-note: "
+                                                  "Capture to daily-note: "))))
+         (time (org-read-date nil t time-str)))
+    (org-roam-dailies--capture time goto)
+    (when goto
+      (run-hooks 'org-roam-dailies-find-file-hook)
+      (message "Showing note for %s" time-str))))
+
+(defun org-roam-dailies-find-date (&optional prefer-future)
+  "Find the daily-note for a date using the calendar, creating it if necessary.
+
+Prefer past dates, unless PREFER-FUTURE is non-nil."
   (interactive)
-  (let ((time (org-read-date nil 'to-time nil "Date:  ")))
+  (org-roam-dailies-capture-date t prefer-future))
-    (org-roam-dailies--file-for-time time)))
+
+;;; Navigation
+(defun org-roam-dailies--list-files (&rest extra-files)
+  "List all files in `org-roam-dailies-directory'.
+
+EXTRA-FILES can be used to append extra files to the list."
+  (let ((dir (org-roam-dailies-directory--get-absolute-path)))
+    (append (--remove (let ((file (file-name-nondirectory it)))
+                        (when (or (auto-save-file-name-p file)
+                                  (backup-file-name-p file)
+                                  (string-match "^\\." file))
+                          it))
+                      (directory-files-recursively dir ""))
+            extra-files)))
+
+(defun org-roam-dailies--find-next-note-path (&optional n file)
+  "Find next daily-note from FILE.
+
+With numeric argument N, find note N days in the future. If N is
+negative, find note N days in the past.
+
+If FILE is not provided, use the file visited by the current
+buffer."
+  (unless (org-roam-dailies--daily-note-p file)
+    (user-error "Not in a daily-note"))
+  (let ((n (or n 1))
+        (file (or file
+                  (-> (buffer-base-buffer)
+                      (buffer-file-name)))))
+    ;; Ensure that the buffer is saved before moving
+    (save-buffer file)
+    (let* ((list (org-roam-dailies--list-files))
+           (position
+            (cl-position-if (lambda (candidate)
+                              (string= file candidate))
+                            list)))
+      (pcase n
+        ((pred (natnump))
+         (if (eq position (- (length list) 1))
+             (user-error "Already at newest note")
+           (message "Showing next daily-note")))
+        ((pred (integerp))
+         (if (eq position 0)
+             (user-error "Already at oldest note")
+           (message "Showing previous daily-note"))))
+      (nth (+ position n) list))))
+
+(defun org-roam-dailies-find-next-note (&optional n)
+  "Find next daily-note.
+
+With numeric argument N, find note N days in the future. If N is
+negative, find note N days in the past."
+  (interactive "p")
+  (let* ((n (or n 1))
+         (next (org-roam-dailies--find-next-note-path n)))
+    (find-file next)
+    (run-hooks 'org-roam-dailies-find-file-hook)))
+
+(defun org-roam-dailies-find-previous-note (&optional n)
+  "Find previous daily-note.
+
+With numeric argument N, find note N days in the past. If N is
+negative, find note N days in the future."
+  (interactive "p")
+  (let ((n (if n (- n) -1)))
+    (org-roam-dailies-find-next-note n)))
+
+;;;; Bindings
+(defvar org-roam-dailies-map (make-sparse-keymap)
+  "Keymap for `org-roam-dailies'.")
+
+(define-prefix-command 'org-roam-dailies-map)
+
+(define-key org-roam-dailies-map (kbd "d") #'org-roam-dailies-find-today)
+(define-key org-roam-dailies-map (kbd "y") #'org-roam-dailies-find-yesterday)
+(define-key org-roam-dailies-map (kbd "t") #'org-roam-dailies-find-tomorrow)
+(define-key org-roam-dailies-map (kbd "n") #'org-roam-dailies-capture-today)
+(define-key org-roam-dailies-map (kbd "f") #'org-roam-dailies-find-next-note)
+(define-key org-roam-dailies-map (kbd "b") #'org-roam-dailies-find-previous-note)
+(define-key org-roam-dailies-map (kbd "c") #'org-roam-dailies-find-date)
+(define-key org-roam-dailies-map (kbd "v") #'org-roam-dailies-capture-date)
+(define-key org-roam-dailies-map (kbd ".") #'org-roam-dailies-find-directory)
 
 (provide 'org-roam-dailies)
 

org-roam-db.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -35,17 +35,24 @@
 (require 'emacsql)
 (require 'emacsql-sqlite3)
 (require 'seq)
-(require 'org-roam-macs)
+
+(eval-and-compile
+  (require 'org-roam-macs)
+  ;; For `org-with-wide-buffer'
+  (require 'org-macs))
 
 (defvar org-roam-directory)
+(defvar org-roam-enable-headline-linking)
 (defvar org-roam-verbose)
 (defvar org-roam-file-name)
 
+(defvar org-agenda-files)
+
 (declare-function org-roam--org-roam-file-p                "org-roam")
 (declare-function org-roam--extract-titles                 "org-roam")
-(declare-function org-roam--extract-ref                    "org-roam")
+(declare-function org-roam--extract-refs                   "org-roam")
 (declare-function org-roam--extract-tags                   "org-roam")
-(declare-function org-roam--extract-headlines              "org-roam")
+(declare-function org-roam--extract-ids                    "org-roam")
 (declare-function org-roam--extract-links                  "org-roam")
 (declare-function org-roam--list-all-files                 "org-roam")
 (declare-function org-roam--path-to-slug                   "org-roam")
@@ -53,7 +60,7 @@
 (declare-function org-roam-buffer--update-maybe            "org-roam-buffer")
 
 ;;;; Options
-(defcustom org-roam-db-location nil
+(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
   "The full path to file where the Org-roam database is stored.
 If this is non-nil, the Org-roam sqlite database is saved here.
 
@@ -77,20 +84,38 @@ value like `most-positive-fixnum'."
   :type 'int
   :group 'org-roam)
 
-(defconst org-roam-db--version 7)
+(defconst org-roam-db--version 10)
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
 
+(defvar org-roam-db-dirty nil
+  "Whether the org-roam database is dirty and requires an update.
+Contains pairs of `org-roam-directory' and `org-roam-db-location'
+so that multi-directories are updated.")
+
+(defcustom org-roam-db-update-method 'idle-timer
+  "Method to update the Org-roam database.
+
+`immediate'
+  Update the database immediately upon file changes.
+
+`idle-timer'
+  Updates the database if dirty, if Emacs idles for `org-roam-db-update-idle-seconds'."
+  :type '(set (const :tag "idle-timer" idle-timer)
+              (const :tag "immediate" immediate))
+  :group 'org-roam)
+
+(defcustom org-roam-db-update-idle-seconds 2
+  "Number of idle seconds before triggering an Org-roam database update."
+  :type 'integer
+  :group 'org-roam)
+
 ;;;; Core Functions
-(defun org-roam-db--get ()
-  "Return the sqlite db file."
-  (or org-roam-db-location
-      (expand-file-name "org-roam.db" org-roam-directory)))
 
 (defun org-roam-db--get-connection ()
   "Return the database connection, if any."
-  (gethash (file-truename org-roam-directory)
+  (gethash (expand-file-name org-roam-directory)
            org-roam-db--connection))
 
 (defun org-roam-db ()
@@ -99,12 +124,11 @@ Initializes and stores the database, and the database connection.
 Performs a database upgrade when required."
   (unless (and (org-roam-db--get-connection)
                (emacsql-live-p (org-roam-db--get-connection)))
-    (let* ((db-file (org-roam-db--get))
+    (let ((init-db (not (file-exists-p org-roam-db-location))))
-           (init-db (not (file-exists-p db-file))))
+      (make-directory (file-name-directory org-roam-db-location) t)
-      (make-directory (file-name-directory db-file) t)
+      (let ((conn (emacsql-sqlite3 org-roam-db-location)))
-      (let ((conn (emacsql-sqlite3 db-file)))
         (set-process-query-on-exit-flag (emacsql-process conn) nil)
-        (puthash (file-truename org-roam-directory)
+        (puthash (expand-file-name org-roam-directory)
                  conn
                  org-roam-db--connection)
         (when init-db
@@ -138,13 +162,14 @@ SQL can be either the emacsql vector representation, or a string."
       (hash :not-null)
       (meta :not-null)])
 
-    (headlines
+    (ids
      [(id :unique :primary-key)
-      (file :not-null)])
+      (file :not-null)
+      (level :not-null)])
 
     (links
-     [(from :not-null)
+     [(source :not-null)
-      (to :not-null)
+      (dest :not-null)
       (type :not-null)
       (properties :not-null)])
 
@@ -193,11 +218,27 @@ the current `org-roam-directory'."
   (dolist (conn (hash-table-values org-roam-db--connection))
     (org-roam-db--close conn)))
 
+;;;; Timer-based updating
+(defvar org-roam-db-file-update-timer nil
+  "Timer for updating the database when dirty.")
+
+(defun org-roam-db-mark-dirty ()
+  "Mark the Org-roam database as dirty."
+  (add-to-list 'org-roam-db-dirty (list org-roam-directory org-roam-db-location)
+               nil #'equal))
+
+(defun org-roam-db-update-cache-on-timer ()
+  "Update the cache if the database is dirty.
+This function is called on `org-roam-db-file-update-timer'."
+  (pcase-dolist (`(,org-roam-directory ,org-roam-db-location) org-roam-db-dirty)
+    (org-roam-db-build-cache))
+  (setq org-roam-db-dirty nil))
+
 ;;;; Database API
 ;;;;; Initialization
 (defun org-roam-db--initialized-p ()
   "Whether the Org-roam cache has been initialized."
-  (and (file-exists-p (org-roam-db--get))
+  (and (file-exists-p org-roam-db-location)
        (> (caar (org-roam-db-query [:select (funcall count) :from titles]))
           0)))
 
@@ -210,75 +251,68 @@ the current `org-roam-directory'."
 (defun org-roam-db-clear ()
   "Clears all entries in the Org-roam cache."
   (interactive)
-  (when (file-exists-p (org-roam-db--get))
+  (when (file-exists-p org-roam-db-location)
     (dolist (table (mapcar #'car org-roam-db--table-schemata))
       (org-roam-db-query `[:delete :from ,table]))))
 
 (defun org-roam-db--clear-file (&optional filepath)
   "Remove any related links to the file at FILEPATH.
 This is equivalent to removing the node from the graph."
-  (let ((file (file-truename (or filepath
+  (let ((file (expand-file-name (or filepath
                                     (buffer-file-name (buffer-base-buffer))))))
     (dolist (table (mapcar #'car org-roam-db--table-schemata))
       (org-roam-db-query `[:delete :from ,table
-                           :where (= ,(if (eq table 'links) 'from 'file) $s1)]
+                           :where (= ,(if (eq table 'links) 'source 'file) $s1)]
                          file))))
 
-;;;;; Insertion
+;;;;; Inserting
-(defun org-roam-db--insert-meta (file hash meta)
+(defun org-roam-db--insert-meta (&optional update-p)
-  "Insert HASH and META for a FILE into the Org-roam cache."
+  "Update the metadata of the current buffer into the cache.
+If UPDATE-P is non-nil, first remove the meta for the file in the database."
+  (let* ((file (or org-roam-file-name (buffer-file-name)))
+         (attr (file-attributes file))
+         (atime (file-attribute-access-time attr))
+         (mtime (file-attribute-modification-time attr))
+         (hash (org-roam-db--file-hash)))
+    (when update-p
+      (org-roam-db-query [:delete :from files
+                          :where (= file $s1)]
+                         file))
     (org-roam-db-query
      [:insert :into files
       :values $v1]
-   (list (vector file hash meta))))
+     (list (vector file hash (list :atime atime :mtime mtime))))))
 
-(defun org-roam-db--insert-links (links)
+(defun org-roam-db--insert-titles (&optional update-p)
-  "Insert LINKS into the Org-roam cache."
+  "Update the titles of the current buffer into the cache.
-  (org-roam-db-query
+If UPDATE-P is non-nil, first remove titles for the file in the database.
-   [:insert :into links
+Returns the number of rows inserted."
-    :values $v1]
+  (let* ((file (or org-roam-file-name (buffer-file-name)))
-   links))
+         (titles (or (org-roam--extract-titles)
-
+                     (list (org-roam--path-to-slug file))))
-(defun org-roam-db--insert-titles (file titles)
+         (rows (mapcar (lambda (title)
-  "Insert TITLES for a FILE into the Org-roam cache."
+                         (vector file title)) titles)))
+    (when update-p
+      (org-roam-db-query [:delete :from titles
+                          :where (= file $s1)]
+                         file))
     (org-roam-db-query
         [:insert :into titles
          :values $v1]
-   (mapcar (lambda (title)
+        rows)
-             (vector file title)) titles)))
+    (length rows)))
 
-(defun org-roam-db--insert-headlines (headlines)
+(defun org-roam-db--insert-refs (&optional update-p)
-  "Insert HEADLINES into the Org-roam cache.
+  "Update the refs of the current buffer into the cache.
-Returns t if the insertion was successful, nil otherwise.
+If UPDATE-P is non-nil, first remove the ref for the file in the database."
-Insertions can fail when there is an ID conflict."
+  (let ((file (or org-roam-file-name (buffer-file-name)))
-  (condition-case nil
+        (count 0))
-      (progn
+    (when update-p
-        (org-roam-db-query
+      (org-roam-db-query [:delete :from refs
-           [:insert :into headlines
+                          :where (= file $s1)]
-            :values $v1]
+                         file))
-           headlines)
+    (when-let ((refs (org-roam--extract-refs)))
-        t)
+      (dolist (ref refs)
-    (error
-     (unless (listp headlines)
-       (setq headlines (list headlines)))
-     (lwarn '(org-roam) :error
-            (format "Duplicate IDs in %s, one of:\n\n%s\n\nskipping..."
-                    (aref (car headlines) 1)
-                    (string-join (mapcar (lambda (hl)
-                                           (aref hl 0)) headlines) "\n")))
-     nil)))
-
-(defun org-roam-db--insert-tags (file tags)
-  "Insert TAGS for a FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into tags
-    :values $v1]
-   (list (vector file tags))))
-
-(defun org-roam-db--insert-ref (file ref)
-  "Insert REF for FILE into the Org-roam cache.
-Returns t if successful, and nil otherwise.
-Insertions can fail if the key is already in the database."
         (let ((key (cdr ref))
               (type (car ref)))
           (condition-case nil
@@ -286,7 +320,7 @@ Insertions can fail if the key is already in the database."
                 (org-roam-db-query
                  [:insert :into refs :values $v1]
                  (list (vector key file type)))
-         t)
+                (cl-incf count))
             (error
              (lwarn '(org-roam) :error
                     (format "Duplicate ref %s in:\n\nA: %s\nB: %s\n\nskipping..."
@@ -295,8 +329,70 @@ Insertions can fail if the key is already in the database."
                             (caar (org-roam-db-query
                                    [:select file :from refs
                                     :where (= ref $v1)]
-                             (vector key)))))
+                                   (vector key))))))))))
-       nil))))
+    count))
+
+(defun org-roam-db--insert-links (&optional update-p)
+  "Update the file links of the current buffer in the cache.
+If UPDATE-P is non-nil, first remove the links for the file in the database.
+Return the number of rows inserted."
+  (let ((file (or org-roam-file-name (buffer-file-name))))
+    (when update-p
+      (org-roam-db-query [:delete :from links
+                          :where (= source $s1)]
+                         file))
+    (if-let ((links (org-roam--extract-links)))
+        (progn
+          (org-roam-db-query
+           [:insert :into links
+            :values $v1]
+           links)
+          (length links))
+      0)))
+
+(defun org-roam-db--insert-ids (&optional update-p)
+  "Update the ids of the current buffer into the cache.
+If UPDATE-P is non-nil, first remove ids for the file in the database.
+Returns the number of rows inserted."
+  (let ((file (or org-roam-file-name (buffer-file-name))))
+    (when update-p
+      (org-roam-db-query [:delete :from ids
+                          :where (= file $s1)]
+                         file))
+    (if-let ((ids (org-roam--extract-ids file)))
+      (condition-case nil
+          (progn
+            (org-roam-db-query
+             [:insert :into ids
+              :values $v1]
+             ids)
+            (length ids))
+        (error
+         (lwarn '(org-roam) :error
+                (format "Duplicate IDs in %s, one of:\n\n%s\n\nskipping..."
+                        (aref (car ids) 1)
+                        (string-join (mapcar (lambda (hl)
+                                               (aref hl 0)) ids) "\n")))
+         0))
+      0)))
+
+(defun org-roam-db--insert-tags (&optional update-p)
+  "Insert tags for the current buffer into the Org-roam cache.
+If UPDATE-P is non-nil, first remove tags for the file in the database.
+Return the number of rows inserted."
+  (let* ((file (or org-roam-file-name (buffer-file-name)))
+         (tags (org-roam--extract-tags file)))
+    (when update-p
+      (org-roam-db-query [:delete :from tags
+                          :where (= file $s1)]
+                         file))
+    (if tags
+        (progn (org-roam-db-query
+                [:insert :into tags
+                 :values $v1]
+                (list (vector file tags)))
+               1)
+      0)))
 
 ;;;;; Fetching
 (defun org-roam-db--get-current-files ()
@@ -314,19 +410,29 @@ Insertions can fail if the key is already in the database."
                             :limit 1]
                            file)))
 
+(defun org-roam-db--get-tags ()
+  "Return all distinct tags from the cache."
+  (let ((rows (org-roam-db-query [:select :distinct [tags] :from tags]))
+        acc)
+    (dolist (row rows)
+      (dolist (tag (car row))
+        (unless (member tag acc)
+          (push tag acc))))
+    acc))
+
 (defun org-roam-db--connected-component (file)
   "Return all files reachable from/connected to FILE, including the file itself.
 If the file does not have any connections, nil is returned."
   (let* ((query "WITH RECURSIVE
                    links_of(file, link) AS
-                     (WITH filelinks AS (SELECT * FROM links WHERE \"type\" = '\"file\"'),
+                     (WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
                            citelinks AS (SELECT * FROM links
-                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
+                                                  JOIN refs ON links.\"dest\" = refs.\"ref\"
                                                             AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM filelinks UNION
+                      SELECT \"source\", \"dest\" FROM filelinks UNION
-                      SELECT \"to\", \"from\" FROM filelinks UNION
+                      SELECT \"dest\", \"source\" FROM filelinks UNION
-                      SELECT \"file\", \"from\" FROM citelinks UNION
+                      SELECT \"file\", \"source\" FROM citelinks UNION
-                      SELECT \"from\", \"file\" FROM citelinks),
+                      SELECT \"dest\", \"file\" FROM citelinks),
                    connected_component(file) AS
                      (SELECT link FROM links_of WHERE file = $s1
                       UNION
@@ -341,14 +447,14 @@ This includes the file itself. If the file does not have any
 connections, nil is returned."
   (let* ((query "WITH RECURSIVE
                    links_of(file, link) AS
-                     (WITH filelinks AS (SELECT * FROM links WHERE \"type\" = '\"file\"'),
+                     (WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
                            citelinks AS (SELECT * FROM links
-                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
+                                                  JOIN refs ON links.\"dest\" = refs.\"ref\"
                                                             AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM filelinks UNION
+                      SELECT \"source\", \"dest\" FROM filelinks UNION
-                      SELECT \"to\", \"from\" FROM filelinks UNION
+                      SELECT \"dest\", \"source\" FROM filelinks UNION
-                      SELECT \"file\", \"from\" FROM citelinks UNION
+                      SELECT \"file\", \"source\" FROM citelinks UNION
-                      SELECT \"from\", \"file\" FROM citelinks),
+                      SELECT \"source\", \"file\" FROM citelinks),
                    -- Links are traversed in a breadth-first search.  In order to calculate the
                    -- distance of nodes and to avoid following cyclic links, the visited nodes
                    -- are tracked in 'trace'.
@@ -370,177 +476,123 @@ connections, nil is returned."
 
 (defun org-roam-db--file-hash (&optional file-path)
   "Compute the hash of FILE-PATH, a file or current buffer."
-  (let* ((file-p (and file-path))
+  (if file-path
-         (file-path (or file-path
-                        (buffer-file-name (current-buffer))))
-         (encrypted-p (and file-path
-                           (string= (org-roam--file-name-extension file-path)
-                                    "gpg"))))
-    (cond ((and encrypted-p file-p)
       (with-temp-buffer
         (set-buffer-multibyte nil)
         (insert-file-contents-literally file-path)
-             (secure-hash 'sha1 (current-buffer))))
+        (secure-hash 'sha1 (current-buffer)))
-          (file-p
+    (org-with-wide-buffer
-           (with-temp-buffer
+     (secure-hash 'sha1 (current-buffer)))))
-             (insert-file-contents file-path)
-             (secure-hash 'sha1 (current-buffer))))
-          (t
-           (secure-hash 'sha1 (current-buffer))))))
 
 ;;;;; Updating
-(defun org-roam-db--update-meta ()
-  "Update the metadata of the current buffer into the cache."
-  (let* ((file (file-truename (buffer-file-name)))
-         (attr (file-attributes file))
-         (atime (file-attribute-access-time attr))
-         (mtime (file-attribute-modification-time attr))
-         (hash (org-roam-db--file-hash)))
-    (org-roam-db-query [:delete :from files
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db--insert-meta file hash (list :atime atime :mtime mtime))))
-
-(defun org-roam-db--update-titles ()
-  "Update the title of the current buffer into the cache."
-  (let* ((file (file-truename (buffer-file-name)))
-         (titles (or (org-roam--extract-titles)
-                     (list (org-roam--path-to-slug file)))))
-    (org-roam-db-query [:delete :from titles
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db--insert-titles file titles)))
-
-(defun org-roam-db--update-tags ()
-  "Update the tags of the current buffer into the cache."
-  (let ((file (file-truename (buffer-file-name)))
-        (tags (org-roam--extract-tags)))
-    (org-roam-db-query [:delete :from tags
-                        :where (= file $s1)]
-                       file)
-    (when tags
-      (org-roam-db--insert-tags file tags))))
-
-(defun org-roam-db--update-refs ()
-  "Update the ref of the current buffer into the cache."
-  (let ((file (file-truename (buffer-file-name))))
-    (org-roam-db-query [:delete :from refs
-                        :where (= file $s1)]
-                       file)
-    (when-let ((ref (org-roam--extract-ref)))
-      (org-roam-db--insert-ref file ref))))
-
-(defun org-roam-db--update-links ()
-  "Update the file links of the current buffer in the cache."
-  (let ((file (file-truename (buffer-file-name))))
-    (org-roam-db-query [:delete :from links
-                        :where (= from $s1)]
-                       file)
-    (when-let ((links (org-roam--extract-links)))
-      (org-roam-db--insert-links links))))
-
-(defun org-roam-db--update-headlines ()
-  "Update the file headlines of the current buffer into the cache."
-  (let* ((file (file-truename (buffer-file-name))))
-    (org-roam-db-query [:delete :from headlines
-                        :where (= file $s1)]
-                       file)
-    (when-let ((headlines (org-roam--extract-headlines)))
-      (org-roam-db--insert-headlines headlines))))
-
 (defun org-roam-db--update-file (&optional file-path)
-  "Update Org-roam cache for FILE-PATH."
+  "Update Org-roam cache for FILE-PATH.
-  (when (org-roam--org-roam-file-p file-path)
+If the file does not exist anymore, remove it from the cache.
-    (let ((buf (or (and file-path
+If the file exists, update the cache with information."
-                        (find-file-noselect file-path t))
+  (setq file-path (or file-path
-                   (current-buffer))))
+                      (buffer-file-name (buffer-base-buffer))))
+  (if (not (file-exists-p file-path))
+      (org-roam-db--clear-file file-path)
+    ;; save the file before performing a database update
+    (when-let ((buf (find-buffer-visiting file-path)))
       (with-current-buffer buf
-        (save-excursion
+        (save-buffer)))
+    (org-roam--with-temp-buffer file-path
       (emacsql-with-transaction (org-roam-db)
-            (org-roam-db--update-meta)
+        (org-roam-db--insert-meta 'update)
-            (org-roam-db--update-tags)
+        (org-roam-db--insert-tags 'update)
-            (org-roam-db--update-titles)
+        (org-roam-db--insert-titles 'update)
-            (org-roam-db--update-refs)
+        (org-roam-db--insert-refs 'update)
-            (org-roam-db--update-headlines)
+        (when org-roam-enable-headline-linking
-            (org-roam-db--update-links))
+          (org-roam-db--insert-ids 'update))
-          (org-roam-buffer--update-maybe :redisplay t))))))
+        (org-roam-db--insert-links 'update)))))
 
 (defun org-roam-db-build-cache (&optional force)
   "Build the cache for `org-roam-directory'.
 If FORCE, force a rebuild of the cache from scratch."
   (interactive "P")
-  (when force (delete-file (org-roam-db--get)))
+  (when force (delete-file org-roam-db-location))
   (org-roam-db--close) ;; Force a reconnect
   (org-roam-db) ;; To initialize the database, no-op if already initialized
   (let* ((gc-cons-threshold org-roam-db-gc-threshold)
+         (org-agenda-files nil)
          (org-roam-files (org-roam--list-all-files))
          (current-files (org-roam-db--get-current-files))
-         (file-count 0)
+         (id-count 0)
-         (headline-count 0)
          (link-count 0)
          (tag-count 0)
          (title-count 0)
          (ref-count 0)
-         (deleted-count 0))
+         (deleted-count 0)
-    (emacsql-with-transaction (org-roam-db)
+         (modified-count 0)
-      ;; Two-step building
+         (modified-files nil))
-      ;; First step: Rebuild files and headlines
     (dolist (file org-roam-files)
-        (let* ((attr (file-attributes file))
-               (atime (file-attribute-access-time attr))
-               (mtime (file-attribute-modification-time attr)))
       (let ((contents-hash (org-roam-db--file-hash file)))
         (unless (string= (gethash file current-files)
                        contents-hash)
-              (org-roam--with-temp-buffer file
+          (push (cons file contents-hash) modified-files)))
+      (remhash file current-files))
+    (dolist (file (hash-table-keys current-files))
+        ;; These files are no longer around, remove from cache...
         (org-roam-db--clear-file file)
+        (setq deleted-count (1+ deleted-count)))
+    (pcase-dolist (`(,file . _) modified-files)
+      (org-roam-db--clear-file file))
+    ;; Process all the files for IDs first
+    ;;
+    ;; We do this so that link extraction is cheaper: this eliminates the need
+    ;; to read the file to check if the ID really exists
+    (pcase-dolist (`(,file . ,contents-hash) modified-files)
+      (let* ((attr (file-attributes file))
+             (atime (file-attribute-access-time attr))
+             (mtime (file-attribute-modification-time attr)))
+        (condition-case nil
+            (org-roam--with-temp-buffer file
               (org-roam-db-query
                [:insert :into files
                 :values $v1]
                (vector file contents-hash (list :atime atime :mtime mtime)))
-               (setq file-count (1+ file-count))
+              (when org-roam-enable-headline-linking
-               (when-let ((headlines (org-roam--extract-headlines file)))
+                (setq id-count (+ id-count (org-roam-db--insert-ids)))))
-                 (when (org-roam-db--insert-headlines headlines)
+          (file-error
-                   (setq headline-count (1+ headline-count)))))))))
+           (setq org-roam-files (remove file org-roam-files))
-      ;; Second step: Rebuild the rest
-      (dolist (file org-roam-files)
-        (let ((contents-hash (org-roam-db--file-hash file)))
-          (unless (string= (gethash file current-files)
-                           contents-hash)
-            (org-roam--with-temp-buffer file
-             (when-let (links (org-roam--extract-links file))
-               (org-roam-db-query
-                [:insert :into links
-                 :values $v1]
-                links)
-               (setq link-count (1+ link-count)))
-             (when-let (tags (org-roam--extract-tags file))
-               (org-roam-db-query
-                [:insert :into tags
-                 :values $v1]
-                (vector file tags))
-               (setq tag-count (1+ tag-count)))
-             (let ((titles (or (org-roam--extract-titles)
-                               (list (org-roam--path-to-slug file)))))
-               (org-roam-db--insert-titles file titles)
-               (setq title-count (+ title-count (length titles))))
-             (when-let* ((ref (org-roam--extract-ref)))
-               (when (org-roam-db--insert-ref file ref)
-                 (setq ref-count (1+ ref-count))))))
-          (remhash file current-files)))
-      (dolist (file (hash-table-keys current-files))
-        ;; These files are no longer around, remove from cache...
            (org-roam-db--clear-file file)
-        (setq deleted-count (1+ deleted-count))))
+           (lwarn '(org-roam) :warning
-    (org-roam-message "files: Δ%s, headlines: Δ%s, links: Δ%s, tags: Δ%s, titles: Δ%s, refs: Δ%s, deleted: Δ%s"
+                  "Skipping unreadable file while building cache: %s" file)))))
-                      file-count
+    (pcase-dolist (`(,file . _) modified-files)
-                      headline-count
+      (org-roam-message "Processed %s/%s modified files..." modified-count (length modified-files))
+      (condition-case nil
+            (org-roam--with-temp-buffer file
+              (setq modified-count (1+ modified-count))
+              (setq link-count (+ link-count (org-roam-db--insert-links)))
+              (setq tag-count (+ tag-count (org-roam-db--insert-tags)))
+              (setq title-count (+ title-count (org-roam-db--insert-titles)))
+              (setq ref-count (+ ref-count (org-roam-db--insert-refs))))
+          (file-error
+           (setq org-roam-files (remove file org-roam-files))
+           (org-roam-db--clear-file file)
+           (lwarn '(org-roam) :warning
+                  "Skipping unreadable file while building cache: %s" file))))
+    (org-roam-message "total: Δ%s, files-modified: Δ%s, ids: Δ%s, links: Δ%s, tags: Δ%s, titles: Δ%s, refs: Δ%s, deleted: Δ%s"
+                      (length org-roam-files)
+                      modified-count
+                      id-count
                       link-count
                       tag-count
                       title-count
                       ref-count
                       deleted-count)))
 
+(defun org-roam-db-update ()
+  "Update the database."
+  (pcase org-roam-db-update-method
+    ('immediate
+     (org-roam-db-build-cache))
+    ('idle-timer
+     (org-roam-db-mark-dirty))
+    (_
+     (user-error "Invalid `org-roam-db-update-method'"))))
+
 (provide 'org-roam-db)
 
 ;;; org-roam-db.el ends here

org-roam-dev.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-doctor.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/jethrokuan/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -59,6 +59,15 @@
 (defvar org-roam-verbose)
 (defvar org-roam-mode)
 
+(defcustom org-roam-doctor-inhibit-startup t
+  "Inhibit `org-mode' startup when processing files with `org-doctor'.
+When non-nil, images and LaTeX preview will not be generated,
+tables will not be aligned, and headlines will not respect
+startup visability. This significantly improves performance when
+processing multiple files"
+  :type 'boolean
+  :group 'org-roam)
+
 (cl-defstruct (org-roam-doctor-checker (:copier nil))
   (name 'missing-checker-name)
   (description "")
@@ -294,7 +303,8 @@ If CHECKALL, run the check for all Org-roam files."
 (defun org-roam-doctor-start (files checkers)
   "Lint FILES using CHECKERS."
   (save-window-excursion
-    (let ((existing-buffers (org-roam--get-roam-buffers)))
+    (let ((existing-buffers (org-roam--get-roam-buffers))
+          (org-inhibit-startup org-roam-doctor-inhibit-startup))
       (dolist (f files)
         (let ((buf (find-file-noselect f)))
           (org-roam-doctor--check buf checkers)

org-roam-faces.el

@@ -0,0 +1,77 @@
+;;; org-roam-faces.el --- Face definitions -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.2.3
+;; Package-Requires: ((emacs "26.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+
+;; This file contains the face definitions for Org-roam.
+
+;;; Code:
+
+(defgroup org-roam-faces nil
+  "Faces used by Org-roam."
+  :group 'org-roam
+  :group 'faces)
+
+;;; Definitions
+(defface org-roam-link
+  '((t :inherit org-link))
+  "Face for Org-roam links."
+  :group 'org-roam-faces)
+
+(defface org-roam-tag
+  '((t :weight bold))
+  "Face for Org-roam tags in minibuffer commands."
+  :group 'org-roam-faces)
+
+(defface org-roam-link-current
+  '((t :inherit org-link))
+  "Face for Org-roam links pointing to the current buffer."
+  :group 'org-roam-faces)
+
+(defface org-roam-link-invalid
+  '((t :inherit (error org-link)))
+  "Face for Org-roam links that are not valid.
+This face is used for links without a destination."
+  :group 'org-roam-faces)
+
+(defface org-roam-link-shielded
+  '((t :inherit (warning org-link)))
+  "Face for Org-roam links that are shielded.
+This face is used on the region target by `org-roam-insertion'
+during an `org-roam-capture'."
+  :group 'org-roam-faces)
+
+(defface org-roam-dailies-calendar-note
+  '((t :inherit (org-roam-link) :underline nil))
+  "Face for dates with a daily-note in the calendar"
+  :group 'org-roam-faces)
+
+;;; _
+
+(provide 'org-roam-faces)
+
+;;; org-roam-faces.el ends here

org-roam-graph.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -32,7 +32,8 @@
 ;;; Code:
 (require 'xml) ;xml-escape-string
 (require 's)   ;s-truncate, s-replace
-(require 'org-roam-macs)
+(eval-and-compile
+  (require 'org-roam-macs))
 (require 'org-roam-db)
 
 ;;;; Declarations
@@ -169,15 +170,15 @@ into a digraph."
     (let* ((nodes (org-roam-db-query node-query))
            (edges-query
             `[:with selected :as [:select [file] :from ,node-query]
-              :select :distinct [to from] :from links
+              :select :distinct [dest source] :from links
-              :where (and (in to selected) (in from selected))])
+              :where (and (in dest selected) (in source selected))])
            (edges-cites-query
             `[:with selected :as [:select [file] :from ,node-query]
-              :select :distinct [file from]
+              :select :distinct [file source]
-              :from links :inner :join refs :on (and (= links:to refs:ref)
+              :from links :inner :join refs :on (and (= links:dest refs:ref)
                                                      (= links:type "cite")
                                                      (= refs:type "cite"))
-              :where (and (in file selected) (in from selected))])
+              :where (and (in file selected) (in source selected))])
            (edges       (org-roam-db-query edges-query))
            (edges-cites (org-roam-db-query edges-cites-query)))
       (insert "digraph \"org-roam\" {\n")
@@ -265,7 +266,7 @@ CALLBACK is passed the graph file as its sole argument."
   "Build a graph of nodes connected to FILE.
 If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps.
 CALLBACK is passed to `org-roam-graph--build'."
-  (let* ((file (file-truename file))
+  (let* ((file (expand-file-name 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))

org-roam-link.el

@@ -0,0 +1,314 @@
+;;; org-roam-link.el --- Custom links for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;;                  Alan Carroll
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.2.3
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This adds the custom `roam:' link to Org-roam. `roam:' links allow linking to
+;; Org-roam files via their titles and headlines.
+;;
+;;; Code:
+;;;; Dependencies
+
+(require 'ol)
+(require 'org-roam-compat)
+(require 'org-roam-macs)
+(require 'org-roam-db)
+
+(require 'org-element)
+
+(defvar org-roam-completion-ignore-case)
+(defvar org-roam-directory)
+(declare-function  org-roam--find-file                  "org-roam")
+(declare-function  org-roam-find-file                   "org-roam")
+(declare-function org-roam-format-link                  "org-roam")
+
+(defcustom org-roam-link-auto-replace t
+  "When non-nil, replace Org-roam's roam links with file or id links whenever possible."
+  :group 'org-roam
+  :type 'boolean)
+
+(defcustom org-roam-link-file-path-type 'relative
+  "How the path name in file links should be stored.
+Valid values are:
+
+relative  Relative to the current directory, i.e. the directory of the file
+          into which the link is being inserted.
+absolute  Absolute path, if possible with ~ for home directory.
+noabbrev  Absolute path, no abbreviation of home directory."
+  :group 'org-roam
+  :type '(choice
+          (const relative)
+          (const absolute)
+          (const noabbrev))
+  :safe #'symbolp)
+
+;;; the roam: link
+(org-link-set-parameters "roam"
+                         :follow #'org-roam-link-follow-link)
+
+(defun org-roam-link-follow-link (path)
+  "Navigates to location specified by PATH."
+  (pcase-let ((`(,link-type ,loc ,desc ,mkr) (org-roam-link--get-location path)))
+    (when (and org-roam-link-auto-replace loc desc)
+      (org-roam-link--replace-link link-type loc desc))
+    (pcase link-type
+          ("file"
+           (if loc
+               (org-roam--find-file loc)
+             (org-roam-find-file desc nil nil t)))
+          ("id"
+           (org-goto-marker-or-bmk mkr)))))
+
+;;; Retrieval Functions
+(defun org-roam-link--get-titles ()
+  "Return all titles within Org-roam."
+  (mapcar #'car (org-roam-db-query [:select [titles:title] :from titles])))
+
+(defun org-roam-link--get-headlines (&optional file with-marker use-stack)
+  "Return all outline headings for the current buffer.
+If FILE, return outline headings for passed FILE instead.
+If WITH-MARKER, return a cons cell of (headline . marker).
+If USE-STACK, include the parent paths as well."
+  (let* ((buf (or (and file
+                       (or (find-buffer-visiting file)
+                           (find-file-noselect file)))
+                  (current-buffer)))
+         (outline-level-fn outline-level)
+         (path-separator "/")
+         (stack-level 0)
+         stack cands name level marker)
+    (with-current-buffer buf
+      (save-excursion
+        (goto-char (point-min))
+        (while (re-search-forward org-complex-heading-regexp nil t)
+          (save-excursion
+            (setq name (substring-no-properties (or (match-string 4) "")))
+            (setq marker (point-marker))
+            (when use-stack
+              (goto-char (match-beginning 0))
+              (setq level (funcall outline-level-fn))
+              ;; Update stack.  The empty entry guards against incorrect
+              ;; headline hierarchies, e.g. a level 3 headline
+              ;; immediately following a level 1 entry.
+              (while (<= level stack-level)
+                (pop stack)
+                (cl-decf stack-level))
+              (while (> level stack-level)
+                (push name stack)
+                (cl-incf stack-level))
+              (setq name (mapconcat #'identity
+                                    (reverse stack)
+                                    path-separator)))
+            (push (if with-marker
+                      (cons name marker)
+                    name) cands)))))
+    (nreverse cands)))
+
+(defun org-roam-link--get-file-from-title (title &optional no-interactive)
+  "Return the file path corresponding to TITLE.
+When NO-INTERACTIVE, return nil if there are multiple options."
+  (let ((files (mapcar #'car (org-roam-db-query [:select [titles:file] :from titles
+                                                 :where (= titles:title $v1)]
+                                                (vector title)))))
+    (pcase files
+      ('nil nil)
+      (`(,file) file)
+      (_
+       (unless no-interactive
+         (completing-read "Select file: " files))))))
+
+(defun org-roam-link--get-id-from-headline (headline &optional file)
+  "Return (marker . id) correspondng to HEADLINE.
+If FILE, get headline from FILE instead.
+If there is no corresponding headline, return nil."
+  (save-excursion
+    (with-current-buffer (or (and file
+                                  (or (find-buffer-visiting file)
+                                      (find-file-noselect file)))
+                             (current-buffer))
+      (let ((headlines (org-roam-link--get-headlines file 'with-markers)))
+        (when-let ((marker (cdr (assoc-string headline headlines))))
+          (goto-char marker)
+          (cons marker
+                (when org-roam-link-auto-replace
+                  (org-id-get-create))))))))
+
+;;; Path-related functions
+(defun org-roam-link-get-path (path &optional type)
+  "Return the PATH of the link to use.
+If TYPE is non-nil, create a link of TYPE. Otherwise, respect
+`org-link-file-path-type'."
+  (pcase (or type org-roam-link-file-path-type)
+      ('absolute
+       (abbreviate-file-name (expand-file-name path)))
+      ('noabbrev
+       (expand-file-name path))
+      ('relative
+       (file-relative-name path))))
+
+(defun org-roam-link--split-path (path)
+  "Splits PATH into title and headline.
+Return a list of the form (type title has-headline-p headline star-idx).
+type is one of `title', `headline', `title+headline'.
+title is the title component of the path.
+headline is the headline component of the path.
+star-idx is the index of the asterisk, if any."
+  (save-match-data
+    (let* ((star-index (string-match-p "\\*" path))
+           (title (substring-no-properties path 0 star-index))
+           (headline (if star-index
+                         (substring-no-properties path (+ 1 star-index))
+                       ""))
+           (type (cond ((not star-index)
+                        'title)
+                       ((= 0 star-index)
+                        'headline)
+                       (t 'title+headline))))
+      (list type title headline star-index))))
+
+(defun org-roam-link--get-location (link)
+  "Return the location of Org-roam fuzzy LINK.
+The location is returned as a list containing (link-type loc desc marker).
+nil is returned if there is no matching location.
+
+link-type is either \"file\" or \"id\".
+loc is the target location: e.g. a file path, or an id.
+marker is a marker to the headline, if applicable."
+  (let (mkr link-type desc loc)
+    (pcase-let ((`(,type ,title ,headline _) (org-roam-link--split-path link)))
+      (pcase type
+        ('title+headline
+         (let ((file (org-roam-link--get-file-from-title title)))
+           (if (not file)
+               (org-roam-message "Cannot find matching file")
+             (setq mkr (org-roam-link--get-id-from-headline headline file))
+             (pcase mkr
+               (`(,marker . ,target-id)
+                (setq mkr marker
+                      loc target-id
+                      link-type "id"
+                      desc headline))
+               (_ (org-roam-message "cannot find matching id"))))))
+        ('title
+         (setq loc (org-roam-link--get-file-from-title title)
+               desc title
+               link-type "file"))
+        ('headline
+         (setq mkr (org-roam-link--get-id-from-headline headline))
+         (pcase mkr
+           (`(,marker . ,target-id)
+            (setq mkr marker
+                  loc target-id
+                  desc headline
+                  link-type "id"))
+           (_ (org-roam-message "Cannot find matching headline")))))
+      (list link-type loc desc mkr))))
+
+;;; Conversion Functions
+(defun org-roam-link--replace-link (link-type loc &optional desc)
+  "Replace link at point with a vanilla Org link.
+LINK-TYPE is the Org link type, typically \"file\" or \"id\".
+LOC is path for the Org link.
+DESC is the link description."
+  (save-excursion
+    (save-match-data
+      (unless (org-in-regexp org-link-bracket-re 1)
+        (user-error "No link at point"))
+      (replace-match "")
+      (insert (org-roam-format-link loc desc link-type)))))
+
+(defun org-roam-link-replace-all ()
+  "Replace all roam links in the current buffer."
+  (interactive)
+  (save-excursion
+    (goto-char (point-min))
+    (while (re-search-forward org-link-bracket-re nil t)
+      (let ((context (org-element-context)))
+          (pcase (org-element-lineage context '(link) t)
+            (`nil nil)
+            (link
+             (when (string-equal "roam" (org-element-property :type link))
+               (pcase-let ((`(,link-type ,loc ,desc _) (org-roam-link--get-location (org-element-property :path link))))
+                 (when (and link-type loc)
+                   (org-roam-link--replace-link link-type loc desc))))))))))
+
+(defun org-roam-link--replace-link-on-save ()
+  "Hook to replace all roam links on save."
+  (when org-roam-link-auto-replace
+    (org-roam-link-replace-all)))
+
+;;; Completion
+(defun org-roam-link-complete-at-point ()
+  "Do appropriate completion for the link at point."
+  (let ((end (point))
+        (start (point))
+        collection link-type headline-only-p)
+    (when (org-in-regexp org-link-bracket-re 1)
+      (setq start (match-beginning 1)
+            end (match-end 1))
+      (let ((context (org-element-context)))
+        (pcase (org-element-lineage context '(link) t)
+          (`nil nil)
+          (link
+           (setq link-type (org-element-property :type link))
+           (when (member link-type '("roam" "fuzzy"))
+             (when (string= link-type "roam") (setq start (+ start (length "roam:"))))
+             (pcase-let ((`(,type ,title _ ,star-idx)
+                          (org-roam-link--split-path (org-element-property :path link))))
+               (pcase type
+                 ('title+headline
+                  (when-let ((file (org-roam-link--get-file-from-title title t)))
+                    (setq collection (apply-partially #'org-roam-link--get-headlines file))
+                    (setq start (+ start star-idx 1))))
+                 ('title
+                  (setq collection #'org-roam-link--get-titles))
+                 ('headline
+                  (setq collection #'org-roam-link--get-headlines)
+                  (setq start (+ start star-idx 1))
+                  (setq headline-only-p t)))))))))
+    (when collection
+      (let ((prefix (buffer-substring-no-properties start end)))
+        (list start end
+              (if (functionp collection)
+                  (completion-table-case-fold
+                   (completion-table-dynamic
+                    (lambda (_)
+                      (cl-remove-if (apply-partially #'string= prefix)
+                                    (funcall collection))))
+                   (not org-roam-completion-ignore-case))
+                collection)
+              :exit-function
+              (lambda (str &rest _)
+                (delete-char (- 0 (length str)
+                                (if headline-only-p 1 0)))
+                (insert (concat (unless (string= link-type "roam") "roam:")
+                                (when headline-only-p "*")
+                                str))))))))
+
+(provide 'org-roam-link)
+;;; org-roam-link.el ends here

org-roam-macs.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,9 +34,24 @@
 ;;; Code:
 ;;;; Library Requires
 (require 'dash)
+(require 's)
 
 (defvar org-roam-verbose)
 
+;; This is necessary to ensure all dependents on this module see
+;; `org-mode-hook' and `org-inhibit-startup' as dynamic variables,
+;; regardless of whether Org is loaded before their compilation.
+(require 'org)
+
+;;;; Utility Functions
+(defun org-roam--list-interleave (lst separator)
+  "Interleaves elements in LST with SEPARATOR."
+  (when lst
+    (let ((new-lst (list (pop lst))))
+      (dolist (it lst)
+        (nconc new-lst (list separator it)))
+      new-lst)))
+
 (defmacro org-roam--with-temp-buffer (file &rest body)
   "Execute BODY within a temp buffer.
 Like `with-temp-buffer', but propagates `org-roam-directory'.
@@ -46,26 +61,14 @@ If FILE, set `org-roam-temp-file-name' to file and insert its contents."
     `(let ((,current-org-roam-directory org-roam-directory))
        (with-temp-buffer
          (let ((org-roam-directory ,current-org-roam-directory)
-               (org-mode-hook nil))
+               (org-mode-hook nil)
+               (org-inhibit-startup t))
            (org-mode)
            (when ,file
              (insert-file-contents ,file)
              (setq-local org-roam-file-name ,file))
            ,@body)))))
 
-(defmacro org-roam--with-template-error (templates &rest body)
-  "Eval BODY, and point to TEMPLATES on error.
-Provides more informative error messages so that users know where
-to look.
-
-\(fn TEMPLATES BODY...)"
-  (declare (debug (form body)) (indent 1))
-  `(condition-case err
-       ,@body
-     (error (user-error "%s.  Please adjust `%s'"
-                        (error-message-string err)
-                        ,templates))))
-
 (defun org-roam-message (format-string &rest args)
   "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
   (when org-roam-verbose
@@ -77,6 +80,28 @@ to look.
        (s-replace "\\" "\\\\")
        (s-replace "\"" "\\\"")))
 
+;;; Shielding regions
+(defun org-roam-shield-region (beg end)
+  "Shield REGION against modifications.
+REGION must be a cons-cell containing the marker to the region
+beginning and maximum values."
+  (when (and beg end)
+    (add-text-properties beg end
+                           '(font-lock-face org-roam-link-shielded
+                                            read-only t)
+                           (marker-buffer beg))
+    (cons beg end)))
+
+(defun org-roam-unshield-region (beg end)
+  "Unshield the shielded REGION."
+  (when (and beg end)
+    (let ((inhibit-read-only t))
+      (remove-text-properties beg end
+                              '(font-lock-face org-roam-link-shielded
+                                               read-only t)
+                              (marker-buffer beg)))
+    (cons beg end)))
+
 (provide 'org-roam-macs)
 
 ;;; org-roam-macs.el ends here

org-roam-protocol.el

@@ -4,7 +4,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.1
+;; Version: 1.2.3
 ;; Package-Requires: ((emacs "26.1") (org "9.3"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -37,6 +37,12 @@
 ;;; Code:
 (require 'org-protocol)
 (require 'org-roam)
+(require 'ol) ;; for org-link-decode
+
+(defcustom org-roam-protocol-store-links nil
+  "Whether to store links when capturing websites with `org-roam-protocol'."
+  :type 'boolean
+  :group 'org-roam)
 
 ;;;; Functions
 (defun org-roam-protocol-open-ref (info)
@@ -45,7 +51,7 @@
 It opens or creates a note with the given ref.
 
   javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
-        encodeURIComponent(location.href) + \\='&title=\\=' \\
+        encodeURIComponent(location.href) + \\='&title=\\=' + \\
         encodeURIComponent(document.title) + \\='&body=\\=' + \\
         encodeURIComponent(window.getSelection())"
   (when-let* ((alist (org-roam--plist-to-alist info))
@@ -57,13 +63,26 @@ It opens or creates a note with the given ref.
       (error "No ref key provided"))
     (when-let ((title (cdr (assoc 'title decoded-alist))))
       (push (cons 'slug (funcall org-roam-title-to-slug-function title)) decoded-alist))
+    (let-alist decoded-alist
+      (let* ((ref (org-protocol-sanitize-uri .ref))
+             (type (and (string-match "^\\([a-z]+\\):" ref)
+                        (match-string 1 ref)))
+             (title (or .title ""))
+             (body (or .body ""))
+             (orglink
+              (org-link-make-string ref (or (org-string-nw-p title) ref))))
+        (when org-roam-protocol-store-links
+          (push (list ref title) org-stored-links))
+        (org-link-store-props :type type
+                              :link ref
+                              :annotation orglink
+                              :initial body)))
     (let* ((org-roam-capture-templates org-roam-capture-ref-templates)
            (org-roam-capture--context 'ref)
            (org-roam-capture--info decoded-alist)
            (template (cdr (assoc 'template decoded-alist))))
       (raise-frame)
-      (org-roam--with-template-error 'org-roam-capture-ref-templates
+      (org-roam-capture--capture nil template)
-        (org-roam-capture--capture nil template))
       (org-roam-message "Item captured.")))
   nil)
 

tests/roam-files/cite_ref.org

@@ -0,0 +1 @@
+#+roam_key: cite:mitsuha2007

tests/roam-files/multiple-refs.org

@@ -0,0 +1,2 @@
+#+roam_key: https://www.orgroam.com/
+#+roam_key: cite:orgroam2020

tests/test-org-roam-perf.el

@@ -29,7 +29,7 @@
 
 (defun test-org-roam-perf--abs-path (file-path)
   "Get absolute FILE-PATH from `org-roam-directory'."
-  (file-truename (expand-file-name file-path org-roam-directory)))
+  (expand-file-name file-path org-roam-directory))
 
 (defun test-org-roam-perf--init ()
   "."
@@ -45,7 +45,7 @@
     (pcase (benchmark-run 1 (org-roam-db-build-cache t))
       (`(,time ,gcs ,time-in-gc)
        (message "Elapsed time: %fs (%fs in %d GCs)" time time-in-gc gcs)
-       (expect time :to-be-less-than 100))))
+       (expect time :to-be-less-than 110))))
   (it "builds quickly without change"
     (pcase (benchmark-run 1 (org-roam-db-build-cache))
       (`(,time ,gcs ,time-in-gc)

tests/test-org-roam.el

@@ -27,7 +27,7 @@
 
 (defun test-org-roam--abs-path (file-path)
   "Get absolute FILE-PATH from `org-roam-directory'."
-  (file-truename (expand-file-name file-path org-roam-directory)))
+  (expand-file-name file-path org-roam-directory))
 
 (defun test-org-roam--find-file (path)
   "PATH."
@@ -35,7 +35,7 @@
     (make-directory (file-name-directory path) t)
     (find-file path)))
 
-(defvar test-org-roam-directory (file-truename (concat default-directory "tests/roam-files"))
+(defvar test-org-roam-directory (expand-file-name "tests/roam-files")
   "Directory containing org-roam test org files.")
 
 (defun test-org-roam--init ()
@@ -49,7 +49,7 @@
 
 (defun test-org-roam--teardown ()
   (org-roam-mode -1)
-  (delete-file (org-roam-db--get))
+  (delete-file org-roam-db-location)
   (org-roam-db--close))
 
 (describe "org-roam--str-to-list"
@@ -71,6 +71,40 @@
     (expect (org-roam--str-to-list "\"hello")
             :to-throw)))
 
+(describe "Ref extraction"
+  (before-all
+    (test-org-roam--init))
+
+  (after-all
+    (test-org-roam--teardown))
+
+  (cl-flet
+      ((test (fn file)
+             (let* ((fname (test-org-roam--abs-path file))
+                    (buf (find-file-noselect fname)))
+               (with-current-buffer buf
+                 ;; Unlike tag extraction, it doesn't make sense to
+                 ;; pass a filename.
+                 (funcall fn)))))
+    ;; Enable "cite:" link parsing
+    (org-link-set-parameters "cite")
+    (it "extracts web keys"
+      (expect (test #'org-roam--extract-ref
+                    "web_ref.org")
+              :to-equal
+              '("website" . "//google.com/")))
+    (it "extracts cite keys"
+      (expect (test #'org-roam--extract-ref
+                    "cite_ref.org")
+              :to-equal
+              '("cite" . "mitsuha2007")))
+    (it "extracts all keys"
+      (expect (test #'org-roam--extract-refs
+                    "multiple-refs.org")
+              :to-have-same-items-as
+              '(("cite" . "orgroam2020")
+                ("website" . "//www.orgroam.com/"))))))
+
 (describe "Title extraction"
   :var (org-roam-title-sources)
   (before-all
@@ -239,7 +273,7 @@
                 :to-equal
                 '("t1" "t2 with space" "t3" "tags"))))))
 
-(describe "Headline extraction"
+(describe "ID extraction"
   (before-all
     (test-org-roam--init))
 
@@ -252,12 +286,34 @@
                     (buf (find-file-noselect fname)))
                (with-current-buffer buf
                  (funcall fn fname)))))
-    (it "extracts headlines"
+    (it "extracts ids"
-      (expect (test #'org-roam--extract-headlines
+      (expect (test #'org-roam--extract-ids
                     "headlines/headline.org")
+              :to-have-same-items-as
+              `(["e84d0630-efad-4017-9059-5ef917908823" ,(test-org-roam--abs-path "headlines/headline.org") 1]
+                ["801b58eb-97e2-435f-a33e-ff59a2f0c213" ,(test-org-roam--abs-path "headlines/headline.org") 1])))))
+
+(describe "Test roam links"
+  (it ""
+    (expect (org-roam-link--split-path "")
             :to-equal
-              `(["e84d0630-efad-4017-9059-5ef917908823" ,(test-org-roam--abs-path "headlines/headline.org")]
+            '(title "" "" nil)))
-                ["801b58eb-97e2-435f-a33e-ff59a2f0c213" ,(test-org-roam--abs-path "headlines/headline.org")])))))
+  (it "title"
+    (expect (org-roam-link--split-path "title")
+            :to-equal
+            '(title "title" "" nil)))
+  (it "title*"
+    (expect (org-roam-link--split-path "title*")
+            :to-equal
+            '(title+headline "title" "" 5)))
+  (it "title*headline"
+    (expect (org-roam-link--split-path "title*headline")
+            :to-equal
+            '(title+headline "title" "headline" 5)))
+  (it "*headline"
+    (expect (org-roam-link--split-path "*headline")
+            :to-equal
+            '(headline "" "headline" 0))))
 
 ;;; Tests
 (xdescribe "org-roam-db-build-cache"
@@ -278,21 +334,21 @@
 
     ;; Links
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= from $s1)]
+                                      :where (= source $s1)]
                                      (test-org-roam--abs-path "foo.org"))) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= from $s1)]
+                                      :where (= source $s1)]
                                      (test-org-roam--abs-path "nested/bar.org"))) :to-be 2)
 
     ;; Links -- File-to
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= to $s1)]
+                                      :where (= dest $s1)]
                                      (test-org-roam--abs-path "nested/foo.org"))) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= to $s1)]
+                                      :where (= dest $s1)]
                                      (test-org-roam--abs-path "nested/bar.org"))) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= to $s1)]
+                                      :where (= dest $s1)]
                                      (test-org-roam--abs-path "unlinked.org"))) :to-be 0)
     ;; TODO Test titles
     (expect (org-roam-db-query [:select * :from titles])