(fix) make roam headline link completion robust (#1473)

Fixes  #1472

.dir-locals.el

@@ -1,4 +1,6 @@
 ;;; Directory Local Variables
 ;;; For more information see (info "(emacs) Directory Variables")
 
-((emacs-lisp-mode . ((eval . (require 'org-roam-dev)))))
+((emacs-lisp-mode
+  (eval . (require 'org-roam-dev))
+  (eval . (org-roam-dev-mode))))

.github/workflows/stale.yml

@@ -1,19 +0,0 @@
-name: Mark stale issues and pull requests
-
-on:
-  schedule:
-  - cron: "0 0 * * *"
-
-jobs:
-  stale:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/stale@v1
-      with:
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-issue-message: 'Stale issue message'
-        stale-pr-message: 'Stale pull request message'
-        stale-issue-label: 'no-issue-activity'
-        stale-pr-label: 'no-pr-activity'

.github/workflows/test.yml

@@ -45,18 +45,23 @@ jobs:
 
     - uses: actions/checkout@v2
 
-    - name: Initialize sandbox
+    - name: Create Sandbox Directory
       run: |
         SANDBOX_DIR=$(mktemp -d) || exit 1
-        echo ::set-env name=SANDBOX_DIR::$SANDBOX_DIR
+        echo "SANDBOX_DIR=$SANDBOX_DIR" >> $GITHUB_ENV
+
+    - name: Initialize Sandbox
+      run: |
         ./makem.sh -vv --sandbox $SANDBOX_DIR --install-deps --install-linters
 
     # The "all" rule is not used, because it treats compilation warnings
     # as failures, so linting and testing are run as separate steps.
 
+    # org-roam-compat is excluded from linting because it contains
+    # symbols/aliases from other packages
     - name: Lint
       continue-on-error: false
-      run: ./makem.sh -vv --sandbox $SANDBOX_DIR lint
+      run: ./makem.sh -vv --sandbox $SANDBOX_DIR --exclude org-roam-compat.el lint
 
     - name: Test
       if: always()  # Run test even if linting fails.

.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

BACKERS.md

@@ -0,0 +1,8 @@
+# Backers
+
+Many thanks to the following backers, your contributions are greatly appreciated!
+
+- Nathan Tran
+- Burke Libbey
+- forkrul
+- Andreas Stuhlmüller

CHANGELOG.md

@@ -1,11 +1,160 @@
 # Changelog
+## 1.2.4 (TBD)
+
+### Added
+- [#1396](https://github.com/org-roam/org-roam/pull/1396) add option to choose between prepending, appending, and omitting `roam_tags` in file completion
+- [#1270](https://github.com/org-roam/org-roam/pull/1270) capture: create OLP if it does not exist. Removes need for OLP setup in `:head`.
+- [#1353](https://github.com/org-roam/org-roam/pull/1353) support file-level property drawers
+
+### Changed
+- [#1352](https://github.com/org-roam/org-roam/pull/1352) prefer lower-case for roam_tag and roam_alias in interactive commands
+
+### Fixed
+- [#1281](https://github.com/org-roam/org-roam/pull/1281) fixed idle-timer not instantiated on `org-roam-mode`
+- [#1308](https://github.com/org-roam/org-roam/pull/1308) fixed file renames corrupting database
+- [#1325](https://github.com/org-roam/org-roam/pull/1325) make titles and tags extracted unique per note
+- [#1327](https://github.com/org-roam/org-roam/pull/1327) preserve existing link description during automatic replacement
+- [#1346](https://github.com/org-roam/org-roam/pull/1346) prevent malformed path to `org-roam-index-file`
+- [#1347](https://github.com/org-roam/org-roam/pull/1347) allow use of `%a` element in regular Org-roam captures
+- [#1352](https://github.com/org-roam/org-roam/pull/1352) fixed org-roam-{tag/alias}-{add/delete} altering the original case of the Org property
+- [#1374](https://github.com/org-roam/org-roam/pull/1374) fix headline completions erroring out
+- [#1375](https://github.com/org-roam/org-roam/pull/1375) fix org-roam-protocol to use existing ref file 
+- [#1403](https://github.com/org-roam/org-roam/issues/1403) fixed inconsistency between how we write and read props like alias and tags
+- [#1409](https://github.com/org-roam/org-roam/issues/1398) prevent inclusion of non-org-roam files in `org-roam-dailies--list-files`
+
+## 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.
+
+We also added some new features that had been a long time coming:
+
+1. We made the backlinks more outline-friendly by also showing the outline hierarchy for a backlink (#863)
+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`
+- [#847](https://github.com/org-roam/org-roam/pull/847) Add GC threshold `org-roam-db-gc-threshold` to temporarily change the threshold on expensive operations.
+- [#847](https://github.com/org-roam/org-roam/pull/847) Use sqlite3 transactions instead of storing the values to be inserted.
+- [#851](https://github.com/org-roam/org-roam/pull/851) Add `'first-directory'` option for `org-roam-tag-sources`
+- [#863](https://github.com/org-roam/org-roam/pull/863) Display outline hierarchy in backlinks buffer
+- [#898](https://github.com/org-roam/org-roam/pull/898) Add `org-roam-random-note` to browse a random note.
+- [#900](https://github.com/org-roam/org-roam/pull/900) Support and index all valid org links
+- [#966](https://github.com/org-roam/org-roam/pull/966) Enable nested captures
+
+### Bugfixes
+
+- [#854](https://github.com/org-roam/org-roam/pull/854) Warn instead of fail when duplicate refs and IDs exist.
+- [#857](https://github.com/org-roam/org-roam/pull/857) Fix tag extraction for symlinked directories.
+- [#894](https://github.com/org-roam/org-roam/pull/894) Perform link fixes on all Org-roam files
+- [#952](https://github.com/org-roam/org-roam/pull/952) Cache `${foo}` template variables so they do not need to be re-entered twice
+
+## 1.2.0 (12-06-2020)
+
+In this release, we improved the linking process by achieving feature parity between links to files and links to headlines. Before, we used the `file:foo::*bar` format to link to the headline `bar` in file `foo`, but this was prone to breakage upon renaming the file or modifying the headline. This is not the case anymore. Now, we use `org-id` to create IDs for those headlines, which are then stored in our database to compute the relationships and jump around. Note that this will work even if you’re not using `org-id` in your global configuration for Org-mode.
+
+This is a major step forward. Supporting the in-file structure of Org-mode files means that we can interface with many of its core-features like TODOs, properties, priorities, etc. UX will have to be figured out, but this release ushers in a new age in terms of functionalities.
+
+We also add `org-roam-unlinked-references`, which naively finds text that could be references to the current Org-roam file.
+
+### Breaking Changes
+
+- [#701](https://github.com/org-roam/org-roam/pull/701) Use `emacsql-sqlite3` instead of `emacsql-sqlite` for better Windows compatibility. This requires the presence of the standard `sqlite3` binary on your machine.
+- [#750](https://github.com/org-roam/org-roam/pull/750) Deprecate `org-roam-buffer-no-delete-other-windows` in favour of `org-roam-buffer-window-parameters`.
+
+### Features
+
+- [#787](https://github.com/org-roam/org-roam/pull/787) Add `org-roam-unlinked-references`
+- [#783](https://github.com/org-roam/org-roam/pull/783) Add support for headlines
+- [#757](https://github.com/org-roam/org-roam/pull/757) Roam global properties are now case-insensitive
+- [#680](https://github.com/org-roam/org-roam/pull/680) , [#703](https://github.com/org-roam/org-roam/pull/703), [#708](https://github.com/org-roam/org-roam/pull/708) Add `org-roam-doctor` checkers for `ROAM_*` properties
+- [#664](https://github.com/org-roam/org-roam/pull/664) Add support for shelling out to `rg` and `find` in `org-roam--list-files`
+- [#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
 
 ## 1.1.1 (18-05-2020)
 
 In this release, we added two new features:
 
 1. `org-roam-doctor`: a linting system that helps you discover possible problems with your Org-roam files. This is in the spirit of keeping notes in top quality.
-2. A tagging system: one can now use sub-directories, and the `#+ROAM_TAG` key add additional meta data to notes. For more information, see [here](https://org-roam.github.io/org-roam/manual/Tags.html#Tags).
+2. A tagging system: one can now use sub-directories, and the `#+roam_tags` key add additional meta data to notes. For more information, see [here](https://www.orgroam.com/manual/Tags.html#Tags).
 
 As usual, this release comes with a multitude of bug-fixes and refactorings.
 

README.md

@@ -1,42 +1,35 @@
-[![License GPL 3][badge-license]](http://www.gnu.org/licenses/gpl-3.0.txt)
-[![GitHub Release](https://img.shields.io/github/v/release/org-roam/org-roam)](https://img.shields.io/github/v/release/org-roam/org-roam)
-[![MELPA](https://melpa.org/packages/org-roam-badge.svg)](https://melpa.org/#/org-roam)
+# Org-roam [![GitHub Release][release-badge]][release] [![MELPA][melpa-badge]][melpa] [![License GPL 3][gpl3-badge]][gpl3]
+ 
+<img src="https://www.orgroam.com/img/logo.svg" align="right" alt="Org-roam Logo" width="240">
 
-## Synopsis
+Org-roam is a plain-text knowledge management system. It brings some of
+[Roam's][roamresearch] more powerful features into the [Org-mode][org]
+ecosystem.
 
-Org-roam is a [Roam][roamresearch] replica built on top of the
-all-powerful [Org-mode][org].
+Org-roam borrows principles from the Zettelkasten method, providing a solution
+for non-hierarchical note-taking. It should also work as a plug-and-play
+solution for anyone already using Org-mode for their personal wiki.
 
-Org-roam is a solution for effortless non-hierarchical note-taking
-with Org-mode. With Org-roam, notes flow naturally, making note-taking
-fun and easy. Org-roam should also work as a plug-and-play solution
-for anyone already using Org-mode for their personal wiki.
+- **Private and Secure**: Edit your personal wiki completely offline, entirely
+  in your control. Encrypt your notes with GPG. Take lasting notes in
+  plain-text.
+- **Networked Thought**: Connect notes and thoughts together with ease using
+  backlinks. Discover surprising and previously unseen connections in your notes
+  with the built-in graph visualization.
+- **Extensible and Powerful**: Leverage Emacs' fantastic text-editing interface,
+  and the mature Emacs and Org-mode ecosystem of packages.
+- **Free and Open Source**: Org-roam is licensed under the GNU General Public
+  License version 3 or later.
 
-Org-roam aims to implement the core features of Roam, leveraging the
-mature ecosystem around Org-mode where possible. Eventually, we hope
-to further introduce features enabled by the Emacs ecosystem.
-
-[@technovangelist](https://github.com/technovangelist/) has produced a video
-describing Org-roam and the concepts behind it:
-
-[![Making Connections in your Notes](http://img.youtube.com/vi/Lg61ocfxk3c/0.jpg)](http://www.youtube.com/watch?v=Lg61ocfxk3c "Making Connections in your Notes")
-
-Important links:
+<p align="center">
+  <img src="https://www.orgroam.com/img/screenshot.png" alt="Org-roam Screenshot" width="738">
+</p>
 
 - **[Documentation][docs]**
 - **[Discourse][discourse]**
 - **[Slack][slack]**
-
-## A Preview
-
-Here's a screencast of Org-roam. The `org-roam-buffer` (window on the
-right) shows backlinks for the active Org-roam buffer (window on the
-left), as well as the surrounding content in the backlink file. The
-database is built once, and updated incrementally. The graph is
-generated from the link structure, and can be used to navigate to the
-respective files.
-
-![img](doc/images/org-roam-graph.gif)
+- **[Frequently Asked Questions][faq]**
+- **[Changelog](CHANGELOG.md)**
 
 ## Installation
 
@@ -46,10 +39,11 @@ You can install `org-roam` using `package.el`:
 M-x package-install RET org-roam RET
 ```
 
-Here's a sample configuration with using `use-package`:
+Here's a sample configuration with `use-package`:
 
 ```emacs-lisp
 (use-package org-roam
+      :ensure t
       :hook
       (after-init . org-roam-mode)
       :custom
@@ -57,29 +51,36 @@ 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-show-graph))
+               ("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))
+              (("C-c n I" . org-roam-insert-immediate))))
 ```
 
-`org-roam-graph` by default expects to find the `dot` executable
-from the `graphviz` package in the `exec-path`.
-Ensure `graphviz` is installed and found if you want to use this
-feature or customize your configuration for `org-roam-graph` to use a
-different tool.
+Org-roam requires sqlite to function. Org-roam optionally uses Graphviz for
+graph-related functionality. It is recommended to install PCRE-enabled ripgrep
+for better performance and extended functionality.
 
-For more detailed installation and configuration instructions (including for
-Doom and Spacemacs users), please see [the
-documentation][docs].
+## Getting Help
+
+Before creating a new topic/issue, please be mindful of our time and ensure that
+it has not already been addressed on [GitHub][issues] or on
+[Discourse][discourse].
+
+- If you are new to Emacs and have problem setting up Org-roam, please ask your
+  question on [Slack, channel #how-do-i][slack].
+- For quick questions, please ask them on [Slack, channel
+  #troubleshooting][slack].
+- If something is not working as it should, or if you would like to suggest a
+  new feature, please [create a new issue][issues].
+- If you have questions about your workflow with the slip-box method, please
+  find a relevant topic on [Discourse][discourse], or create a new one.
 
 ## Knowledge Bases using Org-roam
 
 - [Jethro Kuan](https://braindump.jethro.dev/)
   ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
-
-## Changelog
-
-A changelog is being maintained [here](CHANGELOG.md)
+- [Alexey Shmalko](https://braindump.rasen.dev/)
 
 ## Contributing
 
@@ -90,11 +91,18 @@ request. Please also see [CONTRIBUTING.md](.github/CONTRIBUTING.md).
 ## License
 
 Copyright © Jethro Kuan and contributors. Distributed under the GNU
-General Public License, Version 3
+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://org-roam.github.io/org-roam/manual/
+[gpl3-badge]: https://img.shields.io/badge/license-GPL_3-green.svg
+[gpl3]: http://www.gnu.org/licenses/gpl-3.0.txt
+[melpa-badge]: https://melpa.org/packages/org-roam-badge.svg
+[melpa]: https://melpa.org/#/org-roam
+[release-badge]: https://img.shields.io/github/v/release/org-roam/org-roam
+[release]: https://github.com/org-roam/org-roam/releases
+[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
+[faq]: https://www.orgroam.com/manual.html#FAQ

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

@@ -27,12 +27,9 @@ dir: org-roam.info
 	@printf "Generating $@\n"
 	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) $<
 
-html-dir: 
-	@printf "Generating org-roam/*.html\n"
-	@$(MAKEINFO) --html $(MANUAL_HTML_ARGS) org-roam.texi
-	mv org-roam manual
-	cp -r assets manual
-	cp -r images manual
+html-dir:
+	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) org-roam.texi
+	mv org-roam.html manual.html
 
 %.pdf: %.texi
 	@printf "Generating $@\n"

doc/assets/page.css

@@ -1,442 +1,68 @@
-/* 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,
-    Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif,
-    "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);
+  --border: #526980;
+  --code: #007;
 }
 
 body {
-  /* Center body in page */
-  margin: 0 auto;
-  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;
+    margin: 5ex 10ex;
+    max-width: 80ex;
+    line-height: 1.5;
+    font-family: sans-serif;
 }
 
-::selection {
-  /* Set background color for selected text */
-  background: var(--nc-ac-1);
-  color: var(--nc-ac-tx);
+h1, h2, h3 {
+    font-weight: normal;
 }
 
-p {
-  margin-bottom: 1rem;
-}
-
-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, code {
+    font-family: x, monospace;
 }
 
 pre {
-  padding: 1rem 1.4rem;
-  max-width: 100%;
-  overflow: auto;
+    padding: 1ex;
+    background: #eee;
+    border: solid 1px #ddd;
+    min-width: 0;
+    font-size: 80%;
+    overflow: auto;
 }
 
-pre code {
-  /* When <code> is in a <pre>, reset it's formatting to blend in */
-  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;
+code {
+    color: var(--code);
 }
 
 img {
-  max-width: 100%;
+    max-width: 100%;
 }
 
-/* Customizations */
-.menu-comment {
-  font-weight: bold;
-  border: 0;
-  margin: 0;
-  padding: 0;
-  font-size: 1.2rem;
+table {
+  border-collapse: collapse;
+  width: 100%;
+}
+
+pre.menu-comment {
+  background: none;
+  border: none;
+  font-family: sans-serif;
+  padding: 0;
+  margin: 0;
+  font-size: 100%;
+}
+
+thead {
+  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/css/styles.css

@@ -0,0 +1,85 @@
+body {
+  margin: 20px;
+  background: #303030;
+  color: #f5f5f5;
+  font-size: 1.6rem;
+  font-weight: 300;
+}
+
+.container {
+  max-width: 800px;
+}
+
+.nav {
+  margin-top: 5rem;
+}
+
+.nav-item a {
+  /* color: #797979; */
+  color: #bebebe;
+  text-decoration: none;
+  font-family: "Consolas", "Monaco", "Menlo", monospace;
+}
+
+.nav-item a:hover {
+  cursor: pointer;
+  /* color: #4d4a4a; */
+  color: #dcdcdc;
+  border: none;
+}
+
+.hero {
+  color: #f5f5f5;
+}
+
+.hero div {
+  margin-bottom: 5rem;
+}
+
+.hero h3 {
+  /* font-family: "Edelsans", sans-serif; */
+  font-size: 5rem;
+  margin-bottom: 0;
+}
+
+.hero h5 {
+  margin-top: 1rem;
+  margin-bottom: 0;
+  /* font-weight: 200; */
+  font-weight: 250;
+}
+
+.grid-demo-col {
+  background: #e4e4e4;
+}
+
+a {
+  color: #cd86ff;
+}
+
+a:hover {
+  color: #dbb9f3;
+}
+
+img {
+  max-width: 100%;
+}
+
+.footer-links {
+  font-size: 1.5rem;
+  color: #f5f5f5;
+  text-decoration: none;
+  font-weight: 250;
+}
+
+.header {
+  font-weight: 200;
+}
+
+#footer {
+  margin-bottom: 3rem;
+}
+
+#footer h5 {
+  margin-bottom: 1.5rem;
+}

doc/index.html

@@ -1,3 +1,168 @@
-<html>
-  <h1>--> <a href="manual/index.html">MANUAL HERE</a> <--</h1>
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="description" content="An Effortless PKM System." />
+    <meta name="author" content="Org-roam Contributors" />
+
+    <title>Org-roam</title>
+
+    <link rel="stylesheet" href="https://unpkg.com/wingcss" />
+    <link rel="stylesheet" type="text/css" href="./css/styles.css" />
+
+    <script src="https://code.iconify.design/1/1.0.6/iconify.min.js"></script>
+  </head>
+
+  <body>
+    <section class="hero container center text-center">
+      <div>
+        <img src="./img/logo.png" alt="Org-roam Logo" height="200" />
+        <h3>Org-roam</h3>
+        <h5>A plain-text personal knowledge management system.</h5>
+      </div>
+    </section>
+
+    <section class="container center">
+      <div>
+        <img src="./img/screenshot.png" alt="screenshot" />
+      </div>
+    </section>
+
+    <section id="features" class="container center">
+      <div>
+        <h3 class="header">FEATURES</h3>
+        <div class="row">
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="fxemoji:lock"></iconify-icon> &nbsp;
+              Private and Secure
+            </h5>
+            <p class="content">
+              Edit your personal wiki completely offline, entirely in your
+              control. Encrypt your notes with GPG. Take lasting notes in
+              plain-text.
+            </p>
+          </div>
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="flat-color-icons:link"></iconify-icon>
+              &nbsp; Make Connections
+            </h5>
+            <p class="content">
+              Connect notes and thoughts together with ease using backlinks.
+              Discover surprising and previously unseen connections in your
+              notes with the built-in graph visualization.
+            </p>
+          </div>
+        </div>
+
+        <div class="row">
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="twemoji:puzzle-piece"></iconify-icon>
+              &nbsp; Extensible and Powerful
+            </h5>
+            <p class="content">
+              Leverage Emacs' fantastic text-editing interface, and the mature
+              Emacs and Org-mode ecosystem of packages.
+            </p>
+          </div>
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="logos:git-icon"></iconify-icon> &nbsp;
+              Free and Open Source
+            </h5>
+            <p class="content">
+              Org-roam is licensed under the GNU General Public License version
+              3 or later. You are free to extend its functionality and
+              contribute back. Find
+              us <a href="https://github.com/org-roam/org-roam">here</a>.
+            </p>
+          </div>
+        </div>
+      </div>
+    </section>
+    
+    <section id="links" class="container">
+      <div>
+        <h3 class="header">LINKS</h3> New to Emacs and Org-mode, and trying to
+        find your way around? Org-roam has an inclusive community of users
+        passionate about Personal Knowledge Management -- we're happy to help!
+        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.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>
+      </div>
+    </section>
+
+    <section id="footer" class="row container">
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Ecosystem</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam-bibtex"
+            >org-roam-bibtex</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam-server"
+            >org-roam-server</a
+          >
+        </div>
+      </div>
+
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Resources</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc"
+            >Open Issues</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam/releases"
+            >Releases</a
+          >
+        </div>
+      </div>
+
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Connect</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg"
+            >Slack</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://org-roam.discourse.group/"
+            >Discourse</a
+          >
+        </div>
+      </div>
+    </section>
+  </body>
 </html>

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

mkdocs.yml

@@ -1,40 +0,0 @@
-site_name: "Org-roam"
-repo_url: https://github.com/org-roam/org-roam/
-edit_uri: edit/master/doc/
-copyright: "Copyright (C) 2020 Jethro Kuan and contributors"
-docs_dir: doc
-extra:
-  social:
-    - type: 'slack'
-      link: 'https://join.slack.com/t/orgroam/shared_invite/zt-clh0g0tx-j8xg1kVxnrWdKt16gmSGPQ'
-nav:
-- Home: index.md
-- A Tour of Org-roam: tour.md
-- Installation: installation.md
-- Configuration: configuration.md
-- Anatomy of an Org-roam file: anatomy.md
-- The Templating System: templating.md
-- Ecosystem: ecosystem.md
-- Similar Packages: comparison.md
-- "Appendix: Note-taking Workflow": notetaking_workflow.md
-- "Appendix: Roam Protocol": roam_protocol.md
-- "Appendix: Org Export": org_export.md
-markdown_extensions:
-  - admonition
-  - pymdownx.betterem:
-      smart_enable: all
-  - pymdownx.caret
-  - pymdownx.critic
-  - pymdownx.details
-  - pymdownx.mark
-  - pymdownx.smartsymbols
-  - pymdownx.superfences
-  - pymdownx.tasklist:
-      custom_checkbox: true
-  - pymdownx.tilde
-
-theme:
-  name: 'material'
-  palette:
-    primary: 'deep purple'
-    accent: 'deep purple'

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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -34,6 +34,10 @@
 (require 'cl-lib)
 (require 'dash)
 (require 's)
+(require 'f)
+(require 'ol)
+(require 'org-element)
+(require 'org-roam-macs)
 
 (defvar org-roam-directory)
 (defvar org-link-frame-setup)
@@ -41,12 +45,20 @@
 (defvar org-roam-backlinks-mode)
 (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--get-title-or-slug "org-roam")
+(declare-function org-roam-db--get-title      "org-roam-db")
+(declare-function org-roam-db-has-file-p      "org-roam-db")
+(declare-function org-roam--extract-refs      "org-roam")
+(declare-function org-roam--extract-titles    "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.
@@ -54,11 +66,13 @@ Valid values are
  * left,
  * right,
  * top,
- * bottom."
+ * bottom,
+ * a function returning one of the above."
   :type '(choice (const left)
                  (const right)
                  (const top)
-                 (const bottom))
+                 (const bottom)
+                 function)
   :group 'org-roam)
 
 (defcustom org-roam-buffer-width 0.33
@@ -81,26 +95,54 @@ Has an effect if and only if `org-roam-buffer-position' is `top' or `bottom'."
 
 (defcustom org-roam-buffer-prepare-hook '(org-roam-buffer--insert-title
                                           org-roam-buffer--insert-backlinks
-                                          org-roam-buffer--insert-citelinks)
+                                          org-roam-buffer--insert-ref-links)
   "Hook run in the `org-roam-buffer' before it is displayed."
   :type 'hook
   :group 'org-roam)
 
-(defcustom org-roam-buffer-no-delete-other-windows nil
-  "The `no-delete-other-windows' parameter of the `org-roam-buffer' window.
-When non-nil, the window will not be closed when deleting other windows."
-  :type 'boolean
+(defcustom org-roam-buffer-preview-function #'org-roam-buffer--preview
+  "Function to obtain preview contents for a given link.
+The function takes in two arguments, the FILE containing the
+link, and the POINT of the link."
+  :type 'function
+  :group 'org-roam)
+
+(defcustom org-roam-buffer-window-parameters nil
+  "Additional window parameters for the `org-roam-buffer' side window.
+For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
+  :type '(alist)
   :group 'org-roam)
 
 (defvar org-roam-buffer--current nil
   "Currently displayed file in `org-roam' buffer.")
 
+(defun org-roam-buffer--find-file (file)
+  "Open FILE in the window `org-roam' was called from."
+  (setq file (expand-file-name file))
+  (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 last-window))
+      (org-roam--find-file file))))
+
 (defun org-roam-buffer--insert-title ()
   "Insert the org-roam-buffer title."
-  (insert (propertize (org-roam--get-title-or-slug
+  (insert (propertize (org-roam-db--get-title
                        (buffer-file-name org-roam-buffer--current))
-                       'font-lock-face
-                       'org-document-title)))
+                      'font-lock-face
+                      'org-document-title)))
+
+(defun org-roam-buffer--preview (file point)
+  "Get preview content for FILE at POINT."
+  (save-excursion
+    (org-roam--with-temp-buffer file
+      (goto-char point)
+      (let ((elem (org-element-at-point)))
+        (or (org-element-property :raw-value elem)
+            (when-let ((begin (org-element-property :begin elem))
+                       (end (org-element-property :end elem)))
+              (string-trim (buffer-substring-no-properties begin end))))))))
 
 (defun org-roam-buffer--pluralize (string number)
   "Conditionally pluralize STRING if NUMBER is above 1."
@@ -112,63 +154,93 @@ When non-nil, the window will not be closed when deleting other windows."
                                    ,wrong-type))))))
     (concat string (when (> l 1) "s"))))
 
-(defun org-roam-buffer--insert-citelinks ()
-  "Insert citation backlinks for the current buffer."
-  (if-let* ((ref (with-temp-buffer
-                   (insert-buffer-substring org-roam-buffer--current)
-                   (org-roam--extract-ref)))
-            (org-ref-p (require 'org-ref nil t)) ; Ensure that org-ref is present
-            (key-backlinks (org-roam--get-backlinks (cdr ref)))
-            (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
-      (progn
-        (insert (let ((l (length key-backlinks)))
-                  (format "\n\n* %d %s\n"
-                          l (org-roam-buffer--pluralize "Cite backlink" l))))
-        (dolist (group grouped-backlinks)
-          (let ((file-from (car group))
-                (bls (cdr group)))
-            (insert (format "** [[file:%s][%s]]\n"
-                            file-from
-                            (org-roam--get-title-or-slug file-from)))
-            (dolist (backlink bls)
-              (pcase-let ((`(,file-from _ ,props) backlink))
-                (insert (propertize
-                         (s-trim (s-replace "\n" " "
-                                            (plist-get props :content)))
-                         'help-echo "mouse-1: visit backlinked note"
-                         'file-from file-from
-                         'file-from-point (plist-get props :point)))
-                (insert "\n\n"))))))
-    (insert "\n\n* No cite backlinks!")))
+(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* ((refs (with-temp-buffer
+                      (insert-buffer-substring org-roam-buffer--current)
+                      (org-roam--extract-refs)))
+              (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)))
+                    (format "\n\n* %d %s\n"
+                            l (org-roam-buffer--pluralize "Ref Backlink" l))))
+          (dolist (group grouped-backlinks)
+            (let ((file-from (car group))
+                  (bls (cdr group)))
+              (insert (format "** %s\n"
+                              (org-roam-format-link file-from
+                                                    (org-roam-db--get-title file-from)
+                                                    "file")))
+              (dolist (backlink bls)
+                (pcase-let ((`(,file-from _ ,props) backlink))
+                  (insert (if-let ((content (funcall org-roam-buffer-preview-function file-from (plist-get props :point))))
+                              (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))
+                            "")
+                          "\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."
-  (if-let* ((file-path (buffer-file-name org-roam-buffer--current))
-            (backlinks (org-roam--get-backlinks file-path))
-            (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))
-                (bls (cdr group)))
-            (insert (format "** [[file:%s][%s]]\n"
-                            file-from
-                            (org-roam--get-title-or-slug file-from)))
-            (dolist (backlink bls)
-              (pcase-let ((`(,file-from _ ,props) backlink))
-                (insert (propertize
-                         (s-trim (s-replace "\n" " "
-                                            (plist-get props :content)))
-                         'help-echo "mouse-1: visit backlinked note"
-                         'file-from file-from
-                         'file-from-point (plist-get props :point)))
-                (insert "\n\n"))))))
-    (insert "\n\n* No backlinks!")))
+  (let (props file-from)
+    (if-let* ((file-path (buffer-file-name org-roam-buffer--current))
+              (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)
+            (setq file-from (car group))
+            (setq props (mapcar (lambda (row) (nth 2 row)) (cdr group)))
+            (setq props (seq-sort-by (lambda (p) (plist-get p :point)) #'< props))
+            (insert (format "** %s\n"
+                            (org-roam-format-link file-from
+                                                  (org-roam-db--get-title file-from)
+                                                  "file")))
+            (dolist (prop props)
+              (insert "*** "
+                      (if-let ((outline (plist-get prop :outline)))
+                          (-> outline
+                              (string-join " > ")
+                              (org-roam-buffer-expand-links file-from))
+                        "Top")
+                      "\n"
+                      (if-let ((content (funcall org-roam-buffer-preview-function file-from (plist-get prop :point))))
+                          (propertize
+                           (s-trim (s-replace "\n" " " (org-roam-buffer-expand-links content file-from)))
+                           'help-echo "mouse-1: visit backlinked note"
+                           'file-from file-from
+                           'file-from-point (plist-get prop :point))
+                        "")
+                      "\n\n"))))
+      (insert "\n\n* No backlinks!"))))
 
 (defun org-roam-buffer-update ()
   "Update the `org-roam-buffer'."
+  (interactive)
   (org-roam-db--ensure-built)
   (let* ((source-org-roam-directory org-roam-directory))
     (with-current-buffer org-roam-buffer
@@ -203,7 +275,8 @@ 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)
+               (org-roam-db-has-file-p (buffer-file-name buffer)))
       (setq org-roam-buffer--current buffer)
       (org-roam-buffer-update))))
 
@@ -242,34 +315,42 @@ Valid states are 'visible, 'exists and 'none."
 
 (defun org-roam-buffer--get-create ()
   "Set up the `org-roam' buffer at `org-roam-buffer-position'."
-  (let ((window (get-buffer-window))
-        (position
-         (if (member org-roam-buffer-position '(right left top bottom))
-             org-roam-buffer-position
-           (let ((text-quoting-style 'grave))
-             (lwarn '(org-roam) :error
-                    "Invalid org-roam-buffer-position: %s. Defaulting to \\='right"
-                    org-roam-buffer-position))
-           'right)))
-    (-> (get-buffer-create org-roam-buffer)
-        (display-buffer-in-side-window
-         `((side . ,position)
-           (window-parameters . ((no-delete-other-windows . ,org-roam-buffer-no-delete-other-windows)))))
-        (select-window))
-    (pcase position
-      ((or 'right 'left)
-       (org-roam-buffer--set-width  (round (* (frame-width)  org-roam-buffer-width))))
-      ((or 'top  'bottom)
-       (org-roam-buffer--set-height (round (* (frame-height) org-roam-buffer-height)))))
-    (select-window window)))
+  (let ((position (if (functionp org-roam-buffer-position)
+                      (funcall org-roam-buffer-position)
+                    org-roam-buffer-position)))
+    (save-selected-window
+      (-> (get-buffer-create org-roam-buffer)
+          (display-buffer-in-side-window
+           `((side . ,position)
+             (window-parameters . ,org-roam-buffer-window-parameters)))
+          (select-window))
+      (pcase position
+        ((or 'right 'left)
+         (org-roam-buffer--set-width
+          (round (* (frame-width)  org-roam-buffer-width))))
+        ((or 'top  'bottom)
+         (org-roam-buffer--set-height
+          (round (* (frame-height) org-roam-buffer-height))))))))
+
+(defun org-roam-buffer-activate ()
+  "Activate display of the `org-roam-buffer'."
+  (interactive)
+  (unless org-roam-mode (org-roam-mode))
+  (setq org-roam-last-window (get-buffer-window))
+  (org-roam-buffer--get-create))
+
+(defun org-roam-buffer-deactivate ()
+  "Deactivate display of the `org-roam-buffer'."
+  (interactive)
+  (setq org-roam-last-window (get-buffer-window))
+  (delete-window (get-buffer-window org-roam-buffer)))
 
 (defun org-roam-buffer-toggle-display ()
   "Toggle display of the `org-roam-buffer'."
   (interactive)
-  (setq org-roam-last-window (get-buffer-window))
   (pcase (org-roam-buffer--visibility)
-    ('visible (delete-window (get-buffer-window org-roam-buffer)))
-    ((or 'exists 'none) (org-roam-buffer--get-create))))
+    ('visible (org-roam-buffer-deactivate))
+    ((or 'exists 'none) (org-roam-buffer-activate))))
 
 (provide 'org-roam-buffer)
 

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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -31,6 +31,8 @@
 ;;; Code:
 ;;;; Library Requires
 (require 'org-capture)
+(require 'org-roam-macs)
+(require 'org-roam-db)
 (require 'dash)
 (require 's)
 (require 'cl-lib)
@@ -38,19 +40,18 @@
 ;; Declarations
 (defvar org-roam-encrypt-files)
 (defvar org-roam-directory)
+(defvar org-roam-mode)
+(defvar org-roam-title-to-slug-function)
+(defvar org-roam-file-extensions)
+
 (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--format-link                "org-roam")
-(declare-function  org-roam--title-to-slug              "org-roam")
+(declare-function  org-roam--find-file                  "org-roam")
+(declare-function  org-roam-format-link                "org-roam")
+(declare-function  org-roam--split-ref                 "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.")
@@ -76,71 +77,290 @@ 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.")
 
-(defvar org-roam-capture-templates
-  '(("d" "default" plain (function org-roam-capture--get-point)
+(defcustom org-roam-capture-templates
+  `(("d" "default" plain (function org-roam-capture--get-point)
      "%?"
      :file-name "%<%Y%m%d%H%M%S>-${slug}"
-     :head "#+TITLE: ${title}\n"
+     :head "#+title: ${title}\n"
      :unnarrowed t))
   "Capture templates for Org-roam.
-The capture templates are an extension of
-`org-capture-templates', and the documentation there also
-applies.
+The Org-roam capture-templates  builds on the default behaviours of
+`org-capture-templates' by expanding them in 3 areas:
 
-`org-capture-templates' are extended in 3 ways:
+1. Template-expansion capabilities are extended with additional
+   custom syntax. See `org-roam-capture--fill-template' for more
+   details.
 
-1. Template expansion capabilities are extended with additional custom syntax.
-   See `org-roam-capture--fill-template' for more details.
-
-2. The `:file-name' key is added, which expands to the file-name
-   of the note if it creates a new file.  This file-name is
-   relative to `org-roam-directory', and is without the
-   file-extension.
+2. The `:file-name' key is added, which defines the naming format
+   to use when creating new notes. This file-name is relative to
+   `org-roam-directory', and is without the file-extension.
 
 3. The `:head' key is added, which contains the template that is
-   inserted on initial creation (added only once).  This is where
-   insertion of any note metadata should go.")
+   inserted upon the creation of a new file. This is where you
+   your note metadata should go.
 
-(defvar org-roam-capture-ref-templates
-  '(("r" "ref" plain (function org-roam-capture--get-point)
-     ""
+Each template should have the following structure:
+
+\(KEY DESCRIPTION `plain' `(function org-roam-capture--get-point)'
+  TEMPLATE
+  `:file-name' FILENAME-FORMAT
+  `:head' HEADER-FORMAT
+  `:unnarrowed t'
+  OPTIONS-PLIST)
+
+The elements of a template-entry and their placement are the same
+as in `org-capture-templates', except that the entry type must
+always be the symbol `plain', and that the target must always be
+the list `(function org-roam-capture--get-point)'.
+
+Org-roam requires the plist elements `:file-name' and `:head' to
+be present, and it’s recommended that `:unnarrowed' be set to t."
+  :group 'org-roam
+  ;; Adapted from `org-capture-templates'
+  :type
+  '(repeat
+    (choice :value ("d" "default" plain (function org-roam-capture--get-point)
+                    "%?"
+                    :file-name "%<%Y%m%d%H%M%S>-${slug}"
+                    :head "#+title: ${title}\n"
+                    :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)
+                  (const :format "" (function org-roam-capture--get-point))
+                  (choice :tag "Template          "
+                          (string :tag "String"
+                                  :format "String:\n            \
+Template string   :\n%v")
+                          (list :tag "File"
+                                (const :format "" file)
+                                (file :tag "Template file     "))
+                          (list :tag "Function"
+                                (const :format "" function)
+                                (function :tag "Template function ")))
+                  (const :format "File name format  :" :file-name)
+                  (string :format " %v" :value "#+title: ${title}\n")
+                  (const :format "Header format     :" :head)
+                  (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
+                  (const :format "" :unnarrowed) (const :format "" t)
+                  (plist :inline t
+                         :tag "Options"
+                         ;; Give the most common options as checkboxes
+                         :options
+                         (((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))
+                          ((const :format "%v " :empty-lines-after) (const 1))
+                          ((const :format "%v " :clock-in) (const t))
+                          ((const :format "%v " :clock-keep) (const t))
+                          ((const :format "%v " :clock-resume) (const t))
+                          ((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))))))))
+
+(defcustom org-roam-capture-immediate-template
+  (append (car org-roam-capture-templates) '(:immediate-finish t))
+  "Capture template to use for immediate captures in Org-roam.
+This is a single template, so do not enclose it into a list.
+See `org-roam-capture-templates' for details on templates."
+  :group 'org-roam
+  ;; Adapted from `org-capture-templates'
+  :type
+  '(list :tag "Template entry"
+         :value ("d" "default" plain (function org-roam-capture--get-point)
+                 "%?"
+                 :file-name "%<%Y%m%d%H%M%S>-${slug}"
+                 :head "#+title: ${title}\n"
+                 :unnarrowed t
+                 :immediate-finish t)
+         (string :tag "Keys              ")
+         (string :tag "Description       ")
+         (const :format "" plain)
+         (const :format "" (function org-roam-capture--get-point))
+         (choice :tag "Template          "
+                 (string :tag "String"
+                         :format "String:\n            \
+Template string   :\n%v")
+                 (list :tag "File"
+                       (const :format "" file)
+                       (file :tag "Template file     "))
+                 (list :tag "Function"
+                       (const :format "" function)
+                       (function :tag "Template function ")))
+         (const :format "File name format  :" :file-name)
+         (string :format " %v" :value "#+title: ${title}\n")
+         (const :format "Header format     :" :head)
+         (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
+         (const :format "" :unnarrowed) (const :format "" t)
+         (const :format "" :immediate-finish) (const :format "" t)
+         (plist :inline t
+                :tag "Options"
+                ;; Give the most common options as checkboxes
+                :options
+                (((const :format "%v " :prepend) (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))
+                 ((const :format "%v " :empty-lines-after) (const 1))
+                 ((const :format "%v " :clock-in) (const t))
+                 ((const :format "%v " :clock-keep) (const t))
+                 ((const :format "%v " :clock-resume) (const t))
+                 ((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))))))
+
+(defcustom org-roam-capture-ref-templates
+  '(("r" "ref" plain #'org-roam-capture--get-point
+     "%?"
      :file-name "${slug}"
-     :head "#+TITLE: ${title}
-#+ROAM_KEY: ${ref}\n"
+     :head "#+title: ${title}\n#+roam_key: ${ref}"
      :unnarrowed t))
   "The Org-roam templates used during a capture from the roam-ref protocol.
-Details on how to specify for the template is given in `org-roam-capture-templates'.")
+Details on how to specify for the template is given in `org-roam-capture-templates'."
+  :group 'org-roam
+  ;; Adapted from `org-capture-templates'
+  :type
+  '(repeat
+    (choice :value ("d" "default" plain (function org-roam-capture--get-point)
+                    "%?"
+                    :file-name "${slug}"
+                    :head "#+title: ${title}\n#+roam_key: ${ref}\n"
+                    :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)
+                  (const :format "" (function org-roam-capture--get-point))
+                  (choice :tag "Template          "
+                          (string :tag "String"
+                                  :format "String:\n            \
+Template string   :\n%v")
+                          (list :tag "File"
+                                (const :format "" file)
+                                (file :tag "Template file     "))
+                          (list :tag "Function"
+                                (const :format "" function)
+                                (function :tag "Template function ")))
+                  (const :format "File name format  :" :file-name)
+                  (string :format " %v" :value "#+title: ${title}\n")
+                  (const :format "Header format     :" :head)
+                  (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
+                  (const :format "" :unnarrowed) (const :format "" t)
+                  (plist :inline t
+                         :tag "Options"
+                         ;; Give the most common options as checkboxes
+                         :options
+                         (((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))
+                          ((const :format "%v " :empty-lines-after) (const 1))
+                          ((const :format "%v " :clock-in) (const t))
+                          ((const :format "%v " :clock-keep) (const t))
+                          ((const :format "%v " :clock-resume) (const t))
+                          ((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))))))))
+
+(defun org-roam-capture-p ()
+  "Return t if the current capture process is an Org-roam capture.
+This function is to only be called when org-capture-plist is
+valid for the capture (i.e. initialization, and finalization of
+the capture)."
+  (plist-get org-capture-plist :org-roam))
 
 (defun org-roam-capture--get (keyword)
-  "Gets the value for KEYWORD from the `org-roam-capture-template'."
+  "Get the value for KEYWORD from the `org-roam-capture-template'."
   (plist-get (plist-get org-capture-plist :org-roam) keyword))
 
 (defun org-roam-capture--put (&rest stuff)
-  "Puts properties from STUFF into the `org-roam-capture-template'."
+  "Put properties from STUFF into the `org-roam-capture-template'."
   (let ((p (plist-get org-capture-plist :org-roam)))
     (while stuff
-      (setq p (plist-put p
-                         (pop stuff) (pop stuff))))
+      (setq p (plist-put p (pop stuff) (pop stuff))))
     (setq org-capture-plist
           (plist-put org-capture-plist :org-roam p))))
 
-(defun org-roam-capture--in-process-p ()
-  "Return non-nil if a `org-roam-capture' buffer exists."
-  (cl-some (lambda (buffer)
-             (and (eq (buffer-local-value 'major-mode buffer)
-                      'org-mode)
-                  (plist-get (buffer-local-value 'org-capture-current-plist buffer)
-                             :org-roam)))
-           (buffer-list)))
+;; FIXME: Pending upstream patch
+;; https://orgmode.org/list/87h7tv9pkm.fsf@hidden/T/#u
+;;
+;; Org-capture's behaviour right now is that `org-capture-plist' is valid only
+;; during the initialization of the Org-capture buffer. The value of
+;; `org-capture-plist' is saved into buffer-local `org-capture-current-plist'.
+;; However, the value for that particular capture is no longer accessible for
+;; hooks in `org-capture-after-finalize-hook', since the capture buffer has been
+;; cleaned up.
+;;
+;; This advice restores the global `org-capture-plist' during finalization, so
+;; the plist is valid during both initialization and finalization of the
+;; capture.
+(defun org-roam-capture--update-plist (&optional _)
+  "Update global plist from local var."
+  (setq org-capture-plist org-capture-current-plist))
 
-(defun org-roam-capture--fill-template (str &optional info)
-  "Expands the template STR, returning the string.
+(advice-add 'org-capture-finalize :before #'org-roam-capture--update-plist)
+
+(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 finalize
+        ('find-file
+         (when-let ((file-path (org-roam-capture--get :file-path)))
+           (org-roam--find-file file-path)
+           (run-hooks 'org-roam-capture-after-find-file-hook)))
+        ('insert-link
+         (when-let* ((mkr (org-roam-capture--get :insert-at))
+                     (buf (marker-buffer mkr)))
+           (with-current-buffer buf
+             (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 type))
+                 (org-with-point-at mkr
+                   (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)))
+
+(defun org-roam-capture--install-finalize ()
+  "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
+  (when (org-roam-capture-p)
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
+
+(add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize)
+
+(defun org-roam-capture--fill-template (str)
+  "Expand the template STR, returning the string.
 This is an extension of org-capture's template expansion.
 
-First, it expands ${var} occurrences in STR, using the INFO alist.
+First, it expands ${var} occurrences in STR, using `org-roam-capture--info'.
 If there is a ${var} with no matching var in the alist, the value
 of var is prompted for via `completing-read'.
 
@@ -148,23 +368,13 @@ Next, it expands the remaining template string using
 `org-capture-fill-template'."
   (-> str
       (s-format (lambda (key)
-                  (or (s--aget info key)
-                      (completing-read (format "%s: " key ) nil))) nil)
+                  (or (s--aget org-roam-capture--info key)
+                      (when-let ((val (completing-read (format "%s: " key) nil)))
+                        (push (cons key val) org-roam-capture--info)
+                        val))) nil)
       (org-capture-fill-template)))
 
-(defun org-roam-capture--insert-link-h ()
-  "Insert the link into the original buffer, after the capture process is done.
-This is added as a hook to `org-capture-after-finalize-hook'."
-  (when (and (not org-note-abort)
-             (eq (org-roam-capture--get :capture-fn)
-                 'org-roam-insert))
-    (when-let ((region (org-roam-capture--get :region))) ;; Remove previously selected text.
-      (delete-region (car region) (cdr region)))
-    (insert (org-roam--format-link (org-roam-capture--get :file-path)
-                                   (org-roam-capture--get :link-description))))
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--insert-link-h))
-
-(defun org-roam-capture--save-file-maybe-h ()
+(defun org-roam-capture--save-file-maybe ()
   "Save the file conditionally.
 The file is saved if the original value of :no-save is not t and
 `org-note-abort' is not t. It is added to
@@ -178,16 +388,27 @@ The file is saved if the original value of :no-save is not t and
    ((and (not (org-roam-capture--get :orig-no-save))
          (not org-note-abort))
     (with-current-buffer (org-capture-get :buffer)
-      (save-buffer))))
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h))
+      (save-buffer)))))
 
-(defun org-roam-capture--new-file ()
-  "Return the path to the new file during an Org-roam capture.
+(defun org-roam-capture--get-file-path (basename)
+  "Return path for Org-roam file with BASENAME."
+  (let* ((ext (or (car org-roam-file-extensions)
+                  "org"))
+         (file (concat basename "." ext)))
+    (expand-file-name
+     (if org-roam-encrypt-files
+         (concat file ".gpg")
+       file)
+     org-roam-directory)))
+
+(defun org-roam-capture--new-file (&optional allow-existing-file-p)
+  "Return the path to file during an Org-roam capture.
 
 This function reads the file-name attribute of the currently
 active Org-roam template.
 
-If the file path already exists, it throw an error.
+If the file path already exists, and not ALLOW-EXISTING-FILE-P,
+raise a warning.
 
 Else, to insert the header content in the file, `org-capture'
 prepends the `:head' property of the Org-roam capture template.
@@ -196,46 +417,98 @@ To prevent the creation of a new file if the capture process is
 aborted, we do the following:
 
 1. Save the original value of the capture template's :no-save.
-
 2. Set the capture template's :no-save to t.
-
-3. Add a function on `org-capture-after-finalize-hook' that saves
+3. Add a function on `org-capture-before-finalize-hook' that saves
 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
-                          org-roam-capture--info)))
-         (file-path (org-roam--file-path-from-id new-id))
+                          name-templ)))
+         (file-path (org-roam-capture--get-file-path 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)
+    (if (or (file-exists-p file-path)
+            (find-buffer-visiting file-path))
+        (unless allow-existing-file-p
+          (lwarn '(org-roam) :warning
+                 "Attempted to recreate existing file: %s.
+This can happen when your org-roam db is not in sync with your notes.
+Using existing file..." file-path))
       (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
-                       ;; Fixes org-capture-place-plain-text throwing 'invalid search bound'
-                       ;; when both :unnarowed t and "%?" is missing from the template string;
-                       ;; may become unnecessary when the upstream bug is fixed
-                       (if (s-contains-p "%?" roam-template)
-                           roam-template
-                         (concat roam-template "%?"))
-                       :type 'plain
-                       :no-save t))
+      (pcase org-roam-capture--context
+        ('dailies
+         ;; Populate the header of the daily file before capture to prevent it
+         ;; from appearing in the buffer-restriction
+         (save-window-excursion
+           (find-file file-path)
+           (insert (substring (org-capture-fill-template (concat roam-head "*"))
+                              0 -2))
+           (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--expand-template ()
-  "Expand capture template with information from `org-roam-capture--info'."
-  (org-capture-put :template
-                   (s-format (org-capture-get :template)
-                             (lambda (key)
-                               (or (s--aget org-roam-capture--info key)
-                                   (when-let ((v (completing-read (format "%s: " key ) nil)))
-                                     (push (cons key v) org-roam-capture--info)
-                                     v))) nil)))
+(defun org-roam-capture-find-or-create-olp (olp)
+  "Return a marker pointing to the entry at OLP in the current buffer.
+If OLP does not exist, create it. If anything goes wrong, throw
+an error, and if you need to do something based on this error,
+you can catch it with `condition-case'."
+  (let* ((level 1)
+         (lmin 1)
+         (lmax 1)
+         (start (point-min))
+         (end (point-max))
+         found flevel)
+    (unless (derived-mode-p 'org-mode)
+      (error "Buffer %s needs to be in Org mode" (current-buffer)))
+    (org-with-wide-buffer
+     (goto-char start)
+     (dolist (heading olp)
+       (let ((re (format org-complex-heading-regexp-format
+                         (regexp-quote heading)))
+             (cnt 0))
+         (while (re-search-forward re end t)
+           (setq level (- (match-end 1) (match-beginning 1)))
+           (when (and (>= level lmin) (<= level lmax))
+             (setq found (match-beginning 0) flevel level cnt (1+ cnt))))
+         (when (> cnt 1)
+           (error "Heading not unique on level %d: %s" lmax heading))
+         (when (= cnt 0)
+           ;; Create heading if it doesn't exist
+           (goto-char end)
+           (unless (bolp) (newline))
+           (org-insert-heading nil nil t)
+           (unless (= lmax 1) (org-do-demote))
+           (insert heading)
+           (setq end (point))
+           (goto-char start)
+           (while (re-search-forward re end t)
+             (setq level (- (match-end 1) (match-beginning 1)))
+             (when (and (>= level lmin) (<= level lmax))
+               (setq found (match-beginning 0) flevel level cnt (1+ cnt))))))
+       (goto-char found)
+       (setq lmin (1+ flevel) lmax (+ lmin (if org-odd-levels-only 1 0)))
+       (setq start found
+             end (save-excursion (org-end-of-subtree t t))))
+     (point-marker))))
+
+(defun org-roam-capture--get-ref-path (type path)
+  "Get the file path to the ref with TYPE and PATH."
+  (caar (org-roam-db-query
+         [:select [file]
+          :from refs
+          :where (= type $s1)
+          :and (= ref $s2)
+          :limit 1]
+         type path)))
 
 (defun org-roam-capture--get-point ()
   "Return exact point to file for org-capture-template.
@@ -253,30 +526,45 @@ 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
-                     ('capture
-                      (or (cdr (assoc 'file org-roam-capture--info))
-                          (org-roam-capture--new-file)))
-                     ('title
-                      (org-roam-capture--new-file))
-                     ('dailies
-                      (org-capture-put :default-time (cdr (assoc 'time org-roam-capture--info)))
-                      (org-roam-capture--new-file))
-                     ('ref
-                      (let ((completions (org-roam--get-ref-path-completions))
-                            (ref (cdr (assoc 'ref org-roam-capture--info))))
-                        (or (cdr (assoc ref completions))
-                            (org-roam-capture--new-file))))
-                     (_ (error "Invalid org-roam-capture-context")))))
-    (org-roam-capture--expand-template)
-    (org-roam-capture--put :file-path file-path)
+  (let* ((file-path (pcase org-roam-capture--context
+                      ('capture
+                       (or (cdr (assoc 'file org-roam-capture--info))
+                           (org-roam-capture--new-file)))
+                      ('title
+                       (org-roam-capture--new-file))
+                      ('dailies
+                       (org-capture-put :default-time (cdr (assoc 'time org-roam-capture--info)))
+                       (org-roam-capture--new-file 'allow-existing))
+                      ('ref
+                       (if-let ((ref (cdr (assoc 'ref org-roam-capture--info))))
+                           (pcase (org-roam--split-ref ref)
+                             (`(,type . ,path)
+                              (or (org-roam-capture--get-ref-path type path)
+                                  (org-roam-capture--new-file)))
+                             (_ (user-error "%s is not a valid ref" ref)))
+                         (error "Ref not found in `org-roam-capture--info'")))
+                      (_ (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
+                           :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 (org-roam-capture--get :olp)))
+        (condition-case err
+            (when-let ((marker (org-roam-capture-find-or-create-olp 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-max)))))
 
 (defun org-roam-capture--convert-template (template)
   "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax."
@@ -291,59 +579,59 @@ 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))))
     (_ (user-error "Invalid capture template format: %s" template))))
 
-(defun org-roam-capture--find-file-h ()
-  "Opens the newly created template file.
-This is added as a hook to `org-capture-after-finalize-hook'.
-Run the hooks defined in `org-roam-capture-after-find-file-hook'."
-  (unless org-note-abort
-    (when-let ((file-path (org-roam-capture--get :file-path)))
-      (find-file file-path))
-    (run-hooks 'org-roam-capture-after-find-file-hook))
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h))
-
 (defcustom org-roam-capture-after-find-file-hook nil
   "Hook that is run right after an Org-roam capture process is finalized.
 Suitable for moving point."
   :group 'org-roam
   :type 'hook)
 
+(defcustom org-roam-capture-function #'org-capture
+  "Function that is invoked to start the `org-capture' process."
+  :group 'org-roam
+  :type 'function)
+
 (defun org-roam-capture--capture (&optional goto keys)
   "Create a new file, and return the path to the edited file.
 The templates are defined at `org-roam-capture-templates'.  The
 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))
-        org-capture-templates-contexts)
-    (when (= (length org-capture-templates) 1)
+  (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)
+    (when one-template-p
       (setq keys (caar org-capture-templates)))
-    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h)
-    (org-capture goto keys)))
+    (if (or one-template-p
+            (eq org-roam-capture-function 'org-capture))
+        (org-capture goto keys)
+      (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'."
-  (interactive)
-  (when (org-roam-capture--in-process-p)
-    (user-error "Nested Org-roam capture processes not supported"))
+This uses the templates defined at `org-roam-capture-templates'.
+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: "
                                                                 completions))
          (res (cdr (assoc title-with-keys completions)))
          (title (or (plist-get res :title) title-with-keys))
-         (file-path (plist-get res :file-path)))
+         (file-path (plist-get res :path)))
     (let ((org-roam-capture--info (list (cons 'title title)
-                                        (cons 'slug (org-roam--title-to-slug title))
+                                        (cons 'slug (funcall org-roam-title-to-slug-function title))
                                         (cons 'file file-path)))
           (org-roam-capture--context 'capture))
-      (setq org-roam-capture-additional-template-props (list :capture-fn 'org-roam-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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -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
@@ -77,8 +75,16 @@
   "org-roam 1.1.0")
 (define-obsolete-function-alias 'org-roam--capture 'org-roam-capture--capture
   "org-roam 1.1.0")
-(define-obsolete-function-alias 'org-roam-db--maybe-update 'org-roam-db--update-maybe
-  "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
+  "org-roam 1.2.2")
+(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
@@ -95,6 +101,11 @@
   '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")
 
 (provide 'org-roam-compat)
 

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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -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:
@@ -35,49 +37,311 @@
 (require 'org-capture)
 (require 'org-roam-capture)
 (require 'org-roam-macs)
+(require 'f)
 
-(defvar org-roam-dailies-capture-templates
-  '(("d" "daily" plain (function org-roam-capture--get-point)
-     ""
-     :immediate-finish t
-     :file-name "%<%Y-%m-%d>"
-     :head "#+TITLE: %<%Y-%m-%d>"))
-  "Capture templates for daily notes in Org-roam.")
+;;;; Declarations
+(defvar org-roam-mode)
+(defvar org-roam-directory)
+(defvar org-roam-file-extensions)
+(declare-function org-roam--org-file-p        "org-roam")
+(declare-function org-roam--find-file         "org-roam")
+(declare-function org-roam-mode               "org-roam")
 
-;; Declarations
-(declare-function org-roam--file-path-from-id "org-roam")
+;;;; Customizable variables
+(defcustom org-roam-dailies-directory "daily/"
+  "Path to daily-notes."
+  :group 'org-roam
+  :type 'string)
 
-(defun org-roam-dailies--file-for-time (time)
-  "Create and find file for TIME."
-  (let ((org-roam-capture-templates org-roam-dailies-capture-templates)
+(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" "default" entry (function org-roam-capture--get-point)
+     "* %?"
+     :file-name ,(concat org-roam-dailies-directory "%<%Y-%m-%d>")
+     :head "#+title: %<%Y-%m-%d>\n"))
+  "Capture templates for daily-notes in Org-roam."
+  :group 'org-roam
+  ;; Adapted from `org-capture-templates'
+  :type
+  `(repeat
+    (choice :value ("d" "default" plain (function org-roam-capture--get-point)
+                    "%?"
+                    :file-name ,(concat org-roam-dailies-directory
+					"%<%Y-%m-%d>")
+                    :head "#+title: %<%Y-%m-%d>\n"
+                    :unnarrowed t)
+      (list :tag "Multikey description"
+        (string :tag "Keys       ")
+        (string :tag "Description"))
+      (list :tag "Template entry"
+        (string :tag "Keys              ")
+        (string :tag "Description       ")
+        (choice :tag "Type              "
+         (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            \
+Template string   :\n%v")
+          (list :tag "File"
+            (const :format "" file)
+            (file :tag "Template file     "))
+          (list :tag "Function"
+            (const :format "" function)
+            (function :tag "Template function ")))
+        (const :format "File name format  :" :file-name)
+        (string :format " %v" :value ,(concat org-roam-dailies-directory
+					      "%<%Y-%m-%d>"))
+        (const :format "Header format     :" :head)
+        (string :format " %v" :value "#+title: ${title}\n")
+        (plist :inline t
+               :tag "Options"
+          ;; Give the most common options as checkboxes
+               :options
+               (((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))
+                ((const :format "%v " :empty-lines-after) (const 1))
+                ((const :format "%v " :clock-in) (const t))
+                ((const :format "%v " :clock-keep) (const t))
+                ((const :format "%v " :clock-resume) (const t))
+                ((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))))))))
+
+;;;; Utilities
+(defun org-roam-dailies-directory--get-absolute-path ()
+  "Get absolute path to `org-roam-dailies-directory'."
+  (expand-file-name org-roam-dailies-directory org-roam-directory))
+
+(defun org-roam-dailies-find-directory ()
+  "Find and open `org-roam-dailies-directory'."
+  (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 (expand-file-name 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))
-    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h)
-    (org-roam--with-template-error 'org-roam-dailies-capture-templates
-      (org-roam-capture--capture))))
+    (org-roam-capture--capture (when goto '(4)))))
 
-(defun org-roam-dailies-today ()
-  "Create and find the daily note for today."
+;;;; Commands
+;;; 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)))
+
+(defun org-roam-dailies-find-today ()
+  "Find the daily-note for today, creating it if necessary."
   (interactive)
-  (org-roam-dailies--file-for-time (current-time)))
+  (org-roam-dailies-capture-today t))
 
-(defun org-roam-dailies-tomorrow (n)
-  "Create and find the daily note for tomorrow.
-With numeric argument N, use N days in the future."
+;;; Tomorrow
+(defun org-roam-dailies-capture-tomorrow (n &optional goto)
+  "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")
-  (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
 
-(defun org-roam-dailies-yesterday (n)
-  "Create and find the file for yesterday.
-With numeric argument N, use N days in the past."
+(defun org-roam-dailies-find-tomorrow (n)
+  "Find the daily-note for tomorrow, creating it if necessary.
+
+With numeric argument N, use the daily-note N days in the
+future."
   (interactive "p")
-  (org-roam-dailies-tomorrow (- n)))
+  (org-roam-dailies-capture-tomorrow n t))
 
-(defun org-roam-dailies-date ()
-  "Create the file for any date using the calendar interface."
+;;; Yesterday
+(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))))
+
+(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--file-for-time time)))
+  (org-roam-dailies-capture-date t prefer-future))
+
+;;; 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))
+	(regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
+    (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 regexp))
+            extra-files)))
+
+(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")
+  (unless (org-roam-dailies--daily-note-p)
+    (user-error "Not in a daily-note"))
+  (setq n (or n 1))
+  (let* ((dailies (org-roam-dailies--list-files))
+         (position
+          (cl-position-if (lambda (candidate)
+                            (string= (buffer-file-name (buffer-base-buffer)) candidate))
+                          dailies))
+         note)
+      (unless position
+        (user-error "Can't find current note file - have you saved it yet?"))
+      (pcase n
+        ((pred (natnump))
+         (when (eq position (- (length dailies) 1))
+           (user-error "Already at newest note")))
+        ((pred (integerp))
+         (when (eq position 0)
+             (user-error "Already at oldest note"))))
+      (setq note (nth (+ position n) dailies))
+      (find-file note)
+      (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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -33,23 +33,35 @@
 ;;;; Library Requires
 (eval-when-compile (require 'subr-x))
 (require 'emacsql)
-(require 'emacsql-sqlite)
-(require 'org-roam-macs)
+(require 'emacsql-sqlite3)
+(require 'seq)
+
+(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-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")
+(declare-function org-roam--file-name-extension            "org-roam")
 (declare-function org-roam-buffer--update-maybe            "org-roam-buffer")
 
 ;;;; Options
-(defcustom org-roam-db-location nil
-  "Location of the Org-roam database.
+(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.
 
 It is the user's responsibility to set this correctly, especially
@@ -57,25 +69,53 @@ when used with multiple Org-roam instances."
   :type 'string
   :group 'org-roam)
 
-(defconst org-roam-db--version 5)
-(defconst org-roam-db--sqlite-available-p
-  (with-demoted-errors "Org-roam initialization: %S"
-    (emacsql-sqlite-ensure-binary)
-    t))
+(defcustom org-roam-db-gc-threshold gc-cons-threshold
+  "The value to temporarily set the `gc-cons-threshold' threshold to.
+During large, heavy operations like `org-roam-db-build-cache',
+many GC operations happen because of the large number of
+temporary structures generated (e.g. parsed ASTs). Temporarily
+increasing `gc-cons-threshold' will help reduce the number of GC
+operations, at the cost of temporary memory usage.
+
+This defaults to the original value of `gc-cons-threshold', but
+tweaking this number may lead to better overall performance. For
+example, to reduce the number of GCs, one may set it to a large
+value like `most-positive-fixnum'."
+  :type 'int
+  :group 'org-roam)
+
+(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 '(choice (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."
-  (interactive "P")
-  (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 ()
@@ -84,18 +124,17 @@ 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))
-           (init-db (not (file-exists-p db-file))))
-      (make-directory (file-name-directory db-file) t)
-      (let ((conn (emacsql-sqlite db-file)))
+    (let ((init-db (not (file-exists-p org-roam-db-location))))
+      (make-directory (file-name-directory org-roam-db-location) t)
+      (let ((conn (emacsql-sqlite3 org-roam-db-location)))
         (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
           (org-roam-db--init conn))
         (let* ((version (caar (emacsql conn "PRAGMA user_version")))
-               (version (org-roam-db--update-maybe conn version)))
+               (version (org-roam-db--upgrade-maybe conn version)))
           (cond
            ((> version org-roam-db--version)
             (emacsql-close conn)
@@ -123,9 +162,14 @@ SQL can be either the emacsql vector representation, or a string."
       (hash :not-null)
       (meta :not-null)])
 
+    (ids
+     [(id :unique :primary-key)
+      (file :not-null)
+      (level :not-null)])
+
     (links
-     [(from :not-null)
-      (to :not-null)
+     [(source :not-null)
+      (dest :not-null)
       (type :not-null)
       (properties :not-null)])
 
@@ -135,7 +179,7 @@ SQL can be either the emacsql vector representation, or a string."
 
     (titles
      [(file :not-null)
-      titles])
+      title])
 
     (refs
      [(ref :unique :not-null)
@@ -149,7 +193,7 @@ SQL can be either the emacsql vector representation, or a string."
       (emacsql db [:create-table $i1 $S2] table schema))
     (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
 
-(defun org-roam-db--update-maybe (db version)
+(defun org-roam-db--upgrade-maybe (db version)
   "Upgrades the database schema for DB, if VERSION is old."
   (emacsql-with-transaction db
     'ignore
@@ -174,11 +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 cache has been initialized."
-  (and (file-exists-p (org-roam-db--get))
+  "Whether the Org-roam cache has been initialized."
+  (and (file-exists-p org-roam-db-location)
        (> (caar (org-roam-db-query [:select (funcall count) :from titles]))
           0)))
 
@@ -188,61 +248,159 @@ the current `org-roam-directory'."
     (error "[Org-roam] your cache isn't built yet! Please run org-roam-db-build-cache")))
 
 ;;;;; Clearing
-(defun org-roam-db--clear ()
-  "Clears all entries in the caches."
+(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.
+(defun org-roam-db--clear-file (&optional file)
+  "Remove any related links to the FILE.
 This is equivalent to removing the node from the graph."
-  (let ((file (file-truename (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)]
-                         file))))
+  (setq file (or file (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) 'source 'file) $s1)]
+                       file)))
 
-;;;;; Insertion
-(defun org-roam-db--insert-meta (file hash meta)
-  "Insert HASH and META for a FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into files
-    :values $v1]
-   (list (vector file hash meta))))
-
-(defun org-roam-db--insert-links (links)
-  "Insert LINKS into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into links
-    :values $v1]
-   links))
-
-(defun org-roam-db--insert-titles (file titles)
-  "Insert TITLES for a FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into titles
-    :values $v1]
-   (list (vector file titles))))
-
-(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."
-  (let ((key (cdr ref))
-        (type (car ref)))
+;;;;; Inserting
+(defun org-roam-db--insert-meta (&optional update-p)
+  "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 refs :values $v1]
-     (list (vector key file type)))))
+     [:insert :into files
+      :values $v1]
+     (list (vector file hash (list :atime atime :mtime mtime))))))
+
+(defun org-roam-db--insert-titles (&optional update-p)
+  "Update the titles of the current buffer into the cache.
+If UPDATE-P is non-nil, first remove titles for the file in the database.
+Returns the number of rows inserted."
+  (let* ((file (or org-roam-file-name (buffer-file-name)))
+         (titles (or (org-roam--extract-titles)
+                     (list (org-roam--path-to-slug file))))
+         (rows (mapcar (lambda (title)
+                         (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]
+        rows)
+    (length rows)))
+
+(defun org-roam-db--insert-refs (&optional update-p)
+  "Update the refs of the current buffer into the cache.
+If UPDATE-P is non-nil, first remove the ref for the file in the database."
+  (let ((file (or org-roam-file-name (buffer-file-name)))
+        (count 0))
+    (when update-p
+      (org-roam-db-query [:delete :from refs
+                          :where (= file $s1)]
+                         file))
+    (when-let ((refs (org-roam--extract-refs)))
+      (dolist (ref refs)
+        (let ((key (cdr ref))
+              (type (car ref)))
+          (condition-case nil
+              (progn
+                (org-roam-db-query
+                 [:insert :into refs :values $v1]
+                 (list (vector key file type)))
+                (cl-incf count))
+            (error
+             (lwarn '(org-roam) :error
+                    (format "Duplicate ref %s in:\n\nA: %s\nB: %s\n\nskipping..."
+                            key
+                            file
+                            (caar (org-roam-db-query
+                                   [:select file :from refs
+                                    :where (= ref $v1)]
+                                   (vector key))))))))))
+    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-has-file-p (file)
+  "Return t if FILE is in the database, nil otherwise."
+  (> (caar (org-roam-db-query [:select (funcall count) :from files
+                              :where (= file $s1)]
+                              file))
+     0))
+
 (defun org-roam-db--get-current-files ()
   "Return a hash-table of file to the hash of its file contents."
   (let* ((current-files (org-roam-db-query [:select * :from files]))
@@ -251,26 +409,36 @@ This is equivalent to removing the node from the graph."
       (puthash (car row) (cadr row) ht))
     ht))
 
-(defun org-roam-db--get-titles (file)
-  "Return the titles of FILE from the cache."
-  (caar (org-roam-db-query [:select [titles] :from titles
-                            :where (= file $s1)]
-                           file
-                           :limit 1)))
+(defun org-roam-db--get-title (file)
+  "Return the main title of FILE from the cache."
+  (caar (org-roam-db-query [:select [title] :from titles
+                            :where (= file $s1)
+                            :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 roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                     (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 roamlinks UNION
-                      SELECT \"to\", \"from\" FROM roamlinks UNION
-                      SELECT \"file\", \"from\" FROM citelinks UNION
-                      SELECT \"from\", \"file\" FROM citelinks),
+                      SELECT \"source\", \"dest\" FROM filelinks UNION
+                      SELECT \"dest\", \"source\" FROM filelinks UNION
+                      SELECT \"file\", \"source\" FROM citelinks UNION
+                      SELECT \"dest\", \"file\" FROM citelinks),
                    connected_component(file) AS
                      (SELECT link FROM links_of WHERE file = $s1
                       UNION
@@ -285,14 +453,14 @@ 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 roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                     (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 roamlinks UNION
-                      SELECT \"to\", \"from\" FROM roamlinks UNION
-                      SELECT \"file\", \"from\" FROM citelinks UNION
-                      SELECT \"from\", \"file\" FROM citelinks),
+                      SELECT \"source\", \"dest\" FROM filelinks UNION
+                      SELECT \"dest\", \"source\" FROM filelinks UNION
+                      SELECT \"file\", \"source\" FROM citelinks UNION
+                      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'.
@@ -312,146 +480,153 @@ connections, nil is returned."
          (files (mapcar 'car-safe (emacsql (org-roam-db) query file max-distance))))
     files))
 
+(defun org-roam-db--file-hash (&optional file-path)
+  "Compute the hash of FILE-PATH, a file or current buffer."
+  (if file-path
+      (with-temp-buffer
+        (set-buffer-multibyte nil)
+        (insert-file-contents-literally file-path)
+        (secure-hash 'sha1 (current-buffer)))
+    (org-with-wide-buffer
+     (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 (secure-hash 'sha1 (current-buffer))))
-    (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)))
-         (title (org-roam--extract-titles)))
-    (org-roam-db-query [:delete :from titles
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db--insert-titles file title)))
-
-(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)
-    (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-cache-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-file (&optional file-path)
-  "Update Org-roam cache for FILE-PATH."
-  (when (org-roam--org-roam-file-p file-path)
-    (let ((buf (or (and file-path
-                        (find-file-noselect file-path t))
-                   (current-buffer))))
+  "Update Org-roam cache for FILE-PATH.
+If the file does not exist anymore, remove it from the cache.
+If the file exists, update the cache with information."
+  (setq file-path (or file-path
+                      (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
-          (org-roam-db--update-meta)
-          (org-roam-db--update-tags)
-          (org-roam-db--update-titles)
-          (org-roam-db--update-refs)
-          (org-roam-db--update-cache-links)
-          (org-roam-buffer--update-maybe :redisplay t))))))
+        (save-buffer)))
+    (org-roam--with-temp-buffer file-path
+      (emacsql-with-transaction (org-roam-db)
+        (org-roam-db--insert-meta 'update)
+        (org-roam-db--insert-tags 'update)
+        (org-roam-db--insert-titles 'update)
+        (org-roam-db--insert-refs 'update)
+        (when org-roam-enable-headline-linking
+          (org-roam-db--insert-ids 'update))
+        (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* ((org-roam-files (org-roam--list-all-files))
+  (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))
-         all-files all-links all-titles all-refs all-tags)
+         (count-plist nil)
+         (deleted-count 0)
+         (modified-files nil))
     (dolist (file org-roam-files)
+      (let ((contents-hash (org-roam-db--file-hash file)))
+        (unless (string= (gethash file current-files)
+                       contents-hash)
+          (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)))
+    (setq count-plist (org-roam-db--update-files modified-files))
+    (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) (plist-get count-plist :error-count))
+                      (plist-get count-plist :modified-count)
+                      (plist-get count-plist :id-count)
+                      (plist-get count-plist :link-count)
+                      (plist-get count-plist :tag-count)
+                      (plist-get count-plist :title-count)
+                      (plist-get count-plist :ref-count)
+                      deleted-count)))
+
+(defun org-roam-db--get-file-hash-from-db (&optional file-path)
+  "Get hash from Org-roam database for FILE-PATH."
+  (setq file-path (or file-path
+                      (buffer-file-name (buffer-base-buffer))))
+  (caar (org-roam-db-query [:select hash :from files
+                              :where (= file $s1)] file-path)))
+
+(defun org-roam-db-update-file (file-path)
+  "Update Org-roam cache for FILE-PATH.
+If the file does not exist anymore, remove it from the cache.
+If the file exists, update the cache with information."
+  (let ((content-hash (org-roam-db--file-hash file-path))
+        (db-hash  (org-roam-db--get-file-hash-from-db file-path)))
+    (unless (string= content-hash db-hash)
+      (org-roam-db--update-files (list (cons file-path content-hash)))
+      (org-roam-message "Updated: %s" file-path))))
+
+(defun org-roam-db--update-files (modified-files)
+  "Update Org-roam cache for a list of MODIFIED-FILES.
+FILES is a list of (file . hash) pairs."
+  (let* ((gc-cons-threshold org-roam-db-gc-threshold)
+         (org-agenda-files nil)
+         (error-count 0)
+         (id-count 0)
+         (link-count 0)
+         (tag-count 0)
+         (title-count 0)
+         (ref-count 0)
+         (modified-count 0))
+    (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)))
-        (org-roam--with-temp-buffer
-          (insert-file-contents file)
-          (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
-            (unless (string= (gethash file current-files)
-                             contents-hash)
-              (org-roam-db--clear-file file)
-              (push (vector file contents-hash (list :atime atime :mtime mtime))
-                    all-files)
-              (when-let (links (org-roam--extract-links file))
-                (push links all-links))
-              (when-let (tags (org-roam--extract-tags file))
-                (push (vector file tags) all-tags))
-              (let ((titles (org-roam--extract-titles)))
-                (push (vector file titles)
-                      all-titles))
-              (when-let* ((ref (org-roam--extract-ref))
-                          (type (car ref))
-                          (key (cdr ref)))
-                (setq all-refs (cons (vector key file type) all-refs))))
-            (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))
-    (when all-files
-      (org-roam-db-query
-       [:insert :into files
-        :values $v1]
-       all-files))
-    (when all-links
-      (org-roam-db-query
-       [:insert :into links
-        :values $v1]
-       all-links))
-    (when all-titles
-      (org-roam-db-query
-       [:insert :into titles
-        :values $v1]
-       all-titles))
-    (when all-tags
-      (org-roam-db-query
-       [:insert :into tags
-        :values $v1]
-       all-tags))
-    (when all-refs
-      (org-roam-db-query
-       [:insert :into refs
-        :values $v1]
-       all-refs))
-    (let ((stats (list :files (length all-files)
-                       :links (length all-links)
-                       :tags (length all-tags)
-                       :titles (length all-titles)
-                       :refs (length all-refs)
-                       :deleted (length (hash-table-keys current-files)))))
-      (org-roam-message "files: %s, links: %s, tags: %s, titles: %s, refs: %s, deleted: %s"
-                        (plist-get stats :files)
-                        (plist-get stats :links)
-                        (plist-get stats :tags)
-                        (plist-get stats :titles)
-                        (plist-get stats :refs)
-                        (plist-get stats :deleted))
-      stats)))
+        (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)))
+              (when org-roam-enable-headline-linking
+                (setq id-count (+ id-count (org-roam-db--insert-ids)))))
+          (file-error
+           (setq error-count (1+ error-count))
+           (org-roam-db--clear-file file)
+           (lwarn '(org-roam) :warning
+                  "Skipping unreadable file while building cache: %s" file)))))
+
+    ;; Process titles, tags, links and ref links of file
+    (pcase-dolist (`(,file . _) modified-files)
+      (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 error-count (1+ error-count))
+         (org-roam-db--clear-file file)
+         (lwarn '(org-roam) :warning
+                "Skipping unreadable file while building cache: %s" file))))
+    (list :error-count error-count :modified-count modified-count :id-count id-count :title-count title-count :tag-count tag-count :link-count link-count :ref-count ref-count)))
+
+(defun org-roam-db-update ()
+  "Update the database."
+  (pcase org-roam-db-update-method
+    ('immediate
+     (org-roam-db-update-file (buffer-file-name (buffer-base-buffer))))
+    ('idle-timer
+     (org-roam-db-mark-dirty))
+    (_
+     (user-error "Invalid `org-roam-db-update-method'"))))
 
 (provide 'org-roam-db)
 

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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -33,8 +33,14 @@
 ;;
 ;;; Code:
 (require 'emacsql)
-(emacsql-fix-vector-indentation)
-(setq-local sentence-end-double-space nil)
-(provide 'org-roam-dev)
 
+;;;###autoload
+(define-minor-mode org-roam-dev-mode
+  "Minor mode for setting the dev environment of Org-roam."
+  :lighter " ORD"
+  (when org-roam-dev-mode
+    (emacsql-fix-vector-indentation)
+    (setq-local sentence-end-double-space nil)))
+
+(provide 'org-roam-dev)
 ;;; org-roam-dev.el ends here

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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -44,15 +44,28 @@
 ;; Library Requires
 (require 'cl-lib)
 (require 'org)
-(require 'org-roam-macs)
 (require 'org-element)
+(require 's)
+(require 'dash)
+(require 'org-roam-macs)
 
 (declare-function org-roam-insert "org-roam")
 (declare-function org-roam--get-roam-buffers "org-roam")
 (declare-function org-roam--list-all-files "org-roam")
 (declare-function org-roam--org-roam-file-p "org-roam")
+(declare-function org-roam-mode "org-roam")
 
 (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)
@@ -66,7 +79,78 @@
     :description "Fix broken links."
     :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
                ("r" . ("Replace link" . org-roam-doctor--replace-link))
-               ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))))
+               ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-roam-props
+    :description "Check #+roam_* properties.")
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-tags
+    :description "Check #+roam_tags.")
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-alias
+    :description "Check #+roam_alias.")))
+
+(defconst org-roam-doctor--supported-roam-properties
+  '("roam_tags" "roam_alias" "roam_key")
+  "List of supported Org-roam properties.")
+
+(defun org-roam-doctor-check-roam-props (ast)
+  "Checker for detecting invalid #+roam_* properties.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (let ((key (org-element-property :key kw)))
+          (when (and (string-prefix-p "ROAM_" key t)
+                     (not (member (downcase key) org-roam-doctor--supported-roam-properties)))
+            (push
+             `(,(org-element-property :begin kw)
+               ,(concat "Possible mispelled key: "
+                        (prin1-to-string key)
+                        "\nOrg-roam supports the following keys: "
+                        (s-join ", " org-roam-doctor--supported-roam-properties)))
+             reports)))))
+    reports))
+
+(defun org-roam-doctor-check-tags (ast)
+  "Checker for detecting invalid #+roam_tags.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (when (string-collate-equalp (org-element-property :key kw) "roam_tags" nil t)
+          (let ((tags (org-element-property :value kw)))
+            (condition-case nil
+                (split-string-and-unquote tags)
+              (error
+               (push
+                `(,(org-element-property :begin kw)
+                  ,(concat "Unable to parse tags: "
+                           tags
+                           (when (s-contains? "," tags)
+                             "\nCheck that your tags are not comma-separated.")))
+                reports)))))))
+    reports))
+
+(defun org-roam-doctor-check-alias (ast)
+  "Checker for detecting invalid #+roam_alias.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (when (string-collate-equalp (org-element-property :key kw) "roam_alias" nil t)
+          (let ((aliases (org-element-property :value kw)))
+            (condition-case nil
+              (split-string-and-unquote aliases)
+              (error
+               (push
+                `(,(org-element-property :begin kw)
+                  ,(concat "Unable to parse aliases: "
+                           aliases
+                           (when (s-contains? "," aliases)
+                             "\nCheck that your aliases are not comma-separated.")))
+                reports)))))))
+    reports))
 
 (defun org-roam-doctor-broken-links (ast)
   "Checker for detecting broken links.
@@ -207,6 +291,7 @@ CHECKER is a org-roam-doctor checker instance."
   "Perform a check on the current buffer to ensure cleanliness.
 If CHECKALL, run the check for all Org-roam files."
   (interactive "P")
+  (unless org-roam-mode (org-roam-mode))
   (let ((files (if checkall
                   (org-roam--list-all-files)
                 (unless (org-roam--org-roam-file-p)
@@ -217,7 +302,8 @@ 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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -32,13 +32,16 @@
 ;;; 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
 (defvar org-roam-directory)
+(defvar org-roam-mode)
 (declare-function org-roam--org-roam-file-p  "org-roam")
 (declare-function org-roam--path-to-slug     "org-roam")
+(declare-function org-roam-mode              "org-roam")
 
 ;;;; Options
 (defcustom org-roam-graph-viewer (executable-find "firefox")
@@ -163,19 +166,19 @@ The Org-roam database titles table is read, to obtain the list of titles.
 The links table is then read to obtain all directed links, and formatted
 into a digraph."
   (org-roam-db--ensure-built)
-  (org-roam--with-temp-buffer
+  (org-roam--with-temp-buffer nil
     (let* ((nodes (org-roam-db-query node-query))
            (edges-query
             `[:with selected :as [:select [file] :from ,node-query]
-              :select :distinct [to from] :from links
-              :where (and (in to selected) (in from selected))])
+              :select :distinct [dest source] :from links
+              :where (and (in dest selected) (in source selected))])
            (edges-cites-query
             `[:with selected :as [:select [file] :from ,node-query]
-              :select :distinct [file from]
-              :from links :inner :join refs :on (and (= links:to refs:ref)
+              :select :distinct [file source]
+              :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")
@@ -190,14 +193,16 @@ into a digraph."
                                    ","))))
       (dolist (node nodes)
         (let* ((file (xml-escape-string (car node)))
-               (title (or (caadr node)
+               (title (or (cadr node)
                           (org-roam--path-to-slug file)))
                (shortened-title (pcase org-roam-graph-shorten-titles
                                   (`truncate (s-truncate org-roam-graph-max-title-length title))
                                   (`wrap (s-word-wrap org-roam-graph-max-title-length title))
                                   (_ title)))
+               (shortened-title (org-roam-string-quote shortened-title))
+               (title (org-roam-string-quote title))
                (node-properties
-                `(("label"   . ,(s-replace "\"" "\\\"" shortened-title))
+                `(("label"   . ,shortened-title)
                   ("URL"     . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
                   ("tooltip" . ,(xml-escape-string title)))))
           (insert
@@ -217,24 +222,32 @@ into a digraph."
       (insert "}")
       (buffer-string))))
 
-(defun org-roam-graph--build (&optional node-query)
-  "Generate a graph showing the relations between nodes in NODE-QUERY."
-  (let ((name org-roam-graph-executable))
-    (unless (stringp name)
-      (user-error "`org-roam-graph-executable' is not a string"))
-    (unless (executable-find org-roam-graph-executable)
-      (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
-                          "Please adjust `org-roam-graph-executable'")
-                  name))
-    (let* ((node-query (or node-query
-                           `[:select [file titles]
-                             :from titles
-                             ,@(org-roam-graph--expand-matcher 'file t)]))
-           (graph (org-roam-graph--dot node-query))
-           (temp-dot (make-temp-file "graph." nil ".dot" graph))
-           (temp-graph (make-temp-file "graph." nil ".svg")))
-      (call-process name nil 0 nil temp-dot "-Tsvg" "-o" temp-graph)
-      temp-graph)))
+(defun org-roam-graph--build (&optional node-query callback)
+  "Generate a graph showing the relations between nodes in NODE-QUERY.
+Execute CALLBACK when process exits successfully.
+CALLBACK is passed the graph file as its sole argument."
+  (unless (stringp org-roam-graph-executable)
+    (user-error "`org-roam-graph-executable' is not a string"))
+  (unless (executable-find org-roam-graph-executable)
+    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
+                        "Please adjust `org-roam-graph-executable'")
+                org-roam-graph-executable))
+  (let* ((node-query (or node-query
+                         `[:select [file title] :from titles
+                           ,@(org-roam-graph--expand-matcher 'file t)
+                           :group :by file]))
+         (graph      (org-roam-graph--dot node-query))
+         (temp-dot   (make-temp-file "graph." nil ".dot" graph))
+         (temp-graph (make-temp-file "graph." nil ".svg")))
+    (org-roam-message "building graph")
+    (make-process
+     :name "*org-roam-graph--build-process*"
+     :buffer "*org-roam-graph--build-process*"
+     :command `(,org-roam-graph-executable ,temp-dot "-Tsvg" "-o" ,temp-graph)
+     :sentinel (when callback
+                 (lambda (process _event)
+                   (when (= 0 (process-exit-status process))
+                     (funcall callback temp-graph)))))))
 
 (defun org-roam-graph--open (file)
   "Open FILE using `org-roam-graph-viewer' with `view-file' as a fallback."
@@ -249,18 +262,19 @@ into a digraph."
     ('nil (view-file file))
     (_ (signal 'wrong-type-argument `((functionp stringp null) ,org-roam-graph-viewer)))))
 
-(defun org-roam-graph--build-connected-component (file &optional max-distance)
+(defun org-roam-graph--build-connected-component (file &optional max-distance callback)
   "Build a graph of nodes connected to FILE.
-If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
-  (let* ((file (file-truename file))
+If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps.
+CALLBACK is passed to `org-roam-graph--build'."
+  (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))
                     (list file)))
-         (query `[:select [file titles]
+         (query `[:select [file title]
                   :from titles
                   :where (in file [,@files])]))
-    (org-roam-graph--build query)))
+    (org-roam-graph--build query callback)))
 
 ;;;; Commands
 ;;;###autoload
@@ -275,6 +289,7 @@ ARG may be any of the following values:
   - `\\[universal-argument]' -   build the graph for FILE.
   - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
   (interactive "P")
+  (unless org-roam-mode (org-roam-mode))
   (let ((file (or file (buffer-file-name (buffer-base-buffer)))))
     (unless (or (not arg) (equal arg '(16)))
       (unless file
@@ -282,11 +297,9 @@ ARG may be any of the following values:
       (unless (org-roam--org-roam-file-p file)
         (user-error "\"%s\" is not an org-roam file" file)))
     (pcase arg
-      ('nil            (org-roam-graph--open (org-roam-graph--build node-query)))
-      ('(4)            (org-roam-graph--open (org-roam-graph--build-connected-component file)))
-      ((pred integerp) (let ((graph (org-roam-graph--build-connected-component file (abs arg))))
-                         (when (>= arg 0)
-                           (org-roam-graph--open graph))))
+      ('nil            (org-roam-graph--build node-query #'org-roam-graph--open))
+      ('(4)            (org-roam-graph--build-connected-component file nil #'org-roam-graph--open))
+      ((pred integerp) (org-roam-graph--build-connected-component file (abs arg) (when (>= arg 0) #'org-roam-graph--open)))
       ('(16)           (org-roam-graph--build node-query))
       ('-              (org-roam-graph--build-connected-component file))
       (_ (user-error "Unrecognized ARG: %s" arg)))))

org-roam-link.el

@@ -0,0 +1,324 @@
+;;; 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 in Org-roam link.
+This function is called by Org when following links of the type
+`roam'. While the path is passed, assume that the cursor is on
+the link."
+  (pcase-let ((`(,link-type ,loc ,desc ,mkr) (org-roam-link--get-location)))
+    (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."
+  (org-roam-with-file file (when with-marker 'keep)
+    (let* ((outline-level-fn outline-level)
+           (path-separator "/")
+           (stack-level 0)
+           stack cands name level marker)
+      (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 in FILE.
+If FILE is nil, get ID from current buffer.
+If there is no corresponding headline, return nil."
+  (save-excursion
+    (org-roam-with-file file 'keep
+      (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 ()
+  "Return the location of the Org-roam fuzzy link at point.
+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.
+
+desc is either the the description of the link under point, or
+the target of LINK (title or heading content)."
+  (let ((context (org-element-context))
+        mkr link-type desc loc)
+    (pcase (org-element-lineage context '(link) t)
+      (`nil (error "Not at an Org link"))
+      (link
+       (if (not (string-equal "roam" (org-element-property :type link)))
+           (error "Not at Org-roam link")
+         (setq desc (and (org-element-property :contents-begin link)
+                         (org-element-property :contents-end link)
+                         (buffer-substring-no-properties
+                          (org-element-property :contents-begin link)
+                          (org-element-property :contents-end link))))
+         (pcase-let ((`(,type ,title ,headline _) (org-roam-link--split-path
+                                                   (org-element-property :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)
+                     (progn
+                       (setq mkr marker
+                             loc target-id
+                             desc (or desc headline)
+                             link-type "id")))
+                    (_ (org-roam-message "Cannot find matching id"))))))
+             ('title
+              (setq loc (org-roam-link--get-file-from-title title)
+                    link-type "file"
+                    desc (or desc title)))
+             ('headline
+              (setq mkr (org-roam-link--get-id-from-headline headline))
+              (pcase mkr
+                (`(,marker . ,target-id)
+                 (setq mkr marker
+                       loc target-id
+                       link-type "id"
+                       desc (or desc headline)))
+                (_ (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)
+      (condition-case nil
+          (pcase-let ((`(,link-type ,loc ,desc _) (org-roam-link--get-location)))
+            (when (and link-type loc)
+              (org-roam-link--replace-link link-type loc desc)))
+        (error nil)))))
+
+(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 "*")
+                                (org-link-escape 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: 1.1.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; 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.
 
@@ -33,37 +33,98 @@
 ;;
 ;;; Code:
 ;;;; Library Requires
+(require 'dash)
+(require 's)
 
 (defvar org-roam-verbose)
 
-(defmacro org-roam--with-temp-buffer (&rest body)
+;; 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-file (file keep-buf-p &rest body)
+  "Execute BODY within FILE.
+If FILE is nil, execute BODY in the current buffer.
+Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
+  (declare (indent 2) (debug t))
+  `(let* (new-buf
+          (buf (or (and (not ,file)
+                        (current-buffer)) ;If FILE is nil, use current buffer
+                   (find-buffer-visiting ,file) ; If FILE is already visited, find buffer
+                   (progn
+                     (setq new-buf t)
+                     (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
+          res)
+     (with-current-buffer buf
+       (setq res (progn ,@body))
+       (unless (and new-buf (not ,keep-buf-p))
+         (save-buffer)))
+     (if (and new-buf (not ,keep-buf-p))
+       (when (find-buffer-visiting ,file)
+         (kill-buffer (find-buffer-visiting ,file))))
+     res))
+
+(defmacro org-roam--with-temp-buffer (file &rest body)
   "Execute BODY within a temp buffer.
-Like `with-temp-buffer', but propagates `org-roam-directory'."
-  (declare (indent 0) (debug t))
+Like `with-temp-buffer', but propagates `org-roam-directory'.
+If FILE, set `org-roam-temp-file-name' to file and insert its contents."
+  (declare (indent 1) (debug t))
   (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
     `(let ((,current-org-roam-directory org-roam-directory))
        (with-temp-buffer
-         (let ((org-roam-directory ,current-org-roam-directory))
+         (let ((org-roam-directory ,current-org-roam-directory)
+               (org-mode-hook nil)
+               (org-inhibit-startup t))
+           (org-mode)
+           (when ,file
+             (insert-file-contents ,file)
+             (setq-local org-roam-file-name ,file)
+             (setq-local default-directory (file-name-directory ,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
     (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
 
+(defun org-roam-string-quote (str)
+  "Quote STR."
+  (->> str
+       (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: 1.1.1
+;; 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))
@@ -56,14 +62,28 @@ It opens or creates a note with the given ref.
     (unless (assoc 'ref decoded-alist)
       (error "No ref key provided"))
     (when-let ((title (cdr (assoc 'title decoded-alist))))
-      (push (cons 'slug (org-roam--title-to-slug 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 org-link-plain-re 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)
+           (org-capture-link-is-already-stored t)
            (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)
 
@@ -78,7 +98,7 @@ It should contain the FILE key, pointing to the path of the file to open.
 org-protocol://roam-file?file=/path/to/file.org"
   (when-let ((file (plist-get info :file)))
     (raise-frame)
-    (find-file file))
+    (org-roam--find-file file))
   nil)
 
 (push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)

tests/roam-files/alias.org

@@ -1,2 +1,2 @@
-#+ROAM_ALIAS: "a1" "a 2"
-#+TITLE: t1
+#+roam_alias: "a1" "a 2"
+#+title: t1

tests/roam-files/bar.org

@@ -1,3 +1,3 @@
-#+TITLE: Bar
+#+title: Bar
 
 This is file bar. Bar links to [[file:nested/bar.org][Nested Bar]].

tests/roam-files/base.org

@@ -1 +1 @@
-#+TITLE: Base
+#+title: Base

tests/roam-files/cite_ref.org

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

tests/roam-files/foo.org

@@ -1,4 +1,4 @@
-#+TITLE: Foo
+#+title: Foo
 
 This is the foo file. It contains a link to [[file:bar.org][Bar]].
 

tests/roam-files/headlines/headline.org

@@ -0,0 +1,14 @@
+#+TITLE: Headline
+
+* Headline 1
+:PROPERTIES:
+:ID:       e84d0630-efad-4017-9059-5ef917908823
+:END:
+
+* No headline here
+Oops.
+
+* Headline 2
+:PROPERTIES:
+:ID:       801b58eb-97e2-435f-a33e-ff59a2f0c213
+:END:

tests/roam-files/multiple-refs.org

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

tests/roam-files/nested/bar.org

@@ -1,3 +1,3 @@
-#+TITLE: Nested Bar
+#+title: Nested Bar
 
 This file is nested, 1 level deeper. It links to both [[file:../foo.org][Foo]] and [[file:foo.org][Nested Foo]].

tests/roam-files/nested/deeply/deeply_nested_file.org

@@ -1 +1 @@
-#+TITLE: Deeply Nested File
+#+title: Deeply Nested File

tests/roam-files/nested/foo.org

@@ -1,3 +1,3 @@
-#+TITLE: Nested Foo
+#+title: Nested Foo
 
 This file has no links.

tests/roam-files/tags/no_tag.org

@@ -1,3 +1,3 @@
-#+TITLE: Tagless File
+#+title: Tagless File
 
-This file has no tags, and should not yield any tags on extracting via =#+ROAM_TAGS=.
+This file has no tags, and should not yield any tags on extracting via ~#+roam_tags~.

tests/roam-files/tags/tag.org

@@ -1,4 +1,4 @@
-#+ROAM_TAGS: "t1" "t2 with space" t3
-#+TITLE: Tags
+#+roam_tags: "t1" "t2 with space" t3
+#+title: Tags
 
 This file is used to test functionality for =(org-roam--extract-tags)=

tests/roam-files/titles/aliases.org

@@ -1 +1 @@
-#+ROAM_ALIAS: "roam" "alias"
+#+roam_alias: "roam" "alias"

tests/roam-files/titles/combination.org

@@ -1,4 +1,4 @@
-#+TITLE: TITLE PROP
-#+ROAM_ALIAS: "roam" "alias"
+#+title: TITLE PROP
+#+roam_alias: "roam" "alias"
 
 * Headline

tests/roam-files/titles/title.org

@@ -1 +1 @@
-#+TITLE: Title
+#+title: Title

tests/roam-files/unlinked.org

@@ -1,3 +1,3 @@
-#+TITLE: Unlinked
+#+title: Unlinked
 
 Nothing links here :(

tests/roam-files/web_ref.org

@@ -1 +1 @@
-#+ROAM_KEY: https://google.com/
+#+roam_key: https://google.com/

tests/test-org-roam-perf.el

@@ -0,0 +1,53 @@
+;;; test-org-roam-perf.el --- Performance Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; 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 of the License, 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 this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(defconst test-org-roam-perf-zip-url "https://github.com/org-roam/test-org-files/archive/master.zip"
+  "Path to zip for test org-roam files.")
+
+(defun test-org-roam-perf--abs-path (file-path)
+  "Get absolute FILE-PATH from `org-roam-directory'."
+  (expand-file-name file-path org-roam-directory))
+
+(defun test-org-roam-perf--init ()
+  "."
+  (let* ((temp-loc (expand-file-name (make-temp-name "test-org-files-") temporary-file-directory))
+         (zip-file-loc (concat temp-loc ".zip"))
+         (_ (url-copy-file test-org-roam-perf-zip-url zip-file-loc))
+         (_ (shell-command (format "mkdir -p %s && unzip -j -qq %s -d %s" temp-loc zip-file-loc temp-loc))))
+    (setq org-roam-directory temp-loc)))
+
+(describe "Cache Build"
+  (it "cache build from scratch time to be acceptable"
+    (test-org-roam-perf--init)
+    (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 110))))
+  (it "builds quickly without change"
+    (pcase (benchmark-run 1 (org-roam-db-build-cache))
+      (`(,time ,gcs ,time-in-gc)
+       (message "Elapsed time: %fs (%fs in %d GCs)" time time-in-gc gcs)
+       (expect time :to-be-less-than 5)))))

tests/test-org-roam.el

@@ -3,7 +3,7 @@
 ;; Copyright (C) 2020 Jethro Kuan
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup) (with-simulated-input))
+;; Package-Requires: ((buttercup))
 
 ;; 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
@@ -22,13 +22,12 @@
 ;;; Code:
 
 (require 'buttercup)
-(require 'with-simulated-input)
 (require 'org-roam)
 (require 'dash)
 
 (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."
@@ -36,7 +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 ()
@@ -50,9 +49,43 @@
 
 (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 "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
@@ -193,6 +226,20 @@
               :to-equal
               '("deeply")))
 
+    (it "extracts from first directory"
+      (expect (test #'org-roam--extract-tags-first-directory
+                    "base.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-tags-first-directory
+                    "tags/tag.org")
+              :to-equal
+              '("tags"))
+      (expect (test #'org-roam--extract-tags-first-directory
+                    "nested/deeply/deeply_nested_file.org")
+              :to-equal
+              '("nested")))
+
     (describe "uses org-roam-tag-sources correctly"
       (it "'(prop)"
         (expect (let ((org-roam-tag-sources '(prop)))
@@ -207,6 +254,48 @@
                 :to-equal
                 '("t1" "t2 with space" "t3" "tags"))))))
 
+(describe "ID 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
+                 (funcall fn fname)))))
+    (it "extracts ids"
+      (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
+            '(title "" "" nil)))
+  (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"
   (before-each
@@ -226,21 +315,21 @@
 
     ;; 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])
@@ -270,199 +359,6 @@
             :to-equal
             (list :files 0 :links 0 :tags 0 :titles 0 :refs 0 :deleted 0))))
 
-(xdescribe "org-roam-insert"
-  (before-each
-    (test-org-roam--init))
-
-  (after-each
-    (test-org-roam--teardown))
-
-  (it "temp1 -> foo"
-    (let ((buf (test-org-roam--find-file "temp1.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "Foo RET"
-         (org-roam-insert))))
-    (expect (buffer-string) :to-match (regexp-quote "file:foo.org")))
-
-  (it "temp2 -> nested/foo"
-    (let ((buf (test-org-roam--find-file "temp2.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "(nested) SPC Nested SPC Foo RET"
-         (org-roam-insert))))
-    (expect (buffer-string) :to-match (regexp-quote "file:nested/foo.org")))
-
-  (it "nested/temp3 -> foo"
-    (let ((buf (test-org-roam--find-file "nested/temp3.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "Foo RET"
-         (org-roam-insert))))
-    (expect (buffer-string) :to-match (regexp-quote "file:../foo.org")))
-
-  (it "a/b/temp4 -> nested/foo"
-    (let ((buf (test-org-roam--find-file "a/b/temp4.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "(nested) SPC Nested SPC Foo RET"
-         (org-roam-insert))))
-    (expect (buffer-string) :to-match (regexp-quote "file:../../nested/foo.org"))))
-
-(xdescribe "rename file updates cache"
-  (before-each
-    (test-org-roam--init))
-
-  (after-each
-    (test-org-roam--teardown))
-
-  (it "foo -> new_foo"
-    (rename-file (test-org-roam--abs-path "foo.org")
-                 (test-org-roam--abs-path "new_foo.org"))
-    ;; Cache should be cleared of old file
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-
-    ;; Cache should be updated
-    (expect (org-roam-db-query [:select [to]
-                                :from links
-                                :where (= from $s1)]
-                               (test-org-roam--abs-path "new_foo.org"))
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "bar.org"))))
-    (expect (org-roam-db-query [:select [from]
-                                :from links
-                                :where (= to $s1)]
-                               (test-org-roam--abs-path "new_foo.org"))
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "nested/bar.org"))))
-
-    ;; Links are updated
-    (expect (with-temp-buffer
-              (insert-file-contents (test-org-roam--abs-path "nested/bar.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:../new_foo.org][Foo]]")))
-
-  (it "foo -> foo with spaces"
-    (rename-file (test-org-roam--abs-path "foo.org")
-                 (test-org-roam--abs-path "foo with spaces.org"))
-    ;; Cache should be cleared of old file
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-
-    ;; Cache should be updated
-    (expect (org-roam-db-query [:select [to]
-                                :from links
-                                :where (= from $s1)]
-                               (test-org-roam--abs-path "foo with spaces.org"))
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "bar.org"))))
-    (expect (org-roam-db-query [:select [from]
-                                :from links
-                                :where (= to $s1)]
-                               (test-org-roam--abs-path "foo with spaces.org"))
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "nested/bar.org"))))
-
-    ;; Links are updated
-    (expect (with-temp-buffer
-              (insert-file-contents (test-org-roam--abs-path "nested/bar.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:../foo with spaces.org][Foo]]")))
-
-  (it "no-title -> meaningful-title"
-    (rename-file (test-org-roam--abs-path "no-title.org")
-                 (test-org-roam--abs-path "meaningful-title.org"))
-    ;; File has no forward links
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "no-title.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "meaningful-title.org"))) :to-be 1)
-
-    ;; Links are updated with the appropriate name
-    (expect (with-temp-buffer
-              (insert-file-contents (test-org-roam--abs-path "meaningful-title.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:meaningful-title.org][meaningful-title]]")))
-
-  (it "web_ref -> hello"
-    (expect (org-roam-db-query
-             [:select [file] :from refs
-              :where (= ref $s1)]
-             "https://google.com/")
-            :to-equal
-            (list (list (test-org-roam--abs-path "web_ref.org"))))
-    (rename-file (test-org-roam--abs-path "web_ref.org")
-                 (test-org-roam--abs-path "hello.org"))
-    (expect (org-roam-db-query
-             [:select [file] :from refs
-              :where (= ref $s1)]
-             "https://google.com/")
-            :to-equal (list (list (test-org-roam--abs-path "hello.org"))))
-    (expect (caar (org-roam-db-query
-                   [:select [ref] :from refs
-                    :where (= file $s1)]
-                   (test-org-roam--abs-path "web_ref.org")))
-            :to-equal nil)))
-
-(xdescribe "delete file updates cache"
-  (before-each
-    (test-org-roam--init))
-
-  (after-each
-    (test-org-roam--teardown))
-
-  (it "delete foo"
-    (delete-file (test-org-roam--abs-path "foo.org"))
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0))
-
-  (it "delete web_ref"
-    (expect (org-roam-db-query [:select * :from refs])
-            :to-have-same-items-as
-            (list (list "https://google.com/" (test-org-roam--abs-path "web_ref.org") "website")))
-    (delete-file (test-org-roam--abs-path "web_ref.org"))
-    (expect (org-roam-db-query [:select * :from refs])
-            :to-have-same-items-as
-            (list))))
-
 (provide 'test-org-roam)
 
 ;;; test-org-roam.el ends here