Second Reader

An Obsidian plugin for the Second Reader literature-note workflow. One plugin covers the whole loop:

• Import a paper from Zotero into a structured literature note (title, authors, citekey, APA reference).
• Sync highlights while you type. Read in Zotero's PDF reader with the note open beside it; click the highlighter button at the top-right of the note (also in the left ribbon), or run "Sync highlights into current note", and every new highlight and comment lands under "Quotes worth keeping" with its printed page number — without touching anything typed in the note.
• Progress-colored syllabus links. Links to literature notes show whether the student has made the note, synced highlights into it, or written in it.
• "open pdf" that works for every student. A class copy of the instructor's syllabus links each reading through the student's own literature note to their own copy of the PDF.
• Package a week's notes for upload. A link under each week of the class copy of the syllabus zips the student's literature notes for that week (one file per reading, the student's name in the zip's name) and shows the zip, ready for Canvas.
• Promote candidates. Checking a box under ## Permanent note candidates in a note tagged literature-note creates a permanent note from a template and turns the line into a link to it.

Students' setup instructions: STUDENT-SETUP-GUIDE.md. Students upgrading from 1.x: UPDATING.md. Overview of what's new and how to use it: UPDATE-REPORT-2.3.md.

Desktop only (macOS, Windows, Linux) — Zotero import talks to the Zotero desktop app and runs a PDF helper, which Obsidian mobile can't do.

Install

1. In Obsidian, open Settings → Community plugins and turn off Restricted mode if it's on.
2. Click Browse, search for "Second Reader", and click Install.
3. Click Enable.
4. Open Settings → Second Reader and click the download button next to "PDF Utility". Highlight sync and PDF import need it.

Requires Zotero 7 with the Better BibTeX plugin, and Zotero's "Allow other applications to communicate with Zotero" setting turned on.

Installing through BRAT

Until Second Reader appears in the community directory, install it with BRAT instead of steps 1–3:

1. Install the BRAT community plugin (Settings → Community plugins → Browse → search "BRAT").
2. Command Palette → "BRAT: Add a beta plugin for testing."
3. Paste this repo: kevinmil54/second-reader-obsidian-promote
4. Enable "Second Reader" in Settings → Community plugins.

If you installed it through BRAT and it's now in the directory, open BRAT's settings and remove kevinmil54/second-reader-obsidian-promote from its list of beta plugins, leaving Second Reader installed. Obsidian then updates it from the community directory. The plugin ID hasn't changed, so your settings carry over.

Keeping figures and tables

To keep a figure or table, draw a box around it with the select-area tool in Zotero's PDF reader, then sync highlights. The image comes into the note under "Quotes worth keeping" with its page number. To add a screenshot from somewhere else, put it in the note's "Figures & images" section with ![[filename]].

Network use and access outside your vault

Second Reader works with the Zotero desktop app and a small PDF utility, so it does a few things beyond reading and writing notes in your vault.

Network use

• Zotero on your own computer. The plugin talks to Zotero's Better BibTeX plugin at http://127.0.0.1 (port 23119 for Zotero, 24119 for Juris-M, or a port you set). This is how it looks up citations, imports papers, and reads your highlights. The connection stays on your computer.
• Downloading the PDF utility from GitHub. Highlight sync and PDF import use pdfannots2json, a program by mgmeyers that reads annotations out of PDF files. Second Reader downloads the version for your operating system from that project's GitHub releases page. The first download happens when you click the download button next to "PDF Utility" in the plugin's settings. After a Second Reader update that needs a newer version of the utility, the plugin downloads it again when Obsidian starts. To manage the utility yourself, enter the path to your own copy under "PDF Utility Path Override" in the settings, and Second Reader will never download it. Before anything is installed, the download is checked against a SHA-256 checksum built into the plugin, and a file that does not match is discarded.

The plugin makes no other network connections. It does not send your notes, highlights or reading activity anywhere, and it collects no usage data.

Files and programs outside your vault

• Zotero attachments. To import highlights and images, the plugin reads PDF files and image files from Zotero's storage folder and copies the images it needs into your vault.
• Running the PDF utility. The plugin runs pdfannots2json on the PDF you're importing from. It also runs Tesseract, if you've installed it and turned on "Image OCR" in the settings.
• Showing a week's package. Packaging a week's notes makes a zip file in the vault's Uploads folder and then opens Finder (or Explorer) to show it.

No account or payment is needed. Second Reader is free and open source under the GPL-3.0 license.

Upgrading from 1.x (Promote Candidates + Zotero Integration)

The plugin id is unchanged (second-reader-promote), so BRAT updates 1.x installs in place and promote settings carry over. On first start, 2.x copies the import formats and other settings from the community Zotero Integration plugin (obsidian-zotero-desktop-connector), then shows a reminder until that plugin is turned off. Commands are renamed from "Zotero Integration: …" to "Second Reader: …".

For instructors: preparing a class

Students get the readings as a Zotero RDF file and the syllabus as an Obsidian note. Each student's notes are built from their own Zotero copy of each reading, so highlight sync and "open pdf" work on their machine and their highlights stay private.

1. Export the readings from Zotero. Right-click the course collection → Export Collection… → Format Zotero RDF:

• check Export Files (so the PDFs are included);
• uncheck Export Notes (your Zotero notes stay yours);
• if Include Annotations appears, leave it unchecked — otherwise your highlights are written into the students' PDFs.

Zip the exported folder (the .rdf file plus its files folder) and post it on Canvas. Students import it per the setup guide (step 3b). For readings added later, export just those into a new file.

Item IDs and citekeys are not preserved by an import — each student's Zotero assigns its own — which is why the syllabus can't link straight to PDFs and uses the student's literature note instead (below).

2. Make the students' copy of the syllabus. Keep one master syllabus in your own vault, with your own zotero://open-pdf/... links (they work only on your computer). Open it and run "Second Reader: Make class copy of syllabus." It writes <syllabus name> - student copy.md next to it, with every Zotero link rewritten to obsidian://second-reader?open-pdf=<literature note title> — the literature note named on the same line (the link after "Literature note:", else the line's first [[link]]). On a student's computer that opens their copy: the note's pdf: property, or, for notes made before 2.2, the PDF found in Zotero by the note's citekey (then saved into the note). Zotero links with no note on their line become plain text and are listed in the notice. Literature-note links are also pointed at the name each student's import will give the note — computed from the linked note's title with the import's file-name rules — when that differs from your note's name (e.g. a Zotero title ending in a period); they keep displaying as written ([[Student name|Your name]]). Re-run the command after every syllabus edit; the copy carries a do-not-edit banner.

Literature-note links in the syllabus only resolve if students keep the note names the import produces, so the output path template should name notes the way the syllabus links do (e.g. Literature notes/{{title}}.md).

Packaging links. The class copy also gets a line under every Week N heading (any heading level) whose section links to a note: [Package my Week N literature notes for upload](obsidian://second-reader?package-week=N&syllabus=<copy name>). On a student's computer it collects the literature notes linked in that week's section that the student has made, writes Uploads/<course> Week NN literature notes - <student name>.zip (the notes sit in a folder of that name inside the zip, with any embedded images under attachments/), and shows the zip in Finder or Explorer. <course> comes from the syllabus's course property ("ED 336/536 & …" → "ED 336"). The notes are copied only into the zip, never into the vault, so they can't make [[links]] ambiguous. Readings without a note, and notes that are still blank (nothing but template text, as for link colors), are skipped and named in the notice. The student's name is asked for once and stored in the plugin settings.

3. Link colors. Any link to a literature note (frontmatter citekey or tag literature-note) is colored by the student's progress, in reading view and the editor: no class while the note doesn't exist (Obsidian's unresolved style), sr-lit-untouched, sr-lit-highlights, sr-lit-worked. Colors are the CSS variables --sr-lit-highlights-color and --sr-lit-worked-color (yellow and green by default) — override them in a CSS snippet. "Worked" means any body line that isn't template text (src/litNoteState.ts; the import formats' own template files count as template text too); frontmatter and synced quotes don't count.

Going to the next class session

In a long syllabus, run Second Reader: Go to the next class session in this syllabus (assign a hotkey under Settings > Hotkeys) to scroll to the week the class meets next. It reads the Week N (Month day) headings and picks the earliest week whose date is today or later, so on a class day it goes to today's class and in between classes to the next one. Before the course starts it goes to the first week, after the last class to the last. It scrolls in editing or reading view and never changes the note.

Zotero links in handed-out notes

Literature notes from early course packages have an empty zotero: property and no "Open PDF · Open in Zotero" line under the title. Second Reader fills these in when Obsidian starts, when the student clicks "open pdf" for that reading, and when they sync highlights into the note; Second Reader: Fill in Zotero links in literature notes does it for every note at once. Only those lines change (and a pdf: property is added if missing), so nothing a student has written is touched (src/zoteroLinks.ts).

Course updates

To send students new or revised literature notes partway through a term, give them a folder that holds Literature notes/ (and, if needed, Attachments/ and Templates/). Students put the whole folder anywhere in their vault and run Second Reader: Bring in course update (new literature notes) from the command palette. For each note in the update:

• if the student has no note with that name, it's added to Literature notes/;
• if the student's note is still blank (only template text), it's replaced with the new version;
• if the student has written anything in it or synced highlights into it, it's left alone.

Images and other files are added only where nothing with that name exists, and the update's templates replace the vault's. The update folder then goes to the trash, so no note name appears twice. A message lists the notes that were kept.

Templates

• Literature Note Template - Zotero Import.md — set as the template of an Import Format (plugin settings → Zotero import & highlight sync → Import Formats). Sync uses the format whose template path contains "Literature Note" (else the first format).
• Permanent Note Template.md — filled in when a candidate is promoted. Supports {{title}}, {{date}}, {{source}}, {{tags}}, {{topics}}, {{details}}. {{topics}} is the literature note's topics: property (list or comma-separated text), so a paper's topics become the starting topics of each permanent note promoted from it; edit them on the permanent note when one idea belongs to a different topic. A template with no {{topics}} and no topics: line gets a topics: [...] line added to the note being made (never to the template) when the literature note has topics.

Synthesis notes

A synthesis note gathers what you think about one topic from the permanent notes that share it. Second Reader creates the note and keeps one list in it: the permanent notes on the topic that the note does not link to yet. As you cite a permanent note in your own writing, it leaves the list. Everything else in the note is yours and is never changed or reordered.

• A permanent note is one tagged permanent-note; its topics are its topics: property (a list, or comma-separated text).
• When a topic reaches the minimum number of permanent notes (default 4) and no synthesis note has that topic, a note is created in the synthesis folder (default Synthesis notes) and a notice says so. This happens when a permanent note that lists the topic is added or edited. It does not run at startup, and a note you delete is not made again automatically.
• A synthesis note is any note in the synthesis folder, or with type: synthesis, whose topic: property names the topic (case ignored).
• New notes use the template at the synthesis template path (default Templates/Synthesis Note Template.md). {{title}}, {{date}} and {{topic}} are filled in, as are the Templater title, date and topic prompt used in the instructor template, and the topic is written to the topic: property. A template with any other Templater expression falls back to a built-in note. A Dataview query under "Permanent notes not yet used" is replaced by the plugin's list so the notes aren't shown twice.
• The list lives between %% begin synthesis-notes %% and %% end synthesis-notes %% under the "Permanent notes not yet used" heading (2.11 called it "Permanent notes on this topic"; the old heading is renamed on the next refresh). It is refreshed when permanent notes are added, edited, renamed or deleted, and a few seconds after you stop editing the synthesis note, since a note you link there leaves the list. Any link to the permanent note counts, whether plain, aliased or to a heading. Only notes that already have the markers are refreshed on their own; a synthesis note you wrote yourself is left alone.
• Each entry is shown with the permanent note's full title: as the link text, so a long claim whose file name was shortened is still readable.
• Commands: Create synthesis notes for topics with enough permanent notes (all topics, including ones made before the plugin was updated) and Add or refresh the permanent-notes list in this synthesis note.
• Cite a permanent note here (in a synthesis or project note): opens a search box of the permanent notes that the note does not link to yet. In a synthesis note these are the permanent notes on its topic; in a project note (type: project) they are all permanent notes, with those that share a topic with the project's synthesis: notes listed first. The search box shows full titles and inserts a link at the cursor. With text selected, the selection becomes the link text; otherwise the title is inserted and selected so you can type your own words over it. A note you have linked is no longer offered. Assign a hotkey under Settings > Hotkeys.
• Settings: Synthesis notes (automatic creation on or off, minimum notes, folder, template path).

The logic is in src/synthesisCore.ts (no Obsidian imports, covered by synthesis.test.ts); src/synthesis.ts does the vault work.

Template settings

The literature-note template starts with a few settings, written as template comments so they never appear in notes:

{#- Second Reader settings. These lines never appear in your notes. -#}
{#- reference-style: apa -#}
{#- author-info: photos -#}

• reference-style is the Zotero style used for {{bibliography}}, the "Reference" line. Use the style's ID as Zotero knows it, for example apa, chicago-author-date or modern-language-association; the style must be installed in Zotero. It takes priority over the import format's Bibliography Style. If you change it, also change the "(APA)" in the template's Reference (APA): label.
• author-info is read by the separate author-information program (add_author_info.py), not by Second Reader itself: none adds nothing, basic adds the lead author's name, affiliation and links, and photos also adds a photo, dates and a Wikipedia link from Wikidata.

Keep the dashes inside {#- and -#}; they stop the comments from leaving blank lines above the note's properties.

Template upgrades

The current literature-note template ships inside the plugin (esbuild text loader; jest.text-transform.js does the same for tests). If an import format points at a Second Reader literature-note template that predates highlight import (no newAnnotations) or the PDF link (no pdfURI), the plugin offers to upgrade it: at startup (until declined for that plugin version), before a sync (only if highlight import is missing — the sync would add nothing, so it's blocked if declined), before an import (optional), and via "Update literature-note template." Only the ## Quotes worth keeping section and the pdf: / Open PDF lines are patched, so other customizations survive; the old file is first saved as … (before Second Reader update).md. The upgrade also adds a topics: [] line after tags: when the template has none. Templates without that heading are never touched (src/templateUpgrade.ts).

How highlight sync works

Quotes live in a plugin-owned block (%% begin annotations %% … %% end annotations %%, hidden in Live Preview). Sync and re-import touch only that block, through the live editor when the note is open, so typed text, cursor, undo history, and unsaved keystrokes are preserved; if a student edits a quote while Zotero is being queried, their edit wins and new quotes are appended after it. Each quote carries a block id ^nb-<Zotero annotation key>; a highlight is added only if its id isn't already anywhere in the note, so edited, trimmed, or moved quotes are never duplicated (and can be linked to: [[smith2023#^nb-ABCD1234]]). Re-importing an existing note never overwrites it. Page numbers use Zotero's page label (the printed page) and fall back to the PDF page.

Template variables added for this: newAnnotations (annotations not yet in the note) and a.nbId (the block-id-safe annotation id).

Development

The Zotero import code is a fork of obsidian-zotero-integration v3.2.1 by mgmeyers, which is GPL-3.0; this plugin is therefore distributed under GPL-3.0 (LICENSE.md). Changes from upstream: highlight sync and merge-instead-of-overwrite (src/bbt/sync.ts, src/bbt/export.ts), the promote feature (src/promote.ts), a one-time settings import from the upstream plugin, the PDF helper stored in this plugin's own folder instead of upstream's hardcoded one, and a fix for first-page highlights getting no page number.

npm install
npm test         # one known upstream failure: "sanely handles new lines"
npm run build    # produces main.js

Changing the literature-note template: before committing a change to Templates/Literature Note Template - Zotero Import.md, append the outgoing version to src/pastLiteratureTemplates.md, followed by a line containing only <<<SECOND-READER-TEMPLATE-VERSION>>>. That file is how the link colors recognize template text in notes students made with older templates; without it, an untouched old note would show as "worked." The tests render every past version and check that it reads as untouched and upgrades cleanly. The current template is bundled into main.js, so template changes ship with a plugin release.

Releasing: bump version in manifest.json and package.json, add it to versions.json, build, then create a GitHub release tagged with the version (no v prefix) with main.js, manifest.json, and styles.css attached. main.js is build output and isn't committed.