@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.20

package/dist/services/ncbi/parsing/pmc-article-parser.js

@@ -7,7 +7,7 @@
  * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import { attrOf, childrenOf, findAll, findAllDescendants, findOne, isTextNode, rawTextContent, selectAlternative, tagNameOf, textContent, textContentExcluding, textOf, } from './pmc-xml-helpers.js';
+import { attrOf, childrenOf, findAll, findAllDescendants, findOne, IDENTIFIER_TAGS, isTextNode, lineTextContent, rawTextContent, selectAlternative, TextAssembler, tagNameOf, textContent, textContentExcluding, textOf, } from './pmc-xml-helpers.js';
 /**
  * Block content extracted into a field of its own and therefore left out of the
  * prose a section contributes. Each one nested inside a `<p>` would otherwise be
@@ -116,14 +116,22 @@ function extractArticleId(articleMeta, pubIdType) {
     return;
 }
 // ─── Authors & Affiliations ─────────────────────────────────────────────────
+/**
+ * True for a `<contrib>` that is an author: `contrib-type="author"` or no type
+ * at all. Editors, reviewers and every other typed contributor are not, and
+ * neither they nor their affiliations reach the output.
+ */
+function isAuthorContrib(contrib) {
+    const contribType = attrOf(contrib, 'contrib-type');
+    return !contribType || contribType === 'author';
+}
 /** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
 export function extractJatsAuthors(contribGroup) {
     if (!contribGroup)
         return [];
     const authors = [];
     for (const contrib of findAll(contribGroup, 'contrib')) {
-        const contribType = attrOf(contrib, 'contrib-type');
-        if (contribType && contribType !== 'author')
+        if (!isAuthorContrib(contrib))
             continue;
         const collab = findOne(contrib, 'collab');
         if (collab) {
@@ -144,16 +152,42 @@ export function extractJatsAuthors(contribGroup) {
     }
     return authors;
 }
+/**
+ * Every `<aff>` in the front matter, in document order: directly under
+ * `<article-meta>`, inside a `<contrib-group>`, or inside one `<contrib>` of it.
+ * Most deposits put them under `<contrib-group>` — 131 articles of a
+ * 187-article draw carried theirs only there — and reading `<article-meta>`
+ * alone returned none for those. Some deposits repeat one affiliation as a separate
+ * `<aff>` in every `<contrib>` it applies to; the text is reported once. (#196)
+ *
+ * An affiliation belongs to the authors only: an `<aff>` inside a non-author
+ * `<contrib>` (PMC10666927's reviewing editors), and one directly under a
+ * `<contrib-group>` that holds no author, are left out, as those contributors are
+ * left out of `authors`. A group mixing authors and others keeps its direct
+ * `<aff>`s.
+ */
 function extractAffiliations(articleMeta) {
     if (!articleMeta)
         return [];
-    const result = [];
-    for (const aff of findAll(articleMeta, 'aff')) {
-        const text = textContent(aff);
-        if (text)
-            result.push(text);
+    const affs = [];
+    for (const child of childrenOf(articleMeta)) {
+        const tag = tagNameOf(child);
+        if (tag === 'aff')
+            affs.push(child);
+        if (tag !== 'contrib-group')
+            continue;
+        const contribs = findAll(child, 'contrib');
+        const holdsAuthor = contribs.length === 0 || contribs.some(isAuthorContrib);
+        for (const member of childrenOf(child)) {
+            const memberTag = tagNameOf(member);
+            if (memberTag === 'aff' && holdsAuthor)
+                affs.push(member);
+            else if (memberTag === 'contrib' && isAuthorContrib(member)) {
+                affs.push(...findAll(member, 'aff'));
+            }
+        }
     }
-    return result;
+    return [...new Set(affs.map(textContent).filter(Boolean))];
 }
 // ─── Journal & Publication Date ─────────────────────────────────────────────
 function extractJournal(journalMeta, articleMeta) {
@@ -210,6 +244,8 @@ function extractPubDate(articleMeta) {
     };
 }
 // ─── Abstract & Keywords ────────────────────────────────────────────────────
+/** Closing punctuation a deposited section title can already end in. */
+const TERMINAL_PUNCTUATION_RE = /[:.?!]$/;
 /**
  * Read the article's own abstract.
  *
@@ -226,6 +262,20 @@ function extractPubDate(articleMeta) {
  * abstract leaves its marker and its caption reaches `assets[]` alone —
  * {@link extractPmcAssets} already walks `<front>` — instead of concatenating
  * into the prose, and a `<list>` renders as list lines rather than a token run.
+ * A section that opens with a list starts it on the line below its
+ * `Title:` heading. (#202)
+ *
+ * A structured abstract is read child by child in source order: each `<sec>`
+ * as `Title: text`, and each run of content outside any `<sec>` as an untitled
+ * section reads — its statements space-joined, a blank line between it and the
+ * sections around it. A lead paragraph before the first section therefore
+ * opens the abstract as a paragraph of its own above the first `Title:` line.
+ * Springer deposits the whole abstract that way, ahead of a "Supplementary
+ * Information" section (PMC11281965), and reading the `<sec>`s alone returned
+ * that notice as the abstract. (#204)
+ *
+ * A section title deposited with its own closing punctuation (`Background:`,
+ * `Study Design.`, `What is known?`) keeps it in place of the added colon. (#205)
  */
 function extractAbstract(articleMeta) {
     if (!articleMeta)
@@ -234,33 +284,64 @@ function extractAbstract(articleMeta) {
     const abstractNode = abstracts.find((node) => !attrOf(node, 'abstract-type')) ?? abstracts[0];
     if (!abstractNode)
         return;
-    const sections = findAll(abstractNode, 'sec');
-    if (sections.length > 0) {
-        const parts = [];
-        for (const sec of sections) {
-            const title = textContent(findOne(sec, 'title'));
-            const text = abstractProse(sec);
-            if (title && text)
-                parts.push(`${title}: ${text}`);
-            else if (text)
-                parts.push(text);
+    const children = childrenOf(abstractNode);
+    if (!findOne(abstractNode, 'sec'))
+        return abstractProse(children).text || undefined;
+    const parts = [];
+    let outside = [];
+    const addOutside = () => {
+        const { text } = abstractProse(outside);
+        if (text)
+            parts.push(text);
+        outside = [];
+    };
+    for (const child of children) {
+        if (tagNameOf(child) !== 'sec') {
+            outside.push(child);
+            continue;
         }
-        return parts.join('\n\n').trim() || undefined;
+        addOutside();
+        const title = textContent(findOne(child, 'title'));
+        const { ownLineFirst, text } = abstractProse(childrenOf(child));
+        const heading = TERMINAL_PUNCTUATION_RE.test(title) ? title : `${title}:`;
+        if (title && text)
+            parts.push(`${heading}${ownLineFirst ? '\n' : ' '}${text}`);
+        else if (text)
+            parts.push(text);
     }
-    return abstractProse(abstractNode) || undefined;
+    addOutside();
+    return parts.join('\n\n').trim() || undefined;
 }
 /**
- * The prose of an `<abstract>` or one of its `<sec>`s: every child but the
- * heading the caller reports separately, space-joined. The single space is the
- * spacing the paragraph-only read this replaces already produced, so a record
- * depositing one untyped abstract of plain `<p>`s comes back byte-identical.
+ * The prose of a run of abstract content — an `<abstract>`'s or a `<sec>`'s
+ * children, or what an abstract holds outside its sections — leaving out the
+ * `<title>` and `<label>` the caller reports separately or not at all.
+ * Statements are space-joined — the spacing the paragraph-only read this
+ * replaces already produced, so a record depositing one untyped abstract of
+ * plain `<p>`s comes back byte-identical.
+ *
+ * A list reads on lines of its own, as it does in a body section: a blank line
+ * rather than a space separates it from the statement before and after it, so
+ * neither its first item runs onto the text before it nor its last item onto
+ * the heading or sentence after it (PMC8533648). A delimited box does the same,
+ * so its `[Box]` and `[End of box]` lines stand alone. `ownLineFirst` reports
+ * either on the first line, which the caller starts below the section's
+ * heading (PMC10869376). (#202, #210)
  */
-function abstractProse(node) {
-    const prose = childrenOf(node).filter((child) => {
-        const tag = tagNameOf(child);
+function abstractProse(nodes) {
+    const prose = nodes.filter((node) => {
+        const tag = tagNameOf(node);
         return tag !== 'title' && tag !== 'label';
     });
-    return flowBlocks(prose, STATEMENT_BLOCK_TAGS).join(' ');
+    const blocks = flowParts(prose, STATEMENT_BLOCK_TAGS);
+    let text = '';
+    for (const [i, block] of blocks.entries()) {
+        const previous = blocks[i - 1];
+        if (previous)
+            text += previous.ownLineLast || block.ownLineFirst ? '\n\n' : ' ';
+        text += block.text;
+    }
+    return { ownLineFirst: blocks[0]?.ownLineFirst ?? false, text };
 }
 function extractKeywords(articleMeta) {
     if (!articleMeta)
@@ -278,12 +359,18 @@ function extractKeywords(articleMeta) {
 // ─── Block Rendering ────────────────────────────────────────────────────────
 /** Indent one nesting level of a `<list>`/`<def-list>` nested in a `<list-item>`. */
 const NESTED_LIST_INDENT = '  ';
+/** A {@link FlowBlock} whose edges both stand on their own lines (`ownLines`), or neither does. */
+const flowBlock = (text, ownLines = false) => ({
+    text,
+    ownLineFirst: ownLines,
+    ownLineLast: ownLines,
+});
 /** Close the prose run in progress, discarding it when it holds only whitespace. */
 function flushRun(flow) {
-    const text = flow.run.replace(/\s+/g, ' ').trim();
+    const text = flow.run.toString().replace(/\s+/g, ' ').trim();
     if (text)
-        flow.out.push(text);
-    flow.run = '';
+        flow.out.push(flowBlock(text));
+    flow.run = new TextAssembler();
 }
 /**
  * Walk a mixed-content child list, accumulating inline text into a prose run and
@@ -299,20 +386,28 @@ function flushRun(flow) {
  * prose, {@link STATEMENT_BLOCK_TAGS} for a container whose `<title>` and `<p>`
  * children are separate statements rather than one continuous sentence.
  *
- * `<tex-math>` and `<alternatives>` are the two elements whose text is not the
- * concatenation of their subtree, so this walk defers to the shared rule rather
- * than reading their children one at a time: a `<tex-math>` contributes its
- * LaTeX document body via `rawTextContent`, and an `<alternatives>` re-enters
- * this walk with its single chosen child, which keeps a `<disp-formula>` found
- * there at block position. (#135)
+ * `<tex-math>`, `<alternatives>` and the {@link IDENTIFIER_TAGS} are the elements
+ * whose text is not the concatenation of their subtree, so this walk defers to
+ * the shared rule rather than reading their children one at a time: a
+ * `<tex-math>` contributes its LaTeX document body via `rawTextContent`, an
+ * `<alternatives>` re-enters this walk with its single chosen child, which keeps
+ * a `<disp-formula>` found there at block position, and an `<institution-id>`
+ * in a funding statement contributes nothing. (#135, #208)
+ *
+ * The run is a {@link TextAssembler}, so prose follows the separator rules every
+ * other text field does: a `<break/>`, an inline `<fn>` or a `<label>` beside its
+ * text reads as one space rather than fusing the words on either side, and a run
+ * of `<xref>` markers with nothing between them reads `[1,2,3,4]`. (#185, #197)
  */
 function walkFlow(nodes, flow, blockTags) {
     for (const node of nodes) {
         if (isTextNode(node)) {
-            flow.run += textOf(node);
+            flow.run.text(textOf(node));
             continue;
         }
         const tag = tagNameOf(node) ?? '';
+        if (IDENTIFIER_TAGS.has(tag))
+            continue;
         if (tag === 'alternatives') {
             const chosen = selectAlternative(node);
             if (chosen)
@@ -320,26 +415,32 @@ function walkFlow(nodes, flow, blockTags) {
             continue;
         }
         if (tag === 'tex-math') {
-            flow.run += rawTextContent(node);
+            flow.run.text(rawTextContent(node));
             continue;
         }
         if (blockTags.has(tag)) {
             flushRun(flow);
-            const rendered = renderBlock(node);
-            if (rendered)
-                flow.out.push(rendered);
+            const block = renderBlock(node);
+            if (block.text)
+                flow.out.push(block);
             continue;
         }
+        flow.run.open(tag);
         walkFlow(childrenOf(node), flow, blockTags);
+        flow.run.close(tag);
     }
 }
-/** Ordered text blocks contributed by one `<p>` — or any other flow container. */
-function flowBlocks(nodes, blockTags = BLOCK_TAGS) {
-    const flow = { out: [], run: '' };
+/** Ordered blocks contributed by one `<p>` — or any other flow container — with their list edges. */
+function flowParts(nodes, blockTags = BLOCK_TAGS) {
+    const flow = { out: [], run: new TextAssembler() };
     walkFlow(nodes, flow, blockTags);
     flushRun(flow);
     return flow.out;
 }
+/** Ordered text blocks contributed by one `<p>` — or any other flow container. */
+function flowBlocks(nodes, blockTags = BLOCK_TAGS) {
+    return flowParts(nodes, blockTags).map((block) => block.text);
+}
 /**
  * Block tags for a container whose `<title>` and `<p>` children each carry a
  * statement of their own — a `<caption>`, an `<abstract>`, an abstract `<sec>`.
@@ -369,30 +470,40 @@ function renderCaption(caption) {
  * sat; `<ref-list>` is carried by `references[]` and likewise contributes
  * nothing, which is what keeps a `<sec>` that only wraps one from surviving as
  * an empty "References" heading. (#116, #130)
+ *
+ * A `<list>` or `<def-list>`, and a delimited `<boxed-text>`, stand on lines of
+ * their own at both edges; a container read through the default arm takes the
+ * edges of its first and last blocks. (#202, #210)
  */
 function renderBlock(node) {
     switch (tagNameOf(node)) {
         case 'table-wrap':
         case 'ref-list':
-            return '';
+            return flowBlock('');
         case 'fig':
-            return assetMarker(node, 'Figure');
+            return flowBlock(assetMarker(node, 'Figure'));
         case 'supplementary-material':
-            return assetMarker(node, 'Supplementary');
+            return flowBlock(assetMarker(node, 'Supplementary'));
         case 'list':
-            return renderList(node, 0);
+            return flowBlock(renderList(node, 0), true);
         case 'def-list':
-            return renderDefList(node, 0);
+            return flowBlock(renderDefList(node, 0), true);
         case 'disp-quote':
-            return renderDispQuote(node);
+            return flowBlock(renderDispQuote(node));
         case 'boxed-text':
-            return renderBoxedText(node);
+            return flowBlock(renderFloatingBox(node), true);
         case 'preformat':
-            return renderPreformat(node);
+            return flowBlock(renderPreformat(node));
         case 'disp-formula':
-            return renderDispFormula(node);
-        default:
-            return flowBlocks(childrenOf(node)).join('\n\n');
+            return flowBlock(renderDispFormula(node));
+        default: {
+            const blocks = flowParts(childrenOf(node));
+            return {
+                text: blocks.map((block) => block.text).join('\n\n'),
+                ownLineFirst: blocks[0]?.ownLineFirst ?? false,
+                ownLineLast: blocks.at(-1)?.ownLineLast ?? false,
+            };
+        }
     }
 }
 /**
@@ -458,6 +569,25 @@ function assetMarker(node, kind) {
  * `<def-list>` nested inside a `<list-item>` — both in the JATS content model —
  * indents one level per depth. (#130)
  *
+ * Publishers nest a sub-list either as a child of the `<list-item>` or inside
+ * the item's `<p>` (PMC12892673), and both render the same way: below the
+ * item's line, one level deeper. Read as paragraph flow instead, the inner
+ * list's first item ran onto its parent's line. The item's `<p>` is split at
+ * the lists it holds, so the item reads in document order: prose before the
+ * first nested list stays on the item's line, and prose after one — the rest
+ * of that `<p>` or a later `<p>` — keeps its place below the list on a line of
+ * its own, one level deeper, rather than running onto the last nested item
+ * (PMC8533647) or moving above the list onto the item's line. An item whose
+ * text all follows its nested list still prints its marker, alone on the
+ * item's line, so that text stays under its own item rather than reading as
+ * the item before it; an item holding nothing but a nested list prints no line
+ * of its own. (#200, #203)
+ *
+ * A `simple` list prints no marker of its own, so an item's `<label>` is its
+ * only numbering and leads the item's line (`1. Cereals …`); dropping it lost
+ * the source numbering of every labeled simple list. Other list types print
+ * their own marker and leave the label out. (#185)
+ *
  * `withTitle: false` leaves the title out, for a list whose title has become
  * the heading of the section it forms (see {@link extractBodySections}).
  */
@@ -474,26 +604,64 @@ function renderList(list, depth, withTitle = true) {
         const marker = listType === 'simple' ? '' : listType === 'order' ? `${ordinal}. ` : '- ';
         const parts = [];
         const nested = [];
+        /** Prose read after a nested list, kept below that list. */
+        let after;
+        let proseAfter = false;
+        const flushAfter = () => {
+            const text = after?.filter(Boolean).join(' ');
+            if (!text)
+                return;
+            nested.push(`${pad}${NESTED_LIST_INDENT}${text}`);
+            proseAfter = true;
+        };
+        const addNested = (block) => {
+            flushAfter();
+            nested.push(block);
+            after = [];
+        };
         for (const child of childrenOf(item)) {
             const tag = tagNameOf(child);
-            if (tag === 'label')
+            if (tag === 'label') {
+                if (listType === 'simple' && parts.length === 0)
+                    parts.push(textContent(child));
                 continue;
-            if (tag === 'list')
-                nested.push(renderList(child, depth + 1));
-            else if (tag === 'def-list')
-                nested.push(renderDefList(child, depth + 1));
-            else
-                parts.push(...flowBlocks([child]));
+            }
+            // A `<p>` is read child by child, so a list inside it splits its prose;
+            // any other child is one unit, itself a nested list or not.
+            let prose = [];
+            for (const node of tag === 'p' ? childrenOf(child) : [child]) {
+                const inner = renderNestedList(node, depth + 1);
+                if (inner === undefined) {
+                    prose.push(node);
+                    continue;
+                }
+                (after ?? parts).push(...flowBlocks(prose));
+                prose = [];
+                addNested(inner);
+            }
+            (after ?? parts).push(...flowBlocks(prose));
         }
-        const text = parts.join(' ');
+        flushAfter();
+        const text = parts.filter(Boolean).join(' ');
         if (text)
             lines.push(`${pad}${marker}${text}`);
+        else if (proseAfter && marker)
+            lines.push(`${pad}${marker.trimEnd()}`);
         for (const block of nested)
             if (block)
                 lines.push(block);
     }
     return lines.join('\n');
 }
+/** A `<list>` or `<def-list>` rendered at `depth`; undefined for any other node. (#200) */
+function renderNestedList(node, depth) {
+    const tag = tagNameOf(node);
+    if (tag === 'list')
+        return renderList(node, depth);
+    if (tag === 'def-list')
+        return renderDefList(node, depth);
+    return;
+}
 /**
  * Render a `<def-list>`: its title on a line of its own, then
  * `- term — definition` per item. `withTitle: false` leaves the title out, as
@@ -541,9 +709,10 @@ function renderDispQuote(quote) {
  *
  * `withTitle: false` leaves out the `<caption>`'s `<title>` — the box's title in
  * the JATS content model — for a box whose title has become the heading of the
- * section it forms (see {@link extractBodySections}).
+ * section it forms (see {@link extractBodySections}). `withLabel: false` leaves
+ * out its `<label>`, for a box whose label {@link renderFloatingBox} names it by.
  */
-function renderBoxedText(boxedText, withTitle = true) {
+function renderBoxedText(boxedText, { withLabel = true, withTitle = true } = {}) {
     const blocks = [];
     for (const child of childrenOf(boxedText)) {
         const tag = tagNameOf(child);
@@ -553,11 +722,38 @@ function renderBoxedText(boxedText, withTitle = true) {
             const parts = childrenOf(child).filter((c) => withTitle || tagNameOf(c) !== 'title');
             blocks.push(...flowBlocks(parts, STATEMENT_BLOCK_TAGS));
         }
-        else
+        else if (withLabel || tag !== 'label')
             blocks.push(...flowBlocks([child]));
     }
     return blocks.join('\n\n');
 }
+/** The line that closes a {@link renderFloatingBox} box. */
+const BOX_END = '[End of box]';
+/**
+ * Render a `<boxed-text>` that sits in the body flow — a "Box 1", a highlights
+ * panel, a sidebar — set apart from the prose around it. Read as plain
+ * paragraphs, nothing marked where the box ended, so the body text after it
+ * read as part of the box (PMC10666927). The box opens with a line naming it by
+ * its label and `<caption>` title (`[Box: Box 1. Virtual unconference format]`,
+ * or `[Box]` when it carries neither), its content follows as
+ * {@link renderBoxedText} reads it, and {@link BOX_END} closes it. A box with no
+ * readable content — a lone `<graphic>` — keeps only its opening line when it
+ * is named, and renders nothing when it is not. (#210)
+ *
+ * A box that forms a section of its own (see {@link extractBodySections})
+ * needs none of this: its title is the section heading, and the next heading
+ * ends it.
+ */
+function renderFloatingBox(boxedText) {
+    const label = textContent(findOne(boxedText, 'label'));
+    const title = textContent(findOne(findOne(boxedText, 'caption'), 'title'));
+    const heading = [label, title].filter(Boolean).join(' ');
+    const opening = heading ? `[Box: ${heading}]` : '[Box]';
+    const content = renderBoxedText(boxedText, { withLabel: false, withTitle: false });
+    if (!content)
+        return heading ? opening : '';
+    return [opening, content, BOX_END].join('\n\n');
+}
 /**
  * A `<sec>` subtree as flat text blocks: each heading on its own line above its
  * prose, descendants following in document order. Used where a section has no
@@ -722,9 +918,9 @@ function renderBlockWithoutTitle(node) {
         case 'list':
             return renderList(node, 0, false);
         case 'boxed-text':
-            return renderBoxedText(node, false);
+            return renderBoxedText(node, { withTitle: false });
         default:
-            return renderBlock(node);
+            return renderBlock(node).text;
     }
 }
 /**
@@ -849,7 +1045,9 @@ function parseTableWrap(tableWrap, sectionTitle) {
     const id = attrOf(tableWrap, 'id');
     const label = textContent(findOne(tableWrap, 'label')) || undefined;
     const caption = renderCaption(findOne(tableWrap, 'caption'));
-    const footnotes = textContent(findOne(tableWrap, 'table-wrap-foot')) || undefined;
+    // One line per footnote or paragraph: a footer is a list of statements, and a
+    // marker run into the previous note (`…dose.*No patient…`) misattributes it. (#185)
+    const footnotes = lineTextContent(findOne(tableWrap, 'table-wrap-foot')) || undefined;
     // Some deposits offer both renderings inside <alternatives>; prefer the markup.
     const table = findOne(tableWrap, 'table') ?? findOne(findOne(tableWrap, 'alternatives'), 'table');
     const { rows, headerRowCount } = table
@@ -940,7 +1138,8 @@ function extractTableRows(table) {
                 allHeaderCells = false;
             sourceCells += 1;
             col = drainCarried(row, col);
-            const value = textContent(cell);
+            // `\n` wherever the cell breaks a line: `1.08<break/>2.44` is two values. (#185)
+            const value = lineTextContent(cell);
             const rowspan = spanOf(cell, 'rowspan');
             const width = Math.min(spanOf(cell, 'colspan'), MAX_TABLE_COLUMNS - col);
             for (let i = 0; i < width; i++) {
@@ -1059,30 +1258,41 @@ function renderCitationName(node) {
  * direct children in document order, joining author names with `, ` and
  * labeling typed `<pub-id>`s, so the output reads as a citation rather than a
  * token run. (#69)
+ *
+ * Two field pairs are joined the way a citation prints them rather than by a
+ * space, which read as two unrelated numbers: an `<fpage>` followed by its
+ * `<lpage>` is a page range (`56–71`, `i1–i51`), and a `<volume>` followed by
+ * its `<issue>` reads `16(1)`. Each token is kept verbatim. (#209)
  */
 function renderElementCitation(node) {
     const parts = [];
+    /** The field element that contributed the last part; undefined after anything else. */
+    let previous;
     for (const child of childrenOf(node)) {
         const tag = tagNameOf(child);
+        let part;
         if (tag === 'person-group') {
-            const names = childrenOf(child).map(renderCitationName).filter(Boolean);
-            if (names.length > 0)
-                parts.push(names.join(', '));
+            part = childrenOf(child).map(renderCitationName).filter(Boolean).join(', ');
         }
         else if (tag === 'pub-id') {
             const value = textContent(child);
-            if (value) {
-                const label = PUB_ID_LABELS[attrOf(child, 'pub-id-type') ?? ''];
-                parts.push(label ? `${label} ${value}` : value);
-            }
+            const label = PUB_ID_LABELS[attrOf(child, 'pub-id-type') ?? ''];
+            part = value && label ? `${label} ${value}` : value;
         }
         else {
             // Element field (source, volume, year, fpage, …) or a bare text node;
             // textContent renders both, and empty results drop out of the join.
-            const text = textContent(child);
-            if (text)
-                parts.push(text);
+            part = textContent(child);
         }
+        if (!part)
+            continue;
+        if (tag === 'lpage' && previous === 'fpage')
+            parts.push(`${parts.pop()}–${part}`);
+        else if (tag === 'issue' && previous === 'volume')
+            parts.push(`${parts.pop()}(${part})`);
+        else
+            parts.push(part);
+        previous = tag;
     }
     return parts.join(' ');
 }
@@ -1096,38 +1306,103 @@ function renderElementCitation(node) {
  */
 const NAME_WRAPPER_TAGS = new Set(['name', 'string-name', 'person-group']);
 /**
- * Serialize a `<name>` / `<string-name>` / `<person-group>` subtree, applying
- * the same rule `renderMixedCitation` applies to its own children: a single
- * space between two adjacent elements that carry nothing between them, and
- * source text emitted verbatim. `<person-group>` separates its names with real
- * `, ` text nodes and `<string-name>` usually separates surname from given
- * names with a newline, so a fixed separator would double punctuation the
- * source already has — spacing only the zero-gap transitions leaves those
- * records byte-identical. Returns raw text; the caller collapses whitespace
- * once over the finished citation.
+ * The members of an author list: each names one contributor, or (`<etal>`)
+ * stands for the rest. Two of them with nothing but whitespace between them are
+ * two list entries, which the source left for the reader to separate. (#209)
  */
-function renderNameWrapper(node) {
-    let rendered = '';
-    let prevWasElement = false;
+const PERSON_TAGS = new Set(['name', 'string-name', 'collab', 'etal']);
+/** What an empty `<etal/>` stands for. (#209) */
+const SUPPLIED_ETAL = 'et al.';
+/** Any character other than whitespace. */
+const VISIBLE_TEXT = /\S/;
+/**
+ * Render one child element of a `<mixed-citation>` or name wrapper. `before` is
+ * the citation text written so far, which a `<pub-id>` reads for a literal
+ * prefix already naming its type. An `<etal>` reads as its own text, or as
+ * `et al.` when it is empty — as nearly every deposit leaves it.
+ */
+function renderCitationPart(child, tag, before) {
+    if (tag === 'pub-id') {
+        const value = textContent(child);
+        const type = attrOf(child, 'pub-id-type') ?? '';
+        const label = PUB_ID_LABELS[type];
+        if (value && label && !hasLiteralIdPrefix(before, type)) {
+            return { text: `${label} ${value}`, labeled: true, suppliedEtal: false };
+        }
+        return { text: value, labeled: false, suppliedEtal: false };
+    }
+    if (NAME_WRAPPER_TAGS.has(tag))
+        return { ...renderCitationRun(child, true), labeled: false };
+    const text = rawTextContent(child);
+    if (tag === 'etal' && !text)
+        return { text: SUPPLIED_ETAL, labeled: false, suppliedEtal: true };
+    return { text, labeled: false, suppliedEtal: false };
+}
+/**
+ * Serialize a `<mixed-citation>` (`wrapper: false`) or a `<name>` /
+ * `<string-name>` / `<person-group>` inside one (`wrapper: true`), emitting
+ * source text verbatim and writing a separator only where the source left
+ * none:
+ *
+ * - Two adjacent author-list members ({@link PERSON_TAGS}) with nothing but
+ *   whitespace between them are joined by `, `: `Zwierenga F, van Veggel B,
+ *   Hendriks LEL, et al.` rather than `Zwierenga F van Veggel B Hendriks LEL`.
+ *   (#209)
+ * - Any other two elements with nothing between them get one space: a
+ *   `<surname>` and its `<given-names>`, a title and the volume after it.
+ *   (#115, #123, #124)
+ * - A label this renderer inserts is separated from whatever precedes it. (#115)
+ * - A source `.` straight after a supplied `et al.` closes it rather than
+ *   doubling its period (`<etal/></person-group>. <article-title>`). (#209)
+ *
+ * Gaps the source already fills — `, ` text between names, a newline between a
+ * `<string-name>`'s parts — are kept as written, so a fixed separator never
+ * doubles punctuation the source has. Inside a wrapper an element that renders
+ * nothing is skipped; at the citation's own level it still counts as the
+ * element the next one follows. Returns raw text; the caller collapses
+ * whitespace once over the finished citation.
+ *
+ * Whitespace is held in `gap` until what follows it decides whether it is
+ * written, so no step re-reads the text already written and the cost stays
+ * linear in the size of the citation.
+ */
+function renderCitationRun(node, wrapper) {
+    let text = '';
+    /** Whitespace not yet written: the end of the last element's text, then source whitespace after it. */
+    let gap = '';
+    /** The element written last, while no visible source text has followed it. */
+    let previous;
+    let suppliedEtal = false;
     for (const child of childrenOf(node)) {
         if (isTextNode(child)) {
-            const raw = textOf(child);
-            if (raw) {
-                rendered += raw;
-                prevWasElement = false;
+            let raw = textOf(child);
+            if (!VISIBLE_TEXT.test(raw)) {
+                gap += raw;
+                continue;
             }
+            if (suppliedEtal)
+                raw = raw.replace(/^(\s*)\./, '$1');
+            text += gap + raw;
+            gap = '';
+            previous = undefined;
+            suppliedEtal = false;
             continue;
         }
         const tag = tagNameOf(child) ?? '';
-        const part = NAME_WRAPPER_TAGS.has(tag) ? renderNameWrapper(child) : rawTextContent(child);
-        if (!part)
+        const part = renderCitationPart(child, tag, text);
+        if (!part.text && (wrapper || tag === 'pub-id'))
             continue;
-        if (prevWasElement)
-            rendered += ' ';
-        rendered += part;
-        prevWasElement = true;
+        if (previous && PERSON_TAGS.has(previous) && PERSON_TAGS.has(tag))
+            text += ', ';
+        else
+            text += (previous && !gap) || part.labeled ? `${gap} ` : gap;
+        const body = part.text.trimEnd();
+        text += body;
+        gap = part.text.slice(body.length);
+        previous = tag;
+        suppliedEtal = part.suppliedEtal;
     }
-    return rendered;
+    return { text: text + gap, suppliedEtal };
 }
 /**
  * True when the citation text emitted so far already ends with a literal prefix
@@ -1158,49 +1433,22 @@ function hasLiteralIdPrefix(rendered, pubIdType) {
  * styles routinely close the prose on punctuation (`… (2020).`, `…021]`) and a
  * label butted against that reads as one token. Source transitions that already
  * carry punctuation or whitespace are emitted unchanged; the trailing whitespace
- * collapse keeps a whitespace-only gap at one space.
+ * collapse keeps a whitespace-only gap at one space. An author list whose names
+ * the source left unseparated reads with `, ` between them and `et al.` for an
+ * empty `<etal/>` (see {@link renderCitationRun}). (#209)
  */
 function renderMixedCitation(node) {
-    let rendered = '';
-    let prevWasElement = false;
-    for (const child of childrenOf(node)) {
-        if (isTextNode(child)) {
-            const raw = textOf(child);
-            if (raw) {
-                rendered += raw;
-                prevWasElement = false;
-            }
-            continue;
-        }
-        const tag = tagNameOf(child) ?? '';
-        let part;
-        let labeled = false;
-        if (tag === 'pub-id') {
-            const value = textContent(child);
-            if (!value)
-                continue;
-            const type = attrOf(child, 'pub-id-type') ?? '';
-            const label = PUB_ID_LABELS[type];
-            if (label && !hasLiteralIdPrefix(rendered, type)) {
-                labeled = true;
-                part = `${label} ${value}`;
-            }
-            else {
-                part = value;
-            }
-        }
-        else if (NAME_WRAPPER_TAGS.has(tag)) {
-            part = renderNameWrapper(child);
-        }
-        else {
-            part = rawTextContent(child);
-        }
-        if (prevWasElement || labeled)
-            rendered += ' ';
-        rendered += part;
-        prevWasElement = true;
-    }
-    return rendered.replace(/\s+/g, ' ').trim();
+    return renderCitationRun(node, false).text.replace(/\s+/g, ' ').trim();
+}
+/**
+ * A `<ref>`'s `<label>`, without the one pair of square brackets some deposits
+ * print it in: `[19]` is reference 19, and the tool already writes each
+ * reference's label and id inside brackets of its own (`[19 R19]`, not
+ * `[[19] R19]`). Any other label — `1.`, `(3)`, `A12` — is kept as printed.
+ * (#209)
+ */
+function referenceLabel(label) {
+    return textContent(label).replace(/^\[([^[\]]+)\]$/, '$1') || undefined;
 }
 /**
  * Extract references from anywhere under `root` — pass the `<article>` node to
@@ -1247,7 +1495,7 @@ export function extractReferences(root) {
                 continue;
             if (id)
                 seenIds.add(id);
-            const label = textContent(findOne(ref, 'label')) || undefined;
+            const label = referenceLabel(findOne(ref, 'label'));
             results.push({
                 ...(id && { id }),
                 ...(label && { label }),