pubmed_parser/pmc/
domain.rs

1//! PMC domain models based on JATS Archiving 1.4 DTD
2//!
3//! **This module is the single model layer for PMC full-text articles.**
4//! All parsing produces these types directly; there is no separate
5//! intermediate parser model.
6//!
7//! The type hierarchy mirrors the JATS `<article>` content model:
8//!
9//! ```text
10//! <article>            → PmcArticle
11//!   <front>            → Front
12//!     <journal-meta>   → JournalMeta
13//!     <article-meta>   → ArticleMeta (ids, TitleGroup, contributors,
14//!                         pub info, history, Permissions, Abstract,
15//!                         keywords, funding)
16//!   <body>             → Body (Vec<Section>, recursive)
17//!   <back>             → Back (ack, COI, Vec<Reference>, appendices, glossary)
18//! ```
19//!
20//! Design principles:
21//! - DTD-faithful: every field maps to a JATS element/attribute, structured
22//!   following the DTD hierarchy and declaration order
23//! - No extraction concerns: fields like `file_path` or inferred `file_type` are excluded
24//! - Type-safe IDs: uses `PmcId` / `PubMedId` instead of raw strings
25//! - Reuses shared types: `Author` and `HistoryDate` from `common::models`
26//! - Text mining ready: structured abstracts, table content, formulas, definitions
27//!
28//! Documented deviations from strict DTD structure:
29//! - `supplementary_materials` and `data_availability` live on [`PmcArticle`]
30//!   because in real PMC XML they appear in `<body>` sections, `<back>`, or
31//!   `<floats-group>`; the parser collects them document-wide without
32//!   tracking their position
33//! - `<contrib-group>` is flattened to `Vec<Author>` (only author contribs
34//!   are modeled)
35//!
36//! Flattened read access is provided through accessor methods on
37//! [`PmcArticle`] (e.g. [`PmcArticle::title`], [`PmcArticle::sections`]).
38
39use crate::common::{Author, HistoryDate, PmcId, PubMedId, PublicationDate};
40use serde::{Deserialize, Serialize};
41
42// ============================================================================
43// Top-level article
44// ============================================================================
45
46/// PMC full-text article.
47///
48/// Maps to JATS `<article>`: `front, body?, back?`.
49///
50/// DTD: <https://jats.nlm.nih.gov/archiving/tag-library/1.4/element/article.html>
51#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
52pub struct PmcArticle {
53    /// Article type. From `<article article-type="...">` attribute.
54    pub article_type: Option<String>,
55    /// Front matter. From `<front>`.
56    pub front: Front,
57    /// Article body. From `<body>`. `None` when the article has no body
58    /// (e.g., metadata-only records).
59    pub body: Option<Body>,
60    /// Back matter. From `<back>`. `None` when the article has no back matter.
61    pub back: Option<Back>,
62
63    // --- Document-wide collections (deviation from strict DTD placement) ---
64    /// Supplementary materials. From `<supplementary-material>`, collected
65    /// from the entire document (`<body>` sections, `<back>`, or `<floats-group>`).
66    pub supplementary_materials: Vec<SupplementaryMaterial>,
67    /// Data availability statement. From `<sec sec-type="data-availability">`
68    /// or `<notes notes-type="data-availability">`, wherever it appears.
69    pub data_availability: Option<String>,
70}
71
72// ============================================================================
73// Front matter (<front>)
74// ============================================================================
75
76/// Front matter.
77///
78/// Maps to JATS `<front>`: `journal-meta?, article-meta?`.
79#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
80pub struct Front {
81    /// Journal metadata. From `<journal-meta>`.
82    pub journal_meta: JournalMeta,
83    /// Article metadata. From `<article-meta>`.
84    pub article_meta: ArticleMeta,
85}
86
87/// Journal metadata.
88///
89/// Maps to JATS `<journal-meta>`. Note that `volume` and `issue` are intentionally
90/// excluded here — in the DTD they belong to `<article-meta>`, not `<journal-meta>`,
91/// and are placed on [`ArticleMeta`] accordingly.
92#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
93pub struct JournalMeta {
94    /// Journal title. From `<journal-title-group>/<journal-title>`.
95    pub title: String,
96    /// Abbreviated journal title. From `<journal-id journal-id-type="iso-abbrev">`
97    /// or `<abbrev-journal-title>`.
98    pub abbreviation: Option<String>,
99    /// Print ISSN. From `<issn pub-type="ppub">`.
100    pub issn_print: Option<String>,
101    /// Electronic ISSN. From `<issn pub-type="epub">`.
102    pub issn_electronic: Option<String>,
103    /// Publisher name. From `<publisher>/<publisher-name>`.
104    pub publisher: Option<String>,
105}
106
107/// Article metadata.
108///
109/// Maps to JATS `<article-meta>`. Fields follow the DTD declaration order:
110/// `article-id*, article-categories?, title-group, contrib-group*, pub-date*,
111/// volume?, issue?, fpage?, lpage?, elocation-id?, history?, permissions?,
112/// abstract*, kwd-group*, funding-group*`.
113#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
114pub struct ArticleMeta {
115    // --- Identifiers (<article-id>) ---
116    /// PMC ID (e.g., PMC7906746). From `<article-id pub-id-type="pmc">`.
117    pub pmcid: PmcId,
118    /// PubMed ID. From `<article-id pub-id-type="pmid">`.
119    pub pmid: Option<PubMedId>,
120    /// DOI. From `<article-id pub-id-type="doi">`.
121    pub doi: Option<String>,
122
123    /// Subject categories. From `<article-categories>/<subj-group>/<subject>`.
124    pub categories: Vec<String>,
125
126    /// Title group. From `<title-group>`.
127    pub title_group: TitleGroup,
128
129    /// Authors. From `<contrib-group>/<contrib contrib-type="author">`.
130    pub authors: Vec<Author>,
131
132    /// Publication dates (epub, ppub, collection, etc.). From `<pub-date>`.
133    pub pub_dates: Vec<PublicationDate>,
134    /// Volume number. From `<volume>`.
135    pub volume: Option<String>,
136    /// Issue number. From `<issue>`.
137    pub issue: Option<String>,
138    /// First page. From `<fpage>`.
139    pub fpage: Option<String>,
140    /// Last page. From `<lpage>`.
141    pub lpage: Option<String>,
142    /// Electronic location ID. From `<elocation-id>`.
143    pub elocation_id: Option<String>,
144
145    /// Publication history dates. From `<history>/<date>`.
146    pub history: Vec<HistoryDate>,
147
148    /// Copyright and licensing. From `<permissions>`.
149    pub permissions: Option<Permissions>,
150
151    /// Abstracts. From `<abstract>` (repeatable in the DTD, e.g. a main
152    /// abstract plus a graphical or teaser abstract).
153    pub abstracts: Vec<Abstract>,
154
155    /// Keywords. From `<kwd-group>/<kwd>`.
156    pub keywords: Vec<String>,
157
158    /// Funding information. From `<funding-group>/<award-group>`.
159    pub funding: Vec<FundingInfo>,
160}
161
162/// Title group.
163///
164/// Maps to JATS `<title-group>`.
165#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
166pub struct TitleGroup {
167    /// Article title. From `<article-title>`.
168    pub article_title: String,
169    /// Article subtitle. From `<subtitle>`.
170    pub subtitle: Option<String>,
171}
172
173/// Copyright and licensing information.
174///
175/// Maps to JATS `<permissions>`.
176#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
177pub struct Permissions {
178    /// Copyright statement. From `<copyright-statement>`
179    /// (falls back to `<copyright-year>`).
180    pub copyright_statement: Option<String>,
181    /// License. From `<license>`.
182    pub license: Option<License>,
183}
184
185/// License information.
186///
187/// Maps to JATS `<license>`.
188#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
189pub struct License {
190    /// License URL. From `<license xlink:href="...">` or `<ali:license_ref>`.
191    pub href: Option<String>,
192    /// License text. From `<license-p>` content.
193    pub text: Option<String>,
194}
195
196/// Abstract.
197///
198/// Maps to JATS `<abstract>`. The DTD allows multiple abstracts
199/// distinguished by `@abstract-type`.
200#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
201pub struct Abstract {
202    /// Abstract type (e.g., "graphical", "teaser"). From `<abstract abstract-type="...">`.
203    pub abstract_type: Option<String>,
204    /// Plain abstract text (flattened). Concatenation of all `<p>` texts.
205    pub text: String,
206    /// Structured abstract sections. From `<abstract>/<sec>`.
207    /// Present when the abstract has labeled sections (e.g., Background, Methods, Results).
208    pub sections: Vec<AbstractSection>,
209}
210
211/// Structured abstract section.
212///
213/// Maps to `<abstract>/<sec>`. Many biomedical journals use structured abstracts
214/// with labeled sections (Background, Methods, Results, Conclusions).
215/// This structure preserves the section boundaries for text mining pipelines
216/// that need to process abstract sections independently.
217#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
218pub struct AbstractSection {
219    /// Section label (e.g., "Background", "Methods", "Results", "Conclusions").
220    /// From `<title>` inside `<abstract>/<sec>`.
221    pub label: Option<String>,
222    /// Section text content. From `<p>` inside `<abstract>/<sec>`.
223    pub text: String,
224}
225
226// ============================================================================
227// Body content (<body>)
228// ============================================================================
229
230/// Article body.
231///
232/// Maps to JATS `<body>`: `(p | sec | ...)*`.
233#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
234pub struct Body {
235    /// Article sections. From `<body>/<sec>`.
236    pub sections: Vec<Section>,
237}
238
239/// Article section.
240///
241/// Maps to JATS `<sec>`. Sections form a recursive tree via `subsections`.
242/// Figures, tables, and formulas that appear inline within the section are
243/// collected in their respective fields.
244#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
245pub struct Section {
246    /// Section ID. From `<sec id="...">`.
247    pub id: Option<String>,
248    /// Section type. From `<sec sec-type="...">`.
249    /// Common values: `"intro"`, `"methods"`, `"results"`, `"discussion"`,
250    /// `"conclusions"`, `"supplementary-material"`, `"data-availability"`.
251    pub section_type: Option<String>,
252    /// Section label/number (e.g., "1.", "2.1"). From `<label>`.
253    pub label: Option<String>,
254    /// Section title. From `<title>`.
255    pub title: Option<String>,
256    /// Concatenated paragraph text. From `<p>` elements.
257    pub content: String,
258    /// Nested subsections. From child `<sec>` elements.
259    pub subsections: Vec<Section>,
260    /// Figures within this section. From `<fig>` elements.
261    pub figures: Vec<Figure>,
262    /// Tables within this section. From `<table-wrap>` elements.
263    pub tables: Vec<Table>,
264    /// Display formulas within this section. From `<disp-formula>` elements.
265    pub formulas: Vec<Formula>,
266}
267
268/// Figure.
269///
270/// Maps to JATS `<fig>`. The `graphic_href` field contains the domain-level
271/// reference to the graphic file (from `<graphic xlink:href="...">`).
272/// Actual file extraction paths and sizes belong to the client layer's
273/// `ExtractedFigure` type, not here.
274#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
275pub struct Figure {
276    /// Figure ID. From `<fig id="...">`.
277    pub id: String,
278    /// Figure label (e.g., "Figure 1"). From `<label>`.
279    pub label: Option<String>,
280    /// Figure caption. From `<caption>/<p>`.
281    pub caption: String,
282    /// Alt text. From `<alt-text>`.
283    pub alt_text: Option<String>,
284    /// Figure type (e.g., "figure", "scheme", "chart"). From `<fig fig-type="...">`.
285    pub fig_type: Option<String>,
286    /// Graphic href from the XML. From `<graphic xlink:href="...">`.
287    pub graphic_href: Option<String>,
288}
289
290/// Table wrapper.
291///
292/// Maps to JATS `<table-wrap>`. Table body is parsed into structured rows/cells
293/// for direct programmatic access without requiring downstream HTML parsing.
294#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
295pub struct Table {
296    /// Table ID. From `<table-wrap id="...">`.
297    pub id: String,
298    /// Table label (e.g., "Table 1"). From `<label>`.
299    pub label: Option<String>,
300    /// Table caption. From `<caption>/<p>`.
301    pub caption: String,
302    /// Header rows. From `<thead>/<tr>`.
303    pub head: Vec<TableRow>,
304    /// Body rows. From `<tbody>/<tr>` (or direct `<tr>` if no `<tbody>`).
305    pub body: Vec<TableRow>,
306    /// Table footnotes. From `<table-wrap-foot>/<fn>`.
307    pub footnotes: Vec<String>,
308}
309
310/// A single table row.
311///
312/// Maps to XHTML `<tr>` inside JATS `<table>`.
313#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
314pub struct TableRow {
315    /// Cells in this row. From `<th>` or `<td>` elements.
316    pub cells: Vec<TableCell>,
317}
318
319/// A single table cell.
320///
321/// Maps to XHTML `<th>` or `<td>` inside JATS `<table>`.
322#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
323pub struct TableCell {
324    /// Cell text content (XML tags stripped).
325    pub content: String,
326    /// Whether this is a header cell (`<th>`) vs data cell (`<td>`).
327    pub is_header: bool,
328    /// Column span. From `@colspan` attribute.
329    pub colspan: Option<u32>,
330    /// Row span. From `@rowspan` attribute.
331    pub rowspan: Option<u32>,
332}
333
334/// Display formula.
335///
336/// Maps to JATS `<disp-formula>`. Formulas can be represented as MathML,
337/// TeX/LaTeX, plain text, or as graphic images. The `notation` field indicates
338/// which representation is stored in `content`.
339#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
340pub struct Formula {
341    /// Formula ID. From `<disp-formula id="...">`.
342    pub id: Option<String>,
343    /// Formula label (e.g., "1", "(1)"). From `<label>`.
344    pub label: Option<String>,
345    /// Formula content. From `<tex-math>`, `<mml:math>`, or text content.
346    pub content: Option<String>,
347    /// Notation type indicating the format of `content`.
348    /// `"tex"` for `<tex-math>`, `"mathml"` for `<mml:math>`, `"text"` for plain text.
349    pub notation: Option<String>,
350    /// Graphic href for image-based formulas. From `<graphic xlink:href="...">`.
351    pub graphic_href: Option<String>,
352}
353
354// ============================================================================
355// Back matter (<back>)
356// ============================================================================
357
358/// Back matter.
359///
360/// Maps to JATS `<back>`: `(ack | app-group | bio | fn-group | glossary |
361/// ref-list | notes | sec)*`.
362#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
363pub struct Back {
364    /// Acknowledgments. From `<ack>`.
365    pub acknowledgments: Option<String>,
366    /// Conflict of interest statement. From `<fn-group>/<fn fn-type="COI-statement">`
367    /// or `<sec>` whose title mentions conflicts/competing interests.
368    pub conflict_of_interest: Option<String>,
369    /// Reference list. From `<ref-list>/<ref>`.
370    pub references: Vec<Reference>,
371    /// Appendices. From `<app-group>/<app>`.
372    pub appendices: Vec<Section>,
373    /// Glossary definitions. From `<glossary>/<def-list>`.
374    pub glossary: Vec<Definition>,
375}
376
377/// Reference citation.
378///
379/// Maps to JATS `<ref>` containing `<element-citation>` or `<mixed-citation>`.
380#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
381pub struct Reference {
382    /// Reference ID. From `<ref id="...">`.
383    pub id: String,
384    /// Publication type. From `<element-citation publication-type="...">`.
385    /// Common values: `"journal"`, `"book"`, `"web"`, `"other"`.
386    pub publication_type: Option<String>,
387    /// Article or chapter title. From `<article-title>` or `<chapter-title>`.
388    pub title: Option<String>,
389    /// Authors. From `<person-group>/<name>`.
390    pub authors: Vec<Author>,
391    /// Source (journal name or book title). From `<source>`.
392    pub source: Option<String>,
393    /// Publication year. From `<year>`.
394    pub year: Option<String>,
395    /// Volume. From `<volume>`.
396    pub volume: Option<String>,
397    /// Issue. From `<issue>`.
398    pub issue: Option<String>,
399    /// Page range. From `<fpage>`-`<lpage>`.
400    pub pages: Option<String>,
401    /// PubMed ID. From `<pub-id pub-id-type="pmid">`.
402    pub pmid: Option<String>,
403    /// DOI. From `<pub-id pub-id-type="doi">`.
404    pub doi: Option<String>,
405}
406
407impl Reference {
408    /// Format a human-readable citation string.
409    pub fn format_citation(&self) -> String {
410        let mut parts = Vec::new();
411
412        if !self.authors.is_empty() {
413            let author_names: Vec<String> = self
414                .authors
415                .iter()
416                .map(|a| a.full_name.clone())
417                .filter(|n| !n.trim().is_empty())
418                .collect();
419            if !author_names.is_empty() {
420                parts.push(author_names.join(", "));
421            }
422        }
423
424        if let Some(title) = &self.title
425            && !title.trim().is_empty()
426        {
427            parts.push(title.clone());
428        }
429
430        if let Some(source) = &self.source
431            && !source.trim().is_empty()
432        {
433            let mut source_part = source.clone();
434            if let Some(year) = &self.year
435                && !year.trim().is_empty()
436                && year != "n.d."
437            {
438                source_part.push_str(&format!(" ({year})"));
439            }
440            if let Some(volume) = &self.volume
441                && !volume.trim().is_empty()
442            {
443                source_part.push_str(&format!(" {volume}"));
444                if let Some(issue) = &self.issue
445                    && !issue.trim().is_empty()
446                {
447                    source_part.push_str(&format!("({issue})"));
448                }
449            }
450            if let Some(pages) = &self.pages
451                && !pages.trim().is_empty()
452            {
453                source_part.push_str(&format!(": {pages}"));
454            }
455            parts.push(source_part);
456        }
457
458        let result = parts.join(". ");
459        if result.trim().is_empty() {
460            format!("Reference {}", self.id)
461        } else {
462            result
463        }
464    }
465}
466
467/// Funding information.
468///
469/// Maps to JATS `<funding-group>/<award-group>`.
470#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
471pub struct FundingInfo {
472    /// Funding source/agency. From `<funding-source>`.
473    pub source: String,
474    /// Grant/award ID. From `<award-id>`.
475    pub award_id: Option<String>,
476    /// Funding statement. From `<funding-statement>`.
477    pub statement: Option<String>,
478}
479
480/// Supplementary material.
481///
482/// Maps to JATS `<supplementary-material>`. Only contains domain-level
483/// data from the XML. Inferred values like file type (derived from URL extension)
484/// and layout attributes like `position` are excluded.
485#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
486pub struct SupplementaryMaterial {
487    /// Material ID. From `<supplementary-material id="...">`.
488    pub id: String,
489    /// Content type. From `<supplementary-material content-type="...">`.
490    pub content_type: Option<String>,
491    /// Title or label. From `<label>` or `<caption>/<title>`.
492    pub title: Option<String>,
493    /// Description. From `<caption>/<p>`.
494    pub description: Option<String>,
495    /// Resource href. From `<supplementary-material xlink:href="...">`.
496    pub href: Option<String>,
497}
498
499impl SupplementaryMaterial {
500    /// Check if this material is a tar archive based on the href extension.
501    pub fn is_tar_file(&self) -> bool {
502        if let Some(url) = &self.href {
503            url.ends_with(".tar")
504                || url.ends_with(".tar.gz")
505                || url.ends_with(".tar.bz2")
506                || url.ends_with(".tgz")
507        } else {
508            false
509        }
510    }
511
512    /// Get file extension from the href.
513    pub fn get_file_extension(&self) -> Option<String> {
514        if let Some(url) = &self.href
515            && let Some(filename) = url.split('/').next_back()
516            && let Some(dot_index) = filename.rfind('.')
517        {
518            return Some(filename[dot_index + 1..].to_lowercase());
519        }
520        None
521    }
522
523    /// Check if this is an archive file (zip, tar, etc.).
524    pub fn is_archive(&self) -> bool {
525        if let Some(ext) = self.get_file_extension() {
526            matches!(
527                ext.as_str(),
528                "zip" | "tar" | "gz" | "bz2" | "tgz" | "rar" | "7z"
529            )
530        } else {
531            false
532        }
533    }
534}
535
536// ============================================================================
537// Text mining support types
538// ============================================================================
539
540/// Term definition.
541///
542/// Maps to JATS `<def-list>/<def-item>`. Used for abbreviation lists and
543/// glossaries commonly found in biomedical articles.
544///
545/// Example XML:
546/// ```xml
547/// <def-item>
548///   <term>HPV</term>
549///   <def><p>Human papillomavirus</p></def>
550/// </def-item>
551/// ```
552#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
553pub struct Definition {
554    /// Term being defined. From `<term>`.
555    pub term: String,
556    /// Definition text. From `<def>/<p>`.
557    pub definition: String,
558}
559
560// ============================================================================
561// Aggregate accessors
562// ============================================================================
563
564impl PmcArticle {
565    /// PMC ID of this article (aggregate identity).
566    pub fn pmcid(&self) -> &PmcId {
567        &self.front.article_meta.pmcid
568    }
569
570    /// PubMed ID, if present.
571    pub fn pmid(&self) -> Option<&PubMedId> {
572        self.front.article_meta.pmid.as_ref()
573    }
574
575    /// DOI, if present.
576    pub fn doi(&self) -> Option<&str> {
577        self.front.article_meta.doi.as_deref()
578    }
579
580    /// Article title.
581    pub fn title(&self) -> &str {
582        &self.front.article_meta.title_group.article_title
583    }
584
585    /// Article subtitle, if present.
586    pub fn subtitle(&self) -> Option<&str> {
587        self.front.article_meta.title_group.subtitle.as_deref()
588    }
589
590    /// Authors.
591    pub fn authors(&self) -> &[Author] {
592        &self.front.article_meta.authors
593    }
594
595    /// Journal metadata.
596    pub fn journal(&self) -> &JournalMeta {
597        &self.front.journal_meta
598    }
599
600    /// Publication dates.
601    pub fn pub_dates(&self) -> &[PublicationDate] {
602        &self.front.article_meta.pub_dates
603    }
604
605    /// Subject categories.
606    pub fn categories(&self) -> &[String] {
607        &self.front.article_meta.categories
608    }
609
610    /// Volume number, if present.
611    pub fn volume(&self) -> Option<&str> {
612        self.front.article_meta.volume.as_deref()
613    }
614
615    /// Issue number, if present.
616    pub fn issue(&self) -> Option<&str> {
617        self.front.article_meta.issue.as_deref()
618    }
619
620    /// Keywords.
621    pub fn keywords(&self) -> &[String] {
622        &self.front.article_meta.keywords
623    }
624
625    /// Funding information.
626    pub fn funding(&self) -> &[FundingInfo] {
627        &self.front.article_meta.funding
628    }
629
630    /// Publication history dates.
631    pub fn history(&self) -> &[HistoryDate] {
632        &self.front.article_meta.history
633    }
634
635    /// Text of the main abstract (first `<abstract>`), if present.
636    pub fn abstract_text(&self) -> Option<&str> {
637        self.front
638            .article_meta
639            .abstracts
640            .first()
641            .map(|a| a.text.as_str())
642    }
643
644    /// Copyright statement, if present.
645    pub fn copyright(&self) -> Option<&str> {
646        self.front
647            .article_meta
648            .permissions
649            .as_ref()
650            .and_then(|p| p.copyright_statement.as_deref())
651    }
652
653    /// License text, if present.
654    pub fn license_text(&self) -> Option<&str> {
655        self.front
656            .article_meta
657            .permissions
658            .as_ref()
659            .and_then(|p| p.license.as_ref())
660            .and_then(|l| l.text.as_deref())
661    }
662
663    /// License URL, if present.
664    pub fn license_url(&self) -> Option<&str> {
665        self.front
666            .article_meta
667            .permissions
668            .as_ref()
669            .and_then(|p| p.license.as_ref())
670            .and_then(|l| l.href.as_deref())
671    }
672
673    /// Body sections (empty slice when the article has no body).
674    pub fn sections(&self) -> &[Section] {
675        self.body.as_ref().map_or(&[], |b| b.sections.as_slice())
676    }
677
678    /// References (empty slice when the article has no back matter).
679    pub fn references(&self) -> &[Reference] {
680        self.back.as_ref().map_or(&[], |b| b.references.as_slice())
681    }
682
683    /// Acknowledgments, if present.
684    pub fn acknowledgments(&self) -> Option<&str> {
685        self.back
686            .as_ref()
687            .and_then(|b| b.acknowledgments.as_deref())
688    }
689
690    /// Conflict of interest statement, if present.
691    pub fn conflict_of_interest(&self) -> Option<&str> {
692        self.back
693            .as_ref()
694            .and_then(|b| b.conflict_of_interest.as_deref())
695    }
696
697    /// Get tar files from supplementary materials.
698    pub fn get_tar_files(&self) -> Vec<&SupplementaryMaterial> {
699        self.supplementary_materials
700            .iter()
701            .filter(|m| m.is_tar_file())
702            .collect()
703    }
704
705    /// Get all archive files from supplementary materials.
706    pub fn get_archive_files(&self) -> Vec<&SupplementaryMaterial> {
707        self.supplementary_materials
708            .iter()
709            .filter(|m| m.is_archive())
710            .collect()
711    }
712
713    /// Check if the article has supplementary materials.
714    pub fn has_supplementary_materials(&self) -> bool {
715        !self.supplementary_materials.is_empty()
716    }
717
718    /// Get supplementary materials by content type.
719    pub fn get_supplementary_materials_by_type(
720        &self,
721        content_type: &str,
722    ) -> Vec<&SupplementaryMaterial> {
723        self.supplementary_materials
724            .iter()
725            .filter(|m| m.content_type.as_ref().is_some_and(|ct| ct == content_type))
726            .collect()
727    }
728}
pubmed_parser/pmc/domain.rs

pubmed_parser/pmc/
domain.rs
