import { describe, it, expect } from "vitest";
import { parseArticles, extractTag, stripTags, extractAllTags } from "../src/xml-utils.js";
const SAMPLE_XML = `<?xml version="1.0" ?>
<PubmedArticleSet>
<PubmedArticle>
<MedlineCitation>
<PMID Version="1">12345678</PMID>
<Article>
<Journal>
<Title>Nature Medicine</Title>
<JournalIssue>
<PubDate>
<Year>2024</Year>
<Month>Jan</Month>
<Day>15</Day>
</PubDate>
</JournalIssue>
</Journal>
<ArticleTitle>CRISPR-based gene therapy for sickle cell disease</ArticleTitle>
<Abstract>
<AbstractText Label="BACKGROUND">Sickle cell disease affects millions worldwide.</AbstractText>
<AbstractText Label="METHODS">We conducted a phase 3 trial.</AbstractText>
</Abstract>
<AuthorList>
<Author>
<LastName>Smith</LastName>
<ForeName>John A</ForeName>
</Author>
<Author>
<LastName>Doe</LastName>
<ForeName>Jane B</ForeName>
</Author>
</AuthorList>
</Article>
<MeshHeadingList>
<MeshHeading>
<DescriptorName>CRISPR-Cas Systems</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName>Anemia, Sickle Cell</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData>
<ArticleIdList>
<ArticleId IdType="doi">10.1038/s41591-024-00001-1</ArticleId>
</ArticleIdList>
</PubmedData>
</PubmedArticle>
</PubmedArticleSet>`;
describe("XML parsing", () => {
it("extractTag gets content", () => {
expect(extractTag("<Foo>bar</Foo>", "Foo")).toBe("bar");
});
it("extractTag returns empty for missing tag", () => {
expect(extractTag("<Foo>bar</Foo>", "Baz")).toBe("");
});
it("stripTags removes XML tags", () => {
expect(stripTags("<b>hello</b> <i>world</i>")).toBe("hello world");
});
it("extractAllTags gets multiple matches", () => {
const result = extractAllTags("<A>1</A><A>2</A><A>3</A>", "A");
expect(result).toEqual(["1", "2", "3"]);
});
});
describe("parseArticles", () => {
it("parses a PubMed XML article correctly", () => {
const articles = parseArticles(SAMPLE_XML);
expect(articles).toHaveLength(1);
const a = articles[0];
expect(a.pmid).toBe("12345678");
expect(a.title).toBe("CRISPR-based gene therapy for sickle cell disease");
expect(a.authors).toEqual(["John A Smith", "Jane B Doe"]);
expect(a.journal).toBe("Nature Medicine");
expect(a.pubDate).toBe("2024 Jan 15");
expect(a.doi).toBe("10.1038/s41591-024-00001-1");
expect(a.meshTerms).toContain("CRISPR-Cas Systems");
expect(a.meshTerms).toContain("Anemia, Sickle Cell");
expect(a.abstract).toContain("Sickle cell disease");
expect(a.abstract).toContain("phase 3 trial");
});
});
