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mode 100644 index 0000000..5ad24db --- /dev/null +++ b/Cargo.toml @@ -0,0 +1,9 @@ +[workspace] +resolver = "2" +members = ["feeder-plugin/*"] + +[workspace.package] +edition = "2021" +rust-version = "1.85" +license = "MIT" +repository = "https://github.com/worph/meta-feeder-europepmc" diff --git a/feeder-plugin/europepmc-feeder/Cargo.toml b/feeder-plugin/europepmc-feeder/Cargo.toml new file mode 100644 index 0000000..a7295e1 --- /dev/null +++ b/feeder-plugin/europepmc-feeder/Cargo.toml @@ -0,0 +1,40 @@ +[package] +name = "europepmc-feeder" +version = "0.1.0" +edition.workspace = true +rust-version.workspace = true +license.workspace = true +publish = false + +# Europe PMC open-access life-science literature. Open, keyless. +# Upstream: Europe PMC (www.ebi.ac.uk/europepmc/webservices/rest) + +[lib] +name = "europepmc_feeder" +path = "src/lib.rs" + +[[bin]] +name = "europepmc-feeder" +path = "src/main.rs" + +[dependencies] +# The SDK is a dependency, not a vendored copy. Pinned by rev until the first +# tag; see docs/project-architecture/feeder-architecture.md §8. +meta-feeder-sdk = { git = "https://github.com/worph/meta-feeder-sdk", rev = "d2c6ef4c1887be9ae9f92ebedc39a810aa57c7e4" } + +tokio = { version = "1.40", features = ["full"] } +axum = { version = "0.7", features = ["json"] } +anyhow = "1" +async-trait = "0.1" +serde = { version = "1", features = ["derive"] } +serde_json = "1" +reqwest = { version = "0.12", features = ["json", "rustls-tls", "stream"], default-features = false } +futures = "0.3" +tracing = "0.1" +tracing-subscriber = { version = "0.3", features = ["env-filter", "fmt"] } +bytes = "1" + +[dev-dependencies] +wiremock = "0.6" +tempfile = "3" +tokio = { version = "1.40", features = ["full", "test-util"] } diff --git a/feeder-plugin/europepmc-feeder/Dockerfile b/feeder-plugin/europepmc-feeder/Dockerfile new file mode 100644 index 0000000..0b159da --- /dev/null +++ b/feeder-plugin/europepmc-feeder/Dockerfile @@ -0,0 +1,44 @@ +# syntax=docker/dockerfile:1 +# europepmc-feeder sidecar. Multi-stage build; build context is this repo's root. +# meta-feeder-sdk arrives as a git dependency, so no vendored crate is copied +# in — `git` must be present in the builder for cargo to fetch it. + +FROM rust:1.89-slim-bookworm AS builder +WORKDIR /build + +RUN apt-get update && apt-get install -y --no-install-recommends \ + pkg-config libssl-dev ca-certificates git \ + && rm -rf /var/lib/apt/lists/* + +COPY Cargo.toml rust-toolchain.toml ./ +COPY feeder-plugin/ feeder-plugin/ + +RUN --mount=type=cache,id=cargo-registry,target=/usr/local/cargo/registry \ + --mount=type=cache,id=cargo-git,target=/usr/local/cargo/git \ + --mount=type=cache,id=europepmc-feeder-target,target=/build/target \ + cargo build --release --bin europepmc-feeder \ + && cp target/release/europepmc-feeder /europepmc-feeder + +# ----------------------------------------------------------------------------- +FROM debian:bookworm-slim AS runtime + +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates curl \ + && rm -rf /var/lib/apt/lists/* + +COPY --from=builder /europepmc-feeder /usr/local/bin/europepmc-feeder + +RUN useradd --system --uid 10001 --no-create-home metafeeder \ + && mkdir -p /data/meta-feeder \ + && chown metafeeder:metafeeder /data/meta-feeder + +USER metafeeder +WORKDIR /data/meta-feeder + +EXPOSE 8080 + +ENV META_FEEDER_HTTP_LISTEN=0.0.0.0:8080 \ + META_FEEDER_STATE_DIR=/data/meta-feeder \ + RUST_LOG=info + +ENTRYPOINT ["/usr/local/bin/europepmc-feeder"] diff --git a/feeder-plugin/europepmc-feeder/src/europepmc.rs b/feeder-plugin/europepmc-feeder/src/europepmc.rs new file mode 100644 index 0000000..618e3b1 --- /dev/null +++ b/feeder-plugin/europepmc-feeder/src/europepmc.rs @@ -0,0 +1,617 @@ +//! PubMed Central bridge via the [Europe PMC REST API](https://europepmc.org/RestfulWebService). +//! +//! - Search: `GET /search?query=&format=json&pageSize=N&resultType=lite` +//! → JSON `resultList.result[]`; filter to entries with a `pmcid` +//! (full-text open-access subset). +//! - PDF fetch: `GET /articles/?pdf=render` → binary PDF. +//! +//! No auth, no API key. Europe PMC is a public mirror of NIH's PubMed +//! Central with developer-friendly REST endpoints. NIH's own `efetch.fcgi` +//! returns JATS XML by default and would need a separate URL-discovery +//! step to land on the PDF; Europe PMC's `?pdf=render` is the single +//! direct fetch this plugin is built around. +//! +//! **Open-access only.** Records without a `pmcid` field have no full +//! text in Europe PMC and are filtered out at search time — there's +//! nothing for `compute_outcomes` to hash. The PMC OA subset is large +//! (~5 M articles) so the filter still surfaces plenty. +//! +//! See `docs/gateway-feature.md` §4 for the v0 plugin role. + +use std::collections::BTreeMap; +use std::path::Path; + +use async_trait::async_trait; +use serde::Deserialize; + +use meta_feeder_sdk::common; +use meta_feeder_sdk::cache::MidhashCache; +#[cfg(test)] +use meta_feeder_sdk::plugin::HashKind; +use meta_feeder_sdk::plugin::{upstream_id_field, ConfigError, FeederPlugin, GatewayQuery, HashOutcome}; +use meta_feeder_sdk::types::{DiscoveryRecord, GatewayError, PluginHealth}; + +/// Default Europe PMC REST API root. Used for `/search` and the +/// `?query=PMCID:` single-record lookup that powers `compute_outcomes`. +const DEFAULT_SEARCH_BASE: &str = "https://www.ebi.ac.uk/europepmc/webservices/rest"; + +/// Default Europe PMC web host. Hosts the `/articles/?pdf=render` +/// endpoint that streams the rendered PDF directly. Different host from +/// the REST API root (Europe PMC splits API and content hosting). +const DEFAULT_PDF_BASE: &str = "https://europepmc.org"; + +/// HTTP timeout per upstream call. Generous: Europe PMC's PDF render can +/// take 5–10 s on cold articles (it composes the PDF on demand from +/// JATS XML for some entries). +const HTTP_TIMEOUT_SECS: u64 = 30; + +/// Polite identification per the Europe PMC API guidelines. +const USER_AGENT: &str = concat!( + "meta-share/", + env!("CARGO_PKG_VERSION"), + " (gateway:pubmed)" +); + +/// PubMed Central gateway plugin. Same structural shape as the other +/// fetch-capable v0 plugins: cheap to construct; `configure()` opens the +/// per-plugin redb cache; per-record fetches are memoized so repeated +/// "add" clicks for the same article don't re-download the PDF. +pub struct PubmedPlugin { + http: reqwest::Client, + search_base: String, + pdf_base: String, + cache: Option, +} + +impl Default for PubmedPlugin { + fn default() -> Self { + Self::new() + } +} + +impl PubmedPlugin { + pub fn new() -> Self { + Self::with_bases( + DEFAULT_SEARCH_BASE.to_string(), + DEFAULT_PDF_BASE.to_string(), + ) + } + + /// Single-base constructor used by tests against a `wiremock::MockServer`: + /// the mock serves both `/search` (JSON) and `/articles/` (PDF) under + /// one host. Production uses [`with_bases`] / [`new`] with two distinct + /// hosts. + pub fn with_base_url(base: String) -> Self { + Self::with_bases(base.clone(), base) + } + + pub fn with_bases(search_base: String, pdf_base: String) -> Self { + let http = common::build_http_client(HTTP_TIMEOUT_SECS, USER_AGENT, None); + Self { + http, + search_base, + pdf_base, + cache: None, + } + } + + fn cache(&self) -> Result<&MidhashCache, GatewayError> { + common::require_cache(self.cache.as_ref(), "pubmed") + } + + /// Run a free-text query against Europe PMC's `/search`. Returns the + /// raw JSON parsed into our internal shape; downstream filters drop + /// any record without a `pmcid` (the OA filter). + async fn search_json( + &self, + query: &str, + max_results: usize, + ) -> Result { + let url = format!( + "{}/search?query={}&format=json&pageSize={}&resultType=lite", + self.search_base.trim_end_matches('/'), + common::urlencode(query), + max_results + ); + let resp = self + .http + .get(&url) + .send() + .await + .map_err(|e| GatewayError::Transient(format!("GET {url}: {e}")))?; + common::map_status(&resp)?; + resp.json::() + .await + .map_err(|e| GatewayError::Permanent(format!("decode europe-pmc search response: {e}"))) + } + + /// Single-record lookup by PMC id. Used by `compute_outcomes` to + /// refresh the record metadata before the PDF pull. Europe PMC's + /// search supports `query=PMCID:` to find exactly one article + /// (the indexed pmcid → pmid mapping is unambiguous). + async fn fetch_entry(&self, pmcid: &str) -> Result { + let body = self.search_json(&format!("PMCID:{pmcid}"), 1).await?; + body.result_list + .result + .into_iter() + .next() + .ok_or(GatewayError::NotFound) + } + + /// GET the rendered PDF from Europe PMC. The `?pdf=render` query + /// triggers an on-demand render for articles that aren't pre-baked + /// (most modern OA papers ARE pre-baked; render is sub-second). + async fn fetch_pdf(&self, pmcid: &str) -> Result { + let url = format!( + "{}/articles/{}?pdf=render", + self.pdf_base.trim_end_matches('/'), + pmcid + ); + let bytes = common::fetch_bytes(&self.http, &url).await?; + // Europe PMC occasionally returns a 200 HTML page ("PDF not + // available") for articles in the OA index whose render failed. + // Cheapest guard: insist on the PDF magic bytes; reject anything + // else as a permanent failure so the cache doesn't store junk + // and the caller gets a clear error. + if !bytes.starts_with(b"%PDF") { + return Err(GatewayError::Permanent(format!( + "europe-pmc returned non-PDF body for {pmcid} (article may have no rendered PDF)" + ))); + } + Ok(bytes) + } +} + +#[async_trait] +impl FeederPlugin for PubmedPlugin { + fn upstream_id(&self) -> &'static str { + "pubmed" + } + + fn configure(&mut self, cache_dir: &Path) -> Result<(), ConfigError> { + self.cache = Some(common::open_midhash_cache(cache_dir, "pubmed")?); + Ok(()) + } + + async fn handle_query( + &self, + query: &GatewayQuery, + max_results: usize, + ) -> Result, GatewayError> { + // Layer A early-return: PubMed/Europe PMC only serves + // `document` / `paper`. A non-paper filter can never match — + // skip the upstream call entirely. + if !meta_feeder_sdk::query_eval::query_accepts_plugin( + query, + self.served_file_types(), + self.served_content_kinds(), + ) { + return Ok(Vec::new()); + } + let q = query.free_text_or_star(); + // Europe PMC returns mixed PubMed + PMC + PPR records; only those + // with a `pmcid` field have a fetchable full text. Filter out + // metadata-only entries early so a later `compute_outcomes` for + // a returned record_id always has a chance of succeeding. + let body = self.search_json(q, max_results).await?; + let records: Vec = body + .result_list + .result + .into_iter() + .filter_map(|r| r.pmcid.clone().map(|pmcid| into_discovery_record(r, pmcid))) + .take(max_results) + .collect(); + Ok(records) + } + + async fn compute_outcomes(&self, record_id: &str) -> Result, GatewayError> { + let cache = self.cache()?; + if let Some(hit) = common::cached_outcome(cache, record_id, "pubmed")? { + return Ok(hit); + } + + let entry = self.fetch_entry(record_id).await?; + let pmcid = entry.pmcid.clone().ok_or_else(|| { + // Defensive: `fetch_entry` queried by PMCID, so a missing + // pmcid in the response means the upstream gave us back the + // wrong record. Treat as NotFound so the caller can move on. + GatewayError::NotFound + })?; + let bytes = self.fetch_pdf(&pmcid).await?; + let cid = meta_feeder_sdk::hash::compute_ipfs_cid(&bytes); + + common::store_midhash(cache, record_id, "pubmed", &cid); + + let record = into_discovery_record(entry, pmcid); + Ok(common::single_outcome( + cid, + bytes, + record, + Some("pdf".to_string()), + )) + } + + fn health(&self) -> PluginHealth { + if self.cache.is_some() { + PluginHealth::Ok + } else { + PluginHealth::Degraded { + reason: "configure() not yet called".to_string(), + } + } + } + + fn served_file_types(&self) -> &'static [&'static str] { + &["document"] + } + + fn served_content_kinds(&self) -> &'static [&'static str] { + &["paper"] + } +} + +// -- Europe PMC JSON shapes (subset we use) ---------------------------------- + +#[derive(Debug, Deserialize)] +struct EuropePmcSearchResponse { + #[serde(rename = "resultList", default)] + result_list: EuropePmcResultList, +} + +#[derive(Debug, Default, Deserialize)] +struct EuropePmcResultList { + #[serde(default)] + result: Vec, +} + +/// One record from Europe PMC search. Field names match the API's +/// camelCase JSON keys via `rename_all`; missing fields default to +/// `None`. Everything past `pmcid` is surfaced into the DiscoveryRecord +/// when present. +#[derive(Debug, Default, Deserialize)] +#[serde(default, rename_all = "camelCase")] +struct EuropePmcResult { + /// PubMed numeric id (e.g. "12345678"). Always present for MED-source + /// records; absent for preprints (`PPR…`). + pmid: Option, + /// PMC id (e.g. "PMC2868305"). **Present only when the article has + /// full text in PMC's OA subset** — this is the discriminator we + /// filter on at search time. + pmcid: Option, + /// Article DOI when registered with CrossRef. + doi: Option, + title: Option, + /// Comma-separated author list, e.g. "Smith J, Doe J". + author_string: Option, + journal_title: Option, + pub_year: Option, + /// Full abstract text — multi-paragraph. We pass through verbatim; + /// the UI trims for display. + abstract_text: Option, + is_open_access: Option, +} + +/// Convert a Europe PMC search result into a `DiscoveryRecord`. The +/// caller is responsible for confirming `pmcid` is `Some` (handle_query +/// filters first) — we accept it as a separate arg so the conversion +/// can't accidentally emit a recordless of full-text availability. +fn into_discovery_record(r: EuropePmcResult, pmcid: String) -> DiscoveryRecord { + let mut fields: BTreeMap = BTreeMap::new(); + if let Some(t) = r.title { + fields.insert("title".to_string(), t); + } + fields.insert("fileType".to_string(), "document".to_string()); + fields.insert("contentKind".to_string(), "paper".to_string()); + fields.insert( + "sourceUrl".to_string(), + format!("https://europepmc.org/article/PMC/{pmcid}"), + ); + fields.insert("fileName".to_string(), format!("pubmed-{pmcid}.pdf")); + fields.insert(upstream_id_field("pubmed"), pmcid.clone()); + fields.insert("format".to_string(), "pdf".to_string()); + if let Some(p) = r.pmid { + fields.insert("pmid".to_string(), p); + } + if let Some(d) = r.doi { + fields.insert("doi".to_string(), d); + } + if let Some(a) = r.author_string { + fields.insert("author".to_string(), a); + } + if let Some(j) = r.journal_title { + fields.insert("journal".to_string(), j); + } + if let Some(y) = r.pub_year { + fields.insert("year".to_string(), y); + } + if let Some(s) = r.abstract_text { + fields.insert("summary".to_string(), s); + } + if let Some(o) = r.is_open_access { + fields.insert("openAccess".to_string(), o); + } + + DiscoveryRecord { + upstream_id: "pubmed".to_string(), + record_id: pmcid, + fields, + } +} + +#[cfg(test)] +mod tests { + use super::*; + + /// Minimal search response with one OA record + one non-OA record + /// (no pmcid). `handle_query` should keep only the OA one. + const SAMPLE_SEARCH: &str = r#"{ + "hitCount": 2, + "request": {}, + "resultList": { + "result": [ + { + "id": "12345678", + "source": "MED", + "pmid": "12345678", + "pmcid": "PMC2868305", + "doi": "10.1371/journal.pone.0010068", + "title": "Discovery of a new species", + "authorString": "Smith J, Doe J", + "journalTitle": "PLoS One", + "pubYear": "2010", + "abstractText": "We describe a new species discovered in...", + "isOpenAccess": "Y" + }, + { + "id": "98765432", + "source": "MED", + "pmid": "98765432", + "title": "Closed-access paper", + "authorString": "Other A", + "journalTitle": "Some Journal", + "pubYear": "2018", + "isOpenAccess": "N" + } + ] + } + }"#; + + #[test] + fn parses_europe_pmc_search_response() { + let body: EuropePmcSearchResponse = serde_json::from_str(SAMPLE_SEARCH).expect("parse"); + assert_eq!(body.result_list.result.len(), 2); + assert_eq!( + body.result_list.result[0].pmcid.as_deref(), + Some("PMC2868305") + ); + assert!(body.result_list.result[1].pmcid.is_none()); + } + + #[test] + fn into_discovery_record_emits_required_fields() { + let body: EuropePmcSearchResponse = serde_json::from_str(SAMPLE_SEARCH).unwrap(); + let r0 = body.result_list.result.into_iter().next().unwrap(); + let pmcid = r0.pmcid.clone().unwrap(); + let rec = into_discovery_record(r0, pmcid); + assert_eq!(rec.upstream_id, "pubmed"); + assert_eq!(rec.record_id, "PMC2868305"); + // §6.4 conventions. + assert_eq!( + rec.fields.get("fileType").map(String::as_str), + Some("document") + ); + assert_eq!( + rec.fields.get("contentKind").map(String::as_str), + Some("paper") + ); + assert_eq!(rec.fields.get("format").map(String::as_str), Some("pdf")); + assert_eq!( + rec.fields.get("sourceUrl").map(String::as_str), + Some("https://europepmc.org/article/PMC/PMC2868305") + ); + assert_eq!( + rec.fields.get("fileName").map(String::as_str), + Some("pubmed-PMC2868305.pdf") + ); + // Canonical `id` field — `format!("{upstream_id}id")` + // gives "pubmedid"; value is the PMC id. + assert_eq!( + rec.fields.get("pubmedid").map(String::as_str), + Some("PMC2868305") + ); + // Bibliographic surface. + assert_eq!(rec.fields.get("year").map(String::as_str), Some("2010")); + assert_eq!( + rec.fields.get("author").map(String::as_str), + Some("Smith J, Doe J") + ); + assert_eq!( + rec.fields.get("journal").map(String::as_str), + Some("PLoS One") + ); + assert_eq!( + rec.fields.get("doi").map(String::as_str), + Some("10.1371/journal.pone.0010068") + ); + } + + // -- HTTP integration tests against a wiremock server ---------------- + + use wiremock::matchers::{method, path, query_param}; + use wiremock::{Mock, MockServer, ResponseTemplate}; + + fn configured_plugin_against(server: &MockServer) -> (PubmedPlugin, tempfile::TempDir) { + let dir = tempfile::tempdir().expect("tempdir"); + let mut plugin = PubmedPlugin::with_base_url(server.uri()); + plugin.configure(dir.path()).expect("configure"); + (plugin, dir) + } + + #[tokio::test] + async fn handle_query_drops_non_oa_records() { + let server = MockServer::start().await; + Mock::given(method("GET")) + .and(path("/search")) + .and(query_param("query", "species")) + .respond_with( + ResponseTemplate::new(200) + .set_body_string(SAMPLE_SEARCH) + .insert_header("content-type", "application/json"), + ) + .mount(&server) + .await; + let (plugin, _dir) = configured_plugin_against(&server); + let records = plugin + .handle_query(&GatewayQuery::from_free_text("species"), 10) + .await + .expect("handle_query"); + // Two records in the mock; only the one with `pmcid` survives. + assert_eq!(records.len(), 1); + assert_eq!(records[0].record_id, "PMC2868305"); + } + + #[tokio::test] + async fn handle_query_truncates_to_max_results() { + let server = MockServer::start().await; + // Build a synthetic response with several OA records. + let mut results = String::new(); + for i in 0..5 { + if i > 0 { + results.push(','); + } + results.push_str(&format!( + r#"{{ "pmcid": "PMC{i}", "title": "Paper {i}", "pubYear": "2020" }}"#, + i = i + 100 + )); + } + let body = format!(r#"{{ "hitCount": 5, "resultList": {{ "result": [{results}] }} }}"#); + Mock::given(method("GET")) + .and(path("/search")) + .respond_with(ResponseTemplate::new(200).set_body_string(body)) + .mount(&server) + .await; + let (plugin, _dir) = configured_plugin_against(&server); + let records = plugin + .handle_query(&GatewayQuery::from_free_text("anything"), 2) + .await + .expect("handle_query"); + assert_eq!(records.len(), 2); + } + + #[tokio::test] + async fn compute_outcomes_fetches_pdf_and_caches() { + let server = MockServer::start().await; + // PMCID lookup: search?query=PMCID:PMC2868305 + Mock::given(method("GET")) + .and(path("/search")) + .and(query_param("query", "PMCID:PMC2868305")) + .respond_with( + ResponseTemplate::new(200) + .set_body_string(SAMPLE_SEARCH) + .insert_header("content-type", "application/json"), + ) + .mount(&server) + .await; + // PDF response — bytes get hashed. + let pdf_bytes = b"%PDF-1.4 mock pubmed pdf\n".to_vec(); + let expected_cid = meta_feeder_sdk::hash::compute_ipfs_cid(&pdf_bytes); + Mock::given(method("GET")) + .and(path("/articles/PMC2868305")) + .and(query_param("pdf", "render")) + .respond_with( + ResponseTemplate::new(200) + .set_body_bytes(pdf_bytes.clone()) + .insert_header("content-type", "application/pdf"), + ) + .mount(&server) + .await; + let (plugin, _dir) = configured_plugin_against(&server); + let mut outcomes = plugin + .compute_outcomes("PMC2868305") + .await + .expect("compute"); + assert_eq!(outcomes.len(), 1, "pubmed is single-outcome"); + let outcome = outcomes.remove(0); + assert_eq!(outcome.hash.as_str(), expected_cid); + assert_eq!(outcome.hash_kind, HashKind::Sha2_256); + // Auto-store inputs. + assert_eq!(outcome.bytes.as_deref(), Some(pdf_bytes.as_slice())); + assert_eq!(outcome.file_extension.as_deref(), Some("pdf")); + let rec = outcome.record.expect("record present on fresh compute"); + assert_eq!(rec.record_id, "PMC2868305"); + assert_eq!( + rec.fields.get("doi").map(String::as_str), + Some("10.1371/journal.pone.0010068") + ); + } + + #[tokio::test] + async fn compute_outcomes_cache_hit_skips_http() { + let server = MockServer::start().await; + let (plugin, _dir) = configured_plugin_against(&server); + plugin + .cache + .as_ref() + .unwrap() + .put_midhash("PMC2868305", "bafyCACHED") + .unwrap(); + let mut outcomes = plugin + .compute_outcomes("PMC2868305") + .await + .expect("cache hit"); + assert_eq!(outcomes.len(), 1); + let outcome = outcomes.remove(0); + assert_eq!(outcome.hash.as_str(), "bafyCACHED"); + assert!(outcome.bytes.is_none()); + assert!(outcome.record.is_none()); + } + + #[tokio::test] + async fn compute_outcomes_rejects_non_pdf_response() { + let server = MockServer::start().await; + Mock::given(method("GET")) + .and(path("/search")) + .respond_with( + ResponseTemplate::new(200) + .set_body_string(SAMPLE_SEARCH) + .insert_header("content-type", "application/json"), + ) + .mount(&server) + .await; + // Upstream returns an HTML "PDF not available" page with 200 OK + // — Europe PMC actually does this for articles in the OA index + // whose render failed. The plugin must reject rather than store + // junk bytes. + Mock::given(method("GET")) + .and(path("/articles/PMC2868305")) + .respond_with( + ResponseTemplate::new(200) + .set_body_string("PDF not available") + .insert_header("content-type", "text/html"), + ) + .mount(&server) + .await; + let (plugin, _dir) = configured_plugin_against(&server); + let err = plugin + .compute_outcomes("PMC2868305") + .await + .expect_err("non-PDF"); + assert!(matches!(err, GatewayError::Permanent(_)), "got {err:?}"); + } + + #[tokio::test] + async fn upstream_404_maps_to_not_found() { + let server = MockServer::start().await; + Mock::given(method("GET")) + .and(path("/search")) + .respond_with(ResponseTemplate::new(404)) + .mount(&server) + .await; + let (plugin, _dir) = configured_plugin_against(&server); + let err = plugin + .compute_outcomes("PMC-does-not-exist") + .await + .expect_err("expected NotFound"); + assert!(matches!(err, GatewayError::NotFound), "got {err:?}"); + } +} diff --git a/feeder-plugin/europepmc-feeder/src/lib.rs b/feeder-plugin/europepmc-feeder/src/lib.rs new file mode 100644 index 0000000..fa5f52a --- /dev/null +++ b/feeder-plugin/europepmc-feeder/src/lib.rs @@ -0,0 +1,4 @@ +//! `europepmc-feeder` library surface. The binary (`main.rs`) wraps the plugin in +//! [`meta_feeder_sdk::serve_feeders`]. + +pub mod europepmc; diff --git a/feeder-plugin/europepmc-feeder/src/main.rs b/feeder-plugin/europepmc-feeder/src/main.rs new file mode 100644 index 0000000..969d998 --- /dev/null +++ b/feeder-plugin/europepmc-feeder/src/main.rs @@ -0,0 +1,30 @@ +//! `europepmc-feeder` — a single-upstream feeder sidecar. +//! +//! Upstream: Europe PMC (www.ebi.ac.uk/europepmc/webservices/rest) +//! +//! Env: +//! - `META_FEEDER_HTTP_LISTEN` — listen addr (default `0.0.0.0:8080`) +//! - `META_FEEDER_STATE_DIR` — per-plugin cache root (default `/data/meta-feeder`) +//! - `RUST_LOG` — tracing filter (default `info`) + +use std::net::SocketAddr; + +use meta_feeder_sdk::{serve_feeders, FeederPlugin}; +use europepmc_feeder::europepmc::PubmedPlugin; +use tracing_subscriber::EnvFilter; + +#[tokio::main] +async fn main() -> anyhow::Result<()> { + tracing_subscriber::fmt() + .with_env_filter(EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new("info"))) + .init(); + + let listen: SocketAddr = std::env::var("META_FEEDER_HTTP_LISTEN") + .unwrap_or_else(|_| "0.0.0.0:8080".to_string()) + .parse()?; + let state_dir = + std::env::var("META_FEEDER_STATE_DIR").unwrap_or_else(|_| "/data/meta-feeder".to_string()); + + let plugins: Vec> = vec![Box::new(PubmedPlugin::new())]; + serve_feeders(plugins, state_dir, listen).await +} diff --git a/rust-toolchain.toml b/rust-toolchain.toml new file mode 100644 index 0000000..1c0730c --- /dev/null +++ b/rust-toolchain.toml @@ -0,0 +1,3 @@ +[toolchain] +channel = "1.89" +components = ["rustfmt", "clippy"]