file = files.get(stId);
if (file.isEmpty()) return reason(HttpStatus.NOT_FOUND, "No event " + stId + " in the graph");
Resource body = new FileSystemResource(file.get());
- return ResponseEntity.ok().contentType(SBML).body(body);
- } catch (SbmlFiles.DiagramUnavailable e) {
+ return ResponseEntity.ok().contentType(type).body(body);
+ } catch (ExportFiles.DiagramUnavailable e) {
logger.warn("{}: {}", stId, e.getMessage());
return reason(HttpStatus.SERVICE_UNAVAILABLE, e.getMessage());
} catch (RuntimeException e) {
diff --git a/deploy/java-library/src/main/java/org/reactome/server/library/SbmlFiles.java b/deploy/java-library/src/main/java/org/reactome/server/library/ExportFiles.java
similarity index 77%
rename from deploy/java-library/src/main/java/org/reactome/server/library/SbmlFiles.java
rename to deploy/java-library/src/main/java/org/reactome/server/library/ExportFiles.java
index 83a0a89e7..97f8b063e 100644
--- a/deploy/java-library/src/main/java/org/reactome/server/library/SbmlFiles.java
+++ b/deploy/java-library/src/main/java/org/reactome/server/library/ExportFiles.java
@@ -20,17 +20,18 @@
import org.slf4j.LoggerFactory;
/**
- * The SBML files, kept on disk per release as ContentService keeps its exports.
+ * One export's files (SBML, BioPAX), kept on disk per release as ContentService keeps its exports.
*
* The release is the graph's, read for every request, so a graph moved to a new release is never answered from the
* old one's files, and the old release's files are removed when it is first seen. One id is converted once at a time:
- * a second request for it waits for the first. Node's share of 2 is the limit on conversions (spec 015 T065); the cap
- * here is a backstop.
+ * a second request for it waits for the first. Node gives each export a share of 2 (spec 015 T065, T070); the
+ * conversions' cap is shared by every export in the service, so the heap holds at most that many at once whatever
+ * node sends (T069).
*
*
Removing files is best effort: a release can change while a conversion of the old one is still writing, and that
* must not fail the new release's request. What is left behind goes when the next release is first seen.
*/
-public class SbmlFiles {
+public class ExportFiles {
/** What the service needs from the graph. */
public interface Graph {
@@ -42,7 +43,7 @@ public interface Graph {
/** An event, as far as the diagram files are concerned. */
public static final class Event {
- /** A pathway the graph says has a diagram of its own: its layout needs the diagram file. */
+ /** A pathway the graph says has a diagram of its own: its SBML layout needs the diagram file. */
public final boolean hasDiagram;
public Event(boolean hasDiagram) {
@@ -50,7 +51,7 @@ public Event(boolean hasDiagram) {
}
}
- /** sbml-exporter's library, writing {@code {stId}.sbml} into a folder. */
+ /** An exporter's library, writing {@code {stId}{extension}} into a folder. */
public interface Converter {
void convert(String stId, int release, Path diagrams, Path into) throws Exception;
}
@@ -72,34 +73,50 @@ public DiagramUnavailable(String message, Throwable cause) {
}
}
- private static final Logger logger = LoggerFactory.getLogger(SbmlFiles.class);
+ private static final Logger logger = LoggerFactory.getLogger(ExportFiles.class);
+ private final String kind;
+ private final String extension;
private final Graph graph;
private final Converter converter;
private final DiagramSource diagrams;
private final Path cache;
- private final Semaphore conversions = new Semaphore(2);
+ private final Semaphore conversions;
private final Map> running = new ConcurrentHashMap<>();
private volatile int seen = -1;
- public SbmlFiles(Graph graph, Converter converter, DiagramSource diagrams, Path cache) {
+ /**
+ * @param kind the export's folder in the cache, {@code sbml} or {@code biopax}
+ * @param extension what the converter names its file, {@code .sbml} or {@code .owl}
+ * @param diagrams where a pathway's diagram file comes from, or null for an export that needs none
+ * @param conversions the cap on conversions at once, shared by the service's exports
+ */
+ public ExportFiles(String kind, String extension, Graph graph, Converter converter, DiagramSource diagrams,
+ Path cache, Semaphore conversions) {
+ this.kind = kind;
+ this.extension = extension;
this.graph = graph;
this.converter = converter;
this.diagrams = diagrams;
this.cache = cache;
+ this.conversions = conversions;
// Work in progress when the service last stopped, which nothing will finish
- delete(cache.resolve("tmp"));
+ delete(work());
+ }
+
+ private Path work() {
+ return cache.resolve("tmp").resolve(kind);
}
/**
- * The event's SBML file, or empty when the graph has no such event.
+ * The event's file, or empty when the graph has no such event.
*
* @throws DiagramUnavailable when its diagram file cannot be had
*/
public Optional get(String stId) throws DiagramUnavailable, InterruptedException {
int release = graph.release();
forgetOtherReleases(release);
- Path file = cache.resolve("sbml").resolve(String.valueOf(release)).resolve(stId + ".sbml");
+ Path file = cache.resolve(kind).resolve(String.valueOf(release)).resolve(stId + extension);
if (Files.isRegularFile(file)) return Optional.of(file);
Optional event = graph.event(stId);
@@ -124,13 +141,13 @@ private Path convert(String stId, int release, Event event, Path file) throws Ex
conversions.acquire();
try {
Path diagramFolder = Files.createDirectories(cache.resolve("diagram").resolve(String.valueOf(release)));
- if (event.hasDiagram && !Files.isRegularFile(diagramFolder.resolve(stId + ".json"))) {
+ if (diagrams != null && event.hasDiagram && !Files.isRegularFile(diagramFolder.resolve(stId + ".json"))) {
diagrams.fetch(stId, release, diagramFolder);
}
- Path work = Files.createDirectories(cache.resolve("tmp").resolve(UUID.randomUUID().toString()));
+ Path work = Files.createDirectories(work().resolve(UUID.randomUUID().toString()));
try {
converter.convert(stId, release, diagramFolder, work);
- Path written = work.resolve(stId + ".sbml");
+ Path written = work.resolve(stId + extension);
if (!Files.isRegularFile(written)) throw new IllegalStateException("The converter wrote no " + written);
Files.createDirectories(file.getParent());
return Files.move(written, file, StandardCopyOption.ATOMIC_MOVE, StandardCopyOption.REPLACE_EXISTING);
@@ -159,8 +176,8 @@ private void forgetOtherReleases(int release) {
if (seen == release) return;
synchronized (this) {
if (seen == release) return;
- for (String kind : new String[]{"sbml", "diagram"}) {
- Path folder = cache.resolve(kind);
+ for (String folderName : new String[]{kind, "diagram"}) {
+ Path folder = cache.resolve(folderName);
if (!Files.isDirectory(folder)) continue;
try (DirectoryStream releases = Files.newDirectoryStream(folder)) {
for (Path other : releases) {
diff --git a/deploy/java-library/src/main/java/org/reactome/server/library/HttpDiagramSource.java b/deploy/java-library/src/main/java/org/reactome/server/library/HttpDiagramSource.java
index 6f61034f1..c31c02f4f 100644
--- a/deploy/java-library/src/main/java/org/reactome/server/library/HttpDiagramSource.java
+++ b/deploy/java-library/src/main/java/org/reactome/server/library/HttpDiagramSource.java
@@ -23,7 +23,7 @@
* per converted pathway that has a diagram; the caller keeps it per release, so a file is kept only once it is
* whole and is the pathway's: the converter would refuse anything else on every request until the next release.
*/
-public class HttpDiagramSource implements SbmlFiles.DiagramSource {
+public class HttpDiagramSource implements ExportFiles.DiagramSource {
private static final ObjectMapper JSON = new ObjectMapper();
@@ -45,7 +45,7 @@ public HttpDiagramSource(URI base) {
}
@Override
- public void fetch(String stId, int release, Path into) throws SbmlFiles.DiagramUnavailable {
+ public void fetch(String stId, int release, Path into) throws ExportFiles.DiagramUnavailable {
URI uri = base.resolve(release + "/diagram/" + stId + ".json");
Path part = into.resolve(stId + ".json.part");
try {
@@ -59,27 +59,27 @@ public void fetch(String stId, int release, Path into) throws SbmlFiles.DiagramU
response = download.get(timeout.toMillis(), TimeUnit.MILLISECONDS);
} catch (TimeoutException e) {
download.cancel(true);
- throw new SbmlFiles.DiagramUnavailable(uri + " did not arrive within " + timeout.toSeconds() + " s", e);
+ throw new ExportFiles.DiagramUnavailable(uri + " did not arrive within " + timeout.toSeconds() + " s", e);
} catch (ExecutionException e) {
- throw new SbmlFiles.DiagramUnavailable("Cannot fetch " + uri + ": " + e.getCause(), e.getCause());
+ throw new ExportFiles.DiagramUnavailable("Cannot fetch " + uri + ": " + e.getCause(), e.getCause());
} catch (InterruptedException e) {
// Waiting is interrupted, not the transfer: it is stopped here, as on a timeout
download.cancel(true);
throw e;
}
if (response.statusCode() != 200) {
- throw new SbmlFiles.DiagramUnavailable(uri + " answered " + response.statusCode(), null);
+ throw new ExportFiles.DiagramUnavailable(uri + " answered " + response.statusCode(), null);
}
if (!isTheDiagramOf(stId, part)) {
- throw new SbmlFiles.DiagramUnavailable(uri + " is not " + stId + "'s diagram", null);
+ throw new ExportFiles.DiagramUnavailable(uri + " is not " + stId + "'s diagram", null);
}
Files.move(part, into.resolve(stId + ".json"), StandardCopyOption.ATOMIC_MOVE,
StandardCopyOption.REPLACE_EXISTING);
} catch (IOException e) {
- throw new SbmlFiles.DiagramUnavailable("Cannot fetch " + uri + ": " + e.getMessage(), e);
+ throw new ExportFiles.DiagramUnavailable("Cannot fetch " + uri + ": " + e.getMessage(), e);
} catch (InterruptedException e) {
Thread.currentThread().interrupt();
- throw new SbmlFiles.DiagramUnavailable("Interrupted fetching " + uri, e);
+ throw new ExportFiles.DiagramUnavailable("Interrupted fetching " + uri, e);
} finally {
try {
Files.deleteIfExists(part);
diff --git a/deploy/java-library/src/main/java/org/reactome/server/library/LibraryApplication.java b/deploy/java-library/src/main/java/org/reactome/server/library/LibraryApplication.java
index 7384af2d3..f4995633d 100644
--- a/deploy/java-library/src/main/java/org/reactome/server/library/LibraryApplication.java
+++ b/deploy/java-library/src/main/java/org/reactome/server/library/LibraryApplication.java
@@ -1,9 +1,11 @@
package org.reactome.server.library;
+import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.Optional;
import java.util.Properties;
+import java.util.concurrent.Semaphore;
import org.reactome.server.graph.config.GraphCoreNeo4jConfig;
import org.reactome.server.graph.domain.model.Event;
@@ -11,6 +13,7 @@
import org.reactome.server.graph.service.AdvancedDatabaseObjectService;
import org.reactome.server.graph.service.DatabaseObjectService;
import org.reactome.server.graph.service.GeneralService;
+import org.reactome.server.tools.WriteBioPAX3;
import org.reactome.server.tools.sbml.converter.SbmlConverter;
import org.reactome.server.tools.sbml.layout.DiagramFiles;
import org.springframework.boot.SpringApplication;
@@ -19,8 +22,8 @@
import org.springframework.context.annotation.Import;
/**
- * Spec 010's library service, started in this repository with SBML as its only operation (spec 015 T063). Node
- * answers the public URLs and calls this over loopback; this writes only the body.
+ * Spec 010's library service, started in this repository with SBML (spec 015 T063) and BioPAX Level 3 (T069) as its
+ * operations. Node answers the public URLs and calls this over loopback; this writes only the body.
*/
@SpringBootApplication
@Import(GraphCoreNeo4jConfig.class)
@@ -39,36 +42,53 @@ public static void main(String[] args) {
}
@Bean
- public SbmlFiles.Graph graph(DatabaseObjectService ds, GeneralService general) {
- return new SbmlFiles.Graph() {
+ public ExportFiles.Graph graph(DatabaseObjectService ds, GeneralService general) {
+ return new ExportFiles.Graph() {
@Override
public int release() {
return general.getDBInfo().getVersion();
}
@Override
- public Optional event(String stId) {
+ public Optional event(String stId) {
Object found = ds.findById(stId);
if (!(found instanceof Event)) return Optional.empty();
boolean hasDiagram = found instanceof Pathway && Boolean.TRUE.equals(((Pathway) found).getHasDiagram());
- return Optional.of(new SbmlFiles.Event(hasDiagram));
+ return Optional.of(new ExportFiles.Event(hasDiagram));
}
};
}
+ /** The conversions at once, across every export: two, within the heap (spec 015 T069). */
@Bean
- public SbmlFiles.Converter converter(DatabaseObjectService ds, AdvancedDatabaseObjectService ads) {
- return (stId, release, diagrams, into) -> {
+ public Semaphore conversions() {
+ return new Semaphore(2);
+ }
+
+ @Bean
+ public ExportFiles sbmlFiles(Settings settings, ExportFiles.Graph graph, DatabaseObjectService ds,
+ AdvancedDatabaseObjectService ads, Semaphore conversions) {
+ ExportFiles.Converter converter = (stId, release, diagrams, into) -> {
Event event = ds.findById(stId);
- SbmlConverter converter = new SbmlConverter(event, release, ds, ads, new DiagramFiles(diagrams, release, release));
- converter.convert();
- converter.writeToFile(into.toString());
+ SbmlConverter sbml = new SbmlConverter(event, release, ds, ads, new DiagramFiles(diagrams, release, release));
+ sbml.convert();
+ sbml.writeToFile(into.toString());
};
+ return new ExportFiles("sbml", ".sbml", graph, converter, new HttpDiagramSource(settings.diagramBase),
+ settings.cache, conversions);
}
+ /** BioPAX3Exporter's library: one event with all it holds, with the release's per-event xml:base. */
@Bean
- public SbmlFiles sbmlFiles(Settings settings, SbmlFiles.Graph graph, SbmlFiles.Converter converter) {
- return new SbmlFiles(graph, converter, new HttpDiagramSource(settings.diagramBase), settings.cache);
+ public ExportFiles biopaxFiles(Settings settings, ExportFiles.Graph graph, DatabaseObjectService ds,
+ Semaphore conversions) {
+ ExportFiles.Converter converter = (stId, release, diagrams, into) -> {
+ Event event = ds.findById(stId);
+ WriteBioPAX3 biopax = new WriteBioPAX3(event, release);
+ biopax.createModel();
+ biopax.toFile(new File(into.toFile(), stId + ".owl"));
+ };
+ return new ExportFiles("biopax", ".owl", graph, converter, null, settings.cache, conversions);
}
/** The pinned commits the image was built from, written by the Dockerfile (deploy/java/PINS.md). */
diff --git a/deploy/java-library/src/test/java/org/reactome/server/library/ExportControllerTest.java b/deploy/java-library/src/test/java/org/reactome/server/library/ExportControllerTest.java
new file mode 100644
index 000000000..480eea7bf
--- /dev/null
+++ b/deploy/java-library/src/test/java/org/reactome/server/library/ExportControllerTest.java
@@ -0,0 +1,117 @@
+package org.reactome.server.library;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Map;
+import java.util.Optional;
+import java.util.Properties;
+import java.util.concurrent.Semaphore;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.springframework.http.ResponseEntity;
+
+class ExportControllerTest {
+
+ @TempDir
+ Path cache;
+
+ private final ExportFiles.Graph graph = new ExportFiles.Graph() {
+ @Override
+ public int release() {
+ return 97;
+ }
+
+ @Override
+ public Optional event(String stId) {
+ return stId.equals("R-HSA-1") ? Optional.of(new ExportFiles.Event(true)) : Optional.empty();
+ }
+ };
+
+ private final ExportFiles.Converter owl = (stId, rel, d, into) -> Files.writeString(into.resolve(stId + ".owl"), "");
+
+ private ExportController controller(ExportFiles.DiagramSource diagrams, ExportFiles.Converter converter) {
+ return controller(diagrams, converter, owl);
+ }
+
+ private ExportController controller(ExportFiles.DiagramSource diagrams, ExportFiles.Converter converter,
+ ExportFiles.Converter biopax) {
+ Semaphore cap = new Semaphore(2);
+ return new ExportController(new ExportFiles("sbml", ".sbml", graph, converter, diagrams, cache, cap),
+ new ExportFiles("biopax", ".owl", graph, biopax, null, cache, cap), graph, new Properties());
+ }
+
+ private final ExportFiles.Converter writes = (stId, rel, d, into) -> Files.writeString(into.resolve(stId + ".sbml"), "");
+ private final ExportFiles.DiagramSource fetches = (stId, rel, into) -> {
+ try {
+ Files.writeString(into.resolve(stId + ".json"), "{}");
+ } catch (java.io.IOException e) {
+ throw new ExportFiles.DiagramUnavailable(e.getMessage(), e);
+ }
+ };
+
+ @Test
+ void answersTheFileAsSbml() throws Exception {
+ ResponseEntity answer = controller(fetches, writes).sbml("R-HSA-1");
+ assertEquals(200, answer.getStatusCodeValue());
+ assertEquals(ExportController.SBML, answer.getHeaders().getContentType());
+ }
+
+ @Test
+ void anIdNotInTheGraphIs404() throws Exception {
+ assertEquals(404, controller(fetches, writes).sbml("R-HSA-9").getStatusCodeValue());
+ }
+
+ @Test
+ void anythingButAStableIdIs400() throws Exception {
+ for (String id : new String[]{"R-HSA-1.2", "123", "../R-HSA-1", "r-hsa-1"}) {
+ assertEquals(400, controller(fetches, writes).sbml(id).getStatusCodeValue(), id);
+ }
+ }
+
+ @Test
+ void aDiagramThatCannotBeHadIs503() throws Exception {
+ ExportFiles.DiagramSource failing = (stId, rel, into) -> {
+ throw new ExportFiles.DiagramUnavailable("answered 404", null);
+ };
+ ResponseEntity answer = controller(failing, writes).sbml("R-HSA-1");
+ assertEquals(503, answer.getStatusCodeValue());
+ assertEquals(Map.of("error", "answered 404"), answer.getBody());
+ }
+
+ @Test
+ void aConversionThatFailsIs500() throws Exception {
+ ExportFiles.Converter failing = (stId, rel, d, into) -> {
+ throw new IllegalStateException("no reactions");
+ };
+ assertEquals(500, controller(fetches, failing).sbml("R-HSA-1").getStatusCodeValue());
+ }
+
+ @Test
+ void answersBiopaxAsRdf() throws Exception {
+ ResponseEntity answer = controller(fetches, writes).biopax("R-HSA-1");
+ assertEquals(200, answer.getStatusCodeValue());
+ assertEquals(ExportController.BIOPAX, answer.getHeaders().getContentType());
+ assertEquals("R-HSA-1.owl", ((org.springframework.core.io.Resource) answer.getBody()).getFilename());
+ }
+
+ @Test
+ void biopaxNeedsNoDiagram() throws Exception {
+ ExportFiles.DiagramSource failing = (stId, rel, into) -> {
+ throw new ExportFiles.DiagramUnavailable("answered 404", null);
+ };
+ assertEquals(200, controller(failing, writes).biopax("R-HSA-1").getStatusCodeValue());
+ }
+
+ @Test
+ void biopaxAnswersTheSameErrors() throws Exception {
+ assertEquals(404, controller(fetches, writes).biopax("R-HSA-9").getStatusCodeValue());
+ assertEquals(400, controller(fetches, writes).biopax("R-HSA-1.2").getStatusCodeValue());
+ ExportFiles.Converter failing = (stId, rel, d, into) -> {
+ throw new IllegalStateException("no model");
+ };
+ assertEquals(500, controller(fetches, writes, failing).biopax("R-HSA-1").getStatusCodeValue());
+ }
+}
diff --git a/deploy/java-library/src/test/java/org/reactome/server/library/SbmlFilesTest.java b/deploy/java-library/src/test/java/org/reactome/server/library/ExportFilesTest.java
similarity index 51%
rename from deploy/java-library/src/test/java/org/reactome/server/library/SbmlFilesTest.java
rename to deploy/java-library/src/test/java/org/reactome/server/library/ExportFilesTest.java
index 37bf24688..9cecb3b9b 100644
--- a/deploy/java-library/src/test/java/org/reactome/server/library/SbmlFilesTest.java
+++ b/deploy/java-library/src/test/java/org/reactome/server/library/ExportFilesTest.java
@@ -15,13 +15,14 @@
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
+import java.util.concurrent.Semaphore;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
-class SbmlFilesTest {
+class ExportFilesTest {
@TempDir
Path cache;
@@ -31,45 +32,115 @@ class SbmlFilesTest {
private final AtomicInteger lookups = new AtomicInteger();
/** A graph with a pathway that has a diagram, one that has none, and nothing else. */
- private final SbmlFiles.Graph graph = new SbmlFiles.Graph() {
+ private final ExportFiles.Graph graph = new ExportFiles.Graph() {
@Override
public int release() {
return release;
}
@Override
- public Optional event(String stId) {
+ public Optional event(String stId) {
lookups.incrementAndGet();
- if (stId.equals("R-HSA-1")) return Optional.of(new SbmlFiles.Event(true));
- if (stId.equals("R-HSA-2")) return Optional.of(new SbmlFiles.Event(false));
+ if (stId.equals("R-HSA-1")) return Optional.of(new ExportFiles.Event(true));
+ if (stId.equals("R-HSA-2")) return Optional.of(new ExportFiles.Event(false));
return Optional.empty();
}
};
- private final SbmlFiles.Converter converter = (stId, rel, diagrams, into) -> {
+ private final ExportFiles.Converter converter = (stId, rel, diagrams, into) -> {
calls.add("convert " + stId + " " + rel + " diagram=" + Files.exists(diagrams.resolve(stId + ".json")));
Files.writeString(into.resolve(stId + ".sbml"), "");
};
- private final SbmlFiles.DiagramSource diagrams = (stId, rel, into) -> {
+ private final ExportFiles.DiagramSource diagrams = (stId, rel, into) -> {
calls.add("fetch " + stId + " " + rel);
try {
Files.writeString(into.resolve(stId + ".json"), "{}");
} catch (java.io.IOException e) {
- throw new SbmlFiles.DiagramUnavailable(e.getMessage(), e);
+ throw new ExportFiles.DiagramUnavailable(e.getMessage(), e);
}
};
+ private final Semaphore cap = new Semaphore(2);
+
+ private ExportFiles sbml(ExportFiles.Converter converter, ExportFiles.DiagramSource diagrams) {
+ return new ExportFiles("sbml", ".sbml", graph, converter, diagrams, cache, cap);
+ }
+
+ /** BioPAX needs no diagram file: the export is made with none. */
+ private final ExportFiles.Converter owl = (stId, rel, diagrams, into) -> {
+ calls.add("biopax " + stId + " " + rel);
+ Files.writeString(into.resolve(stId + ".owl"), "");
+ };
+
+ private ExportFiles biopax(ExportFiles.Converter converter) {
+ return new ExportFiles("biopax", ".owl", graph, converter, null, cache, cap);
+ }
+
+ @Test
+ void anExportWithNoDiagramSourceNeverFetchesOne() throws Exception {
+ ExportFiles files = biopax(owl);
+ Path file = files.get("R-HSA-1").orElseThrow();
+ assertEquals(cache.resolve("biopax/97/R-HSA-1.owl"), file);
+ assertEquals(List.of("biopax R-HSA-1 97"), calls);
+ }
+
+ @Test
+ void eachExportKeepsItsOwnFiles() throws Exception {
+ ExportFiles sbml = sbml(converter, diagrams);
+ ExportFiles biopax = biopax(owl);
+ assertEquals("", Files.readString(sbml.get("R-HSA-2").orElseThrow()));
+ assertEquals("", Files.readString(biopax.get("R-HSA-2").orElseThrow()));
+ // A new release seen by one export leaves the other's files to it, and each then converts afresh
+ release = 98;
+ biopax.get("R-HSA-2");
+ assertTrue(Files.exists(cache.resolve("sbml/97/R-HSA-2.sbml")));
+ assertFalse(Files.exists(cache.resolve("biopax/97")));
+ }
+
+ @Test
+ void theCapIsSharedByTheExports() throws Exception {
+ CountDownLatch inside = new CountDownLatch(2);
+ CountDownLatch release = new CountDownLatch(1);
+ AtomicInteger at = new AtomicInteger();
+ AtomicInteger most = new AtomicInteger();
+ ExportFiles.Converter held = (stId, rel, d, into) -> {
+ most.accumulateAndGet(at.incrementAndGet(), Math::max);
+ inside.countDown();
+ assertTrue(release.await(10, TimeUnit.SECONDS));
+ at.decrementAndGet();
+ Files.writeString(into.resolve(stId + (into.toString().contains("biopax") ? ".owl" : ".sbml")), "x");
+ };
+ ExportFiles sbml = sbml(held, diagrams);
+ ExportFiles biopax = biopax(held);
+ ExecutorService pool = Executors.newFixedThreadPool(3);
+ try {
+ Future> a = pool.submit(() -> sbml.get("R-HSA-2"));
+ Future> b = pool.submit(() -> biopax.get("R-HSA-2"));
+ assertTrue(inside.await(10, TimeUnit.SECONDS));
+ Future> c = pool.submit(() -> biopax.get("R-HSA-1"));
+ Thread.sleep(200); // c waits for a place: two conversions are running, one of each export
+ assertEquals(2, at.get());
+ release.countDown();
+ a.get(10, TimeUnit.SECONDS);
+ b.get(10, TimeUnit.SECONDS);
+ c.get(10, TimeUnit.SECONDS);
+ } finally {
+ pool.shutdownNow();
+ }
+ assertEquals(2, most.get());
+ }
+
@Test
void anIdNotInTheGraphIsEmpty() throws Exception {
- SbmlFiles files = new SbmlFiles(graph, converter, diagrams, cache);
+ ExportFiles files = sbml(converter, diagrams);
assertTrue(files.get("R-HSA-3").isEmpty());
assertTrue(calls.isEmpty());
}
@Test
void convertsOnceAndKeepsTheFile() throws Exception {
- SbmlFiles files = new SbmlFiles(graph, converter, diagrams, cache);
+ ExportFiles files = sbml(converter, diagrams);
Path first = files.get("R-HSA-2").orElseThrow();
Path second = files.get("R-HSA-2").orElseThrow();
assertEquals(first, second);
@@ -81,7 +152,7 @@ void convertsOnceAndKeepsTheFile() throws Exception {
@Test
void fetchesTheDiagramOfAPathwayThatHasOne() throws Exception {
- SbmlFiles files = new SbmlFiles(graph, converter, diagrams, cache);
+ ExportFiles files = sbml(converter, diagrams);
files.get("R-HSA-1");
files.get("R-HSA-2");
assertEquals(List.of("fetch R-HSA-1 97", "convert R-HSA-1 97 diagram=true", "convert R-HSA-2 97 diagram=false"),
@@ -90,11 +161,11 @@ void fetchesTheDiagramOfAPathwayThatHasOne() throws Exception {
@Test
void aDiagramThatCannotBeHadIsNeverSbmlWithoutItsLayout() throws Exception {
- SbmlFiles.DiagramSource failing = (stId, rel, into) -> {
- throw new SbmlFiles.DiagramUnavailable("answered 503", null);
+ ExportFiles.DiagramSource failing = (stId, rel, into) -> {
+ throw new ExportFiles.DiagramUnavailable("answered 503", null);
};
- SbmlFiles files = new SbmlFiles(graph, converter, failing, cache);
- assertThrows(SbmlFiles.DiagramUnavailable.class, () -> files.get("R-HSA-1"));
+ ExportFiles files = sbml(converter, failing);
+ assertThrows(ExportFiles.DiagramUnavailable.class, () -> files.get("R-HSA-1"));
assertTrue(calls.isEmpty());
assertFalse(Files.exists(cache.resolve("sbml/97/R-HSA-1.sbml")));
}
@@ -102,11 +173,11 @@ void aDiagramThatCannotBeHadIsNeverSbmlWithoutItsLayout() throws Exception {
@Test
void aFailedConversionIsTriedAgain() throws Exception {
AtomicInteger attempts = new AtomicInteger();
- SbmlFiles.Converter once = (stId, rel, d, into) -> {
+ ExportFiles.Converter once = (stId, rel, d, into) -> {
if (attempts.incrementAndGet() == 1) throw new IllegalStateException("the first attempt fails");
Files.writeString(into.resolve(stId + ".sbml"), "");
};
- SbmlFiles files = new SbmlFiles(graph, once, diagrams, cache);
+ ExportFiles files = sbml(once, diagrams);
assertThrows(IllegalStateException.class, () -> files.get("R-HSA-2"));
assertEquals("", Files.readString(files.get("R-HSA-2").orElseThrow()));
assertEquals(2, attempts.get());
@@ -114,15 +185,18 @@ void aFailedConversionIsTriedAgain() throws Exception {
@Test
void workLeftByAStoppedServiceIsRemoved() throws Exception {
- Path stale = Files.createDirectories(cache.resolve("tmp/left-by-a-killed-run"));
+ Path stale = Files.createDirectories(cache.resolve("tmp/sbml/left-by-a-killed-run"));
Files.writeString(stale.resolve("R-HSA-2.sbml"), " {
+ ExportFiles.Converter slow = (stId, rel, d, into) -> {
conversions.incrementAndGet();
started.countDown();
assertTrue(release.await(10, TimeUnit.SECONDS));
Files.writeString(into.resolve(stId + ".sbml"), "");
};
- SbmlFiles files = new SbmlFiles(graph, slow, diagrams, cache);
+ ExportFiles files = sbml(slow, diagrams);
ExecutorService pool = Executors.newFixedThreadPool(2);
try {
Future> a = pool.submit(() -> files.get("R-HSA-2"));
diff --git a/deploy/java-library/src/test/java/org/reactome/server/library/HttpDiagramSourceTest.java b/deploy/java-library/src/test/java/org/reactome/server/library/HttpDiagramSourceTest.java
index 8b26e5793..ce88a0022 100644
--- a/deploy/java-library/src/test/java/org/reactome/server/library/HttpDiagramSourceTest.java
+++ b/deploy/java-library/src/test/java/org/reactome/server/library/HttpDiagramSourceTest.java
@@ -124,7 +124,7 @@ void writesTheReleasesFile() throws Exception {
@Test
void aMissingFileIsUnavailableAndLeavesNothing() throws Exception {
- SbmlFiles.DiagramUnavailable e = assertThrows(SbmlFiles.DiagramUnavailable.class,
+ ExportFiles.DiagramUnavailable e = assertThrows(ExportFiles.DiagramUnavailable.class,
() -> source().fetch("R-HSA-2", 97, into));
assertTrue(e.getMessage().contains("answered 404"), e.getMessage());
try (var left = Files.list(into)) {
@@ -134,7 +134,7 @@ void aMissingFileIsUnavailableAndLeavesNothing() throws Exception {
@Test
void aPageInPlaceOfTheFileIsUnavailableAndNotKept() throws Exception {
- SbmlFiles.DiagramUnavailable e = assertThrows(SbmlFiles.DiagramUnavailable.class,
+ ExportFiles.DiagramUnavailable e = assertThrows(ExportFiles.DiagramUnavailable.class,
() -> source().fetch("R-HSA-3", 97, into));
assertTrue(e.getMessage().contains("not R-HSA-3's diagram"), e.getMessage());
try (var left = Files.list(into)) {
@@ -144,7 +144,7 @@ void aPageInPlaceOfTheFileIsUnavailableAndNotKept() throws Exception {
@Test
void anotherPathwaysDiagramIsUnavailableAndNotKept() throws Exception {
- SbmlFiles.DiagramUnavailable e = assertThrows(SbmlFiles.DiagramUnavailable.class,
+ ExportFiles.DiagramUnavailable e = assertThrows(ExportFiles.DiagramUnavailable.class,
() -> source().fetch("R-HSA-4", 97, into));
assertTrue(e.getMessage().contains("not R-HSA-4's diagram"), e.getMessage());
try (var left = Files.list(into)) {
@@ -156,7 +156,7 @@ void anotherPathwaysDiagramIsUnavailableAndNotKept() throws Exception {
void aBodyThatStallsIsUnavailableWithinTheTimeout() throws Exception {
// The request's own timeout covers only the wait for the headers
assertTimeoutPreemptively(Duration.ofSeconds(15),
- () -> assertThrows(SbmlFiles.DiagramUnavailable.class, () -> source().fetch("R-HSA-5", 97, into)));
+ () -> assertThrows(ExportFiles.DiagramUnavailable.class, () -> source().fetch("R-HSA-5", 97, into)));
try (var left = Files.list(into)) {
assertEquals(0, left.count());
}
@@ -164,7 +164,7 @@ void aBodyThatStallsIsUnavailableWithinTheTimeout() throws Exception {
@Test
void aDownloadThatTimesOutIsAbandoned() throws Exception {
- assertThrows(SbmlFiles.DiagramUnavailable.class, () -> source().fetch("R-HSA-6", 97, into));
+ assertThrows(ExportFiles.DiagramUnavailable.class, () -> source().fetch("R-HSA-6", 97, into));
assertTrue(abandoned.await(10, TimeUnit.SECONDS), "the server was still sending");
}
@@ -187,7 +187,7 @@ void anInterruptedDownloadIsAbandoned() throws Exception {
fetching.interrupt();
fetching.join(10_000);
assertFalse(fetching.isAlive(), "the fetch did not return");
- assertTrue(outcome.get() instanceof SbmlFiles.DiagramUnavailable, String.valueOf(outcome.get()));
+ assertTrue(outcome.get() instanceof ExportFiles.DiagramUnavailable, String.valueOf(outcome.get()));
assertTrue(stillInterrupted.get(), "the interrupt was swallowed");
assertTrue(abandoned.await(10, TimeUnit.SECONDS), "the server was still sending");
}
diff --git a/deploy/java-library/src/test/java/org/reactome/server/library/SbmlControllerTest.java b/deploy/java-library/src/test/java/org/reactome/server/library/SbmlControllerTest.java
deleted file mode 100644
index f3ba26905..000000000
--- a/deploy/java-library/src/test/java/org/reactome/server/library/SbmlControllerTest.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package org.reactome.server.library;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.Map;
-import java.util.Optional;
-import java.util.Properties;
-
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.io.TempDir;
-import org.springframework.http.ResponseEntity;
-
-class SbmlControllerTest {
-
- @TempDir
- Path cache;
-
- private final SbmlFiles.Graph graph = new SbmlFiles.Graph() {
- @Override
- public int release() {
- return 97;
- }
-
- @Override
- public Optional event(String stId) {
- return stId.equals("R-HSA-1") ? Optional.of(new SbmlFiles.Event(true)) : Optional.empty();
- }
- };
-
- private SbmlController controller(SbmlFiles.DiagramSource diagrams, SbmlFiles.Converter converter) {
- return new SbmlController(new SbmlFiles(graph, converter, diagrams, cache), graph, new Properties());
- }
-
- private final SbmlFiles.Converter writes = (stId, rel, d, into) -> Files.writeString(into.resolve(stId + ".sbml"), "");
- private final SbmlFiles.DiagramSource fetches = (stId, rel, into) -> {
- try {
- Files.writeString(into.resolve(stId + ".json"), "{}");
- } catch (java.io.IOException e) {
- throw new SbmlFiles.DiagramUnavailable(e.getMessage(), e);
- }
- };
-
- @Test
- void answersTheFileAsSbml() throws Exception {
- ResponseEntity answer = controller(fetches, writes).sbml("R-HSA-1");
- assertEquals(200, answer.getStatusCodeValue());
- assertEquals(SbmlController.SBML, answer.getHeaders().getContentType());
- }
-
- @Test
- void anIdNotInTheGraphIs404() throws Exception {
- assertEquals(404, controller(fetches, writes).sbml("R-HSA-9").getStatusCodeValue());
- }
-
- @Test
- void anythingButAStableIdIs400() throws Exception {
- for (String id : new String[]{"R-HSA-1.2", "123", "../R-HSA-1", "r-hsa-1"}) {
- assertEquals(400, controller(fetches, writes).sbml(id).getStatusCodeValue(), id);
- }
- }
-
- @Test
- void aDiagramThatCannotBeHadIs503() throws Exception {
- SbmlFiles.DiagramSource failing = (stId, rel, into) -> {
- throw new SbmlFiles.DiagramUnavailable("answered 404", null);
- };
- ResponseEntity answer = controller(failing, writes).sbml("R-HSA-1");
- assertEquals(503, answer.getStatusCodeValue());
- assertEquals(Map.of("error", "answered 404"), answer.getBody());
- }
-
- @Test
- void aConversionThatFailsIs500() throws Exception {
- SbmlFiles.Converter failing = (stId, rel, d, into) -> {
- throw new IllegalStateException("no reactions");
- };
- assertEquals(500, controller(fetches, failing).sbml("R-HSA-1").getStatusCodeValue());
- }
-}
diff --git a/deploy/java/PINS.md b/deploy/java/PINS.md
index f982e5b60..30fbf42ef 100644
--- a/deploy/java/PINS.md
+++ b/deploy/java/PINS.md
@@ -17,6 +17,7 @@ The Reactome Java this deployment builds (spec 010), each pinned to the commit t
| reactome-parent 1.0.5-SNAPSHOT (and its BOM) | `reactome/reactome-parent` | `d93ad5a` (branch `feature/new-pwb`) | the BOM equal to the published snapshot; the parent differs only in Batik and FOP's versions (published 1.18 and 2.10, here 1.16 and 2.8), which nothing built on it here uses: the published snapshot matches no pushed commit | 17 |
| graph-core 3.0.0-SNAPSHOT | `reactome/graph-core` | `62aef35` | the deployed ContentService's jar is the published snapshot of 25 Sep 2025, byte for byte; rebuilt here, 172/377 classes identical, 203 identical by `javap`, 2 differ only in order (a method's place; which of three identical handlers each exception jumps to) | 17 |
| sbml-exporter-lib 3.0.0-SNAPSHOT | `reactome/sbml-exporter` | `f7b1034` (branch `graph-only`) | not Java's relational answer, so no byte comparison: proven by `ci/compare.py` against today's files (spec 015 T037, T039) | 17 |
+| biopax3-exporter-lib 0.0.1-SNAPSHOT | `reactome/BioPAX3Exporter` | `64c716a` (`main`) | not Java's relational answer, so no byte comparison: proven by its own `ci/compare.py` and `ci/contained.py` against release 98's published files (its spec 001 T020, T021), and here by spec 015 T049 against the legacy service | 17 |
## Frozen on purpose
@@ -27,9 +28,9 @@ The Reactome Java this deployment builds (spec 010), each pinned to the commit t
- **What uses it:** only diagram-exporter's PPTX path, which no Java-homed operation uses, and it runs unlicensed today (research R8).
- **To use it again:** a licence, and an operation that needs it.
-## The library service (spec 015 T063)
+## The library service (spec 015 T063, T069)
-`deploy/java-library/Dockerfile` builds the last three rows from these commits, and checks that its jar carries the libraries it built, byte for byte. `deploy/java-library/pins.spec.ts` checks that the Dockerfile's commits are this table's. Changing `sbml-exporter-lib`'s pin means rerunning spec 015 T067's comparison, not `tools/java-parity`: its body is not Java's.
+`deploy/java-library/Dockerfile` builds the last four rows from these commits, and checks that its jar carries the libraries it built, byte for byte. `deploy/java-library/pins.spec.ts` checks that the Dockerfile's commits are this table's. Changing `sbml-exporter-lib`'s pin means rerunning spec 015 T067's comparison, not `tools/java-parity`: its body is not Java's. Changing `biopax3-exporter-lib`'s likewise means rerunning spec 015 T049's comparison and T072's check.
## Changing a pin
diff --git a/docker-compose.yml b/docker-compose.yml
index 2a557d7ba..a1b6ad1dc 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -317,10 +317,11 @@ services:
# fails to build its lists, and rebuilds on the next request -- which is
# the behaviour specs/006 D10 asks for -- rather than refusing to start.
- # The library service (spec 015 T063, T064): the website's SBML, made on
- # demand from the graph by sbml-exporter's library. Spec 010's Java library
- # service, started here with SBML as its only operation. Node is its only
- # client (T065); nginx never names it.
+ # The library service (spec 015 T063, T064, T069): the website's SBML and
+ # BioPAX Level 3, made on demand from the graph by sbml-exporter's and
+ # BioPAX3Exporter's libraries. Spec 010's Java library service, started here
+ # with those two operations. Node is its only client (T065, T070); nginx
+ # never names it.
#
# Built here, on this host and in CI, from the commits deploy/java/PINS.md
# pins, and never pushed to a registry: no `image:` to pull or push
@@ -404,7 +405,7 @@ volumes:
# Survives a container replacement, which is the point: a cached figure is a
# file read, and rebuilding the cache means paying for every render again.
render-cache:
- # The library service's SBML and diagram files, per release: kept across a
+ # The library service's SBML, BioPAX and diagram files, per release: kept across a
# container replacement, as render's figures are.
java-library-cache:
graphdb-release98:
diff --git a/specs/015-graph-exports/tasks.md b/specs/015-graph-exports/tasks.md
index c1a14540e..cffa18f28 100644
--- a/specs/015-graph-exports/tasks.md
+++ b/specs/015-graph-exports/tasks.md
@@ -265,7 +265,10 @@ Both exporters' adoption pull requests found that their own checks do not run ye
- [ ] T050 [US2] (The species files are done: the validator gives no error a published file lacks, its T020, [BioPAX3Exporter#79](https://github.com/reactome/BioPAX3Exporter/pull/79).) What is left: validate the sample's per-event files from the library, and the legacy service's, and record any error the library's has that the legacy's lacks.
- [x] T051 [US2] [ext] In `BioPAX3Exporter`'s CI: the validator over its output for a small fixture graph, failing on any error in the reports. — its T004 ([BioPAX3Exporter#15](https://github.com/reactome/BioPAX3Exporter/pull/15)) and T007 ([BioPAX3Exporter#27](https://github.com/reactome/BioPAX3Exporter/pull/27)).
- [ ] T052 [US2] Serve the website's BioPAX through the library service in `deploy/java-library/`, as R10's amendment of 29 Oct 2026 decided: T069–T072, in that order. T071 waits for T049 and T050.
-- [ ] T069 [US2] The BioPAX operation in the library service, on T063's terms:
+- [x] T069 [US2] The BioPAX operation in the library service, on T063's terms: — #755. `SbmlFiles` and `SbmlController` became `ExportFiles` and `ExportController`, one `ExportFiles` per export, with the conversions' cap of two shared by both. BioPAX3Exporter `main` at `64c716a` is pinned (PINS.md; `pins.spec.ts`, whose ARG pattern now allows a digit). The Dockerfile checks the jar's `kotlin-stdlib` 2.4.21 and `paxtools-core` 6.0.0. `check.sh` gains a BioPAX stage and a `SERVICE_PORT`, so it runs beside a deployment's service.
+ - **Checked here:** the image built and `check.sh` passed over both fixtures: SBML's three files valid and equal to expected; five BioPAX events, one of each kind across both species, each contained and whole in its species' expected file, with the per-event base. Against beta's image, which has no BioPAX, it failed: five 404s.
+ - **Measured** on a private copy of release 98's graph, in a container held to 1.5 GiB with T064's 1 GiB heap: BioPAX and SBML of Signal Transduction and Metabolism, all four asked at once. Peak 1.10 GiB, no kill. The cap converted two at once: Metabolism's pair in 156–158 s, then Signal Transduction's pair, finished at 300–310 s. Alone, a conversion of either is about 150 s, under node's 290 s. In that worst case the queued pair's readers get node's 503 ("took too long"); the service finishes and keeps the files, so a second request is answered at once. Files: BioPAX 47 MB and 41 MB, SBML 23 MB and 19 MB.
+ - **Unit tests:** `ExportFilesTest` (11) and `ExportControllerTest` (8). The new ones: an export with no diagram source never fetches one; each export keeps its own files; the cap is shared, at most two at once across both; BioPAX answered as RDF, needing no diagram, with SBML's errors. From #754's review, in the same PR: node's comment on the shares, and BioPAX's 503s tested.
- **The library from source:** the Dockerfile builds `biopax3-exporter-lib` from a pinned commit of `BioPAX3Exporter`'s `main`, with its row in `deploy/java/PINS.md` and `pins.spec.ts` following. Its graph-core must be the build already pinned, or the PR says why not. The service's pom sets `kotlin.version` to the library's: Spring Boot 2.7's dependency management would otherwise bring Kotlin's standard library down to 1.6.21 under a library compiled with 2.4. The Dockerfile's jar check `cmp`s `biopax3-exporter-lib` as it does `sbml-exporter-lib`, and requires the jar's `kotlin-stdlib` and `paxtools-core` to be the library's versions.
- **Its operation:** `GET /biopax/{stId}` answers the library's one-event conversion, with the release's per-event `xml:base`, and 404 for an id that is not a pathway or reaction in the graph, a backstop: node decides 404 and 400 first (T070).
- **The files** are kept on disk per release, written beside and moved into place. One id is never converted twice at the same time.
diff --git a/tools/content-node/biopax-export.spec.ts b/tools/content-node/biopax-export.spec.ts
index c492ce357..eaa9a83b3 100644
--- a/tools/content-node/biopax-export.spec.ts
+++ b/tools/content-node/biopax-export.spec.ts
@@ -105,15 +105,15 @@ describe('the file', () => {
res.writeHead(200, { 'Content-Type': 'application/rdf+xml;charset=UTF-8' });
res.end('');
};
- for (const form of ['R-HSA-1', 'R-HSA-1.4', '1']) {
- const answer = await answers(`event/${form}.biopax`);
+ for (const path of ['R-HSA-1.biopax', 'R-HSA-1.4.biopax', '1.biopax', 'R-HSA-1.biopax/']) {
+ const answer = await answers(`event/${path}`);
expect(answer.status).toBe(200);
expect(answer.type).toBe('application/rdf+xml;charset=UTF-8');
expect(answer.headers?.['Content-Disposition']).toBe('attachment; filename="R-HSA-1.biopax"');
expect(await text(answer)).toBe('');
}
// The service is asked for BioPAX, by the bare stable id
- expect(asked).toEqual(['/biopax/R-HSA-1', '/biopax/R-HSA-1', '/biopax/R-HSA-1']);
+ expect(asked).toEqual(Array(4).fill('/biopax/R-HSA-1'));
});
it('the service’s 404 is a 404, and its failure a 500 without its own reason', async () => {
@@ -134,6 +134,27 @@ describe('the file', () => {
]);
});
+ it('the service’s 503 is a 503 to try again, and a service not there is a 503, in BioPAX’s words', async () => {
+ withService();
+ behave = (_path, res) => {
+ res.writeHead(503, { 'Content-Type': 'application/json' });
+ res.end('{"error":"/cache busy"}');
+ };
+ const busy = await answers('event/R-HSA-1.biopax');
+ expect(envelope(busy)).toEqual([
+ 503,
+ 'SERVICE_UNAVAILABLE',
+ ['The BioPAX file cannot be made just now; try again shortly'],
+ ]);
+ expect(busy.headers?.['Retry-After']).toBe('30');
+ process.env['SBML_SERVICE'] = 'http://127.0.0.1:9';
+ expect(envelope(await answers('event/R-HSA-1.biopax'))).toEqual([
+ 503,
+ 'SERVICE_UNAVAILABLE',
+ ['The BioPAX service cannot be reached'],
+ ]);
+ });
+
it('a service that sends no headers in time is a 503', async () => {
withService();
behave = () => undefined;
diff --git a/tools/content-node/exporters-endpoints.ts b/tools/content-node/exporters-endpoints.ts
index 89f1e2f2f..1fa0afc9c 100644
--- a/tools/content-node/exporters-endpoints.ts
+++ b/tools/content-node/exporters-endpoints.ts
@@ -370,11 +370,12 @@ async function exportEvent(raw: string): Promise {
}
/**
- * Each export's own share (research R6): Java made one file at a time, and the
- * service two at once across its exports (its backstop, spec 015 T069); past
- * a share, a 503 with Retry-After, as the deep pool answers. Separate from the
- * deep pool and from each other, so a burst of one cannot starve the queries
- * the pages need, or the other export.
+ * Each export's own share (research R6): Java made one file at a time; past a
+ * share, a 503 with Retry-After, as the deep pool answers. Separate from the
+ * deep pool, so a burst of exports cannot starve the queries the pages need,
+ * and from each other, so one export cannot take the other's places here. The
+ * service converts two at once across both (spec 015 T069), for its heap: a
+ * BioPAX file may wait there behind two SBML ones, within the headers' time.
*/
const SBML_SHARE = deepShare(2);
const BIOPAX_SHARE = deepShare(2);