Spec 015 T069, from #755's review: check.sh's silent stop, old work, a fair cap

deploy/java-library/check.sh

@@ -142,7 +142,12 @@ candidates=$(docker exec "$neo2" cypher-shell -u neo4j -p fixturepass -d graph.d
   RETURN kind + " " + e.stId + " " + e.dbId + " " + replace(e.speciesName, " ", "_")
   ORDER BY kind, e.dbId' | tail -n +2 | tr -d '"')
 events=$(while read -r kind id dbid species; do
-  grep -q ">$dbid</bp:id>" "$bci/fixture/expected/$species.owl" && echo "$kind $id $dbid $species"
+  # The event's own database-id xref, whose comment ends with its id: not any
+  # numeric id (a PubMed id) that happens to match. An if, not &&: under
+  # pipefail a last candidate not in its file would end the script silently.
+  if grep -q "&amp;ID=$dbid</bp:comment>" "$bci/fixture/expected/$species.owl"; then
+    echo "$kind $id $dbid $species"
+  fi
 done <<<"$candidates" | sort -u -k1,1 | cut -d' ' -f2-)
 [ "$(printf '%s\n' "$events" | wc -l)" -eq 5 ] || { echo "Expected one event of each of five kinds in the fixture's files, got: $events" >&2; exit 1; }
 

deploy/java-library/src/main/java/org/reactome/server/library/ExportFiles.java

@@ -74,6 +74,8 @@ public DiagramUnavailable(String message, Throwable cause) {
     }
 
     private static final Logger logger = LoggerFactory.getLogger(ExportFiles.class);
+    private static final java.util.regex.Pattern OLD_WORK =
+            java.util.regex.Pattern.compile("[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}");
 
     private final String kind;
     private final String extension;
@@ -100,8 +102,16 @@ public ExportFiles(String kind, String extension, Graph graph, Converter convert
         this.diagrams = diagrams;
         this.cache = cache;
         this.conversions = conversions;
-        // Work in progress when the service last stopped, which nothing will finish
+        // Work in progress when the service last stopped, which nothing will finish: this export's, and any left
+        // in the layout before exports had a folder each (cache/tmp/{uuid})
         delete(work());
+        try (DirectoryStream<Path> left = Files.newDirectoryStream(cache.resolve("tmp"))) {
+            for (Path old : left) {
+                if (OLD_WORK.matcher(old.getFileName().toString()).matches()) delete(old);
+            }
+        } catch (IOException e) {
+            // No tmp folder yet, or none readable: nothing to clear
+        }
     }
 
     private Path work() {

deploy/java-library/src/main/java/org/reactome/server/library/LibraryApplication.java

@@ -59,10 +59,13 @@ public Optional<ExportFiles.Event> event(String stId) {
         };
     }
 
-    /** The conversions at once, across every export: two, within the heap (spec 015 T069). */
+    /**
+     * The conversions at once, across every export: two, within the heap (spec 015 T069). Fair, so a request
+     * waiting for a place is not overtaken by later ones of the other export.
+     */
     @Bean
     public Semaphore conversions() {
-        return new Semaphore(2);
+        return new Semaphore(2, true);
     }
 
     @Bean

deploy/java-library/src/test/java/org/reactome/server/library/ExportFilesTest.java

@@ -194,6 +194,16 @@ void workLeftByAStoppedServiceIsRemoved() throws Exception {
         assertTrue(Files.exists(others));
     }
 
+    @Test
+    void workLeftInTheLayoutBeforeExportsHadFoldersIsRemoved() throws Exception {
+        Path old = Files.createDirectories(cache.resolve("tmp/0f8fad5b-d9cb-469f-a165-70867728950e"));
+        Files.writeString(old.resolve("R-HSA-2.sbml"), "<sbml");
+        Path others = Files.createDirectories(cache.resolve("tmp/biopax"));
+        sbml(converter, diagrams);
+        assertFalse(Files.exists(old));
+        assertTrue(Files.exists(others));
+    }
+
     @Test
     void aNewReleaseIsNeverAnsweredFromTheOldOnesFiles() throws Exception {
         ExportFiles files = sbml(converter, diagrams);

tools/content-node/exporters-endpoints.ts

@@ -375,7 +375,9 @@ async function exportEvent(raw: string): Promise<ExportEvent | null> {
  * 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.
+ * BioPAX file may wait there behind two SBML ones, and past the headers' time
+ * at the worst (T069 measured 300–310 s): the reader then gets the 503 below,
+ * and the service, finishing, keeps the file for the next request.
  */
 const SBML_SHARE = deepShare(2);
 const BIOPAX_SHARE = deepShare(2);