failing tests on master

Trying to run gradle build yields two assertion errors:

RegistryTest > retrieveNamespaceNonCanonical() STANDARD_ERROR
    May 03, 2022 8:53:47 PM edu.ucsd.sbrg.miriam.Registry checkResourceUrl
    SEVERE: Please report this URI http://purl.obolibrary.org/obo/GSSO_002368

RegistryTest > retrieveNamespaceNonCanonical() FAILED
    org.opentest4j.AssertionFailedError at RegistryTest.java:53

RegistryTest > getPartsFromCanonicalURITest() FAILED
    org.opentest4j.AssertionFailedError at RegistryTest.java:119

this happens via

    Miriam miriam = RegistryProvider.getInstance().getMiriam();
    namespaces = new LinkedHashSet<>(miriam.getNamespaces().values());

and

    for (Namespace ns : namespaces) {
      // Given sample identifier does not match provided pattern for GWAS and Pattern is wrong for GOLD genome
      String name = ns.getName();
      if (name.equals("GWAS Central Phenotype") || name.equals("GOLD genome")) {
        continue;
      }
      for (Resource res : ns.getResources()) {
        // id from sciwalker is slightly different, ignore for now
        // Panther Pattern is interpreted incorrectly - '^G|P|U|C|S\\d{5}$' should be '^[GPUCS]\\d{5}$' instead
        // Onto bee has a weird id pattern that we currently don't handle, ignore for now
        name = res.getName();
        if (name.equals("SciWalker Open Data") || name.equals("PANTHER Pathway Component at USC (Los Angeles)") || name.equals("VariO at Lund University")) {
          continue;
        }
        String id = res.getSampleId();
        String urlPattern = res.getUrlPattern();
        String sourceURL = urlPattern.replaceAll("\\{\\$id}", id);
        Optional<String> canonicalURL = Registry.checkResourceUrl(sourceURL);
        assertTrue(canonicalURL.isPresent());
        canonicalURL.ifPresent(url -> {
          assertTrue(url.startsWith("https://identifiers.org"));

This seems to boil down to some messy code in Registry::checkResourceUrl which could be hotfixed by exiting on empty "NonCanonical" return pair.

draeger-lab / ModelPolisher

failing tests on master #109