Class GeoBrowserTest

java.lang.Object
ubic.gemma.core.loader.expression.geo.service.GeoBrowserTest
@Tag("geo") @Tag("slow") @NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi") @ExtendWith(NetworkAvailableExtension.class) public class GeoBrowserTest extends Object
Author:
pavlidis

  • Constructor Details

    • GeoBrowserTest

      public GeoBrowserTest()

  • Method Details

    • testGetDetailedGeoRecord

      @Test @Tag("slow") public void testGetDetailedGeoRecord() throws IOException
      Throws:
      IOException

    • testSearchGeoRecords

      @Test @Tag("slow") public void testSearchGeoRecords() throws IOException
      Throws:
      IOException

    • testRetrieveDetailedGeoRecords

      @Test @Disabled("This test started breaking around March 25 2025.") public void testRetrieveDetailedGeoRecords() throws IOException
      Exercises getting details
      Throws:
      IOException

    • testGetGeoRecordB

      @Test @Tag("slow") public void testGetGeoRecordB() throws IOException
      Throws:
      IOException

    • testGetGeoRecordGSE93825

      @Test public void testGetGeoRecordGSE93825() throws IOException
      Throws:
      IOException

    • testGSE97948

      @Test @Tag("slow") public void testGSE97948() throws IOException
      This GEO record has ~1000 samples with hundreds of characteristics each.
      Throws:
      IOException

    • testGeoEmptyMINiML

      @Test @Tag("slow") public void testGeoEmptyMINiML() throws IOException
      GEO returns an empty document when retrieving the samples for this document.
      Throws:
      IOException

    • testGetGeoRecordWithMeshHeadings

      @Test @Tag("slow") public void testGetGeoRecordWithMeshHeadings() throws IOException
      This dataset has MESH headings.
      Throws:
      IOException

    • testSearchGeoRecordWithMeshHeadings

      @Test @Tag("slow") public void testSearchGeoRecordWithMeshHeadings() throws IOException
      Throws:
      IOException

    • testGSE2569

      @Test @Tag("slow") public void testGSE2569() throws IOException
      This dataset has incorrect UTF-8 characters in its MINiML file on GEO FTP server. It is re-attempted with Windows-1252 encoding.
      Throws:
      IOException

    • testGSE8579

      @Test @Tag("slow") public void testGSE8579() throws IOException
      THis dataset has invalid 1-byte UTF-8 sequence (0x1b)
      Throws:
      IOException

    • testFetchDetailedGeoSeries

      @Test @Tag("slow") public void testFetchDetailedGeoSeries() throws IOException
      There are two strategies to retrieve detailed GEO series and those should produce identical documents.
      Throws:
      IOException

    • testFetchDetailedGeoSeriesWithInvalidUtf8Characters

      @Test @Tag("slow") public void testFetchDetailedGeoSeriesWithInvalidUtf8Characters() throws IOException
      Throws:
      IOException

    • testGetAllGeoRecords

      @Test @Tag("slow") public void testGetAllGeoRecords() throws IOException
      Throws:
      IOException