@Test public void goodButEmptyAnnotationFileWithUnknownSpeciesIsGonnaBeABlankFieldInSolrButIsOtherwiseOkayForNow() throws Exception { addTemporaryFile( "annotations", "Unknown_species.ensgene.tsv", ImmutableList.of( new String[]{"ensgene", "synonym", "ensfamily_description", "goterm"})); assertHasOneGoodResource(subject.getAnnotationFiles()); assertThat( subject.getAnnotationFiles() .findFirst() .orElseThrow(RuntimeException::new) .species .getEnsemblName(), is(SpeciesProperties.UNKNOWN.ensemblName())); }
Stream<AnnotationFile> getAnnotationFiles() { return getBioentityPropertyFiles(annotationsDirPath, ANNOTATION_FILE_NAME_PATTERN, AnnotationFile::new); }
BioentityPropertiesSource { Stream<AnnotationFile> getAnnotationFiles() { return getBioentityPropertyFiles(annotationsDirPath, ANNOTATION_FILE_NAME_PATTERN, AnnotationFile::new); } }
BioentityPropertiesSource { Stream<AnnotationFile> getAnnotationFiles() { return getBioentityPropertyFiles(annotationsDirPath, ANNOTATION_FILE_NAME_PATTERN, AnnotationFile::new); } BioentityPropertiesSource(Path annotationsDirPath,
                                     Path arrayDesignsDirPath,
                                     Path reactomeDirPath,
                                     SpeciesFactory speciesFactory); }
BioentityPropertiesSource { Stream<AnnotationFile> getAnnotationFiles() { return getBioentityPropertyFiles(annotationsDirPath, ANNOTATION_FILE_NAME_PATTERN, AnnotationFile::new); } BioentityPropertiesSource(Path annotationsDirPath,
                                     Path arrayDesignsDirPath,
                                     Path reactomeDirPath,
                                     SpeciesFactory speciesFactory);  }
BioentityPropertiesSource { Stream<AnnotationFile> getAnnotationFiles() { return getBioentityPropertyFiles(annotationsDirPath, ANNOTATION_FILE_NAME_PATTERN, AnnotationFile::new); } BioentityPropertiesSource(Path annotationsDirPath,
                                     Path arrayDesignsDirPath,
                                     Path reactomeDirPath,
                                     SpeciesFactory speciesFactory);   }