@Test public void goodMirnaFile() throws Exception { addTemporaryFile( "annotations", "Homo_sapiens.mature_mirna.tsv", ImmutableList.of( new String[]{"mirbase_accession", "symbol", "mirbase_name", "mirbase_sequence"}, new String[]{"MIMAT0001535", "cfa-miR-448", "miR-448", "UUGCAUAUGUAGGAUGUCCCAU"})); assertHasOneGoodResource(subject.getAnnotationFiles()); assertThat( subject.getAnnotationFiles() .findFirst() .orElseThrow(RuntimeException::new) .get() .collect(toList()), containsInAnyOrder( new BioentityProperty( "MIMAT0001535", "Homo_sapiens", "mirbase_accession", "MIMAT0001535"), new BioentityProperty( "MIMAT0001535", "Homo_sapiens", "symbol", "cfa-miR-448"), new BioentityProperty( "MIMAT0001535", "Homo_sapiens", "mirbase_name", "miR-448"), new BioentityProperty( "MIMAT0001535", "Homo_sapiens", "mirbase_sequence", "UUGCAUAUGUAGGAUGUCCCAU"))); }
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);   }