GitHub PullRequestReviewCommentEvent at 2014-03-07 10:55:33
Repository: molgenis
Actor: bartcharbon
Payload: {"comment":{"url":"https://api.github.com/repos/molgenis/molgenis/pulls/comments/10379425","id":10379425,"diff_hunk":"@@ -0,0 +1,164 @@\n+package org.molgenis.data.annotation.impl;\n+\n+import static org.mockito.Mockito.mock;\n+import static org.mockito.Mockito.when;\n+import static org.testng.Assert.assertEquals;\n+\n+import java.util.ArrayList;\n+import java.util.Iterator;\n+import java.util.LinkedHashMap;\n+import java.util.List;\n+import java.util.Map;\n+\n+import org.molgenis.MolgenisFieldTypes;\n+import org.molgenis.MolgenisFieldTypes.FieldTypeEnum;\n+import org.molgenis.data.AttributeMetaData;\n+import org.molgenis.data.Entity;\n+import org.molgenis.data.EntityMetaData;\n+import org.molgenis.data.support.MapEntity;\n+import org.testng.annotations.BeforeMethod;\n+import org.testng.annotations.Test;\n+\n+public class OmimHpoAnnotatorTest\n+{\n+\tprivate EntityMetaData metaDataCanAnnotate;\n+\tprivate EntityMetaData metaDataCantAnnotate;\n+\tprivate OmimHpoAnnotator annotator;\n+\tprivate AttributeMetaData attributeMetaDataChrom;\n+\tprivate AttributeMetaData attributeMetaDataPos;\n+\tprivate AttributeMetaData attributeMetaDataCantAnnotateFeature;\n+\tprivate AttributeMetaData attributeMetaDataCantAnnotateChrom;\n+\tprivate AttributeMetaData attributeMetaDataCantAnnotatePos;\n+\tprivate String annotatorOutput;\n+\tprivate Entity entity;\n+\tprivate ArrayList<Entity> input;\n+\t\n+\t@BeforeMethod\n+\tpublic void beforeMethod(){\n+\t\tannotator = new OmimHpoAnnotator();\n+\n+\t\tmetaDataCanAnnotate = mock(EntityMetaData.class);\n+\n+\t\tattributeMetaDataChrom = mock(AttributeMetaData.class);\n+\t\tattributeMetaDataPos = mock(AttributeMetaData.class);\n+\n+\t\twhen(attributeMetaDataChrom.getName()).thenReturn(OmimHpoAnnotator.CHROMOSOME);\n+\t\twhen(attributeMetaDataPos.getName()).thenReturn(OmimHpoAnnotator.POSITION);\n+\n+\t\twhen(attributeMetaDataChrom.getDataType()).thenReturn(\n+\t\t\t\tMolgenisFieldTypes.getType(FieldTypeEnum.STRING.toString().toLowerCase()));\n+\t\twhen(attributeMetaDataPos.getDataType()).thenReturn(\n+\t\t\t\tMolgenisFieldTypes.getType(FieldTypeEnum.LONG.toString().toLowerCase()));\n+\n+\t\twhen(metaDataCanAnnotate.getAttribute(OmimHpoAnnotator.CHROMOSOME))\n+\t\t\t\t.thenReturn(attributeMetaDataChrom);\n+\t\twhen(metaDataCanAnnotate.getAttribute(OmimHpoAnnotator.POSITION)).thenReturn(attributeMetaDataPos);\n+\n+\t\tmetaDataCantAnnotate = mock(EntityMetaData.class);\n+\t\tattributeMetaDataCantAnnotateFeature = mock(AttributeMetaData.class);\n+\n+\t\twhen(attributeMetaDataCantAnnotateFeature.getName()).thenReturn(\"otherID\");\n+\t\twhen(attributeMetaDataCantAnnotateFeature.getDataType()).thenReturn(\n+\t\t\t\tMolgenisFieldTypes.getType(FieldTypeEnum.STRING.toString().toLowerCase()));\n+\n+\t\tattributeMetaDataCantAnnotateChrom = mock(AttributeMetaData.class);\n+\t\twhen(attributeMetaDataCantAnnotateChrom.getName()).thenReturn(OmimHpoAnnotator.CHROMOSOME);\n+\t\twhen(attributeMetaDataCantAnnotateFeature.getDataType()).thenReturn(\n+\t\t\t\tMolgenisFieldTypes.getType(FieldTypeEnum.INT.toString().toLowerCase()));\n+\n+\t\tattributeMetaDataCantAnnotatePos = mock(AttributeMetaData.class);\n+\t\twhen(attributeMetaDataCantAnnotatePos.getName()).thenReturn(OmimHpoAnnotator.POSITION);\n+\t\twhen(attributeMetaDataCantAnnotatePos.getDataType()).thenReturn(\n+\t\t\t\tMolgenisFieldTypes.getType(FieldTypeEnum.STRING.toString().toLowerCase()));\n+\n+\t\twhen(metaDataCantAnnotate.getAttribute(OmimHpoAnnotator.CHROMOSOME)).thenReturn(\n+\t\t\t\tattributeMetaDataChrom);\n+\t\twhen(metaDataCantAnnotate.getAttribute(OmimHpoAnnotator.POSITION)).thenReturn(\n+\t\t\t\tattributeMetaDataCantAnnotatePos);\n+\n+\t\tentity = mock(Entity.class);\n+\n+\t\twhen(entity.getString(OmimHpoAnnotator.CHROMOSOME)).thenReturn(\"2\");\n+\t\twhen(entity.getLong(OmimHpoAnnotator.POSITION)).thenReturn(new Long(58453844l));\n+\n+\t\tinput = new ArrayList<Entity>();\n+\t\tinput.add(entity);\n+\n+\t\tannotatorOutput = \"\";\n+\t}\n+\t\n+\t@Test\n+\tpublic void annotateTest()\n+\t{\n+\t\tList<Entity> expectedList = new ArrayList<Entity>();\n+\t\tMap<String, Object> resultMap = new LinkedHashMap<String, Object>();\n+\n+\t\t\n+\t\t//Full_info_HPO='[HPOTerm{id='HP:0001639', description='Hypertrophic cardiomyopathy', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000532', description='Chorioretinal abnormality', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000505', description='Visual impairment', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000388', description='Otitis media', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000613', description='Photophobia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001956', description='Truncal obesity', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000858', description='Menstrual irregularities', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001970', description='Tubulointerstitial nephritis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002149', description='Hyperuricemia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001596', description='Alopecia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000873', description='Diabetes insipidus', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0200120', description='Chronic active hepatitis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001155', description='Abnormality of the hand', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002910', description='Elevated hepatic transaminases', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000842', description='Hyperinsulinemia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002650', description='Scoliosis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000824', description='Growth hormone deficiency', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000639', description='Nystagmus', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0003233', description='Hypoalphalipoproteinemia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002099', description='Asthma', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000083', description='Renal insufficiency', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001394', description='Cirrhosis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000548', description='Cone-rod dystrophy', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000121', description='Nephrocalcinosis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0100820', description='Glomerulopathy', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000822', description='Hypertension', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0007360', description='Aplasia/Hypoplasia of the cerebellum', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0005616', description='Accelerated skeletal maturation', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002205', description='Recurrent respiratory infections', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000580', description='Pigmentary retinopathy', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000717', description='Autism', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000144', description='Decreased fertility', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000164', description='Abnormality of the teeth', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001397', description='Hepatic steatosis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000408', description='Progressive sensorineural hearing impairment', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000956', description='Acanthosis nigricans', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000091', description='Abnormality of the renal tubule', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000123', description='Nephritis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001635', description='Congestive heart failure', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002808', description='Kyphosis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000518', description='Cataract', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0100543', description='Cognitive impairment', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000618', description='Blindness', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0004438', description='Hyperostosis frontalis interna', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001644', description='Dilated cardiomyopathy', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000407', description='Sensorineural hearing impairment', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000795', description='Abnormality of the urethra', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000821', description='Hypothyroidism', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0004322', description='Short stature', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0009124', description='Abnormality of adipose tissue', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000771', description='Gynecomastia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001409', description='Portal hypertension', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002240', description='Hepatomegaly', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000076', description='Vesicoureteral reflux', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0100817', description='Renovascular hypertension', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0006532', description='Recurrent pneumonia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0003119', description='Abnormality of lipid metabolism', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001250', description='Seizures', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000998', description='Hypertrichosis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000523', description='Subcapsular cataract', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000815', description='Hypergonadotropic hypogonadism', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000490', description='Deeply set eye', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001763', description='Pes planus', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000831', description='Insulin-resistant diabetes mellitus', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000855', description='Insulin resistance', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0005978', description='Type II diabetes mellitus', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000055', description='Abnormality of female external genitalia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000035', description='Abnormality of the testis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002092', description='Pulmonary hypertension', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000230', description='Gingivitis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000311', description='Round face', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000007', description='Autosomal recessive inheritance', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000722', description='Obsessive-compulsive disorder', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002621', description='Atherosclerosis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002093', description='Respiratory insufficiency', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0100626', description='Chronic hepatic failure', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002155', description='Hypertriglyceridemia', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000826', description='Precocious puberty', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0005987', description='Multinodular goiter', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0002206', description='Pulmonary fibrosis', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001263', description='Global developmental delay', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0001744', description='Splenomegaly', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}, HPOTerm{id='HP:0000147', description='Polycystic ovaries', diseaseDb='OMIM', diseaseDbEntry=203800, geneName='ALMS1', geneEntrezID=7840}]', Hyperlink_OMIM='<a href=\"http://www.omim.org/entry/203800\">203800</a>', Hyperlinks_HPO='<a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001639\">HP:0001639</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000532\">HP:0000532</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000505\">HP:0000505</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000388\">HP:0000388</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000613\">HP:0000613</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001956\">HP:0001956</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000858\">HP:0000858</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001970\">HP:0001970</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002149\">HP:0002149</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001596\">HP:0001596</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000873\">HP:0000873</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0200120\">HP:0200120</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001155\">HP:0001155</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002910\">HP:0002910</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000842\">HP:0000842</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002650\">HP:0002650</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000824\">HP:0000824</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000639\">HP:0000639</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0003233\">HP:0003233</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002099\">HP:0002099</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000083\">HP:0000083</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001394\">HP:0001394</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000548\">HP:0000548</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000121\">HP:0000121</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0100820\">HP:0100820</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000822\">HP:0000822</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0007360\">HP:0007360</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0005616\">HP:0005616</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002205\">HP:0002205</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000580\">HP:0000580</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000717\">HP:0000717</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000144\">HP:0000144</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000164\">HP:0000164</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001397\">HP:0001397</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000408\">HP:0000408</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000956\">HP:0000956</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000091\">HP:0000091</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000123\">HP:0000123</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001635\">HP:0001635</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002808\">HP:0002808</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000518\">HP:0000518</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0100543\">HP:0100543</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000618\">HP:0000618</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0004438\">HP:0004438</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001644\">HP:0001644</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000407\">HP:0000407</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000795\">HP:0000795</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000821\">HP:0000821</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0004322\">HP:0004322</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0009124\">HP:0009124</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000771\">HP:0000771</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001409\">HP:0001409</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002240\">HP:0002240</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000076\">HP:0000076</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0100817\">HP:0100817</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0006532\">HP:0006532</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0003119\">HP:0003119</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001250\">HP:0001250</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000998\">HP:0000998</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000523\">HP:0000523</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000815\">HP:0000815</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000490\">HP:0000490</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001763\">HP:0001763</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000831\">HP:0000831</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000855\">HP:0000855</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0005978\">HP:0005978</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000055\">HP:0000055</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000035\">HP:0000035</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002092\">HP:0002092</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000230\">HP:0000230</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000311\">HP:0000311</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000007\">HP:0000007</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000722\">HP:0000722</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002621\">HP:0002621</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002093\">HP:0002093</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0100626\">HP:0100626</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002155\">HP:0002155</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000826\">HP:0000826</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0005987\">HP:0005987</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002206\">HP:0002206</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001263\">HP:0001263</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001744\">HP:0001744</a> / <a href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000147\">HP:0000147</a>', Disease_OMIM='Alstrom syndrome', Symptoms_HPO='Hypertrophic cardiomyopathy / Chorioretinal abnormality / Visual impairment / Otitis media / Photophobia / Truncal obesity / Menstrual irregularities / Tubulointerstitial nephritis / Hyperuricemia / Alopecia / Diabetes insipidus / Chronic active hepatitis / Abnormality of the hand / Elevated hepatic transaminases / Hyperinsulinemia / Scoliosis / Growth hormone deficiency / Nystagmus / Hypoalphalipoproteinemia / Asthma / Renal insufficiency / Cirrhosis / Cone-rod dystrophy / Nephrocalcinosis / Glomerulopathy / Hypertension / Aplasia/Hypoplasia of the cerebellum / Accelerated skeletal maturation / Recurrent respiratory infections / Pigmentary retinopathy / Autism / Decreased fertility / Abnormality of the teeth / Hepatic steatosis / Progressive sensorineural hearing impairment / Acanthosis nigricans / Abnormality of the renal tubule / Nephritis / Congestive heart failure / Kyphosis / Cataract / Cognitive impairment / Blindness / Hyperostosis frontalis interna / Dilated cardiomyopathy / Sensorineural hearing impairment / Abnormality of the urethra / Hypothyroidism / Short stature / Abnormality of adipose tissue / Gynecomastia / Portal hypertension / Hepatomegaly / Vesicoureteral reflux / Renovascular hypertension / Recurrent pneumonia / Abnormality of lipid metabolism / Seizures / Hypertrichosis / Subcapsular cataract / Hypergonadotropic hypogonadism / Deeply set eye / Pes planus / Insulin-resistant diabetes mellitus / Insulin resistance / Type II diabetes mellitus / Abnormality of female external genitalia / Abnormality of the testis / Pulmonary hypertension / Gingivitis / Round face / Autosomal recessive inheritance / Obsessive-compulsive disorder / Atherosclerosis / Respiratory insufficiency / Chronic hepatic failure / Hypertriglyceridemia / Precocious puberty / Multinodular goiter / Pulmonary fibrosis / Global developmental delay / Splenomegaly / Polycystic ovaries', Full_info_OMIM='[OMIMTerm{entry=203800, name='Alstrom syndrome', type=3, causedBy=606844, cytoLoc='2p13.1', hgncIds=[ALMS1, ALSS, KIAA0328]}]', pos='73679116', chrom='2'}\n+\t\tresultMap.put(OmimHpoAnnotator.OMIM_ALL, \"\");\n+\t\tresultMap.put(OmimHpoAnnotator.OMIM_LINK, \"http://www.omim.org/entry/203800\");\n+\t\tresultMap.put(OmimHpoAnnotator.OMIM_DISO, \"\");\n+\t\tresultMap.put(OmimHpoAnnotator.HPO_ALL, \"\");\n+\t\tresultMap.put(OmimHpoAnnotator.HPO_LINK, \"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001639\");\n+\t\tresultMap.put(OmimHpoAnnotator.HPO_DESC, \"\");\n+\n+\t\tEntity expectedEntity = new MapEntity(resultMap);\n+\n+\t\texpectedList.add(expectedEntity);\n+\n+\t\tIterator<Entity> results = annotator.annotate(input.iterator());\n+\n+\t\tEntity resultEntity = results.next();\n+\n+\t\tassertEquals(resultEntity.get(OmimHpoAnnotator.OMIM_ALL), expectedEntity.get(OmimHpoAnnotator.OMIM_ALL));\n+\t\tassertEquals(resultEntity.get(OmimHpoAnnotator.OMIM_LINK),\n+\t\t\t\texpectedEntity.get(OmimHpoAnnotator.OMIM_LINK));\n+\t\tassertEquals(resultEntity.get(OmimHpoAnnotator.OMIM_DISO),\n+\t\t\t\texpectedEntity.get(OmimHpoAnnotator.OMIM_DISO));\n+\t\tassertEquals(resultEntity.get(OmimHpoAnnotator.HPO_ALL),\n+\t\t\t\texpectedEntity.get(OmimHpoAnnotator.HPO_ALL));\n+\t\tassertEquals(resultEntity.get(OmimHpoAnnotator.HPO_LINK),\n+\t\t\t\texpectedEntity.get(OmimHpoAnnotator.HPO_LINK));\n+\t\tassertEquals(resultEntity.get(OmimHpoAnnotator.HPO_DESC),\n+\t\t\t\texpectedEntity.get(OmimHpoAnnotator.HPO_DESC));\n+\t\t\n+\t}\n+\t\n+\t@Test\n+\tpublic void canAnnotateTrueTest()\n+\t{\n+\t\tassertEquals(annotator.canAnnotate(metaDataCanAnnotate), true);\n+\t}\n+\n+\t@Test\n+\tpublic void canAnnotateFalseTest()\n+\t{\n+\t\tassertEquals(annotator.canAnnotate(metaDataCantAnnotate), false);\n+\t}\n+\t\n+//\t public static void main(String [ ] args) throws Exception","path":"molgenis-data-annotators/src/test/java/org/molgenis/data/annotation/impl/OmimHpoAnnotatorTest.java","position":139,"original_position":139,"commit_id":"479bc0fb743a2f41a3455d3285a529d57db3a64f","original_commit_id":"479bc0fb743a2f41a3455d3285a529d57db3a64f","user":{"login":"bartcharbon","id":3714029,"avatar_url":"https://gravatar.com/avatar/3e6df5a1baa7dfc05cdd7c43007eada4?d=https%3A%2F%2Fidenticons.github.com%2Fb1b7ff88b3f5022b0457f4b3fabb202c.png&r=x","gravatar_id":"3e6df5a1baa7dfc05cdd7c43007eada4","url":"https://api.github.com/users/bartcharbon","html_url":"https://github.com/bartcharbon","followers_url":"https://api.github.com/users/bartcharbon/followers","following_url":"https://api.github.com/users/bartcharbon/following{/other_user}","gists_url":"https://api.github.com/users/bartcharbon/gists{/gist_id}","starred_url":"https://api.github.com/users/bartcharbon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bartcharbon/subscriptions","organizations_url":"https://api.github.com/users/bartcharbon/orgs","repos_url":"https://api.github.com/users/bartcharbon/repos","events_url":"https://api.github.com/users/bartcharbon/events{/privacy}","received_events_url":"https://api.github.com/users/bartcharbon/received_events","type":"User","site_admin":false},"body":"remove commented code","created_at":"2014-03-07T10:55:33Z","updated_at":"2014-03-07T10:55:33Z","html_url":"https://github.com/molgenis/molgenis/pull/1260#discussion_r10379425","pull_request_url":"https://api.github.com/repos/molgenis/molgenis/pulls/1260","_links":{"self":{"href":"https://api.github.com/repos/molgenis/molgenis/pulls/comments/10379425"},"html":{"href":"https://github.com/molgenis/molgenis/pull/1260#discussion_r10379425"},"pull_request":{"href":"https://api.github.com/repos/molgenis/molgenis/pulls/1260"}}}}