def test_read(self):
with open("Medline/pubmed_result1.txt") as handle:
record = Medline.read(handle)
self.assertEqual(record["PMID"], "12230038")
self.assertEqual(record["OWN"], "NLM")
self.assertEqual(record["STAT"], "MEDLINE")
self.assertEqual(record["DA"], "20020916")
self.assertEqual(record["DCOM"], "20030606")
self.assertEqual(record["LR"], "20041117")
self.assertEqual(record["PUBM"], "Print")
self.assertEqual(record["IS"], "1467-5463 (Print)")
self.assertEqual(record["VI"], "3")
self.assertEqual(record["IP"], "3")
self.assertEqual(record["DP"], "2002 Sep")
self.assertEqual(record["TI"], "The Bio* toolkits--a brief overview.")
self.assertEqual(record["PG"], "296-302")
self.assertEqual(record["AB"], "Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.")
self.assertEqual(record["AD"], "tacg Informatics, Irvine, CA 92612, USA. [email protected]")
self.assertEqual(record["FAU"], ["Mangalam, Harry"])
self.assertEqual(record["AU"], ["Mangalam H"])
self.assertEqual(record["LA"], ["eng"])
self.assertEqual(record["PT"], ["Journal Article"])
self.assertEqual(record["PL"], "England")
self.assertEqual(record["TA"], "Brief Bioinform")
self.assertEqual(record["JT"], "Briefings in bioinformatics")
self.assertEqual(record["JID"], "100912837")
self.assertEqual(record["SB"], "IM")
self.assertEqual(record["MH"], ["*Computational Biology", "Computer Systems", "Humans", "Internet", "*Programming Languages", "*Software", "User-Computer Interface"])
self.assertEqual(record["EDAT"], "2002/09/17 10:00")
self.assertEqual(record["MHDA"], "2003/06/07 05:00")
self.assertEqual(record["PST"], "ppublish")
self.assertEqual(record["SO"], "Brief Bioinform. 2002 Sep;3(3):296-302.")
def test_multiline_mesh(self):
with open("Medline/pubmed_result3.txt") as handle:
record = Medline.read(handle)
self.assertEqual(record["PMID"], "23039619")
self.assertEqual(record["MH"], ["Blood Circulation",
"High-Intensity Focused Ultrasound Ablation/adverse effects/instrumentation/*methods",
"Humans",
"Models, Biological",
"Sonication",
"Temperature",
"Time Factors",
"Transducers"])
