def test_standard(self):
# test that we can read values for bibcodes
with patch('builtins.open',
return_value=StringIO("""AAAAAAAAAAAAAAAAAAA\tA
BBBBBBBBBBBBBBBBBBB\tB
DDDDDDDDDDDDDDDDDDD\tD
EEEEEEEEEEEEEEEEEEE\tE""")):
f = reader.NonbibFileReader('reads', data_files['reads'])
self.assertEqual({'reads': ['A']},
f.read_value_for('AAAAAAAAAAAAAAAAAAA'))
self.assertEqual({'reads': ['B']},
f.read_value_for('BBBBBBBBBBBBBBBBBBB'))
self.assertEqual({'reads': []},
f.read_value_for('CCCCCCCCCCCCCCCCCCC'))
self.assertEqual({'reads': ['D']},
f.read_value_for('DDDDDDDDDDDDDDDDDDD'))
self.assertEqual({'reads': ['E']},
f.read_value_for('EEEEEEEEEEEEEEEEEEE'))
self.assertEqual({'reads': []},
f.read_value_for('FFFFFFFFFFFFFFFFFFF'))
# test we can skip bibcodes that are in the file
with patch('builtins.open',
return_value=StringIO("""AAAAAAAAAAAAAAAAAAA\tA
BBBBBBBBBBBBBBBBBBB\tB
DDDDDDDDDDDDDDDDDDD\tD
EEEEEEEEEEEEEEEEEEE\tE""")):
f = reader.NonbibFileReader('reads', data_files['reads'])
self.assertEqual({'reads': ['B']},
f.read_value_for('BBBBBBBBBBBBBBBBBBB'))
self.assertEqual({'reads': ['D']},
f.read_value_for('DDDDDDDDDDDDDDDDDDD'))
self.assertEqual({'reads': ['E']},
f.read_value_for('EEEEEEEEEEEEEEEEEEE'))
# test that we receive no value when we read a bibcode that isn't present
with patch('builtins.open',
return_value=StringIO("""AAAAAAAAAAAAAAAAAAA\tA
BBBBBBBBBBBBBBBBBBB\tB
DDDDDDDDDDDDDDDDDDD\tD
EEEEEEEEEEEEEEEEEEE\tE""")):
f = reader.NonbibFileReader('reads', data_files['reads'])
self.assertEqual({'reads': []},
f.read_value_for('CCCCCCCCCCCCCCCCCCC'))
self.assertEqual({'reads': ['E']},
f.read_value_for('EEEEEEEEEEEEEEEEEEE'))
self.assertEqual({'reads': []},
f.read_value_for('FFFFFFFFFFFFFFFFFFF'))
def test_convert_scalar(self):
with patch('builtins.open', return_value=StringIO('')):
f = reader.NonbibFileReader('refereed', data_files['refereed'])
self.assertEqual(f._convert_scalar('1'), 1)
self.assertAlmostEqual(f._convert_scalar('1.2'), 1.2)
self.assertEqual(f._convert_scalar('abc'), 'abc')
self.assertEqual(f._convert_scalar('ab.c'), 'ab.c')
def test_invalid_bibcode(self):
"""verify short input lines are skipped and logged as errors"""
with patch(
'builtins.open',
return_value=StringIO(
'AAAAAAAAAAAAAAAAAAA\nBBB\nDDDDDDDDDDDDDDDDDDD\nEEEEEEEEEEEEEEEEEEE'
)):
with patch('adsdata.tasks.app.logger') as m:
f = reader.NonbibFileReader('refereed', data_files['refereed'])
self.assertEqual(
{'refereed': {
'refereed': True,
'property': ['REFEREED']
}}, f.read_value_for('AAAAAAAAAAAAAAAAAAA'))
self.assertEqual({'refereed': {
'refereed': False
}}, f.read_value_for('BBBBBBBBBBBBBBBBBBB'))
self.assertEqual({'refereed': {
'refereed': False
}}, f.read_value_for('CCCCCCCCCCCCCCCCCCC'))
self.assertEqual(
{'refereed': {
'refereed': True,
'property': ['REFEREED']
}}, f.read_value_for('DDDDDDDDDDDDDDDDDDD'))
self.assertTrue(m.error.called)
def test_deleted(self):
with patch('builtins.open',
return_value=StringIO(
'2013MNRAS.435.1904M\t2013MNRAS.tmp.2206M')):
f = reader.NonbibFileReader('deleted', data_files['deleted'])
a = f.read_value_for('2013MNRAS.435.1904M')
self.assertEqual({'deleted': ['2013MNRAS.tmp.2206M']}, a)
def test_doi(self):
with patch('builtins.open',
return_value=StringIO(
'2013MNRAS.435.1904M\t10.1093/mnras/stt1379')):
f = reader.NonbibFileReader('doi', data_files['doi'])
a = f.read_value_for('2013MNRAS.435.1904M')
self.assertEqual({'doi': ['10.1093/mnras/stt1379']}, a)
def test_refereed_from_file(self):
self.maxDiff = None
with patch('adsputils.load_config',
return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('refereed', data_files['refereed'])
v = r.read_value_for('2004MNRAS.354L..31M')
a = {'refereed': {'refereed': True, 'property': ['REFEREED']}}
self.assertEqual(a, v)
def test_pub2arxiv(self):
# where is this file?!
with patch('builtins.open',
return_value=StringIO(
'2013MNRAS.435.1904M\t2013arXiv1307.6556M')):
f = reader.NonbibFileReader('pub2arxiv', data_files['pub2arxiv'])
a = f.read_value_for('2013MNRAS.435.1904M')
self.assertEqual({'pub2arxiv': ['2013arXiv1307.6556M']}, a)
def test_inspire(self):
self.maxDiff = None
with patch('adsputils.load_config', return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('inspire', data_files['inspire'])
v = r.read_value_for('2004MNRAS.354L..31M')
a = {'inspire': {"url": ["http://inspirehep.net/search?p=find+j+MNRAA,354,L31"],
"link_type": "INSPIRE", "link_sub_type": "NA"}}
self.assertEqual(a, v)
def test_simbad(self):
self.maxDiff = None
with patch('builtins.open',
return_value=StringIO('1857AN.....45...89S\t1500441\tLP*')):
f = reader.NonbibFileReader('simbad_objects',
data_files['simbad_objects'])
v = f.read_value_for('1857AN.....45...89S')
self.assertEqual({'simbad_objects': ['1500441 LP*']}, v)
with patch(
'builtins.open',
return_value=StringIO(
'2010A&A...521A..55C\t2419335\treg\n2010A&A...521A..55C\t3754378\tGrG'
)):
f = reader.NonbibFileReader('simbad_objects',
data_files['simbad_objects'])
v = f.read_value_for('2010A&A...521A..55C')
self.assertEqual(
{'simbad_objects': ['2419335 reg', '3754378 GrG']}, v)
def test_pub_html(self):
self.maxDiff = None
with patch('adsputils.load_config', return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('pub_html', data_files['pub_html'])
links_value = r.read_value_for('1498esap.book.....R')
self.assertEqual({'pub_html': {'link_type': 'ESOURCE',
'link_sub_type': 'PUB_HTML',
'url': ['https://doi.org/10.3931%2Fe-rara-477']}},
links_value)
def test_associated(self):
self.maxDiff = None
with patch('adsputils.load_config', return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('associated', data_files['associated'])
v = r.read_value_for('2004MNRAS.354L..31M')
a = {'associated': {"url": ["2004MNRAS.354L..31M", "2005yCat..73549031M"],
"title": ["Source Paper", "Catalog Description"],
"link_type": "ASSOCIATED", "link_sub_type": "NA"}}
self.assertEqual(a, v)
def test_ads_scan(self):
self.maxDiff = None
with patch('adsputils.load_config', return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('ads_scan', data_files['ads_scan'])
v = r.read_value_for('2004MNRAS.354L..31M')
a = {'ads_scan': {"url": ["http://articles.adsabs.harvard.edu/full/2004MNRAS.354L..31M"],
"link_type": "ESOURCE", "link_sub_type": "ADS_SCAN",
"property": ["ADS_OPENACCESS", "OPENACCESS"]}}
self.assertEqual(a, v)
def test_datasources(self):
self.maxDiff = None
with patch('adsputils.load_config',
return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('data_link', data_files['data_link'])
v = r.read_value_for('2004MNRAS.354L..31M')
a = {
'data_link': [{
"url":
["http://$VIZIER$/viz-bin/VizieR?-source=J/MNRAS/354/L31"],
"title": [""],
"item_count":
1,
"link_type":
"DATA",
"property": ["DATA"],
"link_sub_type":
"CDS"
}, {
"url": [
"https://$NED$/cgi-bin/objsearch?search_type=Search&refcode=2004MNRAS.354L..31M"
],
"property": ["DATA"],
"title": ["NED Objects (1953)"],
"item_count":
1953,
"link_type":
"DATA",
"link_sub_type":
"NED"
}, {
"url":
["http://$SIMBAD$/simbo.pl?bibcode=2004MNRAS.354L..31M"],
"property": ["DATA"],
"title": ["SIMBAD Objects (1)"],
"item_count":
1,
"link_type":
"DATA",
"link_sub_type":
"SIMBAD"
}, {
"url":
["http://$VIZIER$/viz-bin/VizieR?-source=J/MNRAS/354/L31"],
"property": ["DATA"],
"title": [""],
"item_count":
1,
"link_type":
"DATA",
"link_sub_type":
"Vizier"
}]
}
self.assertEqual(a, v)
def test_list(self):
# first line of config/links/reads/downloads.links
self.maxDiff = None
download_line = '1057wjlf.book.....C\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1'
with patch('builtins.open', return_value=StringIO(download_line)):
f = reader.NonbibFileReader('download', data_files['download'])
x = f.read_value_for('1057wjlf.book.....C')
self.assertEqual(
{'download': [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]}, x)
citation_lines = '1890GSAB....1..411D\t2011ESRv..106..215H\n1890GSAB....1..411D\t2014SedG..311...60T\n1890GSAB....1..411D\t2015GSAB..127.1816C'
with patch('builtins.open', return_value=StringIO(citation_lines)):
f = reader.NonbibFileReader('citation', data_files['citation'])
x = f.read_value_for('1890GSAB....1..411D')
self.assertEqual(
{
'citation': [
'2011ESRv..106..215H', '2014SedG..311...60T',
'2015GSAB..127.1816C'
]
}, x)
def test_private(self):
self.maxDiff = None
with patch('adsputils.load_config',
return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('private', data_files['private'])
v = r.read_value_for('1920NW......8..958S')
a = {'private': {'private': True, 'property': ['PRIVATE']}}
self.assertEqual(a, v)
v = r.read_value_for('2003ASPC..295..361M')
a = {'private': {'private': False}}
self.assertEqual(a, v)
def test_grants(self):
with patch('adsputils.load_config',
return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('grants', data_files['grants'])
v = r.read_value_for('1980AJ.....85..780L')
self.assertTrue('grants' in v)
self.assertEqual(v['grants'],
['NSF-AST 0725267', 'NSF-AST 1211349'])
v = r.read_value_for('2010AJ....140..933R')
self.assertTrue('grants' in v)
self.assertEqual(v['grants'], ['NSF-AST 0706980'])
def test_get_rest(self):
with patch('builtins.open', return_value=StringIO('')):
with patch('adsdata.tasks.app.logger') as m:
f = reader.NonbibFileReader('citation', data_files['citation'])
x = f._get_rest('short')
self.assertEqual(x, '')
self.assertTrue(m.error.called)
m.reset_mock()
x = f._get_rest('1234567890123456789\tvalue\n')
self.assertEqual('value', x)
self.assertFalse(m.error.called)
def test_ned(self):
self.maxDiff = None
with patch(
'builtins.open',
return_value=StringIO(
'1885AN....112..285E\tMESSIER_031\tG\n1885AN....112..285E\tSN_1885A\tSN'
)):
f = reader.NonbibFileReader('ned_objects',
data_files['ned_objects'])
v = f.read_value_for('1885AN....112..285E')
self.assertEqual({'ned_objects': ["MESSIER_031 G", "SN_1885A SN"]},
v)
def test_bibgroup(self):
with patch(
'builtins.open',
return_value=StringIO(
'2003ASPC..295..361M\tChandra/Technical\n2021MNRAS.502..510J\tGTC\n2021MNRAS.502..510J\tKeck'
)):
f = reader.NonbibFileReader('bibgroup', data_files['bibgroup'])
self.assertEqual({'bibgroup': ["Chandra/Technical"]},
f.read_value_for('2003ASPC..295..361M'))
self.assertEqual({'bibgroup': []},
f.read_value_for('2004zzzz..295..361M'))
self.assertEqual({"bibgroup": ["GTC", "Keck"]},
f.read_value_for('2021MNRAS.502..510J'))
self.assertEqual({"bibgroup": []},
f.read_value_for('2021ZZZZZ.502..510J'))
def test_ocrabstract(self):
self.maxDiff = None
with patch('builtins.open',
return_value=StringIO(
'1886Natur..34Q.131.\n1954PhRv...96..730K\n')):
f = reader.NonbibFileReader('ocrabstract',
data_files['ocrabstract'])
v = f.read_value_for('1954PhRv...96..730K')
a = {
'ocrabstract': {
'property': ['OCRABSTRACT'],
'ocrabstract': True
}
}
self.assertEqual(a, v)
def test_associated(self):
self.maxDiff = None
with patch(
'builtins.open',
return_value=StringIO(
'1850AJ......1...72H\t1850AJ......1...57H Main Paper\n1850AJ......1...72H\t1850AJ......1...72H Erratum'
)):
f = reader.NonbibFileReader('associated', data_files['associated'])
v = f.read_value_for('1850AJ......1...72H')
a = {
'associated': {
'link_type': 'ASSOCIATED',
'link_sub_type': 'NA',
'url': ['1850AJ......1...57H', '1850AJ......1...72H'],
'title': ['Main Paper', 'Erratum']
}
}
self.assertEqual(a, v)
# a few bibcodes only have one entry in associated
with patch(
'builtins.open',
return_value=StringIO(
'1993yCat.3135....0C\t1993yCat.3135....0C Catalog Description'
)):
f = reader.NonbibFileReader('associated', data_files['associated'])
v = f.read_value_for('1993yCat.3135....0C')
a = {
'associated': {
'link_type': 'ASSOCIATED',
'link_sub_type': 'NA',
'url': ['1993yCat.3135....0C'],
'title': ['Catalog Description']
}
}
self.assertEqual(a, v)
def test_toc(self):
self.maxDiff = None
with patch('adsputils.load_config',
return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('toc', data_files['toc'])
v = r.read_value_for('2003ASPC..295..361M')
a = {
'toc': {
'toc': True,
'link_type': 'TOC',
'link_sub_type': 'NA'
}
}
self.assertEqual(a, v)
v = r.read_value_for('2004ASPC..295..361M')
a = {'toc': {'toc': False}}
self.assertEqual(a, v)
def test_librarycatalog(self):
self.maxDiff = None
with patch(
'builtins.open',
return_value=StringIO(
'1810hdla.book.....V\thttp://www.worldcat.org/oclc/02869597'
)):
f = reader.NonbibFileReader('librarycatalog',
data_files['librarycatalog'])
v = f.read_value_for('1810hdla.book.....V')
a = {
'librarycatalog': {
'link_type': 'LIBRARYCATALOG',
'link_sub_type': 'NA',
'url': ['http://www.worldcat.org/oclc/02869597']
}
}
self.assertEqual(a, v)
def test_presentation(self):
self.maxDiff = None
with patch(
'builtins.open',
return_value=StringIO(
'1997kbls.confE..10C\thttp://online.kitp.ucsb.edu/online/bblunch/carroll/'
)):
f = reader.NonbibFileReader('presentation',
data_files['presentation'])
v = f.read_value_for('1997kbls.confE..10C')
a = {
'presentation': {
'link_type': 'PRESENTATION',
'link_sub_type': 'NA',
'url':
['http://online.kitp.ucsb.edu/online/bblunch/carroll/']
}
}
self.assertEqual(a, v)
def test_downloads(self):
self.maxDiff = None
bibcodes = [
'1057wjlf.book.....C', '1886Natur..34Q.131.',
'1905PhRvI..21..247N', '1908PhRvI..27..367N', '2003ASPC..295..361M'
]
downloads = [
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 1, 0, 0, 1, 0, 0, 0, 0, 0]
]
with patch('adsputils.load_config',
return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('download', data_files['download'])
for i in range(0, len(bibcodes)):
x = r.read_value_for(bibcodes[i])
a = {'download': downloads[i]}
self.assertEqual(a, x, 'for bibcode ' + bibcodes[i])
def test_relevance(self):
self.maxDiff = None
with patch('adsputils.load_config',
return_value={'INPUT_DATA_ROOT': './test/data1/config/'}):
r = reader.NonbibFileReader('relevance', data_files['relevance'])
v = r.read_value_for('1905PhRvI..21..247N')
self.assertTrue('relevance' in v)
# self.assertEqual(4, len(v['relevance'].keys()))
self.assertAlmostEqual(.11, v['relevance']['boost'])
self.assertEqual(2, v['relevance']['citation_count'])
self.assertEqual(0, v['relevance']['read_count'])
self.assertEqual(2386, v['relevance']['norm_cites'])
v = r.read_value_for('2003ASPC..295..361M')
self.assertTrue('relevance' in v)
# self.assertEqual(4, len(v['relevance'].keys()))
self.assertAlmostEqual(.15, v['relevance']['boost'])
self.assertEqual(0, v['relevance']['citation_count'])
self.assertEqual(4, v['relevance']['read_count'])
self.assertEqual(0, v['relevance']['norm_cites'])
def test_repeated_bibcode(self):
# test that repeated bibcodes are properly rolled up
with patch('builtins.open',
return_value=StringIO("""AAAAAAAAAAAAAAAAAAA\tA
AAAAAAAAAAAAAAAAAAA\tAA
AAAAAAAAAAAAAAAAAAA\tAAA
BBBBBBBBBBBBBBBBBBB\tB
DDDDDDDDDDDDDDDDDDD\tD
DDDDDDDDDDDDDDDDDDD\tDD
EEEEEEEEEEEEEEEEEEE\tE""")):
f = reader.NonbibFileReader('citation', data_files['citation'])
self.assertEqual({'citation': ['A', 'AA', 'AAA']},
f.read_value_for('AAAAAAAAAAAAAAAAAAA'))
self.assertEqual({'citation': ['B']},
f.read_value_for('BBBBBBBBBBBBBBBBBBB'))
self.assertEqual({'citation': []},
f.read_value_for('CCCCCCCCCCCCCCCCCCC'))
self.assertEqual({'citation': ['D', 'DD']},
f.read_value_for('DDDDDDDDDDDDDDDDDDD'))
self.assertEqual({'citation': ['E']},
f.read_value_for('EEEEEEEEEEEEEEEEEEE'))
self.assertEqual({'citation': []},
f.read_value_for('FFFFFFFFFFFFFFFFFFF'))
def _open_all(self):
"""open all input files"""
self.readers = {}
for x in data_files.keys():
self.readers[x] = reader.NonbibFileReader(x, data_files[x])
def test_preprint(self):
with patch('builtins.open',
return_value=StringIO('2013MNRAS.435.1904M\t1307.6556')):
f = reader.NonbibFileReader('preprint', data_files['preprint'])
a = f.read_value_for('2013MNRAS.435.1904M')
self.assertEqual({'preprint': ['1307.6556']}, a)
def test_links(self):
"""read in data links files"""
# facet_datasources/datasources.links
self.maxDiff = None
with patch(
'builtins.open',
return_value=StringIO(
'AAAAAAAAAAAAAAAAAAA\tARI\t1\thttp://dc.g-vo.org/arigfh/katkat/byhdw/qp/1202'
)):
f = reader.NonbibFileReader('data_link', data_files['data_link'])
v = f.read_value_for('AAAAAAAAAAAAAAAAAAA')
a = {
'data_link': {
'link_type': 'DATA',
'link_sub_type': 'ARI',
'item_count': 1,
'property': ['DATA'],
'url': ['http://dc.g-vo.org/arigfh/katkat/byhdw/qp/1202'],
'title': ['']
}
}
self.assertEqual(a, v)
with patch(
'builtins.open',
return_value=StringIO(
'2004MNRAS.354L..31M\tCDS\t2\thttp://$VIZIER$/viz-bin/VizieR?-source=J/MNRAS/354/L31\n2004MNRAS.354L..31M\tVizier\t1\thttp://$VIZIER$/viz-bin/VizieR?-source=J/MNRAS/354/L31'
)):
f = reader.NonbibFileReader('data_link', data_files['data_link'])
v = f.read_value_for('2004MNRAS.354L..31M')
a = {
'data_link': [{
"url":
["http://$VIZIER$/viz-bin/VizieR?-source=J/MNRAS/354/L31"],
"title": [""],
"item_count":
2,
"link_type":
"DATA",
"link_sub_type":
"CDS",
'property': ['DATA']
}, {
"url":
["http://$VIZIER$/viz-bin/VizieR?-source=J/MNRAS/354/L31"],
"title": [""],
"item_count":
1,
"link_type":
"DATA",
"link_sub_type":
"Vizier",
'property': ['DATA']
}]
}
self.assertEqual(a, v)
# electr/all.links
with patch(
'builtins.open',
return_value=StringIO(
'AAAAAAAAAAAAAAAAAAA\thttps://doi.org/10.3931%2Fe-rara-477'
)):
f = reader.NonbibFileReader('pub_html', data_files['pub_html'])
x = f.read_value_for('AAAAAAAAAAAAAAAAAAA')
self.assertEqual(
{
'pub_html': {
'link_type': 'ESOURCE',
'link_sub_type': 'PUB_HTML',
'url': ['https://doi.org/10.3931%2Fe-rara-477']
}
}, x)
# eprint_html/all.links
with patch(
'builtins.open',
return_value=StringIO(
'AAAAAAAAAAAAAAAAAAA\thttps://arxiv.org/abs/0908.1823')):
f = reader.NonbibFileReader('eprint_html',
data_files['eprint_html'])
v = f.read_value_for('AAAAAAAAAAAAAAAAAAA')
a = {
'eprint_html': {
'link_type': 'ESOURCE',
'link_sub_type': 'EPRINT_HTML',
'url': 'https://arxiv.org/abs/0908.1823',
'property': ['EPRINT_OPENACCESS', 'OPENACCESS']
}
}
self.assertEqual(a, v)
