def testLCheck(self):
self.setup()
lcheck = self.result1.lcheck(EUtils.databases.PUBMED)
self.assertEquals(lcheck.dbfrom, "protein")
self.assertEquals(lcheck.idchecks,
[Datatypes.IdCheck("4579714", 1, 0)])
lcheck = self.result2.lcheck(EUtils.databases.PUBMED)
self.assertEquals(lcheck.idchecks,
[Datatypes.IdCheck("18250303", 1, 0)])
def testPRLinks(self):
self.setup()
self.assertEquals(
self.result1.prlinks(),
Datatypes.LinksLinkSet('protein',
[Datatypes.IdUrlSet('4579714', [])]))
self.assertEquals(
self.result2.prlinks(),
Datatypes.LinksLinkSet('nucleotide',
[Datatypes.IdUrlSet('18250303', [])]))
def testPostHistory(self):
entrez = HistoryClient.HistoryClient(eutils=picklestore.client())
# Upload a couple nucleotide record identifiers
dbids = Datatypes.DBIds("nucleotide", ["26285514", "16445404"])
results = entrez.post(dbids)
self.assertEquals(dbids, results.dbids)
# Restrict to those which also mention "dopamine"
results2 = entrez.search("#%s AND dopamine" % results.query_key,
db=results.db)
# Should be one hit
self.assertEquals(Datatypes.DBIds("nucleotide", ["16445404"]),
results2.dbids)
summary = results2[0].summary()
self.assertEquals(summary.id, "16445404")
gold_data = {
"16445404":
(("Caption", "NM_000794"),
("Title", "H**o sapiens dopamine receptor D1 (DRD1), mRNA"),
("Extra", "gi|16445404|ref|NM_000794.2|"), ("Gi", 16445404),
("CreateDate", "1999/03/19"), ("UpdateDate", "2002/11/05"),
("Flags", 0), ("TaxId", 9606)),
"26285514":
(("Caption", "AY165035"),
("Title",
"Saccharomyces cerevisiae scavenger mRNA decapping enzyme (DCS1) mRNA, complete cds"
), ("Extra", "gi|26285514|gb|AY165035.1|"), ("Gi", 26285514),
("CreateDate", "2002/12/10"), ("UpdateDate", "2002/12/10"),
("Flags", 0), ("TaxId", 4932)),
}
for fieldname, value in gold_data[summary.id]:
self.assertEquals(summary.dataitems[fieldname], value)
for x in results2.summary():
for fieldname, value in gold_data[x.id]:
self.assertEquals(x.dataitems[fieldname], value)
def testNeighborLinks(self):
self.setup()
# Get the document neighbors in PubMed
neighbors = self.result1.neighbor_links(EUtils.databases.PUBMED)
self.assertEquals(neighbors.dbids, self.result1.dbids)
expected = MultiDict.OrderedMultiDict([
("protein_pubmed",
Datatypes.LinkSetDb("pubmed", "protein_pubmed",
[Datatypes.Link("9878396")]))
])
self.assertEquals(neighbors.linksetdbs, expected)
# Get protein neighbors
neighbors = self.result2.neighbor_links(EUtils.databases.PROTEIN)
self.assertEquals(neighbors.dbids, self.result2.dbids)
self.assertEquals(
neighbors.linksetdbs,
MultiDict.OrderedMultiDict([
("nucleotide_protein",
Datatypes.LinkSetDb("protein", "nucleotide_protein",
[Datatypes.Link("18250304")]))
]))
def testLLinks(self):
self.setup()
self.assertEquals(
self.result1.llinks(),
Datatypes.LinksLinkSet("protein", [
Datatypes.IdUrlSet("4579714", [
Datatypes.ObjUrl(
["protein identification/characterization"],
Datatypes.Provider(
"Domain Architecture Retrieval Tool", "DART",
"3240", None, None), "Domain Neighbors",
"http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=seq&FILTER=on&EXPECT=0.01&DATALIB=oasis_sap&fasta=4579714",
[])
])
]))
self.assertEquals(
self.result2.llinks(),
Datatypes.LinksLinkSet("nucleotide", [
Datatypes.IdUrlSet("18250303", [
Datatypes.ObjUrl(
[],
Datatypes.Provider(
"NCBI LocusLink", "LocusLink", "3086",
"http://www.ncbi.nlm.nih.gov/LocusLink",
"http://www.ncbi.nlm.nih.gov/LocusLink/IMG/LLogo.gif"
), None,
"http://www.ncbi.nlm.nih.gov/LocusLink/list.cgi?V=0&Q=18250303[ngi]",
[]),
Datatypes.ObjUrl(
["sequence screening/similarity/alignment"],
Datatypes.Provider(
"UCSC Genome Browser", "UCSCgb", "3715",
"http://www.cse.ucsc.edu/centers/cbe/Genome/",
"http://www.cse.ucsc.edu/cbe/images/ucsc.gif"),
None,
"http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg11&position=NM_080831",
[]),
Datatypes.ObjUrl(
["DNA/protein sequence"],
Datatypes.Provider(
"UniGene", "UniGene", "3170",
"http://www.ncbi.nlm.nih.gov/UniGene/",
"http://www.ncbi.nlm.nih.gov/UniGene/IMG/button.gif"
), None,
"http://www.ncbi.nlm.nih.gov/UniGene/query.cgi?TEXT=@gi(18250303)&ORG=Hs",
[])
])
]))
def testHistory(self):
entrez = HistoryClient.HistoryClient(eutils=picklestore.client())
results1 = entrez.search("Dalke",
field="au",
daterange=EUtils.DateRange("1995", "1998"))
self.assertEquals(len(results1), 10)
sizes = []
expression = results1.metadata.expression
for x in expression:
if isinstance(x, Datatypes.Term):
n = x.count
assert n, n # cannot be 0 or None
sizes.append(n)
self.assertEquals(len(sizes), 3)
if sizes[0] < 30:
raise AssertionError(sizes)
self.assertEquals(sizes[1], -1)
self.assertEquals(sizes[2], -1)
self.assertEquals(expression.left.term, "Dalke[Author]")
self.assertEquals(expression.left.field, "Author")
self.assertEquals(expression.right.left.term, "1995[EDAT]")
self.assertEquals(expression.right.left.field, "EDAT")
self.assertEquals(expression.right.right.term, "1998[EDAT]")
self.assertEquals(expression.right.right.field, "EDAT")
expected_dbids = Datatypes.DBIds("pubmed", [
"9454215", "9454196", "9454186", "9390282", "9303476", "9300720",
"8763495", "8744570", "8566008", "7648552"
])
self.assertEquals(results1.dbids, expected_dbids)
# this is a no-no, since EDAT isn't a searchable field
self.failUnlessRaises(EUtils.EUtilsSearchError,
entrez.search,
"poliovirus AND 1995:1998[EDAT]",
db="nucleotide")
results2 = entrez.search("poliovirus AND 1995:1998[PDAT]", db="pubmed")
if len(results2) < 1160:
raise AssertionError(len(results2))
all_ids = results2.dbids
self.assertEquals(len(all_ids), len(results2))
self.assertEquals(all_ids[:20], results2[:20].dbids)
self.assertEquals(all_ids[5:20], results2[5:20].dbids)
self.assertEquals(all_ids[-5:], results2[-5:].dbids)
self.assertEquals(all_ids[-5:-1], results2[-5:-1].dbids)
self.assertEquals(all_ids[10:-14], results2[10:-14].dbids)
# This is illegal because pubmed isn't a sequence database
self.failUnlessRaises(TypeError, results2.efetch, seq_start=0)
# Try a different database
results3 = entrez.search("poliovirus AND 1995:1998[PDAT]",
db="nucleotide")
# Make sure I can still access fields from the first database
self.assertEquals(results1.dbids, expected_dbids)
# This is illegal because it mixes databases
self.failUnlessRaises(
EUtils.EUtilsSearchError, entrez.search,
"#%s OR #%s" % (results1.query_key, results3.query_key))
# However, this should yield the same as results3
results4 = entrez.search("poliovirus", db="nucleotide")
results5 = entrez.search("#%s AND 1995:1998[PDAT]" %
results4.query_key,
db=results4.db)
self.assertEquals(len(results3), len(results5))
results3_dbids = results3.dbids
self.assertEquals(results3_dbids, results5.dbids)
# Get the sequence as FASTA one way
s = results3[0].efetch(retmode='text', rettype='fasta').read()
# And another way
t = entrez.eutils.efetch_using_dbids(results3_dbids[:1],
retmode='text',
rettype='fasta').read()
self.assertEquals(s, t)