def testGetRegionSequence(self):
rows = self.queries.getRegionSequence("Pf3D7_01")
row = rows[0]
length = row["length"]
start = 1
end = 10
dna = row["dna"]
dna = dna[start-1:end-1]
data = {
"response" : {
"name" : "region/sequence",
"sequence" : {
"start" : start,
"end" : end,
"length" : length,
"dna" : dna
}
}
}
formatter = Formatter(data, os.path.dirname(__file__) + "/../tpl/")
print formatter.formatJSON()
def testAllOrganisms(self):
since = "2009-06-01"
organism_list = self.queries.getAllOrganismsAndTaxonIDs()
organismIDs = []
organismHash = {}
for organism_details in organism_list:
organism_details["count"] = 0
organismIDs.append(organism_details["organism_id"])
organismHash [organism_details["organism_id"]] = organism_details
counts = self.queries.countAllChangedFeaturesForOrganisms(since, organismIDs)
for count in counts:
organismID = str(count[0])
print organismID
org = organismHash[organismID]
org["count"] = count[1]
data = {
"response" : {
"name" : "genomes/changes",
"since" : since,
"results" : organismHash.values()
}
}
formatter = Formatter(data, os.path.dirname(__file__) + "/../tpl/")
print formatter.formatXML('genomes_changed.xml.tpl')
def testGetGenesWithPrivateAnnotationChanges(self):
since = "2009-06-01"
rows = self.queries.getGenesWithPrivateAnnotationChanges(14, since)
data = {
"response" : {
"name" : "genome/recorded_annotation_changes",
"taxonID" : "420245",
"count" : len(rows),
"results" : rows
}
}
formatter = Formatter(data, os.path.dirname(__file__) + "/../tpl/")
formatter.formatXML('private_annotations.xml.tpl')
formatter.formatJSON()
def testAllChanged(self):
since = "2009-06-01"
organism_id = 14
changed_features = self.queries.getAllChangedFeaturesForOrganism(since, organism_id)
data = {
"response" : {
"name" : "genome/changes",
"taxonID" : "420245",
"count" : len(changed_features),
"since" : since,
"results" : changed_features
}
}
formatter = Formatter(data, os.path.dirname(__file__) + "/../tpl/")
formatter.formatJSON()
formatter.formatXML("changes.xml.tpl")