def newTreeInProjectFromString(self,treename,treestring,projectTitle, description,treetype):
import phyloimport_algorithm, root_phylotree_algorithm
collectionName = self.prefixString+projectTitle+self.separatorString+"PhyloTree"+self.separatorString+treename
treeCollection = self.db[collectionName]
treeCollection.drop()
print "uploading tree to collection: ",collectionName
print "treetype is: ",treetype
# if the project does not exist, create it
projectCollectionName = self.prefixString + 'projects'
if self.db[projectCollectionName].find_one({"name": projectTitle}) == None:
self.newProject(projectTitle)
# create the new collection in mongo for this tree. The tree is encoded
# in a string, so it needs to be processed slightly different than from a file
from StringIO import StringIO
handle = StringIO(treestring)
trees = Phylo.parse(handle, treetype)
#print "length of trees list: ",len(trees)
for tree in trees:
phyloimport_algorithm.recursive_clade(tree, treeCollection)
# add a tree record entry to the 'PyloTree' array in the project record
self.db[self.projectCollectionName].update({"name": projectTitle}, { '$push': {u'PhyloTree': {treename:str(description)}}})
self.db[self.projectCollectionName].update({"name": projectTitle}, { '$addToSet': {u'datatypes': u'PhyloTree'}})
# make sure the tree is rooted, so viewers work
root_phylotree_algorithm.addRootToTree(treeCollection)
# emit a signal so the GUI knows to update
if (self.QtGuiEnabled):
self.datatypeListChangedSignal.emit();
self.datasetListChangedSignal.emit();
def newTreeInProject(self, treename, treefile, projectTitle, treetype):
import phyloimport_algorithm, root_phylotree_algorithm
collectionName = self.returnCollectionForObjectByName(
projectTitle, 'PhyloTree', treename)
#collectionName = self.prefixString+projectTitle+self.separatorString+"PhyloTree"+self.separatorString+treename
treeCollection = self.db[collectionName]
print "uploading tree to collection: ", collectionName
print "treetype is: ", treetype
# create the new collection in mongo for this tree
trees = Phylo.parse(treefile, treetype)
#print "length of trees list: ",len(trees)
for tree in trees:
#process tree
phyloimport_algorithm.recursive_clade(tree, treeCollection)
root_phylotree_algorithm.addRootToTree(treeCollection)
# add a tree record entry to the 'PyloTree' array in the project record
self.db[self.projectCollectionName].update(
{"name": projectTitle},
{'$push': {
u'PhyloTree': {
treename: treefile
}
}})
self.db[self.projectCollectionName].update(
{"name": projectTitle},
{'$addToSet': {
u'datatypes': u'PhyloTree'
}})
def newTreeInProject(self,treename,treefile,projectTitle, treetype):
import phyloimport_algorithm, root_phylotree_algorithm
collectionName = self.returnCollectionForObjectByName(projectTitle, 'PhyloTree', treename)
#collectionName = self.prefixString+projectTitle+self.separatorString+"PhyloTree"+self.separatorString+treename
treeCollection = self.db[collectionName]
print "uploading tree to collection: ",collectionName
print "treetype is: ",treetype
# create the new collection in mongo for this tree
trees = Phylo.parse(treefile, treetype)
#print "length of trees list: ",len(trees)
for tree in trees:
#process tree
phyloimport_algorithm.recursive_clade(tree, treeCollection)
root_phylotree_algorithm.addRootToTree(treeCollection)
# add a tree record entry to the 'PyloTree' array in the project record
self.db[self.projectCollectionName].update({"name": projectTitle}, { '$push': {u'PhyloTree': {treename:treefile}}})
self.db[self.projectCollectionName].update({"name": projectTitle}, { '$addToSet': {u'datatypes': u'PhyloTree'}})
def newTreeInProjectFromString(self, treename, treestring, projectTitle,
description, treetype):
import phyloimport_algorithm, root_phylotree_algorithm
collectionName = self.prefixString + projectTitle + self.separatorString + "PhyloTree" + self.separatorString + treename
treeCollection = self.db[collectionName]
treeCollection.drop()
print "uploading tree to collection: ", collectionName
print "treetype is: ", treetype
# if the project does not exist, create it
projectCollectionName = self.prefixString + 'projects'
if self.db[projectCollectionName].find_one({"name":
projectTitle}) == None:
self.newProject(projectTitle)
# create the new collection in mongo for this tree. The tree is encoded
# in a string, so it needs to be processed slightly different than from a file
from StringIO import StringIO
handle = StringIO(treestring)
trees = Phylo.parse(handle, treetype)
#print "length of trees list: ",len(trees)
for tree in trees:
phyloimport_algorithm.recursive_clade(tree, treeCollection)
# add a tree record entry to the 'PyloTree' array in the project record
self.db[self.projectCollectionName].update(
{"name": projectTitle},
{'$push': {
u'PhyloTree': {
treename: str(description)
}
}})
self.db[self.projectCollectionName].update(
{"name": projectTitle},
{'$addToSet': {
u'datatypes': u'PhyloTree'
}})
# make sure the tree is rooted, so viewers work
root_phylotree_algorithm.addRootToTree(treeCollection)
# emit a signal so the GUI knows to update
if (self.QtGuiEnabled):
self.datatypeListChangedSignal.emit()
self.datasetListChangedSignal.emit()
def newTreeInProjectFromString(self,treename,treestring,projectTitle, description,treetype):
collectionName = self.prefixString+projectTitle+"_"+"PhyloTree"+"_"+treename
treeCollection = self.db[collectionName]
print "uploading tree to collection: ",collectionName
print "treetype is: ",treetype
# create the new collection in mongo for this tree. The tree is encoded
# in a string, so it needs to be processed slightly different than from a file
from StringIO import StringIO
handle = StringIO(treestring)
trees = Phylo.parse(handle, treetype)
#print "length of trees list: ",len(trees)
for tree in trees:
phyloimport_algorithm.recursive_clade(tree, treeCollection)
# add a tree record entry to the 'PyloTree' array in the project record
self.db.ar_projects.update({"name": projectTitle}, { '$push': {u'PhyloTree': {treename:str(description)}}})
self.db.ar_projects.update({"name": projectTitle}, { '$addToSet': {u'datatypes': u'PhyloTree'}})
# make sure the tree is rooted, so viewers work
root_phylotree_algorithm.addRootToTree(treeCollection)
# emit a signal so the GUI knows to update
self.datatypeListChangedSignal.emit();
self.datasetListChangedSignal.emit();