ott_ncbi = "../ott_ncbi" #TODO config file
Entrez.email = "*****@*****.**"
phy = Phylesystem()
n = phy.return_study(study_id)[0]
api_wrapper.study.get(study_id, tree=tree_id)
##This is a weird way to get the ingroup node, but I need the OTT ids anyhow.
m = extract_tree(n,
tree_id,
PhyloSchema('newick',
output_nexml2json='1.2.1',
content="tree",
tip_label="ot:ottId"),
subtree_id="ingroup")
otu_dict = gen_otu_dict(n)
ottids = []
for oid, o in otu_dict.items():
try:
ottid = o[u'^ot:ottId']
if ("{}:".format(ottid) in m) or ("{})".format(ottid)
in m) or ("{},".format(ottid) in m):
ottids.append(ottid)
else:
print(o)
except:
pass
mrca_node = tree_of_life.mrca(ott_ids=ottids, wrap_response=True)
newick = extract_tree(
def add_study(study_id):
_LOG.debug('adding study {s}'.format(s=study_id))
# get latest version of nexson
# location of repo (test vs dev) dependent on peyotl config
phy = create_phylesystem_obj()
try:
studyobj = phy.get_study(study_id)['data']
except:
_LOG.debug('did not find study {s} in phylesystem'.format(s=study_id))
raise HTTPNotFound("Study {s} not found in phylesystem".format(s=study_id))
nexml = get_nexml_el(studyobj)
proposedTrees = nexml.get('^ot:candidateTreeForSynthesis')
if proposedTrees is None:
proposedTrees = []
# create a new Study object
new_study = Study(id=study_id)
DBSession.add(new_study)
# update with treebase id, if exists
datadeposit = nexml.get('^ot:dataDeposit')
if (datadeposit):
url = datadeposit['@href']
if (url):
pattern = re.compile(u'.+TB2:(.+)$')
matchobj = re.match(pattern,url)
if (matchobj):
tb_id = matchobj.group(1)
new_study.treebase_id=tb_id
# get curator(s), noting that ot:curators might be a
# string or a list
c = nexml.get('^ot:curatorName')
# create list of curator objects
curator_list=[]
if (isinstance(c,basestring)):
curator_list.append(c)
else:
curator_list = c
for curator in curator_list:
test_c = DBSession.query(Curator).filter(Curator.name==curator).first()
if test_c:
_LOG.debug("curator {c} already exists".format(c=curator))
#DBSession.add(curator)
new_study.curators.append(test_c)
else:
_LOG.debug("curator {c} does not yet exist".format(c=curator))
new_study.curators.append(Curator(name=curator))
# mapped otus in this study
otu_dict = gen_otu_dict(studyobj)
# iterate over the OTUs in the study, collecting the mapped
# ones (oid to ott_id mapping held at the study level)
mapped_otus = {}
for oid, o in otu_dict.items():
ottID = o.get('^ot:ottId')
if ottID is not None:
mapped_otus[oid]=ottID
# iterate over trees and insert tree data
ntrees = 0
for trees_group_id, tree_id, tree in iter_trees(studyobj):
_LOG.debug(' tree : {t}'.format(t=tree_id))
ntrees+=1
proposedForSynth = False
if (tree_id in proposedTrees):
proposedForSynth = True
treejson = json.dumps(tree)
new_tree = Tree(
tree_id=tree_id,
study_id=study_id,
proposed=proposedForSynth,
data=treejson
)
# get otus
ottIDs = set() # ott ids for this tree
ntips=0
for node_id, node in iter_node(tree):
oid = node.get('@otu')
# no @otu property on internal nodes
if oid is not None:
ntips+=1
#ottID = mapped_otus[oid]
if oid in mapped_otus:
ottID = mapped_otus[oid]
# _LOG.debug(' mapped ottID: {m}'.format(m=ottID))
# check that this exists in the taxonomy
# (it might not, if the ID has been deprecated)
taxon = DBSession.query(Taxonomy).filter(
Taxonomy.id==ottID
).first()
if taxon:
lineage = get_lineage(ottID)
_LOG.debug(' lineage of {m} = {l}'.format(m=ottID,l=lineage))
for t in lineage:
ottIDs.add(t)
new_tree.ntips = ntips
for t in ottIDs:
taxon = DBSession.query(Taxonomy).filter(
Taxonomy.id==t
).first()
# _LOG.debug(' adding {t},{n} to tree {tid}'.format(
# t=t,
# n=taxon.name,
# tid=tree_id)
# )
new_tree.otus.append(taxon)
# add the tree
DBSession.add(new_tree)
# now that we have added the tree info, update the study record
# with the json data (minus the tree info)
del nexml['treesById']
studyjson = json.dumps(nexml)
new_study.data=studyjson
new_study.ntrees = ntrees
reported_study_count = 0
study_count = 0
OTU_count = 0
unmapped_OTU_count = 0
unique_OTU_count = 0
nominated_study_count = 0
nominated_study_OTU_count = 0
nominated_study_unique_OTU_count = 0
nominated_study_unmapped_OTU_count = 0
run_time = 0
ott_id_set = set()
nominated_ott_id_set = set()
for study_id, n in phy.iter_study_objs():
reported_study_count += 1
otu_dict = gen_otu_dict(n)
if not bool(otu_dict):
continue
nex_obj = get_nexml_el(n)
study_count += 1
not_intended_for_synth = nex_obj.get('^ot:notIntendedForSynthesis')
intended_for_synth = (not_intended_for_synth is None) or (not_intended_for_synth is False)
if intended_for_synth:
nominated_study_count += 1
nominated_study_OTU_count += len(otu_dict)
OTU_count += len(otu_dict)
for oid, o in otu_dict.items():
ott_id = o.get('^ot:ottId')
if ott_id is None:
unmapped_OTU_count += 1
def addStudy(session, study_id):
# get latest version of nexson
print "adding study {s}".format(s=study_id)
phy = PhylesystemAPI(get_from="local")
studyobj = phy.get_study(study_id)["data"]
nexml = get_nexml_el(studyobj)
year = nexml.get("^ot:studyYear")
proposedTrees = nexml.get("^ot:candidateTreeForSynthesis")
if proposedTrees is None:
proposedTrees = []
# create a new Study object
new_study = Study(id=study_id, year=year)
session.add(new_study)
# session.commit()
# get curator(s), noting that ot:curators might be a
# string or a list
c = nexml.get("^ot:curatorName")
print " ot:curatorName: ", c
# create list of curator objects
curator_list = []
if isinstance(c, basestring):
curator_list.append(c)
else:
curator_list = c
for curator in curator_list:
test_c = session.query(Curator).filter(Curator.name == curator).first()
if test_c:
print "curator {c} already exists".format(c=curator)
# session.add(curator)
new_study.curators.append(test_c)
else:
print "curator {c} does no exist".format(c=curator)
new_study.curators.append(Curator(name=curator))
# mapped otus in this study
otu_dict = gen_otu_dict(studyobj)
# iterate over the OTUs in the study, collecting the mapped
# ones (oid to ott_id mapping held at the study level)
mapped_otus = {}
for oid, o in otu_dict.items():
ottID = o.get("^ot:ottId")
if ottID is not None:
mapped_otus[oid] = ottID
# iterate over trees and insert tree data
for trees_group_id, tree_id, tree in iter_trees(studyobj):
print " tree :", tree_id
proposedForSynth = False
if tree_id in proposedTrees:
proposedForSynth = True
treejson = json.dumps(tree)
new_tree = Tree(tree_id=tree_id, study_id=study_id, proposed=proposedForSynth, data=treejson)
# get otus
ottIDs = set() # ott ids for this tree
ntips = 0
for node_id, node in iter_node(tree):
oid = node.get("@otu")
# no @otu property on internal nodes
if oid is not None:
ntips += 1
# ottID = mapped_otus[oid]
if oid in mapped_otus:
ottID = mapped_otus[oid]
# check that this exists in the taxonomy
# (it might not, if the ID has been deprecated)
taxon = session.query(Taxonomy).filter(Taxonomy.id == ottID).first()
if taxon:
new_tree.otus.append(taxon)
ottIDs.add(ottID)
new_tree.ntips = ntips
# need to write function for recursive query of Taxonomy table
# ottIDs = parent_closure(ottIDs,taxonomy)
# update with treebase id, if exists
datadeposit = nexml.get("^ot:dataDeposit")
if datadeposit:
url = datadeposit["@href"]
pattern = re.compile(u".+TB2:(.+)$")
matchobj = re.match(pattern, url)
if matchobj:
tb_id = matchobj.group(1)
new_tree.treebase_id = tb_id
session.add(new_tree)
# now that we have added the tree info, update the study record
# with the json data (minus the tree info)
del nexml["treesById"]
studyjson = json.dumps(nexml)
new_study.data = studyjson
session.commit()