def html():
i = int(request.args(0) or 0)
root = build.stree(db, i)
nodes = list(root.iternodes())
for node in nodes:
label = node.rec.label or node.label
if node.rec.ott_node:
label = db.ott_node[node.rec.ott_node].name
node.label = label
modal = PluginMModal(id="mymodal",
title="Edit node properties",
content="")
mid = modal.id
cid = "c" + mid
def onclick(nid):
u = URL(c="snode", f="update_snode.load", args=[nid])
return "hbranch_clicked(%s, '%s', '%s', '%s');" % (nid, u, mid, cid)
if auth.has_membership(role="contributor"): f = onclick
else: f = ""
div, mapping, w, h = tree.render_html(root,
session,
request,
db,
onclick=f)
return dict(tree=div, root=root, modal=modal, w=w, h=h)
def newick():
"""
return newick string for stree.id = request.args(0)
optional request.variables are 'lfmt' (leaf format) and 'ifmt'
(internal node format), which are comma-separated table.field
values to be pulled out of the node.rec Row objects. These are
converted to strings, joined by '_', and attached to nodes as
labels to be written in the newick string.
"""
treeid = int(request.args(0) or 0)
assert treeid
root = build.stree(db, treeid)
lfmt = [ x.split('.') for x in
(request.vars['lfmt'] or 'snode.id,otu.label').split(',')
if x ]
ifmt = [ x.split('.') for x in
(request.vars['ifmt'] or '').split(',')
if x ]
def proc(node, table, field):
try: s = str(getattr(getattr(node.rec, table), field))
except AttributeError: s = ''
return '_'.join(s.split())
for n in root:
n.label = ''
if n.isleaf: n.label = '_'.join([ proc(n, t, f) for t, f in lfmt ])
else:
if ifmt: n.label = '_'.join([ proc(n, t, f) for t, f in ifmt ])
n.label = n.label.replace('(','--').replace(')','--')
return dict(newick=root.write())
def treediv():
i = int(request.args(0) or 0)
root = build.stree(db, i)
nodes = list(root.iternodes())
for node in nodes:
label = node.rec.label or node.label
if node.rec.ott_node:
label = db.ott_node[node.rec.ott_node].name
node.label = label
def onclick(nid):
u = URL(c="snode", f="update_snode.load", args=[nid])
return ("hbranch_clicked(%s, '%s', 'modal', 'modal_content');" %
(nid, u))
if auth.has_membership(role="contributor"): f = onclick
else: f = ""
wscale = float(request.vars.wscale or 0.9)
div, mapping, w, h = tree.render_html(root,
session,
request,
db,
onclick=f,
wscale=wscale)
return div.xml()
def newick():
"""
return newick string for stree.id = request.args(0)
optional request.variables are 'lfmt' (leaf format) and 'ifmt'
(internal node format), which are comma-separated table.field
values to be pulled out of the node.rec Row objects. These are
converted to strings, joined by '_', and attached to nodes as
labels to be written in the newick string.
"""
treeid = int(request.args(0) or 0)
assert treeid
root = build.stree(db, treeid)
lfmt = [
x.split('.')
for x in (request.vars['lfmt'] or 'snode.id,otu.label').split(',') if x
]
ifmt = [x.split('.') for x in (request.vars['ifmt'] or '').split(',') if x]
def proc(node, table, field):
try:
s = str(getattr(getattr(node.rec, table), field))
except AttributeError:
s = ''
return '_'.join(s.split())
for n in root:
n.label = ''
if n.isleaf: n.label = '_'.join([proc(n, t, f) for t, f in lfmt])
else:
if ifmt: n.label = '_'.join([proc(n, t, f) for t, f in ifmt])
n.label = n.label.replace('(', '--').replace(')', '--')
return dict(newick=root.write())
def forcenodepos():
t = request.args(0)
i = int(request.args(1))
if t == "stree":
r = build.stree(db, i)
elif t == "gtree":
r = build.gtree(db, i)
nodes = [ dict(index=i, id=n.id, label=n.label) for i, n in enumerate(r) ]
id2i = dict([ (n.id, i) for i, n in enumerate(r) ])
links = [ dict(source=i, target=id2i[n.parent.id])
for i, n in enumerate(r) if n.parent ]
return dict(nodes=nodes, links=links)
def nodepos():
t = request.args(0)
i = int(request.args(1))
if t == "stree":
root = build.stree(db, i)
elif t == "gtree":
root = build.gtree(db, i)
n2c = layout.calc_node_positions(root, 0.95, 0.95, scaled=False)
return response.json(
[ dict(id=k.id, x=v.x, y=v.y,
px=n2c[k.parent].x if n2c.get(k.parent) else None,
py=n2c[k.parent].y if n2c.get(k.parent) else None)
for k,v in n2c.items() ]
)
def forcenodepos():
t = request.args(0)
i = int(request.args(1))
if t == "stree":
r = build.stree(db, i)
elif t == "gtree":
r = build.gtree(db, i)
nodes = [dict(index=i, id=n.id, label=n.label) for i, n in enumerate(r)]
id2i = dict([(n.id, i) for i, n in enumerate(r)])
links = [
dict(source=i, target=id2i[n.parent.id]) for i, n in enumerate(r)
if n.parent
]
return dict(nodes=nodes, links=links)
def nodepos():
t = request.args(0)
i = int(request.args(1))
if t == "stree":
root = build.stree(db, i)
elif t == "gtree":
root = build.gtree(db, i)
n2c = layout.calc_node_positions(root, 0.95, 0.95, scaled=False)
return response.json([
dict(id=k.id,
x=v.x,
y=v.y,
px=n2c[k.parent].x if n2c.get(k.parent) else None,
py=n2c[k.parent].y if n2c.get(k.parent) else None)
for k, v in n2c.items()
])
def load_html():
i = int(request.args(0) or 0)
root = build.stree(db, i)
nodes = list(root.iternodes())
for node in nodes:
label = node.rec.label or node.label
if node.rec.ott_node:
label = db.ott_node[node.rec.ott_node].name
node.label = label
def onclick(nid):
u = URL(c="snode",f="update_snode.load", args=[nid])
return ("hbranch_clicked(%s, '%s', 'modal', 'modal_content');"
% (nid, u))
if auth.has_membership(role="contributor"): f = onclick
else: f = ""
div, mapping, w, h = tree.render_html(root, session, request,
db, onclick=f)
return dict(tree=div)
def treediv():
i = int(request.args(0) or 0)
root = build.stree(db, i)
nodes = list(root.iternodes())
for node in nodes:
label = node.rec.label or node.label
if node.rec.taxon:
label = db.taxon[node.rec.taxon].name
node.label = label
def onclick(nid):
u = URL(c="snode",f="update_snode.load", args=[nid])
return ("hbranch_clicked(%s, '%s', 'modal', 'modal_content');"
% (nid, u))
if auth.has_membership(role="contributor"): f = onclick
else: f = ""
wscale = float(request.vars.wscale or 0.9)
div, mapping, w, h = tree.render_html(root, session, request,
db, onclick=f,
wscale=wscale)
return div.xml()
def html():
i = int(request.args(0) or 0)
root = build.stree(db, i)
nodes = list(root.iternodes())
for node in nodes:
label = node.rec.label or node.label
if node.rec.ott_node:
label = db.ott_node[node.rec.ott_node].name
node.label = label
modal = PluginMModal(id="mymodal", title="Edit node properties", content="")
mid = modal.id; cid = "c"+mid
def onclick(nid):
u = URL(c="snode",f="update_snode.load", args=[nid])
return "hbranch_clicked(%s, '%s', '%s', '%s');" % (nid, u, mid, cid)
if auth.has_membership(role="contributor"): f = onclick
else: f = ""
div, mapping, w, h = tree.render_html(root, session, request,
db, onclick=f)
return dict(tree=div, root=root, modal=modal, w=w, h=h)
def suggest():
i = int(request.args(0) or 0)
root = build.stree(db, i)
def modalTreeObj():
return dict( tree = build.stree( db, request.args[0] ) )
def suggest():
i = int(request.args(0) or 0)
root = build.stree(db, i)
def modalTreeObj():
return dict(tree=build.stree(db, request.args[0]))