def load_sif(args):
conn = gripql.Connection(args.server)
O = conn.graph(args.db)
proteins = set()
with open(args.input) as handle:
rows = []
for line in handle:
row = line.rstrip().split("\t")
if not (row[0].startswith("CHEBI:")
or row[2].startswith("CHEBI:")):
rows.append(row)
proteins.add(row[0])
proteins.add(row[2])
print("Loading Proteins")
for i in proteins:
O.addVertex(i, "Protein", {})
def chunks(l, n):
"""Yield successive n-sized chunks from l."""
for i in range(0, len(l), n):
yield l[i:i + n]
i = 0
for chunk in chunks(rows, 10000):
b = O.bulkAdd()
for row in chunk:
b.addEdge(row[0], row[2], row[1], {})
b.execute()
i += len(chunk)
print("Loaded %s edges" % i)
def load_matrix(args):
conn = gripql.Connection(args.server)
O = conn.graph(args.db)
matrix = pandas.read_csv(args.input, sep="\t", index_col=0)
for name, row in matrix.iterrows():
data = {}
for k, v in row.iteritems():
if not isinstance(v, float) or not math.isnan(v):
data[k] = v
O.addVertex(name, "Sample", data)
def __init__(self):
if not os.path.exists(credential_file):
with open(credential_file, 'w') as cfile:
cdata = {
'OauthEmail': os.environ.get('BMEGAOauthEmail', ''),
'OauthAccessToken': os.environ.get('BMEGAOauthAccessToken',
''),
'OauthExpires': os.environ.get('BMEGAOauthExpires', '')
}
json.dump(cdata, cfile)
conn = gripql.Connection('https://bmeg.io/api',
credential_file=credentials_dir +
"bmeg_credentials.json")
self.O = conn.graph("rc5")
print("Connected to bmeg")
def render_page_content(pathname):
c = gripql.Connection(conn.GRIP, credential_file=conn.CRED)
graphs = []
for i in c.listGraphs():
if not i.endswith("__schema__"):
graphs.append(i)
if pathname == "/" or pathname == "/query":
return query_view.setup(graphs)
elif pathname == "/facet":
return facet_view.setup(graphs)
return dbc.Jumbotron([
html.H1("404: Not found", className="text-danger"),
html.Hr(),
html.P(f"The pathname {pathname} was not recognised..."),
])
import pandas as pd
import json
import gripql
import datetime
import dash_core_components as dcc
import dash_html_components as html
from app import app
import dash
import plotly.express as px
import plotly.graph_objects as go
# https://towardsdatascience.com/build-an-interactive-choropleth-map-with-plotly-and-dash-1de0de00dce0
conn = gripql.Connection("http://localhost:8201")
G = conn.graph("covid")
with open("geojson-counties-fips.json") as handle:
counties = json.loads(handle.read())
countiesSub = {"type": "FeatureCollection", "features": []}
for c in counties['features']:
if c['properties']['STATE'] == "41":
countiesSub['features'].append(c)
curDate = "2020-04-14 23:33:31"
q = G.query().V().hasLabel("SummaryLocation").has(
gripql.eq("province_state", "OR")).as_("a")
q = q.out("summary_reports").has(gripql.eq("date", curDate)).as_("b")
q = q.render(["$a._gid", "$b.confirmed", "$b.deaths", "$b.recovered"])
def __init__(self):
conn = gripql.Connection('https://bmeg.io/api',
credential_file=credentials_dir +
"bmeg_credentials.json")
self.O = conn.graph("bmeg_rc1_2")
print("Connected to bmeg")
def load_matrix(args):
conn = gripql.Connection(args.server)
if args.db not in list(conn.listGraphs()):
conn.addGraph(args.db)
O = conn.graph(args.db)
if args.columns is not None:
matrix = pandas.read_csv(args.input,
sep=args.sep,
index_col=args.index_col,
header=None,
names=args.columns,
skiprows=args.skiprows)
else:
matrix = pandas.read_csv(args.input,
sep=args.sep,
index_col=args.index_col,
skiprows=args.skiprows)
if args.transpose:
matrix = matrix.transpose()
if args.dump is not None:
dump_vertex_file = open(args.dump + ".vertex", "w")
dump_edge_file = open(args.dump + ".edge", "w")
def dump_vertex(gid, label, data):
print("Add Vertex: %s" % (gid))
dump_vertex_file.write(
json.dumps({
"gid": gid,
"label": label,
"data": data
}) + "\n")
def dump_edge(src, dst, label, data):
print("Add Edge: %s %s" % (src, dst))
dump_edge_file.write(
json.dumps({
"from": src,
"to": dst,
"label": label,
"data": data
}) + "\n")
if args.connect:
if not args.no_vertex:
#every row x col creates an edge with the weight value
for c in matrix.columns:
cname = "%s%s" % (args.col_prefix, c)
if list(O.query().V(c).count())[0]['count'] == 0:
if args.dump is not None:
dump_vertex(c, args.col_label, {})
else:
O.addVertex(c, args.col_label)
for r in matrix.index:
rname = "%s%s" % (args.row_prefix, r)
if list(O.query().V(r).count())[0]['count'] == 0:
if args.dump:
dump_vertex(r, args.row_label, {})
else:
O.addVertex(r, args.row_label)
for name, row in matrix.iterrows():
rname = "%s%s" % (args.row_prefix, name)
print("Loading: %s" % (rname))
b = O.bulkAdd()
for c in matrix.columns:
cname = "%s%s" % (args.col_prefix, c)
v = row[c]
if not math.isnan(v):
if args.dump:
dump_edge(rname, cname, args.edge_label,
{args.edge_prop: v})
else:
b.addEdge(rname, cname, args.edge_label,
{args.edge_prop: v})
b.execute()
else:
if args.col_regex is not None:
col_map = {}
for col in matrix.columns:
new_col = re.sub(args.col_regex[0], args.col_regex[1], col)
col_map[col] = new_col
matrix = matrix.rename(columns=col_map)
for name, row in matrix.iterrows():
rname = "%s%s" % (args.row_prefix, name)
print("Loading: %s" % (rname))
data = {}
for c in matrix.columns:
v = row[c]
if args.column_include is None or c in args.column_include:
if c not in args.column_exclude:
if not isinstance(v, float) or not math.isnan(v):
data[c] = v
for col, reg, rep in args.regex:
data[col] = re.sub(reg, rep, data[col])
if not args.no_vertex and rname not in args.exclude:
if args.dump:
dump_vertex(rname, args.row_label, data)
else:
O.addVertex(rname, args.row_label, data)
data["_rowname"] = name
data["_gid"] = rname
for dst, edge in args.edge:
try:
dstFmt = dst.format(**data)
except KeyError:
print("Formatting Error")
dstFmt = None
if dstFmt is not None:
if args.dump:
dump_edge(rname, dstFmt, edge, {})
else:
O.addEdge(rname, dstFmt, edge)
for dst, label in args.dst_vertex:
try:
dstFmt = dst.format(**data)
except KeyError:
dstFmt = None
if dstFmt is not None:
if list(O.query().V(dstFmt).count())[0]['count'] == 0:
if args.dump:
dump_vertex(dstFmt, label, {})
else:
O.addVertex(dstFmt, label, {})
if args.dump is not None:
dump_vertex_file.close()
dump_edge_file.close()
nargs="+",
default=[],
help="Exclude test suite(s)")
args = parser.parse_args()
server = args.server
if len(args.tests) > 0:
tests = ["ot_" + t for t in args.tests]
else:
tests = [
os.path.basename(a)[:-3]
for a in glob(os.path.join(TESTS, "ot_*.py"))
]
# filter out excluded tests
tests = [t for t in tests if t[3:] not in args.exclude]
conn = gripql.Connection(server)
correct = 0
total = 0
for name in tests:
mod = imp.load_source('test.%s' % name,
os.path.join(TESTS, name + ".py"))
for f in dir(mod):
if f.startswith("test_"):
func = getattr(mod, f)
if callable(func):
try:
print("Running: %s %s " % (name, f[5:]))
GRAPH = "test_graph_" + id_generator()
conn.addGraph(GRAPH)
e = func(conn.graph(GRAPH))
def __init__(self, bmeg_url, bmeg_graph, bmeg_credential_file):
# Set up connection to server and create graph handle
conn = gripql.Connection(bmeg_url,
credential_file=bmeg_credential_file)
self.O = conn.graph(bmeg_graph) # noqa E741
def connect():
return gripql.Connection(GRIP, credential_file=CRED)
